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jpayne@69
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1 /* Generated by Cython 3.0.11 */
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jpayne@69
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2
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jpayne@69
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3 /* BEGIN: Cython Metadata
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jpayne@69
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4 {
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jpayne@69
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5 "distutils": {
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jpayne@69
|
6 "define_macros": [
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jpayne@69
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7 [
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jpayne@69
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8 "BUILDING_WHEEL",
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jpayne@69
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9 null
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jpayne@69
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10 ]
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jpayne@69
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11 ],
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jpayne@69
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12 "depends": [
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jpayne@69
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13 "/project/htslib/htslib/bgzf.h",
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jpayne@69
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14 "/project/htslib/htslib/cram.h",
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jpayne@69
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15 "/project/htslib/htslib/faidx.h",
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jpayne@69
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16 "/project/htslib/htslib/hfile.h",
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jpayne@69
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17 "/project/htslib/htslib/hts.h",
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jpayne@69
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18 "/project/htslib/htslib/kstring.h",
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jpayne@69
|
19 "/project/htslib/htslib/sam.h",
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jpayne@69
|
20 "/project/htslib/htslib/tbx.h",
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jpayne@69
|
21 "/project/htslib/htslib/vcf.h",
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jpayne@69
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22 "/project/htslib/htslib/vcfutils.h",
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jpayne@69
|
23 "/project/pysam/htslib_util.h",
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jpayne@69
|
24 "/project/pysam/pysam_stream.h"
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jpayne@69
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25 ],
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jpayne@69
|
26 "extra_compile_args": [
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jpayne@69
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27 "-Wno-unused",
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jpayne@69
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28 "-Wno-strict-prototypes",
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jpayne@69
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29 "-Wno-sign-compare",
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jpayne@69
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30 "-Wno-error=declaration-after-statement"
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jpayne@69
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31 ],
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jpayne@69
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32 "extra_link_args": [
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jpayne@69
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33 "-Wl,-rpath,$ORIGIN"
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jpayne@69
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34 ],
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jpayne@69
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35 "include_dirs": [
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jpayne@69
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36 "pysam",
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jpayne@69
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37 "/project/pysam",
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jpayne@69
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38 "/project/htslib",
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jpayne@69
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39 "/project/samtools",
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jpayne@69
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40 "/project/samtools/lz4",
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jpayne@69
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41 "/project/bcftools",
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jpayne@69
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42 "/project"
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jpayne@69
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43 ],
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jpayne@69
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44 "language": "c",
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jpayne@69
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45 "libraries": [
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jpayne@69
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46 "z",
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jpayne@69
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47 "lzma",
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jpayne@69
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48 "bz2",
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jpayne@69
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49 "z",
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jpayne@69
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50 "m",
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jpayne@69
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51 "curl",
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jpayne@69
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52 "crypto",
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jpayne@69
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53 "chtslib.cpython-37m-x86_64-linux-gnu",
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jpayne@69
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54 "cutils.cpython-37m-x86_64-linux-gnu"
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jpayne@69
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55 ],
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jpayne@69
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56 "library_dirs": [
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jpayne@69
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57 "/project/pysam",
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jpayne@69
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58 "/project",
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jpayne@69
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59 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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60 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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61 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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62 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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63 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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64 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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65 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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66 "build/lib.linux-x86_64-cpython-37/pysam"
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jpayne@69
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67 ],
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jpayne@69
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68 "name": "pysam.libctabix",
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jpayne@69
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69 "sources": [
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jpayne@69
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70 "pysam/libctabix.pyx"
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jpayne@69
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71 ]
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jpayne@69
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72 },
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jpayne@69
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73 "module_name": "pysam.libctabix"
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jpayne@69
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74 }
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jpayne@69
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75 END: Cython Metadata */
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jpayne@69
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76
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jpayne@69
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77 #ifndef PY_SSIZE_T_CLEAN
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jpayne@69
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78 #define PY_SSIZE_T_CLEAN
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jpayne@69
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79 #endif /* PY_SSIZE_T_CLEAN */
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jpayne@69
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80 #if defined(CYTHON_LIMITED_API) && 0
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jpayne@69
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81 #ifndef Py_LIMITED_API
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jpayne@69
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82 #if CYTHON_LIMITED_API+0 > 0x03030000
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jpayne@69
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83 #define Py_LIMITED_API CYTHON_LIMITED_API
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jpayne@69
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84 #else
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jpayne@69
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85 #define Py_LIMITED_API 0x03030000
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jpayne@69
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86 #endif
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jpayne@69
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87 #endif
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jpayne@69
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88 #endif
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jpayne@69
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89
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jpayne@69
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90 #include "Python.h"
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jpayne@69
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91
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jpayne@69
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92 #if PY_MAJOR_VERSION >= 3
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jpayne@69
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93 #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj)
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jpayne@69
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94 #else
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jpayne@69
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95 #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj, NULL)
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jpayne@69
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96 #endif
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jpayne@69
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97
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jpayne@69
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98
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jpayne@69
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99 #if PY_MAJOR_VERSION <= 2
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jpayne@69
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100 #define PyDict_GetItemWithError _PyDict_GetItemWithError
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jpayne@69
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101 #endif
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jpayne@69
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102
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jpayne@69
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103
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jpayne@69
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104 #if (PY_VERSION_HEX < 0x030700b1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030600)) && !defined(PyContextVar_Get)
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jpayne@69
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105 #define PyContextVar_Get(var, d, v) ((d) ? ((void)(var), Py_INCREF(d), (v)[0] = (d), 0) : ((v)[0] = NULL, 0) )
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jpayne@69
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106 #endif
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jpayne@69
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107
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jpayne@69
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108 #ifndef Py_PYTHON_H
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jpayne@69
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109 #error Python headers needed to compile C extensions, please install development version of Python.
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jpayne@69
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110 #elif PY_VERSION_HEX < 0x02070000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
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jpayne@69
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111 #error Cython requires Python 2.7+ or Python 3.3+.
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jpayne@69
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112 #else
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jpayne@69
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113 #if defined(CYTHON_LIMITED_API) && CYTHON_LIMITED_API
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jpayne@69
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114 #define __PYX_EXTRA_ABI_MODULE_NAME "limited"
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jpayne@69
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115 #else
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jpayne@69
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116 #define __PYX_EXTRA_ABI_MODULE_NAME ""
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jpayne@69
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117 #endif
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jpayne@69
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118 #define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME
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jpayne@69
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119 #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI
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jpayne@69
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120 #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "."
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jpayne@69
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121 #define CYTHON_HEX_VERSION 0x03000BF0
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jpayne@69
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122 #define CYTHON_FUTURE_DIVISION 1
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jpayne@69
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123 #include <stddef.h>
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jpayne@69
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124 #ifndef offsetof
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jpayne@69
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125 #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
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jpayne@69
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126 #endif
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jpayne@69
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127 #if !defined(_WIN32) && !defined(WIN32) && !defined(MS_WINDOWS)
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jpayne@69
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128 #ifndef __stdcall
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jpayne@69
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129 #define __stdcall
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jpayne@69
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130 #endif
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jpayne@69
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131 #ifndef __cdecl
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jpayne@69
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132 #define __cdecl
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jpayne@69
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133 #endif
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jpayne@69
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134 #ifndef __fastcall
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jpayne@69
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135 #define __fastcall
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jpayne@69
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136 #endif
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jpayne@69
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137 #endif
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jpayne@69
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138 #ifndef DL_IMPORT
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jpayne@69
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139 #define DL_IMPORT(t) t
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jpayne@69
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140 #endif
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jpayne@69
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141 #ifndef DL_EXPORT
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jpayne@69
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142 #define DL_EXPORT(t) t
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jpayne@69
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143 #endif
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jpayne@69
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144 #define __PYX_COMMA ,
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jpayne@69
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145 #ifndef HAVE_LONG_LONG
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jpayne@69
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146 #define HAVE_LONG_LONG
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jpayne@69
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147 #endif
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jpayne@69
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148 #ifndef PY_LONG_LONG
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jpayne@69
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149 #define PY_LONG_LONG LONG_LONG
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jpayne@69
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150 #endif
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jpayne@69
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151 #ifndef Py_HUGE_VAL
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jpayne@69
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152 #define Py_HUGE_VAL HUGE_VAL
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jpayne@69
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153 #endif
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jpayne@69
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154 #define __PYX_LIMITED_VERSION_HEX PY_VERSION_HEX
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jpayne@69
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155 #if defined(GRAALVM_PYTHON)
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jpayne@69
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156 /* For very preliminary testing purposes. Most variables are set the same as PyPy.
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157 The existence of this section does not imply that anything works or is even tested */
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jpayne@69
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158 #define CYTHON_COMPILING_IN_PYPY 0
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jpayne@69
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159 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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160 #define CYTHON_COMPILING_IN_LIMITED_API 0
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jpayne@69
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161 #define CYTHON_COMPILING_IN_GRAAL 1
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jpayne@69
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162 #define CYTHON_COMPILING_IN_NOGIL 0
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jpayne@69
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163 #undef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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164 #define CYTHON_USE_TYPE_SLOTS 0
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jpayne@69
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165 #undef CYTHON_USE_TYPE_SPECS
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jpayne@69
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166 #define CYTHON_USE_TYPE_SPECS 0
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jpayne@69
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167 #undef CYTHON_USE_PYTYPE_LOOKUP
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jpayne@69
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168 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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169 #if PY_VERSION_HEX < 0x03050000
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jpayne@69
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170 #undef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
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171 #define CYTHON_USE_ASYNC_SLOTS 0
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jpayne@69
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172 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
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jpayne@69
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173 #define CYTHON_USE_ASYNC_SLOTS 1
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jpayne@69
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174 #endif
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jpayne@69
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175 #undef CYTHON_USE_PYLIST_INTERNALS
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jpayne@69
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176 #define CYTHON_USE_PYLIST_INTERNALS 0
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jpayne@69
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177 #undef CYTHON_USE_UNICODE_INTERNALS
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jpayne@69
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178 #define CYTHON_USE_UNICODE_INTERNALS 0
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jpayne@69
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179 #undef CYTHON_USE_UNICODE_WRITER
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jpayne@69
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180 #define CYTHON_USE_UNICODE_WRITER 0
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jpayne@69
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181 #undef CYTHON_USE_PYLONG_INTERNALS
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jpayne@69
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182 #define CYTHON_USE_PYLONG_INTERNALS 0
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jpayne@69
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183 #undef CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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184 #define CYTHON_AVOID_BORROWED_REFS 1
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jpayne@69
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185 #undef CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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186 #define CYTHON_ASSUME_SAFE_MACROS 0
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jpayne@69
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187 #undef CYTHON_UNPACK_METHODS
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jpayne@69
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188 #define CYTHON_UNPACK_METHODS 0
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jpayne@69
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189 #undef CYTHON_FAST_THREAD_STATE
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jpayne@69
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190 #define CYTHON_FAST_THREAD_STATE 0
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jpayne@69
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191 #undef CYTHON_FAST_GIL
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jpayne@69
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192 #define CYTHON_FAST_GIL 0
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jpayne@69
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193 #undef CYTHON_METH_FASTCALL
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jpayne@69
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194 #define CYTHON_METH_FASTCALL 0
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jpayne@69
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195 #undef CYTHON_FAST_PYCALL
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jpayne@69
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196 #define CYTHON_FAST_PYCALL 0
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jpayne@69
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197 #ifndef CYTHON_PEP487_INIT_SUBCLASS
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jpayne@69
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198 #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3)
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jpayne@69
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199 #endif
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jpayne@69
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200 #undef CYTHON_PEP489_MULTI_PHASE_INIT
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jpayne@69
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201 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
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jpayne@69
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202 #undef CYTHON_USE_MODULE_STATE
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jpayne@69
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203 #define CYTHON_USE_MODULE_STATE 0
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jpayne@69
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204 #undef CYTHON_USE_TP_FINALIZE
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jpayne@69
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205 #define CYTHON_USE_TP_FINALIZE 0
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jpayne@69
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206 #undef CYTHON_USE_DICT_VERSIONS
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jpayne@69
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207 #define CYTHON_USE_DICT_VERSIONS 0
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jpayne@69
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208 #undef CYTHON_USE_EXC_INFO_STACK
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jpayne@69
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209 #define CYTHON_USE_EXC_INFO_STACK 0
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jpayne@69
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210 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
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jpayne@69
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211 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
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jpayne@69
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212 #endif
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jpayne@69
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213 #undef CYTHON_USE_FREELISTS
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jpayne@69
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214 #define CYTHON_USE_FREELISTS 0
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jpayne@69
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215 #elif defined(PYPY_VERSION)
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jpayne@69
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216 #define CYTHON_COMPILING_IN_PYPY 1
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jpayne@69
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217 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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218 #define CYTHON_COMPILING_IN_LIMITED_API 0
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jpayne@69
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219 #define CYTHON_COMPILING_IN_GRAAL 0
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jpayne@69
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220 #define CYTHON_COMPILING_IN_NOGIL 0
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jpayne@69
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221 #undef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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222 #define CYTHON_USE_TYPE_SLOTS 0
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jpayne@69
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223 #ifndef CYTHON_USE_TYPE_SPECS
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jpayne@69
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224 #define CYTHON_USE_TYPE_SPECS 0
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jpayne@69
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225 #endif
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jpayne@69
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226 #undef CYTHON_USE_PYTYPE_LOOKUP
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jpayne@69
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227 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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228 #if PY_VERSION_HEX < 0x03050000
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jpayne@69
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229 #undef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
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230 #define CYTHON_USE_ASYNC_SLOTS 0
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jpayne@69
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231 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
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jpayne@69
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232 #define CYTHON_USE_ASYNC_SLOTS 1
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jpayne@69
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233 #endif
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jpayne@69
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234 #undef CYTHON_USE_PYLIST_INTERNALS
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jpayne@69
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235 #define CYTHON_USE_PYLIST_INTERNALS 0
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jpayne@69
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236 #undef CYTHON_USE_UNICODE_INTERNALS
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jpayne@69
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237 #define CYTHON_USE_UNICODE_INTERNALS 0
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jpayne@69
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238 #undef CYTHON_USE_UNICODE_WRITER
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jpayne@69
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239 #define CYTHON_USE_UNICODE_WRITER 0
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jpayne@69
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240 #undef CYTHON_USE_PYLONG_INTERNALS
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jpayne@69
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241 #define CYTHON_USE_PYLONG_INTERNALS 0
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jpayne@69
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242 #undef CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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243 #define CYTHON_AVOID_BORROWED_REFS 1
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jpayne@69
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244 #undef CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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245 #define CYTHON_ASSUME_SAFE_MACROS 0
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jpayne@69
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246 #undef CYTHON_UNPACK_METHODS
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jpayne@69
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247 #define CYTHON_UNPACK_METHODS 0
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jpayne@69
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248 #undef CYTHON_FAST_THREAD_STATE
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jpayne@69
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249 #define CYTHON_FAST_THREAD_STATE 0
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jpayne@69
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250 #undef CYTHON_FAST_GIL
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jpayne@69
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251 #define CYTHON_FAST_GIL 0
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jpayne@69
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252 #undef CYTHON_METH_FASTCALL
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jpayne@69
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253 #define CYTHON_METH_FASTCALL 0
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jpayne@69
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254 #undef CYTHON_FAST_PYCALL
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jpayne@69
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255 #define CYTHON_FAST_PYCALL 0
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jpayne@69
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256 #ifndef CYTHON_PEP487_INIT_SUBCLASS
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|
jpayne@69
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257 #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3)
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jpayne@69
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258 #endif
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|
jpayne@69
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259 #if PY_VERSION_HEX < 0x03090000
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jpayne@69
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260 #undef CYTHON_PEP489_MULTI_PHASE_INIT
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|
jpayne@69
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261 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
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|
jpayne@69
|
262 #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
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jpayne@69
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263 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
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|
jpayne@69
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264 #endif
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jpayne@69
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265 #undef CYTHON_USE_MODULE_STATE
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jpayne@69
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266 #define CYTHON_USE_MODULE_STATE 0
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jpayne@69
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267 #undef CYTHON_USE_TP_FINALIZE
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jpayne@69
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268 #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1 && PYPY_VERSION_NUM >= 0x07030C00)
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jpayne@69
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269 #undef CYTHON_USE_DICT_VERSIONS
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jpayne@69
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270 #define CYTHON_USE_DICT_VERSIONS 0
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jpayne@69
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271 #undef CYTHON_USE_EXC_INFO_STACK
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jpayne@69
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272 #define CYTHON_USE_EXC_INFO_STACK 0
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jpayne@69
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273 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
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jpayne@69
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274 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
|
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jpayne@69
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275 #endif
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jpayne@69
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276 #undef CYTHON_USE_FREELISTS
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jpayne@69
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277 #define CYTHON_USE_FREELISTS 0
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jpayne@69
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278 #elif defined(CYTHON_LIMITED_API)
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jpayne@69
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279 #ifdef Py_LIMITED_API
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jpayne@69
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280 #undef __PYX_LIMITED_VERSION_HEX
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jpayne@69
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281 #define __PYX_LIMITED_VERSION_HEX Py_LIMITED_API
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jpayne@69
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282 #endif
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jpayne@69
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283 #define CYTHON_COMPILING_IN_PYPY 0
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jpayne@69
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284 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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285 #define CYTHON_COMPILING_IN_LIMITED_API 1
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jpayne@69
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286 #define CYTHON_COMPILING_IN_GRAAL 0
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|
jpayne@69
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287 #define CYTHON_COMPILING_IN_NOGIL 0
|
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jpayne@69
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288 #undef CYTHON_CLINE_IN_TRACEBACK
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jpayne@69
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289 #define CYTHON_CLINE_IN_TRACEBACK 0
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jpayne@69
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290 #undef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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291 #define CYTHON_USE_TYPE_SLOTS 0
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jpayne@69
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292 #undef CYTHON_USE_TYPE_SPECS
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jpayne@69
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293 #define CYTHON_USE_TYPE_SPECS 1
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jpayne@69
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294 #undef CYTHON_USE_PYTYPE_LOOKUP
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jpayne@69
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295 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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296 #undef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
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297 #define CYTHON_USE_ASYNC_SLOTS 0
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jpayne@69
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298 #undef CYTHON_USE_PYLIST_INTERNALS
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jpayne@69
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299 #define CYTHON_USE_PYLIST_INTERNALS 0
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jpayne@69
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300 #undef CYTHON_USE_UNICODE_INTERNALS
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jpayne@69
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301 #define CYTHON_USE_UNICODE_INTERNALS 0
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jpayne@69
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302 #ifndef CYTHON_USE_UNICODE_WRITER
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jpayne@69
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303 #define CYTHON_USE_UNICODE_WRITER 0
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jpayne@69
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304 #endif
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jpayne@69
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305 #undef CYTHON_USE_PYLONG_INTERNALS
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jpayne@69
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306 #define CYTHON_USE_PYLONG_INTERNALS 0
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jpayne@69
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307 #ifndef CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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308 #define CYTHON_AVOID_BORROWED_REFS 0
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jpayne@69
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309 #endif
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jpayne@69
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310 #undef CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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311 #define CYTHON_ASSUME_SAFE_MACROS 0
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jpayne@69
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312 #undef CYTHON_UNPACK_METHODS
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jpayne@69
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313 #define CYTHON_UNPACK_METHODS 0
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|
jpayne@69
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314 #undef CYTHON_FAST_THREAD_STATE
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jpayne@69
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315 #define CYTHON_FAST_THREAD_STATE 0
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jpayne@69
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316 #undef CYTHON_FAST_GIL
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jpayne@69
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317 #define CYTHON_FAST_GIL 0
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jpayne@69
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318 #undef CYTHON_METH_FASTCALL
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jpayne@69
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319 #define CYTHON_METH_FASTCALL 0
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jpayne@69
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320 #undef CYTHON_FAST_PYCALL
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jpayne@69
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321 #define CYTHON_FAST_PYCALL 0
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jpayne@69
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322 #ifndef CYTHON_PEP487_INIT_SUBCLASS
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jpayne@69
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323 #define CYTHON_PEP487_INIT_SUBCLASS 1
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jpayne@69
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324 #endif
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jpayne@69
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325 #undef CYTHON_PEP489_MULTI_PHASE_INIT
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jpayne@69
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326 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
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jpayne@69
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327 #undef CYTHON_USE_MODULE_STATE
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jpayne@69
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328 #define CYTHON_USE_MODULE_STATE 1
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jpayne@69
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329 #ifndef CYTHON_USE_TP_FINALIZE
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jpayne@69
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330 #define CYTHON_USE_TP_FINALIZE 0
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jpayne@69
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331 #endif
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jpayne@69
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332 #undef CYTHON_USE_DICT_VERSIONS
|
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jpayne@69
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333 #define CYTHON_USE_DICT_VERSIONS 0
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jpayne@69
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334 #undef CYTHON_USE_EXC_INFO_STACK
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jpayne@69
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335 #define CYTHON_USE_EXC_INFO_STACK 0
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jpayne@69
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336 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
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jpayne@69
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337 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
|
|
jpayne@69
|
338 #endif
|
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jpayne@69
|
339 #undef CYTHON_USE_FREELISTS
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jpayne@69
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340 #define CYTHON_USE_FREELISTS 0
|
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jpayne@69
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341 #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL)
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jpayne@69
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342 #define CYTHON_COMPILING_IN_PYPY 0
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jpayne@69
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343 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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344 #define CYTHON_COMPILING_IN_LIMITED_API 0
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jpayne@69
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345 #define CYTHON_COMPILING_IN_GRAAL 0
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jpayne@69
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346 #define CYTHON_COMPILING_IN_NOGIL 1
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jpayne@69
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347 #ifndef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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348 #define CYTHON_USE_TYPE_SLOTS 1
|
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jpayne@69
|
349 #endif
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jpayne@69
|
350 #ifndef CYTHON_USE_TYPE_SPECS
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jpayne@69
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351 #define CYTHON_USE_TYPE_SPECS 0
|
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jpayne@69
|
352 #endif
|
|
jpayne@69
|
353 #undef CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
354 #define CYTHON_USE_PYTYPE_LOOKUP 0
|
|
jpayne@69
|
355 #ifndef CYTHON_USE_ASYNC_SLOTS
|
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jpayne@69
|
356 #define CYTHON_USE_ASYNC_SLOTS 1
|
|
jpayne@69
|
357 #endif
|
|
jpayne@69
|
358 #ifndef CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
359 #define CYTHON_USE_PYLONG_INTERNALS 0
|
|
jpayne@69
|
360 #endif
|
|
jpayne@69
|
361 #undef CYTHON_USE_PYLIST_INTERNALS
|
|
jpayne@69
|
362 #define CYTHON_USE_PYLIST_INTERNALS 0
|
|
jpayne@69
|
363 #ifndef CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
364 #define CYTHON_USE_UNICODE_INTERNALS 1
|
|
jpayne@69
|
365 #endif
|
|
jpayne@69
|
366 #undef CYTHON_USE_UNICODE_WRITER
|
|
jpayne@69
|
367 #define CYTHON_USE_UNICODE_WRITER 0
|
|
jpayne@69
|
368 #ifndef CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
369 #define CYTHON_AVOID_BORROWED_REFS 0
|
|
jpayne@69
|
370 #endif
|
|
jpayne@69
|
371 #ifndef CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
372 #define CYTHON_ASSUME_SAFE_MACROS 1
|
|
jpayne@69
|
373 #endif
|
|
jpayne@69
|
374 #ifndef CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
375 #define CYTHON_UNPACK_METHODS 1
|
|
jpayne@69
|
376 #endif
|
|
jpayne@69
|
377 #undef CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
378 #define CYTHON_FAST_THREAD_STATE 0
|
|
jpayne@69
|
379 #undef CYTHON_FAST_GIL
|
|
jpayne@69
|
380 #define CYTHON_FAST_GIL 0
|
|
jpayne@69
|
381 #ifndef CYTHON_METH_FASTCALL
|
|
jpayne@69
|
382 #define CYTHON_METH_FASTCALL 1
|
|
jpayne@69
|
383 #endif
|
|
jpayne@69
|
384 #undef CYTHON_FAST_PYCALL
|
|
jpayne@69
|
385 #define CYTHON_FAST_PYCALL 0
|
|
jpayne@69
|
386 #ifndef CYTHON_PEP487_INIT_SUBCLASS
|
|
jpayne@69
|
387 #define CYTHON_PEP487_INIT_SUBCLASS 1
|
|
jpayne@69
|
388 #endif
|
|
jpayne@69
|
389 #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
390 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
|
|
jpayne@69
|
391 #endif
|
|
jpayne@69
|
392 #ifndef CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
393 #define CYTHON_USE_MODULE_STATE 0
|
|
jpayne@69
|
394 #endif
|
|
jpayne@69
|
395 #ifndef CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
396 #define CYTHON_USE_TP_FINALIZE 1
|
|
jpayne@69
|
397 #endif
|
|
jpayne@69
|
398 #undef CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
399 #define CYTHON_USE_DICT_VERSIONS 0
|
|
jpayne@69
|
400 #undef CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
401 #define CYTHON_USE_EXC_INFO_STACK 0
|
|
jpayne@69
|
402 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
403 #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
|
|
jpayne@69
|
404 #endif
|
|
jpayne@69
|
405 #ifndef CYTHON_USE_FREELISTS
|
|
jpayne@69
|
406 #define CYTHON_USE_FREELISTS 0
|
|
jpayne@69
|
407 #endif
|
|
jpayne@69
|
408 #else
|
|
jpayne@69
|
409 #define CYTHON_COMPILING_IN_PYPY 0
|
|
jpayne@69
|
410 #define CYTHON_COMPILING_IN_CPYTHON 1
|
|
jpayne@69
|
411 #define CYTHON_COMPILING_IN_LIMITED_API 0
|
|
jpayne@69
|
412 #define CYTHON_COMPILING_IN_GRAAL 0
|
|
jpayne@69
|
413 #define CYTHON_COMPILING_IN_NOGIL 0
|
|
jpayne@69
|
414 #ifndef CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
415 #define CYTHON_USE_TYPE_SLOTS 1
|
|
jpayne@69
|
416 #endif
|
|
jpayne@69
|
417 #ifndef CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
418 #define CYTHON_USE_TYPE_SPECS 0
|
|
jpayne@69
|
419 #endif
|
|
jpayne@69
|
420 #ifndef CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
421 #define CYTHON_USE_PYTYPE_LOOKUP 1
|
|
jpayne@69
|
422 #endif
|
|
jpayne@69
|
423 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
424 #undef CYTHON_USE_ASYNC_SLOTS
|
|
jpayne@69
|
425 #define CYTHON_USE_ASYNC_SLOTS 0
|
|
jpayne@69
|
426 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
|
|
jpayne@69
|
427 #define CYTHON_USE_ASYNC_SLOTS 1
|
|
jpayne@69
|
428 #endif
|
|
jpayne@69
|
429 #ifndef CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
430 #define CYTHON_USE_PYLONG_INTERNALS 1
|
|
jpayne@69
|
431 #endif
|
|
jpayne@69
|
432 #ifndef CYTHON_USE_PYLIST_INTERNALS
|
|
jpayne@69
|
433 #define CYTHON_USE_PYLIST_INTERNALS 1
|
|
jpayne@69
|
434 #endif
|
|
jpayne@69
|
435 #ifndef CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
436 #define CYTHON_USE_UNICODE_INTERNALS 1
|
|
jpayne@69
|
437 #endif
|
|
jpayne@69
|
438 #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
|
|
jpayne@69
|
439 #undef CYTHON_USE_UNICODE_WRITER
|
|
jpayne@69
|
440 #define CYTHON_USE_UNICODE_WRITER 0
|
|
jpayne@69
|
441 #elif !defined(CYTHON_USE_UNICODE_WRITER)
|
|
jpayne@69
|
442 #define CYTHON_USE_UNICODE_WRITER 1
|
|
jpayne@69
|
443 #endif
|
|
jpayne@69
|
444 #ifndef CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
445 #define CYTHON_AVOID_BORROWED_REFS 0
|
|
jpayne@69
|
446 #endif
|
|
jpayne@69
|
447 #ifndef CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
448 #define CYTHON_ASSUME_SAFE_MACROS 1
|
|
jpayne@69
|
449 #endif
|
|
jpayne@69
|
450 #ifndef CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
451 #define CYTHON_UNPACK_METHODS 1
|
|
jpayne@69
|
452 #endif
|
|
jpayne@69
|
453 #ifndef CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
454 #define CYTHON_FAST_THREAD_STATE 1
|
|
jpayne@69
|
455 #endif
|
|
jpayne@69
|
456 #ifndef CYTHON_FAST_GIL
|
|
jpayne@69
|
457 #define CYTHON_FAST_GIL (PY_MAJOR_VERSION < 3 || PY_VERSION_HEX >= 0x03060000 && PY_VERSION_HEX < 0x030C00A6)
|
|
jpayne@69
|
458 #endif
|
|
jpayne@69
|
459 #ifndef CYTHON_METH_FASTCALL
|
|
jpayne@69
|
460 #define CYTHON_METH_FASTCALL (PY_VERSION_HEX >= 0x030700A1)
|
|
jpayne@69
|
461 #endif
|
|
jpayne@69
|
462 #ifndef CYTHON_FAST_PYCALL
|
|
jpayne@69
|
463 #define CYTHON_FAST_PYCALL 1
|
|
jpayne@69
|
464 #endif
|
|
jpayne@69
|
465 #ifndef CYTHON_PEP487_INIT_SUBCLASS
|
|
jpayne@69
|
466 #define CYTHON_PEP487_INIT_SUBCLASS 1
|
|
jpayne@69
|
467 #endif
|
|
jpayne@69
|
468 #if PY_VERSION_HEX < 0x03050000
|
|
jpayne@69
|
469 #undef CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
470 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
|
|
jpayne@69
|
471 #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
|
|
jpayne@69
|
472 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
|
|
jpayne@69
|
473 #endif
|
|
jpayne@69
|
474 #ifndef CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
475 #define CYTHON_USE_MODULE_STATE 0
|
|
jpayne@69
|
476 #endif
|
|
jpayne@69
|
477 #if PY_VERSION_HEX < 0x030400a1
|
|
jpayne@69
|
478 #undef CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
479 #define CYTHON_USE_TP_FINALIZE 0
|
|
jpayne@69
|
480 #elif !defined(CYTHON_USE_TP_FINALIZE)
|
|
jpayne@69
|
481 #define CYTHON_USE_TP_FINALIZE 1
|
|
jpayne@69
|
482 #endif
|
|
jpayne@69
|
483 #if PY_VERSION_HEX < 0x030600B1
|
|
jpayne@69
|
484 #undef CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
485 #define CYTHON_USE_DICT_VERSIONS 0
|
|
jpayne@69
|
486 #elif !defined(CYTHON_USE_DICT_VERSIONS)
|
|
jpayne@69
|
487 #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX < 0x030C00A5)
|
|
jpayne@69
|
488 #endif
|
|
jpayne@69
|
489 #if PY_VERSION_HEX < 0x030700A3
|
|
jpayne@69
|
490 #undef CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
491 #define CYTHON_USE_EXC_INFO_STACK 0
|
|
jpayne@69
|
492 #elif !defined(CYTHON_USE_EXC_INFO_STACK)
|
|
jpayne@69
|
493 #define CYTHON_USE_EXC_INFO_STACK 1
|
|
jpayne@69
|
494 #endif
|
|
jpayne@69
|
495 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
496 #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
|
|
jpayne@69
|
497 #endif
|
|
jpayne@69
|
498 #ifndef CYTHON_USE_FREELISTS
|
|
jpayne@69
|
499 #define CYTHON_USE_FREELISTS 1
|
|
jpayne@69
|
500 #endif
|
|
jpayne@69
|
501 #endif
|
|
jpayne@69
|
502 #if !defined(CYTHON_FAST_PYCCALL)
|
|
jpayne@69
|
503 #define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
|
|
jpayne@69
|
504 #endif
|
|
jpayne@69
|
505 #if !defined(CYTHON_VECTORCALL)
|
|
jpayne@69
|
506 #define CYTHON_VECTORCALL (CYTHON_FAST_PYCCALL && PY_VERSION_HEX >= 0x030800B1)
|
|
jpayne@69
|
507 #endif
|
|
jpayne@69
|
508 #define CYTHON_BACKPORT_VECTORCALL (CYTHON_METH_FASTCALL && PY_VERSION_HEX < 0x030800B1)
|
|
jpayne@69
|
509 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
510 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
511 #include "longintrepr.h"
|
|
jpayne@69
|
512 #endif
|
|
jpayne@69
|
513 #undef SHIFT
|
|
jpayne@69
|
514 #undef BASE
|
|
jpayne@69
|
515 #undef MASK
|
|
jpayne@69
|
516 #ifdef SIZEOF_VOID_P
|
|
jpayne@69
|
517 enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) };
|
|
jpayne@69
|
518 #endif
|
|
jpayne@69
|
519 #endif
|
|
jpayne@69
|
520 #ifndef __has_attribute
|
|
jpayne@69
|
521 #define __has_attribute(x) 0
|
|
jpayne@69
|
522 #endif
|
|
jpayne@69
|
523 #ifndef __has_cpp_attribute
|
|
jpayne@69
|
524 #define __has_cpp_attribute(x) 0
|
|
jpayne@69
|
525 #endif
|
|
jpayne@69
|
526 #ifndef CYTHON_RESTRICT
|
|
jpayne@69
|
527 #if defined(__GNUC__)
|
|
jpayne@69
|
528 #define CYTHON_RESTRICT __restrict__
|
|
jpayne@69
|
529 #elif defined(_MSC_VER) && _MSC_VER >= 1400
|
|
jpayne@69
|
530 #define CYTHON_RESTRICT __restrict
|
|
jpayne@69
|
531 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
|
|
jpayne@69
|
532 #define CYTHON_RESTRICT restrict
|
|
jpayne@69
|
533 #else
|
|
jpayne@69
|
534 #define CYTHON_RESTRICT
|
|
jpayne@69
|
535 #endif
|
|
jpayne@69
|
536 #endif
|
|
jpayne@69
|
537 #ifndef CYTHON_UNUSED
|
|
jpayne@69
|
538 #if defined(__cplusplus)
|
|
jpayne@69
|
539 /* for clang __has_cpp_attribute(maybe_unused) is true even before C++17
|
|
jpayne@69
|
540 * but leads to warnings with -pedantic, since it is a C++17 feature */
|
|
jpayne@69
|
541 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
|
|
jpayne@69
|
542 #if __has_cpp_attribute(maybe_unused)
|
|
jpayne@69
|
543 #define CYTHON_UNUSED [[maybe_unused]]
|
|
jpayne@69
|
544 #endif
|
|
jpayne@69
|
545 #endif
|
|
jpayne@69
|
546 #endif
|
|
jpayne@69
|
547 #endif
|
|
jpayne@69
|
548 #ifndef CYTHON_UNUSED
|
|
jpayne@69
|
549 # if defined(__GNUC__)
|
|
jpayne@69
|
550 # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
|
|
jpayne@69
|
551 # define CYTHON_UNUSED __attribute__ ((__unused__))
|
|
jpayne@69
|
552 # else
|
|
jpayne@69
|
553 # define CYTHON_UNUSED
|
|
jpayne@69
|
554 # endif
|
|
jpayne@69
|
555 # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
|
|
jpayne@69
|
556 # define CYTHON_UNUSED __attribute__ ((__unused__))
|
|
jpayne@69
|
557 # else
|
|
jpayne@69
|
558 # define CYTHON_UNUSED
|
|
jpayne@69
|
559 # endif
|
|
jpayne@69
|
560 #endif
|
|
jpayne@69
|
561 #ifndef CYTHON_UNUSED_VAR
|
|
jpayne@69
|
562 # if defined(__cplusplus)
|
|
jpayne@69
|
563 template<class T> void CYTHON_UNUSED_VAR( const T& ) { }
|
|
jpayne@69
|
564 # else
|
|
jpayne@69
|
565 # define CYTHON_UNUSED_VAR(x) (void)(x)
|
|
jpayne@69
|
566 # endif
|
|
jpayne@69
|
567 #endif
|
|
jpayne@69
|
568 #ifndef CYTHON_MAYBE_UNUSED_VAR
|
|
jpayne@69
|
569 #define CYTHON_MAYBE_UNUSED_VAR(x) CYTHON_UNUSED_VAR(x)
|
|
jpayne@69
|
570 #endif
|
|
jpayne@69
|
571 #ifndef CYTHON_NCP_UNUSED
|
|
jpayne@69
|
572 # if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
573 # define CYTHON_NCP_UNUSED
|
|
jpayne@69
|
574 # else
|
|
jpayne@69
|
575 # define CYTHON_NCP_UNUSED CYTHON_UNUSED
|
|
jpayne@69
|
576 # endif
|
|
jpayne@69
|
577 #endif
|
|
jpayne@69
|
578 #ifndef CYTHON_USE_CPP_STD_MOVE
|
|
jpayne@69
|
579 #if defined(__cplusplus) && (\
|
|
jpayne@69
|
580 __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600))
|
|
jpayne@69
|
581 #define CYTHON_USE_CPP_STD_MOVE 1
|
|
jpayne@69
|
582 #else
|
|
jpayne@69
|
583 #define CYTHON_USE_CPP_STD_MOVE 0
|
|
jpayne@69
|
584 #endif
|
|
jpayne@69
|
585 #endif
|
|
jpayne@69
|
586 #define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
|
|
jpayne@69
|
587 #ifdef _MSC_VER
|
|
jpayne@69
|
588 #ifndef _MSC_STDINT_H_
|
|
jpayne@69
|
589 #if _MSC_VER < 1300
|
|
jpayne@69
|
590 typedef unsigned char uint8_t;
|
|
jpayne@69
|
591 typedef unsigned short uint16_t;
|
|
jpayne@69
|
592 typedef unsigned int uint32_t;
|
|
jpayne@69
|
593 #else
|
|
jpayne@69
|
594 typedef unsigned __int8 uint8_t;
|
|
jpayne@69
|
595 typedef unsigned __int16 uint16_t;
|
|
jpayne@69
|
596 typedef unsigned __int32 uint32_t;
|
|
jpayne@69
|
597 #endif
|
|
jpayne@69
|
598 #endif
|
|
jpayne@69
|
599 #if _MSC_VER < 1300
|
|
jpayne@69
|
600 #ifdef _WIN64
|
|
jpayne@69
|
601 typedef unsigned long long __pyx_uintptr_t;
|
|
jpayne@69
|
602 #else
|
|
jpayne@69
|
603 typedef unsigned int __pyx_uintptr_t;
|
|
jpayne@69
|
604 #endif
|
|
jpayne@69
|
605 #else
|
|
jpayne@69
|
606 #ifdef _WIN64
|
|
jpayne@69
|
607 typedef unsigned __int64 __pyx_uintptr_t;
|
|
jpayne@69
|
608 #else
|
|
jpayne@69
|
609 typedef unsigned __int32 __pyx_uintptr_t;
|
|
jpayne@69
|
610 #endif
|
|
jpayne@69
|
611 #endif
|
|
jpayne@69
|
612 #else
|
|
jpayne@69
|
613 #include <stdint.h>
|
|
jpayne@69
|
614 typedef uintptr_t __pyx_uintptr_t;
|
|
jpayne@69
|
615 #endif
|
|
jpayne@69
|
616 #ifndef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
617 #if defined(__cplusplus)
|
|
jpayne@69
|
618 /* for clang __has_cpp_attribute(fallthrough) is true even before C++17
|
|
jpayne@69
|
619 * but leads to warnings with -pedantic, since it is a C++17 feature */
|
|
jpayne@69
|
620 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
|
|
jpayne@69
|
621 #if __has_cpp_attribute(fallthrough)
|
|
jpayne@69
|
622 #define CYTHON_FALLTHROUGH [[fallthrough]]
|
|
jpayne@69
|
623 #endif
|
|
jpayne@69
|
624 #endif
|
|
jpayne@69
|
625 #ifndef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
626 #if __has_cpp_attribute(clang::fallthrough)
|
|
jpayne@69
|
627 #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
|
|
jpayne@69
|
628 #elif __has_cpp_attribute(gnu::fallthrough)
|
|
jpayne@69
|
629 #define CYTHON_FALLTHROUGH [[gnu::fallthrough]]
|
|
jpayne@69
|
630 #endif
|
|
jpayne@69
|
631 #endif
|
|
jpayne@69
|
632 #endif
|
|
jpayne@69
|
633 #ifndef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
634 #if __has_attribute(fallthrough)
|
|
jpayne@69
|
635 #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
|
|
jpayne@69
|
636 #else
|
|
jpayne@69
|
637 #define CYTHON_FALLTHROUGH
|
|
jpayne@69
|
638 #endif
|
|
jpayne@69
|
639 #endif
|
|
jpayne@69
|
640 #if defined(__clang__) && defined(__apple_build_version__)
|
|
jpayne@69
|
641 #if __apple_build_version__ < 7000000
|
|
jpayne@69
|
642 #undef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
643 #define CYTHON_FALLTHROUGH
|
|
jpayne@69
|
644 #endif
|
|
jpayne@69
|
645 #endif
|
|
jpayne@69
|
646 #endif
|
|
jpayne@69
|
647 #ifdef __cplusplus
|
|
jpayne@69
|
648 template <typename T>
|
|
jpayne@69
|
649 struct __PYX_IS_UNSIGNED_IMPL {static const bool value = T(0) < T(-1);};
|
|
jpayne@69
|
650 #define __PYX_IS_UNSIGNED(type) (__PYX_IS_UNSIGNED_IMPL<type>::value)
|
|
jpayne@69
|
651 #else
|
|
jpayne@69
|
652 #define __PYX_IS_UNSIGNED(type) (((type)-1) > 0)
|
|
jpayne@69
|
653 #endif
|
|
jpayne@69
|
654 #if CYTHON_COMPILING_IN_PYPY == 1
|
|
jpayne@69
|
655 #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x030A0000)
|
|
jpayne@69
|
656 #else
|
|
jpayne@69
|
657 #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000)
|
|
jpayne@69
|
658 #endif
|
|
jpayne@69
|
659 #define __PYX_REINTERPRET_FUNCION(func_pointer, other_pointer) ((func_pointer)(void(*)(void))(other_pointer))
|
|
jpayne@69
|
660
|
|
jpayne@69
|
661 #ifndef CYTHON_INLINE
|
|
jpayne@69
|
662 #if defined(__clang__)
|
|
jpayne@69
|
663 #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
|
|
jpayne@69
|
664 #elif defined(__GNUC__)
|
|
jpayne@69
|
665 #define CYTHON_INLINE __inline__
|
|
jpayne@69
|
666 #elif defined(_MSC_VER)
|
|
jpayne@69
|
667 #define CYTHON_INLINE __inline
|
|
jpayne@69
|
668 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
|
|
jpayne@69
|
669 #define CYTHON_INLINE inline
|
|
jpayne@69
|
670 #else
|
|
jpayne@69
|
671 #define CYTHON_INLINE
|
|
jpayne@69
|
672 #endif
|
|
jpayne@69
|
673 #endif
|
|
jpayne@69
|
674
|
|
jpayne@69
|
675 #define __PYX_BUILD_PY_SSIZE_T "n"
|
|
jpayne@69
|
676 #define CYTHON_FORMAT_SSIZE_T "z"
|
|
jpayne@69
|
677 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
678 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
|
|
jpayne@69
|
679 #define __Pyx_DefaultClassType PyClass_Type
|
|
jpayne@69
|
680 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
|
|
jpayne@69
|
681 PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
|
|
jpayne@69
|
682 #else
|
|
jpayne@69
|
683 #define __Pyx_BUILTIN_MODULE_NAME "builtins"
|
|
jpayne@69
|
684 #define __Pyx_DefaultClassType PyType_Type
|
|
jpayne@69
|
685 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
686 static CYTHON_INLINE PyObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f,
|
|
jpayne@69
|
687 PyObject *code, PyObject *c, PyObject* n, PyObject *v,
|
|
jpayne@69
|
688 PyObject *fv, PyObject *cell, PyObject* fn,
|
|
jpayne@69
|
689 PyObject *name, int fline, PyObject *lnos) {
|
|
jpayne@69
|
690 PyObject *exception_table = NULL;
|
|
jpayne@69
|
691 PyObject *types_module=NULL, *code_type=NULL, *result=NULL;
|
|
jpayne@69
|
692 #if __PYX_LIMITED_VERSION_HEX < 0x030B0000
|
|
jpayne@69
|
693 PyObject *version_info;
|
|
jpayne@69
|
694 PyObject *py_minor_version = NULL;
|
|
jpayne@69
|
695 #endif
|
|
jpayne@69
|
696 long minor_version = 0;
|
|
jpayne@69
|
697 PyObject *type, *value, *traceback;
|
|
jpayne@69
|
698 PyErr_Fetch(&type, &value, &traceback);
|
|
jpayne@69
|
699 #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000
|
|
jpayne@69
|
700 minor_version = 11;
|
|
jpayne@69
|
701 #else
|
|
jpayne@69
|
702 if (!(version_info = PySys_GetObject("version_info"))) goto end;
|
|
jpayne@69
|
703 if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end;
|
|
jpayne@69
|
704 minor_version = PyLong_AsLong(py_minor_version);
|
|
jpayne@69
|
705 Py_DECREF(py_minor_version);
|
|
jpayne@69
|
706 if (minor_version == -1 && PyErr_Occurred()) goto end;
|
|
jpayne@69
|
707 #endif
|
|
jpayne@69
|
708 if (!(types_module = PyImport_ImportModule("types"))) goto end;
|
|
jpayne@69
|
709 if (!(code_type = PyObject_GetAttrString(types_module, "CodeType"))) goto end;
|
|
jpayne@69
|
710 if (minor_version <= 7) {
|
|
jpayne@69
|
711 (void)p;
|
|
jpayne@69
|
712 result = PyObject_CallFunction(code_type, "iiiiiOOOOOOiOO", a, k, l, s, f, code,
|
|
jpayne@69
|
713 c, n, v, fn, name, fline, lnos, fv, cell);
|
|
jpayne@69
|
714 } else if (minor_version <= 10) {
|
|
jpayne@69
|
715 result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOiOO", a,p, k, l, s, f, code,
|
|
jpayne@69
|
716 c, n, v, fn, name, fline, lnos, fv, cell);
|
|
jpayne@69
|
717 } else {
|
|
jpayne@69
|
718 if (!(exception_table = PyBytes_FromStringAndSize(NULL, 0))) goto end;
|
|
jpayne@69
|
719 result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOOiOO", a,p, k, l, s, f, code,
|
|
jpayne@69
|
720 c, n, v, fn, name, name, fline, lnos, exception_table, fv, cell);
|
|
jpayne@69
|
721 }
|
|
jpayne@69
|
722 end:
|
|
jpayne@69
|
723 Py_XDECREF(code_type);
|
|
jpayne@69
|
724 Py_XDECREF(exception_table);
|
|
jpayne@69
|
725 Py_XDECREF(types_module);
|
|
jpayne@69
|
726 if (type) {
|
|
jpayne@69
|
727 PyErr_Restore(type, value, traceback);
|
|
jpayne@69
|
728 }
|
|
jpayne@69
|
729 return result;
|
|
jpayne@69
|
730 }
|
|
jpayne@69
|
731 #ifndef CO_OPTIMIZED
|
|
jpayne@69
|
732 #define CO_OPTIMIZED 0x0001
|
|
jpayne@69
|
733 #endif
|
|
jpayne@69
|
734 #ifndef CO_NEWLOCALS
|
|
jpayne@69
|
735 #define CO_NEWLOCALS 0x0002
|
|
jpayne@69
|
736 #endif
|
|
jpayne@69
|
737 #ifndef CO_VARARGS
|
|
jpayne@69
|
738 #define CO_VARARGS 0x0004
|
|
jpayne@69
|
739 #endif
|
|
jpayne@69
|
740 #ifndef CO_VARKEYWORDS
|
|
jpayne@69
|
741 #define CO_VARKEYWORDS 0x0008
|
|
jpayne@69
|
742 #endif
|
|
jpayne@69
|
743 #ifndef CO_ASYNC_GENERATOR
|
|
jpayne@69
|
744 #define CO_ASYNC_GENERATOR 0x0200
|
|
jpayne@69
|
745 #endif
|
|
jpayne@69
|
746 #ifndef CO_GENERATOR
|
|
jpayne@69
|
747 #define CO_GENERATOR 0x0020
|
|
jpayne@69
|
748 #endif
|
|
jpayne@69
|
749 #ifndef CO_COROUTINE
|
|
jpayne@69
|
750 #define CO_COROUTINE 0x0080
|
|
jpayne@69
|
751 #endif
|
|
jpayne@69
|
752 #elif PY_VERSION_HEX >= 0x030B0000
|
|
jpayne@69
|
753 static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f,
|
|
jpayne@69
|
754 PyObject *code, PyObject *c, PyObject* n, PyObject *v,
|
|
jpayne@69
|
755 PyObject *fv, PyObject *cell, PyObject* fn,
|
|
jpayne@69
|
756 PyObject *name, int fline, PyObject *lnos) {
|
|
jpayne@69
|
757 PyCodeObject *result;
|
|
jpayne@69
|
758 PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);
|
|
jpayne@69
|
759 if (!empty_bytes) return NULL;
|
|
jpayne@69
|
760 result =
|
|
jpayne@69
|
761 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
762 PyUnstable_Code_NewWithPosOnlyArgs
|
|
jpayne@69
|
763 #else
|
|
jpayne@69
|
764 PyCode_NewWithPosOnlyArgs
|
|
jpayne@69
|
765 #endif
|
|
jpayne@69
|
766 (a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, name, fline, lnos, empty_bytes);
|
|
jpayne@69
|
767 Py_DECREF(empty_bytes);
|
|
jpayne@69
|
768 return result;
|
|
jpayne@69
|
769 }
|
|
jpayne@69
|
770 #elif PY_VERSION_HEX >= 0x030800B2 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
771 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
|
|
jpayne@69
|
772 PyCode_NewWithPosOnlyArgs(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
|
|
jpayne@69
|
773 #else
|
|
jpayne@69
|
774 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
|
|
jpayne@69
|
775 PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
|
|
jpayne@69
|
776 #endif
|
|
jpayne@69
|
777 #endif
|
|
jpayne@69
|
778 #if PY_VERSION_HEX >= 0x030900A4 || defined(Py_IS_TYPE)
|
|
jpayne@69
|
779 #define __Pyx_IS_TYPE(ob, type) Py_IS_TYPE(ob, type)
|
|
jpayne@69
|
780 #else
|
|
jpayne@69
|
781 #define __Pyx_IS_TYPE(ob, type) (((const PyObject*)ob)->ob_type == (type))
|
|
jpayne@69
|
782 #endif
|
|
jpayne@69
|
783 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_Is)
|
|
jpayne@69
|
784 #define __Pyx_Py_Is(x, y) Py_Is(x, y)
|
|
jpayne@69
|
785 #else
|
|
jpayne@69
|
786 #define __Pyx_Py_Is(x, y) ((x) == (y))
|
|
jpayne@69
|
787 #endif
|
|
jpayne@69
|
788 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsNone)
|
|
jpayne@69
|
789 #define __Pyx_Py_IsNone(ob) Py_IsNone(ob)
|
|
jpayne@69
|
790 #else
|
|
jpayne@69
|
791 #define __Pyx_Py_IsNone(ob) __Pyx_Py_Is((ob), Py_None)
|
|
jpayne@69
|
792 #endif
|
|
jpayne@69
|
793 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsTrue)
|
|
jpayne@69
|
794 #define __Pyx_Py_IsTrue(ob) Py_IsTrue(ob)
|
|
jpayne@69
|
795 #else
|
|
jpayne@69
|
796 #define __Pyx_Py_IsTrue(ob) __Pyx_Py_Is((ob), Py_True)
|
|
jpayne@69
|
797 #endif
|
|
jpayne@69
|
798 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsFalse)
|
|
jpayne@69
|
799 #define __Pyx_Py_IsFalse(ob) Py_IsFalse(ob)
|
|
jpayne@69
|
800 #else
|
|
jpayne@69
|
801 #define __Pyx_Py_IsFalse(ob) __Pyx_Py_Is((ob), Py_False)
|
|
jpayne@69
|
802 #endif
|
|
jpayne@69
|
803 #define __Pyx_NoneAsNull(obj) (__Pyx_Py_IsNone(obj) ? NULL : (obj))
|
|
jpayne@69
|
804 #if PY_VERSION_HEX >= 0x030900F0 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
805 #define __Pyx_PyObject_GC_IsFinalized(o) PyObject_GC_IsFinalized(o)
|
|
jpayne@69
|
806 #else
|
|
jpayne@69
|
807 #define __Pyx_PyObject_GC_IsFinalized(o) _PyGC_FINALIZED(o)
|
|
jpayne@69
|
808 #endif
|
|
jpayne@69
|
809 #ifndef CO_COROUTINE
|
|
jpayne@69
|
810 #define CO_COROUTINE 0x80
|
|
jpayne@69
|
811 #endif
|
|
jpayne@69
|
812 #ifndef CO_ASYNC_GENERATOR
|
|
jpayne@69
|
813 #define CO_ASYNC_GENERATOR 0x200
|
|
jpayne@69
|
814 #endif
|
|
jpayne@69
|
815 #ifndef Py_TPFLAGS_CHECKTYPES
|
|
jpayne@69
|
816 #define Py_TPFLAGS_CHECKTYPES 0
|
|
jpayne@69
|
817 #endif
|
|
jpayne@69
|
818 #ifndef Py_TPFLAGS_HAVE_INDEX
|
|
jpayne@69
|
819 #define Py_TPFLAGS_HAVE_INDEX 0
|
|
jpayne@69
|
820 #endif
|
|
jpayne@69
|
821 #ifndef Py_TPFLAGS_HAVE_NEWBUFFER
|
|
jpayne@69
|
822 #define Py_TPFLAGS_HAVE_NEWBUFFER 0
|
|
jpayne@69
|
823 #endif
|
|
jpayne@69
|
824 #ifndef Py_TPFLAGS_HAVE_FINALIZE
|
|
jpayne@69
|
825 #define Py_TPFLAGS_HAVE_FINALIZE 0
|
|
jpayne@69
|
826 #endif
|
|
jpayne@69
|
827 #ifndef Py_TPFLAGS_SEQUENCE
|
|
jpayne@69
|
828 #define Py_TPFLAGS_SEQUENCE 0
|
|
jpayne@69
|
829 #endif
|
|
jpayne@69
|
830 #ifndef Py_TPFLAGS_MAPPING
|
|
jpayne@69
|
831 #define Py_TPFLAGS_MAPPING 0
|
|
jpayne@69
|
832 #endif
|
|
jpayne@69
|
833 #ifndef METH_STACKLESS
|
|
jpayne@69
|
834 #define METH_STACKLESS 0
|
|
jpayne@69
|
835 #endif
|
|
jpayne@69
|
836 #if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL)
|
|
jpayne@69
|
837 #ifndef METH_FASTCALL
|
|
jpayne@69
|
838 #define METH_FASTCALL 0x80
|
|
jpayne@69
|
839 #endif
|
|
jpayne@69
|
840 typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs);
|
|
jpayne@69
|
841 typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
|
|
jpayne@69
|
842 Py_ssize_t nargs, PyObject *kwnames);
|
|
jpayne@69
|
843 #else
|
|
jpayne@69
|
844 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
845 # define __Pyx_PyCFunctionFast PyCFunctionFast
|
|
jpayne@69
|
846 # define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords
|
|
jpayne@69
|
847 #else
|
|
jpayne@69
|
848 # define __Pyx_PyCFunctionFast _PyCFunctionFast
|
|
jpayne@69
|
849 # define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
|
|
jpayne@69
|
850 #endif
|
|
jpayne@69
|
851 #endif
|
|
jpayne@69
|
852 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
853 #define __Pyx_METH_FASTCALL METH_FASTCALL
|
|
jpayne@69
|
854 #define __Pyx_PyCFunction_FastCall __Pyx_PyCFunctionFast
|
|
jpayne@69
|
855 #define __Pyx_PyCFunction_FastCallWithKeywords __Pyx_PyCFunctionFastWithKeywords
|
|
jpayne@69
|
856 #else
|
|
jpayne@69
|
857 #define __Pyx_METH_FASTCALL METH_VARARGS
|
|
jpayne@69
|
858 #define __Pyx_PyCFunction_FastCall PyCFunction
|
|
jpayne@69
|
859 #define __Pyx_PyCFunction_FastCallWithKeywords PyCFunctionWithKeywords
|
|
jpayne@69
|
860 #endif
|
|
jpayne@69
|
861 #if CYTHON_VECTORCALL
|
|
jpayne@69
|
862 #define __pyx_vectorcallfunc vectorcallfunc
|
|
jpayne@69
|
863 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET PY_VECTORCALL_ARGUMENTS_OFFSET
|
|
jpayne@69
|
864 #define __Pyx_PyVectorcall_NARGS(n) PyVectorcall_NARGS((size_t)(n))
|
|
jpayne@69
|
865 #elif CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
866 typedef PyObject *(*__pyx_vectorcallfunc)(PyObject *callable, PyObject *const *args,
|
|
jpayne@69
|
867 size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
868 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET ((size_t)1 << (8 * sizeof(size_t) - 1))
|
|
jpayne@69
|
869 #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(((size_t)(n)) & ~__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET))
|
|
jpayne@69
|
870 #else
|
|
jpayne@69
|
871 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET 0
|
|
jpayne@69
|
872 #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(n))
|
|
jpayne@69
|
873 #endif
|
|
jpayne@69
|
874 #if PY_MAJOR_VERSION >= 0x030900B1
|
|
jpayne@69
|
875 #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_CheckExact(func)
|
|
jpayne@69
|
876 #else
|
|
jpayne@69
|
877 #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_Check(func)
|
|
jpayne@69
|
878 #endif
|
|
jpayne@69
|
879 #define __Pyx_CyOrPyCFunction_Check(func) PyCFunction_Check(func)
|
|
jpayne@69
|
880 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
881 #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) (((PyCFunctionObject*)(func))->m_ml->ml_meth)
|
|
jpayne@69
|
882 #elif !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
883 #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) PyCFunction_GET_FUNCTION(func)
|
|
jpayne@69
|
884 #endif
|
|
jpayne@69
|
885 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
886 #define __Pyx_CyOrPyCFunction_GET_FLAGS(func) (((PyCFunctionObject*)(func))->m_ml->ml_flags)
|
|
jpayne@69
|
887 static CYTHON_INLINE PyObject* __Pyx_CyOrPyCFunction_GET_SELF(PyObject *func) {
|
|
jpayne@69
|
888 return (__Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_STATIC) ? NULL : ((PyCFunctionObject*)func)->m_self;
|
|
jpayne@69
|
889 }
|
|
jpayne@69
|
890 #endif
|
|
jpayne@69
|
891 static CYTHON_INLINE int __Pyx__IsSameCFunction(PyObject *func, void *cfunc) {
|
|
jpayne@69
|
892 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
893 return PyCFunction_Check(func) && PyCFunction_GetFunction(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
894 #else
|
|
jpayne@69
|
895 return PyCFunction_Check(func) && PyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
896 #endif
|
|
jpayne@69
|
897 }
|
|
jpayne@69
|
898 #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCFunction(func, cfunc)
|
|
jpayne@69
|
899 #if __PYX_LIMITED_VERSION_HEX < 0x030900B1
|
|
jpayne@69
|
900 #define __Pyx_PyType_FromModuleAndSpec(m, s, b) ((void)m, PyType_FromSpecWithBases(s, b))
|
|
jpayne@69
|
901 typedef PyObject *(*__Pyx_PyCMethod)(PyObject *, PyTypeObject *, PyObject *const *, size_t, PyObject *);
|
|
jpayne@69
|
902 #else
|
|
jpayne@69
|
903 #define __Pyx_PyType_FromModuleAndSpec(m, s, b) PyType_FromModuleAndSpec(m, s, b)
|
|
jpayne@69
|
904 #define __Pyx_PyCMethod PyCMethod
|
|
jpayne@69
|
905 #endif
|
|
jpayne@69
|
906 #ifndef METH_METHOD
|
|
jpayne@69
|
907 #define METH_METHOD 0x200
|
|
jpayne@69
|
908 #endif
|
|
jpayne@69
|
909 #if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
|
|
jpayne@69
|
910 #define PyObject_Malloc(s) PyMem_Malloc(s)
|
|
jpayne@69
|
911 #define PyObject_Free(p) PyMem_Free(p)
|
|
jpayne@69
|
912 #define PyObject_Realloc(p) PyMem_Realloc(p)
|
|
jpayne@69
|
913 #endif
|
|
jpayne@69
|
914 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
915 #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
|
|
jpayne@69
|
916 #define __Pyx_PyFrame_SetLineNumber(frame, lineno)
|
|
jpayne@69
|
917 #else
|
|
jpayne@69
|
918 #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
|
|
jpayne@69
|
919 #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
|
|
jpayne@69
|
920 #endif
|
|
jpayne@69
|
921 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
922 #define __Pyx_PyThreadState_Current PyThreadState_Get()
|
|
jpayne@69
|
923 #elif !CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
924 #define __Pyx_PyThreadState_Current PyThreadState_GET()
|
|
jpayne@69
|
925 #elif PY_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
926 #define __Pyx_PyThreadState_Current PyThreadState_GetUnchecked()
|
|
jpayne@69
|
927 #elif PY_VERSION_HEX >= 0x03060000
|
|
jpayne@69
|
928 #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet()
|
|
jpayne@69
|
929 #elif PY_VERSION_HEX >= 0x03000000
|
|
jpayne@69
|
930 #define __Pyx_PyThreadState_Current PyThreadState_GET()
|
|
jpayne@69
|
931 #else
|
|
jpayne@69
|
932 #define __Pyx_PyThreadState_Current _PyThreadState_Current
|
|
jpayne@69
|
933 #endif
|
|
jpayne@69
|
934 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
935 static CYTHON_INLINE void *__Pyx_PyModule_GetState(PyObject *op)
|
|
jpayne@69
|
936 {
|
|
jpayne@69
|
937 void *result;
|
|
jpayne@69
|
938 result = PyModule_GetState(op);
|
|
jpayne@69
|
939 if (!result)
|
|
jpayne@69
|
940 Py_FatalError("Couldn't find the module state");
|
|
jpayne@69
|
941 return result;
|
|
jpayne@69
|
942 }
|
|
jpayne@69
|
943 #endif
|
|
jpayne@69
|
944 #define __Pyx_PyObject_GetSlot(obj, name, func_ctype) __Pyx_PyType_GetSlot(Py_TYPE(obj), name, func_ctype)
|
|
jpayne@69
|
945 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
946 #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((func_ctype) PyType_GetSlot((type), Py_##name))
|
|
jpayne@69
|
947 #else
|
|
jpayne@69
|
948 #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((type)->name)
|
|
jpayne@69
|
949 #endif
|
|
jpayne@69
|
950 #if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT)
|
|
jpayne@69
|
951 #include "pythread.h"
|
|
jpayne@69
|
952 #define Py_tss_NEEDS_INIT 0
|
|
jpayne@69
|
953 typedef int Py_tss_t;
|
|
jpayne@69
|
954 static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) {
|
|
jpayne@69
|
955 *key = PyThread_create_key();
|
|
jpayne@69
|
956 return 0;
|
|
jpayne@69
|
957 }
|
|
jpayne@69
|
958 static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) {
|
|
jpayne@69
|
959 Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t));
|
|
jpayne@69
|
960 *key = Py_tss_NEEDS_INIT;
|
|
jpayne@69
|
961 return key;
|
|
jpayne@69
|
962 }
|
|
jpayne@69
|
963 static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) {
|
|
jpayne@69
|
964 PyObject_Free(key);
|
|
jpayne@69
|
965 }
|
|
jpayne@69
|
966 static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) {
|
|
jpayne@69
|
967 return *key != Py_tss_NEEDS_INIT;
|
|
jpayne@69
|
968 }
|
|
jpayne@69
|
969 static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) {
|
|
jpayne@69
|
970 PyThread_delete_key(*key);
|
|
jpayne@69
|
971 *key = Py_tss_NEEDS_INIT;
|
|
jpayne@69
|
972 }
|
|
jpayne@69
|
973 static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) {
|
|
jpayne@69
|
974 return PyThread_set_key_value(*key, value);
|
|
jpayne@69
|
975 }
|
|
jpayne@69
|
976 static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
|
|
jpayne@69
|
977 return PyThread_get_key_value(*key);
|
|
jpayne@69
|
978 }
|
|
jpayne@69
|
979 #endif
|
|
jpayne@69
|
980 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
981 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
982 #if PYPY_VERSION_NUM < 0x07030600
|
|
jpayne@69
|
983 #if defined(__cplusplus) && __cplusplus >= 201402L
|
|
jpayne@69
|
984 [[deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")]]
|
|
jpayne@69
|
985 #elif defined(__GNUC__) || defined(__clang__)
|
|
jpayne@69
|
986 __attribute__ ((__deprecated__("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")))
|
|
jpayne@69
|
987 #elif defined(_MSC_VER)
|
|
jpayne@69
|
988 __declspec(deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6"))
|
|
jpayne@69
|
989 #endif
|
|
jpayne@69
|
990 static CYTHON_INLINE int PyGILState_Check(void) {
|
|
jpayne@69
|
991 return 0;
|
|
jpayne@69
|
992 }
|
|
jpayne@69
|
993 #else // PYPY_VERSION_NUM < 0x07030600
|
|
jpayne@69
|
994 #endif // PYPY_VERSION_NUM < 0x07030600
|
|
jpayne@69
|
995 #else
|
|
jpayne@69
|
996 static CYTHON_INLINE int PyGILState_Check(void) {
|
|
jpayne@69
|
997 PyThreadState * tstate = _PyThreadState_Current;
|
|
jpayne@69
|
998 return tstate && (tstate == PyGILState_GetThisThreadState());
|
|
jpayne@69
|
999 }
|
|
jpayne@69
|
1000 #endif
|
|
jpayne@69
|
1001 #endif
|
|
jpayne@69
|
1002 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030d0000 || defined(_PyDict_NewPresized)
|
|
jpayne@69
|
1003 #define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n))
|
|
jpayne@69
|
1004 #else
|
|
jpayne@69
|
1005 #define __Pyx_PyDict_NewPresized(n) PyDict_New()
|
|
jpayne@69
|
1006 #endif
|
|
jpayne@69
|
1007 #if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION
|
|
jpayne@69
|
1008 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
|
|
jpayne@69
|
1009 #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
|
|
jpayne@69
|
1010 #else
|
|
jpayne@69
|
1011 #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
|
|
jpayne@69
|
1012 #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
|
|
jpayne@69
|
1013 #endif
|
|
jpayne@69
|
1014 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX > 0x030600B4 && PY_VERSION_HEX < 0x030d0000 && CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
1015 #define __Pyx_PyDict_GetItemStrWithError(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash)
|
|
jpayne@69
|
1016 static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStr(PyObject *dict, PyObject *name) {
|
|
jpayne@69
|
1017 PyObject *res = __Pyx_PyDict_GetItemStrWithError(dict, name);
|
|
jpayne@69
|
1018 if (res == NULL) PyErr_Clear();
|
|
jpayne@69
|
1019 return res;
|
|
jpayne@69
|
1020 }
|
|
jpayne@69
|
1021 #elif PY_MAJOR_VERSION >= 3 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07020000)
|
|
jpayne@69
|
1022 #define __Pyx_PyDict_GetItemStrWithError PyDict_GetItemWithError
|
|
jpayne@69
|
1023 #define __Pyx_PyDict_GetItemStr PyDict_GetItem
|
|
jpayne@69
|
1024 #else
|
|
jpayne@69
|
1025 static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict, PyObject *name) {
|
|
jpayne@69
|
1026 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1027 return PyDict_GetItem(dict, name);
|
|
jpayne@69
|
1028 #else
|
|
jpayne@69
|
1029 PyDictEntry *ep;
|
|
jpayne@69
|
1030 PyDictObject *mp = (PyDictObject*) dict;
|
|
jpayne@69
|
1031 long hash = ((PyStringObject *) name)->ob_shash;
|
|
jpayne@69
|
1032 assert(hash != -1);
|
|
jpayne@69
|
1033 ep = (mp->ma_lookup)(mp, name, hash);
|
|
jpayne@69
|
1034 if (ep == NULL) {
|
|
jpayne@69
|
1035 return NULL;
|
|
jpayne@69
|
1036 }
|
|
jpayne@69
|
1037 return ep->me_value;
|
|
jpayne@69
|
1038 #endif
|
|
jpayne@69
|
1039 }
|
|
jpayne@69
|
1040 #define __Pyx_PyDict_GetItemStr PyDict_GetItem
|
|
jpayne@69
|
1041 #endif
|
|
jpayne@69
|
1042 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
1043 #define __Pyx_PyType_GetFlags(tp) (((PyTypeObject *)tp)->tp_flags)
|
|
jpayne@69
|
1044 #define __Pyx_PyType_HasFeature(type, feature) ((__Pyx_PyType_GetFlags(type) & (feature)) != 0)
|
|
jpayne@69
|
1045 #define __Pyx_PyObject_GetIterNextFunc(obj) (Py_TYPE(obj)->tp_iternext)
|
|
jpayne@69
|
1046 #else
|
|
jpayne@69
|
1047 #define __Pyx_PyType_GetFlags(tp) (PyType_GetFlags((PyTypeObject *)tp))
|
|
jpayne@69
|
1048 #define __Pyx_PyType_HasFeature(type, feature) PyType_HasFeature(type, feature)
|
|
jpayne@69
|
1049 #define __Pyx_PyObject_GetIterNextFunc(obj) PyIter_Next
|
|
jpayne@69
|
1050 #endif
|
|
jpayne@69
|
1051 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
1052 #define __Pyx_SetItemOnTypeDict(tp, k, v) PyObject_GenericSetAttr((PyObject*)tp, k, v)
|
|
jpayne@69
|
1053 #else
|
|
jpayne@69
|
1054 #define __Pyx_SetItemOnTypeDict(tp, k, v) PyDict_SetItem(tp->tp_dict, k, v)
|
|
jpayne@69
|
1055 #endif
|
|
jpayne@69
|
1056 #if CYTHON_USE_TYPE_SPECS && PY_VERSION_HEX >= 0x03080000
|
|
jpayne@69
|
1057 #define __Pyx_PyHeapTypeObject_GC_Del(obj) {\
|
|
jpayne@69
|
1058 PyTypeObject *type = Py_TYPE((PyObject*)obj);\
|
|
jpayne@69
|
1059 assert(__Pyx_PyType_HasFeature(type, Py_TPFLAGS_HEAPTYPE));\
|
|
jpayne@69
|
1060 PyObject_GC_Del(obj);\
|
|
jpayne@69
|
1061 Py_DECREF(type);\
|
|
jpayne@69
|
1062 }
|
|
jpayne@69
|
1063 #else
|
|
jpayne@69
|
1064 #define __Pyx_PyHeapTypeObject_GC_Del(obj) PyObject_GC_Del(obj)
|
|
jpayne@69
|
1065 #endif
|
|
jpayne@69
|
1066 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
1067 #define CYTHON_PEP393_ENABLED 1
|
|
jpayne@69
|
1068 #define __Pyx_PyUnicode_READY(op) (0)
|
|
jpayne@69
|
1069 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GetLength(u)
|
|
jpayne@69
|
1070 #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_ReadChar(u, i)
|
|
jpayne@69
|
1071 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((void)u, 1114111U)
|
|
jpayne@69
|
1072 #define __Pyx_PyUnicode_KIND(u) ((void)u, (0))
|
|
jpayne@69
|
1073 #define __Pyx_PyUnicode_DATA(u) ((void*)u)
|
|
jpayne@69
|
1074 #define __Pyx_PyUnicode_READ(k, d, i) ((void)k, PyUnicode_ReadChar((PyObject*)(d), i))
|
|
jpayne@69
|
1075 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GetLength(u))
|
|
jpayne@69
|
1076 #elif PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
|
|
jpayne@69
|
1077 #define CYTHON_PEP393_ENABLED 1
|
|
jpayne@69
|
1078 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
1079 #define __Pyx_PyUnicode_READY(op) (0)
|
|
jpayne@69
|
1080 #else
|
|
jpayne@69
|
1081 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
|
|
jpayne@69
|
1082 0 : _PyUnicode_Ready((PyObject *)(op)))
|
|
jpayne@69
|
1083 #endif
|
|
jpayne@69
|
1084 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
|
|
jpayne@69
|
1085 #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
|
|
jpayne@69
|
1086 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
|
|
jpayne@69
|
1087 #define __Pyx_PyUnicode_KIND(u) ((int)PyUnicode_KIND(u))
|
|
jpayne@69
|
1088 #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
|
|
jpayne@69
|
1089 #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
|
|
jpayne@69
|
1090 #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, (Py_UCS4) ch)
|
|
jpayne@69
|
1091 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
1092 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u))
|
|
jpayne@69
|
1093 #else
|
|
jpayne@69
|
1094 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000
|
|
jpayne@69
|
1095 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length))
|
|
jpayne@69
|
1096 #else
|
|
jpayne@69
|
1097 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
|
|
jpayne@69
|
1098 #endif
|
|
jpayne@69
|
1099 #endif
|
|
jpayne@69
|
1100 #else
|
|
jpayne@69
|
1101 #define CYTHON_PEP393_ENABLED 0
|
|
jpayne@69
|
1102 #define PyUnicode_1BYTE_KIND 1
|
|
jpayne@69
|
1103 #define PyUnicode_2BYTE_KIND 2
|
|
jpayne@69
|
1104 #define PyUnicode_4BYTE_KIND 4
|
|
jpayne@69
|
1105 #define __Pyx_PyUnicode_READY(op) (0)
|
|
jpayne@69
|
1106 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
|
|
jpayne@69
|
1107 #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
|
|
jpayne@69
|
1108 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535U : 1114111U)
|
|
jpayne@69
|
1109 #define __Pyx_PyUnicode_KIND(u) ((int)sizeof(Py_UNICODE))
|
|
jpayne@69
|
1110 #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
|
|
jpayne@69
|
1111 #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
|
|
jpayne@69
|
1112 #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = (Py_UNICODE) ch)
|
|
jpayne@69
|
1113 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
|
|
jpayne@69
|
1114 #endif
|
|
jpayne@69
|
1115 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1116 #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
|
|
jpayne@69
|
1117 #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
|
|
jpayne@69
|
1118 #else
|
|
jpayne@69
|
1119 #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
|
|
jpayne@69
|
1120 #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
|
|
jpayne@69
|
1121 PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
|
|
jpayne@69
|
1122 #endif
|
|
jpayne@69
|
1123 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1124 #if !defined(PyUnicode_DecodeUnicodeEscape)
|
|
jpayne@69
|
1125 #define PyUnicode_DecodeUnicodeEscape(s, size, errors) PyUnicode_Decode(s, size, "unicode_escape", errors)
|
|
jpayne@69
|
1126 #endif
|
|
jpayne@69
|
1127 #if !defined(PyUnicode_Contains) || (PY_MAJOR_VERSION == 2 && PYPY_VERSION_NUM < 0x07030500)
|
|
jpayne@69
|
1128 #undef PyUnicode_Contains
|
|
jpayne@69
|
1129 #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
|
|
jpayne@69
|
1130 #endif
|
|
jpayne@69
|
1131 #if !defined(PyByteArray_Check)
|
|
jpayne@69
|
1132 #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type)
|
|
jpayne@69
|
1133 #endif
|
|
jpayne@69
|
1134 #if !defined(PyObject_Format)
|
|
jpayne@69
|
1135 #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt)
|
|
jpayne@69
|
1136 #endif
|
|
jpayne@69
|
1137 #endif
|
|
jpayne@69
|
1138 #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyString_Check(b) && !PyString_CheckExact(b)))) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
|
|
jpayne@69
|
1139 #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
|
|
jpayne@69
|
1140 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1141 #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
|
|
jpayne@69
|
1142 #else
|
|
jpayne@69
|
1143 #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
|
|
jpayne@69
|
1144 #endif
|
|
jpayne@69
|
1145 #if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
|
|
jpayne@69
|
1146 #define PyObject_ASCII(o) PyObject_Repr(o)
|
|
jpayne@69
|
1147 #endif
|
|
jpayne@69
|
1148 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1149 #define PyBaseString_Type PyUnicode_Type
|
|
jpayne@69
|
1150 #define PyStringObject PyUnicodeObject
|
|
jpayne@69
|
1151 #define PyString_Type PyUnicode_Type
|
|
jpayne@69
|
1152 #define PyString_Check PyUnicode_Check
|
|
jpayne@69
|
1153 #define PyString_CheckExact PyUnicode_CheckExact
|
|
jpayne@69
|
1154 #ifndef PyObject_Unicode
|
|
jpayne@69
|
1155 #define PyObject_Unicode PyObject_Str
|
|
jpayne@69
|
1156 #endif
|
|
jpayne@69
|
1157 #endif
|
|
jpayne@69
|
1158 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1159 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
|
|
jpayne@69
|
1160 #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
|
|
jpayne@69
|
1161 #else
|
|
jpayne@69
|
1162 #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
|
|
jpayne@69
|
1163 #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
|
|
jpayne@69
|
1164 #endif
|
|
jpayne@69
|
1165 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
1166 #define __Pyx_PySequence_ListKeepNew(obj)\
|
|
jpayne@69
|
1167 (likely(PyList_CheckExact(obj) && Py_REFCNT(obj) == 1) ? __Pyx_NewRef(obj) : PySequence_List(obj))
|
|
jpayne@69
|
1168 #else
|
|
jpayne@69
|
1169 #define __Pyx_PySequence_ListKeepNew(obj) PySequence_List(obj)
|
|
jpayne@69
|
1170 #endif
|
|
jpayne@69
|
1171 #ifndef PySet_CheckExact
|
|
jpayne@69
|
1172 #define PySet_CheckExact(obj) __Pyx_IS_TYPE(obj, &PySet_Type)
|
|
jpayne@69
|
1173 #endif
|
|
jpayne@69
|
1174 #if PY_VERSION_HEX >= 0x030900A4
|
|
jpayne@69
|
1175 #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt)
|
|
jpayne@69
|
1176 #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size)
|
|
jpayne@69
|
1177 #else
|
|
jpayne@69
|
1178 #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt)
|
|
jpayne@69
|
1179 #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size)
|
|
jpayne@69
|
1180 #endif
|
|
jpayne@69
|
1181 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
1182 #define __Pyx_PySequence_ITEM(o, i) PySequence_ITEM(o, i)
|
|
jpayne@69
|
1183 #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq)
|
|
jpayne@69
|
1184 #define __Pyx_PyTuple_SET_ITEM(o, i, v) (PyTuple_SET_ITEM(o, i, v), (0))
|
|
jpayne@69
|
1185 #define __Pyx_PyList_SET_ITEM(o, i, v) (PyList_SET_ITEM(o, i, v), (0))
|
|
jpayne@69
|
1186 #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_GET_SIZE(o)
|
|
jpayne@69
|
1187 #define __Pyx_PyList_GET_SIZE(o) PyList_GET_SIZE(o)
|
|
jpayne@69
|
1188 #define __Pyx_PySet_GET_SIZE(o) PySet_GET_SIZE(o)
|
|
jpayne@69
|
1189 #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_GET_SIZE(o)
|
|
jpayne@69
|
1190 #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_GET_SIZE(o)
|
|
jpayne@69
|
1191 #else
|
|
jpayne@69
|
1192 #define __Pyx_PySequence_ITEM(o, i) PySequence_GetItem(o, i)
|
|
jpayne@69
|
1193 #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq)
|
|
jpayne@69
|
1194 #define __Pyx_PyTuple_SET_ITEM(o, i, v) PyTuple_SetItem(o, i, v)
|
|
jpayne@69
|
1195 #define __Pyx_PyList_SET_ITEM(o, i, v) PyList_SetItem(o, i, v)
|
|
jpayne@69
|
1196 #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_Size(o)
|
|
jpayne@69
|
1197 #define __Pyx_PyList_GET_SIZE(o) PyList_Size(o)
|
|
jpayne@69
|
1198 #define __Pyx_PySet_GET_SIZE(o) PySet_Size(o)
|
|
jpayne@69
|
1199 #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o)
|
|
jpayne@69
|
1200 #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o)
|
|
jpayne@69
|
1201 #endif
|
|
jpayne@69
|
1202 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
1203 #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name)
|
|
jpayne@69
|
1204 #else
|
|
jpayne@69
|
1205 static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) {
|
|
jpayne@69
|
1206 PyObject *module = PyImport_AddModule(name);
|
|
jpayne@69
|
1207 Py_XINCREF(module);
|
|
jpayne@69
|
1208 return module;
|
|
jpayne@69
|
1209 }
|
|
jpayne@69
|
1210 #endif
|
|
jpayne@69
|
1211 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1212 #define PyIntObject PyLongObject
|
|
jpayne@69
|
1213 #define PyInt_Type PyLong_Type
|
|
jpayne@69
|
1214 #define PyInt_Check(op) PyLong_Check(op)
|
|
jpayne@69
|
1215 #define PyInt_CheckExact(op) PyLong_CheckExact(op)
|
|
jpayne@69
|
1216 #define __Pyx_Py3Int_Check(op) PyLong_Check(op)
|
|
jpayne@69
|
1217 #define __Pyx_Py3Int_CheckExact(op) PyLong_CheckExact(op)
|
|
jpayne@69
|
1218 #define PyInt_FromString PyLong_FromString
|
|
jpayne@69
|
1219 #define PyInt_FromUnicode PyLong_FromUnicode
|
|
jpayne@69
|
1220 #define PyInt_FromLong PyLong_FromLong
|
|
jpayne@69
|
1221 #define PyInt_FromSize_t PyLong_FromSize_t
|
|
jpayne@69
|
1222 #define PyInt_FromSsize_t PyLong_FromSsize_t
|
|
jpayne@69
|
1223 #define PyInt_AsLong PyLong_AsLong
|
|
jpayne@69
|
1224 #define PyInt_AS_LONG PyLong_AS_LONG
|
|
jpayne@69
|
1225 #define PyInt_AsSsize_t PyLong_AsSsize_t
|
|
jpayne@69
|
1226 #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
|
|
jpayne@69
|
1227 #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
|
|
jpayne@69
|
1228 #define PyNumber_Int PyNumber_Long
|
|
jpayne@69
|
1229 #else
|
|
jpayne@69
|
1230 #define __Pyx_Py3Int_Check(op) (PyLong_Check(op) || PyInt_Check(op))
|
|
jpayne@69
|
1231 #define __Pyx_Py3Int_CheckExact(op) (PyLong_CheckExact(op) || PyInt_CheckExact(op))
|
|
jpayne@69
|
1232 #endif
|
|
jpayne@69
|
1233 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1234 #define PyBoolObject PyLongObject
|
|
jpayne@69
|
1235 #endif
|
|
jpayne@69
|
1236 #if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1237 #ifndef PyUnicode_InternFromString
|
|
jpayne@69
|
1238 #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
|
|
jpayne@69
|
1239 #endif
|
|
jpayne@69
|
1240 #endif
|
|
jpayne@69
|
1241 #if PY_VERSION_HEX < 0x030200A4
|
|
jpayne@69
|
1242 typedef long Py_hash_t;
|
|
jpayne@69
|
1243 #define __Pyx_PyInt_FromHash_t PyInt_FromLong
|
|
jpayne@69
|
1244 #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t
|
|
jpayne@69
|
1245 #else
|
|
jpayne@69
|
1246 #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
|
|
jpayne@69
|
1247 #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t
|
|
jpayne@69
|
1248 #endif
|
|
jpayne@69
|
1249 #if CYTHON_USE_ASYNC_SLOTS
|
|
jpayne@69
|
1250 #if PY_VERSION_HEX >= 0x030500B1
|
|
jpayne@69
|
1251 #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
|
|
jpayne@69
|
1252 #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
|
|
jpayne@69
|
1253 #else
|
|
jpayne@69
|
1254 #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
|
|
jpayne@69
|
1255 #endif
|
|
jpayne@69
|
1256 #else
|
|
jpayne@69
|
1257 #define __Pyx_PyType_AsAsync(obj) NULL
|
|
jpayne@69
|
1258 #endif
|
|
jpayne@69
|
1259 #ifndef __Pyx_PyAsyncMethodsStruct
|
|
jpayne@69
|
1260 typedef struct {
|
|
jpayne@69
|
1261 unaryfunc am_await;
|
|
jpayne@69
|
1262 unaryfunc am_aiter;
|
|
jpayne@69
|
1263 unaryfunc am_anext;
|
|
jpayne@69
|
1264 } __Pyx_PyAsyncMethodsStruct;
|
|
jpayne@69
|
1265 #endif
|
|
jpayne@69
|
1266
|
|
jpayne@69
|
1267 #if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
|
|
jpayne@69
|
1268 #if !defined(_USE_MATH_DEFINES)
|
|
jpayne@69
|
1269 #define _USE_MATH_DEFINES
|
|
jpayne@69
|
1270 #endif
|
|
jpayne@69
|
1271 #endif
|
|
jpayne@69
|
1272 #include <math.h>
|
|
jpayne@69
|
1273 #ifdef NAN
|
|
jpayne@69
|
1274 #define __PYX_NAN() ((float) NAN)
|
|
jpayne@69
|
1275 #else
|
|
jpayne@69
|
1276 static CYTHON_INLINE float __PYX_NAN() {
|
|
jpayne@69
|
1277 float value;
|
|
jpayne@69
|
1278 memset(&value, 0xFF, sizeof(value));
|
|
jpayne@69
|
1279 return value;
|
|
jpayne@69
|
1280 }
|
|
jpayne@69
|
1281 #endif
|
|
jpayne@69
|
1282 #if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
|
|
jpayne@69
|
1283 #define __Pyx_truncl trunc
|
|
jpayne@69
|
1284 #else
|
|
jpayne@69
|
1285 #define __Pyx_truncl truncl
|
|
jpayne@69
|
1286 #endif
|
|
jpayne@69
|
1287
|
|
jpayne@69
|
1288 #define __PYX_MARK_ERR_POS(f_index, lineno) \
|
|
jpayne@69
|
1289 { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
|
|
jpayne@69
|
1290 #define __PYX_ERR(f_index, lineno, Ln_error) \
|
|
jpayne@69
|
1291 { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }
|
|
jpayne@69
|
1292
|
|
jpayne@69
|
1293 #ifdef CYTHON_EXTERN_C
|
|
jpayne@69
|
1294 #undef __PYX_EXTERN_C
|
|
jpayne@69
|
1295 #define __PYX_EXTERN_C CYTHON_EXTERN_C
|
|
jpayne@69
|
1296 #elif defined(__PYX_EXTERN_C)
|
|
jpayne@69
|
1297 #ifdef _MSC_VER
|
|
jpayne@69
|
1298 #pragma message ("Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.")
|
|
jpayne@69
|
1299 #else
|
|
jpayne@69
|
1300 #warning Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.
|
|
jpayne@69
|
1301 #endif
|
|
jpayne@69
|
1302 #else
|
|
jpayne@69
|
1303 #ifdef __cplusplus
|
|
jpayne@69
|
1304 #define __PYX_EXTERN_C extern "C"
|
|
jpayne@69
|
1305 #else
|
|
jpayne@69
|
1306 #define __PYX_EXTERN_C extern
|
|
jpayne@69
|
1307 #endif
|
|
jpayne@69
|
1308 #endif
|
|
jpayne@69
|
1309
|
|
jpayne@69
|
1310 #define __PYX_HAVE__pysam__libctabix
|
|
jpayne@69
|
1311 #define __PYX_HAVE_API__pysam__libctabix
|
|
jpayne@69
|
1312 /* Early includes */
|
|
jpayne@69
|
1313 #include <stdint.h>
|
|
jpayne@69
|
1314 #include <string.h>
|
|
jpayne@69
|
1315 #include <stdlib.h>
|
|
jpayne@69
|
1316 #include <stdio.h>
|
|
jpayne@69
|
1317 #include "fcntl.h"
|
|
jpayne@69
|
1318 #include "unistd.h"
|
|
jpayne@69
|
1319 #include <sys/types.h>
|
|
jpayne@69
|
1320 #include "stdarg.h"
|
|
jpayne@69
|
1321 #include "htslib/kstring.h"
|
|
jpayne@69
|
1322 #include "htslib_util.h"
|
|
jpayne@69
|
1323 #include "htslib/hfile.h"
|
|
jpayne@69
|
1324 #include "htslib/bgzf.h"
|
|
jpayne@69
|
1325 #include "htslib/hts.h"
|
|
jpayne@69
|
1326 #include "htslib/sam.h"
|
|
jpayne@69
|
1327 #include "htslib/faidx.h"
|
|
jpayne@69
|
1328 #include "htslib/tbx.h"
|
|
jpayne@69
|
1329 #include "htslib/vcf.h"
|
|
jpayne@69
|
1330 #include "htslib/vcfutils.h"
|
|
jpayne@69
|
1331 #include "htslib/cram.h"
|
|
jpayne@69
|
1332 #include "pysam_stream.h"
|
|
jpayne@69
|
1333 #include <errno.h>
|
|
jpayne@69
|
1334 #include <unistd.h>
|
|
jpayne@69
|
1335 #include <stddef.h>
|
|
jpayne@69
|
1336 #include "pythread.h"
|
|
jpayne@69
|
1337
|
|
jpayne@69
|
1338 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1339 #ifdef _MSC_VER
|
|
jpayne@69
|
1340 #pragma message ("This module uses CPython specific internals of 'array.array', which are not available in PyPy.")
|
|
jpayne@69
|
1341 #else
|
|
jpayne@69
|
1342 #warning This module uses CPython specific internals of 'array.array', which are not available in PyPy.
|
|
jpayne@69
|
1343 #endif
|
|
jpayne@69
|
1344 #endif
|
|
jpayne@69
|
1345
|
|
jpayne@69
|
1346 #ifdef _OPENMP
|
|
jpayne@69
|
1347 #include <omp.h>
|
|
jpayne@69
|
1348 #endif /* _OPENMP */
|
|
jpayne@69
|
1349
|
|
jpayne@69
|
1350 #if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
|
|
jpayne@69
|
1351 #define CYTHON_WITHOUT_ASSERTIONS
|
|
jpayne@69
|
1352 #endif
|
|
jpayne@69
|
1353
|
|
jpayne@69
|
1354 typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
|
|
jpayne@69
|
1355 const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
|
|
jpayne@69
|
1356
|
|
jpayne@69
|
1357 #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
|
|
jpayne@69
|
1358 #define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0
|
|
jpayne@69
|
1359 #define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8)
|
|
jpayne@69
|
1360 #define __PYX_DEFAULT_STRING_ENCODING ""
|
|
jpayne@69
|
1361 #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
|
|
jpayne@69
|
1362 #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
|
|
jpayne@69
|
1363 #define __Pyx_uchar_cast(c) ((unsigned char)c)
|
|
jpayne@69
|
1364 #define __Pyx_long_cast(x) ((long)x)
|
|
jpayne@69
|
1365 #define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\
|
|
jpayne@69
|
1366 (sizeof(type) < sizeof(Py_ssize_t)) ||\
|
|
jpayne@69
|
1367 (sizeof(type) > sizeof(Py_ssize_t) &&\
|
|
jpayne@69
|
1368 likely(v < (type)PY_SSIZE_T_MAX ||\
|
|
jpayne@69
|
1369 v == (type)PY_SSIZE_T_MAX) &&\
|
|
jpayne@69
|
1370 (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
|
|
jpayne@69
|
1371 v == (type)PY_SSIZE_T_MIN))) ||\
|
|
jpayne@69
|
1372 (sizeof(type) == sizeof(Py_ssize_t) &&\
|
|
jpayne@69
|
1373 (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
|
|
jpayne@69
|
1374 v == (type)PY_SSIZE_T_MAX))) )
|
|
jpayne@69
|
1375 static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) {
|
|
jpayne@69
|
1376 return (size_t) i < (size_t) limit;
|
|
jpayne@69
|
1377 }
|
|
jpayne@69
|
1378 #if defined (__cplusplus) && __cplusplus >= 201103L
|
|
jpayne@69
|
1379 #include <cstdlib>
|
|
jpayne@69
|
1380 #define __Pyx_sst_abs(value) std::abs(value)
|
|
jpayne@69
|
1381 #elif SIZEOF_INT >= SIZEOF_SIZE_T
|
|
jpayne@69
|
1382 #define __Pyx_sst_abs(value) abs(value)
|
|
jpayne@69
|
1383 #elif SIZEOF_LONG >= SIZEOF_SIZE_T
|
|
jpayne@69
|
1384 #define __Pyx_sst_abs(value) labs(value)
|
|
jpayne@69
|
1385 #elif defined (_MSC_VER)
|
|
jpayne@69
|
1386 #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
|
|
jpayne@69
|
1387 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
|
|
jpayne@69
|
1388 #define __Pyx_sst_abs(value) llabs(value)
|
|
jpayne@69
|
1389 #elif defined (__GNUC__)
|
|
jpayne@69
|
1390 #define __Pyx_sst_abs(value) __builtin_llabs(value)
|
|
jpayne@69
|
1391 #else
|
|
jpayne@69
|
1392 #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
|
|
jpayne@69
|
1393 #endif
|
|
jpayne@69
|
1394 static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s);
|
|
jpayne@69
|
1395 static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
|
|
jpayne@69
|
1396 static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
|
|
jpayne@69
|
1397 static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char*);
|
|
jpayne@69
|
1398 #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
|
|
jpayne@69
|
1399 #define __Pyx_PyBytes_FromString PyBytes_FromString
|
|
jpayne@69
|
1400 #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
|
|
jpayne@69
|
1401 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
|
|
jpayne@69
|
1402 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
1403 #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
|
|
jpayne@69
|
1404 #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
|
|
jpayne@69
|
1405 #else
|
|
jpayne@69
|
1406 #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
|
|
jpayne@69
|
1407 #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
|
|
jpayne@69
|
1408 #endif
|
|
jpayne@69
|
1409 #define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1410 #define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1411 #define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1412 #define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1413 #define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1414 #define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1415 #define __Pyx_PyObject_AsWritableString(s) ((char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1416 #define __Pyx_PyObject_AsWritableSString(s) ((signed char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1417 #define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1418 #define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1419 #define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1420 #define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
|
|
jpayne@69
|
1421 #define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
|
|
jpayne@69
|
1422 #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
|
|
jpayne@69
|
1423 #define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
|
|
jpayne@69
|
1424 #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
|
|
jpayne@69
|
1425 #define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o)
|
|
jpayne@69
|
1426 #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
|
|
jpayne@69
|
1427 #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
|
|
jpayne@69
|
1428 #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
|
|
jpayne@69
|
1429 static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
|
|
jpayne@69
|
1430 static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
|
|
jpayne@69
|
1431 static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
|
|
jpayne@69
|
1432 static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
|
|
jpayne@69
|
1433 #define __Pyx_PySequence_Tuple(obj)\
|
|
jpayne@69
|
1434 (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
|
|
jpayne@69
|
1435 static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
|
|
jpayne@69
|
1436 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
|
|
jpayne@69
|
1437 static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
|
|
jpayne@69
|
1438 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
1439 #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
|
|
jpayne@69
|
1440 #else
|
|
jpayne@69
|
1441 #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
|
|
jpayne@69
|
1442 #endif
|
|
jpayne@69
|
1443 #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
|
|
jpayne@69
|
1444 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1445 #define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
|
|
jpayne@69
|
1446 #else
|
|
jpayne@69
|
1447 #define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
|
|
jpayne@69
|
1448 #endif
|
|
jpayne@69
|
1449 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
1450 #if PY_VERSION_HEX >= 0x030C00A7
|
|
jpayne@69
|
1451 #ifndef _PyLong_SIGN_MASK
|
|
jpayne@69
|
1452 #define _PyLong_SIGN_MASK 3
|
|
jpayne@69
|
1453 #endif
|
|
jpayne@69
|
1454 #ifndef _PyLong_NON_SIZE_BITS
|
|
jpayne@69
|
1455 #define _PyLong_NON_SIZE_BITS 3
|
|
jpayne@69
|
1456 #endif
|
|
jpayne@69
|
1457 #define __Pyx_PyLong_Sign(x) (((PyLongObject*)x)->long_value.lv_tag & _PyLong_SIGN_MASK)
|
|
jpayne@69
|
1458 #define __Pyx_PyLong_IsNeg(x) ((__Pyx_PyLong_Sign(x) & 2) != 0)
|
|
jpayne@69
|
1459 #define __Pyx_PyLong_IsNonNeg(x) (!__Pyx_PyLong_IsNeg(x))
|
|
jpayne@69
|
1460 #define __Pyx_PyLong_IsZero(x) (__Pyx_PyLong_Sign(x) & 1)
|
|
jpayne@69
|
1461 #define __Pyx_PyLong_IsPos(x) (__Pyx_PyLong_Sign(x) == 0)
|
|
jpayne@69
|
1462 #define __Pyx_PyLong_CompactValueUnsigned(x) (__Pyx_PyLong_Digits(x)[0])
|
|
jpayne@69
|
1463 #define __Pyx_PyLong_DigitCount(x) ((Py_ssize_t) (((PyLongObject*)x)->long_value.lv_tag >> _PyLong_NON_SIZE_BITS))
|
|
jpayne@69
|
1464 #define __Pyx_PyLong_SignedDigitCount(x)\
|
|
jpayne@69
|
1465 ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * __Pyx_PyLong_DigitCount(x))
|
|
jpayne@69
|
1466 #if defined(PyUnstable_Long_IsCompact) && defined(PyUnstable_Long_CompactValue)
|
|
jpayne@69
|
1467 #define __Pyx_PyLong_IsCompact(x) PyUnstable_Long_IsCompact((PyLongObject*) x)
|
|
jpayne@69
|
1468 #define __Pyx_PyLong_CompactValue(x) PyUnstable_Long_CompactValue((PyLongObject*) x)
|
|
jpayne@69
|
1469 #else
|
|
jpayne@69
|
1470 #define __Pyx_PyLong_IsCompact(x) (((PyLongObject*)x)->long_value.lv_tag < (2 << _PyLong_NON_SIZE_BITS))
|
|
jpayne@69
|
1471 #define __Pyx_PyLong_CompactValue(x) ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * (Py_ssize_t) __Pyx_PyLong_Digits(x)[0])
|
|
jpayne@69
|
1472 #endif
|
|
jpayne@69
|
1473 typedef Py_ssize_t __Pyx_compact_pylong;
|
|
jpayne@69
|
1474 typedef size_t __Pyx_compact_upylong;
|
|
jpayne@69
|
1475 #else
|
|
jpayne@69
|
1476 #define __Pyx_PyLong_IsNeg(x) (Py_SIZE(x) < 0)
|
|
jpayne@69
|
1477 #define __Pyx_PyLong_IsNonNeg(x) (Py_SIZE(x) >= 0)
|
|
jpayne@69
|
1478 #define __Pyx_PyLong_IsZero(x) (Py_SIZE(x) == 0)
|
|
jpayne@69
|
1479 #define __Pyx_PyLong_IsPos(x) (Py_SIZE(x) > 0)
|
|
jpayne@69
|
1480 #define __Pyx_PyLong_CompactValueUnsigned(x) ((Py_SIZE(x) == 0) ? 0 : __Pyx_PyLong_Digits(x)[0])
|
|
jpayne@69
|
1481 #define __Pyx_PyLong_DigitCount(x) __Pyx_sst_abs(Py_SIZE(x))
|
|
jpayne@69
|
1482 #define __Pyx_PyLong_SignedDigitCount(x) Py_SIZE(x)
|
|
jpayne@69
|
1483 #define __Pyx_PyLong_IsCompact(x) (Py_SIZE(x) == 0 || Py_SIZE(x) == 1 || Py_SIZE(x) == -1)
|
|
jpayne@69
|
1484 #define __Pyx_PyLong_CompactValue(x)\
|
|
jpayne@69
|
1485 ((Py_SIZE(x) == 0) ? (sdigit) 0 : ((Py_SIZE(x) < 0) ? -(sdigit)__Pyx_PyLong_Digits(x)[0] : (sdigit)__Pyx_PyLong_Digits(x)[0]))
|
|
jpayne@69
|
1486 typedef sdigit __Pyx_compact_pylong;
|
|
jpayne@69
|
1487 typedef digit __Pyx_compact_upylong;
|
|
jpayne@69
|
1488 #endif
|
|
jpayne@69
|
1489 #if PY_VERSION_HEX >= 0x030C00A5
|
|
jpayne@69
|
1490 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->long_value.ob_digit)
|
|
jpayne@69
|
1491 #else
|
|
jpayne@69
|
1492 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->ob_digit)
|
|
jpayne@69
|
1493 #endif
|
|
jpayne@69
|
1494 #endif
|
|
jpayne@69
|
1495 #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
1496 #include <string.h>
|
|
jpayne@69
|
1497 static int __Pyx_sys_getdefaultencoding_not_ascii;
|
|
jpayne@69
|
1498 static int __Pyx_init_sys_getdefaultencoding_params(void) {
|
|
jpayne@69
|
1499 PyObject* sys;
|
|
jpayne@69
|
1500 PyObject* default_encoding = NULL;
|
|
jpayne@69
|
1501 PyObject* ascii_chars_u = NULL;
|
|
jpayne@69
|
1502 PyObject* ascii_chars_b = NULL;
|
|
jpayne@69
|
1503 const char* default_encoding_c;
|
|
jpayne@69
|
1504 sys = PyImport_ImportModule("sys");
|
|
jpayne@69
|
1505 if (!sys) goto bad;
|
|
jpayne@69
|
1506 default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
|
|
jpayne@69
|
1507 Py_DECREF(sys);
|
|
jpayne@69
|
1508 if (!default_encoding) goto bad;
|
|
jpayne@69
|
1509 default_encoding_c = PyBytes_AsString(default_encoding);
|
|
jpayne@69
|
1510 if (!default_encoding_c) goto bad;
|
|
jpayne@69
|
1511 if (strcmp(default_encoding_c, "ascii") == 0) {
|
|
jpayne@69
|
1512 __Pyx_sys_getdefaultencoding_not_ascii = 0;
|
|
jpayne@69
|
1513 } else {
|
|
jpayne@69
|
1514 char ascii_chars[128];
|
|
jpayne@69
|
1515 int c;
|
|
jpayne@69
|
1516 for (c = 0; c < 128; c++) {
|
|
jpayne@69
|
1517 ascii_chars[c] = (char) c;
|
|
jpayne@69
|
1518 }
|
|
jpayne@69
|
1519 __Pyx_sys_getdefaultencoding_not_ascii = 1;
|
|
jpayne@69
|
1520 ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
|
|
jpayne@69
|
1521 if (!ascii_chars_u) goto bad;
|
|
jpayne@69
|
1522 ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
|
|
jpayne@69
|
1523 if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
|
|
jpayne@69
|
1524 PyErr_Format(
|
|
jpayne@69
|
1525 PyExc_ValueError,
|
|
jpayne@69
|
1526 "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
|
|
jpayne@69
|
1527 default_encoding_c);
|
|
jpayne@69
|
1528 goto bad;
|
|
jpayne@69
|
1529 }
|
|
jpayne@69
|
1530 Py_DECREF(ascii_chars_u);
|
|
jpayne@69
|
1531 Py_DECREF(ascii_chars_b);
|
|
jpayne@69
|
1532 }
|
|
jpayne@69
|
1533 Py_DECREF(default_encoding);
|
|
jpayne@69
|
1534 return 0;
|
|
jpayne@69
|
1535 bad:
|
|
jpayne@69
|
1536 Py_XDECREF(default_encoding);
|
|
jpayne@69
|
1537 Py_XDECREF(ascii_chars_u);
|
|
jpayne@69
|
1538 Py_XDECREF(ascii_chars_b);
|
|
jpayne@69
|
1539 return -1;
|
|
jpayne@69
|
1540 }
|
|
jpayne@69
|
1541 #endif
|
|
jpayne@69
|
1542 #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1543 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
|
|
jpayne@69
|
1544 #else
|
|
jpayne@69
|
1545 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
|
|
jpayne@69
|
1546 #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
|
|
jpayne@69
|
1547 #include <string.h>
|
|
jpayne@69
|
1548 static char* __PYX_DEFAULT_STRING_ENCODING;
|
|
jpayne@69
|
1549 static int __Pyx_init_sys_getdefaultencoding_params(void) {
|
|
jpayne@69
|
1550 PyObject* sys;
|
|
jpayne@69
|
1551 PyObject* default_encoding = NULL;
|
|
jpayne@69
|
1552 char* default_encoding_c;
|
|
jpayne@69
|
1553 sys = PyImport_ImportModule("sys");
|
|
jpayne@69
|
1554 if (!sys) goto bad;
|
|
jpayne@69
|
1555 default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
|
|
jpayne@69
|
1556 Py_DECREF(sys);
|
|
jpayne@69
|
1557 if (!default_encoding) goto bad;
|
|
jpayne@69
|
1558 default_encoding_c = PyBytes_AsString(default_encoding);
|
|
jpayne@69
|
1559 if (!default_encoding_c) goto bad;
|
|
jpayne@69
|
1560 __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
|
|
jpayne@69
|
1561 if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
|
|
jpayne@69
|
1562 strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
|
|
jpayne@69
|
1563 Py_DECREF(default_encoding);
|
|
jpayne@69
|
1564 return 0;
|
|
jpayne@69
|
1565 bad:
|
|
jpayne@69
|
1566 Py_XDECREF(default_encoding);
|
|
jpayne@69
|
1567 return -1;
|
|
jpayne@69
|
1568 }
|
|
jpayne@69
|
1569 #endif
|
|
jpayne@69
|
1570 #endif
|
|
jpayne@69
|
1571
|
|
jpayne@69
|
1572
|
|
jpayne@69
|
1573 /* Test for GCC > 2.95 */
|
|
jpayne@69
|
1574 #if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
|
|
jpayne@69
|
1575 #define likely(x) __builtin_expect(!!(x), 1)
|
|
jpayne@69
|
1576 #define unlikely(x) __builtin_expect(!!(x), 0)
|
|
jpayne@69
|
1577 #else /* !__GNUC__ or GCC < 2.95 */
|
|
jpayne@69
|
1578 #define likely(x) (x)
|
|
jpayne@69
|
1579 #define unlikely(x) (x)
|
|
jpayne@69
|
1580 #endif /* __GNUC__ */
|
|
jpayne@69
|
1581 static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }
|
|
jpayne@69
|
1582
|
|
jpayne@69
|
1583 #if !CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
1584 static PyObject *__pyx_m = NULL;
|
|
jpayne@69
|
1585 #endif
|
|
jpayne@69
|
1586 static int __pyx_lineno;
|
|
jpayne@69
|
1587 static int __pyx_clineno = 0;
|
|
jpayne@69
|
1588 static const char * __pyx_cfilenm = __FILE__;
|
|
jpayne@69
|
1589 static const char *__pyx_filename;
|
|
jpayne@69
|
1590
|
|
jpayne@69
|
1591 /* #### Code section: filename_table ### */
|
|
jpayne@69
|
1592
|
|
jpayne@69
|
1593 static const char *__pyx_f[] = {
|
|
jpayne@69
|
1594 "pysam/libctabix.pyx",
|
|
jpayne@69
|
1595 "<stringsource>",
|
|
jpayne@69
|
1596 "contextvars.pxd",
|
|
jpayne@69
|
1597 "array.pxd",
|
|
jpayne@69
|
1598 "pysam/libctabix.pxd",
|
|
jpayne@69
|
1599 "type.pxd",
|
|
jpayne@69
|
1600 "bool.pxd",
|
|
jpayne@69
|
1601 "complex.pxd",
|
|
jpayne@69
|
1602 "pysam/libctabixproxies.pxd",
|
|
jpayne@69
|
1603 };
|
|
jpayne@69
|
1604 /* #### Code section: utility_code_proto_before_types ### */
|
|
jpayne@69
|
1605 /* ForceInitThreads.proto */
|
|
jpayne@69
|
1606 #ifndef __PYX_FORCE_INIT_THREADS
|
|
jpayne@69
|
1607 #define __PYX_FORCE_INIT_THREADS 0
|
|
jpayne@69
|
1608 #endif
|
|
jpayne@69
|
1609
|
|
jpayne@69
|
1610 /* NoFastGil.proto */
|
|
jpayne@69
|
1611 #define __Pyx_PyGILState_Ensure PyGILState_Ensure
|
|
jpayne@69
|
1612 #define __Pyx_PyGILState_Release PyGILState_Release
|
|
jpayne@69
|
1613 #define __Pyx_FastGIL_Remember()
|
|
jpayne@69
|
1614 #define __Pyx_FastGIL_Forget()
|
|
jpayne@69
|
1615 #define __Pyx_FastGilFuncInit()
|
|
jpayne@69
|
1616
|
|
jpayne@69
|
1617 /* #### Code section: numeric_typedefs ### */
|
|
jpayne@69
|
1618 /* #### Code section: complex_type_declarations ### */
|
|
jpayne@69
|
1619 /* #### Code section: type_declarations ### */
|
|
jpayne@69
|
1620
|
|
jpayne@69
|
1621 /*--- Type declarations ---*/
|
|
jpayne@69
|
1622 #ifndef _ARRAYARRAY_H
|
|
jpayne@69
|
1623 struct arrayobject;
|
|
jpayne@69
|
1624 typedef struct arrayobject arrayobject;
|
|
jpayne@69
|
1625 #endif
|
|
jpayne@69
|
1626 struct __pyx_obj_5pysam_10libchtslib_HTSFile;
|
|
jpayne@69
|
1627 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy;
|
|
jpayne@69
|
1628 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator;
|
|
jpayne@69
|
1629 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy;
|
|
jpayne@69
|
1630 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy;
|
|
jpayne@69
|
1631 struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy;
|
|
jpayne@69
|
1632 struct __pyx_obj_5pysam_16libctabixproxies_BedProxy;
|
|
jpayne@69
|
1633 struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy;
|
|
jpayne@69
|
1634 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator;
|
|
jpayne@69
|
1635 struct __pyx_obj_5pysam_9libctabix_TabixFile;
|
|
jpayne@69
|
1636 struct __pyx_obj_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
1637 struct __pyx_obj_5pysam_9libctabix_asTuple;
|
|
jpayne@69
|
1638 struct __pyx_obj_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
1639 struct __pyx_obj_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
1640 struct __pyx_obj_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
1641 struct __pyx_obj_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
1642 struct __pyx_obj_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
1643 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
1644 struct __pyx_obj_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
1645 struct __pyx_obj_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
1646 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed;
|
|
jpayne@69
|
1647 struct __pyx_obj_5pysam_9libctabix_Tabixfile;
|
|
jpayne@69
|
1648 struct __pyx_opt_args_7cpython_11contextvars_get_value;
|
|
jpayne@69
|
1649 struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default;
|
|
jpayne@69
|
1650
|
|
jpayne@69
|
1651 /* "cpython/contextvars.pxd":112
|
|
jpayne@69
|
1652 *
|
|
jpayne@69
|
1653 *
|
|
jpayne@69
|
1654 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1655 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
1656 * or the default value of the context variable,
|
|
jpayne@69
|
1657 */
|
|
jpayne@69
|
1658 struct __pyx_opt_args_7cpython_11contextvars_get_value {
|
|
jpayne@69
|
1659 int __pyx_n;
|
|
jpayne@69
|
1660 PyObject *default_value;
|
|
jpayne@69
|
1661 };
|
|
jpayne@69
|
1662
|
|
jpayne@69
|
1663 /* "cpython/contextvars.pxd":129
|
|
jpayne@69
|
1664 *
|
|
jpayne@69
|
1665 *
|
|
jpayne@69
|
1666 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1667 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
1668 * or the provided default value if no such value was found.
|
|
jpayne@69
|
1669 */
|
|
jpayne@69
|
1670 struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default {
|
|
jpayne@69
|
1671 int __pyx_n;
|
|
jpayne@69
|
1672 PyObject *default_value;
|
|
jpayne@69
|
1673 };
|
|
jpayne@69
|
1674 struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy;
|
|
jpayne@69
|
1675
|
|
jpayne@69
|
1676 /* "pysam/libctabixproxies.pxd":23
|
|
jpayne@69
|
1677 * cdef take(self, char * buffer, size_t nbytes)
|
|
jpayne@69
|
1678 * cdef present(self, char * buffer, size_t nbytes)
|
|
jpayne@69
|
1679 * cdef copy(self, char * buffer, size_t nbytes, bint reset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1680 * cdef update(self, char * buffer, size_t nbytes)
|
|
jpayne@69
|
1681 *
|
|
jpayne@69
|
1682 */
|
|
jpayne@69
|
1683 struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy {
|
|
jpayne@69
|
1684 int __pyx_n;
|
|
jpayne@69
|
1685 int reset;
|
|
jpayne@69
|
1686 };
|
|
jpayne@69
|
1687 struct __pyx_opt_args_5pysam_9libcutils_parse_region;
|
|
jpayne@69
|
1688 struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array;
|
|
jpayne@69
|
1689 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring;
|
|
jpayne@69
|
1690 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring;
|
|
jpayne@69
|
1691 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str;
|
|
jpayne@69
|
1692 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes;
|
|
jpayne@69
|
1693 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len;
|
|
jpayne@69
|
1694 struct __pyx_opt_args_5pysam_9libcutils_force_str;
|
|
jpayne@69
|
1695 struct __pyx_opt_args_5pysam_9libcutils_force_bytes;
|
|
jpayne@69
|
1696 struct __pyx_opt_args_5pysam_9libcutils_decode_bytes;
|
|
jpayne@69
|
1697
|
|
jpayne@69
|
1698 /* "pysam/libcutils.pxd":8
|
|
jpayne@69
|
1699 * from cpython cimport array as c_array
|
|
jpayne@69
|
1700 *
|
|
jpayne@69
|
1701 * cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1702 *
|
|
jpayne@69
|
1703 * cdef int libc_whence_from_io(int whence)
|
|
jpayne@69
|
1704 */
|
|
jpayne@69
|
1705 struct __pyx_opt_args_5pysam_9libcutils_parse_region {
|
|
jpayne@69
|
1706 int __pyx_n;
|
|
jpayne@69
|
1707 PyObject *contig;
|
|
jpayne@69
|
1708 PyObject *start;
|
|
jpayne@69
|
1709 PyObject *stop;
|
|
jpayne@69
|
1710 PyObject *region;
|
|
jpayne@69
|
1711 PyObject *reference;
|
|
jpayne@69
|
1712 PyObject *end;
|
|
jpayne@69
|
1713 };
|
|
jpayne@69
|
1714
|
|
jpayne@69
|
1715 /* "pysam/libcutils.pxd":15
|
|
jpayne@69
|
1716 * # Utility functions for quality string conversions
|
|
jpayne@69
|
1717 *
|
|
jpayne@69
|
1718 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1719 * cpdef array_to_qualitystring(c_array.array arr, int offset=*)
|
|
jpayne@69
|
1720 * cpdef qualities_to_qualitystring(qualities, int offset=*)
|
|
jpayne@69
|
1721 */
|
|
jpayne@69
|
1722 struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array {
|
|
jpayne@69
|
1723 int __pyx_n;
|
|
jpayne@69
|
1724 int offset;
|
|
jpayne@69
|
1725 };
|
|
jpayne@69
|
1726
|
|
jpayne@69
|
1727 /* "pysam/libcutils.pxd":16
|
|
jpayne@69
|
1728 *
|
|
jpayne@69
|
1729 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
|
|
jpayne@69
|
1730 * cpdef array_to_qualitystring(c_array.array arr, int offset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1731 * cpdef qualities_to_qualitystring(qualities, int offset=*)
|
|
jpayne@69
|
1732 *
|
|
jpayne@69
|
1733 */
|
|
jpayne@69
|
1734 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring {
|
|
jpayne@69
|
1735 int __pyx_n;
|
|
jpayne@69
|
1736 int offset;
|
|
jpayne@69
|
1737 };
|
|
jpayne@69
|
1738
|
|
jpayne@69
|
1739 /* "pysam/libcutils.pxd":17
|
|
jpayne@69
|
1740 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
|
|
jpayne@69
|
1741 * cpdef array_to_qualitystring(c_array.array arr, int offset=*)
|
|
jpayne@69
|
1742 * cpdef qualities_to_qualitystring(qualities, int offset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1743 *
|
|
jpayne@69
|
1744 * ########################################################################
|
|
jpayne@69
|
1745 */
|
|
jpayne@69
|
1746 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring {
|
|
jpayne@69
|
1747 int __pyx_n;
|
|
jpayne@69
|
1748 int offset;
|
|
jpayne@69
|
1749 };
|
|
jpayne@69
|
1750
|
|
jpayne@69
|
1751 /* "pysam/libcutils.pxd":29
|
|
jpayne@69
|
1752 * ## Python 3 compatibility functions
|
|
jpayne@69
|
1753 * ########################################################################
|
|
jpayne@69
|
1754 * cdef charptr_to_str(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1755 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1756 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1757 */
|
|
jpayne@69
|
1758 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str {
|
|
jpayne@69
|
1759 int __pyx_n;
|
|
jpayne@69
|
1760 PyObject *encoding;
|
|
jpayne@69
|
1761 PyObject *errors;
|
|
jpayne@69
|
1762 };
|
|
jpayne@69
|
1763
|
|
jpayne@69
|
1764 /* "pysam/libcutils.pxd":30
|
|
jpayne@69
|
1765 * ########################################################################
|
|
jpayne@69
|
1766 * cdef charptr_to_str(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1767 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1768 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1769 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1770 */
|
|
jpayne@69
|
1771 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes {
|
|
jpayne@69
|
1772 int __pyx_n;
|
|
jpayne@69
|
1773 PyObject *encoding;
|
|
jpayne@69
|
1774 PyObject *errors;
|
|
jpayne@69
|
1775 };
|
|
jpayne@69
|
1776
|
|
jpayne@69
|
1777 /* "pysam/libcutils.pxd":31
|
|
jpayne@69
|
1778 * cdef charptr_to_str(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1779 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1780 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1781 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1782 * cdef bytes force_bytes(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1783 */
|
|
jpayne@69
|
1784 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len {
|
|
jpayne@69
|
1785 int __pyx_n;
|
|
jpayne@69
|
1786 PyObject *encoding;
|
|
jpayne@69
|
1787 PyObject *errors;
|
|
jpayne@69
|
1788 };
|
|
jpayne@69
|
1789
|
|
jpayne@69
|
1790 /* "pysam/libcutils.pxd":32
|
|
jpayne@69
|
1791 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1792 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1793 * cdef force_str(object s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1794 * cdef bytes force_bytes(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1795 * cdef decode_bytes(bytes s, encoding=*, errors=*)
|
|
jpayne@69
|
1796 */
|
|
jpayne@69
|
1797 struct __pyx_opt_args_5pysam_9libcutils_force_str {
|
|
jpayne@69
|
1798 int __pyx_n;
|
|
jpayne@69
|
1799 PyObject *encoding;
|
|
jpayne@69
|
1800 PyObject *errors;
|
|
jpayne@69
|
1801 };
|
|
jpayne@69
|
1802
|
|
jpayne@69
|
1803 /* "pysam/libcutils.pxd":33
|
|
jpayne@69
|
1804 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1805 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1806 * cdef bytes force_bytes(object s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1807 * cdef decode_bytes(bytes s, encoding=*, errors=*)
|
|
jpayne@69
|
1808 * cdef bytes encode_filename(object filename)
|
|
jpayne@69
|
1809 */
|
|
jpayne@69
|
1810 struct __pyx_opt_args_5pysam_9libcutils_force_bytes {
|
|
jpayne@69
|
1811 int __pyx_n;
|
|
jpayne@69
|
1812 PyObject *encoding;
|
|
jpayne@69
|
1813 PyObject *errors;
|
|
jpayne@69
|
1814 };
|
|
jpayne@69
|
1815
|
|
jpayne@69
|
1816 /* "pysam/libcutils.pxd":34
|
|
jpayne@69
|
1817 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1818 * cdef bytes force_bytes(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1819 * cdef decode_bytes(bytes s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1820 * cdef bytes encode_filename(object filename)
|
|
jpayne@69
|
1821 * cdef from_string_and_size(const char *s, size_t length)
|
|
jpayne@69
|
1822 */
|
|
jpayne@69
|
1823 struct __pyx_opt_args_5pysam_9libcutils_decode_bytes {
|
|
jpayne@69
|
1824 int __pyx_n;
|
|
jpayne@69
|
1825 PyObject *encoding;
|
|
jpayne@69
|
1826 PyObject *errors;
|
|
jpayne@69
|
1827 };
|
|
jpayne@69
|
1828
|
|
jpayne@69
|
1829 /* "pysam/libchtslib.pxd":2706
|
|
jpayne@69
|
1830 *
|
|
jpayne@69
|
1831 *
|
|
jpayne@69
|
1832 * cdef class HTSFile(object): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1833 * cdef htsFile *htsfile # pointer to htsFile structure
|
|
jpayne@69
|
1834 * cdef int64_t start_offset # BGZF offset of first record
|
|
jpayne@69
|
1835 */
|
|
jpayne@69
|
1836 struct __pyx_obj_5pysam_10libchtslib_HTSFile {
|
|
jpayne@69
|
1837 PyObject_HEAD
|
|
jpayne@69
|
1838 struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtab;
|
|
jpayne@69
|
1839 htsFile *htsfile;
|
|
jpayne@69
|
1840 int64_t start_offset;
|
|
jpayne@69
|
1841 PyObject *filename;
|
|
jpayne@69
|
1842 PyObject *mode;
|
|
jpayne@69
|
1843 PyObject *threads;
|
|
jpayne@69
|
1844 PyObject *index_filename;
|
|
jpayne@69
|
1845 int is_stream;
|
|
jpayne@69
|
1846 int is_remote;
|
|
jpayne@69
|
1847 int duplicate_filehandle;
|
|
jpayne@69
|
1848 };
|
|
jpayne@69
|
1849
|
|
jpayne@69
|
1850
|
|
jpayne@69
|
1851 /* "pysam/libctabixproxies.pxd":5
|
|
jpayne@69
|
1852 * from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t
|
|
jpayne@69
|
1853 *
|
|
jpayne@69
|
1854 * cdef class TupleProxy: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1855 *
|
|
jpayne@69
|
1856 * cdef:
|
|
jpayne@69
|
1857 */
|
|
jpayne@69
|
1858 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy {
|
|
jpayne@69
|
1859 PyObject_HEAD
|
|
jpayne@69
|
1860 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *__pyx_vtab;
|
|
jpayne@69
|
1861 char *data;
|
|
jpayne@69
|
1862 char **fields;
|
|
jpayne@69
|
1863 int nfields;
|
|
jpayne@69
|
1864 int nbytes;
|
|
jpayne@69
|
1865 int offset;
|
|
jpayne@69
|
1866 int is_modified;
|
|
jpayne@69
|
1867 PyObject *encoding;
|
|
jpayne@69
|
1868 };
|
|
jpayne@69
|
1869
|
|
jpayne@69
|
1870
|
|
jpayne@69
|
1871 /* "pysam/libctabixproxies.pxd":27
|
|
jpayne@69
|
1872 *
|
|
jpayne@69
|
1873 *
|
|
jpayne@69
|
1874 * cdef class TupleProxyIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1875 * cdef TupleProxy proxy
|
|
jpayne@69
|
1876 * cdef int index
|
|
jpayne@69
|
1877 */
|
|
jpayne@69
|
1878 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator {
|
|
jpayne@69
|
1879 PyObject_HEAD
|
|
jpayne@69
|
1880 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *proxy;
|
|
jpayne@69
|
1881 int index;
|
|
jpayne@69
|
1882 };
|
|
jpayne@69
|
1883
|
|
jpayne@69
|
1884
|
|
jpayne@69
|
1885 /* "pysam/libctabixproxies.pxd":32
|
|
jpayne@69
|
1886 *
|
|
jpayne@69
|
1887 *
|
|
jpayne@69
|
1888 * cdef class NamedTupleProxy(TupleProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1889 * pass
|
|
jpayne@69
|
1890 *
|
|
jpayne@69
|
1891 */
|
|
jpayne@69
|
1892 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy {
|
|
jpayne@69
|
1893 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy __pyx_base;
|
|
jpayne@69
|
1894 };
|
|
jpayne@69
|
1895
|
|
jpayne@69
|
1896
|
|
jpayne@69
|
1897 /* "pysam/libctabixproxies.pxd":36
|
|
jpayne@69
|
1898 *
|
|
jpayne@69
|
1899 *
|
|
jpayne@69
|
1900 * cdef class GTFProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1901 * cdef object attribute_dict
|
|
jpayne@69
|
1902 * cpdef int getMaxFields(self)
|
|
jpayne@69
|
1903 */
|
|
jpayne@69
|
1904 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy {
|
|
jpayne@69
|
1905 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
|
|
jpayne@69
|
1906 PyObject *attribute_dict;
|
|
jpayne@69
|
1907 };
|
|
jpayne@69
|
1908
|
|
jpayne@69
|
1909
|
|
jpayne@69
|
1910 /* "pysam/libctabixproxies.pxd":42
|
|
jpayne@69
|
1911 *
|
|
jpayne@69
|
1912 *
|
|
jpayne@69
|
1913 * cdef class GFF3Proxy(GTFProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1914 * pass
|
|
jpayne@69
|
1915 *
|
|
jpayne@69
|
1916 */
|
|
jpayne@69
|
1917 struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy {
|
|
jpayne@69
|
1918 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy __pyx_base;
|
|
jpayne@69
|
1919 };
|
|
jpayne@69
|
1920
|
|
jpayne@69
|
1921
|
|
jpayne@69
|
1922 /* "pysam/libctabixproxies.pxd":46
|
|
jpayne@69
|
1923 *
|
|
jpayne@69
|
1924 *
|
|
jpayne@69
|
1925 * cdef class BedProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1926 *
|
|
jpayne@69
|
1927 * cdef:
|
|
jpayne@69
|
1928 */
|
|
jpayne@69
|
1929 struct __pyx_obj_5pysam_16libctabixproxies_BedProxy {
|
|
jpayne@69
|
1930 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
|
|
jpayne@69
|
1931 char *contig;
|
|
jpayne@69
|
1932 uint32_t start;
|
|
jpayne@69
|
1933 uint32_t end;
|
|
jpayne@69
|
1934 int bedfields;
|
|
jpayne@69
|
1935 };
|
|
jpayne@69
|
1936
|
|
jpayne@69
|
1937
|
|
jpayne@69
|
1938 /* "pysam/libctabixproxies.pxd":58
|
|
jpayne@69
|
1939 * cdef update(self, char * buffer, size_t nbytes)
|
|
jpayne@69
|
1940 *
|
|
jpayne@69
|
1941 * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1942 *
|
|
jpayne@69
|
1943 * cdef:
|
|
jpayne@69
|
1944 */
|
|
jpayne@69
|
1945 struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy {
|
|
jpayne@69
|
1946 struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
|
|
jpayne@69
|
1947 char *contig;
|
|
jpayne@69
|
1948 uint32_t pos;
|
|
jpayne@69
|
1949 };
|
|
jpayne@69
|
1950
|
|
jpayne@69
|
1951
|
|
jpayne@69
|
1952 /* "pysam/libctabix.pxd":48
|
|
jpayne@69
|
1953 *
|
|
jpayne@69
|
1954 *
|
|
jpayne@69
|
1955 * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1956 * cdef BGZF * fh
|
|
jpayne@69
|
1957 * cdef kstream_t * kstream
|
|
jpayne@69
|
1958 */
|
|
jpayne@69
|
1959 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator {
|
|
jpayne@69
|
1960 PyObject_HEAD
|
|
jpayne@69
|
1961 struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *__pyx_vtab;
|
|
jpayne@69
|
1962 BGZF *fh;
|
|
jpayne@69
|
1963 kstream_t *kstream;
|
|
jpayne@69
|
1964 kstring_t buffer;
|
|
jpayne@69
|
1965 size_t size;
|
|
jpayne@69
|
1966 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
|
|
jpayne@69
|
1967 int fd;
|
|
jpayne@69
|
1968 int duplicated_fd;
|
|
jpayne@69
|
1969 PyObject *infile;
|
|
jpayne@69
|
1970 };
|
|
jpayne@69
|
1971
|
|
jpayne@69
|
1972
|
|
jpayne@69
|
1973 /* "pysam/libctabix.pxd":61
|
|
jpayne@69
|
1974 *
|
|
jpayne@69
|
1975 *
|
|
jpayne@69
|
1976 * cdef class TabixFile(HTSFile): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1977 * # pointer to index structure
|
|
jpayne@69
|
1978 * cdef tbx_t * index
|
|
jpayne@69
|
1979 */
|
|
jpayne@69
|
1980 struct __pyx_obj_5pysam_9libctabix_TabixFile {
|
|
jpayne@69
|
1981 struct __pyx_obj_5pysam_10libchtslib_HTSFile __pyx_base;
|
|
jpayne@69
|
1982 tbx_t *index;
|
|
jpayne@69
|
1983 PyObject *filename_index;
|
|
jpayne@69
|
1984 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
|
|
jpayne@69
|
1985 PyObject *encoding;
|
|
jpayne@69
|
1986 };
|
|
jpayne@69
|
1987
|
|
jpayne@69
|
1988
|
|
jpayne@69
|
1989 /* "pysam/libctabix.pxd":72
|
|
jpayne@69
|
1990 *
|
|
jpayne@69
|
1991 *
|
|
jpayne@69
|
1992 * cdef class Parser: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1993 * cdef encoding
|
|
jpayne@69
|
1994 * cdef parse(self, char * buffer, int len)
|
|
jpayne@69
|
1995 */
|
|
jpayne@69
|
1996 struct __pyx_obj_5pysam_9libctabix_Parser {
|
|
jpayne@69
|
1997 PyObject_HEAD
|
|
jpayne@69
|
1998 struct __pyx_vtabstruct_5pysam_9libctabix_Parser *__pyx_vtab;
|
|
jpayne@69
|
1999 PyObject *encoding;
|
|
jpayne@69
|
2000 };
|
|
jpayne@69
|
2001
|
|
jpayne@69
|
2002
|
|
jpayne@69
|
2003 /* "pysam/libctabix.pxd":77
|
|
jpayne@69
|
2004 *
|
|
jpayne@69
|
2005 *
|
|
jpayne@69
|
2006 * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2007 * cdef parse(self, char * buffer, int len)
|
|
jpayne@69
|
2008 *
|
|
jpayne@69
|
2009 */
|
|
jpayne@69
|
2010 struct __pyx_obj_5pysam_9libctabix_asTuple {
|
|
jpayne@69
|
2011 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2012 };
|
|
jpayne@69
|
2013
|
|
jpayne@69
|
2014
|
|
jpayne@69
|
2015 /* "pysam/libctabix.pxd":81
|
|
jpayne@69
|
2016 *
|
|
jpayne@69
|
2017 *
|
|
jpayne@69
|
2018 * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2019 * pass
|
|
jpayne@69
|
2020 *
|
|
jpayne@69
|
2021 */
|
|
jpayne@69
|
2022 struct __pyx_obj_5pysam_9libctabix_asGTF {
|
|
jpayne@69
|
2023 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2024 };
|
|
jpayne@69
|
2025
|
|
jpayne@69
|
2026
|
|
jpayne@69
|
2027 /* "pysam/libctabix.pxd":85
|
|
jpayne@69
|
2028 *
|
|
jpayne@69
|
2029 *
|
|
jpayne@69
|
2030 * cdef class asGFF3(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2031 * pass
|
|
jpayne@69
|
2032 *
|
|
jpayne@69
|
2033 */
|
|
jpayne@69
|
2034 struct __pyx_obj_5pysam_9libctabix_asGFF3 {
|
|
jpayne@69
|
2035 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2036 };
|
|
jpayne@69
|
2037
|
|
jpayne@69
|
2038
|
|
jpayne@69
|
2039 /* "pysam/libctabix.pxd":89
|
|
jpayne@69
|
2040 *
|
|
jpayne@69
|
2041 *
|
|
jpayne@69
|
2042 * cdef class asBed(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2043 * pass
|
|
jpayne@69
|
2044 *
|
|
jpayne@69
|
2045 */
|
|
jpayne@69
|
2046 struct __pyx_obj_5pysam_9libctabix_asBed {
|
|
jpayne@69
|
2047 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2048 };
|
|
jpayne@69
|
2049
|
|
jpayne@69
|
2050
|
|
jpayne@69
|
2051 /* "pysam/libctabix.pxd":93
|
|
jpayne@69
|
2052 *
|
|
jpayne@69
|
2053 *
|
|
jpayne@69
|
2054 * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2055 * pass
|
|
jpayne@69
|
2056 *
|
|
jpayne@69
|
2057 */
|
|
jpayne@69
|
2058 struct __pyx_obj_5pysam_9libctabix_asVCF {
|
|
jpayne@69
|
2059 struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2060 };
|
|
jpayne@69
|
2061
|
|
jpayne@69
|
2062
|
|
jpayne@69
|
2063 /* "pysam/libctabix.pxd":97
|
|
jpayne@69
|
2064 *
|
|
jpayne@69
|
2065 *
|
|
jpayne@69
|
2066 * cdef class TabixIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2067 * cdef hts_itr_t * iterator
|
|
jpayne@69
|
2068 * cdef TabixFile tabixfile
|
|
jpayne@69
|
2069 */
|
|
jpayne@69
|
2070 struct __pyx_obj_5pysam_9libctabix_TabixIterator {
|
|
jpayne@69
|
2071 PyObject_HEAD
|
|
jpayne@69
|
2072 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *__pyx_vtab;
|
|
jpayne@69
|
2073 hts_itr_t *iterator;
|
|
jpayne@69
|
2074 struct __pyx_obj_5pysam_9libctabix_TabixFile *tabixfile;
|
|
jpayne@69
|
2075 kstring_t buffer;
|
|
jpayne@69
|
2076 PyObject *encoding;
|
|
jpayne@69
|
2077 };
|
|
jpayne@69
|
2078
|
|
jpayne@69
|
2079
|
|
jpayne@69
|
2080 /* "pysam/libctabix.pxd":105
|
|
jpayne@69
|
2081 *
|
|
jpayne@69
|
2082 *
|
|
jpayne@69
|
2083 * cdef class TabixIteratorParsed(TabixIterator): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2084 * cdef Parser parser
|
|
jpayne@69
|
2085 *
|
|
jpayne@69
|
2086 */
|
|
jpayne@69
|
2087 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed {
|
|
jpayne@69
|
2088 struct __pyx_obj_5pysam_9libctabix_TabixIterator __pyx_base;
|
|
jpayne@69
|
2089 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
|
|
jpayne@69
|
2090 };
|
|
jpayne@69
|
2091
|
|
jpayne@69
|
2092
|
|
jpayne@69
|
2093 /* "pysam/libctabix.pxd":109
|
|
jpayne@69
|
2094 *
|
|
jpayne@69
|
2095 *
|
|
jpayne@69
|
2096 * cdef class GZIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2097 * cdef object _filename
|
|
jpayne@69
|
2098 * cdef BGZF * gzipfile
|
|
jpayne@69
|
2099 */
|
|
jpayne@69
|
2100 struct __pyx_obj_5pysam_9libctabix_GZIterator {
|
|
jpayne@69
|
2101 PyObject_HEAD
|
|
jpayne@69
|
2102 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *__pyx_vtab;
|
|
jpayne@69
|
2103 PyObject *_filename;
|
|
jpayne@69
|
2104 BGZF *gzipfile;
|
|
jpayne@69
|
2105 kstream_t *kstream;
|
|
jpayne@69
|
2106 kstring_t buffer;
|
|
jpayne@69
|
2107 PyObject *encoding;
|
|
jpayne@69
|
2108 };
|
|
jpayne@69
|
2109
|
|
jpayne@69
|
2110
|
|
jpayne@69
|
2111 /* "pysam/libctabix.pxd":118
|
|
jpayne@69
|
2112 *
|
|
jpayne@69
|
2113 *
|
|
jpayne@69
|
2114 * cdef class GZIteratorHead(GZIterator): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2115 * pass
|
|
jpayne@69
|
2116 *
|
|
jpayne@69
|
2117 */
|
|
jpayne@69
|
2118 struct __pyx_obj_5pysam_9libctabix_GZIteratorHead {
|
|
jpayne@69
|
2119 struct __pyx_obj_5pysam_9libctabix_GZIterator __pyx_base;
|
|
jpayne@69
|
2120 };
|
|
jpayne@69
|
2121
|
|
jpayne@69
|
2122
|
|
jpayne@69
|
2123 /* "pysam/libctabix.pxd":122
|
|
jpayne@69
|
2124 *
|
|
jpayne@69
|
2125 *
|
|
jpayne@69
|
2126 * cdef class GZIteratorParsed(GZIterator): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2127 * cdef Parser parser
|
|
jpayne@69
|
2128 *
|
|
jpayne@69
|
2129 */
|
|
jpayne@69
|
2130 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed {
|
|
jpayne@69
|
2131 struct __pyx_obj_5pysam_9libctabix_GZIterator __pyx_base;
|
|
jpayne@69
|
2132 struct __pyx_obj_5pysam_9libctabix_Parser *parser;
|
|
jpayne@69
|
2133 };
|
|
jpayne@69
|
2134
|
|
jpayne@69
|
2135
|
|
jpayne@69
|
2136 /* "pysam/libctabix.pxd":127
|
|
jpayne@69
|
2137 *
|
|
jpayne@69
|
2138 * # Compatibility Layer for pysam < 0.8
|
|
jpayne@69
|
2139 * cdef class Tabixfile(TabixFile): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2140 * pass
|
|
jpayne@69
|
2141 */
|
|
jpayne@69
|
2142 struct __pyx_obj_5pysam_9libctabix_Tabixfile {
|
|
jpayne@69
|
2143 struct __pyx_obj_5pysam_9libctabix_TabixFile __pyx_base;
|
|
jpayne@69
|
2144 };
|
|
jpayne@69
|
2145
|
|
jpayne@69
|
2146
|
|
jpayne@69
|
2147
|
|
jpayne@69
|
2148 /* "pysam/libchtslib.pxd":2706
|
|
jpayne@69
|
2149 *
|
|
jpayne@69
|
2150 *
|
|
jpayne@69
|
2151 * cdef class HTSFile(object): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2152 * cdef htsFile *htsfile # pointer to htsFile structure
|
|
jpayne@69
|
2153 * cdef int64_t start_offset # BGZF offset of first record
|
|
jpayne@69
|
2154 */
|
|
jpayne@69
|
2155
|
|
jpayne@69
|
2156 struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile {
|
|
jpayne@69
|
2157 htsFile *(*_open_htsfile)(struct __pyx_obj_5pysam_10libchtslib_HTSFile *);
|
|
jpayne@69
|
2158 };
|
|
jpayne@69
|
2159 static struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtabptr_5pysam_10libchtslib_HTSFile;
|
|
jpayne@69
|
2160
|
|
jpayne@69
|
2161
|
|
jpayne@69
|
2162 /* "pysam/libctabixproxies.pxd":5
|
|
jpayne@69
|
2163 * from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t
|
|
jpayne@69
|
2164 *
|
|
jpayne@69
|
2165 * cdef class TupleProxy: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2166 *
|
|
jpayne@69
|
2167 * cdef:
|
|
jpayne@69
|
2168 */
|
|
jpayne@69
|
2169
|
|
jpayne@69
|
2170 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy {
|
|
jpayne@69
|
2171 int (*getMaxFields)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, int __pyx_skip_dispatch);
|
|
jpayne@69
|
2172 int (*getMinFields)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, int __pyx_skip_dispatch);
|
|
jpayne@69
|
2173 PyObject *(*take)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t);
|
|
jpayne@69
|
2174 PyObject *(*present)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t);
|
|
jpayne@69
|
2175 PyObject *(*copy)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t, struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy *__pyx_optional_args);
|
|
jpayne@69
|
2176 PyObject *(*update)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t);
|
|
jpayne@69
|
2177 };
|
|
jpayne@69
|
2178 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy;
|
|
jpayne@69
|
2179
|
|
jpayne@69
|
2180
|
|
jpayne@69
|
2181 /* "pysam/libctabixproxies.pxd":32
|
|
jpayne@69
|
2182 *
|
|
jpayne@69
|
2183 *
|
|
jpayne@69
|
2184 * cdef class NamedTupleProxy(TupleProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2185 * pass
|
|
jpayne@69
|
2186 *
|
|
jpayne@69
|
2187 */
|
|
jpayne@69
|
2188
|
|
jpayne@69
|
2189 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy {
|
|
jpayne@69
|
2190 struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy __pyx_base;
|
|
jpayne@69
|
2191 };
|
|
jpayne@69
|
2192 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy *__pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy;
|
|
jpayne@69
|
2193
|
|
jpayne@69
|
2194
|
|
jpayne@69
|
2195 /* "pysam/libctabixproxies.pxd":36
|
|
jpayne@69
|
2196 *
|
|
jpayne@69
|
2197 *
|
|
jpayne@69
|
2198 * cdef class GTFProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2199 * cdef object attribute_dict
|
|
jpayne@69
|
2200 * cpdef int getMaxFields(self)
|
|
jpayne@69
|
2201 */
|
|
jpayne@69
|
2202
|
|
jpayne@69
|
2203 struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy {
|
|
jpayne@69
|
2204 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
|
|
jpayne@69
|
2205 };
|
|
jpayne@69
|
2206 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy *__pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy;
|
|
jpayne@69
|
2207
|
|
jpayne@69
|
2208
|
|
jpayne@69
|
2209 /* "pysam/libctabixproxies.pxd":42
|
|
jpayne@69
|
2210 *
|
|
jpayne@69
|
2211 *
|
|
jpayne@69
|
2212 * cdef class GFF3Proxy(GTFProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2213 * pass
|
|
jpayne@69
|
2214 *
|
|
jpayne@69
|
2215 */
|
|
jpayne@69
|
2216
|
|
jpayne@69
|
2217 struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy {
|
|
jpayne@69
|
2218 struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy __pyx_base;
|
|
jpayne@69
|
2219 };
|
|
jpayne@69
|
2220 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy *__pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy;
|
|
jpayne@69
|
2221
|
|
jpayne@69
|
2222
|
|
jpayne@69
|
2223 /* "pysam/libctabixproxies.pxd":46
|
|
jpayne@69
|
2224 *
|
|
jpayne@69
|
2225 *
|
|
jpayne@69
|
2226 * cdef class BedProxy(NamedTupleProxy): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2227 *
|
|
jpayne@69
|
2228 * cdef:
|
|
jpayne@69
|
2229 */
|
|
jpayne@69
|
2230
|
|
jpayne@69
|
2231 struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy {
|
|
jpayne@69
|
2232 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
|
|
jpayne@69
|
2233 };
|
|
jpayne@69
|
2234 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy *__pyx_vtabptr_5pysam_16libctabixproxies_BedProxy;
|
|
jpayne@69
|
2235
|
|
jpayne@69
|
2236
|
|
jpayne@69
|
2237 /* "pysam/libctabixproxies.pxd":58
|
|
jpayne@69
|
2238 * cdef update(self, char * buffer, size_t nbytes)
|
|
jpayne@69
|
2239 *
|
|
jpayne@69
|
2240 * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2241 *
|
|
jpayne@69
|
2242 * cdef:
|
|
jpayne@69
|
2243 */
|
|
jpayne@69
|
2244
|
|
jpayne@69
|
2245 struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy {
|
|
jpayne@69
|
2246 struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base;
|
|
jpayne@69
|
2247 };
|
|
jpayne@69
|
2248 static struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy *__pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy;
|
|
jpayne@69
|
2249
|
|
jpayne@69
|
2250
|
|
jpayne@69
|
2251 /* "pysam/libctabix.pyx":1098
|
|
jpayne@69
|
2252 *
|
|
jpayne@69
|
2253 *
|
|
jpayne@69
|
2254 * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2255 * '''iterate over a compressed or uncompressed ``infile``.
|
|
jpayne@69
|
2256 * '''
|
|
jpayne@69
|
2257 */
|
|
jpayne@69
|
2258
|
|
jpayne@69
|
2259 struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator {
|
|
jpayne@69
|
2260 PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *);
|
|
jpayne@69
|
2261 };
|
|
jpayne@69
|
2262 static struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *__pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator;
|
|
jpayne@69
|
2263
|
|
jpayne@69
|
2264
|
|
jpayne@69
|
2265 /* "pysam/libctabix.pyx":287
|
|
jpayne@69
|
2266 *
|
|
jpayne@69
|
2267 *
|
|
jpayne@69
|
2268 * cdef class TabixFile: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2269 * """Random access to bgzf formatted files that
|
|
jpayne@69
|
2270 * have been indexed by :term:`tabix`.
|
|
jpayne@69
|
2271 */
|
|
jpayne@69
|
2272
|
|
jpayne@69
|
2273 struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile {
|
|
jpayne@69
|
2274 struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile __pyx_base;
|
|
jpayne@69
|
2275 };
|
|
jpayne@69
|
2276 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile *__pyx_vtabptr_5pysam_9libctabix_TabixFile;
|
|
jpayne@69
|
2277
|
|
jpayne@69
|
2278
|
|
jpayne@69
|
2279 /* "pysam/libctabix.pyx":82
|
|
jpayne@69
|
2280 * from pysam.libcutils cimport encode_filename, from_string_and_size
|
|
jpayne@69
|
2281 *
|
|
jpayne@69
|
2282 * cdef class Parser: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2283 *
|
|
jpayne@69
|
2284 * def __init__(self, encoding="ascii"):
|
|
jpayne@69
|
2285 */
|
|
jpayne@69
|
2286
|
|
jpayne@69
|
2287 struct __pyx_vtabstruct_5pysam_9libctabix_Parser {
|
|
jpayne@69
|
2288 PyObject *(*parse)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int);
|
|
jpayne@69
|
2289 };
|
|
jpayne@69
|
2290 static struct __pyx_vtabstruct_5pysam_9libctabix_Parser *__pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
2291
|
|
jpayne@69
|
2292
|
|
jpayne@69
|
2293 /* "pysam/libctabix.pyx":101
|
|
jpayne@69
|
2294 *
|
|
jpayne@69
|
2295 *
|
|
jpayne@69
|
2296 * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2297 * '''converts a :term:`tabix row` into a python tuple.
|
|
jpayne@69
|
2298 *
|
|
jpayne@69
|
2299 */
|
|
jpayne@69
|
2300
|
|
jpayne@69
|
2301 struct __pyx_vtabstruct_5pysam_9libctabix_asTuple {
|
|
jpayne@69
|
2302 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2303 };
|
|
jpayne@69
|
2304 static struct __pyx_vtabstruct_5pysam_9libctabix_asTuple *__pyx_vtabptr_5pysam_9libctabix_asTuple;
|
|
jpayne@69
|
2305
|
|
jpayne@69
|
2306
|
|
jpayne@69
|
2307 /* "pysam/libctabix.pyx":151
|
|
jpayne@69
|
2308 *
|
|
jpayne@69
|
2309 *
|
|
jpayne@69
|
2310 * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2311 * '''converts a :term:`tabix row` into a GTF record with the following
|
|
jpayne@69
|
2312 * fields:
|
|
jpayne@69
|
2313 */
|
|
jpayne@69
|
2314
|
|
jpayne@69
|
2315 struct __pyx_vtabstruct_5pysam_9libctabix_asGTF {
|
|
jpayne@69
|
2316 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2317 };
|
|
jpayne@69
|
2318 static struct __pyx_vtabstruct_5pysam_9libctabix_asGTF *__pyx_vtabptr_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
2319
|
|
jpayne@69
|
2320
|
|
jpayne@69
|
2321 /* "pysam/libctabix.pyx":115
|
|
jpayne@69
|
2322 *
|
|
jpayne@69
|
2323 *
|
|
jpayne@69
|
2324 * cdef class asGFF3(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2325 * '''converts a :term:`tabix row` into a GFF record with the following
|
|
jpayne@69
|
2326 * fields:
|
|
jpayne@69
|
2327 */
|
|
jpayne@69
|
2328
|
|
jpayne@69
|
2329 struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 {
|
|
jpayne@69
|
2330 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2331 };
|
|
jpayne@69
|
2332 static struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 *__pyx_vtabptr_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
2333
|
|
jpayne@69
|
2334
|
|
jpayne@69
|
2335 /* "pysam/libctabix.pyx":198
|
|
jpayne@69
|
2336 *
|
|
jpayne@69
|
2337 *
|
|
jpayne@69
|
2338 * cdef class asBed(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2339 * '''converts a :term:`tabix row` into a bed record
|
|
jpayne@69
|
2340 * with the following fields:
|
|
jpayne@69
|
2341 */
|
|
jpayne@69
|
2342
|
|
jpayne@69
|
2343 struct __pyx_vtabstruct_5pysam_9libctabix_asBed {
|
|
jpayne@69
|
2344 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2345 };
|
|
jpayne@69
|
2346 static struct __pyx_vtabstruct_5pysam_9libctabix_asBed *__pyx_vtabptr_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
2347
|
|
jpayne@69
|
2348
|
|
jpayne@69
|
2349 /* "pysam/libctabix.pyx":246
|
|
jpayne@69
|
2350 *
|
|
jpayne@69
|
2351 *
|
|
jpayne@69
|
2352 * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2353 * '''converts a :term:`tabix row` into a VCF record with
|
|
jpayne@69
|
2354 * the following fields:
|
|
jpayne@69
|
2355 */
|
|
jpayne@69
|
2356
|
|
jpayne@69
|
2357 struct __pyx_vtabstruct_5pysam_9libctabix_asVCF {
|
|
jpayne@69
|
2358 struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base;
|
|
jpayne@69
|
2359 };
|
|
jpayne@69
|
2360 static struct __pyx_vtabstruct_5pysam_9libctabix_asVCF *__pyx_vtabptr_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
2361
|
|
jpayne@69
|
2362
|
|
jpayne@69
|
2363 /* "pysam/libctabix.pyx":619
|
|
jpayne@69
|
2364 *
|
|
jpayne@69
|
2365 *
|
|
jpayne@69
|
2366 * cdef class TabixIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2367 * """iterates over rows in *tabixfile* in region
|
|
jpayne@69
|
2368 * given by *tid*, *start* and *end*.
|
|
jpayne@69
|
2369 */
|
|
jpayne@69
|
2370
|
|
jpayne@69
|
2371 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator {
|
|
jpayne@69
|
2372 int (*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_TabixIterator *);
|
|
jpayne@69
|
2373 };
|
|
jpayne@69
|
2374 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *__pyx_vtabptr_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
2375
|
|
jpayne@69
|
2376
|
|
jpayne@69
|
2377 /* "pysam/libctabix.pyx":692
|
|
jpayne@69
|
2378 *
|
|
jpayne@69
|
2379 *
|
|
jpayne@69
|
2380 * cdef class TabixIteratorParsed(TabixIterator): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2381 * """iterates over mapped reads in a region.
|
|
jpayne@69
|
2382 *
|
|
jpayne@69
|
2383 */
|
|
jpayne@69
|
2384
|
|
jpayne@69
|
2385 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed {
|
|
jpayne@69
|
2386 struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator __pyx_base;
|
|
jpayne@69
|
2387 };
|
|
jpayne@69
|
2388 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed *__pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
2389
|
|
jpayne@69
|
2390
|
|
jpayne@69
|
2391 /* "pysam/libctabix.pyx":720
|
|
jpayne@69
|
2392 *
|
|
jpayne@69
|
2393 *
|
|
jpayne@69
|
2394 * cdef class GZIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2395 * def __init__(self, filename, int buffer_size=65536, encoding="ascii"):
|
|
jpayne@69
|
2396 * '''iterate line-by-line through gzip (or bgzip)
|
|
jpayne@69
|
2397 */
|
|
jpayne@69
|
2398
|
|
jpayne@69
|
2399 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator {
|
|
jpayne@69
|
2400 int (*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_GZIterator *);
|
|
jpayne@69
|
2401 };
|
|
jpayne@69
|
2402 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *__pyx_vtabptr_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
2403
|
|
jpayne@69
|
2404
|
|
jpayne@69
|
2405 /* "pysam/libctabix.pyx":775
|
|
jpayne@69
|
2406 *
|
|
jpayne@69
|
2407 *
|
|
jpayne@69
|
2408 * cdef class GZIteratorHead(GZIterator): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2409 * '''iterate line-by-line through gzip (or bgzip)
|
|
jpayne@69
|
2410 * compressed file returning comments at top of file.
|
|
jpayne@69
|
2411 */
|
|
jpayne@69
|
2412
|
|
jpayne@69
|
2413 struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead {
|
|
jpayne@69
|
2414 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_base;
|
|
jpayne@69
|
2415 };
|
|
jpayne@69
|
2416 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead *__pyx_vtabptr_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
2417
|
|
jpayne@69
|
2418
|
|
jpayne@69
|
2419 /* "pysam/libctabix.pyx":792
|
|
jpayne@69
|
2420 *
|
|
jpayne@69
|
2421 *
|
|
jpayne@69
|
2422 * cdef class GZIteratorParsed(GZIterator): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2423 * '''iterate line-by-line through gzip (or bgzip)
|
|
jpayne@69
|
2424 * compressed file returning comments at top of file.
|
|
jpayne@69
|
2425 */
|
|
jpayne@69
|
2426
|
|
jpayne@69
|
2427 struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed {
|
|
jpayne@69
|
2428 struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_base;
|
|
jpayne@69
|
2429 };
|
|
jpayne@69
|
2430 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed *__pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed;
|
|
jpayne@69
|
2431
|
|
jpayne@69
|
2432
|
|
jpayne@69
|
2433 /* "pysam/libctabix.pyx":1251
|
|
jpayne@69
|
2434 *
|
|
jpayne@69
|
2435 *
|
|
jpayne@69
|
2436 * cdef class Tabixfile(TabixFile): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
2437 * """Tabixfile is deprecated: use TabixFile instead"""
|
|
jpayne@69
|
2438 * pass
|
|
jpayne@69
|
2439 */
|
|
jpayne@69
|
2440
|
|
jpayne@69
|
2441 struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile {
|
|
jpayne@69
|
2442 struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile __pyx_base;
|
|
jpayne@69
|
2443 };
|
|
jpayne@69
|
2444 static struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile *__pyx_vtabptr_5pysam_9libctabix_Tabixfile;
|
|
jpayne@69
|
2445 /* #### Code section: utility_code_proto ### */
|
|
jpayne@69
|
2446
|
|
jpayne@69
|
2447 /* --- Runtime support code (head) --- */
|
|
jpayne@69
|
2448 /* Refnanny.proto */
|
|
jpayne@69
|
2449 #ifndef CYTHON_REFNANNY
|
|
jpayne@69
|
2450 #define CYTHON_REFNANNY 0
|
|
jpayne@69
|
2451 #endif
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|
jpayne@69
|
2452 #if CYTHON_REFNANNY
|
|
jpayne@69
|
2453 typedef struct {
|
|
jpayne@69
|
2454 void (*INCREF)(void*, PyObject*, Py_ssize_t);
|
|
jpayne@69
|
2455 void (*DECREF)(void*, PyObject*, Py_ssize_t);
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|
jpayne@69
|
2456 void (*GOTREF)(void*, PyObject*, Py_ssize_t);
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|
jpayne@69
|
2457 void (*GIVEREF)(void*, PyObject*, Py_ssize_t);
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|
jpayne@69
|
2458 void* (*SetupContext)(const char*, Py_ssize_t, const char*);
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jpayne@69
|
2459 void (*FinishContext)(void**);
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jpayne@69
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2460 } __Pyx_RefNannyAPIStruct;
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jpayne@69
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2461 static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
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jpayne@69
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2462 static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
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jpayne@69
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2463 #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
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jpayne@69
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2464 #ifdef WITH_THREAD
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jpayne@69
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2465 #define __Pyx_RefNannySetupContext(name, acquire_gil)\
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|
jpayne@69
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2466 if (acquire_gil) {\
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jpayne@69
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2467 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
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jpayne@69
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2468 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\
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jpayne@69
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2469 PyGILState_Release(__pyx_gilstate_save);\
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jpayne@69
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2470 } else {\
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jpayne@69
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2471 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\
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jpayne@69
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2472 }
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jpayne@69
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2473 #define __Pyx_RefNannyFinishContextNogil() {\
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jpayne@69
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2474 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
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jpayne@69
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2475 __Pyx_RefNannyFinishContext();\
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jpayne@69
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2476 PyGILState_Release(__pyx_gilstate_save);\
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2477 }
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jpayne@69
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2478 #else
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jpayne@69
|
2479 #define __Pyx_RefNannySetupContext(name, acquire_gil)\
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jpayne@69
|
2480 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__))
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jpayne@69
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2481 #define __Pyx_RefNannyFinishContextNogil() __Pyx_RefNannyFinishContext()
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jpayne@69
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2482 #endif
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jpayne@69
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2483 #define __Pyx_RefNannyFinishContextNogil() {\
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jpayne@69
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2484 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
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jpayne@69
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2485 __Pyx_RefNannyFinishContext();\
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jpayne@69
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2486 PyGILState_Release(__pyx_gilstate_save);\
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jpayne@69
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2487 }
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jpayne@69
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2488 #define __Pyx_RefNannyFinishContext()\
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jpayne@69
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2489 __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
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jpayne@69
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2490 #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
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jpayne@69
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2491 #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
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jpayne@69
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2492 #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
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jpayne@69
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2493 #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
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jpayne@69
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2494 #define __Pyx_XINCREF(r) do { if((r) == NULL); else {__Pyx_INCREF(r); }} while(0)
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jpayne@69
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2495 #define __Pyx_XDECREF(r) do { if((r) == NULL); else {__Pyx_DECREF(r); }} while(0)
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jpayne@69
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2496 #define __Pyx_XGOTREF(r) do { if((r) == NULL); else {__Pyx_GOTREF(r); }} while(0)
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jpayne@69
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2497 #define __Pyx_XGIVEREF(r) do { if((r) == NULL); else {__Pyx_GIVEREF(r);}} while(0)
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jpayne@69
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2498 #else
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jpayne@69
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2499 #define __Pyx_RefNannyDeclarations
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jpayne@69
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2500 #define __Pyx_RefNannySetupContext(name, acquire_gil)
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jpayne@69
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2501 #define __Pyx_RefNannyFinishContextNogil()
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jpayne@69
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2502 #define __Pyx_RefNannyFinishContext()
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jpayne@69
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2503 #define __Pyx_INCREF(r) Py_INCREF(r)
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jpayne@69
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2504 #define __Pyx_DECREF(r) Py_DECREF(r)
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jpayne@69
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2505 #define __Pyx_GOTREF(r)
|
|
jpayne@69
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2506 #define __Pyx_GIVEREF(r)
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|
jpayne@69
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2507 #define __Pyx_XINCREF(r) Py_XINCREF(r)
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jpayne@69
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2508 #define __Pyx_XDECREF(r) Py_XDECREF(r)
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|
jpayne@69
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2509 #define __Pyx_XGOTREF(r)
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|
jpayne@69
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2510 #define __Pyx_XGIVEREF(r)
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|
jpayne@69
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2511 #endif
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jpayne@69
|
2512 #define __Pyx_Py_XDECREF_SET(r, v) do {\
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jpayne@69
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2513 PyObject *tmp = (PyObject *) r;\
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jpayne@69
|
2514 r = v; Py_XDECREF(tmp);\
|
|
jpayne@69
|
2515 } while (0)
|
|
jpayne@69
|
2516 #define __Pyx_XDECREF_SET(r, v) do {\
|
|
jpayne@69
|
2517 PyObject *tmp = (PyObject *) r;\
|
|
jpayne@69
|
2518 r = v; __Pyx_XDECREF(tmp);\
|
|
jpayne@69
|
2519 } while (0)
|
|
jpayne@69
|
2520 #define __Pyx_DECREF_SET(r, v) do {\
|
|
jpayne@69
|
2521 PyObject *tmp = (PyObject *) r;\
|
|
jpayne@69
|
2522 r = v; __Pyx_DECREF(tmp);\
|
|
jpayne@69
|
2523 } while (0)
|
|
jpayne@69
|
2524 #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
|
|
jpayne@69
|
2525 #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
|
|
jpayne@69
|
2526
|
|
jpayne@69
|
2527 /* PyErrExceptionMatches.proto */
|
|
jpayne@69
|
2528 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2529 #define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
|
|
jpayne@69
|
2530 static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
|
|
jpayne@69
|
2531 #else
|
|
jpayne@69
|
2532 #define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
|
|
jpayne@69
|
2533 #endif
|
|
jpayne@69
|
2534
|
|
jpayne@69
|
2535 /* PyThreadStateGet.proto */
|
|
jpayne@69
|
2536 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2537 #define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
|
|
jpayne@69
|
2538 #define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
2539 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
2540 #define __Pyx_PyErr_Occurred() (__pyx_tstate->current_exception != NULL)
|
|
jpayne@69
|
2541 #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->current_exception ? (PyObject*) Py_TYPE(__pyx_tstate->current_exception) : (PyObject*) NULL)
|
|
jpayne@69
|
2542 #else
|
|
jpayne@69
|
2543 #define __Pyx_PyErr_Occurred() (__pyx_tstate->curexc_type != NULL)
|
|
jpayne@69
|
2544 #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->curexc_type)
|
|
jpayne@69
|
2545 #endif
|
|
jpayne@69
|
2546 #else
|
|
jpayne@69
|
2547 #define __Pyx_PyThreadState_declare
|
|
jpayne@69
|
2548 #define __Pyx_PyThreadState_assign
|
|
jpayne@69
|
2549 #define __Pyx_PyErr_Occurred() (PyErr_Occurred() != NULL)
|
|
jpayne@69
|
2550 #define __Pyx_PyErr_CurrentExceptionType() PyErr_Occurred()
|
|
jpayne@69
|
2551 #endif
|
|
jpayne@69
|
2552
|
|
jpayne@69
|
2553 /* PyErrFetchRestore.proto */
|
|
jpayne@69
|
2554 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2555 #define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL)
|
|
jpayne@69
|
2556 #define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
|
|
jpayne@69
|
2557 #define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
|
|
jpayne@69
|
2558 #define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
2559 #define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
2560 static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
|
|
jpayne@69
|
2561 static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
2562 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A6
|
|
jpayne@69
|
2563 #define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL))
|
|
jpayne@69
|
2564 #else
|
|
jpayne@69
|
2565 #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
|
|
jpayne@69
|
2566 #endif
|
|
jpayne@69
|
2567 #else
|
|
jpayne@69
|
2568 #define __Pyx_PyErr_Clear() PyErr_Clear()
|
|
jpayne@69
|
2569 #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
|
|
jpayne@69
|
2570 #define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb)
|
|
jpayne@69
|
2571 #define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb)
|
|
jpayne@69
|
2572 #define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb)
|
|
jpayne@69
|
2573 #define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb)
|
|
jpayne@69
|
2574 #define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb)
|
|
jpayne@69
|
2575 #define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb)
|
|
jpayne@69
|
2576 #endif
|
|
jpayne@69
|
2577
|
|
jpayne@69
|
2578 /* PyObjectGetAttrStr.proto */
|
|
jpayne@69
|
2579 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
2580 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name);
|
|
jpayne@69
|
2581 #else
|
|
jpayne@69
|
2582 #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
|
|
jpayne@69
|
2583 #endif
|
|
jpayne@69
|
2584
|
|
jpayne@69
|
2585 /* PyObjectGetAttrStrNoError.proto */
|
|
jpayne@69
|
2586 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name);
|
|
jpayne@69
|
2587
|
|
jpayne@69
|
2588 /* GetBuiltinName.proto */
|
|
jpayne@69
|
2589 static PyObject *__Pyx_GetBuiltinName(PyObject *name);
|
|
jpayne@69
|
2590
|
|
jpayne@69
|
2591 /* TupleAndListFromArray.proto */
|
|
jpayne@69
|
2592 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
2593 static CYTHON_INLINE PyObject* __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n);
|
|
jpayne@69
|
2594 static CYTHON_INLINE PyObject* __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n);
|
|
jpayne@69
|
2595 #endif
|
|
jpayne@69
|
2596
|
|
jpayne@69
|
2597 /* IncludeStringH.proto */
|
|
jpayne@69
|
2598 #include <string.h>
|
|
jpayne@69
|
2599
|
|
jpayne@69
|
2600 /* BytesEquals.proto */
|
|
jpayne@69
|
2601 static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);
|
|
jpayne@69
|
2602
|
|
jpayne@69
|
2603 /* UnicodeEquals.proto */
|
|
jpayne@69
|
2604 static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);
|
|
jpayne@69
|
2605
|
|
jpayne@69
|
2606 /* fastcall.proto */
|
|
jpayne@69
|
2607 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
2608 #define __Pyx_Arg_VARARGS(args, i) PySequence_GetItem(args, i)
|
|
jpayne@69
|
2609 #elif CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
2610 #define __Pyx_Arg_VARARGS(args, i) PyTuple_GET_ITEM(args, i)
|
|
jpayne@69
|
2611 #else
|
|
jpayne@69
|
2612 #define __Pyx_Arg_VARARGS(args, i) PyTuple_GetItem(args, i)
|
|
jpayne@69
|
2613 #endif
|
|
jpayne@69
|
2614 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
2615 #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg)
|
|
jpayne@69
|
2616 #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg)
|
|
jpayne@69
|
2617 #else
|
|
jpayne@69
|
2618 #define __Pyx_Arg_NewRef_VARARGS(arg) arg
|
|
jpayne@69
|
2619 #define __Pyx_Arg_XDECREF_VARARGS(arg)
|
|
jpayne@69
|
2620 #endif
|
|
jpayne@69
|
2621 #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds)
|
|
jpayne@69
|
2622 #define __Pyx_KwValues_VARARGS(args, nargs) NULL
|
|
jpayne@69
|
2623 #define __Pyx_GetKwValue_VARARGS(kw, kwvalues, s) __Pyx_PyDict_GetItemStrWithError(kw, s)
|
|
jpayne@69
|
2624 #define __Pyx_KwargsAsDict_VARARGS(kw, kwvalues) PyDict_Copy(kw)
|
|
jpayne@69
|
2625 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
2626 #define __Pyx_Arg_FASTCALL(args, i) args[i]
|
|
jpayne@69
|
2627 #define __Pyx_NumKwargs_FASTCALL(kwds) PyTuple_GET_SIZE(kwds)
|
|
jpayne@69
|
2628 #define __Pyx_KwValues_FASTCALL(args, nargs) ((args) + (nargs))
|
|
jpayne@69
|
2629 static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s);
|
|
jpayne@69
|
2630 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
2631 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues);
|
|
jpayne@69
|
2632 #else
|
|
jpayne@69
|
2633 #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw)
|
|
jpayne@69
|
2634 #endif
|
|
jpayne@69
|
2635 #define __Pyx_Arg_NewRef_FASTCALL(arg) arg /* no-op, __Pyx_Arg_FASTCALL is direct and this needs
|
|
jpayne@69
|
2636 to have the same reference counting */
|
|
jpayne@69
|
2637 #define __Pyx_Arg_XDECREF_FASTCALL(arg)
|
|
jpayne@69
|
2638 #else
|
|
jpayne@69
|
2639 #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS
|
|
jpayne@69
|
2640 #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS
|
|
jpayne@69
|
2641 #define __Pyx_KwValues_FASTCALL __Pyx_KwValues_VARARGS
|
|
jpayne@69
|
2642 #define __Pyx_GetKwValue_FASTCALL __Pyx_GetKwValue_VARARGS
|
|
jpayne@69
|
2643 #define __Pyx_KwargsAsDict_FASTCALL __Pyx_KwargsAsDict_VARARGS
|
|
jpayne@69
|
2644 #define __Pyx_Arg_NewRef_FASTCALL(arg) __Pyx_Arg_NewRef_VARARGS(arg)
|
|
jpayne@69
|
2645 #define __Pyx_Arg_XDECREF_FASTCALL(arg) __Pyx_Arg_XDECREF_VARARGS(arg)
|
|
jpayne@69
|
2646 #endif
|
|
jpayne@69
|
2647 #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
2648 #define __Pyx_ArgsSlice_VARARGS(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_VARARGS(args, start), stop - start)
|
|
jpayne@69
|
2649 #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_FASTCALL(args, start), stop - start)
|
|
jpayne@69
|
2650 #else
|
|
jpayne@69
|
2651 #define __Pyx_ArgsSlice_VARARGS(args, start, stop) PyTuple_GetSlice(args, start, stop)
|
|
jpayne@69
|
2652 #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) PyTuple_GetSlice(args, start, stop)
|
|
jpayne@69
|
2653 #endif
|
|
jpayne@69
|
2654
|
|
jpayne@69
|
2655 /* RaiseDoubleKeywords.proto */
|
|
jpayne@69
|
2656 static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
|
|
jpayne@69
|
2657
|
|
jpayne@69
|
2658 /* ParseKeywords.proto */
|
|
jpayne@69
|
2659 static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject *const *kwvalues,
|
|
jpayne@69
|
2660 PyObject **argnames[],
|
|
jpayne@69
|
2661 PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,
|
|
jpayne@69
|
2662 const char* function_name);
|
|
jpayne@69
|
2663
|
|
jpayne@69
|
2664 /* RaiseArgTupleInvalid.proto */
|
|
jpayne@69
|
2665 static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
|
|
jpayne@69
|
2666 Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
|
|
jpayne@69
|
2667
|
|
jpayne@69
|
2668 /* Profile.proto */
|
|
jpayne@69
|
2669 #ifndef CYTHON_PROFILE
|
|
jpayne@69
|
2670 #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
2671 #define CYTHON_PROFILE 0
|
|
jpayne@69
|
2672 #else
|
|
jpayne@69
|
2673 #define CYTHON_PROFILE 1
|
|
jpayne@69
|
2674 #endif
|
|
jpayne@69
|
2675 #endif
|
|
jpayne@69
|
2676 #ifndef CYTHON_TRACE_NOGIL
|
|
jpayne@69
|
2677 #define CYTHON_TRACE_NOGIL 0
|
|
jpayne@69
|
2678 #else
|
|
jpayne@69
|
2679 #if CYTHON_TRACE_NOGIL && !defined(CYTHON_TRACE)
|
|
jpayne@69
|
2680 #define CYTHON_TRACE 1
|
|
jpayne@69
|
2681 #endif
|
|
jpayne@69
|
2682 #endif
|
|
jpayne@69
|
2683 #ifndef CYTHON_TRACE
|
|
jpayne@69
|
2684 #define CYTHON_TRACE 0
|
|
jpayne@69
|
2685 #endif
|
|
jpayne@69
|
2686 #if CYTHON_TRACE
|
|
jpayne@69
|
2687 #undef CYTHON_PROFILE_REUSE_FRAME
|
|
jpayne@69
|
2688 #endif
|
|
jpayne@69
|
2689 #ifndef CYTHON_PROFILE_REUSE_FRAME
|
|
jpayne@69
|
2690 #define CYTHON_PROFILE_REUSE_FRAME 0
|
|
jpayne@69
|
2691 #endif
|
|
jpayne@69
|
2692 #if CYTHON_PROFILE || CYTHON_TRACE
|
|
jpayne@69
|
2693 #include "compile.h"
|
|
jpayne@69
|
2694 #include "frameobject.h"
|
|
jpayne@69
|
2695 #include "traceback.h"
|
|
jpayne@69
|
2696 #if PY_VERSION_HEX >= 0x030b00a6
|
|
jpayne@69
|
2697 #ifndef Py_BUILD_CORE
|
|
jpayne@69
|
2698 #define Py_BUILD_CORE 1
|
|
jpayne@69
|
2699 #endif
|
|
jpayne@69
|
2700 #include "internal/pycore_frame.h"
|
|
jpayne@69
|
2701 #endif
|
|
jpayne@69
|
2702 #if CYTHON_PROFILE_REUSE_FRAME
|
|
jpayne@69
|
2703 #define CYTHON_FRAME_MODIFIER static
|
|
jpayne@69
|
2704 #define CYTHON_FRAME_DEL(frame)
|
|
jpayne@69
|
2705 #else
|
|
jpayne@69
|
2706 #define CYTHON_FRAME_MODIFIER
|
|
jpayne@69
|
2707 #define CYTHON_FRAME_DEL(frame) Py_CLEAR(frame)
|
|
jpayne@69
|
2708 #endif
|
|
jpayne@69
|
2709 #define __Pyx_TraceDeclarations\
|
|
jpayne@69
|
2710 static PyCodeObject *__pyx_frame_code = NULL;\
|
|
jpayne@69
|
2711 CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL;\
|
|
jpayne@69
|
2712 int __Pyx_use_tracing = 0;
|
|
jpayne@69
|
2713 #define __Pyx_TraceFrameInit(codeobj)\
|
|
jpayne@69
|
2714 if (codeobj) __pyx_frame_code = (PyCodeObject*) codeobj;
|
|
jpayne@69
|
2715 #if PY_VERSION_HEX >= 0x030b00a2
|
|
jpayne@69
|
2716 #if PY_VERSION_HEX >= 0x030C00b1
|
|
jpayne@69
|
2717 #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\
|
|
jpayne@69
|
2718 ((!(check_tracing) || !(tstate)->tracing) &&\
|
|
jpayne@69
|
2719 (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc)))
|
|
jpayne@69
|
2720 #else
|
|
jpayne@69
|
2721 #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\
|
|
jpayne@69
|
2722 (unlikely((tstate)->cframe->use_tracing) &&\
|
|
jpayne@69
|
2723 (!(check_tracing) || !(tstate)->tracing) &&\
|
|
jpayne@69
|
2724 (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc)))
|
|
jpayne@69
|
2725 #endif
|
|
jpayne@69
|
2726 #define __Pyx_EnterTracing(tstate) PyThreadState_EnterTracing(tstate)
|
|
jpayne@69
|
2727 #define __Pyx_LeaveTracing(tstate) PyThreadState_LeaveTracing(tstate)
|
|
jpayne@69
|
2728 #elif PY_VERSION_HEX >= 0x030a00b1
|
|
jpayne@69
|
2729 #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\
|
|
jpayne@69
|
2730 (unlikely((tstate)->cframe->use_tracing) &&\
|
|
jpayne@69
|
2731 (!(check_tracing) || !(tstate)->tracing) &&\
|
|
jpayne@69
|
2732 (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc)))
|
|
jpayne@69
|
2733 #define __Pyx_EnterTracing(tstate)\
|
|
jpayne@69
|
2734 do { tstate->tracing++; tstate->cframe->use_tracing = 0; } while (0)
|
|
jpayne@69
|
2735 #define __Pyx_LeaveTracing(tstate)\
|
|
jpayne@69
|
2736 do {\
|
|
jpayne@69
|
2737 tstate->tracing--;\
|
|
jpayne@69
|
2738 tstate->cframe->use_tracing = ((CYTHON_TRACE && tstate->c_tracefunc != NULL)\
|
|
jpayne@69
|
2739 || tstate->c_profilefunc != NULL);\
|
|
jpayne@69
|
2740 } while (0)
|
|
jpayne@69
|
2741 #else
|
|
jpayne@69
|
2742 #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\
|
|
jpayne@69
|
2743 (unlikely((tstate)->use_tracing) &&\
|
|
jpayne@69
|
2744 (!(check_tracing) || !(tstate)->tracing) &&\
|
|
jpayne@69
|
2745 (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc)))
|
|
jpayne@69
|
2746 #define __Pyx_EnterTracing(tstate)\
|
|
jpayne@69
|
2747 do { tstate->tracing++; tstate->use_tracing = 0; } while (0)
|
|
jpayne@69
|
2748 #define __Pyx_LeaveTracing(tstate)\
|
|
jpayne@69
|
2749 do {\
|
|
jpayne@69
|
2750 tstate->tracing--;\
|
|
jpayne@69
|
2751 tstate->use_tracing = ((CYTHON_TRACE && tstate->c_tracefunc != NULL)\
|
|
jpayne@69
|
2752 || tstate->c_profilefunc != NULL);\
|
|
jpayne@69
|
2753 } while (0)
|
|
jpayne@69
|
2754 #endif
|
|
jpayne@69
|
2755 #ifdef WITH_THREAD
|
|
jpayne@69
|
2756 #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\
|
|
jpayne@69
|
2757 if (nogil) {\
|
|
jpayne@69
|
2758 if (CYTHON_TRACE_NOGIL) {\
|
|
jpayne@69
|
2759 PyThreadState *tstate;\
|
|
jpayne@69
|
2760 PyGILState_STATE state = PyGILState_Ensure();\
|
|
jpayne@69
|
2761 tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2762 if (__Pyx_IsTracing(tstate, 1, 1)) {\
|
|
jpayne@69
|
2763 __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\
|
|
jpayne@69
|
2764 }\
|
|
jpayne@69
|
2765 PyGILState_Release(state);\
|
|
jpayne@69
|
2766 if (unlikely(__Pyx_use_tracing < 0)) goto_error;\
|
|
jpayne@69
|
2767 }\
|
|
jpayne@69
|
2768 } else {\
|
|
jpayne@69
|
2769 PyThreadState* tstate = PyThreadState_GET();\
|
|
jpayne@69
|
2770 if (__Pyx_IsTracing(tstate, 1, 1)) {\
|
|
jpayne@69
|
2771 __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\
|
|
jpayne@69
|
2772 if (unlikely(__Pyx_use_tracing < 0)) goto_error;\
|
|
jpayne@69
|
2773 }\
|
|
jpayne@69
|
2774 }
|
|
jpayne@69
|
2775 #else
|
|
jpayne@69
|
2776 #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\
|
|
jpayne@69
|
2777 { PyThreadState* tstate = PyThreadState_GET();\
|
|
jpayne@69
|
2778 if (__Pyx_IsTracing(tstate, 1, 1)) {\
|
|
jpayne@69
|
2779 __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\
|
|
jpayne@69
|
2780 if (unlikely(__Pyx_use_tracing < 0)) goto_error;\
|
|
jpayne@69
|
2781 }\
|
|
jpayne@69
|
2782 }
|
|
jpayne@69
|
2783 #endif
|
|
jpayne@69
|
2784 #define __Pyx_TraceException()\
|
|
jpayne@69
|
2785 if (likely(!__Pyx_use_tracing)); else {\
|
|
jpayne@69
|
2786 PyThreadState* tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2787 if (__Pyx_IsTracing(tstate, 0, 1)) {\
|
|
jpayne@69
|
2788 __Pyx_EnterTracing(tstate);\
|
|
jpayne@69
|
2789 PyObject *exc_info = __Pyx_GetExceptionTuple(tstate);\
|
|
jpayne@69
|
2790 if (exc_info) {\
|
|
jpayne@69
|
2791 if (CYTHON_TRACE && tstate->c_tracefunc)\
|
|
jpayne@69
|
2792 tstate->c_tracefunc(\
|
|
jpayne@69
|
2793 tstate->c_traceobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\
|
|
jpayne@69
|
2794 tstate->c_profilefunc(\
|
|
jpayne@69
|
2795 tstate->c_profileobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\
|
|
jpayne@69
|
2796 Py_DECREF(exc_info);\
|
|
jpayne@69
|
2797 }\
|
|
jpayne@69
|
2798 __Pyx_LeaveTracing(tstate);\
|
|
jpayne@69
|
2799 }\
|
|
jpayne@69
|
2800 }
|
|
jpayne@69
|
2801 static void __Pyx_call_return_trace_func(PyThreadState *tstate, PyFrameObject *frame, PyObject *result) {
|
|
jpayne@69
|
2802 PyObject *type, *value, *traceback;
|
|
jpayne@69
|
2803 __Pyx_ErrFetchInState(tstate, &type, &value, &traceback);
|
|
jpayne@69
|
2804 __Pyx_EnterTracing(tstate);
|
|
jpayne@69
|
2805 if (CYTHON_TRACE && tstate->c_tracefunc)
|
|
jpayne@69
|
2806 tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_RETURN, result);
|
|
jpayne@69
|
2807 if (tstate->c_profilefunc)
|
|
jpayne@69
|
2808 tstate->c_profilefunc(tstate->c_profileobj, frame, PyTrace_RETURN, result);
|
|
jpayne@69
|
2809 CYTHON_FRAME_DEL(frame);
|
|
jpayne@69
|
2810 __Pyx_LeaveTracing(tstate);
|
|
jpayne@69
|
2811 __Pyx_ErrRestoreInState(tstate, type, value, traceback);
|
|
jpayne@69
|
2812 }
|
|
jpayne@69
|
2813 #ifdef WITH_THREAD
|
|
jpayne@69
|
2814 #define __Pyx_TraceReturn(result, nogil)\
|
|
jpayne@69
|
2815 if (likely(!__Pyx_use_tracing)); else {\
|
|
jpayne@69
|
2816 if (nogil) {\
|
|
jpayne@69
|
2817 if (CYTHON_TRACE_NOGIL) {\
|
|
jpayne@69
|
2818 PyThreadState *tstate;\
|
|
jpayne@69
|
2819 PyGILState_STATE state = PyGILState_Ensure();\
|
|
jpayne@69
|
2820 tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2821 if (__Pyx_IsTracing(tstate, 0, 0)) {\
|
|
jpayne@69
|
2822 __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\
|
|
jpayne@69
|
2823 }\
|
|
jpayne@69
|
2824 PyGILState_Release(state);\
|
|
jpayne@69
|
2825 }\
|
|
jpayne@69
|
2826 } else {\
|
|
jpayne@69
|
2827 PyThreadState* tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2828 if (__Pyx_IsTracing(tstate, 0, 0)) {\
|
|
jpayne@69
|
2829 __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\
|
|
jpayne@69
|
2830 }\
|
|
jpayne@69
|
2831 }\
|
|
jpayne@69
|
2832 }
|
|
jpayne@69
|
2833 #else
|
|
jpayne@69
|
2834 #define __Pyx_TraceReturn(result, nogil)\
|
|
jpayne@69
|
2835 if (likely(!__Pyx_use_tracing)); else {\
|
|
jpayne@69
|
2836 PyThreadState* tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2837 if (__Pyx_IsTracing(tstate, 0, 0)) {\
|
|
jpayne@69
|
2838 __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\
|
|
jpayne@69
|
2839 }\
|
|
jpayne@69
|
2840 }
|
|
jpayne@69
|
2841 #endif
|
|
jpayne@69
|
2842 static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno);
|
|
jpayne@69
|
2843 static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, PyThreadState* tstate, const char *funcname, const char *srcfile, int firstlineno);
|
|
jpayne@69
|
2844 #else
|
|
jpayne@69
|
2845 #define __Pyx_TraceDeclarations
|
|
jpayne@69
|
2846 #define __Pyx_TraceFrameInit(codeobj)
|
|
jpayne@69
|
2847 #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error) if ((1)); else goto_error;
|
|
jpayne@69
|
2848 #define __Pyx_TraceException()
|
|
jpayne@69
|
2849 #define __Pyx_TraceReturn(result, nogil)
|
|
jpayne@69
|
2850 #endif
|
|
jpayne@69
|
2851 #if CYTHON_TRACE
|
|
jpayne@69
|
2852 static int __Pyx_call_line_trace_func(PyThreadState *tstate, PyFrameObject *frame, int lineno) {
|
|
jpayne@69
|
2853 int ret;
|
|
jpayne@69
|
2854 PyObject *type, *value, *traceback;
|
|
jpayne@69
|
2855 __Pyx_ErrFetchInState(tstate, &type, &value, &traceback);
|
|
jpayne@69
|
2856 __Pyx_PyFrame_SetLineNumber(frame, lineno);
|
|
jpayne@69
|
2857 __Pyx_EnterTracing(tstate);
|
|
jpayne@69
|
2858 ret = tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_LINE, NULL);
|
|
jpayne@69
|
2859 __Pyx_LeaveTracing(tstate);
|
|
jpayne@69
|
2860 if (likely(!ret)) {
|
|
jpayne@69
|
2861 __Pyx_ErrRestoreInState(tstate, type, value, traceback);
|
|
jpayne@69
|
2862 } else {
|
|
jpayne@69
|
2863 Py_XDECREF(type);
|
|
jpayne@69
|
2864 Py_XDECREF(value);
|
|
jpayne@69
|
2865 Py_XDECREF(traceback);
|
|
jpayne@69
|
2866 }
|
|
jpayne@69
|
2867 return ret;
|
|
jpayne@69
|
2868 }
|
|
jpayne@69
|
2869 #ifdef WITH_THREAD
|
|
jpayne@69
|
2870 #define __Pyx_TraceLine(lineno, nogil, goto_error)\
|
|
jpayne@69
|
2871 if (likely(!__Pyx_use_tracing)); else {\
|
|
jpayne@69
|
2872 if (nogil) {\
|
|
jpayne@69
|
2873 if (CYTHON_TRACE_NOGIL) {\
|
|
jpayne@69
|
2874 int ret = 0;\
|
|
jpayne@69
|
2875 PyThreadState *tstate;\
|
|
jpayne@69
|
2876 PyGILState_STATE state = __Pyx_PyGILState_Ensure();\
|
|
jpayne@69
|
2877 tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2878 if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\
|
|
jpayne@69
|
2879 ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\
|
|
jpayne@69
|
2880 }\
|
|
jpayne@69
|
2881 __Pyx_PyGILState_Release(state);\
|
|
jpayne@69
|
2882 if (unlikely(ret)) goto_error;\
|
|
jpayne@69
|
2883 }\
|
|
jpayne@69
|
2884 } else {\
|
|
jpayne@69
|
2885 PyThreadState* tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2886 if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\
|
|
jpayne@69
|
2887 int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\
|
|
jpayne@69
|
2888 if (unlikely(ret)) goto_error;\
|
|
jpayne@69
|
2889 }\
|
|
jpayne@69
|
2890 }\
|
|
jpayne@69
|
2891 }
|
|
jpayne@69
|
2892 #else
|
|
jpayne@69
|
2893 #define __Pyx_TraceLine(lineno, nogil, goto_error)\
|
|
jpayne@69
|
2894 if (likely(!__Pyx_use_tracing)); else {\
|
|
jpayne@69
|
2895 PyThreadState* tstate = __Pyx_PyThreadState_Current;\
|
|
jpayne@69
|
2896 if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\
|
|
jpayne@69
|
2897 int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\
|
|
jpayne@69
|
2898 if (unlikely(ret)) goto_error;\
|
|
jpayne@69
|
2899 }\
|
|
jpayne@69
|
2900 }
|
|
jpayne@69
|
2901 #endif
|
|
jpayne@69
|
2902 #else
|
|
jpayne@69
|
2903 #define __Pyx_TraceLine(lineno, nogil, goto_error) if ((1)); else goto_error;
|
|
jpayne@69
|
2904 #endif
|
|
jpayne@69
|
2905
|
|
jpayne@69
|
2906 /* KeywordStringCheck.proto */
|
|
jpayne@69
|
2907 static int __Pyx_CheckKeywordStrings(PyObject *kw, const char* function_name, int kw_allowed);
|
|
jpayne@69
|
2908
|
|
jpayne@69
|
2909 /* PyObject_Unicode.proto */
|
|
jpayne@69
|
2910 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
2911 #define __Pyx_PyObject_Unicode(obj)\
|
|
jpayne@69
|
2912 (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj))
|
|
jpayne@69
|
2913 #else
|
|
jpayne@69
|
2914 #define __Pyx_PyObject_Unicode(obj)\
|
|
jpayne@69
|
2915 (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Unicode(obj))
|
|
jpayne@69
|
2916 #endif
|
|
jpayne@69
|
2917
|
|
jpayne@69
|
2918 /* PyFunctionFastCall.proto */
|
|
jpayne@69
|
2919 #if CYTHON_FAST_PYCALL
|
|
jpayne@69
|
2920 #if !CYTHON_VECTORCALL
|
|
jpayne@69
|
2921 #define __Pyx_PyFunction_FastCall(func, args, nargs)\
|
|
jpayne@69
|
2922 __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
|
|
jpayne@69
|
2923 static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs);
|
|
jpayne@69
|
2924 #endif
|
|
jpayne@69
|
2925 #define __Pyx_BUILD_ASSERT_EXPR(cond)\
|
|
jpayne@69
|
2926 (sizeof(char [1 - 2*!(cond)]) - 1)
|
|
jpayne@69
|
2927 #ifndef Py_MEMBER_SIZE
|
|
jpayne@69
|
2928 #define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
|
|
jpayne@69
|
2929 #endif
|
|
jpayne@69
|
2930 #if !CYTHON_VECTORCALL
|
|
jpayne@69
|
2931 #if PY_VERSION_HEX >= 0x03080000
|
|
jpayne@69
|
2932 #include "frameobject.h"
|
|
jpayne@69
|
2933 #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2934 #ifndef Py_BUILD_CORE
|
|
jpayne@69
|
2935 #define Py_BUILD_CORE 1
|
|
jpayne@69
|
2936 #endif
|
|
jpayne@69
|
2937 #include "internal/pycore_frame.h"
|
|
jpayne@69
|
2938 #endif
|
|
jpayne@69
|
2939 #define __Pxy_PyFrame_Initialize_Offsets()
|
|
jpayne@69
|
2940 #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus)
|
|
jpayne@69
|
2941 #else
|
|
jpayne@69
|
2942 static size_t __pyx_pyframe_localsplus_offset = 0;
|
|
jpayne@69
|
2943 #include "frameobject.h"
|
|
jpayne@69
|
2944 #define __Pxy_PyFrame_Initialize_Offsets()\
|
|
jpayne@69
|
2945 ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
|
|
jpayne@69
|
2946 (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
|
|
jpayne@69
|
2947 #define __Pyx_PyFrame_GetLocalsplus(frame)\
|
|
jpayne@69
|
2948 (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
|
|
jpayne@69
|
2949 #endif
|
|
jpayne@69
|
2950 #endif
|
|
jpayne@69
|
2951 #endif
|
|
jpayne@69
|
2952
|
|
jpayne@69
|
2953 /* PyObjectCall.proto */
|
|
jpayne@69
|
2954 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
2955 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
|
|
jpayne@69
|
2956 #else
|
|
jpayne@69
|
2957 #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
|
|
jpayne@69
|
2958 #endif
|
|
jpayne@69
|
2959
|
|
jpayne@69
|
2960 /* PyObjectCallMethO.proto */
|
|
jpayne@69
|
2961 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
2962 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
|
|
jpayne@69
|
2963 #endif
|
|
jpayne@69
|
2964
|
|
jpayne@69
|
2965 /* PyObjectFastCall.proto */
|
|
jpayne@69
|
2966 #define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL)
|
|
jpayne@69
|
2967 static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs);
|
|
jpayne@69
|
2968
|
|
jpayne@69
|
2969 /* PyObjectCallOneArg.proto */
|
|
jpayne@69
|
2970 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
|
|
jpayne@69
|
2971
|
|
jpayne@69
|
2972 /* RaiseException.proto */
|
|
jpayne@69
|
2973 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
|
|
jpayne@69
|
2974
|
|
jpayne@69
|
2975 /* GetAttr3.proto */
|
|
jpayne@69
|
2976 static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *);
|
|
jpayne@69
|
2977
|
|
jpayne@69
|
2978 /* PyDictVersioning.proto */
|
|
jpayne@69
|
2979 #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
2980 #define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1)
|
|
jpayne@69
|
2981 #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag)
|
|
jpayne@69
|
2982 #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\
|
|
jpayne@69
|
2983 (version_var) = __PYX_GET_DICT_VERSION(dict);\
|
|
jpayne@69
|
2984 (cache_var) = (value);
|
|
jpayne@69
|
2985 #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\
|
|
jpayne@69
|
2986 static PY_UINT64_T __pyx_dict_version = 0;\
|
|
jpayne@69
|
2987 static PyObject *__pyx_dict_cached_value = NULL;\
|
|
jpayne@69
|
2988 if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\
|
|
jpayne@69
|
2989 (VAR) = __pyx_dict_cached_value;\
|
|
jpayne@69
|
2990 } else {\
|
|
jpayne@69
|
2991 (VAR) = __pyx_dict_cached_value = (LOOKUP);\
|
|
jpayne@69
|
2992 __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\
|
|
jpayne@69
|
2993 }\
|
|
jpayne@69
|
2994 }
|
|
jpayne@69
|
2995 static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj);
|
|
jpayne@69
|
2996 static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj);
|
|
jpayne@69
|
2997 static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version);
|
|
jpayne@69
|
2998 #else
|
|
jpayne@69
|
2999 #define __PYX_GET_DICT_VERSION(dict) (0)
|
|
jpayne@69
|
3000 #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)
|
|
jpayne@69
|
3001 #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP);
|
|
jpayne@69
|
3002 #endif
|
|
jpayne@69
|
3003
|
|
jpayne@69
|
3004 /* GetModuleGlobalName.proto */
|
|
jpayne@69
|
3005 #if CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
3006 #define __Pyx_GetModuleGlobalName(var, name) do {\
|
|
jpayne@69
|
3007 static PY_UINT64_T __pyx_dict_version = 0;\
|
|
jpayne@69
|
3008 static PyObject *__pyx_dict_cached_value = NULL;\
|
|
jpayne@69
|
3009 (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\
|
|
jpayne@69
|
3010 (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\
|
|
jpayne@69
|
3011 __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
|
|
jpayne@69
|
3012 } while(0)
|
|
jpayne@69
|
3013 #define __Pyx_GetModuleGlobalNameUncached(var, name) do {\
|
|
jpayne@69
|
3014 PY_UINT64_T __pyx_dict_version;\
|
|
jpayne@69
|
3015 PyObject *__pyx_dict_cached_value;\
|
|
jpayne@69
|
3016 (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
|
|
jpayne@69
|
3017 } while(0)
|
|
jpayne@69
|
3018 static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value);
|
|
jpayne@69
|
3019 #else
|
|
jpayne@69
|
3020 #define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name)
|
|
jpayne@69
|
3021 #define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name)
|
|
jpayne@69
|
3022 static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name);
|
|
jpayne@69
|
3023 #endif
|
|
jpayne@69
|
3024
|
|
jpayne@69
|
3025 /* RaiseUnexpectedTypeError.proto */
|
|
jpayne@69
|
3026 static int __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj);
|
|
jpayne@69
|
3027
|
|
jpayne@69
|
3028 /* ExtTypeTest.proto */
|
|
jpayne@69
|
3029 static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
|
|
jpayne@69
|
3030
|
|
jpayne@69
|
3031 /* PyIntBinop.proto */
|
|
jpayne@69
|
3032 #if !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
3033 static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
|
|
jpayne@69
|
3034 #else
|
|
jpayne@69
|
3035 #define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\
|
|
jpayne@69
|
3036 (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2))
|
|
jpayne@69
|
3037 #endif
|
|
jpayne@69
|
3038
|
|
jpayne@69
|
3039 /* ListAppend.proto */
|
|
jpayne@69
|
3040 #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
3041 static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
|
|
jpayne@69
|
3042 PyListObject* L = (PyListObject*) list;
|
|
jpayne@69
|
3043 Py_ssize_t len = Py_SIZE(list);
|
|
jpayne@69
|
3044 if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
|
|
jpayne@69
|
3045 Py_INCREF(x);
|
|
jpayne@69
|
3046 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
3047 L->ob_item[len] = x;
|
|
jpayne@69
|
3048 #else
|
|
jpayne@69
|
3049 PyList_SET_ITEM(list, len, x);
|
|
jpayne@69
|
3050 #endif
|
|
jpayne@69
|
3051 __Pyx_SET_SIZE(list, len + 1);
|
|
jpayne@69
|
3052 return 0;
|
|
jpayne@69
|
3053 }
|
|
jpayne@69
|
3054 return PyList_Append(list, x);
|
|
jpayne@69
|
3055 }
|
|
jpayne@69
|
3056 #else
|
|
jpayne@69
|
3057 #define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
|
|
jpayne@69
|
3058 #endif
|
|
jpayne@69
|
3059
|
|
jpayne@69
|
3060 /* WriteUnraisableException.proto */
|
|
jpayne@69
|
3061 static void __Pyx_WriteUnraisable(const char *name, int clineno,
|
|
jpayne@69
|
3062 int lineno, const char *filename,
|
|
jpayne@69
|
3063 int full_traceback, int nogil);
|
|
jpayne@69
|
3064
|
|
jpayne@69
|
3065 /* PyObjectCallNoArg.proto */
|
|
jpayne@69
|
3066 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
|
|
jpayne@69
|
3067
|
|
jpayne@69
|
3068 /* ArgTypeTest.proto */
|
|
jpayne@69
|
3069 #define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\
|
|
jpayne@69
|
3070 ((likely(__Pyx_IS_TYPE(obj, type) | (none_allowed && (obj == Py_None)))) ? 1 :\
|
|
jpayne@69
|
3071 __Pyx__ArgTypeTest(obj, type, name, exact))
|
|
jpayne@69
|
3072 static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact);
|
|
jpayne@69
|
3073
|
|
jpayne@69
|
3074 /* PyObjectFormatAndDecref.proto */
|
|
jpayne@69
|
3075 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f);
|
|
jpayne@69
|
3076 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f);
|
|
jpayne@69
|
3077
|
|
jpayne@69
|
3078 /* JoinPyUnicode.proto */
|
|
jpayne@69
|
3079 static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength,
|
|
jpayne@69
|
3080 Py_UCS4 max_char);
|
|
jpayne@69
|
3081
|
|
jpayne@69
|
3082 /* DictGetItem.proto */
|
|
jpayne@69
|
3083 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
3084 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key);
|
|
jpayne@69
|
3085 #define __Pyx_PyObject_Dict_GetItem(obj, name)\
|
|
jpayne@69
|
3086 (likely(PyDict_CheckExact(obj)) ?\
|
|
jpayne@69
|
3087 __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name))
|
|
jpayne@69
|
3088 #else
|
|
jpayne@69
|
3089 #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
|
|
jpayne@69
|
3090 #define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name)
|
|
jpayne@69
|
3091 #endif
|
|
jpayne@69
|
3092
|
|
jpayne@69
|
3093 /* GetTopmostException.proto */
|
|
jpayne@69
|
3094 #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
3095 static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate);
|
|
jpayne@69
|
3096 #endif
|
|
jpayne@69
|
3097
|
|
jpayne@69
|
3098 /* SaveResetException.proto */
|
|
jpayne@69
|
3099 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
3100 #define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
3101 static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
3102 #define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
3103 static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
|
|
jpayne@69
|
3104 #else
|
|
jpayne@69
|
3105 #define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb)
|
|
jpayne@69
|
3106 #define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
|
|
jpayne@69
|
3107 #endif
|
|
jpayne@69
|
3108
|
|
jpayne@69
|
3109 /* GetException.proto */
|
|
jpayne@69
|
3110 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
3111 #define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
3112 static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
3113 #else
|
|
jpayne@69
|
3114 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
3115 #endif
|
|
jpayne@69
|
3116
|
|
jpayne@69
|
3117 /* py_dict_keys.proto */
|
|
jpayne@69
|
3118 static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d);
|
|
jpayne@69
|
3119
|
|
jpayne@69
|
3120 /* UnpackUnboundCMethod.proto */
|
|
jpayne@69
|
3121 typedef struct {
|
|
jpayne@69
|
3122 PyObject *type;
|
|
jpayne@69
|
3123 PyObject **method_name;
|
|
jpayne@69
|
3124 PyCFunction func;
|
|
jpayne@69
|
3125 PyObject *method;
|
|
jpayne@69
|
3126 int flag;
|
|
jpayne@69
|
3127 } __Pyx_CachedCFunction;
|
|
jpayne@69
|
3128
|
|
jpayne@69
|
3129 /* CallUnboundCMethod0.proto */
|
|
jpayne@69
|
3130 static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self);
|
|
jpayne@69
|
3131 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
3132 #define __Pyx_CallUnboundCMethod0(cfunc, self)\
|
|
jpayne@69
|
3133 (likely((cfunc)->func) ?\
|
|
jpayne@69
|
3134 (likely((cfunc)->flag == METH_NOARGS) ? (*((cfunc)->func))(self, NULL) :\
|
|
jpayne@69
|
3135 (PY_VERSION_HEX >= 0x030600B1 && likely((cfunc)->flag == METH_FASTCALL) ?\
|
|
jpayne@69
|
3136 (PY_VERSION_HEX >= 0x030700A0 ?\
|
|
jpayne@69
|
3137 (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0) :\
|
|
jpayne@69
|
3138 (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0, NULL)) :\
|
|
jpayne@69
|
3139 (PY_VERSION_HEX >= 0x030700A0 && (cfunc)->flag == (METH_FASTCALL | METH_KEYWORDS) ?\
|
|
jpayne@69
|
3140 (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0, NULL) :\
|
|
jpayne@69
|
3141 (likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ? ((*(PyCFunctionWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\
|
|
jpayne@69
|
3142 ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) :\
|
|
jpayne@69
|
3143 __Pyx__CallUnboundCMethod0(cfunc, self)))))) :\
|
|
jpayne@69
|
3144 __Pyx__CallUnboundCMethod0(cfunc, self))
|
|
jpayne@69
|
3145 #else
|
|
jpayne@69
|
3146 #define __Pyx_CallUnboundCMethod0(cfunc, self) __Pyx__CallUnboundCMethod0(cfunc, self)
|
|
jpayne@69
|
3147 #endif
|
|
jpayne@69
|
3148
|
|
jpayne@69
|
3149 /* UnicodeAsUCS4.proto */
|
|
jpayne@69
|
3150 static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject*);
|
|
jpayne@69
|
3151
|
|
jpayne@69
|
3152 /* object_ord.proto */
|
|
jpayne@69
|
3153 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
3154 #define __Pyx_PyObject_Ord(c)\
|
|
jpayne@69
|
3155 (likely(PyUnicode_Check(c)) ? (long)__Pyx_PyUnicode_AsPy_UCS4(c) : __Pyx__PyObject_Ord(c))
|
|
jpayne@69
|
3156 #else
|
|
jpayne@69
|
3157 #define __Pyx_PyObject_Ord(c) __Pyx__PyObject_Ord(c)
|
|
jpayne@69
|
3158 #endif
|
|
jpayne@69
|
3159 static long __Pyx__PyObject_Ord(PyObject* c);
|
|
jpayne@69
|
3160
|
|
jpayne@69
|
3161 /* RaiseTooManyValuesToUnpack.proto */
|
|
jpayne@69
|
3162 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
|
|
jpayne@69
|
3163
|
|
jpayne@69
|
3164 /* RaiseNeedMoreValuesToUnpack.proto */
|
|
jpayne@69
|
3165 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
|
|
jpayne@69
|
3166
|
|
jpayne@69
|
3167 /* IterFinish.proto */
|
|
jpayne@69
|
3168 static CYTHON_INLINE int __Pyx_IterFinish(void);
|
|
jpayne@69
|
3169
|
|
jpayne@69
|
3170 /* UnpackItemEndCheck.proto */
|
|
jpayne@69
|
3171 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
|
|
jpayne@69
|
3172
|
|
jpayne@69
|
3173 /* PyObjectSetAttrStr.proto */
|
|
jpayne@69
|
3174 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
3175 #define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL)
|
|
jpayne@69
|
3176 static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value);
|
|
jpayne@69
|
3177 #else
|
|
jpayne@69
|
3178 #define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
|
|
jpayne@69
|
3179 #define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
|
|
jpayne@69
|
3180 #endif
|
|
jpayne@69
|
3181
|
|
jpayne@69
|
3182 /* AssertionsEnabled.proto */
|
|
jpayne@69
|
3183 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag)
|
|
jpayne@69
|
3184 #define __Pyx_init_assertions_enabled() (0)
|
|
jpayne@69
|
3185 #define __pyx_assertions_enabled() (1)
|
|
jpayne@69
|
3186 #elif CYTHON_COMPILING_IN_LIMITED_API || (CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030C0000)
|
|
jpayne@69
|
3187 static int __pyx_assertions_enabled_flag;
|
|
jpayne@69
|
3188 #define __pyx_assertions_enabled() (__pyx_assertions_enabled_flag)
|
|
jpayne@69
|
3189 static int __Pyx_init_assertions_enabled(void) {
|
|
jpayne@69
|
3190 PyObject *builtins, *debug, *debug_str;
|
|
jpayne@69
|
3191 int flag;
|
|
jpayne@69
|
3192 builtins = PyEval_GetBuiltins();
|
|
jpayne@69
|
3193 if (!builtins) goto bad;
|
|
jpayne@69
|
3194 debug_str = PyUnicode_FromStringAndSize("__debug__", 9);
|
|
jpayne@69
|
3195 if (!debug_str) goto bad;
|
|
jpayne@69
|
3196 debug = PyObject_GetItem(builtins, debug_str);
|
|
jpayne@69
|
3197 Py_DECREF(debug_str);
|
|
jpayne@69
|
3198 if (!debug) goto bad;
|
|
jpayne@69
|
3199 flag = PyObject_IsTrue(debug);
|
|
jpayne@69
|
3200 Py_DECREF(debug);
|
|
jpayne@69
|
3201 if (flag == -1) goto bad;
|
|
jpayne@69
|
3202 __pyx_assertions_enabled_flag = flag;
|
|
jpayne@69
|
3203 return 0;
|
|
jpayne@69
|
3204 bad:
|
|
jpayne@69
|
3205 __pyx_assertions_enabled_flag = 1;
|
|
jpayne@69
|
3206 return -1;
|
|
jpayne@69
|
3207 }
|
|
jpayne@69
|
3208 #else
|
|
jpayne@69
|
3209 #define __Pyx_init_assertions_enabled() (0)
|
|
jpayne@69
|
3210 #define __pyx_assertions_enabled() (!Py_OptimizeFlag)
|
|
jpayne@69
|
3211 #endif
|
|
jpayne@69
|
3212
|
|
jpayne@69
|
3213 /* PySequenceContains.proto */
|
|
jpayne@69
|
3214 static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) {
|
|
jpayne@69
|
3215 int result = PySequence_Contains(seq, item);
|
|
jpayne@69
|
3216 return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
|
|
jpayne@69
|
3217 }
|
|
jpayne@69
|
3218
|
|
jpayne@69
|
3219 /* Import.proto */
|
|
jpayne@69
|
3220 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
|
|
jpayne@69
|
3221
|
|
jpayne@69
|
3222 /* ImportFrom.proto */
|
|
jpayne@69
|
3223 static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
|
|
jpayne@69
|
3224
|
|
jpayne@69
|
3225 /* GetItemInt.proto */
|
|
jpayne@69
|
3226 #define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
3227 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
3228 __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
|
|
jpayne@69
|
3229 (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
|
|
jpayne@69
|
3230 __Pyx_GetItemInt_Generic(o, to_py_func(i))))
|
|
jpayne@69
|
3231 #define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
3232 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
3233 __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
|
|
jpayne@69
|
3234 (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
|
|
jpayne@69
|
3235 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
3236 int wraparound, int boundscheck);
|
|
jpayne@69
|
3237 #define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
3238 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
3239 __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
|
|
jpayne@69
|
3240 (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
|
|
jpayne@69
|
3241 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
3242 int wraparound, int boundscheck);
|
|
jpayne@69
|
3243 static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
|
|
jpayne@69
|
3244 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
3245 int is_list, int wraparound, int boundscheck);
|
|
jpayne@69
|
3246
|
|
jpayne@69
|
3247 /* GetAttr.proto */
|
|
jpayne@69
|
3248 static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *);
|
|
jpayne@69
|
3249
|
|
jpayne@69
|
3250 /* HasAttr.proto */
|
|
jpayne@69
|
3251 static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *);
|
|
jpayne@69
|
3252
|
|
jpayne@69
|
3253 /* CallNextTpDealloc.proto */
|
|
jpayne@69
|
3254 static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
|
|
jpayne@69
|
3255
|
|
jpayne@69
|
3256 /* CallNextTpTraverse.proto */
|
|
jpayne@69
|
3257 static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
|
|
jpayne@69
|
3258
|
|
jpayne@69
|
3259 /* CallNextTpClear.proto */
|
|
jpayne@69
|
3260 static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear);
|
|
jpayne@69
|
3261
|
|
jpayne@69
|
3262 /* IncludeStructmemberH.proto */
|
|
jpayne@69
|
3263 #include <structmember.h>
|
|
jpayne@69
|
3264
|
|
jpayne@69
|
3265 /* FixUpExtensionType.proto */
|
|
jpayne@69
|
3266 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
3267 static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type);
|
|
jpayne@69
|
3268 #endif
|
|
jpayne@69
|
3269
|
|
jpayne@69
|
3270 /* PyObjectGetMethod.proto */
|
|
jpayne@69
|
3271 static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method);
|
|
jpayne@69
|
3272
|
|
jpayne@69
|
3273 /* PyObjectCallMethod0.proto */
|
|
jpayne@69
|
3274 static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name);
|
|
jpayne@69
|
3275
|
|
jpayne@69
|
3276 /* ValidateBasesTuple.proto */
|
|
jpayne@69
|
3277 #if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
3278 static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases);
|
|
jpayne@69
|
3279 #endif
|
|
jpayne@69
|
3280
|
|
jpayne@69
|
3281 /* PyType_Ready.proto */
|
|
jpayne@69
|
3282 CYTHON_UNUSED static int __Pyx_PyType_Ready(PyTypeObject *t);
|
|
jpayne@69
|
3283
|
|
jpayne@69
|
3284 /* PyObject_GenericGetAttrNoDict.proto */
|
|
jpayne@69
|
3285 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
|
|
jpayne@69
|
3286 static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name);
|
|
jpayne@69
|
3287 #else
|
|
jpayne@69
|
3288 #define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr
|
|
jpayne@69
|
3289 #endif
|
|
jpayne@69
|
3290
|
|
jpayne@69
|
3291 /* PyObject_GenericGetAttr.proto */
|
|
jpayne@69
|
3292 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
|
|
jpayne@69
|
3293 static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name);
|
|
jpayne@69
|
3294 #else
|
|
jpayne@69
|
3295 #define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr
|
|
jpayne@69
|
3296 #endif
|
|
jpayne@69
|
3297
|
|
jpayne@69
|
3298 /* SetVTable.proto */
|
|
jpayne@69
|
3299 static int __Pyx_SetVtable(PyTypeObject* typeptr , void* vtable);
|
|
jpayne@69
|
3300
|
|
jpayne@69
|
3301 /* GetVTable.proto */
|
|
jpayne@69
|
3302 static void* __Pyx_GetVtable(PyTypeObject *type);
|
|
jpayne@69
|
3303
|
|
jpayne@69
|
3304 /* MergeVTables.proto */
|
|
jpayne@69
|
3305 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3306 static int __Pyx_MergeVtables(PyTypeObject *type);
|
|
jpayne@69
|
3307 #endif
|
|
jpayne@69
|
3308
|
|
jpayne@69
|
3309 /* SetupReduce.proto */
|
|
jpayne@69
|
3310 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3311 static int __Pyx_setup_reduce(PyObject* type_obj);
|
|
jpayne@69
|
3312 #endif
|
|
jpayne@69
|
3313
|
|
jpayne@69
|
3314 /* TypeImport.proto */
|
|
jpayne@69
|
3315 #ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11
|
|
jpayne@69
|
3316 #define __PYX_HAVE_RT_ImportType_proto_3_0_11
|
|
jpayne@69
|
3317 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L
|
|
jpayne@69
|
3318 #include <stdalign.h>
|
|
jpayne@69
|
3319 #endif
|
|
jpayne@69
|
3320 #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L
|
|
jpayne@69
|
3321 #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s)
|
|
jpayne@69
|
3322 #else
|
|
jpayne@69
|
3323 #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*)
|
|
jpayne@69
|
3324 #endif
|
|
jpayne@69
|
3325 enum __Pyx_ImportType_CheckSize_3_0_11 {
|
|
jpayne@69
|
3326 __Pyx_ImportType_CheckSize_Error_3_0_11 = 0,
|
|
jpayne@69
|
3327 __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1,
|
|
jpayne@69
|
3328 __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2
|
|
jpayne@69
|
3329 };
|
|
jpayne@69
|
3330 static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size);
|
|
jpayne@69
|
3331 #endif
|
|
jpayne@69
|
3332
|
|
jpayne@69
|
3333 /* ImportDottedModule.proto */
|
|
jpayne@69
|
3334 static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple);
|
|
jpayne@69
|
3335 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
3336 static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple);
|
|
jpayne@69
|
3337 #endif
|
|
jpayne@69
|
3338
|
|
jpayne@69
|
3339 /* FetchSharedCythonModule.proto */
|
|
jpayne@69
|
3340 static PyObject *__Pyx_FetchSharedCythonABIModule(void);
|
|
jpayne@69
|
3341
|
|
jpayne@69
|
3342 /* FetchCommonType.proto */
|
|
jpayne@69
|
3343 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
3344 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
|
|
jpayne@69
|
3345 #else
|
|
jpayne@69
|
3346 static PyTypeObject* __Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases);
|
|
jpayne@69
|
3347 #endif
|
|
jpayne@69
|
3348
|
|
jpayne@69
|
3349 /* PyMethodNew.proto */
|
|
jpayne@69
|
3350 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3351 static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) {
|
|
jpayne@69
|
3352 PyObject *typesModule=NULL, *methodType=NULL, *result=NULL;
|
|
jpayne@69
|
3353 CYTHON_UNUSED_VAR(typ);
|
|
jpayne@69
|
3354 if (!self)
|
|
jpayne@69
|
3355 return __Pyx_NewRef(func);
|
|
jpayne@69
|
3356 typesModule = PyImport_ImportModule("types");
|
|
jpayne@69
|
3357 if (!typesModule) return NULL;
|
|
jpayne@69
|
3358 methodType = PyObject_GetAttrString(typesModule, "MethodType");
|
|
jpayne@69
|
3359 Py_DECREF(typesModule);
|
|
jpayne@69
|
3360 if (!methodType) return NULL;
|
|
jpayne@69
|
3361 result = PyObject_CallFunctionObjArgs(methodType, func, self, NULL);
|
|
jpayne@69
|
3362 Py_DECREF(methodType);
|
|
jpayne@69
|
3363 return result;
|
|
jpayne@69
|
3364 }
|
|
jpayne@69
|
3365 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
3366 static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) {
|
|
jpayne@69
|
3367 CYTHON_UNUSED_VAR(typ);
|
|
jpayne@69
|
3368 if (!self)
|
|
jpayne@69
|
3369 return __Pyx_NewRef(func);
|
|
jpayne@69
|
3370 return PyMethod_New(func, self);
|
|
jpayne@69
|
3371 }
|
|
jpayne@69
|
3372 #else
|
|
jpayne@69
|
3373 #define __Pyx_PyMethod_New PyMethod_New
|
|
jpayne@69
|
3374 #endif
|
|
jpayne@69
|
3375
|
|
jpayne@69
|
3376 /* PyVectorcallFastCallDict.proto */
|
|
jpayne@69
|
3377 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
3378 static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw);
|
|
jpayne@69
|
3379 #endif
|
|
jpayne@69
|
3380
|
|
jpayne@69
|
3381 /* CythonFunctionShared.proto */
|
|
jpayne@69
|
3382 #define __Pyx_CyFunction_USED
|
|
jpayne@69
|
3383 #define __Pyx_CYFUNCTION_STATICMETHOD 0x01
|
|
jpayne@69
|
3384 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
|
|
jpayne@69
|
3385 #define __Pyx_CYFUNCTION_CCLASS 0x04
|
|
jpayne@69
|
3386 #define __Pyx_CYFUNCTION_COROUTINE 0x08
|
|
jpayne@69
|
3387 #define __Pyx_CyFunction_GetClosure(f)\
|
|
jpayne@69
|
3388 (((__pyx_CyFunctionObject *) (f))->func_closure)
|
|
jpayne@69
|
3389 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3390 #define __Pyx_CyFunction_GetClassObj(f)\
|
|
jpayne@69
|
3391 (((__pyx_CyFunctionObject *) (f))->func_classobj)
|
|
jpayne@69
|
3392 #else
|
|
jpayne@69
|
3393 #define __Pyx_CyFunction_GetClassObj(f)\
|
|
jpayne@69
|
3394 ((PyObject*) ((PyCMethodObject *) (f))->mm_class)
|
|
jpayne@69
|
3395 #endif
|
|
jpayne@69
|
3396 #define __Pyx_CyFunction_SetClassObj(f, classobj)\
|
|
jpayne@69
|
3397 __Pyx__CyFunction_SetClassObj((__pyx_CyFunctionObject *) (f), (classobj))
|
|
jpayne@69
|
3398 #define __Pyx_CyFunction_Defaults(type, f)\
|
|
jpayne@69
|
3399 ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
|
|
jpayne@69
|
3400 #define __Pyx_CyFunction_SetDefaultsGetter(f, g)\
|
|
jpayne@69
|
3401 ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
|
|
jpayne@69
|
3402 typedef struct {
|
|
jpayne@69
|
3403 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3404 PyObject_HEAD
|
|
jpayne@69
|
3405 PyObject *func;
|
|
jpayne@69
|
3406 #elif PY_VERSION_HEX < 0x030900B1
|
|
jpayne@69
|
3407 PyCFunctionObject func;
|
|
jpayne@69
|
3408 #else
|
|
jpayne@69
|
3409 PyCMethodObject func;
|
|
jpayne@69
|
3410 #endif
|
|
jpayne@69
|
3411 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
3412 __pyx_vectorcallfunc func_vectorcall;
|
|
jpayne@69
|
3413 #endif
|
|
jpayne@69
|
3414 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3415 PyObject *func_weakreflist;
|
|
jpayne@69
|
3416 #endif
|
|
jpayne@69
|
3417 PyObject *func_dict;
|
|
jpayne@69
|
3418 PyObject *func_name;
|
|
jpayne@69
|
3419 PyObject *func_qualname;
|
|
jpayne@69
|
3420 PyObject *func_doc;
|
|
jpayne@69
|
3421 PyObject *func_globals;
|
|
jpayne@69
|
3422 PyObject *func_code;
|
|
jpayne@69
|
3423 PyObject *func_closure;
|
|
jpayne@69
|
3424 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3425 PyObject *func_classobj;
|
|
jpayne@69
|
3426 #endif
|
|
jpayne@69
|
3427 void *defaults;
|
|
jpayne@69
|
3428 int defaults_pyobjects;
|
|
jpayne@69
|
3429 size_t defaults_size;
|
|
jpayne@69
|
3430 int flags;
|
|
jpayne@69
|
3431 PyObject *defaults_tuple;
|
|
jpayne@69
|
3432 PyObject *defaults_kwdict;
|
|
jpayne@69
|
3433 PyObject *(*defaults_getter)(PyObject *);
|
|
jpayne@69
|
3434 PyObject *func_annotations;
|
|
jpayne@69
|
3435 PyObject *func_is_coroutine;
|
|
jpayne@69
|
3436 } __pyx_CyFunctionObject;
|
|
jpayne@69
|
3437 #undef __Pyx_CyOrPyCFunction_Check
|
|
jpayne@69
|
3438 #define __Pyx_CyFunction_Check(obj) __Pyx_TypeCheck(obj, __pyx_CyFunctionType)
|
|
jpayne@69
|
3439 #define __Pyx_CyOrPyCFunction_Check(obj) __Pyx_TypeCheck2(obj, __pyx_CyFunctionType, &PyCFunction_Type)
|
|
jpayne@69
|
3440 #define __Pyx_CyFunction_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_CyFunctionType)
|
|
jpayne@69
|
3441 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc);
|
|
jpayne@69
|
3442 #undef __Pyx_IsSameCFunction
|
|
jpayne@69
|
3443 #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCyOrCFunction(func, cfunc)
|
|
jpayne@69
|
3444 static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml,
|
|
jpayne@69
|
3445 int flags, PyObject* qualname,
|
|
jpayne@69
|
3446 PyObject *closure,
|
|
jpayne@69
|
3447 PyObject *module, PyObject *globals,
|
|
jpayne@69
|
3448 PyObject* code);
|
|
jpayne@69
|
3449 static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj);
|
|
jpayne@69
|
3450 static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
|
|
jpayne@69
|
3451 size_t size,
|
|
jpayne@69
|
3452 int pyobjects);
|
|
jpayne@69
|
3453 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
|
|
jpayne@69
|
3454 PyObject *tuple);
|
|
jpayne@69
|
3455 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m,
|
|
jpayne@69
|
3456 PyObject *dict);
|
|
jpayne@69
|
3457 static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m,
|
|
jpayne@69
|
3458 PyObject *dict);
|
|
jpayne@69
|
3459 static int __pyx_CyFunction_init(PyObject *module);
|
|
jpayne@69
|
3460 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
3461 static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
3462 static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
3463 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
3464 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
3465 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
3466 #define __Pyx_CyFunction_func_vectorcall(f) (((__pyx_CyFunctionObject*)f)->func_vectorcall)
|
|
jpayne@69
|
3467 #else
|
|
jpayne@69
|
3468 #define __Pyx_CyFunction_func_vectorcall(f) (((PyCFunctionObject*)f)->vectorcall)
|
|
jpayne@69
|
3469 #endif
|
|
jpayne@69
|
3470 #endif
|
|
jpayne@69
|
3471
|
|
jpayne@69
|
3472 /* CythonFunction.proto */
|
|
jpayne@69
|
3473 static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml,
|
|
jpayne@69
|
3474 int flags, PyObject* qualname,
|
|
jpayne@69
|
3475 PyObject *closure,
|
|
jpayne@69
|
3476 PyObject *module, PyObject *globals,
|
|
jpayne@69
|
3477 PyObject* code);
|
|
jpayne@69
|
3478
|
|
jpayne@69
|
3479 /* SetNameInClass.proto */
|
|
jpayne@69
|
3480 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
3481 #define __Pyx_SetNameInClass(ns, name, value)\
|
|
jpayne@69
|
3482 (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value))
|
|
jpayne@69
|
3483 #elif CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
3484 #define __Pyx_SetNameInClass(ns, name, value)\
|
|
jpayne@69
|
3485 (likely(PyDict_CheckExact(ns)) ? PyDict_SetItem(ns, name, value) : PyObject_SetItem(ns, name, value))
|
|
jpayne@69
|
3486 #else
|
|
jpayne@69
|
3487 #define __Pyx_SetNameInClass(ns, name, value) PyObject_SetItem(ns, name, value)
|
|
jpayne@69
|
3488 #endif
|
|
jpayne@69
|
3489
|
|
jpayne@69
|
3490 /* CalculateMetaclass.proto */
|
|
jpayne@69
|
3491 static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases);
|
|
jpayne@69
|
3492
|
|
jpayne@69
|
3493 /* PyObjectCall2Args.proto */
|
|
jpayne@69
|
3494 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2);
|
|
jpayne@69
|
3495
|
|
jpayne@69
|
3496 /* PyObjectLookupSpecial.proto */
|
|
jpayne@69
|
3497 #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
3498 #define __Pyx_PyObject_LookupSpecialNoError(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 0)
|
|
jpayne@69
|
3499 #define __Pyx_PyObject_LookupSpecial(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 1)
|
|
jpayne@69
|
3500 static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error);
|
|
jpayne@69
|
3501 #else
|
|
jpayne@69
|
3502 #define __Pyx_PyObject_LookupSpecialNoError(o,n) __Pyx_PyObject_GetAttrStrNoError(o,n)
|
|
jpayne@69
|
3503 #define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n)
|
|
jpayne@69
|
3504 #endif
|
|
jpayne@69
|
3505
|
|
jpayne@69
|
3506 /* Py3ClassCreate.proto */
|
|
jpayne@69
|
3507 static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname,
|
|
jpayne@69
|
3508 PyObject *mkw, PyObject *modname, PyObject *doc);
|
|
jpayne@69
|
3509 static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict,
|
|
jpayne@69
|
3510 PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass);
|
|
jpayne@69
|
3511
|
|
jpayne@69
|
3512 /* CLineInTraceback.proto */
|
|
jpayne@69
|
3513 #ifdef CYTHON_CLINE_IN_TRACEBACK
|
|
jpayne@69
|
3514 #define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
|
|
jpayne@69
|
3515 #else
|
|
jpayne@69
|
3516 static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
|
|
jpayne@69
|
3517 #endif
|
|
jpayne@69
|
3518
|
|
jpayne@69
|
3519 /* CodeObjectCache.proto */
|
|
jpayne@69
|
3520 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3521 typedef struct {
|
|
jpayne@69
|
3522 PyCodeObject* code_object;
|
|
jpayne@69
|
3523 int code_line;
|
|
jpayne@69
|
3524 } __Pyx_CodeObjectCacheEntry;
|
|
jpayne@69
|
3525 struct __Pyx_CodeObjectCache {
|
|
jpayne@69
|
3526 int count;
|
|
jpayne@69
|
3527 int max_count;
|
|
jpayne@69
|
3528 __Pyx_CodeObjectCacheEntry* entries;
|
|
jpayne@69
|
3529 };
|
|
jpayne@69
|
3530 static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
|
|
jpayne@69
|
3531 static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
|
|
jpayne@69
|
3532 static PyCodeObject *__pyx_find_code_object(int code_line);
|
|
jpayne@69
|
3533 static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
|
|
jpayne@69
|
3534 #endif
|
|
jpayne@69
|
3535
|
|
jpayne@69
|
3536 /* AddTraceback.proto */
|
|
jpayne@69
|
3537 static void __Pyx_AddTraceback(const char *funcname, int c_line,
|
|
jpayne@69
|
3538 int py_line, const char *filename);
|
|
jpayne@69
|
3539
|
|
jpayne@69
|
3540 /* GCCDiagnostics.proto */
|
|
jpayne@69
|
3541 #if !defined(__INTEL_COMPILER) && defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
|
|
jpayne@69
|
3542 #define __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
3543 #endif
|
|
jpayne@69
|
3544
|
|
jpayne@69
|
3545 /* ArrayAPI.proto */
|
|
jpayne@69
|
3546 #ifndef _ARRAYARRAY_H
|
|
jpayne@69
|
3547 #define _ARRAYARRAY_H
|
|
jpayne@69
|
3548 typedef struct arraydescr {
|
|
jpayne@69
|
3549 int typecode;
|
|
jpayne@69
|
3550 int itemsize;
|
|
jpayne@69
|
3551 PyObject * (*getitem)(struct arrayobject *, Py_ssize_t);
|
|
jpayne@69
|
3552 int (*setitem)(struct arrayobject *, Py_ssize_t, PyObject *);
|
|
jpayne@69
|
3553 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
3554 char *formats;
|
|
jpayne@69
|
3555 #endif
|
|
jpayne@69
|
3556 } arraydescr;
|
|
jpayne@69
|
3557 struct arrayobject {
|
|
jpayne@69
|
3558 PyObject_HEAD
|
|
jpayne@69
|
3559 Py_ssize_t ob_size;
|
|
jpayne@69
|
3560 union {
|
|
jpayne@69
|
3561 char *ob_item;
|
|
jpayne@69
|
3562 float *as_floats;
|
|
jpayne@69
|
3563 double *as_doubles;
|
|
jpayne@69
|
3564 int *as_ints;
|
|
jpayne@69
|
3565 unsigned int *as_uints;
|
|
jpayne@69
|
3566 unsigned char *as_uchars;
|
|
jpayne@69
|
3567 signed char *as_schars;
|
|
jpayne@69
|
3568 char *as_chars;
|
|
jpayne@69
|
3569 unsigned long *as_ulongs;
|
|
jpayne@69
|
3570 long *as_longs;
|
|
jpayne@69
|
3571 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
3572 unsigned long long *as_ulonglongs;
|
|
jpayne@69
|
3573 long long *as_longlongs;
|
|
jpayne@69
|
3574 #endif
|
|
jpayne@69
|
3575 short *as_shorts;
|
|
jpayne@69
|
3576 unsigned short *as_ushorts;
|
|
jpayne@69
|
3577 Py_UNICODE *as_pyunicodes;
|
|
jpayne@69
|
3578 void *as_voidptr;
|
|
jpayne@69
|
3579 } data;
|
|
jpayne@69
|
3580 Py_ssize_t allocated;
|
|
jpayne@69
|
3581 struct arraydescr *ob_descr;
|
|
jpayne@69
|
3582 PyObject *weakreflist;
|
|
jpayne@69
|
3583 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
3584 int ob_exports;
|
|
jpayne@69
|
3585 #endif
|
|
jpayne@69
|
3586 };
|
|
jpayne@69
|
3587 #ifndef NO_NEWARRAY_INLINE
|
|
jpayne@69
|
3588 static CYTHON_INLINE PyObject * newarrayobject(PyTypeObject *type, Py_ssize_t size,
|
|
jpayne@69
|
3589 struct arraydescr *descr) {
|
|
jpayne@69
|
3590 arrayobject *op;
|
|
jpayne@69
|
3591 size_t nbytes;
|
|
jpayne@69
|
3592 if (size < 0) {
|
|
jpayne@69
|
3593 PyErr_BadInternalCall();
|
|
jpayne@69
|
3594 return NULL;
|
|
jpayne@69
|
3595 }
|
|
jpayne@69
|
3596 nbytes = size * descr->itemsize;
|
|
jpayne@69
|
3597 if (nbytes / descr->itemsize != (size_t)size) {
|
|
jpayne@69
|
3598 return PyErr_NoMemory();
|
|
jpayne@69
|
3599 }
|
|
jpayne@69
|
3600 op = (arrayobject *) type->tp_alloc(type, 0);
|
|
jpayne@69
|
3601 if (op == NULL) {
|
|
jpayne@69
|
3602 return NULL;
|
|
jpayne@69
|
3603 }
|
|
jpayne@69
|
3604 op->ob_descr = descr;
|
|
jpayne@69
|
3605 op->allocated = size;
|
|
jpayne@69
|
3606 op->weakreflist = NULL;
|
|
jpayne@69
|
3607 __Pyx_SET_SIZE(op, size);
|
|
jpayne@69
|
3608 if (size <= 0) {
|
|
jpayne@69
|
3609 op->data.ob_item = NULL;
|
|
jpayne@69
|
3610 }
|
|
jpayne@69
|
3611 else {
|
|
jpayne@69
|
3612 op->data.ob_item = PyMem_NEW(char, nbytes);
|
|
jpayne@69
|
3613 if (op->data.ob_item == NULL) {
|
|
jpayne@69
|
3614 Py_DECREF(op);
|
|
jpayne@69
|
3615 return PyErr_NoMemory();
|
|
jpayne@69
|
3616 }
|
|
jpayne@69
|
3617 }
|
|
jpayne@69
|
3618 return (PyObject *) op;
|
|
jpayne@69
|
3619 }
|
|
jpayne@69
|
3620 #else
|
|
jpayne@69
|
3621 PyObject* newarrayobject(PyTypeObject *type, Py_ssize_t size,
|
|
jpayne@69
|
3622 struct arraydescr *descr);
|
|
jpayne@69
|
3623 #endif
|
|
jpayne@69
|
3624 static CYTHON_INLINE int resize(arrayobject *self, Py_ssize_t n) {
|
|
jpayne@69
|
3625 void *items = (void*) self->data.ob_item;
|
|
jpayne@69
|
3626 PyMem_Resize(items, char, (size_t)(n * self->ob_descr->itemsize));
|
|
jpayne@69
|
3627 if (items == NULL) {
|
|
jpayne@69
|
3628 PyErr_NoMemory();
|
|
jpayne@69
|
3629 return -1;
|
|
jpayne@69
|
3630 }
|
|
jpayne@69
|
3631 self->data.ob_item = (char*) items;
|
|
jpayne@69
|
3632 __Pyx_SET_SIZE(self, n);
|
|
jpayne@69
|
3633 self->allocated = n;
|
|
jpayne@69
|
3634 return 0;
|
|
jpayne@69
|
3635 }
|
|
jpayne@69
|
3636 static CYTHON_INLINE int resize_smart(arrayobject *self, Py_ssize_t n) {
|
|
jpayne@69
|
3637 void *items = (void*) self->data.ob_item;
|
|
jpayne@69
|
3638 Py_ssize_t newsize;
|
|
jpayne@69
|
3639 if (n < self->allocated && n*4 > self->allocated) {
|
|
jpayne@69
|
3640 __Pyx_SET_SIZE(self, n);
|
|
jpayne@69
|
3641 return 0;
|
|
jpayne@69
|
3642 }
|
|
jpayne@69
|
3643 newsize = n + (n / 2) + 1;
|
|
jpayne@69
|
3644 if (newsize <= n) {
|
|
jpayne@69
|
3645 PyErr_NoMemory();
|
|
jpayne@69
|
3646 return -1;
|
|
jpayne@69
|
3647 }
|
|
jpayne@69
|
3648 PyMem_Resize(items, char, (size_t)(newsize * self->ob_descr->itemsize));
|
|
jpayne@69
|
3649 if (items == NULL) {
|
|
jpayne@69
|
3650 PyErr_NoMemory();
|
|
jpayne@69
|
3651 return -1;
|
|
jpayne@69
|
3652 }
|
|
jpayne@69
|
3653 self->data.ob_item = (char*) items;
|
|
jpayne@69
|
3654 __Pyx_SET_SIZE(self, n);
|
|
jpayne@69
|
3655 self->allocated = newsize;
|
|
jpayne@69
|
3656 return 0;
|
|
jpayne@69
|
3657 }
|
|
jpayne@69
|
3658 #endif
|
|
jpayne@69
|
3659
|
|
jpayne@69
|
3660 /* CIntFromPy.proto */
|
|
jpayne@69
|
3661 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
|
|
jpayne@69
|
3662
|
|
jpayne@69
|
3663 /* CIntToPy.proto */
|
|
jpayne@69
|
3664 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
|
|
jpayne@69
|
3665
|
|
jpayne@69
|
3666 /* CIntFromPy.proto */
|
|
jpayne@69
|
3667 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
|
|
jpayne@69
|
3668
|
|
jpayne@69
|
3669 /* CIntFromPy.proto */
|
|
jpayne@69
|
3670 static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *);
|
|
jpayne@69
|
3671
|
|
jpayne@69
|
3672 /* CIntToPy.proto */
|
|
jpayne@69
|
3673 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value);
|
|
jpayne@69
|
3674
|
|
jpayne@69
|
3675 /* CIntToPy.proto */
|
|
jpayne@69
|
3676 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
|
|
jpayne@69
|
3677
|
|
jpayne@69
|
3678 /* CIntFromPy.proto */
|
|
jpayne@69
|
3679 static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *);
|
|
jpayne@69
|
3680
|
|
jpayne@69
|
3681 /* FormatTypeName.proto */
|
|
jpayne@69
|
3682 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
3683 typedef PyObject *__Pyx_TypeName;
|
|
jpayne@69
|
3684 #define __Pyx_FMT_TYPENAME "%U"
|
|
jpayne@69
|
3685 static __Pyx_TypeName __Pyx_PyType_GetName(PyTypeObject* tp);
|
|
jpayne@69
|
3686 #define __Pyx_DECREF_TypeName(obj) Py_XDECREF(obj)
|
|
jpayne@69
|
3687 #else
|
|
jpayne@69
|
3688 typedef const char *__Pyx_TypeName;
|
|
jpayne@69
|
3689 #define __Pyx_FMT_TYPENAME "%.200s"
|
|
jpayne@69
|
3690 #define __Pyx_PyType_GetName(tp) ((tp)->tp_name)
|
|
jpayne@69
|
3691 #define __Pyx_DECREF_TypeName(obj)
|
|
jpayne@69
|
3692 #endif
|
|
jpayne@69
|
3693
|
|
jpayne@69
|
3694 /* FastTypeChecks.proto */
|
|
jpayne@69
|
3695 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
3696 #define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
|
|
jpayne@69
|
3697 #define __Pyx_TypeCheck2(obj, type1, type2) __Pyx_IsAnySubtype2(Py_TYPE(obj), (PyTypeObject *)type1, (PyTypeObject *)type2)
|
|
jpayne@69
|
3698 static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
|
|
jpayne@69
|
3699 static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b);
|
|
jpayne@69
|
3700 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
|
|
jpayne@69
|
3701 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
|
|
jpayne@69
|
3702 #else
|
|
jpayne@69
|
3703 #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
|
|
jpayne@69
|
3704 #define __Pyx_TypeCheck2(obj, type1, type2) (PyObject_TypeCheck(obj, (PyTypeObject *)type1) || PyObject_TypeCheck(obj, (PyTypeObject *)type2))
|
|
jpayne@69
|
3705 #define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
|
|
jpayne@69
|
3706 #define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
|
|
jpayne@69
|
3707 #endif
|
|
jpayne@69
|
3708 #define __Pyx_PyErr_ExceptionMatches2(err1, err2) __Pyx_PyErr_GivenExceptionMatches2(__Pyx_PyErr_CurrentExceptionType(), err1, err2)
|
|
jpayne@69
|
3709 #define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
|
|
jpayne@69
|
3710
|
|
jpayne@69
|
3711 /* CheckBinaryVersion.proto */
|
|
jpayne@69
|
3712 static unsigned long __Pyx_get_runtime_version(void);
|
|
jpayne@69
|
3713 static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer);
|
|
jpayne@69
|
3714
|
|
jpayne@69
|
3715 /* FunctionImport.proto */
|
|
jpayne@69
|
3716 static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig);
|
|
jpayne@69
|
3717
|
|
jpayne@69
|
3718 /* InitStrings.proto */
|
|
jpayne@69
|
3719 static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
|
|
jpayne@69
|
3720
|
|
jpayne@69
|
3721 /* #### Code section: module_declarations ### */
|
|
jpayne@69
|
3722 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
3723 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
3724 static PyObject *__pyx_f_5pysam_9libctabix_6Parser_parse(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, CYTHON_UNUSED char *__pyx_v_buffer, CYTHON_UNUSED int __pyx_v_length); /* proto*/
|
|
jpayne@69
|
3725 static PyObject *__pyx_f_5pysam_9libctabix_7asTuple_parse(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/
|
|
jpayne@69
|
3726 static PyObject *__pyx_f_5pysam_9libctabix_6asGFF3_parse(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/
|
|
jpayne@69
|
3727 static PyObject *__pyx_f_5pysam_9libctabix_5asGTF_parse(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/
|
|
jpayne@69
|
3728 static PyObject *__pyx_f_5pysam_9libctabix_5asBed_parse(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/
|
|
jpayne@69
|
3729 static PyObject *__pyx_f_5pysam_9libctabix_5asVCF_parse(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/
|
|
jpayne@69
|
3730 static int __pyx_f_5pysam_9libctabix_13TabixIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
3731 static int __pyx_f_5pysam_9libctabix_10GZIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
3732 static PyObject *__pyx_f_5pysam_9libctabix_19tabix_file_iterator___cnext__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
3733
|
|
jpayne@69
|
3734 /* Module declarations from "libc.stdint" */
|
|
jpayne@69
|
3735
|
|
jpayne@69
|
3736 /* Module declarations from "libc.string" */
|
|
jpayne@69
|
3737
|
|
jpayne@69
|
3738 /* Module declarations from "libc.stdlib" */
|
|
jpayne@69
|
3739
|
|
jpayne@69
|
3740 /* Module declarations from "libc.stdio" */
|
|
jpayne@69
|
3741
|
|
jpayne@69
|
3742 /* Module declarations from "posix.types" */
|
|
jpayne@69
|
3743
|
|
jpayne@69
|
3744 /* Module declarations from "pysam.libchtslib" */
|
|
jpayne@69
|
3745
|
|
jpayne@69
|
3746 /* Module declarations from "libc.errno" */
|
|
jpayne@69
|
3747
|
|
jpayne@69
|
3748 /* Module declarations from "posix.unistd" */
|
|
jpayne@69
|
3749
|
|
jpayne@69
|
3750 /* Module declarations from "cpython.version" */
|
|
jpayne@69
|
3751
|
|
jpayne@69
|
3752 /* Module declarations from "__builtin__" */
|
|
jpayne@69
|
3753
|
|
jpayne@69
|
3754 /* Module declarations from "cpython.type" */
|
|
jpayne@69
|
3755
|
|
jpayne@69
|
3756 /* Module declarations from "cpython.object" */
|
|
jpayne@69
|
3757
|
|
jpayne@69
|
3758 /* Module declarations from "cpython.ref" */
|
|
jpayne@69
|
3759
|
|
jpayne@69
|
3760 /* Module declarations from "cpython.exc" */
|
|
jpayne@69
|
3761
|
|
jpayne@69
|
3762 /* Module declarations from "cpython.module" */
|
|
jpayne@69
|
3763
|
|
jpayne@69
|
3764 /* Module declarations from "cpython.mem" */
|
|
jpayne@69
|
3765
|
|
jpayne@69
|
3766 /* Module declarations from "cpython.tuple" */
|
|
jpayne@69
|
3767
|
|
jpayne@69
|
3768 /* Module declarations from "cpython.list" */
|
|
jpayne@69
|
3769
|
|
jpayne@69
|
3770 /* Module declarations from "cpython.sequence" */
|
|
jpayne@69
|
3771
|
|
jpayne@69
|
3772 /* Module declarations from "cpython.mapping" */
|
|
jpayne@69
|
3773
|
|
jpayne@69
|
3774 /* Module declarations from "cpython.iterator" */
|
|
jpayne@69
|
3775
|
|
jpayne@69
|
3776 /* Module declarations from "cpython.number" */
|
|
jpayne@69
|
3777
|
|
jpayne@69
|
3778 /* Module declarations from "cpython.int" */
|
|
jpayne@69
|
3779
|
|
jpayne@69
|
3780 /* Module declarations from "__builtin__" */
|
|
jpayne@69
|
3781
|
|
jpayne@69
|
3782 /* Module declarations from "cpython.bool" */
|
|
jpayne@69
|
3783
|
|
jpayne@69
|
3784 /* Module declarations from "cpython.long" */
|
|
jpayne@69
|
3785
|
|
jpayne@69
|
3786 /* Module declarations from "cpython.float" */
|
|
jpayne@69
|
3787
|
|
jpayne@69
|
3788 /* Module declarations from "__builtin__" */
|
|
jpayne@69
|
3789
|
|
jpayne@69
|
3790 /* Module declarations from "cpython.complex" */
|
|
jpayne@69
|
3791
|
|
jpayne@69
|
3792 /* Module declarations from "cpython.string" */
|
|
jpayne@69
|
3793
|
|
jpayne@69
|
3794 /* Module declarations from "libc.stddef" */
|
|
jpayne@69
|
3795
|
|
jpayne@69
|
3796 /* Module declarations from "cpython.unicode" */
|
|
jpayne@69
|
3797
|
|
jpayne@69
|
3798 /* Module declarations from "cpython.pyport" */
|
|
jpayne@69
|
3799
|
|
jpayne@69
|
3800 /* Module declarations from "cpython.dict" */
|
|
jpayne@69
|
3801
|
|
jpayne@69
|
3802 /* Module declarations from "cpython.instance" */
|
|
jpayne@69
|
3803
|
|
jpayne@69
|
3804 /* Module declarations from "cpython.function" */
|
|
jpayne@69
|
3805
|
|
jpayne@69
|
3806 /* Module declarations from "cpython.method" */
|
|
jpayne@69
|
3807
|
|
jpayne@69
|
3808 /* Module declarations from "cpython.weakref" */
|
|
jpayne@69
|
3809
|
|
jpayne@69
|
3810 /* Module declarations from "cpython.getargs" */
|
|
jpayne@69
|
3811
|
|
jpayne@69
|
3812 /* Module declarations from "cpython.pythread" */
|
|
jpayne@69
|
3813
|
|
jpayne@69
|
3814 /* Module declarations from "cpython.pystate" */
|
|
jpayne@69
|
3815
|
|
jpayne@69
|
3816 /* Module declarations from "cpython.cobject" */
|
|
jpayne@69
|
3817
|
|
jpayne@69
|
3818 /* Module declarations from "cpython.oldbuffer" */
|
|
jpayne@69
|
3819
|
|
jpayne@69
|
3820 /* Module declarations from "cpython.set" */
|
|
jpayne@69
|
3821
|
|
jpayne@69
|
3822 /* Module declarations from "cpython.buffer" */
|
|
jpayne@69
|
3823
|
|
jpayne@69
|
3824 /* Module declarations from "cpython.bytes" */
|
|
jpayne@69
|
3825
|
|
jpayne@69
|
3826 /* Module declarations from "cpython.pycapsule" */
|
|
jpayne@69
|
3827
|
|
jpayne@69
|
3828 /* Module declarations from "cpython.contextvars" */
|
|
jpayne@69
|
3829
|
|
jpayne@69
|
3830 /* Module declarations from "cpython" */
|
|
jpayne@69
|
3831
|
|
jpayne@69
|
3832 /* Module declarations from "pysam.libctabixproxies" */
|
|
jpayne@69
|
3833
|
|
jpayne@69
|
3834 /* Module declarations from "cython" */
|
|
jpayne@69
|
3835
|
|
jpayne@69
|
3836 /* Module declarations from "array" */
|
|
jpayne@69
|
3837
|
|
jpayne@69
|
3838 /* Module declarations from "cpython.array" */
|
|
jpayne@69
|
3839 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *, char *, Py_ssize_t); /*proto*/
|
|
jpayne@69
|
3840
|
|
jpayne@69
|
3841 /* Module declarations from "pysam.libcutils" */
|
|
jpayne@69
|
3842 static PyObject *(*__pyx_f_5pysam_9libcutils_charptr_to_str)(char const *, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
3843 static PyObject *(*__pyx_f_5pysam_9libcutils_force_str)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
3844 static PyObject *(*__pyx_f_5pysam_9libcutils_force_bytes)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_bytes *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
3845 static PyObject *(*__pyx_f_5pysam_9libcutils_encode_filename)(PyObject *); /*proto*/
|
|
jpayne@69
|
3846 static PyObject *(*__pyx_f_5pysam_9libcutils_from_string_and_size)(char const *, size_t); /*proto*/
|
|
jpayne@69
|
3847
|
|
jpayne@69
|
3848 /* Module declarations from "pysam.libctabix" */
|
|
jpayne@69
|
3849 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(struct __pyx_obj_5pysam_9libctabix_Parser *, PyObject *); /*proto*/
|
|
jpayne@69
|
3850 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(struct __pyx_obj_5pysam_9libctabix_asTuple *, PyObject *); /*proto*/
|
|
jpayne@69
|
3851 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(struct __pyx_obj_5pysam_9libctabix_asGFF3 *, PyObject *); /*proto*/
|
|
jpayne@69
|
3852 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(struct __pyx_obj_5pysam_9libctabix_asGTF *, PyObject *); /*proto*/
|
|
jpayne@69
|
3853 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(struct __pyx_obj_5pysam_9libctabix_asBed *, PyObject *); /*proto*/
|
|
jpayne@69
|
3854 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(struct __pyx_obj_5pysam_9libctabix_asVCF *, PyObject *); /*proto*/
|
|
jpayne@69
|
3855 /* #### Code section: typeinfo ### */
|
|
jpayne@69
|
3856 /* #### Code section: before_global_var ### */
|
|
jpayne@69
|
3857 #define __Pyx_MODULE_NAME "pysam.libctabix"
|
|
jpayne@69
|
3858 extern int __pyx_module_is_main_pysam__libctabix;
|
|
jpayne@69
|
3859 int __pyx_module_is_main_pysam__libctabix = 0;
|
|
jpayne@69
|
3860
|
|
jpayne@69
|
3861 /* Implementation of "pysam.libctabix" */
|
|
jpayne@69
|
3862 /* #### Code section: global_var ### */
|
|
jpayne@69
|
3863 static PyObject *__pyx_builtin_NotImplementedError;
|
|
jpayne@69
|
3864 static PyObject *__pyx_builtin_ValueError;
|
|
jpayne@69
|
3865 static PyObject *__pyx_builtin_IOError;
|
|
jpayne@69
|
3866 static PyObject *__pyx_builtin_OSError;
|
|
jpayne@69
|
3867 static PyObject *__pyx_builtin_TypeError;
|
|
jpayne@69
|
3868 static PyObject *__pyx_builtin_StopIteration;
|
|
jpayne@69
|
3869 static PyObject *__pyx_builtin_super;
|
|
jpayne@69
|
3870 static PyObject *__pyx_builtin_KeyError;
|
|
jpayne@69
|
3871 static PyObject *__pyx_builtin_AssertionError;
|
|
jpayne@69
|
3872 static PyObject *__pyx_builtin_MemoryError;
|
|
jpayne@69
|
3873 /* #### Code section: string_decls ### */
|
|
jpayne@69
|
3874 static const char __pyx_k_a[] = "a";
|
|
jpayne@69
|
3875 static const char __pyx_k_b[] = "b";
|
|
jpayne@69
|
3876 static const char __pyx_k_c[] = "c";
|
|
jpayne@69
|
3877 static const char __pyx_k_r[] = "r";
|
|
jpayne@69
|
3878 static const char __pyx_k_s[] = "%s";
|
|
jpayne@69
|
3879 static const char __pyx_k_fn[] = "fn";
|
|
jpayne@69
|
3880 static const char __pyx_k_fp[] = "fp";
|
|
jpayne@69
|
3881 static const char __pyx_k_gc[] = "gc";
|
|
jpayne@69
|
3882 static const char __pyx_k_gz[] = ".gz";
|
|
jpayne@69
|
3883 static const char __pyx_k_os[] = "os";
|
|
jpayne@69
|
3884 static const char __pyx_k__16[] = "-";
|
|
jpayne@69
|
3885 static const char __pyx_k__39[] = "#";
|
|
jpayne@69
|
3886 static const char __pyx_k__42[] = "': ";
|
|
jpayne@69
|
3887 static const char __pyx_k__43[] = ",";
|
|
jpayne@69
|
3888 static const char __pyx_k__44[] = "'";
|
|
jpayne@69
|
3889 static const char __pyx_k__56[] = ".";
|
|
jpayne@69
|
3890 static const char __pyx_k__62[] = "*";
|
|
jpayne@69
|
3891 static const char __pyx_k__78[] = "?";
|
|
jpayne@69
|
3892 static const char __pyx_k_all[] = "__all__";
|
|
jpayne@69
|
3893 static const char __pyx_k_bcf[] = "bcf";
|
|
jpayne@69
|
3894 static const char __pyx_k_bed[] = "bed";
|
|
jpayne@69
|
3895 static const char __pyx_k_cfn[] = "cfn";
|
|
jpayne@69
|
3896 static const char __pyx_k_cpy[] = "cpy";
|
|
jpayne@69
|
3897 static const char __pyx_k_csi[] = "csi";
|
|
jpayne@69
|
3898 static const char __pyx_k_doc[] = "__doc__";
|
|
jpayne@69
|
3899 static const char __pyx_k_dup[] = "_dup";
|
|
jpayne@69
|
3900 static const char __pyx_k_end[] = "end";
|
|
jpayne@69
|
3901 static const char __pyx_k_fmt[] = "fmt";
|
|
jpayne@69
|
3902 static const char __pyx_k_gff[] = "gff";
|
|
jpayne@69
|
3903 static const char __pyx_k_itr[] = "itr";
|
|
jpayne@69
|
3904 static const char __pyx_k_new[] = "__new__";
|
|
jpayne@69
|
3905 static const char __pyx_k_s_2[] = "s";
|
|
jpayne@69
|
3906 static const char __pyx_k_s_i[] = "%s:%i";
|
|
jpayne@69
|
3907 static const char __pyx_k_sam[] = "sam";
|
|
jpayne@69
|
3908 static const char __pyx_k_sys[] = "sys";
|
|
jpayne@69
|
3909 static const char __pyx_k_tbi[] = ".tbi";
|
|
jpayne@69
|
3910 static const char __pyx_k_vcf[] = "vcf";
|
|
jpayne@69
|
3911 static const char __pyx_k_conf[] = "conf";
|
|
jpayne@69
|
3912 static const char __pyx_k_cstr[] = "cstr";
|
|
jpayne@69
|
3913 static const char __pyx_k_dict[] = "__dict__";
|
|
jpayne@69
|
3914 static const char __pyx_k_init[] = "__init__";
|
|
jpayne@69
|
3915 static const char __pyx_k_iter[] = "__iter__";
|
|
jpayne@69
|
3916 static const char __pyx_k_keys[] = "keys";
|
|
jpayne@69
|
3917 static const char __pyx_k_line[] = "line";
|
|
jpayne@69
|
3918 static const char __pyx_k_main[] = "__main__";
|
|
jpayne@69
|
3919 static const char __pyx_k_mode[] = "mode";
|
|
jpayne@69
|
3920 static const char __pyx_k_name[] = "__name__";
|
|
jpayne@69
|
3921 static const char __pyx_k_next[] = "__next__";
|
|
jpayne@69
|
3922 static const char __pyx_k_open[] = "_open";
|
|
jpayne@69
|
3923 static const char __pyx_k_path[] = "path";
|
|
jpayne@69
|
3924 static const char __pyx_k_self[] = "self";
|
|
jpayne@69
|
3925 static const char __pyx_k_spec[] = "__spec__";
|
|
jpayne@69
|
3926 static const char __pyx_k_tell[] = "tell";
|
|
jpayne@69
|
3927 static const char __pyx_k_test[] = "__test__";
|
|
jpayne@69
|
3928 static const char __pyx_k_asBed[] = "asBed";
|
|
jpayne@69
|
3929 static const char __pyx_k_asGTF[] = "asGTF";
|
|
jpayne@69
|
3930 static const char __pyx_k_asVCF[] = "asVCF";
|
|
jpayne@69
|
3931 static const char __pyx_k_ascii[] = "ascii";
|
|
jpayne@69
|
3932 static const char __pyx_k_close[] = "close";
|
|
jpayne@69
|
3933 static const char __pyx_k_csi_2[] = ".csi";
|
|
jpayne@69
|
3934 static const char __pyx_k_fetch[] = "fetch";
|
|
jpayne@69
|
3935 static const char __pyx_k_fnidx[] = "fnidx";
|
|
jpayne@69
|
3936 static const char __pyx_k_force[] = "force";
|
|
jpayne@69
|
3937 static const char __pyx_k_index[] = "index";
|
|
jpayne@69
|
3938 static const char __pyx_k_s_i_i[] = "%s:%i-%i";
|
|
jpayne@69
|
3939 static const char __pyx_k_start[] = "start";
|
|
jpayne@69
|
3940 static const char __pyx_k_state[] = "state";
|
|
jpayne@69
|
3941 static const char __pyx_k_super[] = "super";
|
|
jpayne@69
|
3942 static const char __pyx_k_Parser[] = "Parser";
|
|
jpayne@69
|
3943 static const char __pyx_k_asGFF3[] = "asGFF3";
|
|
jpayne@69
|
3944 static const char __pyx_k_buffer[] = "buffer";
|
|
jpayne@69
|
3945 static const char __pyx_k_closed[] = "closed";
|
|
jpayne@69
|
3946 static const char __pyx_k_dict_2[] = "_dict";
|
|
jpayne@69
|
3947 static const char __pyx_k_enable[] = "enable";
|
|
jpayne@69
|
3948 static const char __pyx_k_exists[] = "exists";
|
|
jpayne@69
|
3949 static const char __pyx_k_fd_src[] = "fd_src";
|
|
jpayne@69
|
3950 static const char __pyx_k_format[] = "format";
|
|
jpayne@69
|
3951 static const char __pyx_k_import[] = "__import__";
|
|
jpayne@69
|
3952 static const char __pyx_k_infile[] = "infile";
|
|
jpayne@69
|
3953 static const char __pyx_k_length[] = "length";
|
|
jpayne@69
|
3954 static const char __pyx_k_module[] = "__module__";
|
|
jpayne@69
|
3955 static const char __pyx_k_nbytes[] = "nbytes";
|
|
jpayne@69
|
3956 static const char __pyx_k_parser[] = "parser";
|
|
jpayne@69
|
3957 static const char __pyx_k_pickle[] = "pickle";
|
|
jpayne@69
|
3958 static const char __pyx_k_preset[] = "preset";
|
|
jpayne@69
|
3959 static const char __pyx_k_psltbl[] = "psltbl";
|
|
jpayne@69
|
3960 static const char __pyx_k_reduce[] = "__reduce__";
|
|
jpayne@69
|
3961 static const char __pyx_k_region[] = "region";
|
|
jpayne@69
|
3962 static const char __pyx_k_retval[] = "retval";
|
|
jpayne@69
|
3963 static const char __pyx_k_suffix[] = "suffix";
|
|
jpayne@69
|
3964 static const char __pyx_k_unlink[] = "unlink";
|
|
jpayne@69
|
3965 static const char __pyx_k_update[] = "update";
|
|
jpayne@69
|
3966 static const char __pyx_k_IOError[] = "IOError";
|
|
jpayne@69
|
3967 static const char __pyx_k_OSError[] = "OSError";
|
|
jpayne@69
|
3968 static const char __pyx_k_asTuple[] = "asTuple";
|
|
jpayne@69
|
3969 static const char __pyx_k_contigs[] = "contigs";
|
|
jpayne@69
|
3970 static const char __pyx_k_disable[] = "disable";
|
|
jpayne@69
|
3971 static const char __pyx_k_end_col[] = "end_col";
|
|
jpayne@69
|
3972 static const char __pyx_k_fileobj[] = "fileobj";
|
|
jpayne@69
|
3973 static const char __pyx_k_is_open[] = "is_open";
|
|
jpayne@69
|
3974 static const char __pyx_k_prepare[] = "__prepare__";
|
|
jpayne@69
|
3975 static const char __pyx_k_seq_col[] = "seq_col";
|
|
jpayne@69
|
3976 static const char __pyx_k_threads[] = "threads";
|
|
jpayne@69
|
3977 static const char __pyx_k_KeyError[] = "KeyError";
|
|
jpayne@69
|
3978 static const char __pyx_k_O_RDONLY[] = "O_RDONLY";
|
|
jpayne@69
|
3979 static const char __pyx_k_encoding[] = "encoding";
|
|
jpayne@69
|
3980 static const char __pyx_k_filename[] = "filename";
|
|
jpayne@69
|
3981 static const char __pyx_k_fn_index[] = "fn_index";
|
|
jpayne@69
|
3982 static const char __pyx_k_getstate[] = "__getstate__";
|
|
jpayne@69
|
3983 static const char __pyx_k_is_empty[] = "is_empty";
|
|
jpayne@69
|
3984 static const char __pyx_k_pyx_type[] = "__pyx_type";
|
|
jpayne@69
|
3985 static const char __pyx_k_qualname[] = "__qualname__";
|
|
jpayne@69
|
3986 static const char __pyx_k_readline[] = "readline";
|
|
jpayne@69
|
3987 static const char __pyx_k_set_name[] = "__set_name__";
|
|
jpayne@69
|
3988 static const char __pyx_k_setstate[] = "__setstate__";
|
|
jpayne@69
|
3989 static const char __pyx_k_TabixFile[] = "TabixFile";
|
|
jpayne@69
|
3990 static const char __pyx_k_Tabixfile[] = "Tabixfile";
|
|
jpayne@69
|
3991 static const char __pyx_k_TypeError[] = "TypeError";
|
|
jpayne@69
|
3992 static const char __pyx_k_bytes_cpy[] = "bytes_cpy";
|
|
jpayne@69
|
3993 static const char __pyx_k_cfilename[] = "cfilename";
|
|
jpayne@69
|
3994 static const char __pyx_k_conf_data[] = "conf_data";
|
|
jpayne@69
|
3995 static const char __pyx_k_isenabled[] = "isenabled";
|
|
jpayne@69
|
3996 static const char __pyx_k_line_skip[] = "line_skip";
|
|
jpayne@69
|
3997 static const char __pyx_k_meta_char[] = "meta_char";
|
|
jpayne@69
|
3998 static const char __pyx_k_metaclass[] = "__metaclass__";
|
|
jpayne@69
|
3999 static const char __pyx_k_min_shift[] = "min_shift";
|
|
jpayne@69
|
4000 static const char __pyx_k_pyx_state[] = "__pyx_state";
|
|
jpayne@69
|
4001 static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
|
|
jpayne@69
|
4002 static const char __pyx_k_reference[] = "reference";
|
|
jpayne@69
|
4003 static const char __pyx_k_start_col[] = "start_col";
|
|
jpayne@69
|
4004 static const char __pyx_k_zerobased[] = "zerobased";
|
|
jpayne@69
|
4005 static const char __pyx_k_GZIterator[] = "GZIterator";
|
|
jpayne@69
|
4006 static const char __pyx_k_ValueError[] = "ValueError";
|
|
jpayne@69
|
4007 static const char __pyx_k_pyx_result[] = "__pyx_result";
|
|
jpayne@69
|
4008 static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
|
|
jpayne@69
|
4009 static const char __pyx_k_MemoryError[] = "MemoryError";
|
|
jpayne@69
|
4010 static const char __pyx_k_PickleError[] = "PickleError";
|
|
jpayne@69
|
4011 static const char __pyx_k_WINDOW_SIZE[] = "WINDOW_SIZE";
|
|
jpayne@69
|
4012 static const char __pyx_k_buffer_size[] = "buffer_size";
|
|
jpayne@69
|
4013 static const char __pyx_k_filename_in[] = "filename_in";
|
|
jpayne@69
|
4014 static const char __pyx_k_preset2conf[] = "preset2conf";
|
|
jpayne@69
|
4015 static const char __pyx_k_tabix_index[] = "tabix_index";
|
|
jpayne@69
|
4016 static const char __pyx_k_filename_out[] = "filename_out";
|
|
jpayne@69
|
4017 static const char __pyx_k_get_encoding[] = "get_encoding";
|
|
jpayne@69
|
4018 static const char __pyx_k_initializing[] = "_initializing";
|
|
jpayne@69
|
4019 static const char __pyx_k_is_coroutine[] = "_is_coroutine";
|
|
jpayne@69
|
4020 static const char __pyx_k_pyx_checksum[] = "__pyx_checksum";
|
|
jpayne@69
|
4021 static const char __pyx_k_set_encoding[] = "set_encoding";
|
|
jpayne@69
|
4022 static const char __pyx_k_stringsource[] = "<stringsource>";
|
|
jpayne@69
|
4023 static const char __pyx_k_use_setstate[] = "use_setstate";
|
|
jpayne@69
|
4024 static const char __pyx_k_EmptyIterator[] = "EmptyIterator";
|
|
jpayne@69
|
4025 static const char __pyx_k_StopIteration[] = "StopIteration";
|
|
jpayne@69
|
4026 static const char __pyx_k_TabixIterator[] = "TabixIterator";
|
|
jpayne@69
|
4027 static const char __pyx_k_init_subclass[] = "__init_subclass__";
|
|
jpayne@69
|
4028 static const char __pyx_k_keep_original[] = "keep_original";
|
|
jpayne@69
|
4029 static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
|
|
jpayne@69
|
4030 static const char __pyx_k_start_i_end_i[] = "start (%i) >= end (%i)";
|
|
jpayne@69
|
4031 static const char __pyx_k_AssertionError[] = "AssertionError";
|
|
jpayne@69
|
4032 static const char __pyx_k_GZIteratorHead[] = "GZIteratorHead";
|
|
jpayne@69
|
4033 static const char __pyx_k_TabixFile__dup[] = "TabixFile._dup";
|
|
jpayne@69
|
4034 static const char __pyx_k_empty_iterator[] = "empty iterator";
|
|
jpayne@69
|
4035 static const char __pyx_k_filename_index[] = "filename_index";
|
|
jpayne@69
|
4036 static const char __pyx_k_tabix_compress[] = "tabix_compress";
|
|
jpayne@69
|
4037 static const char __pyx_k_tabix_iterator[] = "tabix_iterator";
|
|
jpayne@69
|
4038 static const char __pyx_k_unknown_preset[] = "unknown preset '";
|
|
jpayne@69
|
4039 static const char __pyx_k_writing_failed[] = "writing failed";
|
|
jpayne@69
|
4040 static const char __pyx_k_TabixFile__open[] = "TabixFile._open";
|
|
jpayne@69
|
4041 static const char __pyx_k_TabixFile_close[] = "TabixFile.close";
|
|
jpayne@69
|
4042 static const char __pyx_k_TabixFile_fetch[] = "TabixFile.fetch";
|
|
jpayne@69
|
4043 static const char __pyx_k_cfilename_index[] = "cfilename_index";
|
|
jpayne@69
|
4044 static const char __pyx_k_pysam_libctabix[] = "pysam.libctabix";
|
|
jpayne@69
|
4045 static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError";
|
|
jpayne@69
|
4046 static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
|
|
jpayne@69
|
4047 static const char __pyx_k_GZIteratorParsed[] = "GZIteratorParsed";
|
|
jpayne@69
|
4048 static const char __pyx_k_file_s_not_found[] = "file `%s` not found";
|
|
jpayne@69
|
4049 static const char __pyx_k_index_s_not_found[] = "index `%s` not found";
|
|
jpayne@69
|
4050 static const char __pyx_k_valid_presets_are[] = "', valid presets are '";
|
|
jpayne@69
|
4051 static const char __pyx_k_asyncio_coroutines[] = "asyncio.coroutines";
|
|
jpayne@69
|
4052 static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
|
|
jpayne@69
|
4053 static const char __pyx_k_end_out_of_range_i[] = "end out of range (%i)";
|
|
jpayne@69
|
4054 static const char __pyx_k_multiple_iterators[] = "multiple_iterators";
|
|
jpayne@69
|
4055 static const char __pyx_k_pyx_unpickle_asBed[] = "__pyx_unpickle_asBed";
|
|
jpayne@69
|
4056 static const char __pyx_k_pyx_unpickle_asGTF[] = "__pyx_unpickle_asGTF";
|
|
jpayne@69
|
4057 static const char __pyx_k_pyx_unpickle_asVCF[] = "__pyx_unpickle_asVCF";
|
|
jpayne@69
|
4058 static const char __pyx_k_Could_not_open_file[] = "Could not open file '";
|
|
jpayne@69
|
4059 static const char __pyx_k_NotImplementedError[] = "NotImplementedError";
|
|
jpayne@69
|
4060 static const char __pyx_k_Parser_get_encoding[] = "Parser.get_encoding";
|
|
jpayne@69
|
4061 static const char __pyx_k_Parser_set_encoding[] = "Parser.set_encoding";
|
|
jpayne@69
|
4062 static const char __pyx_k_TabixIteratorParsed[] = "TabixIteratorParsed";
|
|
jpayne@69
|
4063 static const char __pyx_k_pysam_libctabix_pyx[] = "pysam/libctabix.pyx";
|
|
jpayne@69
|
4064 static const char __pyx_k_pyx_unpickle_Parser[] = "__pyx_unpickle_Parser";
|
|
jpayne@69
|
4065 static const char __pyx_k_pyx_unpickle_asGFF3[] = "__pyx_unpickle_asGFF3";
|
|
jpayne@69
|
4066 static const char __pyx_k_tabix_file_iterator[] = "tabix_file_iterator";
|
|
jpayne@69
|
4067 static const char __pyx_k_EmptyIterator___iter[] = "EmptyIterator.__iter__";
|
|
jpayne@69
|
4068 static const char __pyx_k_EmptyIterator___next[] = "EmptyIterator.__next__";
|
|
jpayne@69
|
4069 static const char __pyx_k_incomplete_line_at_s[] = "incomplete line at %s";
|
|
jpayne@69
|
4070 static const char __pyx_k_pyx_unpickle_asTuple[] = "__pyx_unpickle_asTuple";
|
|
jpayne@69
|
4071 static const char __pyx_k_start_out_of_range_i[] = "start out of range (%i)";
|
|
jpayne@69
|
4072 static const char __pyx_k_asBed___reduce_cython[] = "asBed.__reduce_cython__";
|
|
jpayne@69
|
4073 static const char __pyx_k_asGTF___reduce_cython[] = "asGTF.__reduce_cython__";
|
|
jpayne@69
|
4074 static const char __pyx_k_asVCF___reduce_cython[] = "asVCF.__reduce_cython__";
|
|
jpayne@69
|
4075 static const char __pyx_k_could_not_open_file_s[] = "could not open file `%s`";
|
|
jpayne@69
|
4076 static const char __pyx_k_Parser___reduce_cython[] = "Parser.__reduce_cython__";
|
|
jpayne@69
|
4077 static const char __pyx_k_asGFF3___reduce_cython[] = "asGFF3.__reduce_cython__";
|
|
jpayne@69
|
4078 static const char __pyx_k_tabix_generic_iterator[] = "tabix_generic_iterator";
|
|
jpayne@69
|
4079 static const char __pyx_k_asBed___setstate_cython[] = "asBed.__setstate_cython__";
|
|
jpayne@69
|
4080 static const char __pyx_k_asGTF___setstate_cython[] = "asGTF.__setstate_cython__";
|
|
jpayne@69
|
4081 static const char __pyx_k_asTuple___reduce_cython[] = "asTuple.__reduce_cython__";
|
|
jpayne@69
|
4082 static const char __pyx_k_asVCF___setstate_cython[] = "asVCF.__setstate_cython__";
|
|
jpayne@69
|
4083 static const char __pyx_k_Parser___setstate_cython[] = "Parser.__setstate_cython__";
|
|
jpayne@69
|
4084 static const char __pyx_k_asGFF3___setstate_cython[] = "asGFF3.__setstate_cython__";
|
|
jpayne@69
|
4085 static const char __pyx_k_iteration_on_closed_file[] = "iteration on closed file";
|
|
jpayne@69
|
4086 static const char __pyx_k_TabixFile___reduce_cython[] = "TabixFile.__reduce_cython__";
|
|
jpayne@69
|
4087 static const char __pyx_k_Tabixfile___reduce_cython[] = "Tabixfile.__reduce_cython__";
|
|
jpayne@69
|
4088 static const char __pyx_k_asTuple___setstate_cython[] = "asTuple.__setstate_cython__";
|
|
jpayne@69
|
4089 static const char __pyx_k_GZIterator___reduce_cython[] = "GZIterator.__reduce_cython__";
|
|
jpayne@69
|
4090 static const char __pyx_k_could_not_open_index_for_s[] = "could not open index for `%s`";
|
|
jpayne@69
|
4091 static const char __pyx_k_No_such_file_or_directory_s[] = "No such file or directory: %s";
|
|
jpayne@69
|
4092 static const char __pyx_k_TabixFile___setstate_cython[] = "TabixFile.__setstate_cython__";
|
|
jpayne@69
|
4093 static const char __pyx_k_Tabixfile___setstate_cython[] = "Tabixfile.__setstate_cython__";
|
|
jpayne@69
|
4094 static const char __pyx_k_error_i_when_closing_file_s[] = "error %i when closing file %s";
|
|
jpayne@69
|
4095 static const char __pyx_k_invalid_file_opening_mode_s[] = "invalid file opening mode `%s`";
|
|
jpayne@69
|
4096 static const char __pyx_k_GZIterator___setstate_cython[] = "GZIterator.__setstate_cython__";
|
|
jpayne@69
|
4097 static const char __pyx_k_I_O_operation_on_closed_file[] = "I/O operation on closed file";
|
|
jpayne@69
|
4098 static const char __pyx_k_building_of_index_for_failed[] = "building of index for {} failed";
|
|
jpayne@69
|
4099 static const char __pyx_k_could_not_open_s_for_reading[] = "could not open '%s' for reading";
|
|
jpayne@69
|
4100 static const char __pyx_k_could_not_open_s_for_writing[] = "could not open '%s' for writing";
|
|
jpayne@69
|
4101 static const char __pyx_k_TabixIterator___reduce_cython[] = "TabixIterator.__reduce_cython__";
|
|
jpayne@69
|
4102 static const char __pyx_k_tabix_generic_iterator___init[] = "tabix_generic_iterator.__init__";
|
|
jpayne@69
|
4103 static const char __pyx_k_tabix_generic_iterator___iter[] = "tabix_generic_iterator.__iter__";
|
|
jpayne@69
|
4104 static const char __pyx_k_tabix_generic_iterator___next[] = "tabix_generic_iterator.__next__";
|
|
jpayne@69
|
4105 static const char __pyx_k_GZIteratorHead___reduce_cython[] = "GZIteratorHead.__reduce_cython__";
|
|
jpayne@69
|
4106 static const char __pyx_k_I_O_operation_on_closed_file_2[] = "I/O operation on closed file.";
|
|
jpayne@69
|
4107 static const char __pyx_k_error_i_when_writing_to_file_s[] = "error %i when writing to file %s";
|
|
jpayne@69
|
4108 static const char __pyx_k_TabixIterator___setstate_cython[] = "TabixIterator.__setstate_cython__";
|
|
jpayne@69
|
4109 static const char __pyx_k_could_not_load_tbi_csi_index_of[] = "could not load .tbi/.csi index of {}";
|
|
jpayne@69
|
4110 static const char __pyx_k_iterate_over_infile_Permits_the[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
|
|
jpayne@69
|
4111 static const char __pyx_k_Filename_s_already_exists_use_fo[] = "Filename '%s' already exists, use *force* to overwrite";
|
|
jpayne@69
|
4112 static const char __pyx_k_GZIteratorHead___setstate_cython[] = "GZIteratorHead.__setstate_cython__";
|
|
jpayne@69
|
4113 static const char __pyx_k_GZIteratorParsed___reduce_cython[] = "GZIteratorParsed.__reduce_cython__";
|
|
jpayne@69
|
4114 static const char __pyx_k_GZIteratorParsed___setstate_cyth[] = "GZIteratorParsed.__setstate_cython__";
|
|
jpayne@69
|
4115 static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))";
|
|
jpayne@69
|
4116 static const char __pyx_k_TabixIteratorParsed___reduce_cyt[] = "TabixIteratorParsed.__reduce_cython__";
|
|
jpayne@69
|
4117 static const char __pyx_k_TabixIteratorParsed___setstate_c[] = "TabixIteratorParsed.__setstate_cython__";
|
|
jpayne@69
|
4118 static const char __pyx_k_could_not_create_iterator_for_re[] = "could not create iterator for region '%s'";
|
|
jpayne@69
|
4119 static const char __pyx_k_could_not_create_iterator_possib[] = "could not create iterator, possible tabix version mismatch";
|
|
jpayne@69
|
4120 static const char __pyx_k_could_not_open_for_reading_heade[] = "could not open {} for reading header";
|
|
jpayne@69
|
4121 static const char __pyx_k_filename_s_already_exists_use_fo[] = "filename '%s' already exists, use *force* to overwrite";
|
|
jpayne@69
|
4122 static const char __pyx_k_neither_preset_nor_seq_col_start[] = "neither preset nor seq_col,start_col and end_col given";
|
|
jpayne@69
|
4123 static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__";
|
|
jpayne@69
|
4124 static const char __pyx_k_parse_method_of_s_not_implemente[] = "parse method of %s not implemented";
|
|
jpayne@69
|
4125 static const char __pyx_k_self_gzipfile_self_kstream_canno[] = "self.gzipfile,self.kstream cannot be converted to a Python object for pickling";
|
|
jpayne@69
|
4126 static const char __pyx_k_self_iterator_cannot_be_converte[] = "self.iterator cannot be converted to a Python object for pickling";
|
|
jpayne@69
|
4127 static const char __pyx_k_tabix_file_iterator___reduce_cyt[] = "tabix_file_iterator.__reduce_cython__";
|
|
jpayne@69
|
4128 static const char __pyx_k_tabix_file_iterator___setstate_c[] = "tabix_file_iterator.__setstate_cython__";
|
|
jpayne@69
|
4129 /* #### Code section: decls ### */
|
|
jpayne@69
|
4130 static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags); /* proto */
|
|
jpayne@69
|
4131 static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
|
|
jpayne@69
|
4132 static int __pyx_pf_5pysam_9libctabix_6Parser___init__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */
|
|
jpayne@69
|
4133 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_2set_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */
|
|
jpayne@69
|
4134 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_4get_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4135 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_6__call__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length); /* proto */
|
|
jpayne@69
|
4136 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_8__reduce_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4137 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_10__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4138 static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4139 static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4140 static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4141 static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4142 static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4143 static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4144 static PyObject *__pyx_pf_5pysam_9libctabix_5asBed___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4145 static PyObject *__pyx_pf_5pysam_9libctabix_5asBed_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4146 static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4147 static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4148 static int __pyx_pf_5pysam_9libctabix_9TabixFile___cinit__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_parser, PyObject *__pyx_v_index, PyObject *__pyx_v_encoding, PyObject *__pyx_v_threads, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
|
|
jpayne@69
|
4149 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_2_open(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_index, PyObject *__pyx_v_threads); /* proto */
|
|
jpayne@69
|
4150 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_4_dup(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4151 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6fetch(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser, PyObject *__pyx_v_multiple_iterators); /* proto */
|
|
jpayne@69
|
4152 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6header___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4153 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4154 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_8close(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4155 static void __pyx_pf_5pysam_9libctabix_9TabixFile_10__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4156 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14filename_index___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4157 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_12__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4158 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4159 static int __pyx_pf_5pysam_9libctabix_13TabixIterator___init__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */
|
|
jpayne@69
|
4160 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4161 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4162 static void __pyx_pf_5pysam_9libctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4163 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4164 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4165 static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator___iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4166 static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator_2__next__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4167 static int __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser); /* proto */
|
|
jpayne@69
|
4168 static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4169 static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4170 static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4171 static int __pyx_pf_5pysam_9libctabix_10GZIterator___init__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, PyObject *__pyx_v_filename, int __pyx_v_buffer_size, PyObject *__pyx_v_encoding); /* proto */
|
|
jpayne@69
|
4172 static void __pyx_pf_5pysam_9libctabix_10GZIterator_2__dealloc__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4173 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_4__iter__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4174 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_6__next__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4175 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4176 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4177 static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead___next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4178 static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4179 static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4180 static int __pyx_pf_5pysam_9libctabix_16GZIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, PyObject *__pyx_v_parser); /* proto */
|
|
jpayne@69
|
4181 static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4182 static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4183 static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4184 static PyObject *__pyx_pf_5pysam_9libctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */
|
|
jpayne@69
|
4185 static PyObject *__pyx_pf_5pysam_9libctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, int __pyx_v_line_skip, PyObject *__pyx_v_zerobased, int __pyx_v_min_shift, PyObject *__pyx_v_index, PyObject *__pyx_v_keep_original, PyObject *__pyx_v_csi); /* proto */
|
|
jpayne@69
|
4186 static int __pyx_pf_5pysam_9libctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size); /* proto */
|
|
jpayne@69
|
4187 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4188 static void __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4189 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4190 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4191 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4192 static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
|
|
jpayne@69
|
4193 static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4194 static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4195 static PyObject *__pyx_pf_5pysam_9libctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
|
|
jpayne@69
|
4196 static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile___reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self); /* proto */
|
|
jpayne@69
|
4197 static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile_2__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4198 static PyObject *__pyx_pf_5pysam_9libctabix_6__pyx_unpickle_Parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4199 static PyObject *__pyx_pf_5pysam_9libctabix_8__pyx_unpickle_asTuple(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4200 static PyObject *__pyx_pf_5pysam_9libctabix_10__pyx_unpickle_asGFF3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4201 static PyObject *__pyx_pf_5pysam_9libctabix_12__pyx_unpickle_asGTF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4202 static PyObject *__pyx_pf_5pysam_9libctabix_14__pyx_unpickle_asBed(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4203 static PyObject *__pyx_pf_5pysam_9libctabix_16__pyx_unpickle_asVCF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */
|
|
jpayne@69
|
4204 static PyObject *__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4205 static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4206 static PyObject *__pyx_tp_new_5pysam_9libctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4207 static PyObject *__pyx_tp_new_5pysam_9libctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4208 static PyObject *__pyx_tp_new_5pysam_9libctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4209 static PyObject *__pyx_tp_new_5pysam_9libctabix_asGFF3(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4210 static PyObject *__pyx_tp_new_5pysam_9libctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4211 static PyObject *__pyx_tp_new_5pysam_9libctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4212 static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4213 static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4214 static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4215 static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorHead(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4216 static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4217 static PyObject *__pyx_tp_new_5pysam_9libctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
|
|
jpayne@69
|
4218 static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_keys = {0, 0, 0, 0, 0};
|
|
jpayne@69
|
4219 /* #### Code section: late_includes ### */
|
|
jpayne@69
|
4220 /* #### Code section: module_state ### */
|
|
jpayne@69
|
4221 typedef struct {
|
|
jpayne@69
|
4222 PyObject *__pyx_d;
|
|
jpayne@69
|
4223 PyObject *__pyx_b;
|
|
jpayne@69
|
4224 PyObject *__pyx_cython_runtime;
|
|
jpayne@69
|
4225 PyObject *__pyx_empty_tuple;
|
|
jpayne@69
|
4226 PyObject *__pyx_empty_bytes;
|
|
jpayne@69
|
4227 PyObject *__pyx_empty_unicode;
|
|
jpayne@69
|
4228 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
4229 PyTypeObject *__pyx_CyFunctionType;
|
|
jpayne@69
|
4230 #endif
|
|
jpayne@69
|
4231 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
4232 PyTypeObject *__pyx_FusedFunctionType;
|
|
jpayne@69
|
4233 #endif
|
|
jpayne@69
|
4234 #ifdef __Pyx_Generator_USED
|
|
jpayne@69
|
4235 PyTypeObject *__pyx_GeneratorType;
|
|
jpayne@69
|
4236 #endif
|
|
jpayne@69
|
4237 #ifdef __Pyx_IterableCoroutine_USED
|
|
jpayne@69
|
4238 PyTypeObject *__pyx_IterableCoroutineType;
|
|
jpayne@69
|
4239 #endif
|
|
jpayne@69
|
4240 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
4241 PyTypeObject *__pyx_CoroutineAwaitType;
|
|
jpayne@69
|
4242 #endif
|
|
jpayne@69
|
4243 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
4244 PyTypeObject *__pyx_CoroutineType;
|
|
jpayne@69
|
4245 #endif
|
|
jpayne@69
|
4246 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4247 #endif
|
|
jpayne@69
|
4248 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4249 #endif
|
|
jpayne@69
|
4250 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4251 #endif
|
|
jpayne@69
|
4252 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4253 #endif
|
|
jpayne@69
|
4254 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4255 #endif
|
|
jpayne@69
|
4256 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4257 #endif
|
|
jpayne@69
|
4258 PyTypeObject *__pyx_ptype_5pysam_10libchtslib_HTSFile;
|
|
jpayne@69
|
4259 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4260 #endif
|
|
jpayne@69
|
4261 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4262 #endif
|
|
jpayne@69
|
4263 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4264 #endif
|
|
jpayne@69
|
4265 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4266 #endif
|
|
jpayne@69
|
4267 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4268 #endif
|
|
jpayne@69
|
4269 PyTypeObject *__pyx_ptype_7cpython_4type_type;
|
|
jpayne@69
|
4270 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4271 #endif
|
|
jpayne@69
|
4272 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4273 #endif
|
|
jpayne@69
|
4274 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4275 #endif
|
|
jpayne@69
|
4276 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4277 #endif
|
|
jpayne@69
|
4278 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4279 #endif
|
|
jpayne@69
|
4280 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4281 #endif
|
|
jpayne@69
|
4282 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4283 #endif
|
|
jpayne@69
|
4284 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4285 #endif
|
|
jpayne@69
|
4286 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4287 #endif
|
|
jpayne@69
|
4288 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4289 #endif
|
|
jpayne@69
|
4290 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4291 #endif
|
|
jpayne@69
|
4292 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4293 #endif
|
|
jpayne@69
|
4294 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4295 #endif
|
|
jpayne@69
|
4296 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4297 #endif
|
|
jpayne@69
|
4298 PyTypeObject *__pyx_ptype_7cpython_4bool_bool;
|
|
jpayne@69
|
4299 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4300 #endif
|
|
jpayne@69
|
4301 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4302 #endif
|
|
jpayne@69
|
4303 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4304 #endif
|
|
jpayne@69
|
4305 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4306 #endif
|
|
jpayne@69
|
4307 PyTypeObject *__pyx_ptype_7cpython_7complex_complex;
|
|
jpayne@69
|
4308 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4309 #endif
|
|
jpayne@69
|
4310 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4311 #endif
|
|
jpayne@69
|
4312 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4313 #endif
|
|
jpayne@69
|
4314 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4315 #endif
|
|
jpayne@69
|
4316 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4317 #endif
|
|
jpayne@69
|
4318 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4319 #endif
|
|
jpayne@69
|
4320 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4321 #endif
|
|
jpayne@69
|
4322 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4323 #endif
|
|
jpayne@69
|
4324 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4325 #endif
|
|
jpayne@69
|
4326 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4327 #endif
|
|
jpayne@69
|
4328 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4329 #endif
|
|
jpayne@69
|
4330 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4331 #endif
|
|
jpayne@69
|
4332 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4333 #endif
|
|
jpayne@69
|
4334 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4335 #endif
|
|
jpayne@69
|
4336 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4337 #endif
|
|
jpayne@69
|
4338 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4339 #endif
|
|
jpayne@69
|
4340 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4341 #endif
|
|
jpayne@69
|
4342 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4343 #endif
|
|
jpayne@69
|
4344 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4345 #endif
|
|
jpayne@69
|
4346 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4347 #endif
|
|
jpayne@69
|
4348 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4349 #endif
|
|
jpayne@69
|
4350 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_TupleProxy;
|
|
jpayne@69
|
4351 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator;
|
|
jpayne@69
|
4352 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy;
|
|
jpayne@69
|
4353 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_GTFProxy;
|
|
jpayne@69
|
4354 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy;
|
|
jpayne@69
|
4355 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_BedProxy;
|
|
jpayne@69
|
4356 PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_VCFProxy;
|
|
jpayne@69
|
4357 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4358 #endif
|
|
jpayne@69
|
4359 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4360 #endif
|
|
jpayne@69
|
4361 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4362 #endif
|
|
jpayne@69
|
4363 PyTypeObject *__pyx_ptype_7cpython_5array_array;
|
|
jpayne@69
|
4364 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4365 #endif
|
|
jpayne@69
|
4366 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4367 PyObject *__pyx_type_5pysam_9libctabix_tabix_file_iterator;
|
|
jpayne@69
|
4368 PyObject *__pyx_type_5pysam_9libctabix_TabixFile;
|
|
jpayne@69
|
4369 PyObject *__pyx_type_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
4370 PyObject *__pyx_type_5pysam_9libctabix_asTuple;
|
|
jpayne@69
|
4371 PyObject *__pyx_type_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
4372 PyObject *__pyx_type_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
4373 PyObject *__pyx_type_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
4374 PyObject *__pyx_type_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
4375 PyObject *__pyx_type_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
4376 PyObject *__pyx_type_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
4377 PyObject *__pyx_type_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
4378 PyObject *__pyx_type_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
4379 PyObject *__pyx_type_5pysam_9libctabix_GZIteratorParsed;
|
|
jpayne@69
|
4380 PyObject *__pyx_type_5pysam_9libctabix_Tabixfile;
|
|
jpayne@69
|
4381 #endif
|
|
jpayne@69
|
4382 PyTypeObject *__pyx_ptype_5pysam_9libctabix_tabix_file_iterator;
|
|
jpayne@69
|
4383 PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixFile;
|
|
jpayne@69
|
4384 PyTypeObject *__pyx_ptype_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
4385 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asTuple;
|
|
jpayne@69
|
4386 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
4387 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
4388 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
4389 PyTypeObject *__pyx_ptype_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
4390 PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
4391 PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
4392 PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
4393 PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
4394 PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIteratorParsed;
|
|
jpayne@69
|
4395 PyTypeObject *__pyx_ptype_5pysam_9libctabix_Tabixfile;
|
|
jpayne@69
|
4396 PyObject *__pyx_n_s_AssertionError;
|
|
jpayne@69
|
4397 PyObject *__pyx_kp_u_Could_not_open_file;
|
|
jpayne@69
|
4398 PyObject *__pyx_n_s_EmptyIterator;
|
|
jpayne@69
|
4399 PyObject *__pyx_n_s_EmptyIterator___iter;
|
|
jpayne@69
|
4400 PyObject *__pyx_n_s_EmptyIterator___next;
|
|
jpayne@69
|
4401 PyObject *__pyx_kp_u_Filename_s_already_exists_use_fo;
|
|
jpayne@69
|
4402 PyObject *__pyx_n_s_GZIterator;
|
|
jpayne@69
|
4403 PyObject *__pyx_n_u_GZIterator;
|
|
jpayne@69
|
4404 PyObject *__pyx_n_s_GZIteratorHead;
|
|
jpayne@69
|
4405 PyObject *__pyx_n_u_GZIteratorHead;
|
|
jpayne@69
|
4406 PyObject *__pyx_n_s_GZIteratorHead___reduce_cython;
|
|
jpayne@69
|
4407 PyObject *__pyx_n_s_GZIteratorHead___setstate_cython;
|
|
jpayne@69
|
4408 PyObject *__pyx_n_s_GZIteratorParsed;
|
|
jpayne@69
|
4409 PyObject *__pyx_n_s_GZIteratorParsed___reduce_cython;
|
|
jpayne@69
|
4410 PyObject *__pyx_n_s_GZIteratorParsed___setstate_cyth;
|
|
jpayne@69
|
4411 PyObject *__pyx_n_s_GZIterator___reduce_cython;
|
|
jpayne@69
|
4412 PyObject *__pyx_n_s_GZIterator___setstate_cython;
|
|
jpayne@69
|
4413 PyObject *__pyx_n_s_IOError;
|
|
jpayne@69
|
4414 PyObject *__pyx_kp_u_I_O_operation_on_closed_file;
|
|
jpayne@69
|
4415 PyObject *__pyx_kp_u_I_O_operation_on_closed_file_2;
|
|
jpayne@69
|
4416 PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0;
|
|
jpayne@69
|
4417 PyObject *__pyx_n_s_KeyError;
|
|
jpayne@69
|
4418 PyObject *__pyx_n_s_MemoryError;
|
|
jpayne@69
|
4419 PyObject *__pyx_kp_u_No_such_file_or_directory_s;
|
|
jpayne@69
|
4420 PyObject *__pyx_n_s_NotImplementedError;
|
|
jpayne@69
|
4421 PyObject *__pyx_n_s_OSError;
|
|
jpayne@69
|
4422 PyObject *__pyx_n_s_O_RDONLY;
|
|
jpayne@69
|
4423 PyObject *__pyx_n_s_Parser;
|
|
jpayne@69
|
4424 PyObject *__pyx_n_s_Parser___reduce_cython;
|
|
jpayne@69
|
4425 PyObject *__pyx_n_s_Parser___setstate_cython;
|
|
jpayne@69
|
4426 PyObject *__pyx_n_s_Parser_get_encoding;
|
|
jpayne@69
|
4427 PyObject *__pyx_n_s_Parser_set_encoding;
|
|
jpayne@69
|
4428 PyObject *__pyx_n_s_PickleError;
|
|
jpayne@69
|
4429 PyObject *__pyx_n_s_StopIteration;
|
|
jpayne@69
|
4430 PyObject *__pyx_n_s_TabixFile;
|
|
jpayne@69
|
4431 PyObject *__pyx_n_u_TabixFile;
|
|
jpayne@69
|
4432 PyObject *__pyx_n_s_TabixFile___reduce_cython;
|
|
jpayne@69
|
4433 PyObject *__pyx_n_s_TabixFile___setstate_cython;
|
|
jpayne@69
|
4434 PyObject *__pyx_n_s_TabixFile__dup;
|
|
jpayne@69
|
4435 PyObject *__pyx_n_s_TabixFile__open;
|
|
jpayne@69
|
4436 PyObject *__pyx_n_s_TabixFile_close;
|
|
jpayne@69
|
4437 PyObject *__pyx_n_s_TabixFile_fetch;
|
|
jpayne@69
|
4438 PyObject *__pyx_n_s_TabixIterator;
|
|
jpayne@69
|
4439 PyObject *__pyx_n_s_TabixIteratorParsed;
|
|
jpayne@69
|
4440 PyObject *__pyx_n_s_TabixIteratorParsed___reduce_cyt;
|
|
jpayne@69
|
4441 PyObject *__pyx_n_s_TabixIteratorParsed___setstate_c;
|
|
jpayne@69
|
4442 PyObject *__pyx_n_s_TabixIterator___reduce_cython;
|
|
jpayne@69
|
4443 PyObject *__pyx_n_s_TabixIterator___setstate_cython;
|
|
jpayne@69
|
4444 PyObject *__pyx_n_s_Tabixfile;
|
|
jpayne@69
|
4445 PyObject *__pyx_n_u_Tabixfile;
|
|
jpayne@69
|
4446 PyObject *__pyx_n_s_Tabixfile___reduce_cython;
|
|
jpayne@69
|
4447 PyObject *__pyx_n_s_Tabixfile___setstate_cython;
|
|
jpayne@69
|
4448 PyObject *__pyx_n_s_TypeError;
|
|
jpayne@69
|
4449 PyObject *__pyx_n_s_ValueError;
|
|
jpayne@69
|
4450 PyObject *__pyx_n_s_WINDOW_SIZE;
|
|
jpayne@69
|
4451 PyObject *__pyx_kp_b__16;
|
|
jpayne@69
|
4452 PyObject *__pyx_kp_u__39;
|
|
jpayne@69
|
4453 PyObject *__pyx_kp_u__42;
|
|
jpayne@69
|
4454 PyObject *__pyx_kp_u__43;
|
|
jpayne@69
|
4455 PyObject *__pyx_kp_u__44;
|
|
jpayne@69
|
4456 PyObject *__pyx_kp_u__56;
|
|
jpayne@69
|
4457 PyObject *__pyx_n_s__62;
|
|
jpayne@69
|
4458 PyObject *__pyx_n_s__78;
|
|
jpayne@69
|
4459 PyObject *__pyx_n_s_a;
|
|
jpayne@69
|
4460 PyObject *__pyx_n_s_all;
|
|
jpayne@69
|
4461 PyObject *__pyx_n_s_asBed;
|
|
jpayne@69
|
4462 PyObject *__pyx_n_u_asBed;
|
|
jpayne@69
|
4463 PyObject *__pyx_n_s_asBed___reduce_cython;
|
|
jpayne@69
|
4464 PyObject *__pyx_n_s_asBed___setstate_cython;
|
|
jpayne@69
|
4465 PyObject *__pyx_n_s_asGFF3;
|
|
jpayne@69
|
4466 PyObject *__pyx_n_u_asGFF3;
|
|
jpayne@69
|
4467 PyObject *__pyx_n_s_asGFF3___reduce_cython;
|
|
jpayne@69
|
4468 PyObject *__pyx_n_s_asGFF3___setstate_cython;
|
|
jpayne@69
|
4469 PyObject *__pyx_n_s_asGTF;
|
|
jpayne@69
|
4470 PyObject *__pyx_n_u_asGTF;
|
|
jpayne@69
|
4471 PyObject *__pyx_n_s_asGTF___reduce_cython;
|
|
jpayne@69
|
4472 PyObject *__pyx_n_s_asGTF___setstate_cython;
|
|
jpayne@69
|
4473 PyObject *__pyx_n_s_asTuple;
|
|
jpayne@69
|
4474 PyObject *__pyx_n_u_asTuple;
|
|
jpayne@69
|
4475 PyObject *__pyx_n_s_asTuple___reduce_cython;
|
|
jpayne@69
|
4476 PyObject *__pyx_n_s_asTuple___setstate_cython;
|
|
jpayne@69
|
4477 PyObject *__pyx_n_s_asVCF;
|
|
jpayne@69
|
4478 PyObject *__pyx_n_u_asVCF;
|
|
jpayne@69
|
4479 PyObject *__pyx_n_s_asVCF___reduce_cython;
|
|
jpayne@69
|
4480 PyObject *__pyx_n_s_asVCF___setstate_cython;
|
|
jpayne@69
|
4481 PyObject *__pyx_n_u_ascii;
|
|
jpayne@69
|
4482 PyObject *__pyx_n_s_asyncio_coroutines;
|
|
jpayne@69
|
4483 PyObject *__pyx_n_s_b;
|
|
jpayne@69
|
4484 PyObject *__pyx_n_u_bcf;
|
|
jpayne@69
|
4485 PyObject *__pyx_n_u_bed;
|
|
jpayne@69
|
4486 PyObject *__pyx_n_s_buffer;
|
|
jpayne@69
|
4487 PyObject *__pyx_n_s_buffer_size;
|
|
jpayne@69
|
4488 PyObject *__pyx_kp_u_building_of_index_for_failed;
|
|
jpayne@69
|
4489 PyObject *__pyx_n_s_bytes_cpy;
|
|
jpayne@69
|
4490 PyObject *__pyx_n_s_c;
|
|
jpayne@69
|
4491 PyObject *__pyx_n_s_cfilename;
|
|
jpayne@69
|
4492 PyObject *__pyx_n_s_cfilename_index;
|
|
jpayne@69
|
4493 PyObject *__pyx_n_s_cfn;
|
|
jpayne@69
|
4494 PyObject *__pyx_n_s_cline_in_traceback;
|
|
jpayne@69
|
4495 PyObject *__pyx_n_s_close;
|
|
jpayne@69
|
4496 PyObject *__pyx_n_s_closed;
|
|
jpayne@69
|
4497 PyObject *__pyx_n_s_conf;
|
|
jpayne@69
|
4498 PyObject *__pyx_n_s_conf_data;
|
|
jpayne@69
|
4499 PyObject *__pyx_n_s_contigs;
|
|
jpayne@69
|
4500 PyObject *__pyx_kp_u_could_not_create_iterator_for_re;
|
|
jpayne@69
|
4501 PyObject *__pyx_kp_u_could_not_create_iterator_possib;
|
|
jpayne@69
|
4502 PyObject *__pyx_kp_u_could_not_load_tbi_csi_index_of;
|
|
jpayne@69
|
4503 PyObject *__pyx_kp_u_could_not_open_file_s;
|
|
jpayne@69
|
4504 PyObject *__pyx_kp_u_could_not_open_for_reading_heade;
|
|
jpayne@69
|
4505 PyObject *__pyx_kp_u_could_not_open_index_for_s;
|
|
jpayne@69
|
4506 PyObject *__pyx_kp_u_could_not_open_s_for_reading;
|
|
jpayne@69
|
4507 PyObject *__pyx_kp_u_could_not_open_s_for_writing;
|
|
jpayne@69
|
4508 PyObject *__pyx_n_s_cpy;
|
|
jpayne@69
|
4509 PyObject *__pyx_n_s_csi;
|
|
jpayne@69
|
4510 PyObject *__pyx_kp_u_csi_2;
|
|
jpayne@69
|
4511 PyObject *__pyx_n_s_cstr;
|
|
jpayne@69
|
4512 PyObject *__pyx_n_s_dict;
|
|
jpayne@69
|
4513 PyObject *__pyx_n_s_dict_2;
|
|
jpayne@69
|
4514 PyObject *__pyx_kp_u_disable;
|
|
jpayne@69
|
4515 PyObject *__pyx_n_s_doc;
|
|
jpayne@69
|
4516 PyObject *__pyx_n_s_dup;
|
|
jpayne@69
|
4517 PyObject *__pyx_kp_s_empty_iterator;
|
|
jpayne@69
|
4518 PyObject *__pyx_kp_u_enable;
|
|
jpayne@69
|
4519 PyObject *__pyx_n_s_encoding;
|
|
jpayne@69
|
4520 PyObject *__pyx_n_s_end;
|
|
jpayne@69
|
4521 PyObject *__pyx_n_s_end_col;
|
|
jpayne@69
|
4522 PyObject *__pyx_kp_u_end_out_of_range_i;
|
|
jpayne@69
|
4523 PyObject *__pyx_kp_u_error_i_when_closing_file_s;
|
|
jpayne@69
|
4524 PyObject *__pyx_kp_u_error_i_when_writing_to_file_s;
|
|
jpayne@69
|
4525 PyObject *__pyx_n_s_exists;
|
|
jpayne@69
|
4526 PyObject *__pyx_n_s_fd_src;
|
|
jpayne@69
|
4527 PyObject *__pyx_n_s_fetch;
|
|
jpayne@69
|
4528 PyObject *__pyx_kp_u_file_s_not_found;
|
|
jpayne@69
|
4529 PyObject *__pyx_n_s_filename;
|
|
jpayne@69
|
4530 PyObject *__pyx_n_s_filename_in;
|
|
jpayne@69
|
4531 PyObject *__pyx_n_s_filename_index;
|
|
jpayne@69
|
4532 PyObject *__pyx_n_s_filename_out;
|
|
jpayne@69
|
4533 PyObject *__pyx_kp_u_filename_s_already_exists_use_fo;
|
|
jpayne@69
|
4534 PyObject *__pyx_n_s_fileobj;
|
|
jpayne@69
|
4535 PyObject *__pyx_n_s_fmt;
|
|
jpayne@69
|
4536 PyObject *__pyx_n_s_fn;
|
|
jpayne@69
|
4537 PyObject *__pyx_n_s_fn_index;
|
|
jpayne@69
|
4538 PyObject *__pyx_n_s_fnidx;
|
|
jpayne@69
|
4539 PyObject *__pyx_n_s_force;
|
|
jpayne@69
|
4540 PyObject *__pyx_n_s_format;
|
|
jpayne@69
|
4541 PyObject *__pyx_n_s_fp;
|
|
jpayne@69
|
4542 PyObject *__pyx_kp_u_gc;
|
|
jpayne@69
|
4543 PyObject *__pyx_n_s_get_encoding;
|
|
jpayne@69
|
4544 PyObject *__pyx_n_s_getstate;
|
|
jpayne@69
|
4545 PyObject *__pyx_n_u_gff;
|
|
jpayne@69
|
4546 PyObject *__pyx_kp_u_gz;
|
|
jpayne@69
|
4547 PyObject *__pyx_n_s_import;
|
|
jpayne@69
|
4548 PyObject *__pyx_kp_u_incomplete_line_at_s;
|
|
jpayne@69
|
4549 PyObject *__pyx_n_s_index;
|
|
jpayne@69
|
4550 PyObject *__pyx_kp_u_index_s_not_found;
|
|
jpayne@69
|
4551 PyObject *__pyx_n_s_infile;
|
|
jpayne@69
|
4552 PyObject *__pyx_n_s_init;
|
|
jpayne@69
|
4553 PyObject *__pyx_n_s_init_subclass;
|
|
jpayne@69
|
4554 PyObject *__pyx_n_s_initializing;
|
|
jpayne@69
|
4555 PyObject *__pyx_kp_u_invalid_file_opening_mode_s;
|
|
jpayne@69
|
4556 PyObject *__pyx_n_s_is_coroutine;
|
|
jpayne@69
|
4557 PyObject *__pyx_n_s_is_empty;
|
|
jpayne@69
|
4558 PyObject *__pyx_n_s_is_open;
|
|
jpayne@69
|
4559 PyObject *__pyx_kp_u_isenabled;
|
|
jpayne@69
|
4560 PyObject *__pyx_n_s_iter;
|
|
jpayne@69
|
4561 PyObject *__pyx_kp_s_iterate_over_infile_Permits_the;
|
|
jpayne@69
|
4562 PyObject *__pyx_kp_u_iteration_on_closed_file;
|
|
jpayne@69
|
4563 PyObject *__pyx_n_s_itr;
|
|
jpayne@69
|
4564 PyObject *__pyx_n_s_keep_original;
|
|
jpayne@69
|
4565 PyObject *__pyx_n_s_keys;
|
|
jpayne@69
|
4566 PyObject *__pyx_n_s_length;
|
|
jpayne@69
|
4567 PyObject *__pyx_n_s_line;
|
|
jpayne@69
|
4568 PyObject *__pyx_n_s_line_skip;
|
|
jpayne@69
|
4569 PyObject *__pyx_n_s_main;
|
|
jpayne@69
|
4570 PyObject *__pyx_n_s_meta_char;
|
|
jpayne@69
|
4571 PyObject *__pyx_n_s_metaclass;
|
|
jpayne@69
|
4572 PyObject *__pyx_n_s_min_shift;
|
|
jpayne@69
|
4573 PyObject *__pyx_n_s_mode;
|
|
jpayne@69
|
4574 PyObject *__pyx_n_s_module;
|
|
jpayne@69
|
4575 PyObject *__pyx_n_s_multiple_iterators;
|
|
jpayne@69
|
4576 PyObject *__pyx_n_s_name;
|
|
jpayne@69
|
4577 PyObject *__pyx_n_s_nbytes;
|
|
jpayne@69
|
4578 PyObject *__pyx_kp_u_neither_preset_nor_seq_col_start;
|
|
jpayne@69
|
4579 PyObject *__pyx_n_s_new;
|
|
jpayne@69
|
4580 PyObject *__pyx_n_s_next;
|
|
jpayne@69
|
4581 PyObject *__pyx_kp_s_no_default___reduce___due_to_non;
|
|
jpayne@69
|
4582 PyObject *__pyx_n_s_open;
|
|
jpayne@69
|
4583 PyObject *__pyx_n_s_os;
|
|
jpayne@69
|
4584 PyObject *__pyx_kp_u_parse_method_of_s_not_implemente;
|
|
jpayne@69
|
4585 PyObject *__pyx_n_s_parser;
|
|
jpayne@69
|
4586 PyObject *__pyx_n_s_path;
|
|
jpayne@69
|
4587 PyObject *__pyx_n_s_pickle;
|
|
jpayne@69
|
4588 PyObject *__pyx_n_s_prepare;
|
|
jpayne@69
|
4589 PyObject *__pyx_n_s_preset;
|
|
jpayne@69
|
4590 PyObject *__pyx_n_s_preset2conf;
|
|
jpayne@69
|
4591 PyObject *__pyx_n_u_psltbl;
|
|
jpayne@69
|
4592 PyObject *__pyx_n_s_pysam_libctabix;
|
|
jpayne@69
|
4593 PyObject *__pyx_kp_s_pysam_libctabix_pyx;
|
|
jpayne@69
|
4594 PyObject *__pyx_n_s_pyx_PickleError;
|
|
jpayne@69
|
4595 PyObject *__pyx_n_s_pyx_checksum;
|
|
jpayne@69
|
4596 PyObject *__pyx_n_s_pyx_result;
|
|
jpayne@69
|
4597 PyObject *__pyx_n_s_pyx_state;
|
|
jpayne@69
|
4598 PyObject *__pyx_n_s_pyx_type;
|
|
jpayne@69
|
4599 PyObject *__pyx_n_s_pyx_unpickle_Parser;
|
|
jpayne@69
|
4600 PyObject *__pyx_n_s_pyx_unpickle_asBed;
|
|
jpayne@69
|
4601 PyObject *__pyx_n_s_pyx_unpickle_asGFF3;
|
|
jpayne@69
|
4602 PyObject *__pyx_n_s_pyx_unpickle_asGTF;
|
|
jpayne@69
|
4603 PyObject *__pyx_n_s_pyx_unpickle_asTuple;
|
|
jpayne@69
|
4604 PyObject *__pyx_n_s_pyx_unpickle_asVCF;
|
|
jpayne@69
|
4605 PyObject *__pyx_n_s_pyx_vtable;
|
|
jpayne@69
|
4606 PyObject *__pyx_n_s_qualname;
|
|
jpayne@69
|
4607 PyObject *__pyx_n_s_r;
|
|
jpayne@69
|
4608 PyObject *__pyx_n_u_r;
|
|
jpayne@69
|
4609 PyObject *__pyx_n_s_readline;
|
|
jpayne@69
|
4610 PyObject *__pyx_n_s_reduce;
|
|
jpayne@69
|
4611 PyObject *__pyx_n_s_reduce_cython;
|
|
jpayne@69
|
4612 PyObject *__pyx_n_s_reduce_ex;
|
|
jpayne@69
|
4613 PyObject *__pyx_n_s_reference;
|
|
jpayne@69
|
4614 PyObject *__pyx_n_s_region;
|
|
jpayne@69
|
4615 PyObject *__pyx_n_s_retval;
|
|
jpayne@69
|
4616 PyObject *__pyx_kp_u_s;
|
|
jpayne@69
|
4617 PyObject *__pyx_n_s_s_2;
|
|
jpayne@69
|
4618 PyObject *__pyx_kp_u_s_i;
|
|
jpayne@69
|
4619 PyObject *__pyx_kp_u_s_i_i;
|
|
jpayne@69
|
4620 PyObject *__pyx_n_u_sam;
|
|
jpayne@69
|
4621 PyObject *__pyx_n_s_self;
|
|
jpayne@69
|
4622 PyObject *__pyx_kp_s_self_gzipfile_self_kstream_canno;
|
|
jpayne@69
|
4623 PyObject *__pyx_kp_s_self_iterator_cannot_be_converte;
|
|
jpayne@69
|
4624 PyObject *__pyx_n_s_seq_col;
|
|
jpayne@69
|
4625 PyObject *__pyx_n_s_set_encoding;
|
|
jpayne@69
|
4626 PyObject *__pyx_n_s_set_name;
|
|
jpayne@69
|
4627 PyObject *__pyx_n_s_setstate;
|
|
jpayne@69
|
4628 PyObject *__pyx_n_s_setstate_cython;
|
|
jpayne@69
|
4629 PyObject *__pyx_n_s_spec;
|
|
jpayne@69
|
4630 PyObject *__pyx_n_s_start;
|
|
jpayne@69
|
4631 PyObject *__pyx_n_s_start_col;
|
|
jpayne@69
|
4632 PyObject *__pyx_kp_u_start_i_end_i;
|
|
jpayne@69
|
4633 PyObject *__pyx_kp_u_start_out_of_range_i;
|
|
jpayne@69
|
4634 PyObject *__pyx_n_s_state;
|
|
jpayne@69
|
4635 PyObject *__pyx_kp_s_stringsource;
|
|
jpayne@69
|
4636 PyObject *__pyx_n_s_suffix;
|
|
jpayne@69
|
4637 PyObject *__pyx_n_s_super;
|
|
jpayne@69
|
4638 PyObject *__pyx_n_s_sys;
|
|
jpayne@69
|
4639 PyObject *__pyx_n_s_tabix_compress;
|
|
jpayne@69
|
4640 PyObject *__pyx_n_u_tabix_compress;
|
|
jpayne@69
|
4641 PyObject *__pyx_n_s_tabix_file_iterator;
|
|
jpayne@69
|
4642 PyObject *__pyx_n_u_tabix_file_iterator;
|
|
jpayne@69
|
4643 PyObject *__pyx_n_s_tabix_file_iterator___reduce_cyt;
|
|
jpayne@69
|
4644 PyObject *__pyx_n_s_tabix_file_iterator___setstate_c;
|
|
jpayne@69
|
4645 PyObject *__pyx_n_s_tabix_generic_iterator;
|
|
jpayne@69
|
4646 PyObject *__pyx_n_u_tabix_generic_iterator;
|
|
jpayne@69
|
4647 PyObject *__pyx_n_s_tabix_generic_iterator___init;
|
|
jpayne@69
|
4648 PyObject *__pyx_n_s_tabix_generic_iterator___iter;
|
|
jpayne@69
|
4649 PyObject *__pyx_n_s_tabix_generic_iterator___next;
|
|
jpayne@69
|
4650 PyObject *__pyx_n_s_tabix_index;
|
|
jpayne@69
|
4651 PyObject *__pyx_n_u_tabix_index;
|
|
jpayne@69
|
4652 PyObject *__pyx_n_s_tabix_iterator;
|
|
jpayne@69
|
4653 PyObject *__pyx_n_u_tabix_iterator;
|
|
jpayne@69
|
4654 PyObject *__pyx_kp_u_tbi;
|
|
jpayne@69
|
4655 PyObject *__pyx_n_s_tell;
|
|
jpayne@69
|
4656 PyObject *__pyx_n_s_test;
|
|
jpayne@69
|
4657 PyObject *__pyx_n_s_threads;
|
|
jpayne@69
|
4658 PyObject *__pyx_kp_u_unknown_preset;
|
|
jpayne@69
|
4659 PyObject *__pyx_n_s_unlink;
|
|
jpayne@69
|
4660 PyObject *__pyx_n_s_update;
|
|
jpayne@69
|
4661 PyObject *__pyx_n_s_use_setstate;
|
|
jpayne@69
|
4662 PyObject *__pyx_kp_u_valid_presets_are;
|
|
jpayne@69
|
4663 PyObject *__pyx_n_u_vcf;
|
|
jpayne@69
|
4664 PyObject *__pyx_kp_u_writing_failed;
|
|
jpayne@69
|
4665 PyObject *__pyx_n_s_zerobased;
|
|
jpayne@69
|
4666 PyObject *__pyx_int_0;
|
|
jpayne@69
|
4667 PyObject *__pyx_int_1;
|
|
jpayne@69
|
4668 PyObject *__pyx_int_2;
|
|
jpayne@69
|
4669 PyObject *__pyx_int_3;
|
|
jpayne@69
|
4670 PyObject *__pyx_int_4;
|
|
jpayne@69
|
4671 PyObject *__pyx_int_5;
|
|
jpayne@69
|
4672 PyObject *__pyx_int_15;
|
|
jpayne@69
|
4673 PyObject *__pyx_int_17;
|
|
jpayne@69
|
4674 PyObject *__pyx_int_18;
|
|
jpayne@69
|
4675 PyObject *__pyx_int_35;
|
|
jpayne@69
|
4676 PyObject *__pyx_int_64;
|
|
jpayne@69
|
4677 PyObject *__pyx_int_21667264;
|
|
jpayne@69
|
4678 PyObject *__pyx_int_139192863;
|
|
jpayne@69
|
4679 PyObject *__pyx_int_243541226;
|
|
jpayne@69
|
4680 PyObject *__pyx_int_neg_1;
|
|
jpayne@69
|
4681 PyObject *__pyx_codeobj_;
|
|
jpayne@69
|
4682 PyObject *__pyx_tuple__19;
|
|
jpayne@69
|
4683 PyObject *__pyx_tuple__20;
|
|
jpayne@69
|
4684 PyObject *__pyx_tuple__24;
|
|
jpayne@69
|
4685 PyObject *__pyx_tuple__38;
|
|
jpayne@69
|
4686 PyObject *__pyx_tuple__41;
|
|
jpayne@69
|
4687 PyObject *__pyx_tuple__45;
|
|
jpayne@69
|
4688 PyObject *__pyx_tuple__55;
|
|
jpayne@69
|
4689 PyObject *__pyx_tuple__63;
|
|
jpayne@69
|
4690 PyObject *__pyx_tuple__64;
|
|
jpayne@69
|
4691 PyObject *__pyx_tuple__65;
|
|
jpayne@69
|
4692 PyObject *__pyx_tuple__66;
|
|
jpayne@69
|
4693 PyObject *__pyx_tuple__67;
|
|
jpayne@69
|
4694 PyObject *__pyx_tuple__68;
|
|
jpayne@69
|
4695 PyObject *__pyx_tuple__69;
|
|
jpayne@69
|
4696 PyObject *__pyx_tuple__70;
|
|
jpayne@69
|
4697 PyObject *__pyx_tuple__71;
|
|
jpayne@69
|
4698 PyObject *__pyx_tuple__72;
|
|
jpayne@69
|
4699 PyObject *__pyx_tuple__73;
|
|
jpayne@69
|
4700 PyObject *__pyx_tuple__74;
|
|
jpayne@69
|
4701 PyObject *__pyx_tuple__75;
|
|
jpayne@69
|
4702 PyObject *__pyx_tuple__76;
|
|
jpayne@69
|
4703 PyObject *__pyx_tuple__77;
|
|
jpayne@69
|
4704 PyObject *__pyx_codeobj__2;
|
|
jpayne@69
|
4705 PyObject *__pyx_codeobj__3;
|
|
jpayne@69
|
4706 PyObject *__pyx_codeobj__4;
|
|
jpayne@69
|
4707 PyObject *__pyx_codeobj__5;
|
|
jpayne@69
|
4708 PyObject *__pyx_codeobj__6;
|
|
jpayne@69
|
4709 PyObject *__pyx_codeobj__7;
|
|
jpayne@69
|
4710 PyObject *__pyx_codeobj__8;
|
|
jpayne@69
|
4711 PyObject *__pyx_codeobj__9;
|
|
jpayne@69
|
4712 PyObject *__pyx_codeobj__10;
|
|
jpayne@69
|
4713 PyObject *__pyx_codeobj__11;
|
|
jpayne@69
|
4714 PyObject *__pyx_codeobj__12;
|
|
jpayne@69
|
4715 PyObject *__pyx_codeobj__13;
|
|
jpayne@69
|
4716 PyObject *__pyx_codeobj__14;
|
|
jpayne@69
|
4717 PyObject *__pyx_codeobj__15;
|
|
jpayne@69
|
4718 PyObject *__pyx_codeobj__17;
|
|
jpayne@69
|
4719 PyObject *__pyx_codeobj__18;
|
|
jpayne@69
|
4720 PyObject *__pyx_codeobj__21;
|
|
jpayne@69
|
4721 PyObject *__pyx_codeobj__22;
|
|
jpayne@69
|
4722 PyObject *__pyx_codeobj__23;
|
|
jpayne@69
|
4723 PyObject *__pyx_codeobj__25;
|
|
jpayne@69
|
4724 PyObject *__pyx_codeobj__26;
|
|
jpayne@69
|
4725 PyObject *__pyx_codeobj__27;
|
|
jpayne@69
|
4726 PyObject *__pyx_codeobj__28;
|
|
jpayne@69
|
4727 PyObject *__pyx_codeobj__29;
|
|
jpayne@69
|
4728 PyObject *__pyx_codeobj__30;
|
|
jpayne@69
|
4729 PyObject *__pyx_codeobj__31;
|
|
jpayne@69
|
4730 PyObject *__pyx_codeobj__32;
|
|
jpayne@69
|
4731 PyObject *__pyx_codeobj__33;
|
|
jpayne@69
|
4732 PyObject *__pyx_codeobj__34;
|
|
jpayne@69
|
4733 PyObject *__pyx_codeobj__35;
|
|
jpayne@69
|
4734 PyObject *__pyx_codeobj__36;
|
|
jpayne@69
|
4735 PyObject *__pyx_codeobj__37;
|
|
jpayne@69
|
4736 PyObject *__pyx_codeobj__40;
|
|
jpayne@69
|
4737 PyObject *__pyx_codeobj__46;
|
|
jpayne@69
|
4738 PyObject *__pyx_codeobj__47;
|
|
jpayne@69
|
4739 PyObject *__pyx_codeobj__48;
|
|
jpayne@69
|
4740 PyObject *__pyx_codeobj__49;
|
|
jpayne@69
|
4741 PyObject *__pyx_codeobj__50;
|
|
jpayne@69
|
4742 PyObject *__pyx_codeobj__51;
|
|
jpayne@69
|
4743 PyObject *__pyx_codeobj__52;
|
|
jpayne@69
|
4744 PyObject *__pyx_codeobj__53;
|
|
jpayne@69
|
4745 PyObject *__pyx_codeobj__54;
|
|
jpayne@69
|
4746 PyObject *__pyx_codeobj__57;
|
|
jpayne@69
|
4747 PyObject *__pyx_codeobj__58;
|
|
jpayne@69
|
4748 PyObject *__pyx_codeobj__59;
|
|
jpayne@69
|
4749 PyObject *__pyx_codeobj__60;
|
|
jpayne@69
|
4750 PyObject *__pyx_codeobj__61;
|
|
jpayne@69
|
4751 } __pyx_mstate;
|
|
jpayne@69
|
4752
|
|
jpayne@69
|
4753 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4754 #ifdef __cplusplus
|
|
jpayne@69
|
4755 namespace {
|
|
jpayne@69
|
4756 extern struct PyModuleDef __pyx_moduledef;
|
|
jpayne@69
|
4757 } /* anonymous namespace */
|
|
jpayne@69
|
4758 #else
|
|
jpayne@69
|
4759 static struct PyModuleDef __pyx_moduledef;
|
|
jpayne@69
|
4760 #endif
|
|
jpayne@69
|
4761
|
|
jpayne@69
|
4762 #define __pyx_mstate(o) ((__pyx_mstate *)__Pyx_PyModule_GetState(o))
|
|
jpayne@69
|
4763
|
|
jpayne@69
|
4764 #define __pyx_mstate_global (__pyx_mstate(PyState_FindModule(&__pyx_moduledef)))
|
|
jpayne@69
|
4765
|
|
jpayne@69
|
4766 #define __pyx_m (PyState_FindModule(&__pyx_moduledef))
|
|
jpayne@69
|
4767 #else
|
|
jpayne@69
|
4768 static __pyx_mstate __pyx_mstate_global_static =
|
|
jpayne@69
|
4769 #ifdef __cplusplus
|
|
jpayne@69
|
4770 {};
|
|
jpayne@69
|
4771 #else
|
|
jpayne@69
|
4772 {0};
|
|
jpayne@69
|
4773 #endif
|
|
jpayne@69
|
4774 static __pyx_mstate *__pyx_mstate_global = &__pyx_mstate_global_static;
|
|
jpayne@69
|
4775 #endif
|
|
jpayne@69
|
4776 /* #### Code section: module_state_clear ### */
|
|
jpayne@69
|
4777 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
4778 static int __pyx_m_clear(PyObject *m) {
|
|
jpayne@69
|
4779 __pyx_mstate *clear_module_state = __pyx_mstate(m);
|
|
jpayne@69
|
4780 if (!clear_module_state) return 0;
|
|
jpayne@69
|
4781 Py_CLEAR(clear_module_state->__pyx_d);
|
|
jpayne@69
|
4782 Py_CLEAR(clear_module_state->__pyx_b);
|
|
jpayne@69
|
4783 Py_CLEAR(clear_module_state->__pyx_cython_runtime);
|
|
jpayne@69
|
4784 Py_CLEAR(clear_module_state->__pyx_empty_tuple);
|
|
jpayne@69
|
4785 Py_CLEAR(clear_module_state->__pyx_empty_bytes);
|
|
jpayne@69
|
4786 Py_CLEAR(clear_module_state->__pyx_empty_unicode);
|
|
jpayne@69
|
4787 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
4788 Py_CLEAR(clear_module_state->__pyx_CyFunctionType);
|
|
jpayne@69
|
4789 #endif
|
|
jpayne@69
|
4790 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
4791 Py_CLEAR(clear_module_state->__pyx_FusedFunctionType);
|
|
jpayne@69
|
4792 #endif
|
|
jpayne@69
|
4793 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile);
|
|
jpayne@69
|
4794 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4type_type);
|
|
jpayne@69
|
4795 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4bool_bool);
|
|
jpayne@69
|
4796 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_7complex_complex);
|
|
jpayne@69
|
4797 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy);
|
|
jpayne@69
|
4798 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator);
|
|
jpayne@69
|
4799 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy);
|
|
jpayne@69
|
4800 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy);
|
|
jpayne@69
|
4801 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy);
|
|
jpayne@69
|
4802 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_BedProxy);
|
|
jpayne@69
|
4803 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy);
|
|
jpayne@69
|
4804 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_5array_array);
|
|
jpayne@69
|
4805 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator);
|
|
jpayne@69
|
4806 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_tabix_file_iterator);
|
|
jpayne@69
|
4807 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
4808 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
4809 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_Parser);
|
|
jpayne@69
|
4810 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_Parser);
|
|
jpayne@69
|
4811 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asTuple);
|
|
jpayne@69
|
4812 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asTuple);
|
|
jpayne@69
|
4813 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asGTF);
|
|
jpayne@69
|
4814 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asGTF);
|
|
jpayne@69
|
4815 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asGFF3);
|
|
jpayne@69
|
4816 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asGFF3);
|
|
jpayne@69
|
4817 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asBed);
|
|
jpayne@69
|
4818 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asBed);
|
|
jpayne@69
|
4819 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asVCF);
|
|
jpayne@69
|
4820 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asVCF);
|
|
jpayne@69
|
4821 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixIterator);
|
|
jpayne@69
|
4822 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_TabixIterator);
|
|
jpayne@69
|
4823 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed);
|
|
jpayne@69
|
4824 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_TabixIteratorParsed);
|
|
jpayne@69
|
4825 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIterator);
|
|
jpayne@69
|
4826 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_GZIterator);
|
|
jpayne@69
|
4827 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorHead);
|
|
jpayne@69
|
4828 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_GZIteratorHead);
|
|
jpayne@69
|
4829 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed);
|
|
jpayne@69
|
4830 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_GZIteratorParsed);
|
|
jpayne@69
|
4831 Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_Tabixfile);
|
|
jpayne@69
|
4832 Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_Tabixfile);
|
|
jpayne@69
|
4833 Py_CLEAR(clear_module_state->__pyx_n_s_AssertionError);
|
|
jpayne@69
|
4834 Py_CLEAR(clear_module_state->__pyx_kp_u_Could_not_open_file);
|
|
jpayne@69
|
4835 Py_CLEAR(clear_module_state->__pyx_n_s_EmptyIterator);
|
|
jpayne@69
|
4836 Py_CLEAR(clear_module_state->__pyx_n_s_EmptyIterator___iter);
|
|
jpayne@69
|
4837 Py_CLEAR(clear_module_state->__pyx_n_s_EmptyIterator___next);
|
|
jpayne@69
|
4838 Py_CLEAR(clear_module_state->__pyx_kp_u_Filename_s_already_exists_use_fo);
|
|
jpayne@69
|
4839 Py_CLEAR(clear_module_state->__pyx_n_s_GZIterator);
|
|
jpayne@69
|
4840 Py_CLEAR(clear_module_state->__pyx_n_u_GZIterator);
|
|
jpayne@69
|
4841 Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorHead);
|
|
jpayne@69
|
4842 Py_CLEAR(clear_module_state->__pyx_n_u_GZIteratorHead);
|
|
jpayne@69
|
4843 Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorHead___reduce_cython);
|
|
jpayne@69
|
4844 Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorHead___setstate_cython);
|
|
jpayne@69
|
4845 Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorParsed);
|
|
jpayne@69
|
4846 Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorParsed___reduce_cython);
|
|
jpayne@69
|
4847 Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorParsed___setstate_cyth);
|
|
jpayne@69
|
4848 Py_CLEAR(clear_module_state->__pyx_n_s_GZIterator___reduce_cython);
|
|
jpayne@69
|
4849 Py_CLEAR(clear_module_state->__pyx_n_s_GZIterator___setstate_cython);
|
|
jpayne@69
|
4850 Py_CLEAR(clear_module_state->__pyx_n_s_IOError);
|
|
jpayne@69
|
4851 Py_CLEAR(clear_module_state->__pyx_kp_u_I_O_operation_on_closed_file);
|
|
jpayne@69
|
4852 Py_CLEAR(clear_module_state->__pyx_kp_u_I_O_operation_on_closed_file_2);
|
|
jpayne@69
|
4853 Py_CLEAR(clear_module_state->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0);
|
|
jpayne@69
|
4854 Py_CLEAR(clear_module_state->__pyx_n_s_KeyError);
|
|
jpayne@69
|
4855 Py_CLEAR(clear_module_state->__pyx_n_s_MemoryError);
|
|
jpayne@69
|
4856 Py_CLEAR(clear_module_state->__pyx_kp_u_No_such_file_or_directory_s);
|
|
jpayne@69
|
4857 Py_CLEAR(clear_module_state->__pyx_n_s_NotImplementedError);
|
|
jpayne@69
|
4858 Py_CLEAR(clear_module_state->__pyx_n_s_OSError);
|
|
jpayne@69
|
4859 Py_CLEAR(clear_module_state->__pyx_n_s_O_RDONLY);
|
|
jpayne@69
|
4860 Py_CLEAR(clear_module_state->__pyx_n_s_Parser);
|
|
jpayne@69
|
4861 Py_CLEAR(clear_module_state->__pyx_n_s_Parser___reduce_cython);
|
|
jpayne@69
|
4862 Py_CLEAR(clear_module_state->__pyx_n_s_Parser___setstate_cython);
|
|
jpayne@69
|
4863 Py_CLEAR(clear_module_state->__pyx_n_s_Parser_get_encoding);
|
|
jpayne@69
|
4864 Py_CLEAR(clear_module_state->__pyx_n_s_Parser_set_encoding);
|
|
jpayne@69
|
4865 Py_CLEAR(clear_module_state->__pyx_n_s_PickleError);
|
|
jpayne@69
|
4866 Py_CLEAR(clear_module_state->__pyx_n_s_StopIteration);
|
|
jpayne@69
|
4867 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile);
|
|
jpayne@69
|
4868 Py_CLEAR(clear_module_state->__pyx_n_u_TabixFile);
|
|
jpayne@69
|
4869 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile___reduce_cython);
|
|
jpayne@69
|
4870 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile___setstate_cython);
|
|
jpayne@69
|
4871 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile__dup);
|
|
jpayne@69
|
4872 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile__open);
|
|
jpayne@69
|
4873 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile_close);
|
|
jpayne@69
|
4874 Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile_fetch);
|
|
jpayne@69
|
4875 Py_CLEAR(clear_module_state->__pyx_n_s_TabixIterator);
|
|
jpayne@69
|
4876 Py_CLEAR(clear_module_state->__pyx_n_s_TabixIteratorParsed);
|
|
jpayne@69
|
4877 Py_CLEAR(clear_module_state->__pyx_n_s_TabixIteratorParsed___reduce_cyt);
|
|
jpayne@69
|
4878 Py_CLEAR(clear_module_state->__pyx_n_s_TabixIteratorParsed___setstate_c);
|
|
jpayne@69
|
4879 Py_CLEAR(clear_module_state->__pyx_n_s_TabixIterator___reduce_cython);
|
|
jpayne@69
|
4880 Py_CLEAR(clear_module_state->__pyx_n_s_TabixIterator___setstate_cython);
|
|
jpayne@69
|
4881 Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile);
|
|
jpayne@69
|
4882 Py_CLEAR(clear_module_state->__pyx_n_u_Tabixfile);
|
|
jpayne@69
|
4883 Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile___reduce_cython);
|
|
jpayne@69
|
4884 Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile___setstate_cython);
|
|
jpayne@69
|
4885 Py_CLEAR(clear_module_state->__pyx_n_s_TypeError);
|
|
jpayne@69
|
4886 Py_CLEAR(clear_module_state->__pyx_n_s_ValueError);
|
|
jpayne@69
|
4887 Py_CLEAR(clear_module_state->__pyx_n_s_WINDOW_SIZE);
|
|
jpayne@69
|
4888 Py_CLEAR(clear_module_state->__pyx_kp_b__16);
|
|
jpayne@69
|
4889 Py_CLEAR(clear_module_state->__pyx_kp_u__39);
|
|
jpayne@69
|
4890 Py_CLEAR(clear_module_state->__pyx_kp_u__42);
|
|
jpayne@69
|
4891 Py_CLEAR(clear_module_state->__pyx_kp_u__43);
|
|
jpayne@69
|
4892 Py_CLEAR(clear_module_state->__pyx_kp_u__44);
|
|
jpayne@69
|
4893 Py_CLEAR(clear_module_state->__pyx_kp_u__56);
|
|
jpayne@69
|
4894 Py_CLEAR(clear_module_state->__pyx_n_s__62);
|
|
jpayne@69
|
4895 Py_CLEAR(clear_module_state->__pyx_n_s__78);
|
|
jpayne@69
|
4896 Py_CLEAR(clear_module_state->__pyx_n_s_a);
|
|
jpayne@69
|
4897 Py_CLEAR(clear_module_state->__pyx_n_s_all);
|
|
jpayne@69
|
4898 Py_CLEAR(clear_module_state->__pyx_n_s_asBed);
|
|
jpayne@69
|
4899 Py_CLEAR(clear_module_state->__pyx_n_u_asBed);
|
|
jpayne@69
|
4900 Py_CLEAR(clear_module_state->__pyx_n_s_asBed___reduce_cython);
|
|
jpayne@69
|
4901 Py_CLEAR(clear_module_state->__pyx_n_s_asBed___setstate_cython);
|
|
jpayne@69
|
4902 Py_CLEAR(clear_module_state->__pyx_n_s_asGFF3);
|
|
jpayne@69
|
4903 Py_CLEAR(clear_module_state->__pyx_n_u_asGFF3);
|
|
jpayne@69
|
4904 Py_CLEAR(clear_module_state->__pyx_n_s_asGFF3___reduce_cython);
|
|
jpayne@69
|
4905 Py_CLEAR(clear_module_state->__pyx_n_s_asGFF3___setstate_cython);
|
|
jpayne@69
|
4906 Py_CLEAR(clear_module_state->__pyx_n_s_asGTF);
|
|
jpayne@69
|
4907 Py_CLEAR(clear_module_state->__pyx_n_u_asGTF);
|
|
jpayne@69
|
4908 Py_CLEAR(clear_module_state->__pyx_n_s_asGTF___reduce_cython);
|
|
jpayne@69
|
4909 Py_CLEAR(clear_module_state->__pyx_n_s_asGTF___setstate_cython);
|
|
jpayne@69
|
4910 Py_CLEAR(clear_module_state->__pyx_n_s_asTuple);
|
|
jpayne@69
|
4911 Py_CLEAR(clear_module_state->__pyx_n_u_asTuple);
|
|
jpayne@69
|
4912 Py_CLEAR(clear_module_state->__pyx_n_s_asTuple___reduce_cython);
|
|
jpayne@69
|
4913 Py_CLEAR(clear_module_state->__pyx_n_s_asTuple___setstate_cython);
|
|
jpayne@69
|
4914 Py_CLEAR(clear_module_state->__pyx_n_s_asVCF);
|
|
jpayne@69
|
4915 Py_CLEAR(clear_module_state->__pyx_n_u_asVCF);
|
|
jpayne@69
|
4916 Py_CLEAR(clear_module_state->__pyx_n_s_asVCF___reduce_cython);
|
|
jpayne@69
|
4917 Py_CLEAR(clear_module_state->__pyx_n_s_asVCF___setstate_cython);
|
|
jpayne@69
|
4918 Py_CLEAR(clear_module_state->__pyx_n_u_ascii);
|
|
jpayne@69
|
4919 Py_CLEAR(clear_module_state->__pyx_n_s_asyncio_coroutines);
|
|
jpayne@69
|
4920 Py_CLEAR(clear_module_state->__pyx_n_s_b);
|
|
jpayne@69
|
4921 Py_CLEAR(clear_module_state->__pyx_n_u_bcf);
|
|
jpayne@69
|
4922 Py_CLEAR(clear_module_state->__pyx_n_u_bed);
|
|
jpayne@69
|
4923 Py_CLEAR(clear_module_state->__pyx_n_s_buffer);
|
|
jpayne@69
|
4924 Py_CLEAR(clear_module_state->__pyx_n_s_buffer_size);
|
|
jpayne@69
|
4925 Py_CLEAR(clear_module_state->__pyx_kp_u_building_of_index_for_failed);
|
|
jpayne@69
|
4926 Py_CLEAR(clear_module_state->__pyx_n_s_bytes_cpy);
|
|
jpayne@69
|
4927 Py_CLEAR(clear_module_state->__pyx_n_s_c);
|
|
jpayne@69
|
4928 Py_CLEAR(clear_module_state->__pyx_n_s_cfilename);
|
|
jpayne@69
|
4929 Py_CLEAR(clear_module_state->__pyx_n_s_cfilename_index);
|
|
jpayne@69
|
4930 Py_CLEAR(clear_module_state->__pyx_n_s_cfn);
|
|
jpayne@69
|
4931 Py_CLEAR(clear_module_state->__pyx_n_s_cline_in_traceback);
|
|
jpayne@69
|
4932 Py_CLEAR(clear_module_state->__pyx_n_s_close);
|
|
jpayne@69
|
4933 Py_CLEAR(clear_module_state->__pyx_n_s_closed);
|
|
jpayne@69
|
4934 Py_CLEAR(clear_module_state->__pyx_n_s_conf);
|
|
jpayne@69
|
4935 Py_CLEAR(clear_module_state->__pyx_n_s_conf_data);
|
|
jpayne@69
|
4936 Py_CLEAR(clear_module_state->__pyx_n_s_contigs);
|
|
jpayne@69
|
4937 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_create_iterator_for_re);
|
|
jpayne@69
|
4938 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_create_iterator_possib);
|
|
jpayne@69
|
4939 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_load_tbi_csi_index_of);
|
|
jpayne@69
|
4940 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_file_s);
|
|
jpayne@69
|
4941 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_for_reading_heade);
|
|
jpayne@69
|
4942 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_index_for_s);
|
|
jpayne@69
|
4943 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_s_for_reading);
|
|
jpayne@69
|
4944 Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_s_for_writing);
|
|
jpayne@69
|
4945 Py_CLEAR(clear_module_state->__pyx_n_s_cpy);
|
|
jpayne@69
|
4946 Py_CLEAR(clear_module_state->__pyx_n_s_csi);
|
|
jpayne@69
|
4947 Py_CLEAR(clear_module_state->__pyx_kp_u_csi_2);
|
|
jpayne@69
|
4948 Py_CLEAR(clear_module_state->__pyx_n_s_cstr);
|
|
jpayne@69
|
4949 Py_CLEAR(clear_module_state->__pyx_n_s_dict);
|
|
jpayne@69
|
4950 Py_CLEAR(clear_module_state->__pyx_n_s_dict_2);
|
|
jpayne@69
|
4951 Py_CLEAR(clear_module_state->__pyx_kp_u_disable);
|
|
jpayne@69
|
4952 Py_CLEAR(clear_module_state->__pyx_n_s_doc);
|
|
jpayne@69
|
4953 Py_CLEAR(clear_module_state->__pyx_n_s_dup);
|
|
jpayne@69
|
4954 Py_CLEAR(clear_module_state->__pyx_kp_s_empty_iterator);
|
|
jpayne@69
|
4955 Py_CLEAR(clear_module_state->__pyx_kp_u_enable);
|
|
jpayne@69
|
4956 Py_CLEAR(clear_module_state->__pyx_n_s_encoding);
|
|
jpayne@69
|
4957 Py_CLEAR(clear_module_state->__pyx_n_s_end);
|
|
jpayne@69
|
4958 Py_CLEAR(clear_module_state->__pyx_n_s_end_col);
|
|
jpayne@69
|
4959 Py_CLEAR(clear_module_state->__pyx_kp_u_end_out_of_range_i);
|
|
jpayne@69
|
4960 Py_CLEAR(clear_module_state->__pyx_kp_u_error_i_when_closing_file_s);
|
|
jpayne@69
|
4961 Py_CLEAR(clear_module_state->__pyx_kp_u_error_i_when_writing_to_file_s);
|
|
jpayne@69
|
4962 Py_CLEAR(clear_module_state->__pyx_n_s_exists);
|
|
jpayne@69
|
4963 Py_CLEAR(clear_module_state->__pyx_n_s_fd_src);
|
|
jpayne@69
|
4964 Py_CLEAR(clear_module_state->__pyx_n_s_fetch);
|
|
jpayne@69
|
4965 Py_CLEAR(clear_module_state->__pyx_kp_u_file_s_not_found);
|
|
jpayne@69
|
4966 Py_CLEAR(clear_module_state->__pyx_n_s_filename);
|
|
jpayne@69
|
4967 Py_CLEAR(clear_module_state->__pyx_n_s_filename_in);
|
|
jpayne@69
|
4968 Py_CLEAR(clear_module_state->__pyx_n_s_filename_index);
|
|
jpayne@69
|
4969 Py_CLEAR(clear_module_state->__pyx_n_s_filename_out);
|
|
jpayne@69
|
4970 Py_CLEAR(clear_module_state->__pyx_kp_u_filename_s_already_exists_use_fo);
|
|
jpayne@69
|
4971 Py_CLEAR(clear_module_state->__pyx_n_s_fileobj);
|
|
jpayne@69
|
4972 Py_CLEAR(clear_module_state->__pyx_n_s_fmt);
|
|
jpayne@69
|
4973 Py_CLEAR(clear_module_state->__pyx_n_s_fn);
|
|
jpayne@69
|
4974 Py_CLEAR(clear_module_state->__pyx_n_s_fn_index);
|
|
jpayne@69
|
4975 Py_CLEAR(clear_module_state->__pyx_n_s_fnidx);
|
|
jpayne@69
|
4976 Py_CLEAR(clear_module_state->__pyx_n_s_force);
|
|
jpayne@69
|
4977 Py_CLEAR(clear_module_state->__pyx_n_s_format);
|
|
jpayne@69
|
4978 Py_CLEAR(clear_module_state->__pyx_n_s_fp);
|
|
jpayne@69
|
4979 Py_CLEAR(clear_module_state->__pyx_kp_u_gc);
|
|
jpayne@69
|
4980 Py_CLEAR(clear_module_state->__pyx_n_s_get_encoding);
|
|
jpayne@69
|
4981 Py_CLEAR(clear_module_state->__pyx_n_s_getstate);
|
|
jpayne@69
|
4982 Py_CLEAR(clear_module_state->__pyx_n_u_gff);
|
|
jpayne@69
|
4983 Py_CLEAR(clear_module_state->__pyx_kp_u_gz);
|
|
jpayne@69
|
4984 Py_CLEAR(clear_module_state->__pyx_n_s_import);
|
|
jpayne@69
|
4985 Py_CLEAR(clear_module_state->__pyx_kp_u_incomplete_line_at_s);
|
|
jpayne@69
|
4986 Py_CLEAR(clear_module_state->__pyx_n_s_index);
|
|
jpayne@69
|
4987 Py_CLEAR(clear_module_state->__pyx_kp_u_index_s_not_found);
|
|
jpayne@69
|
4988 Py_CLEAR(clear_module_state->__pyx_n_s_infile);
|
|
jpayne@69
|
4989 Py_CLEAR(clear_module_state->__pyx_n_s_init);
|
|
jpayne@69
|
4990 Py_CLEAR(clear_module_state->__pyx_n_s_init_subclass);
|
|
jpayne@69
|
4991 Py_CLEAR(clear_module_state->__pyx_n_s_initializing);
|
|
jpayne@69
|
4992 Py_CLEAR(clear_module_state->__pyx_kp_u_invalid_file_opening_mode_s);
|
|
jpayne@69
|
4993 Py_CLEAR(clear_module_state->__pyx_n_s_is_coroutine);
|
|
jpayne@69
|
4994 Py_CLEAR(clear_module_state->__pyx_n_s_is_empty);
|
|
jpayne@69
|
4995 Py_CLEAR(clear_module_state->__pyx_n_s_is_open);
|
|
jpayne@69
|
4996 Py_CLEAR(clear_module_state->__pyx_kp_u_isenabled);
|
|
jpayne@69
|
4997 Py_CLEAR(clear_module_state->__pyx_n_s_iter);
|
|
jpayne@69
|
4998 Py_CLEAR(clear_module_state->__pyx_kp_s_iterate_over_infile_Permits_the);
|
|
jpayne@69
|
4999 Py_CLEAR(clear_module_state->__pyx_kp_u_iteration_on_closed_file);
|
|
jpayne@69
|
5000 Py_CLEAR(clear_module_state->__pyx_n_s_itr);
|
|
jpayne@69
|
5001 Py_CLEAR(clear_module_state->__pyx_n_s_keep_original);
|
|
jpayne@69
|
5002 Py_CLEAR(clear_module_state->__pyx_n_s_keys);
|
|
jpayne@69
|
5003 Py_CLEAR(clear_module_state->__pyx_n_s_length);
|
|
jpayne@69
|
5004 Py_CLEAR(clear_module_state->__pyx_n_s_line);
|
|
jpayne@69
|
5005 Py_CLEAR(clear_module_state->__pyx_n_s_line_skip);
|
|
jpayne@69
|
5006 Py_CLEAR(clear_module_state->__pyx_n_s_main);
|
|
jpayne@69
|
5007 Py_CLEAR(clear_module_state->__pyx_n_s_meta_char);
|
|
jpayne@69
|
5008 Py_CLEAR(clear_module_state->__pyx_n_s_metaclass);
|
|
jpayne@69
|
5009 Py_CLEAR(clear_module_state->__pyx_n_s_min_shift);
|
|
jpayne@69
|
5010 Py_CLEAR(clear_module_state->__pyx_n_s_mode);
|
|
jpayne@69
|
5011 Py_CLEAR(clear_module_state->__pyx_n_s_module);
|
|
jpayne@69
|
5012 Py_CLEAR(clear_module_state->__pyx_n_s_multiple_iterators);
|
|
jpayne@69
|
5013 Py_CLEAR(clear_module_state->__pyx_n_s_name);
|
|
jpayne@69
|
5014 Py_CLEAR(clear_module_state->__pyx_n_s_nbytes);
|
|
jpayne@69
|
5015 Py_CLEAR(clear_module_state->__pyx_kp_u_neither_preset_nor_seq_col_start);
|
|
jpayne@69
|
5016 Py_CLEAR(clear_module_state->__pyx_n_s_new);
|
|
jpayne@69
|
5017 Py_CLEAR(clear_module_state->__pyx_n_s_next);
|
|
jpayne@69
|
5018 Py_CLEAR(clear_module_state->__pyx_kp_s_no_default___reduce___due_to_non);
|
|
jpayne@69
|
5019 Py_CLEAR(clear_module_state->__pyx_n_s_open);
|
|
jpayne@69
|
5020 Py_CLEAR(clear_module_state->__pyx_n_s_os);
|
|
jpayne@69
|
5021 Py_CLEAR(clear_module_state->__pyx_kp_u_parse_method_of_s_not_implemente);
|
|
jpayne@69
|
5022 Py_CLEAR(clear_module_state->__pyx_n_s_parser);
|
|
jpayne@69
|
5023 Py_CLEAR(clear_module_state->__pyx_n_s_path);
|
|
jpayne@69
|
5024 Py_CLEAR(clear_module_state->__pyx_n_s_pickle);
|
|
jpayne@69
|
5025 Py_CLEAR(clear_module_state->__pyx_n_s_prepare);
|
|
jpayne@69
|
5026 Py_CLEAR(clear_module_state->__pyx_n_s_preset);
|
|
jpayne@69
|
5027 Py_CLEAR(clear_module_state->__pyx_n_s_preset2conf);
|
|
jpayne@69
|
5028 Py_CLEAR(clear_module_state->__pyx_n_u_psltbl);
|
|
jpayne@69
|
5029 Py_CLEAR(clear_module_state->__pyx_n_s_pysam_libctabix);
|
|
jpayne@69
|
5030 Py_CLEAR(clear_module_state->__pyx_kp_s_pysam_libctabix_pyx);
|
|
jpayne@69
|
5031 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_PickleError);
|
|
jpayne@69
|
5032 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_checksum);
|
|
jpayne@69
|
5033 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_result);
|
|
jpayne@69
|
5034 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_state);
|
|
jpayne@69
|
5035 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_type);
|
|
jpayne@69
|
5036 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_Parser);
|
|
jpayne@69
|
5037 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asBed);
|
|
jpayne@69
|
5038 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asGFF3);
|
|
jpayne@69
|
5039 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asGTF);
|
|
jpayne@69
|
5040 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asTuple);
|
|
jpayne@69
|
5041 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asVCF);
|
|
jpayne@69
|
5042 Py_CLEAR(clear_module_state->__pyx_n_s_pyx_vtable);
|
|
jpayne@69
|
5043 Py_CLEAR(clear_module_state->__pyx_n_s_qualname);
|
|
jpayne@69
|
5044 Py_CLEAR(clear_module_state->__pyx_n_s_r);
|
|
jpayne@69
|
5045 Py_CLEAR(clear_module_state->__pyx_n_u_r);
|
|
jpayne@69
|
5046 Py_CLEAR(clear_module_state->__pyx_n_s_readline);
|
|
jpayne@69
|
5047 Py_CLEAR(clear_module_state->__pyx_n_s_reduce);
|
|
jpayne@69
|
5048 Py_CLEAR(clear_module_state->__pyx_n_s_reduce_cython);
|
|
jpayne@69
|
5049 Py_CLEAR(clear_module_state->__pyx_n_s_reduce_ex);
|
|
jpayne@69
|
5050 Py_CLEAR(clear_module_state->__pyx_n_s_reference);
|
|
jpayne@69
|
5051 Py_CLEAR(clear_module_state->__pyx_n_s_region);
|
|
jpayne@69
|
5052 Py_CLEAR(clear_module_state->__pyx_n_s_retval);
|
|
jpayne@69
|
5053 Py_CLEAR(clear_module_state->__pyx_kp_u_s);
|
|
jpayne@69
|
5054 Py_CLEAR(clear_module_state->__pyx_n_s_s_2);
|
|
jpayne@69
|
5055 Py_CLEAR(clear_module_state->__pyx_kp_u_s_i);
|
|
jpayne@69
|
5056 Py_CLEAR(clear_module_state->__pyx_kp_u_s_i_i);
|
|
jpayne@69
|
5057 Py_CLEAR(clear_module_state->__pyx_n_u_sam);
|
|
jpayne@69
|
5058 Py_CLEAR(clear_module_state->__pyx_n_s_self);
|
|
jpayne@69
|
5059 Py_CLEAR(clear_module_state->__pyx_kp_s_self_gzipfile_self_kstream_canno);
|
|
jpayne@69
|
5060 Py_CLEAR(clear_module_state->__pyx_kp_s_self_iterator_cannot_be_converte);
|
|
jpayne@69
|
5061 Py_CLEAR(clear_module_state->__pyx_n_s_seq_col);
|
|
jpayne@69
|
5062 Py_CLEAR(clear_module_state->__pyx_n_s_set_encoding);
|
|
jpayne@69
|
5063 Py_CLEAR(clear_module_state->__pyx_n_s_set_name);
|
|
jpayne@69
|
5064 Py_CLEAR(clear_module_state->__pyx_n_s_setstate);
|
|
jpayne@69
|
5065 Py_CLEAR(clear_module_state->__pyx_n_s_setstate_cython);
|
|
jpayne@69
|
5066 Py_CLEAR(clear_module_state->__pyx_n_s_spec);
|
|
jpayne@69
|
5067 Py_CLEAR(clear_module_state->__pyx_n_s_start);
|
|
jpayne@69
|
5068 Py_CLEAR(clear_module_state->__pyx_n_s_start_col);
|
|
jpayne@69
|
5069 Py_CLEAR(clear_module_state->__pyx_kp_u_start_i_end_i);
|
|
jpayne@69
|
5070 Py_CLEAR(clear_module_state->__pyx_kp_u_start_out_of_range_i);
|
|
jpayne@69
|
5071 Py_CLEAR(clear_module_state->__pyx_n_s_state);
|
|
jpayne@69
|
5072 Py_CLEAR(clear_module_state->__pyx_kp_s_stringsource);
|
|
jpayne@69
|
5073 Py_CLEAR(clear_module_state->__pyx_n_s_suffix);
|
|
jpayne@69
|
5074 Py_CLEAR(clear_module_state->__pyx_n_s_super);
|
|
jpayne@69
|
5075 Py_CLEAR(clear_module_state->__pyx_n_s_sys);
|
|
jpayne@69
|
5076 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_compress);
|
|
jpayne@69
|
5077 Py_CLEAR(clear_module_state->__pyx_n_u_tabix_compress);
|
|
jpayne@69
|
5078 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_file_iterator);
|
|
jpayne@69
|
5079 Py_CLEAR(clear_module_state->__pyx_n_u_tabix_file_iterator);
|
|
jpayne@69
|
5080 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_file_iterator___reduce_cyt);
|
|
jpayne@69
|
5081 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_file_iterator___setstate_c);
|
|
jpayne@69
|
5082 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator);
|
|
jpayne@69
|
5083 Py_CLEAR(clear_module_state->__pyx_n_u_tabix_generic_iterator);
|
|
jpayne@69
|
5084 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator___init);
|
|
jpayne@69
|
5085 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator___iter);
|
|
jpayne@69
|
5086 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator___next);
|
|
jpayne@69
|
5087 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_index);
|
|
jpayne@69
|
5088 Py_CLEAR(clear_module_state->__pyx_n_u_tabix_index);
|
|
jpayne@69
|
5089 Py_CLEAR(clear_module_state->__pyx_n_s_tabix_iterator);
|
|
jpayne@69
|
5090 Py_CLEAR(clear_module_state->__pyx_n_u_tabix_iterator);
|
|
jpayne@69
|
5091 Py_CLEAR(clear_module_state->__pyx_kp_u_tbi);
|
|
jpayne@69
|
5092 Py_CLEAR(clear_module_state->__pyx_n_s_tell);
|
|
jpayne@69
|
5093 Py_CLEAR(clear_module_state->__pyx_n_s_test);
|
|
jpayne@69
|
5094 Py_CLEAR(clear_module_state->__pyx_n_s_threads);
|
|
jpayne@69
|
5095 Py_CLEAR(clear_module_state->__pyx_kp_u_unknown_preset);
|
|
jpayne@69
|
5096 Py_CLEAR(clear_module_state->__pyx_n_s_unlink);
|
|
jpayne@69
|
5097 Py_CLEAR(clear_module_state->__pyx_n_s_update);
|
|
jpayne@69
|
5098 Py_CLEAR(clear_module_state->__pyx_n_s_use_setstate);
|
|
jpayne@69
|
5099 Py_CLEAR(clear_module_state->__pyx_kp_u_valid_presets_are);
|
|
jpayne@69
|
5100 Py_CLEAR(clear_module_state->__pyx_n_u_vcf);
|
|
jpayne@69
|
5101 Py_CLEAR(clear_module_state->__pyx_kp_u_writing_failed);
|
|
jpayne@69
|
5102 Py_CLEAR(clear_module_state->__pyx_n_s_zerobased);
|
|
jpayne@69
|
5103 Py_CLEAR(clear_module_state->__pyx_int_0);
|
|
jpayne@69
|
5104 Py_CLEAR(clear_module_state->__pyx_int_1);
|
|
jpayne@69
|
5105 Py_CLEAR(clear_module_state->__pyx_int_2);
|
|
jpayne@69
|
5106 Py_CLEAR(clear_module_state->__pyx_int_3);
|
|
jpayne@69
|
5107 Py_CLEAR(clear_module_state->__pyx_int_4);
|
|
jpayne@69
|
5108 Py_CLEAR(clear_module_state->__pyx_int_5);
|
|
jpayne@69
|
5109 Py_CLEAR(clear_module_state->__pyx_int_15);
|
|
jpayne@69
|
5110 Py_CLEAR(clear_module_state->__pyx_int_17);
|
|
jpayne@69
|
5111 Py_CLEAR(clear_module_state->__pyx_int_18);
|
|
jpayne@69
|
5112 Py_CLEAR(clear_module_state->__pyx_int_35);
|
|
jpayne@69
|
5113 Py_CLEAR(clear_module_state->__pyx_int_64);
|
|
jpayne@69
|
5114 Py_CLEAR(clear_module_state->__pyx_int_21667264);
|
|
jpayne@69
|
5115 Py_CLEAR(clear_module_state->__pyx_int_139192863);
|
|
jpayne@69
|
5116 Py_CLEAR(clear_module_state->__pyx_int_243541226);
|
|
jpayne@69
|
5117 Py_CLEAR(clear_module_state->__pyx_int_neg_1);
|
|
jpayne@69
|
5118 Py_CLEAR(clear_module_state->__pyx_codeobj_);
|
|
jpayne@69
|
5119 Py_CLEAR(clear_module_state->__pyx_tuple__19);
|
|
jpayne@69
|
5120 Py_CLEAR(clear_module_state->__pyx_tuple__20);
|
|
jpayne@69
|
5121 Py_CLEAR(clear_module_state->__pyx_tuple__24);
|
|
jpayne@69
|
5122 Py_CLEAR(clear_module_state->__pyx_tuple__38);
|
|
jpayne@69
|
5123 Py_CLEAR(clear_module_state->__pyx_tuple__41);
|
|
jpayne@69
|
5124 Py_CLEAR(clear_module_state->__pyx_tuple__45);
|
|
jpayne@69
|
5125 Py_CLEAR(clear_module_state->__pyx_tuple__55);
|
|
jpayne@69
|
5126 Py_CLEAR(clear_module_state->__pyx_tuple__63);
|
|
jpayne@69
|
5127 Py_CLEAR(clear_module_state->__pyx_tuple__64);
|
|
jpayne@69
|
5128 Py_CLEAR(clear_module_state->__pyx_tuple__65);
|
|
jpayne@69
|
5129 Py_CLEAR(clear_module_state->__pyx_tuple__66);
|
|
jpayne@69
|
5130 Py_CLEAR(clear_module_state->__pyx_tuple__67);
|
|
jpayne@69
|
5131 Py_CLEAR(clear_module_state->__pyx_tuple__68);
|
|
jpayne@69
|
5132 Py_CLEAR(clear_module_state->__pyx_tuple__69);
|
|
jpayne@69
|
5133 Py_CLEAR(clear_module_state->__pyx_tuple__70);
|
|
jpayne@69
|
5134 Py_CLEAR(clear_module_state->__pyx_tuple__71);
|
|
jpayne@69
|
5135 Py_CLEAR(clear_module_state->__pyx_tuple__72);
|
|
jpayne@69
|
5136 Py_CLEAR(clear_module_state->__pyx_tuple__73);
|
|
jpayne@69
|
5137 Py_CLEAR(clear_module_state->__pyx_tuple__74);
|
|
jpayne@69
|
5138 Py_CLEAR(clear_module_state->__pyx_tuple__75);
|
|
jpayne@69
|
5139 Py_CLEAR(clear_module_state->__pyx_tuple__76);
|
|
jpayne@69
|
5140 Py_CLEAR(clear_module_state->__pyx_tuple__77);
|
|
jpayne@69
|
5141 Py_CLEAR(clear_module_state->__pyx_codeobj__2);
|
|
jpayne@69
|
5142 Py_CLEAR(clear_module_state->__pyx_codeobj__3);
|
|
jpayne@69
|
5143 Py_CLEAR(clear_module_state->__pyx_codeobj__4);
|
|
jpayne@69
|
5144 Py_CLEAR(clear_module_state->__pyx_codeobj__5);
|
|
jpayne@69
|
5145 Py_CLEAR(clear_module_state->__pyx_codeobj__6);
|
|
jpayne@69
|
5146 Py_CLEAR(clear_module_state->__pyx_codeobj__7);
|
|
jpayne@69
|
5147 Py_CLEAR(clear_module_state->__pyx_codeobj__8);
|
|
jpayne@69
|
5148 Py_CLEAR(clear_module_state->__pyx_codeobj__9);
|
|
jpayne@69
|
5149 Py_CLEAR(clear_module_state->__pyx_codeobj__10);
|
|
jpayne@69
|
5150 Py_CLEAR(clear_module_state->__pyx_codeobj__11);
|
|
jpayne@69
|
5151 Py_CLEAR(clear_module_state->__pyx_codeobj__12);
|
|
jpayne@69
|
5152 Py_CLEAR(clear_module_state->__pyx_codeobj__13);
|
|
jpayne@69
|
5153 Py_CLEAR(clear_module_state->__pyx_codeobj__14);
|
|
jpayne@69
|
5154 Py_CLEAR(clear_module_state->__pyx_codeobj__15);
|
|
jpayne@69
|
5155 Py_CLEAR(clear_module_state->__pyx_codeobj__17);
|
|
jpayne@69
|
5156 Py_CLEAR(clear_module_state->__pyx_codeobj__18);
|
|
jpayne@69
|
5157 Py_CLEAR(clear_module_state->__pyx_codeobj__21);
|
|
jpayne@69
|
5158 Py_CLEAR(clear_module_state->__pyx_codeobj__22);
|
|
jpayne@69
|
5159 Py_CLEAR(clear_module_state->__pyx_codeobj__23);
|
|
jpayne@69
|
5160 Py_CLEAR(clear_module_state->__pyx_codeobj__25);
|
|
jpayne@69
|
5161 Py_CLEAR(clear_module_state->__pyx_codeobj__26);
|
|
jpayne@69
|
5162 Py_CLEAR(clear_module_state->__pyx_codeobj__27);
|
|
jpayne@69
|
5163 Py_CLEAR(clear_module_state->__pyx_codeobj__28);
|
|
jpayne@69
|
5164 Py_CLEAR(clear_module_state->__pyx_codeobj__29);
|
|
jpayne@69
|
5165 Py_CLEAR(clear_module_state->__pyx_codeobj__30);
|
|
jpayne@69
|
5166 Py_CLEAR(clear_module_state->__pyx_codeobj__31);
|
|
jpayne@69
|
5167 Py_CLEAR(clear_module_state->__pyx_codeobj__32);
|
|
jpayne@69
|
5168 Py_CLEAR(clear_module_state->__pyx_codeobj__33);
|
|
jpayne@69
|
5169 Py_CLEAR(clear_module_state->__pyx_codeobj__34);
|
|
jpayne@69
|
5170 Py_CLEAR(clear_module_state->__pyx_codeobj__35);
|
|
jpayne@69
|
5171 Py_CLEAR(clear_module_state->__pyx_codeobj__36);
|
|
jpayne@69
|
5172 Py_CLEAR(clear_module_state->__pyx_codeobj__37);
|
|
jpayne@69
|
5173 Py_CLEAR(clear_module_state->__pyx_codeobj__40);
|
|
jpayne@69
|
5174 Py_CLEAR(clear_module_state->__pyx_codeobj__46);
|
|
jpayne@69
|
5175 Py_CLEAR(clear_module_state->__pyx_codeobj__47);
|
|
jpayne@69
|
5176 Py_CLEAR(clear_module_state->__pyx_codeobj__48);
|
|
jpayne@69
|
5177 Py_CLEAR(clear_module_state->__pyx_codeobj__49);
|
|
jpayne@69
|
5178 Py_CLEAR(clear_module_state->__pyx_codeobj__50);
|
|
jpayne@69
|
5179 Py_CLEAR(clear_module_state->__pyx_codeobj__51);
|
|
jpayne@69
|
5180 Py_CLEAR(clear_module_state->__pyx_codeobj__52);
|
|
jpayne@69
|
5181 Py_CLEAR(clear_module_state->__pyx_codeobj__53);
|
|
jpayne@69
|
5182 Py_CLEAR(clear_module_state->__pyx_codeobj__54);
|
|
jpayne@69
|
5183 Py_CLEAR(clear_module_state->__pyx_codeobj__57);
|
|
jpayne@69
|
5184 Py_CLEAR(clear_module_state->__pyx_codeobj__58);
|
|
jpayne@69
|
5185 Py_CLEAR(clear_module_state->__pyx_codeobj__59);
|
|
jpayne@69
|
5186 Py_CLEAR(clear_module_state->__pyx_codeobj__60);
|
|
jpayne@69
|
5187 Py_CLEAR(clear_module_state->__pyx_codeobj__61);
|
|
jpayne@69
|
5188 return 0;
|
|
jpayne@69
|
5189 }
|
|
jpayne@69
|
5190 #endif
|
|
jpayne@69
|
5191 /* #### Code section: module_state_traverse ### */
|
|
jpayne@69
|
5192 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5193 static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) {
|
|
jpayne@69
|
5194 __pyx_mstate *traverse_module_state = __pyx_mstate(m);
|
|
jpayne@69
|
5195 if (!traverse_module_state) return 0;
|
|
jpayne@69
|
5196 Py_VISIT(traverse_module_state->__pyx_d);
|
|
jpayne@69
|
5197 Py_VISIT(traverse_module_state->__pyx_b);
|
|
jpayne@69
|
5198 Py_VISIT(traverse_module_state->__pyx_cython_runtime);
|
|
jpayne@69
|
5199 Py_VISIT(traverse_module_state->__pyx_empty_tuple);
|
|
jpayne@69
|
5200 Py_VISIT(traverse_module_state->__pyx_empty_bytes);
|
|
jpayne@69
|
5201 Py_VISIT(traverse_module_state->__pyx_empty_unicode);
|
|
jpayne@69
|
5202 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
5203 Py_VISIT(traverse_module_state->__pyx_CyFunctionType);
|
|
jpayne@69
|
5204 #endif
|
|
jpayne@69
|
5205 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
5206 Py_VISIT(traverse_module_state->__pyx_FusedFunctionType);
|
|
jpayne@69
|
5207 #endif
|
|
jpayne@69
|
5208 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile);
|
|
jpayne@69
|
5209 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4type_type);
|
|
jpayne@69
|
5210 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4bool_bool);
|
|
jpayne@69
|
5211 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_7complex_complex);
|
|
jpayne@69
|
5212 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy);
|
|
jpayne@69
|
5213 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator);
|
|
jpayne@69
|
5214 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy);
|
|
jpayne@69
|
5215 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy);
|
|
jpayne@69
|
5216 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy);
|
|
jpayne@69
|
5217 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_BedProxy);
|
|
jpayne@69
|
5218 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy);
|
|
jpayne@69
|
5219 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_5array_array);
|
|
jpayne@69
|
5220 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator);
|
|
jpayne@69
|
5221 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_tabix_file_iterator);
|
|
jpayne@69
|
5222 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
5223 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
5224 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_Parser);
|
|
jpayne@69
|
5225 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_Parser);
|
|
jpayne@69
|
5226 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asTuple);
|
|
jpayne@69
|
5227 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asTuple);
|
|
jpayne@69
|
5228 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asGTF);
|
|
jpayne@69
|
5229 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asGTF);
|
|
jpayne@69
|
5230 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asGFF3);
|
|
jpayne@69
|
5231 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asGFF3);
|
|
jpayne@69
|
5232 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asBed);
|
|
jpayne@69
|
5233 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asBed);
|
|
jpayne@69
|
5234 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asVCF);
|
|
jpayne@69
|
5235 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asVCF);
|
|
jpayne@69
|
5236 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixIterator);
|
|
jpayne@69
|
5237 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_TabixIterator);
|
|
jpayne@69
|
5238 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed);
|
|
jpayne@69
|
5239 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_TabixIteratorParsed);
|
|
jpayne@69
|
5240 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIterator);
|
|
jpayne@69
|
5241 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_GZIterator);
|
|
jpayne@69
|
5242 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorHead);
|
|
jpayne@69
|
5243 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_GZIteratorHead);
|
|
jpayne@69
|
5244 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed);
|
|
jpayne@69
|
5245 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_GZIteratorParsed);
|
|
jpayne@69
|
5246 Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_Tabixfile);
|
|
jpayne@69
|
5247 Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_Tabixfile);
|
|
jpayne@69
|
5248 Py_VISIT(traverse_module_state->__pyx_n_s_AssertionError);
|
|
jpayne@69
|
5249 Py_VISIT(traverse_module_state->__pyx_kp_u_Could_not_open_file);
|
|
jpayne@69
|
5250 Py_VISIT(traverse_module_state->__pyx_n_s_EmptyIterator);
|
|
jpayne@69
|
5251 Py_VISIT(traverse_module_state->__pyx_n_s_EmptyIterator___iter);
|
|
jpayne@69
|
5252 Py_VISIT(traverse_module_state->__pyx_n_s_EmptyIterator___next);
|
|
jpayne@69
|
5253 Py_VISIT(traverse_module_state->__pyx_kp_u_Filename_s_already_exists_use_fo);
|
|
jpayne@69
|
5254 Py_VISIT(traverse_module_state->__pyx_n_s_GZIterator);
|
|
jpayne@69
|
5255 Py_VISIT(traverse_module_state->__pyx_n_u_GZIterator);
|
|
jpayne@69
|
5256 Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorHead);
|
|
jpayne@69
|
5257 Py_VISIT(traverse_module_state->__pyx_n_u_GZIteratorHead);
|
|
jpayne@69
|
5258 Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorHead___reduce_cython);
|
|
jpayne@69
|
5259 Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorHead___setstate_cython);
|
|
jpayne@69
|
5260 Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorParsed);
|
|
jpayne@69
|
5261 Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorParsed___reduce_cython);
|
|
jpayne@69
|
5262 Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorParsed___setstate_cyth);
|
|
jpayne@69
|
5263 Py_VISIT(traverse_module_state->__pyx_n_s_GZIterator___reduce_cython);
|
|
jpayne@69
|
5264 Py_VISIT(traverse_module_state->__pyx_n_s_GZIterator___setstate_cython);
|
|
jpayne@69
|
5265 Py_VISIT(traverse_module_state->__pyx_n_s_IOError);
|
|
jpayne@69
|
5266 Py_VISIT(traverse_module_state->__pyx_kp_u_I_O_operation_on_closed_file);
|
|
jpayne@69
|
5267 Py_VISIT(traverse_module_state->__pyx_kp_u_I_O_operation_on_closed_file_2);
|
|
jpayne@69
|
5268 Py_VISIT(traverse_module_state->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0);
|
|
jpayne@69
|
5269 Py_VISIT(traverse_module_state->__pyx_n_s_KeyError);
|
|
jpayne@69
|
5270 Py_VISIT(traverse_module_state->__pyx_n_s_MemoryError);
|
|
jpayne@69
|
5271 Py_VISIT(traverse_module_state->__pyx_kp_u_No_such_file_or_directory_s);
|
|
jpayne@69
|
5272 Py_VISIT(traverse_module_state->__pyx_n_s_NotImplementedError);
|
|
jpayne@69
|
5273 Py_VISIT(traverse_module_state->__pyx_n_s_OSError);
|
|
jpayne@69
|
5274 Py_VISIT(traverse_module_state->__pyx_n_s_O_RDONLY);
|
|
jpayne@69
|
5275 Py_VISIT(traverse_module_state->__pyx_n_s_Parser);
|
|
jpayne@69
|
5276 Py_VISIT(traverse_module_state->__pyx_n_s_Parser___reduce_cython);
|
|
jpayne@69
|
5277 Py_VISIT(traverse_module_state->__pyx_n_s_Parser___setstate_cython);
|
|
jpayne@69
|
5278 Py_VISIT(traverse_module_state->__pyx_n_s_Parser_get_encoding);
|
|
jpayne@69
|
5279 Py_VISIT(traverse_module_state->__pyx_n_s_Parser_set_encoding);
|
|
jpayne@69
|
5280 Py_VISIT(traverse_module_state->__pyx_n_s_PickleError);
|
|
jpayne@69
|
5281 Py_VISIT(traverse_module_state->__pyx_n_s_StopIteration);
|
|
jpayne@69
|
5282 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile);
|
|
jpayne@69
|
5283 Py_VISIT(traverse_module_state->__pyx_n_u_TabixFile);
|
|
jpayne@69
|
5284 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile___reduce_cython);
|
|
jpayne@69
|
5285 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile___setstate_cython);
|
|
jpayne@69
|
5286 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile__dup);
|
|
jpayne@69
|
5287 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile__open);
|
|
jpayne@69
|
5288 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile_close);
|
|
jpayne@69
|
5289 Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile_fetch);
|
|
jpayne@69
|
5290 Py_VISIT(traverse_module_state->__pyx_n_s_TabixIterator);
|
|
jpayne@69
|
5291 Py_VISIT(traverse_module_state->__pyx_n_s_TabixIteratorParsed);
|
|
jpayne@69
|
5292 Py_VISIT(traverse_module_state->__pyx_n_s_TabixIteratorParsed___reduce_cyt);
|
|
jpayne@69
|
5293 Py_VISIT(traverse_module_state->__pyx_n_s_TabixIteratorParsed___setstate_c);
|
|
jpayne@69
|
5294 Py_VISIT(traverse_module_state->__pyx_n_s_TabixIterator___reduce_cython);
|
|
jpayne@69
|
5295 Py_VISIT(traverse_module_state->__pyx_n_s_TabixIterator___setstate_cython);
|
|
jpayne@69
|
5296 Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile);
|
|
jpayne@69
|
5297 Py_VISIT(traverse_module_state->__pyx_n_u_Tabixfile);
|
|
jpayne@69
|
5298 Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile___reduce_cython);
|
|
jpayne@69
|
5299 Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile___setstate_cython);
|
|
jpayne@69
|
5300 Py_VISIT(traverse_module_state->__pyx_n_s_TypeError);
|
|
jpayne@69
|
5301 Py_VISIT(traverse_module_state->__pyx_n_s_ValueError);
|
|
jpayne@69
|
5302 Py_VISIT(traverse_module_state->__pyx_n_s_WINDOW_SIZE);
|
|
jpayne@69
|
5303 Py_VISIT(traverse_module_state->__pyx_kp_b__16);
|
|
jpayne@69
|
5304 Py_VISIT(traverse_module_state->__pyx_kp_u__39);
|
|
jpayne@69
|
5305 Py_VISIT(traverse_module_state->__pyx_kp_u__42);
|
|
jpayne@69
|
5306 Py_VISIT(traverse_module_state->__pyx_kp_u__43);
|
|
jpayne@69
|
5307 Py_VISIT(traverse_module_state->__pyx_kp_u__44);
|
|
jpayne@69
|
5308 Py_VISIT(traverse_module_state->__pyx_kp_u__56);
|
|
jpayne@69
|
5309 Py_VISIT(traverse_module_state->__pyx_n_s__62);
|
|
jpayne@69
|
5310 Py_VISIT(traverse_module_state->__pyx_n_s__78);
|
|
jpayne@69
|
5311 Py_VISIT(traverse_module_state->__pyx_n_s_a);
|
|
jpayne@69
|
5312 Py_VISIT(traverse_module_state->__pyx_n_s_all);
|
|
jpayne@69
|
5313 Py_VISIT(traverse_module_state->__pyx_n_s_asBed);
|
|
jpayne@69
|
5314 Py_VISIT(traverse_module_state->__pyx_n_u_asBed);
|
|
jpayne@69
|
5315 Py_VISIT(traverse_module_state->__pyx_n_s_asBed___reduce_cython);
|
|
jpayne@69
|
5316 Py_VISIT(traverse_module_state->__pyx_n_s_asBed___setstate_cython);
|
|
jpayne@69
|
5317 Py_VISIT(traverse_module_state->__pyx_n_s_asGFF3);
|
|
jpayne@69
|
5318 Py_VISIT(traverse_module_state->__pyx_n_u_asGFF3);
|
|
jpayne@69
|
5319 Py_VISIT(traverse_module_state->__pyx_n_s_asGFF3___reduce_cython);
|
|
jpayne@69
|
5320 Py_VISIT(traverse_module_state->__pyx_n_s_asGFF3___setstate_cython);
|
|
jpayne@69
|
5321 Py_VISIT(traverse_module_state->__pyx_n_s_asGTF);
|
|
jpayne@69
|
5322 Py_VISIT(traverse_module_state->__pyx_n_u_asGTF);
|
|
jpayne@69
|
5323 Py_VISIT(traverse_module_state->__pyx_n_s_asGTF___reduce_cython);
|
|
jpayne@69
|
5324 Py_VISIT(traverse_module_state->__pyx_n_s_asGTF___setstate_cython);
|
|
jpayne@69
|
5325 Py_VISIT(traverse_module_state->__pyx_n_s_asTuple);
|
|
jpayne@69
|
5326 Py_VISIT(traverse_module_state->__pyx_n_u_asTuple);
|
|
jpayne@69
|
5327 Py_VISIT(traverse_module_state->__pyx_n_s_asTuple___reduce_cython);
|
|
jpayne@69
|
5328 Py_VISIT(traverse_module_state->__pyx_n_s_asTuple___setstate_cython);
|
|
jpayne@69
|
5329 Py_VISIT(traverse_module_state->__pyx_n_s_asVCF);
|
|
jpayne@69
|
5330 Py_VISIT(traverse_module_state->__pyx_n_u_asVCF);
|
|
jpayne@69
|
5331 Py_VISIT(traverse_module_state->__pyx_n_s_asVCF___reduce_cython);
|
|
jpayne@69
|
5332 Py_VISIT(traverse_module_state->__pyx_n_s_asVCF___setstate_cython);
|
|
jpayne@69
|
5333 Py_VISIT(traverse_module_state->__pyx_n_u_ascii);
|
|
jpayne@69
|
5334 Py_VISIT(traverse_module_state->__pyx_n_s_asyncio_coroutines);
|
|
jpayne@69
|
5335 Py_VISIT(traverse_module_state->__pyx_n_s_b);
|
|
jpayne@69
|
5336 Py_VISIT(traverse_module_state->__pyx_n_u_bcf);
|
|
jpayne@69
|
5337 Py_VISIT(traverse_module_state->__pyx_n_u_bed);
|
|
jpayne@69
|
5338 Py_VISIT(traverse_module_state->__pyx_n_s_buffer);
|
|
jpayne@69
|
5339 Py_VISIT(traverse_module_state->__pyx_n_s_buffer_size);
|
|
jpayne@69
|
5340 Py_VISIT(traverse_module_state->__pyx_kp_u_building_of_index_for_failed);
|
|
jpayne@69
|
5341 Py_VISIT(traverse_module_state->__pyx_n_s_bytes_cpy);
|
|
jpayne@69
|
5342 Py_VISIT(traverse_module_state->__pyx_n_s_c);
|
|
jpayne@69
|
5343 Py_VISIT(traverse_module_state->__pyx_n_s_cfilename);
|
|
jpayne@69
|
5344 Py_VISIT(traverse_module_state->__pyx_n_s_cfilename_index);
|
|
jpayne@69
|
5345 Py_VISIT(traverse_module_state->__pyx_n_s_cfn);
|
|
jpayne@69
|
5346 Py_VISIT(traverse_module_state->__pyx_n_s_cline_in_traceback);
|
|
jpayne@69
|
5347 Py_VISIT(traverse_module_state->__pyx_n_s_close);
|
|
jpayne@69
|
5348 Py_VISIT(traverse_module_state->__pyx_n_s_closed);
|
|
jpayne@69
|
5349 Py_VISIT(traverse_module_state->__pyx_n_s_conf);
|
|
jpayne@69
|
5350 Py_VISIT(traverse_module_state->__pyx_n_s_conf_data);
|
|
jpayne@69
|
5351 Py_VISIT(traverse_module_state->__pyx_n_s_contigs);
|
|
jpayne@69
|
5352 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_create_iterator_for_re);
|
|
jpayne@69
|
5353 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_create_iterator_possib);
|
|
jpayne@69
|
5354 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_load_tbi_csi_index_of);
|
|
jpayne@69
|
5355 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_file_s);
|
|
jpayne@69
|
5356 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_for_reading_heade);
|
|
jpayne@69
|
5357 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_index_for_s);
|
|
jpayne@69
|
5358 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_s_for_reading);
|
|
jpayne@69
|
5359 Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_s_for_writing);
|
|
jpayne@69
|
5360 Py_VISIT(traverse_module_state->__pyx_n_s_cpy);
|
|
jpayne@69
|
5361 Py_VISIT(traverse_module_state->__pyx_n_s_csi);
|
|
jpayne@69
|
5362 Py_VISIT(traverse_module_state->__pyx_kp_u_csi_2);
|
|
jpayne@69
|
5363 Py_VISIT(traverse_module_state->__pyx_n_s_cstr);
|
|
jpayne@69
|
5364 Py_VISIT(traverse_module_state->__pyx_n_s_dict);
|
|
jpayne@69
|
5365 Py_VISIT(traverse_module_state->__pyx_n_s_dict_2);
|
|
jpayne@69
|
5366 Py_VISIT(traverse_module_state->__pyx_kp_u_disable);
|
|
jpayne@69
|
5367 Py_VISIT(traverse_module_state->__pyx_n_s_doc);
|
|
jpayne@69
|
5368 Py_VISIT(traverse_module_state->__pyx_n_s_dup);
|
|
jpayne@69
|
5369 Py_VISIT(traverse_module_state->__pyx_kp_s_empty_iterator);
|
|
jpayne@69
|
5370 Py_VISIT(traverse_module_state->__pyx_kp_u_enable);
|
|
jpayne@69
|
5371 Py_VISIT(traverse_module_state->__pyx_n_s_encoding);
|
|
jpayne@69
|
5372 Py_VISIT(traverse_module_state->__pyx_n_s_end);
|
|
jpayne@69
|
5373 Py_VISIT(traverse_module_state->__pyx_n_s_end_col);
|
|
jpayne@69
|
5374 Py_VISIT(traverse_module_state->__pyx_kp_u_end_out_of_range_i);
|
|
jpayne@69
|
5375 Py_VISIT(traverse_module_state->__pyx_kp_u_error_i_when_closing_file_s);
|
|
jpayne@69
|
5376 Py_VISIT(traverse_module_state->__pyx_kp_u_error_i_when_writing_to_file_s);
|
|
jpayne@69
|
5377 Py_VISIT(traverse_module_state->__pyx_n_s_exists);
|
|
jpayne@69
|
5378 Py_VISIT(traverse_module_state->__pyx_n_s_fd_src);
|
|
jpayne@69
|
5379 Py_VISIT(traverse_module_state->__pyx_n_s_fetch);
|
|
jpayne@69
|
5380 Py_VISIT(traverse_module_state->__pyx_kp_u_file_s_not_found);
|
|
jpayne@69
|
5381 Py_VISIT(traverse_module_state->__pyx_n_s_filename);
|
|
jpayne@69
|
5382 Py_VISIT(traverse_module_state->__pyx_n_s_filename_in);
|
|
jpayne@69
|
5383 Py_VISIT(traverse_module_state->__pyx_n_s_filename_index);
|
|
jpayne@69
|
5384 Py_VISIT(traverse_module_state->__pyx_n_s_filename_out);
|
|
jpayne@69
|
5385 Py_VISIT(traverse_module_state->__pyx_kp_u_filename_s_already_exists_use_fo);
|
|
jpayne@69
|
5386 Py_VISIT(traverse_module_state->__pyx_n_s_fileobj);
|
|
jpayne@69
|
5387 Py_VISIT(traverse_module_state->__pyx_n_s_fmt);
|
|
jpayne@69
|
5388 Py_VISIT(traverse_module_state->__pyx_n_s_fn);
|
|
jpayne@69
|
5389 Py_VISIT(traverse_module_state->__pyx_n_s_fn_index);
|
|
jpayne@69
|
5390 Py_VISIT(traverse_module_state->__pyx_n_s_fnidx);
|
|
jpayne@69
|
5391 Py_VISIT(traverse_module_state->__pyx_n_s_force);
|
|
jpayne@69
|
5392 Py_VISIT(traverse_module_state->__pyx_n_s_format);
|
|
jpayne@69
|
5393 Py_VISIT(traverse_module_state->__pyx_n_s_fp);
|
|
jpayne@69
|
5394 Py_VISIT(traverse_module_state->__pyx_kp_u_gc);
|
|
jpayne@69
|
5395 Py_VISIT(traverse_module_state->__pyx_n_s_get_encoding);
|
|
jpayne@69
|
5396 Py_VISIT(traverse_module_state->__pyx_n_s_getstate);
|
|
jpayne@69
|
5397 Py_VISIT(traverse_module_state->__pyx_n_u_gff);
|
|
jpayne@69
|
5398 Py_VISIT(traverse_module_state->__pyx_kp_u_gz);
|
|
jpayne@69
|
5399 Py_VISIT(traverse_module_state->__pyx_n_s_import);
|
|
jpayne@69
|
5400 Py_VISIT(traverse_module_state->__pyx_kp_u_incomplete_line_at_s);
|
|
jpayne@69
|
5401 Py_VISIT(traverse_module_state->__pyx_n_s_index);
|
|
jpayne@69
|
5402 Py_VISIT(traverse_module_state->__pyx_kp_u_index_s_not_found);
|
|
jpayne@69
|
5403 Py_VISIT(traverse_module_state->__pyx_n_s_infile);
|
|
jpayne@69
|
5404 Py_VISIT(traverse_module_state->__pyx_n_s_init);
|
|
jpayne@69
|
5405 Py_VISIT(traverse_module_state->__pyx_n_s_init_subclass);
|
|
jpayne@69
|
5406 Py_VISIT(traverse_module_state->__pyx_n_s_initializing);
|
|
jpayne@69
|
5407 Py_VISIT(traverse_module_state->__pyx_kp_u_invalid_file_opening_mode_s);
|
|
jpayne@69
|
5408 Py_VISIT(traverse_module_state->__pyx_n_s_is_coroutine);
|
|
jpayne@69
|
5409 Py_VISIT(traverse_module_state->__pyx_n_s_is_empty);
|
|
jpayne@69
|
5410 Py_VISIT(traverse_module_state->__pyx_n_s_is_open);
|
|
jpayne@69
|
5411 Py_VISIT(traverse_module_state->__pyx_kp_u_isenabled);
|
|
jpayne@69
|
5412 Py_VISIT(traverse_module_state->__pyx_n_s_iter);
|
|
jpayne@69
|
5413 Py_VISIT(traverse_module_state->__pyx_kp_s_iterate_over_infile_Permits_the);
|
|
jpayne@69
|
5414 Py_VISIT(traverse_module_state->__pyx_kp_u_iteration_on_closed_file);
|
|
jpayne@69
|
5415 Py_VISIT(traverse_module_state->__pyx_n_s_itr);
|
|
jpayne@69
|
5416 Py_VISIT(traverse_module_state->__pyx_n_s_keep_original);
|
|
jpayne@69
|
5417 Py_VISIT(traverse_module_state->__pyx_n_s_keys);
|
|
jpayne@69
|
5418 Py_VISIT(traverse_module_state->__pyx_n_s_length);
|
|
jpayne@69
|
5419 Py_VISIT(traverse_module_state->__pyx_n_s_line);
|
|
jpayne@69
|
5420 Py_VISIT(traverse_module_state->__pyx_n_s_line_skip);
|
|
jpayne@69
|
5421 Py_VISIT(traverse_module_state->__pyx_n_s_main);
|
|
jpayne@69
|
5422 Py_VISIT(traverse_module_state->__pyx_n_s_meta_char);
|
|
jpayne@69
|
5423 Py_VISIT(traverse_module_state->__pyx_n_s_metaclass);
|
|
jpayne@69
|
5424 Py_VISIT(traverse_module_state->__pyx_n_s_min_shift);
|
|
jpayne@69
|
5425 Py_VISIT(traverse_module_state->__pyx_n_s_mode);
|
|
jpayne@69
|
5426 Py_VISIT(traverse_module_state->__pyx_n_s_module);
|
|
jpayne@69
|
5427 Py_VISIT(traverse_module_state->__pyx_n_s_multiple_iterators);
|
|
jpayne@69
|
5428 Py_VISIT(traverse_module_state->__pyx_n_s_name);
|
|
jpayne@69
|
5429 Py_VISIT(traverse_module_state->__pyx_n_s_nbytes);
|
|
jpayne@69
|
5430 Py_VISIT(traverse_module_state->__pyx_kp_u_neither_preset_nor_seq_col_start);
|
|
jpayne@69
|
5431 Py_VISIT(traverse_module_state->__pyx_n_s_new);
|
|
jpayne@69
|
5432 Py_VISIT(traverse_module_state->__pyx_n_s_next);
|
|
jpayne@69
|
5433 Py_VISIT(traverse_module_state->__pyx_kp_s_no_default___reduce___due_to_non);
|
|
jpayne@69
|
5434 Py_VISIT(traverse_module_state->__pyx_n_s_open);
|
|
jpayne@69
|
5435 Py_VISIT(traverse_module_state->__pyx_n_s_os);
|
|
jpayne@69
|
5436 Py_VISIT(traverse_module_state->__pyx_kp_u_parse_method_of_s_not_implemente);
|
|
jpayne@69
|
5437 Py_VISIT(traverse_module_state->__pyx_n_s_parser);
|
|
jpayne@69
|
5438 Py_VISIT(traverse_module_state->__pyx_n_s_path);
|
|
jpayne@69
|
5439 Py_VISIT(traverse_module_state->__pyx_n_s_pickle);
|
|
jpayne@69
|
5440 Py_VISIT(traverse_module_state->__pyx_n_s_prepare);
|
|
jpayne@69
|
5441 Py_VISIT(traverse_module_state->__pyx_n_s_preset);
|
|
jpayne@69
|
5442 Py_VISIT(traverse_module_state->__pyx_n_s_preset2conf);
|
|
jpayne@69
|
5443 Py_VISIT(traverse_module_state->__pyx_n_u_psltbl);
|
|
jpayne@69
|
5444 Py_VISIT(traverse_module_state->__pyx_n_s_pysam_libctabix);
|
|
jpayne@69
|
5445 Py_VISIT(traverse_module_state->__pyx_kp_s_pysam_libctabix_pyx);
|
|
jpayne@69
|
5446 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_PickleError);
|
|
jpayne@69
|
5447 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_checksum);
|
|
jpayne@69
|
5448 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_result);
|
|
jpayne@69
|
5449 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_state);
|
|
jpayne@69
|
5450 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_type);
|
|
jpayne@69
|
5451 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_Parser);
|
|
jpayne@69
|
5452 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asBed);
|
|
jpayne@69
|
5453 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asGFF3);
|
|
jpayne@69
|
5454 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asGTF);
|
|
jpayne@69
|
5455 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asTuple);
|
|
jpayne@69
|
5456 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asVCF);
|
|
jpayne@69
|
5457 Py_VISIT(traverse_module_state->__pyx_n_s_pyx_vtable);
|
|
jpayne@69
|
5458 Py_VISIT(traverse_module_state->__pyx_n_s_qualname);
|
|
jpayne@69
|
5459 Py_VISIT(traverse_module_state->__pyx_n_s_r);
|
|
jpayne@69
|
5460 Py_VISIT(traverse_module_state->__pyx_n_u_r);
|
|
jpayne@69
|
5461 Py_VISIT(traverse_module_state->__pyx_n_s_readline);
|
|
jpayne@69
|
5462 Py_VISIT(traverse_module_state->__pyx_n_s_reduce);
|
|
jpayne@69
|
5463 Py_VISIT(traverse_module_state->__pyx_n_s_reduce_cython);
|
|
jpayne@69
|
5464 Py_VISIT(traverse_module_state->__pyx_n_s_reduce_ex);
|
|
jpayne@69
|
5465 Py_VISIT(traverse_module_state->__pyx_n_s_reference);
|
|
jpayne@69
|
5466 Py_VISIT(traverse_module_state->__pyx_n_s_region);
|
|
jpayne@69
|
5467 Py_VISIT(traverse_module_state->__pyx_n_s_retval);
|
|
jpayne@69
|
5468 Py_VISIT(traverse_module_state->__pyx_kp_u_s);
|
|
jpayne@69
|
5469 Py_VISIT(traverse_module_state->__pyx_n_s_s_2);
|
|
jpayne@69
|
5470 Py_VISIT(traverse_module_state->__pyx_kp_u_s_i);
|
|
jpayne@69
|
5471 Py_VISIT(traverse_module_state->__pyx_kp_u_s_i_i);
|
|
jpayne@69
|
5472 Py_VISIT(traverse_module_state->__pyx_n_u_sam);
|
|
jpayne@69
|
5473 Py_VISIT(traverse_module_state->__pyx_n_s_self);
|
|
jpayne@69
|
5474 Py_VISIT(traverse_module_state->__pyx_kp_s_self_gzipfile_self_kstream_canno);
|
|
jpayne@69
|
5475 Py_VISIT(traverse_module_state->__pyx_kp_s_self_iterator_cannot_be_converte);
|
|
jpayne@69
|
5476 Py_VISIT(traverse_module_state->__pyx_n_s_seq_col);
|
|
jpayne@69
|
5477 Py_VISIT(traverse_module_state->__pyx_n_s_set_encoding);
|
|
jpayne@69
|
5478 Py_VISIT(traverse_module_state->__pyx_n_s_set_name);
|
|
jpayne@69
|
5479 Py_VISIT(traverse_module_state->__pyx_n_s_setstate);
|
|
jpayne@69
|
5480 Py_VISIT(traverse_module_state->__pyx_n_s_setstate_cython);
|
|
jpayne@69
|
5481 Py_VISIT(traverse_module_state->__pyx_n_s_spec);
|
|
jpayne@69
|
5482 Py_VISIT(traverse_module_state->__pyx_n_s_start);
|
|
jpayne@69
|
5483 Py_VISIT(traverse_module_state->__pyx_n_s_start_col);
|
|
jpayne@69
|
5484 Py_VISIT(traverse_module_state->__pyx_kp_u_start_i_end_i);
|
|
jpayne@69
|
5485 Py_VISIT(traverse_module_state->__pyx_kp_u_start_out_of_range_i);
|
|
jpayne@69
|
5486 Py_VISIT(traverse_module_state->__pyx_n_s_state);
|
|
jpayne@69
|
5487 Py_VISIT(traverse_module_state->__pyx_kp_s_stringsource);
|
|
jpayne@69
|
5488 Py_VISIT(traverse_module_state->__pyx_n_s_suffix);
|
|
jpayne@69
|
5489 Py_VISIT(traverse_module_state->__pyx_n_s_super);
|
|
jpayne@69
|
5490 Py_VISIT(traverse_module_state->__pyx_n_s_sys);
|
|
jpayne@69
|
5491 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_compress);
|
|
jpayne@69
|
5492 Py_VISIT(traverse_module_state->__pyx_n_u_tabix_compress);
|
|
jpayne@69
|
5493 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_file_iterator);
|
|
jpayne@69
|
5494 Py_VISIT(traverse_module_state->__pyx_n_u_tabix_file_iterator);
|
|
jpayne@69
|
5495 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_file_iterator___reduce_cyt);
|
|
jpayne@69
|
5496 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_file_iterator___setstate_c);
|
|
jpayne@69
|
5497 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator);
|
|
jpayne@69
|
5498 Py_VISIT(traverse_module_state->__pyx_n_u_tabix_generic_iterator);
|
|
jpayne@69
|
5499 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator___init);
|
|
jpayne@69
|
5500 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator___iter);
|
|
jpayne@69
|
5501 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator___next);
|
|
jpayne@69
|
5502 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_index);
|
|
jpayne@69
|
5503 Py_VISIT(traverse_module_state->__pyx_n_u_tabix_index);
|
|
jpayne@69
|
5504 Py_VISIT(traverse_module_state->__pyx_n_s_tabix_iterator);
|
|
jpayne@69
|
5505 Py_VISIT(traverse_module_state->__pyx_n_u_tabix_iterator);
|
|
jpayne@69
|
5506 Py_VISIT(traverse_module_state->__pyx_kp_u_tbi);
|
|
jpayne@69
|
5507 Py_VISIT(traverse_module_state->__pyx_n_s_tell);
|
|
jpayne@69
|
5508 Py_VISIT(traverse_module_state->__pyx_n_s_test);
|
|
jpayne@69
|
5509 Py_VISIT(traverse_module_state->__pyx_n_s_threads);
|
|
jpayne@69
|
5510 Py_VISIT(traverse_module_state->__pyx_kp_u_unknown_preset);
|
|
jpayne@69
|
5511 Py_VISIT(traverse_module_state->__pyx_n_s_unlink);
|
|
jpayne@69
|
5512 Py_VISIT(traverse_module_state->__pyx_n_s_update);
|
|
jpayne@69
|
5513 Py_VISIT(traverse_module_state->__pyx_n_s_use_setstate);
|
|
jpayne@69
|
5514 Py_VISIT(traverse_module_state->__pyx_kp_u_valid_presets_are);
|
|
jpayne@69
|
5515 Py_VISIT(traverse_module_state->__pyx_n_u_vcf);
|
|
jpayne@69
|
5516 Py_VISIT(traverse_module_state->__pyx_kp_u_writing_failed);
|
|
jpayne@69
|
5517 Py_VISIT(traverse_module_state->__pyx_n_s_zerobased);
|
|
jpayne@69
|
5518 Py_VISIT(traverse_module_state->__pyx_int_0);
|
|
jpayne@69
|
5519 Py_VISIT(traverse_module_state->__pyx_int_1);
|
|
jpayne@69
|
5520 Py_VISIT(traverse_module_state->__pyx_int_2);
|
|
jpayne@69
|
5521 Py_VISIT(traverse_module_state->__pyx_int_3);
|
|
jpayne@69
|
5522 Py_VISIT(traverse_module_state->__pyx_int_4);
|
|
jpayne@69
|
5523 Py_VISIT(traverse_module_state->__pyx_int_5);
|
|
jpayne@69
|
5524 Py_VISIT(traverse_module_state->__pyx_int_15);
|
|
jpayne@69
|
5525 Py_VISIT(traverse_module_state->__pyx_int_17);
|
|
jpayne@69
|
5526 Py_VISIT(traverse_module_state->__pyx_int_18);
|
|
jpayne@69
|
5527 Py_VISIT(traverse_module_state->__pyx_int_35);
|
|
jpayne@69
|
5528 Py_VISIT(traverse_module_state->__pyx_int_64);
|
|
jpayne@69
|
5529 Py_VISIT(traverse_module_state->__pyx_int_21667264);
|
|
jpayne@69
|
5530 Py_VISIT(traverse_module_state->__pyx_int_139192863);
|
|
jpayne@69
|
5531 Py_VISIT(traverse_module_state->__pyx_int_243541226);
|
|
jpayne@69
|
5532 Py_VISIT(traverse_module_state->__pyx_int_neg_1);
|
|
jpayne@69
|
5533 Py_VISIT(traverse_module_state->__pyx_codeobj_);
|
|
jpayne@69
|
5534 Py_VISIT(traverse_module_state->__pyx_tuple__19);
|
|
jpayne@69
|
5535 Py_VISIT(traverse_module_state->__pyx_tuple__20);
|
|
jpayne@69
|
5536 Py_VISIT(traverse_module_state->__pyx_tuple__24);
|
|
jpayne@69
|
5537 Py_VISIT(traverse_module_state->__pyx_tuple__38);
|
|
jpayne@69
|
5538 Py_VISIT(traverse_module_state->__pyx_tuple__41);
|
|
jpayne@69
|
5539 Py_VISIT(traverse_module_state->__pyx_tuple__45);
|
|
jpayne@69
|
5540 Py_VISIT(traverse_module_state->__pyx_tuple__55);
|
|
jpayne@69
|
5541 Py_VISIT(traverse_module_state->__pyx_tuple__63);
|
|
jpayne@69
|
5542 Py_VISIT(traverse_module_state->__pyx_tuple__64);
|
|
jpayne@69
|
5543 Py_VISIT(traverse_module_state->__pyx_tuple__65);
|
|
jpayne@69
|
5544 Py_VISIT(traverse_module_state->__pyx_tuple__66);
|
|
jpayne@69
|
5545 Py_VISIT(traverse_module_state->__pyx_tuple__67);
|
|
jpayne@69
|
5546 Py_VISIT(traverse_module_state->__pyx_tuple__68);
|
|
jpayne@69
|
5547 Py_VISIT(traverse_module_state->__pyx_tuple__69);
|
|
jpayne@69
|
5548 Py_VISIT(traverse_module_state->__pyx_tuple__70);
|
|
jpayne@69
|
5549 Py_VISIT(traverse_module_state->__pyx_tuple__71);
|
|
jpayne@69
|
5550 Py_VISIT(traverse_module_state->__pyx_tuple__72);
|
|
jpayne@69
|
5551 Py_VISIT(traverse_module_state->__pyx_tuple__73);
|
|
jpayne@69
|
5552 Py_VISIT(traverse_module_state->__pyx_tuple__74);
|
|
jpayne@69
|
5553 Py_VISIT(traverse_module_state->__pyx_tuple__75);
|
|
jpayne@69
|
5554 Py_VISIT(traverse_module_state->__pyx_tuple__76);
|
|
jpayne@69
|
5555 Py_VISIT(traverse_module_state->__pyx_tuple__77);
|
|
jpayne@69
|
5556 Py_VISIT(traverse_module_state->__pyx_codeobj__2);
|
|
jpayne@69
|
5557 Py_VISIT(traverse_module_state->__pyx_codeobj__3);
|
|
jpayne@69
|
5558 Py_VISIT(traverse_module_state->__pyx_codeobj__4);
|
|
jpayne@69
|
5559 Py_VISIT(traverse_module_state->__pyx_codeobj__5);
|
|
jpayne@69
|
5560 Py_VISIT(traverse_module_state->__pyx_codeobj__6);
|
|
jpayne@69
|
5561 Py_VISIT(traverse_module_state->__pyx_codeobj__7);
|
|
jpayne@69
|
5562 Py_VISIT(traverse_module_state->__pyx_codeobj__8);
|
|
jpayne@69
|
5563 Py_VISIT(traverse_module_state->__pyx_codeobj__9);
|
|
jpayne@69
|
5564 Py_VISIT(traverse_module_state->__pyx_codeobj__10);
|
|
jpayne@69
|
5565 Py_VISIT(traverse_module_state->__pyx_codeobj__11);
|
|
jpayne@69
|
5566 Py_VISIT(traverse_module_state->__pyx_codeobj__12);
|
|
jpayne@69
|
5567 Py_VISIT(traverse_module_state->__pyx_codeobj__13);
|
|
jpayne@69
|
5568 Py_VISIT(traverse_module_state->__pyx_codeobj__14);
|
|
jpayne@69
|
5569 Py_VISIT(traverse_module_state->__pyx_codeobj__15);
|
|
jpayne@69
|
5570 Py_VISIT(traverse_module_state->__pyx_codeobj__17);
|
|
jpayne@69
|
5571 Py_VISIT(traverse_module_state->__pyx_codeobj__18);
|
|
jpayne@69
|
5572 Py_VISIT(traverse_module_state->__pyx_codeobj__21);
|
|
jpayne@69
|
5573 Py_VISIT(traverse_module_state->__pyx_codeobj__22);
|
|
jpayne@69
|
5574 Py_VISIT(traverse_module_state->__pyx_codeobj__23);
|
|
jpayne@69
|
5575 Py_VISIT(traverse_module_state->__pyx_codeobj__25);
|
|
jpayne@69
|
5576 Py_VISIT(traverse_module_state->__pyx_codeobj__26);
|
|
jpayne@69
|
5577 Py_VISIT(traverse_module_state->__pyx_codeobj__27);
|
|
jpayne@69
|
5578 Py_VISIT(traverse_module_state->__pyx_codeobj__28);
|
|
jpayne@69
|
5579 Py_VISIT(traverse_module_state->__pyx_codeobj__29);
|
|
jpayne@69
|
5580 Py_VISIT(traverse_module_state->__pyx_codeobj__30);
|
|
jpayne@69
|
5581 Py_VISIT(traverse_module_state->__pyx_codeobj__31);
|
|
jpayne@69
|
5582 Py_VISIT(traverse_module_state->__pyx_codeobj__32);
|
|
jpayne@69
|
5583 Py_VISIT(traverse_module_state->__pyx_codeobj__33);
|
|
jpayne@69
|
5584 Py_VISIT(traverse_module_state->__pyx_codeobj__34);
|
|
jpayne@69
|
5585 Py_VISIT(traverse_module_state->__pyx_codeobj__35);
|
|
jpayne@69
|
5586 Py_VISIT(traverse_module_state->__pyx_codeobj__36);
|
|
jpayne@69
|
5587 Py_VISIT(traverse_module_state->__pyx_codeobj__37);
|
|
jpayne@69
|
5588 Py_VISIT(traverse_module_state->__pyx_codeobj__40);
|
|
jpayne@69
|
5589 Py_VISIT(traverse_module_state->__pyx_codeobj__46);
|
|
jpayne@69
|
5590 Py_VISIT(traverse_module_state->__pyx_codeobj__47);
|
|
jpayne@69
|
5591 Py_VISIT(traverse_module_state->__pyx_codeobj__48);
|
|
jpayne@69
|
5592 Py_VISIT(traverse_module_state->__pyx_codeobj__49);
|
|
jpayne@69
|
5593 Py_VISIT(traverse_module_state->__pyx_codeobj__50);
|
|
jpayne@69
|
5594 Py_VISIT(traverse_module_state->__pyx_codeobj__51);
|
|
jpayne@69
|
5595 Py_VISIT(traverse_module_state->__pyx_codeobj__52);
|
|
jpayne@69
|
5596 Py_VISIT(traverse_module_state->__pyx_codeobj__53);
|
|
jpayne@69
|
5597 Py_VISIT(traverse_module_state->__pyx_codeobj__54);
|
|
jpayne@69
|
5598 Py_VISIT(traverse_module_state->__pyx_codeobj__57);
|
|
jpayne@69
|
5599 Py_VISIT(traverse_module_state->__pyx_codeobj__58);
|
|
jpayne@69
|
5600 Py_VISIT(traverse_module_state->__pyx_codeobj__59);
|
|
jpayne@69
|
5601 Py_VISIT(traverse_module_state->__pyx_codeobj__60);
|
|
jpayne@69
|
5602 Py_VISIT(traverse_module_state->__pyx_codeobj__61);
|
|
jpayne@69
|
5603 return 0;
|
|
jpayne@69
|
5604 }
|
|
jpayne@69
|
5605 #endif
|
|
jpayne@69
|
5606 /* #### Code section: module_state_defines ### */
|
|
jpayne@69
|
5607 #define __pyx_d __pyx_mstate_global->__pyx_d
|
|
jpayne@69
|
5608 #define __pyx_b __pyx_mstate_global->__pyx_b
|
|
jpayne@69
|
5609 #define __pyx_cython_runtime __pyx_mstate_global->__pyx_cython_runtime
|
|
jpayne@69
|
5610 #define __pyx_empty_tuple __pyx_mstate_global->__pyx_empty_tuple
|
|
jpayne@69
|
5611 #define __pyx_empty_bytes __pyx_mstate_global->__pyx_empty_bytes
|
|
jpayne@69
|
5612 #define __pyx_empty_unicode __pyx_mstate_global->__pyx_empty_unicode
|
|
jpayne@69
|
5613 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
5614 #define __pyx_CyFunctionType __pyx_mstate_global->__pyx_CyFunctionType
|
|
jpayne@69
|
5615 #endif
|
|
jpayne@69
|
5616 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
5617 #define __pyx_FusedFunctionType __pyx_mstate_global->__pyx_FusedFunctionType
|
|
jpayne@69
|
5618 #endif
|
|
jpayne@69
|
5619 #ifdef __Pyx_Generator_USED
|
|
jpayne@69
|
5620 #define __pyx_GeneratorType __pyx_mstate_global->__pyx_GeneratorType
|
|
jpayne@69
|
5621 #endif
|
|
jpayne@69
|
5622 #ifdef __Pyx_IterableCoroutine_USED
|
|
jpayne@69
|
5623 #define __pyx_IterableCoroutineType __pyx_mstate_global->__pyx_IterableCoroutineType
|
|
jpayne@69
|
5624 #endif
|
|
jpayne@69
|
5625 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
5626 #define __pyx_CoroutineAwaitType __pyx_mstate_global->__pyx_CoroutineAwaitType
|
|
jpayne@69
|
5627 #endif
|
|
jpayne@69
|
5628 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
5629 #define __pyx_CoroutineType __pyx_mstate_global->__pyx_CoroutineType
|
|
jpayne@69
|
5630 #endif
|
|
jpayne@69
|
5631 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5632 #endif
|
|
jpayne@69
|
5633 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5634 #endif
|
|
jpayne@69
|
5635 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5636 #endif
|
|
jpayne@69
|
5637 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5638 #endif
|
|
jpayne@69
|
5639 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5640 #endif
|
|
jpayne@69
|
5641 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5642 #endif
|
|
jpayne@69
|
5643 #define __pyx_ptype_5pysam_10libchtslib_HTSFile __pyx_mstate_global->__pyx_ptype_5pysam_10libchtslib_HTSFile
|
|
jpayne@69
|
5644 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5645 #endif
|
|
jpayne@69
|
5646 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5647 #endif
|
|
jpayne@69
|
5648 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5649 #endif
|
|
jpayne@69
|
5650 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5651 #endif
|
|
jpayne@69
|
5652 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5653 #endif
|
|
jpayne@69
|
5654 #define __pyx_ptype_7cpython_4type_type __pyx_mstate_global->__pyx_ptype_7cpython_4type_type
|
|
jpayne@69
|
5655 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5656 #endif
|
|
jpayne@69
|
5657 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5658 #endif
|
|
jpayne@69
|
5659 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5660 #endif
|
|
jpayne@69
|
5661 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5662 #endif
|
|
jpayne@69
|
5663 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5664 #endif
|
|
jpayne@69
|
5665 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5666 #endif
|
|
jpayne@69
|
5667 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5668 #endif
|
|
jpayne@69
|
5669 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5670 #endif
|
|
jpayne@69
|
5671 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5672 #endif
|
|
jpayne@69
|
5673 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5674 #endif
|
|
jpayne@69
|
5675 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5676 #endif
|
|
jpayne@69
|
5677 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5678 #endif
|
|
jpayne@69
|
5679 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5680 #endif
|
|
jpayne@69
|
5681 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5682 #endif
|
|
jpayne@69
|
5683 #define __pyx_ptype_7cpython_4bool_bool __pyx_mstate_global->__pyx_ptype_7cpython_4bool_bool
|
|
jpayne@69
|
5684 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5685 #endif
|
|
jpayne@69
|
5686 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5687 #endif
|
|
jpayne@69
|
5688 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5689 #endif
|
|
jpayne@69
|
5690 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5691 #endif
|
|
jpayne@69
|
5692 #define __pyx_ptype_7cpython_7complex_complex __pyx_mstate_global->__pyx_ptype_7cpython_7complex_complex
|
|
jpayne@69
|
5693 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5694 #endif
|
|
jpayne@69
|
5695 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5696 #endif
|
|
jpayne@69
|
5697 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5698 #endif
|
|
jpayne@69
|
5699 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5700 #endif
|
|
jpayne@69
|
5701 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5702 #endif
|
|
jpayne@69
|
5703 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5704 #endif
|
|
jpayne@69
|
5705 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5706 #endif
|
|
jpayne@69
|
5707 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5708 #endif
|
|
jpayne@69
|
5709 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5710 #endif
|
|
jpayne@69
|
5711 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5712 #endif
|
|
jpayne@69
|
5713 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5714 #endif
|
|
jpayne@69
|
5715 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5716 #endif
|
|
jpayne@69
|
5717 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5718 #endif
|
|
jpayne@69
|
5719 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5720 #endif
|
|
jpayne@69
|
5721 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5722 #endif
|
|
jpayne@69
|
5723 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5724 #endif
|
|
jpayne@69
|
5725 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5726 #endif
|
|
jpayne@69
|
5727 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5728 #endif
|
|
jpayne@69
|
5729 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5730 #endif
|
|
jpayne@69
|
5731 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5732 #endif
|
|
jpayne@69
|
5733 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5734 #endif
|
|
jpayne@69
|
5735 #define __pyx_ptype_5pysam_16libctabixproxies_TupleProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy
|
|
jpayne@69
|
5736 #define __pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator
|
|
jpayne@69
|
5737 #define __pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy
|
|
jpayne@69
|
5738 #define __pyx_ptype_5pysam_16libctabixproxies_GTFProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy
|
|
jpayne@69
|
5739 #define __pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy
|
|
jpayne@69
|
5740 #define __pyx_ptype_5pysam_16libctabixproxies_BedProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_BedProxy
|
|
jpayne@69
|
5741 #define __pyx_ptype_5pysam_16libctabixproxies_VCFProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy
|
|
jpayne@69
|
5742 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5743 #endif
|
|
jpayne@69
|
5744 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5745 #endif
|
|
jpayne@69
|
5746 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5747 #endif
|
|
jpayne@69
|
5748 #define __pyx_ptype_7cpython_5array_array __pyx_mstate_global->__pyx_ptype_7cpython_5array_array
|
|
jpayne@69
|
5749 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5750 #endif
|
|
jpayne@69
|
5751 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
5752 #define __pyx_type_5pysam_9libctabix_tabix_file_iterator __pyx_mstate_global->__pyx_type_5pysam_9libctabix_tabix_file_iterator
|
|
jpayne@69
|
5753 #define __pyx_type_5pysam_9libctabix_TabixFile __pyx_mstate_global->__pyx_type_5pysam_9libctabix_TabixFile
|
|
jpayne@69
|
5754 #define __pyx_type_5pysam_9libctabix_Parser __pyx_mstate_global->__pyx_type_5pysam_9libctabix_Parser
|
|
jpayne@69
|
5755 #define __pyx_type_5pysam_9libctabix_asTuple __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asTuple
|
|
jpayne@69
|
5756 #define __pyx_type_5pysam_9libctabix_asGTF __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asGTF
|
|
jpayne@69
|
5757 #define __pyx_type_5pysam_9libctabix_asGFF3 __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asGFF3
|
|
jpayne@69
|
5758 #define __pyx_type_5pysam_9libctabix_asBed __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asBed
|
|
jpayne@69
|
5759 #define __pyx_type_5pysam_9libctabix_asVCF __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asVCF
|
|
jpayne@69
|
5760 #define __pyx_type_5pysam_9libctabix_TabixIterator __pyx_mstate_global->__pyx_type_5pysam_9libctabix_TabixIterator
|
|
jpayne@69
|
5761 #define __pyx_type_5pysam_9libctabix_TabixIteratorParsed __pyx_mstate_global->__pyx_type_5pysam_9libctabix_TabixIteratorParsed
|
|
jpayne@69
|
5762 #define __pyx_type_5pysam_9libctabix_GZIterator __pyx_mstate_global->__pyx_type_5pysam_9libctabix_GZIterator
|
|
jpayne@69
|
5763 #define __pyx_type_5pysam_9libctabix_GZIteratorHead __pyx_mstate_global->__pyx_type_5pysam_9libctabix_GZIteratorHead
|
|
jpayne@69
|
5764 #define __pyx_type_5pysam_9libctabix_GZIteratorParsed __pyx_mstate_global->__pyx_type_5pysam_9libctabix_GZIteratorParsed
|
|
jpayne@69
|
5765 #define __pyx_type_5pysam_9libctabix_Tabixfile __pyx_mstate_global->__pyx_type_5pysam_9libctabix_Tabixfile
|
|
jpayne@69
|
5766 #endif
|
|
jpayne@69
|
5767 #define __pyx_ptype_5pysam_9libctabix_tabix_file_iterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator
|
|
jpayne@69
|
5768 #define __pyx_ptype_5pysam_9libctabix_TabixFile __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixFile
|
|
jpayne@69
|
5769 #define __pyx_ptype_5pysam_9libctabix_Parser __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_Parser
|
|
jpayne@69
|
5770 #define __pyx_ptype_5pysam_9libctabix_asTuple __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asTuple
|
|
jpayne@69
|
5771 #define __pyx_ptype_5pysam_9libctabix_asGTF __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asGTF
|
|
jpayne@69
|
5772 #define __pyx_ptype_5pysam_9libctabix_asGFF3 __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asGFF3
|
|
jpayne@69
|
5773 #define __pyx_ptype_5pysam_9libctabix_asBed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asBed
|
|
jpayne@69
|
5774 #define __pyx_ptype_5pysam_9libctabix_asVCF __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asVCF
|
|
jpayne@69
|
5775 #define __pyx_ptype_5pysam_9libctabix_TabixIterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixIterator
|
|
jpayne@69
|
5776 #define __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed
|
|
jpayne@69
|
5777 #define __pyx_ptype_5pysam_9libctabix_GZIterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIterator
|
|
jpayne@69
|
5778 #define __pyx_ptype_5pysam_9libctabix_GZIteratorHead __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIteratorHead
|
|
jpayne@69
|
5779 #define __pyx_ptype_5pysam_9libctabix_GZIteratorParsed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed
|
|
jpayne@69
|
5780 #define __pyx_ptype_5pysam_9libctabix_Tabixfile __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_Tabixfile
|
|
jpayne@69
|
5781 #define __pyx_n_s_AssertionError __pyx_mstate_global->__pyx_n_s_AssertionError
|
|
jpayne@69
|
5782 #define __pyx_kp_u_Could_not_open_file __pyx_mstate_global->__pyx_kp_u_Could_not_open_file
|
|
jpayne@69
|
5783 #define __pyx_n_s_EmptyIterator __pyx_mstate_global->__pyx_n_s_EmptyIterator
|
|
jpayne@69
|
5784 #define __pyx_n_s_EmptyIterator___iter __pyx_mstate_global->__pyx_n_s_EmptyIterator___iter
|
|
jpayne@69
|
5785 #define __pyx_n_s_EmptyIterator___next __pyx_mstate_global->__pyx_n_s_EmptyIterator___next
|
|
jpayne@69
|
5786 #define __pyx_kp_u_Filename_s_already_exists_use_fo __pyx_mstate_global->__pyx_kp_u_Filename_s_already_exists_use_fo
|
|
jpayne@69
|
5787 #define __pyx_n_s_GZIterator __pyx_mstate_global->__pyx_n_s_GZIterator
|
|
jpayne@69
|
5788 #define __pyx_n_u_GZIterator __pyx_mstate_global->__pyx_n_u_GZIterator
|
|
jpayne@69
|
5789 #define __pyx_n_s_GZIteratorHead __pyx_mstate_global->__pyx_n_s_GZIteratorHead
|
|
jpayne@69
|
5790 #define __pyx_n_u_GZIteratorHead __pyx_mstate_global->__pyx_n_u_GZIteratorHead
|
|
jpayne@69
|
5791 #define __pyx_n_s_GZIteratorHead___reduce_cython __pyx_mstate_global->__pyx_n_s_GZIteratorHead___reduce_cython
|
|
jpayne@69
|
5792 #define __pyx_n_s_GZIteratorHead___setstate_cython __pyx_mstate_global->__pyx_n_s_GZIteratorHead___setstate_cython
|
|
jpayne@69
|
5793 #define __pyx_n_s_GZIteratorParsed __pyx_mstate_global->__pyx_n_s_GZIteratorParsed
|
|
jpayne@69
|
5794 #define __pyx_n_s_GZIteratorParsed___reduce_cython __pyx_mstate_global->__pyx_n_s_GZIteratorParsed___reduce_cython
|
|
jpayne@69
|
5795 #define __pyx_n_s_GZIteratorParsed___setstate_cyth __pyx_mstate_global->__pyx_n_s_GZIteratorParsed___setstate_cyth
|
|
jpayne@69
|
5796 #define __pyx_n_s_GZIterator___reduce_cython __pyx_mstate_global->__pyx_n_s_GZIterator___reduce_cython
|
|
jpayne@69
|
5797 #define __pyx_n_s_GZIterator___setstate_cython __pyx_mstate_global->__pyx_n_s_GZIterator___setstate_cython
|
|
jpayne@69
|
5798 #define __pyx_n_s_IOError __pyx_mstate_global->__pyx_n_s_IOError
|
|
jpayne@69
|
5799 #define __pyx_kp_u_I_O_operation_on_closed_file __pyx_mstate_global->__pyx_kp_u_I_O_operation_on_closed_file
|
|
jpayne@69
|
5800 #define __pyx_kp_u_I_O_operation_on_closed_file_2 __pyx_mstate_global->__pyx_kp_u_I_O_operation_on_closed_file_2
|
|
jpayne@69
|
5801 #define __pyx_kp_s_Incompatible_checksums_0x_x_vs_0 __pyx_mstate_global->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0
|
|
jpayne@69
|
5802 #define __pyx_n_s_KeyError __pyx_mstate_global->__pyx_n_s_KeyError
|
|
jpayne@69
|
5803 #define __pyx_n_s_MemoryError __pyx_mstate_global->__pyx_n_s_MemoryError
|
|
jpayne@69
|
5804 #define __pyx_kp_u_No_such_file_or_directory_s __pyx_mstate_global->__pyx_kp_u_No_such_file_or_directory_s
|
|
jpayne@69
|
5805 #define __pyx_n_s_NotImplementedError __pyx_mstate_global->__pyx_n_s_NotImplementedError
|
|
jpayne@69
|
5806 #define __pyx_n_s_OSError __pyx_mstate_global->__pyx_n_s_OSError
|
|
jpayne@69
|
5807 #define __pyx_n_s_O_RDONLY __pyx_mstate_global->__pyx_n_s_O_RDONLY
|
|
jpayne@69
|
5808 #define __pyx_n_s_Parser __pyx_mstate_global->__pyx_n_s_Parser
|
|
jpayne@69
|
5809 #define __pyx_n_s_Parser___reduce_cython __pyx_mstate_global->__pyx_n_s_Parser___reduce_cython
|
|
jpayne@69
|
5810 #define __pyx_n_s_Parser___setstate_cython __pyx_mstate_global->__pyx_n_s_Parser___setstate_cython
|
|
jpayne@69
|
5811 #define __pyx_n_s_Parser_get_encoding __pyx_mstate_global->__pyx_n_s_Parser_get_encoding
|
|
jpayne@69
|
5812 #define __pyx_n_s_Parser_set_encoding __pyx_mstate_global->__pyx_n_s_Parser_set_encoding
|
|
jpayne@69
|
5813 #define __pyx_n_s_PickleError __pyx_mstate_global->__pyx_n_s_PickleError
|
|
jpayne@69
|
5814 #define __pyx_n_s_StopIteration __pyx_mstate_global->__pyx_n_s_StopIteration
|
|
jpayne@69
|
5815 #define __pyx_n_s_TabixFile __pyx_mstate_global->__pyx_n_s_TabixFile
|
|
jpayne@69
|
5816 #define __pyx_n_u_TabixFile __pyx_mstate_global->__pyx_n_u_TabixFile
|
|
jpayne@69
|
5817 #define __pyx_n_s_TabixFile___reduce_cython __pyx_mstate_global->__pyx_n_s_TabixFile___reduce_cython
|
|
jpayne@69
|
5818 #define __pyx_n_s_TabixFile___setstate_cython __pyx_mstate_global->__pyx_n_s_TabixFile___setstate_cython
|
|
jpayne@69
|
5819 #define __pyx_n_s_TabixFile__dup __pyx_mstate_global->__pyx_n_s_TabixFile__dup
|
|
jpayne@69
|
5820 #define __pyx_n_s_TabixFile__open __pyx_mstate_global->__pyx_n_s_TabixFile__open
|
|
jpayne@69
|
5821 #define __pyx_n_s_TabixFile_close __pyx_mstate_global->__pyx_n_s_TabixFile_close
|
|
jpayne@69
|
5822 #define __pyx_n_s_TabixFile_fetch __pyx_mstate_global->__pyx_n_s_TabixFile_fetch
|
|
jpayne@69
|
5823 #define __pyx_n_s_TabixIterator __pyx_mstate_global->__pyx_n_s_TabixIterator
|
|
jpayne@69
|
5824 #define __pyx_n_s_TabixIteratorParsed __pyx_mstate_global->__pyx_n_s_TabixIteratorParsed
|
|
jpayne@69
|
5825 #define __pyx_n_s_TabixIteratorParsed___reduce_cyt __pyx_mstate_global->__pyx_n_s_TabixIteratorParsed___reduce_cyt
|
|
jpayne@69
|
5826 #define __pyx_n_s_TabixIteratorParsed___setstate_c __pyx_mstate_global->__pyx_n_s_TabixIteratorParsed___setstate_c
|
|
jpayne@69
|
5827 #define __pyx_n_s_TabixIterator___reduce_cython __pyx_mstate_global->__pyx_n_s_TabixIterator___reduce_cython
|
|
jpayne@69
|
5828 #define __pyx_n_s_TabixIterator___setstate_cython __pyx_mstate_global->__pyx_n_s_TabixIterator___setstate_cython
|
|
jpayne@69
|
5829 #define __pyx_n_s_Tabixfile __pyx_mstate_global->__pyx_n_s_Tabixfile
|
|
jpayne@69
|
5830 #define __pyx_n_u_Tabixfile __pyx_mstate_global->__pyx_n_u_Tabixfile
|
|
jpayne@69
|
5831 #define __pyx_n_s_Tabixfile___reduce_cython __pyx_mstate_global->__pyx_n_s_Tabixfile___reduce_cython
|
|
jpayne@69
|
5832 #define __pyx_n_s_Tabixfile___setstate_cython __pyx_mstate_global->__pyx_n_s_Tabixfile___setstate_cython
|
|
jpayne@69
|
5833 #define __pyx_n_s_TypeError __pyx_mstate_global->__pyx_n_s_TypeError
|
|
jpayne@69
|
5834 #define __pyx_n_s_ValueError __pyx_mstate_global->__pyx_n_s_ValueError
|
|
jpayne@69
|
5835 #define __pyx_n_s_WINDOW_SIZE __pyx_mstate_global->__pyx_n_s_WINDOW_SIZE
|
|
jpayne@69
|
5836 #define __pyx_kp_b__16 __pyx_mstate_global->__pyx_kp_b__16
|
|
jpayne@69
|
5837 #define __pyx_kp_u__39 __pyx_mstate_global->__pyx_kp_u__39
|
|
jpayne@69
|
5838 #define __pyx_kp_u__42 __pyx_mstate_global->__pyx_kp_u__42
|
|
jpayne@69
|
5839 #define __pyx_kp_u__43 __pyx_mstate_global->__pyx_kp_u__43
|
|
jpayne@69
|
5840 #define __pyx_kp_u__44 __pyx_mstate_global->__pyx_kp_u__44
|
|
jpayne@69
|
5841 #define __pyx_kp_u__56 __pyx_mstate_global->__pyx_kp_u__56
|
|
jpayne@69
|
5842 #define __pyx_n_s__62 __pyx_mstate_global->__pyx_n_s__62
|
|
jpayne@69
|
5843 #define __pyx_n_s__78 __pyx_mstate_global->__pyx_n_s__78
|
|
jpayne@69
|
5844 #define __pyx_n_s_a __pyx_mstate_global->__pyx_n_s_a
|
|
jpayne@69
|
5845 #define __pyx_n_s_all __pyx_mstate_global->__pyx_n_s_all
|
|
jpayne@69
|
5846 #define __pyx_n_s_asBed __pyx_mstate_global->__pyx_n_s_asBed
|
|
jpayne@69
|
5847 #define __pyx_n_u_asBed __pyx_mstate_global->__pyx_n_u_asBed
|
|
jpayne@69
|
5848 #define __pyx_n_s_asBed___reduce_cython __pyx_mstate_global->__pyx_n_s_asBed___reduce_cython
|
|
jpayne@69
|
5849 #define __pyx_n_s_asBed___setstate_cython __pyx_mstate_global->__pyx_n_s_asBed___setstate_cython
|
|
jpayne@69
|
5850 #define __pyx_n_s_asGFF3 __pyx_mstate_global->__pyx_n_s_asGFF3
|
|
jpayne@69
|
5851 #define __pyx_n_u_asGFF3 __pyx_mstate_global->__pyx_n_u_asGFF3
|
|
jpayne@69
|
5852 #define __pyx_n_s_asGFF3___reduce_cython __pyx_mstate_global->__pyx_n_s_asGFF3___reduce_cython
|
|
jpayne@69
|
5853 #define __pyx_n_s_asGFF3___setstate_cython __pyx_mstate_global->__pyx_n_s_asGFF3___setstate_cython
|
|
jpayne@69
|
5854 #define __pyx_n_s_asGTF __pyx_mstate_global->__pyx_n_s_asGTF
|
|
jpayne@69
|
5855 #define __pyx_n_u_asGTF __pyx_mstate_global->__pyx_n_u_asGTF
|
|
jpayne@69
|
5856 #define __pyx_n_s_asGTF___reduce_cython __pyx_mstate_global->__pyx_n_s_asGTF___reduce_cython
|
|
jpayne@69
|
5857 #define __pyx_n_s_asGTF___setstate_cython __pyx_mstate_global->__pyx_n_s_asGTF___setstate_cython
|
|
jpayne@69
|
5858 #define __pyx_n_s_asTuple __pyx_mstate_global->__pyx_n_s_asTuple
|
|
jpayne@69
|
5859 #define __pyx_n_u_asTuple __pyx_mstate_global->__pyx_n_u_asTuple
|
|
jpayne@69
|
5860 #define __pyx_n_s_asTuple___reduce_cython __pyx_mstate_global->__pyx_n_s_asTuple___reduce_cython
|
|
jpayne@69
|
5861 #define __pyx_n_s_asTuple___setstate_cython __pyx_mstate_global->__pyx_n_s_asTuple___setstate_cython
|
|
jpayne@69
|
5862 #define __pyx_n_s_asVCF __pyx_mstate_global->__pyx_n_s_asVCF
|
|
jpayne@69
|
5863 #define __pyx_n_u_asVCF __pyx_mstate_global->__pyx_n_u_asVCF
|
|
jpayne@69
|
5864 #define __pyx_n_s_asVCF___reduce_cython __pyx_mstate_global->__pyx_n_s_asVCF___reduce_cython
|
|
jpayne@69
|
5865 #define __pyx_n_s_asVCF___setstate_cython __pyx_mstate_global->__pyx_n_s_asVCF___setstate_cython
|
|
jpayne@69
|
5866 #define __pyx_n_u_ascii __pyx_mstate_global->__pyx_n_u_ascii
|
|
jpayne@69
|
5867 #define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines
|
|
jpayne@69
|
5868 #define __pyx_n_s_b __pyx_mstate_global->__pyx_n_s_b
|
|
jpayne@69
|
5869 #define __pyx_n_u_bcf __pyx_mstate_global->__pyx_n_u_bcf
|
|
jpayne@69
|
5870 #define __pyx_n_u_bed __pyx_mstate_global->__pyx_n_u_bed
|
|
jpayne@69
|
5871 #define __pyx_n_s_buffer __pyx_mstate_global->__pyx_n_s_buffer
|
|
jpayne@69
|
5872 #define __pyx_n_s_buffer_size __pyx_mstate_global->__pyx_n_s_buffer_size
|
|
jpayne@69
|
5873 #define __pyx_kp_u_building_of_index_for_failed __pyx_mstate_global->__pyx_kp_u_building_of_index_for_failed
|
|
jpayne@69
|
5874 #define __pyx_n_s_bytes_cpy __pyx_mstate_global->__pyx_n_s_bytes_cpy
|
|
jpayne@69
|
5875 #define __pyx_n_s_c __pyx_mstate_global->__pyx_n_s_c
|
|
jpayne@69
|
5876 #define __pyx_n_s_cfilename __pyx_mstate_global->__pyx_n_s_cfilename
|
|
jpayne@69
|
5877 #define __pyx_n_s_cfilename_index __pyx_mstate_global->__pyx_n_s_cfilename_index
|
|
jpayne@69
|
5878 #define __pyx_n_s_cfn __pyx_mstate_global->__pyx_n_s_cfn
|
|
jpayne@69
|
5879 #define __pyx_n_s_cline_in_traceback __pyx_mstate_global->__pyx_n_s_cline_in_traceback
|
|
jpayne@69
|
5880 #define __pyx_n_s_close __pyx_mstate_global->__pyx_n_s_close
|
|
jpayne@69
|
5881 #define __pyx_n_s_closed __pyx_mstate_global->__pyx_n_s_closed
|
|
jpayne@69
|
5882 #define __pyx_n_s_conf __pyx_mstate_global->__pyx_n_s_conf
|
|
jpayne@69
|
5883 #define __pyx_n_s_conf_data __pyx_mstate_global->__pyx_n_s_conf_data
|
|
jpayne@69
|
5884 #define __pyx_n_s_contigs __pyx_mstate_global->__pyx_n_s_contigs
|
|
jpayne@69
|
5885 #define __pyx_kp_u_could_not_create_iterator_for_re __pyx_mstate_global->__pyx_kp_u_could_not_create_iterator_for_re
|
|
jpayne@69
|
5886 #define __pyx_kp_u_could_not_create_iterator_possib __pyx_mstate_global->__pyx_kp_u_could_not_create_iterator_possib
|
|
jpayne@69
|
5887 #define __pyx_kp_u_could_not_load_tbi_csi_index_of __pyx_mstate_global->__pyx_kp_u_could_not_load_tbi_csi_index_of
|
|
jpayne@69
|
5888 #define __pyx_kp_u_could_not_open_file_s __pyx_mstate_global->__pyx_kp_u_could_not_open_file_s
|
|
jpayne@69
|
5889 #define __pyx_kp_u_could_not_open_for_reading_heade __pyx_mstate_global->__pyx_kp_u_could_not_open_for_reading_heade
|
|
jpayne@69
|
5890 #define __pyx_kp_u_could_not_open_index_for_s __pyx_mstate_global->__pyx_kp_u_could_not_open_index_for_s
|
|
jpayne@69
|
5891 #define __pyx_kp_u_could_not_open_s_for_reading __pyx_mstate_global->__pyx_kp_u_could_not_open_s_for_reading
|
|
jpayne@69
|
5892 #define __pyx_kp_u_could_not_open_s_for_writing __pyx_mstate_global->__pyx_kp_u_could_not_open_s_for_writing
|
|
jpayne@69
|
5893 #define __pyx_n_s_cpy __pyx_mstate_global->__pyx_n_s_cpy
|
|
jpayne@69
|
5894 #define __pyx_n_s_csi __pyx_mstate_global->__pyx_n_s_csi
|
|
jpayne@69
|
5895 #define __pyx_kp_u_csi_2 __pyx_mstate_global->__pyx_kp_u_csi_2
|
|
jpayne@69
|
5896 #define __pyx_n_s_cstr __pyx_mstate_global->__pyx_n_s_cstr
|
|
jpayne@69
|
5897 #define __pyx_n_s_dict __pyx_mstate_global->__pyx_n_s_dict
|
|
jpayne@69
|
5898 #define __pyx_n_s_dict_2 __pyx_mstate_global->__pyx_n_s_dict_2
|
|
jpayne@69
|
5899 #define __pyx_kp_u_disable __pyx_mstate_global->__pyx_kp_u_disable
|
|
jpayne@69
|
5900 #define __pyx_n_s_doc __pyx_mstate_global->__pyx_n_s_doc
|
|
jpayne@69
|
5901 #define __pyx_n_s_dup __pyx_mstate_global->__pyx_n_s_dup
|
|
jpayne@69
|
5902 #define __pyx_kp_s_empty_iterator __pyx_mstate_global->__pyx_kp_s_empty_iterator
|
|
jpayne@69
|
5903 #define __pyx_kp_u_enable __pyx_mstate_global->__pyx_kp_u_enable
|
|
jpayne@69
|
5904 #define __pyx_n_s_encoding __pyx_mstate_global->__pyx_n_s_encoding
|
|
jpayne@69
|
5905 #define __pyx_n_s_end __pyx_mstate_global->__pyx_n_s_end
|
|
jpayne@69
|
5906 #define __pyx_n_s_end_col __pyx_mstate_global->__pyx_n_s_end_col
|
|
jpayne@69
|
5907 #define __pyx_kp_u_end_out_of_range_i __pyx_mstate_global->__pyx_kp_u_end_out_of_range_i
|
|
jpayne@69
|
5908 #define __pyx_kp_u_error_i_when_closing_file_s __pyx_mstate_global->__pyx_kp_u_error_i_when_closing_file_s
|
|
jpayne@69
|
5909 #define __pyx_kp_u_error_i_when_writing_to_file_s __pyx_mstate_global->__pyx_kp_u_error_i_when_writing_to_file_s
|
|
jpayne@69
|
5910 #define __pyx_n_s_exists __pyx_mstate_global->__pyx_n_s_exists
|
|
jpayne@69
|
5911 #define __pyx_n_s_fd_src __pyx_mstate_global->__pyx_n_s_fd_src
|
|
jpayne@69
|
5912 #define __pyx_n_s_fetch __pyx_mstate_global->__pyx_n_s_fetch
|
|
jpayne@69
|
5913 #define __pyx_kp_u_file_s_not_found __pyx_mstate_global->__pyx_kp_u_file_s_not_found
|
|
jpayne@69
|
5914 #define __pyx_n_s_filename __pyx_mstate_global->__pyx_n_s_filename
|
|
jpayne@69
|
5915 #define __pyx_n_s_filename_in __pyx_mstate_global->__pyx_n_s_filename_in
|
|
jpayne@69
|
5916 #define __pyx_n_s_filename_index __pyx_mstate_global->__pyx_n_s_filename_index
|
|
jpayne@69
|
5917 #define __pyx_n_s_filename_out __pyx_mstate_global->__pyx_n_s_filename_out
|
|
jpayne@69
|
5918 #define __pyx_kp_u_filename_s_already_exists_use_fo __pyx_mstate_global->__pyx_kp_u_filename_s_already_exists_use_fo
|
|
jpayne@69
|
5919 #define __pyx_n_s_fileobj __pyx_mstate_global->__pyx_n_s_fileobj
|
|
jpayne@69
|
5920 #define __pyx_n_s_fmt __pyx_mstate_global->__pyx_n_s_fmt
|
|
jpayne@69
|
5921 #define __pyx_n_s_fn __pyx_mstate_global->__pyx_n_s_fn
|
|
jpayne@69
|
5922 #define __pyx_n_s_fn_index __pyx_mstate_global->__pyx_n_s_fn_index
|
|
jpayne@69
|
5923 #define __pyx_n_s_fnidx __pyx_mstate_global->__pyx_n_s_fnidx
|
|
jpayne@69
|
5924 #define __pyx_n_s_force __pyx_mstate_global->__pyx_n_s_force
|
|
jpayne@69
|
5925 #define __pyx_n_s_format __pyx_mstate_global->__pyx_n_s_format
|
|
jpayne@69
|
5926 #define __pyx_n_s_fp __pyx_mstate_global->__pyx_n_s_fp
|
|
jpayne@69
|
5927 #define __pyx_kp_u_gc __pyx_mstate_global->__pyx_kp_u_gc
|
|
jpayne@69
|
5928 #define __pyx_n_s_get_encoding __pyx_mstate_global->__pyx_n_s_get_encoding
|
|
jpayne@69
|
5929 #define __pyx_n_s_getstate __pyx_mstate_global->__pyx_n_s_getstate
|
|
jpayne@69
|
5930 #define __pyx_n_u_gff __pyx_mstate_global->__pyx_n_u_gff
|
|
jpayne@69
|
5931 #define __pyx_kp_u_gz __pyx_mstate_global->__pyx_kp_u_gz
|
|
jpayne@69
|
5932 #define __pyx_n_s_import __pyx_mstate_global->__pyx_n_s_import
|
|
jpayne@69
|
5933 #define __pyx_kp_u_incomplete_line_at_s __pyx_mstate_global->__pyx_kp_u_incomplete_line_at_s
|
|
jpayne@69
|
5934 #define __pyx_n_s_index __pyx_mstate_global->__pyx_n_s_index
|
|
jpayne@69
|
5935 #define __pyx_kp_u_index_s_not_found __pyx_mstate_global->__pyx_kp_u_index_s_not_found
|
|
jpayne@69
|
5936 #define __pyx_n_s_infile __pyx_mstate_global->__pyx_n_s_infile
|
|
jpayne@69
|
5937 #define __pyx_n_s_init __pyx_mstate_global->__pyx_n_s_init
|
|
jpayne@69
|
5938 #define __pyx_n_s_init_subclass __pyx_mstate_global->__pyx_n_s_init_subclass
|
|
jpayne@69
|
5939 #define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing
|
|
jpayne@69
|
5940 #define __pyx_kp_u_invalid_file_opening_mode_s __pyx_mstate_global->__pyx_kp_u_invalid_file_opening_mode_s
|
|
jpayne@69
|
5941 #define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine
|
|
jpayne@69
|
5942 #define __pyx_n_s_is_empty __pyx_mstate_global->__pyx_n_s_is_empty
|
|
jpayne@69
|
5943 #define __pyx_n_s_is_open __pyx_mstate_global->__pyx_n_s_is_open
|
|
jpayne@69
|
5944 #define __pyx_kp_u_isenabled __pyx_mstate_global->__pyx_kp_u_isenabled
|
|
jpayne@69
|
5945 #define __pyx_n_s_iter __pyx_mstate_global->__pyx_n_s_iter
|
|
jpayne@69
|
5946 #define __pyx_kp_s_iterate_over_infile_Permits_the __pyx_mstate_global->__pyx_kp_s_iterate_over_infile_Permits_the
|
|
jpayne@69
|
5947 #define __pyx_kp_u_iteration_on_closed_file __pyx_mstate_global->__pyx_kp_u_iteration_on_closed_file
|
|
jpayne@69
|
5948 #define __pyx_n_s_itr __pyx_mstate_global->__pyx_n_s_itr
|
|
jpayne@69
|
5949 #define __pyx_n_s_keep_original __pyx_mstate_global->__pyx_n_s_keep_original
|
|
jpayne@69
|
5950 #define __pyx_n_s_keys __pyx_mstate_global->__pyx_n_s_keys
|
|
jpayne@69
|
5951 #define __pyx_n_s_length __pyx_mstate_global->__pyx_n_s_length
|
|
jpayne@69
|
5952 #define __pyx_n_s_line __pyx_mstate_global->__pyx_n_s_line
|
|
jpayne@69
|
5953 #define __pyx_n_s_line_skip __pyx_mstate_global->__pyx_n_s_line_skip
|
|
jpayne@69
|
5954 #define __pyx_n_s_main __pyx_mstate_global->__pyx_n_s_main
|
|
jpayne@69
|
5955 #define __pyx_n_s_meta_char __pyx_mstate_global->__pyx_n_s_meta_char
|
|
jpayne@69
|
5956 #define __pyx_n_s_metaclass __pyx_mstate_global->__pyx_n_s_metaclass
|
|
jpayne@69
|
5957 #define __pyx_n_s_min_shift __pyx_mstate_global->__pyx_n_s_min_shift
|
|
jpayne@69
|
5958 #define __pyx_n_s_mode __pyx_mstate_global->__pyx_n_s_mode
|
|
jpayne@69
|
5959 #define __pyx_n_s_module __pyx_mstate_global->__pyx_n_s_module
|
|
jpayne@69
|
5960 #define __pyx_n_s_multiple_iterators __pyx_mstate_global->__pyx_n_s_multiple_iterators
|
|
jpayne@69
|
5961 #define __pyx_n_s_name __pyx_mstate_global->__pyx_n_s_name
|
|
jpayne@69
|
5962 #define __pyx_n_s_nbytes __pyx_mstate_global->__pyx_n_s_nbytes
|
|
jpayne@69
|
5963 #define __pyx_kp_u_neither_preset_nor_seq_col_start __pyx_mstate_global->__pyx_kp_u_neither_preset_nor_seq_col_start
|
|
jpayne@69
|
5964 #define __pyx_n_s_new __pyx_mstate_global->__pyx_n_s_new
|
|
jpayne@69
|
5965 #define __pyx_n_s_next __pyx_mstate_global->__pyx_n_s_next
|
|
jpayne@69
|
5966 #define __pyx_kp_s_no_default___reduce___due_to_non __pyx_mstate_global->__pyx_kp_s_no_default___reduce___due_to_non
|
|
jpayne@69
|
5967 #define __pyx_n_s_open __pyx_mstate_global->__pyx_n_s_open
|
|
jpayne@69
|
5968 #define __pyx_n_s_os __pyx_mstate_global->__pyx_n_s_os
|
|
jpayne@69
|
5969 #define __pyx_kp_u_parse_method_of_s_not_implemente __pyx_mstate_global->__pyx_kp_u_parse_method_of_s_not_implemente
|
|
jpayne@69
|
5970 #define __pyx_n_s_parser __pyx_mstate_global->__pyx_n_s_parser
|
|
jpayne@69
|
5971 #define __pyx_n_s_path __pyx_mstate_global->__pyx_n_s_path
|
|
jpayne@69
|
5972 #define __pyx_n_s_pickle __pyx_mstate_global->__pyx_n_s_pickle
|
|
jpayne@69
|
5973 #define __pyx_n_s_prepare __pyx_mstate_global->__pyx_n_s_prepare
|
|
jpayne@69
|
5974 #define __pyx_n_s_preset __pyx_mstate_global->__pyx_n_s_preset
|
|
jpayne@69
|
5975 #define __pyx_n_s_preset2conf __pyx_mstate_global->__pyx_n_s_preset2conf
|
|
jpayne@69
|
5976 #define __pyx_n_u_psltbl __pyx_mstate_global->__pyx_n_u_psltbl
|
|
jpayne@69
|
5977 #define __pyx_n_s_pysam_libctabix __pyx_mstate_global->__pyx_n_s_pysam_libctabix
|
|
jpayne@69
|
5978 #define __pyx_kp_s_pysam_libctabix_pyx __pyx_mstate_global->__pyx_kp_s_pysam_libctabix_pyx
|
|
jpayne@69
|
5979 #define __pyx_n_s_pyx_PickleError __pyx_mstate_global->__pyx_n_s_pyx_PickleError
|
|
jpayne@69
|
5980 #define __pyx_n_s_pyx_checksum __pyx_mstate_global->__pyx_n_s_pyx_checksum
|
|
jpayne@69
|
5981 #define __pyx_n_s_pyx_result __pyx_mstate_global->__pyx_n_s_pyx_result
|
|
jpayne@69
|
5982 #define __pyx_n_s_pyx_state __pyx_mstate_global->__pyx_n_s_pyx_state
|
|
jpayne@69
|
5983 #define __pyx_n_s_pyx_type __pyx_mstate_global->__pyx_n_s_pyx_type
|
|
jpayne@69
|
5984 #define __pyx_n_s_pyx_unpickle_Parser __pyx_mstate_global->__pyx_n_s_pyx_unpickle_Parser
|
|
jpayne@69
|
5985 #define __pyx_n_s_pyx_unpickle_asBed __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asBed
|
|
jpayne@69
|
5986 #define __pyx_n_s_pyx_unpickle_asGFF3 __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asGFF3
|
|
jpayne@69
|
5987 #define __pyx_n_s_pyx_unpickle_asGTF __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asGTF
|
|
jpayne@69
|
5988 #define __pyx_n_s_pyx_unpickle_asTuple __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asTuple
|
|
jpayne@69
|
5989 #define __pyx_n_s_pyx_unpickle_asVCF __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asVCF
|
|
jpayne@69
|
5990 #define __pyx_n_s_pyx_vtable __pyx_mstate_global->__pyx_n_s_pyx_vtable
|
|
jpayne@69
|
5991 #define __pyx_n_s_qualname __pyx_mstate_global->__pyx_n_s_qualname
|
|
jpayne@69
|
5992 #define __pyx_n_s_r __pyx_mstate_global->__pyx_n_s_r
|
|
jpayne@69
|
5993 #define __pyx_n_u_r __pyx_mstate_global->__pyx_n_u_r
|
|
jpayne@69
|
5994 #define __pyx_n_s_readline __pyx_mstate_global->__pyx_n_s_readline
|
|
jpayne@69
|
5995 #define __pyx_n_s_reduce __pyx_mstate_global->__pyx_n_s_reduce
|
|
jpayne@69
|
5996 #define __pyx_n_s_reduce_cython __pyx_mstate_global->__pyx_n_s_reduce_cython
|
|
jpayne@69
|
5997 #define __pyx_n_s_reduce_ex __pyx_mstate_global->__pyx_n_s_reduce_ex
|
|
jpayne@69
|
5998 #define __pyx_n_s_reference __pyx_mstate_global->__pyx_n_s_reference
|
|
jpayne@69
|
5999 #define __pyx_n_s_region __pyx_mstate_global->__pyx_n_s_region
|
|
jpayne@69
|
6000 #define __pyx_n_s_retval __pyx_mstate_global->__pyx_n_s_retval
|
|
jpayne@69
|
6001 #define __pyx_kp_u_s __pyx_mstate_global->__pyx_kp_u_s
|
|
jpayne@69
|
6002 #define __pyx_n_s_s_2 __pyx_mstate_global->__pyx_n_s_s_2
|
|
jpayne@69
|
6003 #define __pyx_kp_u_s_i __pyx_mstate_global->__pyx_kp_u_s_i
|
|
jpayne@69
|
6004 #define __pyx_kp_u_s_i_i __pyx_mstate_global->__pyx_kp_u_s_i_i
|
|
jpayne@69
|
6005 #define __pyx_n_u_sam __pyx_mstate_global->__pyx_n_u_sam
|
|
jpayne@69
|
6006 #define __pyx_n_s_self __pyx_mstate_global->__pyx_n_s_self
|
|
jpayne@69
|
6007 #define __pyx_kp_s_self_gzipfile_self_kstream_canno __pyx_mstate_global->__pyx_kp_s_self_gzipfile_self_kstream_canno
|
|
jpayne@69
|
6008 #define __pyx_kp_s_self_iterator_cannot_be_converte __pyx_mstate_global->__pyx_kp_s_self_iterator_cannot_be_converte
|
|
jpayne@69
|
6009 #define __pyx_n_s_seq_col __pyx_mstate_global->__pyx_n_s_seq_col
|
|
jpayne@69
|
6010 #define __pyx_n_s_set_encoding __pyx_mstate_global->__pyx_n_s_set_encoding
|
|
jpayne@69
|
6011 #define __pyx_n_s_set_name __pyx_mstate_global->__pyx_n_s_set_name
|
|
jpayne@69
|
6012 #define __pyx_n_s_setstate __pyx_mstate_global->__pyx_n_s_setstate
|
|
jpayne@69
|
6013 #define __pyx_n_s_setstate_cython __pyx_mstate_global->__pyx_n_s_setstate_cython
|
|
jpayne@69
|
6014 #define __pyx_n_s_spec __pyx_mstate_global->__pyx_n_s_spec
|
|
jpayne@69
|
6015 #define __pyx_n_s_start __pyx_mstate_global->__pyx_n_s_start
|
|
jpayne@69
|
6016 #define __pyx_n_s_start_col __pyx_mstate_global->__pyx_n_s_start_col
|
|
jpayne@69
|
6017 #define __pyx_kp_u_start_i_end_i __pyx_mstate_global->__pyx_kp_u_start_i_end_i
|
|
jpayne@69
|
6018 #define __pyx_kp_u_start_out_of_range_i __pyx_mstate_global->__pyx_kp_u_start_out_of_range_i
|
|
jpayne@69
|
6019 #define __pyx_n_s_state __pyx_mstate_global->__pyx_n_s_state
|
|
jpayne@69
|
6020 #define __pyx_kp_s_stringsource __pyx_mstate_global->__pyx_kp_s_stringsource
|
|
jpayne@69
|
6021 #define __pyx_n_s_suffix __pyx_mstate_global->__pyx_n_s_suffix
|
|
jpayne@69
|
6022 #define __pyx_n_s_super __pyx_mstate_global->__pyx_n_s_super
|
|
jpayne@69
|
6023 #define __pyx_n_s_sys __pyx_mstate_global->__pyx_n_s_sys
|
|
jpayne@69
|
6024 #define __pyx_n_s_tabix_compress __pyx_mstate_global->__pyx_n_s_tabix_compress
|
|
jpayne@69
|
6025 #define __pyx_n_u_tabix_compress __pyx_mstate_global->__pyx_n_u_tabix_compress
|
|
jpayne@69
|
6026 #define __pyx_n_s_tabix_file_iterator __pyx_mstate_global->__pyx_n_s_tabix_file_iterator
|
|
jpayne@69
|
6027 #define __pyx_n_u_tabix_file_iterator __pyx_mstate_global->__pyx_n_u_tabix_file_iterator
|
|
jpayne@69
|
6028 #define __pyx_n_s_tabix_file_iterator___reduce_cyt __pyx_mstate_global->__pyx_n_s_tabix_file_iterator___reduce_cyt
|
|
jpayne@69
|
6029 #define __pyx_n_s_tabix_file_iterator___setstate_c __pyx_mstate_global->__pyx_n_s_tabix_file_iterator___setstate_c
|
|
jpayne@69
|
6030 #define __pyx_n_s_tabix_generic_iterator __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator
|
|
jpayne@69
|
6031 #define __pyx_n_u_tabix_generic_iterator __pyx_mstate_global->__pyx_n_u_tabix_generic_iterator
|
|
jpayne@69
|
6032 #define __pyx_n_s_tabix_generic_iterator___init __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator___init
|
|
jpayne@69
|
6033 #define __pyx_n_s_tabix_generic_iterator___iter __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator___iter
|
|
jpayne@69
|
6034 #define __pyx_n_s_tabix_generic_iterator___next __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator___next
|
|
jpayne@69
|
6035 #define __pyx_n_s_tabix_index __pyx_mstate_global->__pyx_n_s_tabix_index
|
|
jpayne@69
|
6036 #define __pyx_n_u_tabix_index __pyx_mstate_global->__pyx_n_u_tabix_index
|
|
jpayne@69
|
6037 #define __pyx_n_s_tabix_iterator __pyx_mstate_global->__pyx_n_s_tabix_iterator
|
|
jpayne@69
|
6038 #define __pyx_n_u_tabix_iterator __pyx_mstate_global->__pyx_n_u_tabix_iterator
|
|
jpayne@69
|
6039 #define __pyx_kp_u_tbi __pyx_mstate_global->__pyx_kp_u_tbi
|
|
jpayne@69
|
6040 #define __pyx_n_s_tell __pyx_mstate_global->__pyx_n_s_tell
|
|
jpayne@69
|
6041 #define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test
|
|
jpayne@69
|
6042 #define __pyx_n_s_threads __pyx_mstate_global->__pyx_n_s_threads
|
|
jpayne@69
|
6043 #define __pyx_kp_u_unknown_preset __pyx_mstate_global->__pyx_kp_u_unknown_preset
|
|
jpayne@69
|
6044 #define __pyx_n_s_unlink __pyx_mstate_global->__pyx_n_s_unlink
|
|
jpayne@69
|
6045 #define __pyx_n_s_update __pyx_mstate_global->__pyx_n_s_update
|
|
jpayne@69
|
6046 #define __pyx_n_s_use_setstate __pyx_mstate_global->__pyx_n_s_use_setstate
|
|
jpayne@69
|
6047 #define __pyx_kp_u_valid_presets_are __pyx_mstate_global->__pyx_kp_u_valid_presets_are
|
|
jpayne@69
|
6048 #define __pyx_n_u_vcf __pyx_mstate_global->__pyx_n_u_vcf
|
|
jpayne@69
|
6049 #define __pyx_kp_u_writing_failed __pyx_mstate_global->__pyx_kp_u_writing_failed
|
|
jpayne@69
|
6050 #define __pyx_n_s_zerobased __pyx_mstate_global->__pyx_n_s_zerobased
|
|
jpayne@69
|
6051 #define __pyx_int_0 __pyx_mstate_global->__pyx_int_0
|
|
jpayne@69
|
6052 #define __pyx_int_1 __pyx_mstate_global->__pyx_int_1
|
|
jpayne@69
|
6053 #define __pyx_int_2 __pyx_mstate_global->__pyx_int_2
|
|
jpayne@69
|
6054 #define __pyx_int_3 __pyx_mstate_global->__pyx_int_3
|
|
jpayne@69
|
6055 #define __pyx_int_4 __pyx_mstate_global->__pyx_int_4
|
|
jpayne@69
|
6056 #define __pyx_int_5 __pyx_mstate_global->__pyx_int_5
|
|
jpayne@69
|
6057 #define __pyx_int_15 __pyx_mstate_global->__pyx_int_15
|
|
jpayne@69
|
6058 #define __pyx_int_17 __pyx_mstate_global->__pyx_int_17
|
|
jpayne@69
|
6059 #define __pyx_int_18 __pyx_mstate_global->__pyx_int_18
|
|
jpayne@69
|
6060 #define __pyx_int_35 __pyx_mstate_global->__pyx_int_35
|
|
jpayne@69
|
6061 #define __pyx_int_64 __pyx_mstate_global->__pyx_int_64
|
|
jpayne@69
|
6062 #define __pyx_int_21667264 __pyx_mstate_global->__pyx_int_21667264
|
|
jpayne@69
|
6063 #define __pyx_int_139192863 __pyx_mstate_global->__pyx_int_139192863
|
|
jpayne@69
|
6064 #define __pyx_int_243541226 __pyx_mstate_global->__pyx_int_243541226
|
|
jpayne@69
|
6065 #define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1
|
|
jpayne@69
|
6066 #define __pyx_codeobj_ __pyx_mstate_global->__pyx_codeobj_
|
|
jpayne@69
|
6067 #define __pyx_tuple__19 __pyx_mstate_global->__pyx_tuple__19
|
|
jpayne@69
|
6068 #define __pyx_tuple__20 __pyx_mstate_global->__pyx_tuple__20
|
|
jpayne@69
|
6069 #define __pyx_tuple__24 __pyx_mstate_global->__pyx_tuple__24
|
|
jpayne@69
|
6070 #define __pyx_tuple__38 __pyx_mstate_global->__pyx_tuple__38
|
|
jpayne@69
|
6071 #define __pyx_tuple__41 __pyx_mstate_global->__pyx_tuple__41
|
|
jpayne@69
|
6072 #define __pyx_tuple__45 __pyx_mstate_global->__pyx_tuple__45
|
|
jpayne@69
|
6073 #define __pyx_tuple__55 __pyx_mstate_global->__pyx_tuple__55
|
|
jpayne@69
|
6074 #define __pyx_tuple__63 __pyx_mstate_global->__pyx_tuple__63
|
|
jpayne@69
|
6075 #define __pyx_tuple__64 __pyx_mstate_global->__pyx_tuple__64
|
|
jpayne@69
|
6076 #define __pyx_tuple__65 __pyx_mstate_global->__pyx_tuple__65
|
|
jpayne@69
|
6077 #define __pyx_tuple__66 __pyx_mstate_global->__pyx_tuple__66
|
|
jpayne@69
|
6078 #define __pyx_tuple__67 __pyx_mstate_global->__pyx_tuple__67
|
|
jpayne@69
|
6079 #define __pyx_tuple__68 __pyx_mstate_global->__pyx_tuple__68
|
|
jpayne@69
|
6080 #define __pyx_tuple__69 __pyx_mstate_global->__pyx_tuple__69
|
|
jpayne@69
|
6081 #define __pyx_tuple__70 __pyx_mstate_global->__pyx_tuple__70
|
|
jpayne@69
|
6082 #define __pyx_tuple__71 __pyx_mstate_global->__pyx_tuple__71
|
|
jpayne@69
|
6083 #define __pyx_tuple__72 __pyx_mstate_global->__pyx_tuple__72
|
|
jpayne@69
|
6084 #define __pyx_tuple__73 __pyx_mstate_global->__pyx_tuple__73
|
|
jpayne@69
|
6085 #define __pyx_tuple__74 __pyx_mstate_global->__pyx_tuple__74
|
|
jpayne@69
|
6086 #define __pyx_tuple__75 __pyx_mstate_global->__pyx_tuple__75
|
|
jpayne@69
|
6087 #define __pyx_tuple__76 __pyx_mstate_global->__pyx_tuple__76
|
|
jpayne@69
|
6088 #define __pyx_tuple__77 __pyx_mstate_global->__pyx_tuple__77
|
|
jpayne@69
|
6089 #define __pyx_codeobj__2 __pyx_mstate_global->__pyx_codeobj__2
|
|
jpayne@69
|
6090 #define __pyx_codeobj__3 __pyx_mstate_global->__pyx_codeobj__3
|
|
jpayne@69
|
6091 #define __pyx_codeobj__4 __pyx_mstate_global->__pyx_codeobj__4
|
|
jpayne@69
|
6092 #define __pyx_codeobj__5 __pyx_mstate_global->__pyx_codeobj__5
|
|
jpayne@69
|
6093 #define __pyx_codeobj__6 __pyx_mstate_global->__pyx_codeobj__6
|
|
jpayne@69
|
6094 #define __pyx_codeobj__7 __pyx_mstate_global->__pyx_codeobj__7
|
|
jpayne@69
|
6095 #define __pyx_codeobj__8 __pyx_mstate_global->__pyx_codeobj__8
|
|
jpayne@69
|
6096 #define __pyx_codeobj__9 __pyx_mstate_global->__pyx_codeobj__9
|
|
jpayne@69
|
6097 #define __pyx_codeobj__10 __pyx_mstate_global->__pyx_codeobj__10
|
|
jpayne@69
|
6098 #define __pyx_codeobj__11 __pyx_mstate_global->__pyx_codeobj__11
|
|
jpayne@69
|
6099 #define __pyx_codeobj__12 __pyx_mstate_global->__pyx_codeobj__12
|
|
jpayne@69
|
6100 #define __pyx_codeobj__13 __pyx_mstate_global->__pyx_codeobj__13
|
|
jpayne@69
|
6101 #define __pyx_codeobj__14 __pyx_mstate_global->__pyx_codeobj__14
|
|
jpayne@69
|
6102 #define __pyx_codeobj__15 __pyx_mstate_global->__pyx_codeobj__15
|
|
jpayne@69
|
6103 #define __pyx_codeobj__17 __pyx_mstate_global->__pyx_codeobj__17
|
|
jpayne@69
|
6104 #define __pyx_codeobj__18 __pyx_mstate_global->__pyx_codeobj__18
|
|
jpayne@69
|
6105 #define __pyx_codeobj__21 __pyx_mstate_global->__pyx_codeobj__21
|
|
jpayne@69
|
6106 #define __pyx_codeobj__22 __pyx_mstate_global->__pyx_codeobj__22
|
|
jpayne@69
|
6107 #define __pyx_codeobj__23 __pyx_mstate_global->__pyx_codeobj__23
|
|
jpayne@69
|
6108 #define __pyx_codeobj__25 __pyx_mstate_global->__pyx_codeobj__25
|
|
jpayne@69
|
6109 #define __pyx_codeobj__26 __pyx_mstate_global->__pyx_codeobj__26
|
|
jpayne@69
|
6110 #define __pyx_codeobj__27 __pyx_mstate_global->__pyx_codeobj__27
|
|
jpayne@69
|
6111 #define __pyx_codeobj__28 __pyx_mstate_global->__pyx_codeobj__28
|
|
jpayne@69
|
6112 #define __pyx_codeobj__29 __pyx_mstate_global->__pyx_codeobj__29
|
|
jpayne@69
|
6113 #define __pyx_codeobj__30 __pyx_mstate_global->__pyx_codeobj__30
|
|
jpayne@69
|
6114 #define __pyx_codeobj__31 __pyx_mstate_global->__pyx_codeobj__31
|
|
jpayne@69
|
6115 #define __pyx_codeobj__32 __pyx_mstate_global->__pyx_codeobj__32
|
|
jpayne@69
|
6116 #define __pyx_codeobj__33 __pyx_mstate_global->__pyx_codeobj__33
|
|
jpayne@69
|
6117 #define __pyx_codeobj__34 __pyx_mstate_global->__pyx_codeobj__34
|
|
jpayne@69
|
6118 #define __pyx_codeobj__35 __pyx_mstate_global->__pyx_codeobj__35
|
|
jpayne@69
|
6119 #define __pyx_codeobj__36 __pyx_mstate_global->__pyx_codeobj__36
|
|
jpayne@69
|
6120 #define __pyx_codeobj__37 __pyx_mstate_global->__pyx_codeobj__37
|
|
jpayne@69
|
6121 #define __pyx_codeobj__40 __pyx_mstate_global->__pyx_codeobj__40
|
|
jpayne@69
|
6122 #define __pyx_codeobj__46 __pyx_mstate_global->__pyx_codeobj__46
|
|
jpayne@69
|
6123 #define __pyx_codeobj__47 __pyx_mstate_global->__pyx_codeobj__47
|
|
jpayne@69
|
6124 #define __pyx_codeobj__48 __pyx_mstate_global->__pyx_codeobj__48
|
|
jpayne@69
|
6125 #define __pyx_codeobj__49 __pyx_mstate_global->__pyx_codeobj__49
|
|
jpayne@69
|
6126 #define __pyx_codeobj__50 __pyx_mstate_global->__pyx_codeobj__50
|
|
jpayne@69
|
6127 #define __pyx_codeobj__51 __pyx_mstate_global->__pyx_codeobj__51
|
|
jpayne@69
|
6128 #define __pyx_codeobj__52 __pyx_mstate_global->__pyx_codeobj__52
|
|
jpayne@69
|
6129 #define __pyx_codeobj__53 __pyx_mstate_global->__pyx_codeobj__53
|
|
jpayne@69
|
6130 #define __pyx_codeobj__54 __pyx_mstate_global->__pyx_codeobj__54
|
|
jpayne@69
|
6131 #define __pyx_codeobj__57 __pyx_mstate_global->__pyx_codeobj__57
|
|
jpayne@69
|
6132 #define __pyx_codeobj__58 __pyx_mstate_global->__pyx_codeobj__58
|
|
jpayne@69
|
6133 #define __pyx_codeobj__59 __pyx_mstate_global->__pyx_codeobj__59
|
|
jpayne@69
|
6134 #define __pyx_codeobj__60 __pyx_mstate_global->__pyx_codeobj__60
|
|
jpayne@69
|
6135 #define __pyx_codeobj__61 __pyx_mstate_global->__pyx_codeobj__61
|
|
jpayne@69
|
6136 /* #### Code section: module_code ### */
|
|
jpayne@69
|
6137
|
|
jpayne@69
|
6138 /* "cpython/complex.pxd":19
|
|
jpayne@69
|
6139 *
|
|
jpayne@69
|
6140 * @property
|
|
jpayne@69
|
6141 * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6142 * return self.cval.real
|
|
jpayne@69
|
6143 *
|
|
jpayne@69
|
6144 */
|
|
jpayne@69
|
6145
|
|
jpayne@69
|
6146 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self) {
|
|
jpayne@69
|
6147 double __pyx_r;
|
|
jpayne@69
|
6148
|
|
jpayne@69
|
6149 /* "cpython/complex.pxd":20
|
|
jpayne@69
|
6150 * @property
|
|
jpayne@69
|
6151 * cdef inline double real(self) noexcept:
|
|
jpayne@69
|
6152 * return self.cval.real # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6153 *
|
|
jpayne@69
|
6154 * @property
|
|
jpayne@69
|
6155 */
|
|
jpayne@69
|
6156 __pyx_r = __pyx_v_self->cval.real;
|
|
jpayne@69
|
6157 goto __pyx_L0;
|
|
jpayne@69
|
6158
|
|
jpayne@69
|
6159 /* "cpython/complex.pxd":19
|
|
jpayne@69
|
6160 *
|
|
jpayne@69
|
6161 * @property
|
|
jpayne@69
|
6162 * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6163 * return self.cval.real
|
|
jpayne@69
|
6164 *
|
|
jpayne@69
|
6165 */
|
|
jpayne@69
|
6166
|
|
jpayne@69
|
6167 /* function exit code */
|
|
jpayne@69
|
6168 __pyx_L0:;
|
|
jpayne@69
|
6169 return __pyx_r;
|
|
jpayne@69
|
6170 }
|
|
jpayne@69
|
6171
|
|
jpayne@69
|
6172 /* "cpython/complex.pxd":23
|
|
jpayne@69
|
6173 *
|
|
jpayne@69
|
6174 * @property
|
|
jpayne@69
|
6175 * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6176 * return self.cval.imag
|
|
jpayne@69
|
6177 *
|
|
jpayne@69
|
6178 */
|
|
jpayne@69
|
6179
|
|
jpayne@69
|
6180 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self) {
|
|
jpayne@69
|
6181 double __pyx_r;
|
|
jpayne@69
|
6182
|
|
jpayne@69
|
6183 /* "cpython/complex.pxd":24
|
|
jpayne@69
|
6184 * @property
|
|
jpayne@69
|
6185 * cdef inline double imag(self) noexcept:
|
|
jpayne@69
|
6186 * return self.cval.imag # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6187 *
|
|
jpayne@69
|
6188 * # PyTypeObject PyComplex_Type
|
|
jpayne@69
|
6189 */
|
|
jpayne@69
|
6190 __pyx_r = __pyx_v_self->cval.imag;
|
|
jpayne@69
|
6191 goto __pyx_L0;
|
|
jpayne@69
|
6192
|
|
jpayne@69
|
6193 /* "cpython/complex.pxd":23
|
|
jpayne@69
|
6194 *
|
|
jpayne@69
|
6195 * @property
|
|
jpayne@69
|
6196 * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6197 * return self.cval.imag
|
|
jpayne@69
|
6198 *
|
|
jpayne@69
|
6199 */
|
|
jpayne@69
|
6200
|
|
jpayne@69
|
6201 /* function exit code */
|
|
jpayne@69
|
6202 __pyx_L0:;
|
|
jpayne@69
|
6203 return __pyx_r;
|
|
jpayne@69
|
6204 }
|
|
jpayne@69
|
6205
|
|
jpayne@69
|
6206 /* "cpython/contextvars.pxd":112
|
|
jpayne@69
|
6207 *
|
|
jpayne@69
|
6208 *
|
|
jpayne@69
|
6209 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6210 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
6211 * or the default value of the context variable,
|
|
jpayne@69
|
6212 */
|
|
jpayne@69
|
6213
|
|
jpayne@69
|
6214 static CYTHON_INLINE PyObject *__pyx_f_7cpython_11contextvars_get_value(PyObject *__pyx_v_var, struct __pyx_opt_args_7cpython_11contextvars_get_value *__pyx_optional_args) {
|
|
jpayne@69
|
6215 PyObject *__pyx_v_default_value = ((PyObject *)Py_None);
|
|
jpayne@69
|
6216 PyObject *__pyx_v_value;
|
|
jpayne@69
|
6217 PyObject *__pyx_v_pyvalue = NULL;
|
|
jpayne@69
|
6218 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
6219 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
6220 int __pyx_t_1;
|
|
jpayne@69
|
6221 int __pyx_t_2;
|
|
jpayne@69
|
6222 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
6223 int __pyx_lineno = 0;
|
|
jpayne@69
|
6224 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6225 int __pyx_clineno = 0;
|
|
jpayne@69
|
6226 __Pyx_RefNannySetupContext("get_value", 1);
|
|
jpayne@69
|
6227 if (__pyx_optional_args) {
|
|
jpayne@69
|
6228 if (__pyx_optional_args->__pyx_n > 0) {
|
|
jpayne@69
|
6229 __pyx_v_default_value = __pyx_optional_args->default_value;
|
|
jpayne@69
|
6230 }
|
|
jpayne@69
|
6231 }
|
|
jpayne@69
|
6232
|
|
jpayne@69
|
6233 /* "cpython/contextvars.pxd":117
|
|
jpayne@69
|
6234 * or None if no such value or default was found.
|
|
jpayne@69
|
6235 * """
|
|
jpayne@69
|
6236 * cdef PyObject *value = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6237 * PyContextVar_Get(var, NULL, &value)
|
|
jpayne@69
|
6238 * if value is NULL:
|
|
jpayne@69
|
6239 */
|
|
jpayne@69
|
6240 __pyx_v_value = NULL;
|
|
jpayne@69
|
6241
|
|
jpayne@69
|
6242 /* "cpython/contextvars.pxd":118
|
|
jpayne@69
|
6243 * """
|
|
jpayne@69
|
6244 * cdef PyObject *value = NULL
|
|
jpayne@69
|
6245 * PyContextVar_Get(var, NULL, &value) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6246 * if value is NULL:
|
|
jpayne@69
|
6247 * # context variable does not have a default
|
|
jpayne@69
|
6248 */
|
|
jpayne@69
|
6249 __pyx_t_1 = PyContextVar_Get(__pyx_v_var, NULL, (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 118, __pyx_L1_error)
|
|
jpayne@69
|
6250
|
|
jpayne@69
|
6251 /* "cpython/contextvars.pxd":119
|
|
jpayne@69
|
6252 * cdef PyObject *value = NULL
|
|
jpayne@69
|
6253 * PyContextVar_Get(var, NULL, &value)
|
|
jpayne@69
|
6254 * if value is NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6255 * # context variable does not have a default
|
|
jpayne@69
|
6256 * pyvalue = default_value
|
|
jpayne@69
|
6257 */
|
|
jpayne@69
|
6258 __pyx_t_2 = (__pyx_v_value == NULL);
|
|
jpayne@69
|
6259 if (__pyx_t_2) {
|
|
jpayne@69
|
6260
|
|
jpayne@69
|
6261 /* "cpython/contextvars.pxd":121
|
|
jpayne@69
|
6262 * if value is NULL:
|
|
jpayne@69
|
6263 * # context variable does not have a default
|
|
jpayne@69
|
6264 * pyvalue = default_value # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6265 * else:
|
|
jpayne@69
|
6266 * # value or default value of context variable
|
|
jpayne@69
|
6267 */
|
|
jpayne@69
|
6268 __Pyx_INCREF(__pyx_v_default_value);
|
|
jpayne@69
|
6269 __pyx_v_pyvalue = __pyx_v_default_value;
|
|
jpayne@69
|
6270
|
|
jpayne@69
|
6271 /* "cpython/contextvars.pxd":119
|
|
jpayne@69
|
6272 * cdef PyObject *value = NULL
|
|
jpayne@69
|
6273 * PyContextVar_Get(var, NULL, &value)
|
|
jpayne@69
|
6274 * if value is NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6275 * # context variable does not have a default
|
|
jpayne@69
|
6276 * pyvalue = default_value
|
|
jpayne@69
|
6277 */
|
|
jpayne@69
|
6278 goto __pyx_L3;
|
|
jpayne@69
|
6279 }
|
|
jpayne@69
|
6280
|
|
jpayne@69
|
6281 /* "cpython/contextvars.pxd":124
|
|
jpayne@69
|
6282 * else:
|
|
jpayne@69
|
6283 * # value or default value of context variable
|
|
jpayne@69
|
6284 * pyvalue = <object>value # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6285 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
6286 * return pyvalue
|
|
jpayne@69
|
6287 */
|
|
jpayne@69
|
6288 /*else*/ {
|
|
jpayne@69
|
6289 __pyx_t_3 = ((PyObject *)__pyx_v_value);
|
|
jpayne@69
|
6290 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
6291 __pyx_v_pyvalue = __pyx_t_3;
|
|
jpayne@69
|
6292 __pyx_t_3 = 0;
|
|
jpayne@69
|
6293
|
|
jpayne@69
|
6294 /* "cpython/contextvars.pxd":125
|
|
jpayne@69
|
6295 * # value or default value of context variable
|
|
jpayne@69
|
6296 * pyvalue = <object>value
|
|
jpayne@69
|
6297 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6298 * return pyvalue
|
|
jpayne@69
|
6299 *
|
|
jpayne@69
|
6300 */
|
|
jpayne@69
|
6301 Py_XDECREF(__pyx_v_value);
|
|
jpayne@69
|
6302 }
|
|
jpayne@69
|
6303 __pyx_L3:;
|
|
jpayne@69
|
6304
|
|
jpayne@69
|
6305 /* "cpython/contextvars.pxd":126
|
|
jpayne@69
|
6306 * pyvalue = <object>value
|
|
jpayne@69
|
6307 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
6308 * return pyvalue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6309 *
|
|
jpayne@69
|
6310 *
|
|
jpayne@69
|
6311 */
|
|
jpayne@69
|
6312 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
6313 __Pyx_INCREF(__pyx_v_pyvalue);
|
|
jpayne@69
|
6314 __pyx_r = __pyx_v_pyvalue;
|
|
jpayne@69
|
6315 goto __pyx_L0;
|
|
jpayne@69
|
6316
|
|
jpayne@69
|
6317 /* "cpython/contextvars.pxd":112
|
|
jpayne@69
|
6318 *
|
|
jpayne@69
|
6319 *
|
|
jpayne@69
|
6320 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6321 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
6322 * or the default value of the context variable,
|
|
jpayne@69
|
6323 */
|
|
jpayne@69
|
6324
|
|
jpayne@69
|
6325 /* function exit code */
|
|
jpayne@69
|
6326 __pyx_L1_error:;
|
|
jpayne@69
|
6327 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
6328 __Pyx_AddTraceback("cpython.contextvars.get_value", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6329 __pyx_r = 0;
|
|
jpayne@69
|
6330 __pyx_L0:;
|
|
jpayne@69
|
6331 __Pyx_XDECREF(__pyx_v_pyvalue);
|
|
jpayne@69
|
6332 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
6333 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
6334 return __pyx_r;
|
|
jpayne@69
|
6335 }
|
|
jpayne@69
|
6336
|
|
jpayne@69
|
6337 /* "cpython/contextvars.pxd":129
|
|
jpayne@69
|
6338 *
|
|
jpayne@69
|
6339 *
|
|
jpayne@69
|
6340 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6341 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
6342 * or the provided default value if no such value was found.
|
|
jpayne@69
|
6343 */
|
|
jpayne@69
|
6344
|
|
jpayne@69
|
6345 static CYTHON_INLINE PyObject *__pyx_f_7cpython_11contextvars_get_value_no_default(PyObject *__pyx_v_var, struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default *__pyx_optional_args) {
|
|
jpayne@69
|
6346 PyObject *__pyx_v_default_value = ((PyObject *)Py_None);
|
|
jpayne@69
|
6347 PyObject *__pyx_v_value;
|
|
jpayne@69
|
6348 PyObject *__pyx_v_pyvalue = NULL;
|
|
jpayne@69
|
6349 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
6350 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
6351 int __pyx_t_1;
|
|
jpayne@69
|
6352 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
6353 int __pyx_lineno = 0;
|
|
jpayne@69
|
6354 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6355 int __pyx_clineno = 0;
|
|
jpayne@69
|
6356 __Pyx_RefNannySetupContext("get_value_no_default", 1);
|
|
jpayne@69
|
6357 if (__pyx_optional_args) {
|
|
jpayne@69
|
6358 if (__pyx_optional_args->__pyx_n > 0) {
|
|
jpayne@69
|
6359 __pyx_v_default_value = __pyx_optional_args->default_value;
|
|
jpayne@69
|
6360 }
|
|
jpayne@69
|
6361 }
|
|
jpayne@69
|
6362
|
|
jpayne@69
|
6363 /* "cpython/contextvars.pxd":135
|
|
jpayne@69
|
6364 * Ignores the default value of the context variable, if any.
|
|
jpayne@69
|
6365 * """
|
|
jpayne@69
|
6366 * cdef PyObject *value = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6367 * PyContextVar_Get(var, <PyObject*>default_value, &value)
|
|
jpayne@69
|
6368 * # value of context variable or 'default_value'
|
|
jpayne@69
|
6369 */
|
|
jpayne@69
|
6370 __pyx_v_value = NULL;
|
|
jpayne@69
|
6371
|
|
jpayne@69
|
6372 /* "cpython/contextvars.pxd":136
|
|
jpayne@69
|
6373 * """
|
|
jpayne@69
|
6374 * cdef PyObject *value = NULL
|
|
jpayne@69
|
6375 * PyContextVar_Get(var, <PyObject*>default_value, &value) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6376 * # value of context variable or 'default_value'
|
|
jpayne@69
|
6377 * pyvalue = <object>value
|
|
jpayne@69
|
6378 */
|
|
jpayne@69
|
6379 __pyx_t_1 = PyContextVar_Get(__pyx_v_var, ((PyObject *)__pyx_v_default_value), (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 136, __pyx_L1_error)
|
|
jpayne@69
|
6380
|
|
jpayne@69
|
6381 /* "cpython/contextvars.pxd":138
|
|
jpayne@69
|
6382 * PyContextVar_Get(var, <PyObject*>default_value, &value)
|
|
jpayne@69
|
6383 * # value of context variable or 'default_value'
|
|
jpayne@69
|
6384 * pyvalue = <object>value # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6385 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
6386 * return pyvalue
|
|
jpayne@69
|
6387 */
|
|
jpayne@69
|
6388 __pyx_t_2 = ((PyObject *)__pyx_v_value);
|
|
jpayne@69
|
6389 __Pyx_INCREF(__pyx_t_2);
|
|
jpayne@69
|
6390 __pyx_v_pyvalue = __pyx_t_2;
|
|
jpayne@69
|
6391 __pyx_t_2 = 0;
|
|
jpayne@69
|
6392
|
|
jpayne@69
|
6393 /* "cpython/contextvars.pxd":139
|
|
jpayne@69
|
6394 * # value of context variable or 'default_value'
|
|
jpayne@69
|
6395 * pyvalue = <object>value
|
|
jpayne@69
|
6396 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6397 * return pyvalue
|
|
jpayne@69
|
6398 */
|
|
jpayne@69
|
6399 Py_XDECREF(__pyx_v_value);
|
|
jpayne@69
|
6400
|
|
jpayne@69
|
6401 /* "cpython/contextvars.pxd":140
|
|
jpayne@69
|
6402 * pyvalue = <object>value
|
|
jpayne@69
|
6403 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
6404 * return pyvalue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6405 */
|
|
jpayne@69
|
6406 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
6407 __Pyx_INCREF(__pyx_v_pyvalue);
|
|
jpayne@69
|
6408 __pyx_r = __pyx_v_pyvalue;
|
|
jpayne@69
|
6409 goto __pyx_L0;
|
|
jpayne@69
|
6410
|
|
jpayne@69
|
6411 /* "cpython/contextvars.pxd":129
|
|
jpayne@69
|
6412 *
|
|
jpayne@69
|
6413 *
|
|
jpayne@69
|
6414 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6415 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
6416 * or the provided default value if no such value was found.
|
|
jpayne@69
|
6417 */
|
|
jpayne@69
|
6418
|
|
jpayne@69
|
6419 /* function exit code */
|
|
jpayne@69
|
6420 __pyx_L1_error:;
|
|
jpayne@69
|
6421 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
6422 __Pyx_AddTraceback("cpython.contextvars.get_value_no_default", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6423 __pyx_r = 0;
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jpayne@69
|
6424 __pyx_L0:;
|
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jpayne@69
|
6425 __Pyx_XDECREF(__pyx_v_pyvalue);
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jpayne@69
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6426 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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6427 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
6428 return __pyx_r;
|
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jpayne@69
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6429 }
|
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jpayne@69
|
6430
|
|
jpayne@69
|
6431 /* "array.pxd":104
|
|
jpayne@69
|
6432 * __data_union data
|
|
jpayne@69
|
6433 *
|
|
jpayne@69
|
6434 * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6435 * # This implementation of getbuffer is geared towards Cython
|
|
jpayne@69
|
6436 * # requirements, and does not yet fulfill the PEP.
|
|
jpayne@69
|
6437 */
|
|
jpayne@69
|
6438
|
|
jpayne@69
|
6439 /* Python wrapper */
|
|
jpayne@69
|
6440 CYTHON_UNUSED static int __pyx_pw_7cpython_5array_5array_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/
|
|
jpayne@69
|
6441 CYTHON_UNUSED static int __pyx_pw_7cpython_5array_5array_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) {
|
|
jpayne@69
|
6442 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
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jpayne@69
|
6443 int __pyx_r;
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jpayne@69
|
6444 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
6445 __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0);
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jpayne@69
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6446 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
6447 __pyx_r = __pyx_pf_7cpython_5array_5array___getbuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags));
|
|
jpayne@69
|
6448
|
|
jpayne@69
|
6449 /* function exit code */
|
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jpayne@69
|
6450 __Pyx_RefNannyFinishContext();
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jpayne@69
|
6451 return __pyx_r;
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jpayne@69
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6452 }
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jpayne@69
|
6453
|
|
jpayne@69
|
6454 static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags) {
|
|
jpayne@69
|
6455 PyObject *__pyx_v_item_count = NULL;
|
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jpayne@69
|
6456 int __pyx_r;
|
|
jpayne@69
|
6457 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
6458 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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6459 char *__pyx_t_2;
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jpayne@69
|
6460 int __pyx_t_3;
|
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jpayne@69
|
6461 PyObject *__pyx_t_4 = NULL;
|
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jpayne@69
|
6462 Py_ssize_t __pyx_t_5;
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jpayne@69
|
6463 int __pyx_t_6;
|
|
jpayne@69
|
6464 char __pyx_t_7;
|
|
jpayne@69
|
6465 int __pyx_lineno = 0;
|
|
jpayne@69
|
6466 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6467 int __pyx_clineno = 0;
|
|
jpayne@69
|
6468 if (unlikely(__pyx_v_info == NULL)) {
|
|
jpayne@69
|
6469 PyErr_SetString(PyExc_BufferError, "PyObject_GetBuffer: view==NULL argument is obsolete");
|
|
jpayne@69
|
6470 return -1;
|
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jpayne@69
|
6471 }
|
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jpayne@69
|
6472 __Pyx_RefNannySetupContext("__getbuffer__", 0);
|
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jpayne@69
|
6473 __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None);
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jpayne@69
|
6474 __Pyx_GIVEREF(__pyx_v_info->obj);
|
|
jpayne@69
|
6475
|
|
jpayne@69
|
6476 /* "array.pxd":109
|
|
jpayne@69
|
6477 * # In particular strided access is always provided regardless
|
|
jpayne@69
|
6478 * # of flags
|
|
jpayne@69
|
6479 * item_count = Py_SIZE(self) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6480 *
|
|
jpayne@69
|
6481 * info.suboffsets = NULL
|
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jpayne@69
|
6482 */
|
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jpayne@69
|
6483 __pyx_t_1 = PyInt_FromSsize_t(Py_SIZE(((PyObject *)__pyx_v_self))); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 109, __pyx_L1_error)
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jpayne@69
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6484 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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6485 __pyx_v_item_count = __pyx_t_1;
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jpayne@69
|
6486 __pyx_t_1 = 0;
|
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jpayne@69
|
6487
|
|
jpayne@69
|
6488 /* "array.pxd":111
|
|
jpayne@69
|
6489 * item_count = Py_SIZE(self)
|
|
jpayne@69
|
6490 *
|
|
jpayne@69
|
6491 * info.suboffsets = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6492 * info.buf = self.data.as_chars
|
|
jpayne@69
|
6493 * info.readonly = 0
|
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jpayne@69
|
6494 */
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jpayne@69
|
6495 __pyx_v_info->suboffsets = NULL;
|
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jpayne@69
|
6496
|
|
jpayne@69
|
6497 /* "array.pxd":112
|
|
jpayne@69
|
6498 *
|
|
jpayne@69
|
6499 * info.suboffsets = NULL
|
|
jpayne@69
|
6500 * info.buf = self.data.as_chars # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6501 * info.readonly = 0
|
|
jpayne@69
|
6502 * info.ndim = 1
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jpayne@69
|
6503 */
|
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jpayne@69
|
6504 __pyx_t_2 = __pyx_v_self->data.as_chars;
|
|
jpayne@69
|
6505 __pyx_v_info->buf = __pyx_t_2;
|
|
jpayne@69
|
6506
|
|
jpayne@69
|
6507 /* "array.pxd":113
|
|
jpayne@69
|
6508 * info.suboffsets = NULL
|
|
jpayne@69
|
6509 * info.buf = self.data.as_chars
|
|
jpayne@69
|
6510 * info.readonly = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6511 * info.ndim = 1
|
|
jpayne@69
|
6512 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
|
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jpayne@69
|
6513 */
|
|
jpayne@69
|
6514 __pyx_v_info->readonly = 0;
|
|
jpayne@69
|
6515
|
|
jpayne@69
|
6516 /* "array.pxd":114
|
|
jpayne@69
|
6517 * info.buf = self.data.as_chars
|
|
jpayne@69
|
6518 * info.readonly = 0
|
|
jpayne@69
|
6519 * info.ndim = 1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6520 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
|
|
jpayne@69
|
6521 * info.len = info.itemsize * item_count
|
|
jpayne@69
|
6522 */
|
|
jpayne@69
|
6523 __pyx_v_info->ndim = 1;
|
|
jpayne@69
|
6524
|
|
jpayne@69
|
6525 /* "array.pxd":115
|
|
jpayne@69
|
6526 * info.readonly = 0
|
|
jpayne@69
|
6527 * info.ndim = 1
|
|
jpayne@69
|
6528 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6529 * info.len = info.itemsize * item_count
|
|
jpayne@69
|
6530 *
|
|
jpayne@69
|
6531 */
|
|
jpayne@69
|
6532 __pyx_t_3 = __pyx_v_self->ob_descr->itemsize;
|
|
jpayne@69
|
6533 __pyx_v_info->itemsize = __pyx_t_3;
|
|
jpayne@69
|
6534
|
|
jpayne@69
|
6535 /* "array.pxd":116
|
|
jpayne@69
|
6536 * info.ndim = 1
|
|
jpayne@69
|
6537 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
|
|
jpayne@69
|
6538 * info.len = info.itemsize * item_count # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6539 *
|
|
jpayne@69
|
6540 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
|
jpayne@69
|
6541 */
|
|
jpayne@69
|
6542 __pyx_t_1 = PyInt_FromSsize_t(__pyx_v_info->itemsize); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 116, __pyx_L1_error)
|
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jpayne@69
|
6543 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
6544 __pyx_t_4 = PyNumber_Multiply(__pyx_t_1, __pyx_v_item_count); if (unlikely(!__pyx_t_4)) __PYX_ERR(3, 116, __pyx_L1_error)
|
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jpayne@69
|
6545 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
|
6546 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
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jpayne@69
|
6547 __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(3, 116, __pyx_L1_error)
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jpayne@69
|
6548 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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|
jpayne@69
|
6549 __pyx_v_info->len = __pyx_t_5;
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jpayne@69
|
6550
|
|
jpayne@69
|
6551 /* "array.pxd":118
|
|
jpayne@69
|
6552 * info.len = info.itemsize * item_count
|
|
jpayne@69
|
6553 *
|
|
jpayne@69
|
6554 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6555 * if not info.shape:
|
|
jpayne@69
|
6556 * raise MemoryError()
|
|
jpayne@69
|
6557 */
|
|
jpayne@69
|
6558 __pyx_v_info->shape = ((Py_ssize_t *)PyObject_Malloc(((sizeof(Py_ssize_t)) + 2)));
|
|
jpayne@69
|
6559
|
|
jpayne@69
|
6560 /* "array.pxd":119
|
|
jpayne@69
|
6561 *
|
|
jpayne@69
|
6562 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
|
jpayne@69
|
6563 * if not info.shape: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6564 * raise MemoryError()
|
|
jpayne@69
|
6565 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
6566 */
|
|
jpayne@69
|
6567 __pyx_t_6 = (!(__pyx_v_info->shape != 0));
|
|
jpayne@69
|
6568 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
6569
|
|
jpayne@69
|
6570 /* "array.pxd":120
|
|
jpayne@69
|
6571 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
|
jpayne@69
|
6572 * if not info.shape:
|
|
jpayne@69
|
6573 * raise MemoryError() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6574 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
6575 * info.strides = &info.itemsize
|
|
jpayne@69
|
6576 */
|
|
jpayne@69
|
6577 PyErr_NoMemory(); __PYX_ERR(3, 120, __pyx_L1_error)
|
|
jpayne@69
|
6578
|
|
jpayne@69
|
6579 /* "array.pxd":119
|
|
jpayne@69
|
6580 *
|
|
jpayne@69
|
6581 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
|
jpayne@69
|
6582 * if not info.shape: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6583 * raise MemoryError()
|
|
jpayne@69
|
6584 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
6585 */
|
|
jpayne@69
|
6586 }
|
|
jpayne@69
|
6587
|
|
jpayne@69
|
6588 /* "array.pxd":121
|
|
jpayne@69
|
6589 * if not info.shape:
|
|
jpayne@69
|
6590 * raise MemoryError()
|
|
jpayne@69
|
6591 * info.shape[0] = item_count # constant regardless of resizing # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6592 * info.strides = &info.itemsize
|
|
jpayne@69
|
6593 *
|
|
jpayne@69
|
6594 */
|
|
jpayne@69
|
6595 __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_item_count); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(3, 121, __pyx_L1_error)
|
|
jpayne@69
|
6596 (__pyx_v_info->shape[0]) = __pyx_t_5;
|
|
jpayne@69
|
6597
|
|
jpayne@69
|
6598 /* "array.pxd":122
|
|
jpayne@69
|
6599 * raise MemoryError()
|
|
jpayne@69
|
6600 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
6601 * info.strides = &info.itemsize # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6602 *
|
|
jpayne@69
|
6603 * info.format = <char*> (info.shape + 1)
|
|
jpayne@69
|
6604 */
|
|
jpayne@69
|
6605 __pyx_v_info->strides = (&__pyx_v_info->itemsize);
|
|
jpayne@69
|
6606
|
|
jpayne@69
|
6607 /* "array.pxd":124
|
|
jpayne@69
|
6608 * info.strides = &info.itemsize
|
|
jpayne@69
|
6609 *
|
|
jpayne@69
|
6610 * info.format = <char*> (info.shape + 1) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6611 * info.format[0] = self.ob_descr.typecode
|
|
jpayne@69
|
6612 * info.format[1] = 0
|
|
jpayne@69
|
6613 */
|
|
jpayne@69
|
6614 __pyx_v_info->format = ((char *)(__pyx_v_info->shape + 1));
|
|
jpayne@69
|
6615
|
|
jpayne@69
|
6616 /* "array.pxd":125
|
|
jpayne@69
|
6617 *
|
|
jpayne@69
|
6618 * info.format = <char*> (info.shape + 1)
|
|
jpayne@69
|
6619 * info.format[0] = self.ob_descr.typecode # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6620 * info.format[1] = 0
|
|
jpayne@69
|
6621 * info.obj = self
|
|
jpayne@69
|
6622 */
|
|
jpayne@69
|
6623 __pyx_t_7 = __pyx_v_self->ob_descr->typecode;
|
|
jpayne@69
|
6624 (__pyx_v_info->format[0]) = __pyx_t_7;
|
|
jpayne@69
|
6625
|
|
jpayne@69
|
6626 /* "array.pxd":126
|
|
jpayne@69
|
6627 * info.format = <char*> (info.shape + 1)
|
|
jpayne@69
|
6628 * info.format[0] = self.ob_descr.typecode
|
|
jpayne@69
|
6629 * info.format[1] = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6630 * info.obj = self
|
|
jpayne@69
|
6631 *
|
|
jpayne@69
|
6632 */
|
|
jpayne@69
|
6633 (__pyx_v_info->format[1]) = 0;
|
|
jpayne@69
|
6634
|
|
jpayne@69
|
6635 /* "array.pxd":127
|
|
jpayne@69
|
6636 * info.format[0] = self.ob_descr.typecode
|
|
jpayne@69
|
6637 * info.format[1] = 0
|
|
jpayne@69
|
6638 * info.obj = self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6639 *
|
|
jpayne@69
|
6640 * def __releasebuffer__(self, Py_buffer* info):
|
|
jpayne@69
|
6641 */
|
|
jpayne@69
|
6642 __Pyx_INCREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
6643 __Pyx_GIVEREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
6644 __Pyx_GOTREF(__pyx_v_info->obj);
|
|
jpayne@69
|
6645 __Pyx_DECREF(__pyx_v_info->obj);
|
|
jpayne@69
|
6646 __pyx_v_info->obj = ((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
6647
|
|
jpayne@69
|
6648 /* "array.pxd":104
|
|
jpayne@69
|
6649 * __data_union data
|
|
jpayne@69
|
6650 *
|
|
jpayne@69
|
6651 * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6652 * # This implementation of getbuffer is geared towards Cython
|
|
jpayne@69
|
6653 * # requirements, and does not yet fulfill the PEP.
|
|
jpayne@69
|
6654 */
|
|
jpayne@69
|
6655
|
|
jpayne@69
|
6656 /* function exit code */
|
|
jpayne@69
|
6657 __pyx_r = 0;
|
|
jpayne@69
|
6658 goto __pyx_L0;
|
|
jpayne@69
|
6659 __pyx_L1_error:;
|
|
jpayne@69
|
6660 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
6661 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
6662 __Pyx_AddTraceback("cpython.array.array.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6663 __pyx_r = -1;
|
|
jpayne@69
|
6664 if (__pyx_v_info->obj != NULL) {
|
|
jpayne@69
|
6665 __Pyx_GOTREF(__pyx_v_info->obj);
|
|
jpayne@69
|
6666 __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0;
|
|
jpayne@69
|
6667 }
|
|
jpayne@69
|
6668 goto __pyx_L2;
|
|
jpayne@69
|
6669 __pyx_L0:;
|
|
jpayne@69
|
6670 if (__pyx_v_info->obj == Py_None) {
|
|
jpayne@69
|
6671 __Pyx_GOTREF(__pyx_v_info->obj);
|
|
jpayne@69
|
6672 __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0;
|
|
jpayne@69
|
6673 }
|
|
jpayne@69
|
6674 __pyx_L2:;
|
|
jpayne@69
|
6675 __Pyx_XDECREF(__pyx_v_item_count);
|
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jpayne@69
|
6676 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
6677 return __pyx_r;
|
|
jpayne@69
|
6678 }
|
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jpayne@69
|
6679
|
|
jpayne@69
|
6680 /* "array.pxd":129
|
|
jpayne@69
|
6681 * info.obj = self
|
|
jpayne@69
|
6682 *
|
|
jpayne@69
|
6683 * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6684 * PyObject_Free(info.shape)
|
|
jpayne@69
|
6685 *
|
|
jpayne@69
|
6686 */
|
|
jpayne@69
|
6687
|
|
jpayne@69
|
6688 /* Python wrapper */
|
|
jpayne@69
|
6689 CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/
|
|
jpayne@69
|
6690 CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) {
|
|
jpayne@69
|
6691 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
6692 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
6693 __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0);
|
|
jpayne@69
|
6694 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
6695 __pyx_pf_7cpython_5array_5array_2__releasebuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info));
|
|
jpayne@69
|
6696
|
|
jpayne@69
|
6697 /* function exit code */
|
|
jpayne@69
|
6698 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
6699 }
|
|
jpayne@69
|
6700
|
|
jpayne@69
|
6701 static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info) {
|
|
jpayne@69
|
6702
|
|
jpayne@69
|
6703 /* "array.pxd":130
|
|
jpayne@69
|
6704 *
|
|
jpayne@69
|
6705 * def __releasebuffer__(self, Py_buffer* info):
|
|
jpayne@69
|
6706 * PyObject_Free(info.shape) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6707 *
|
|
jpayne@69
|
6708 * array newarrayobject(PyTypeObject* type, Py_ssize_t size, arraydescr *descr)
|
|
jpayne@69
|
6709 */
|
|
jpayne@69
|
6710 PyObject_Free(__pyx_v_info->shape);
|
|
jpayne@69
|
6711
|
|
jpayne@69
|
6712 /* "array.pxd":129
|
|
jpayne@69
|
6713 * info.obj = self
|
|
jpayne@69
|
6714 *
|
|
jpayne@69
|
6715 * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6716 * PyObject_Free(info.shape)
|
|
jpayne@69
|
6717 *
|
|
jpayne@69
|
6718 */
|
|
jpayne@69
|
6719
|
|
jpayne@69
|
6720 /* function exit code */
|
|
jpayne@69
|
6721 }
|
|
jpayne@69
|
6722
|
|
jpayne@69
|
6723 /* "array.pxd":141
|
|
jpayne@69
|
6724 *
|
|
jpayne@69
|
6725 *
|
|
jpayne@69
|
6726 * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6727 * """ fast creation of a new array, given a template array.
|
|
jpayne@69
|
6728 * type will be same as template.
|
|
jpayne@69
|
6729 */
|
|
jpayne@69
|
6730
|
|
jpayne@69
|
6731 static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_clone(arrayobject *__pyx_v_template, Py_ssize_t __pyx_v_length, int __pyx_v_zero) {
|
|
jpayne@69
|
6732 arrayobject *__pyx_v_op = 0;
|
|
jpayne@69
|
6733 arrayobject *__pyx_r = NULL;
|
|
jpayne@69
|
6734 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
6735 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
6736 int __pyx_t_2;
|
|
jpayne@69
|
6737 int __pyx_t_3;
|
|
jpayne@69
|
6738 int __pyx_lineno = 0;
|
|
jpayne@69
|
6739 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6740 int __pyx_clineno = 0;
|
|
jpayne@69
|
6741 __Pyx_RefNannySetupContext("clone", 1);
|
|
jpayne@69
|
6742
|
|
jpayne@69
|
6743 /* "array.pxd":145
|
|
jpayne@69
|
6744 * type will be same as template.
|
|
jpayne@69
|
6745 * if zero is true, new array will be initialized with zeroes."""
|
|
jpayne@69
|
6746 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6747 * if zero and op is not None:
|
|
jpayne@69
|
6748 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
6749 */
|
|
jpayne@69
|
6750 __pyx_t_1 = ((PyObject *)newarrayobject(Py_TYPE(((PyObject *)__pyx_v_template)), __pyx_v_length, __pyx_v_template->ob_descr)); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 145, __pyx_L1_error)
|
|
jpayne@69
|
6751 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
6752 __pyx_v_op = ((arrayobject *)__pyx_t_1);
|
|
jpayne@69
|
6753 __pyx_t_1 = 0;
|
|
jpayne@69
|
6754
|
|
jpayne@69
|
6755 /* "array.pxd":146
|
|
jpayne@69
|
6756 * if zero is true, new array will be initialized with zeroes."""
|
|
jpayne@69
|
6757 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
|
|
jpayne@69
|
6758 * if zero and op is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6759 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
6760 * return op
|
|
jpayne@69
|
6761 */
|
|
jpayne@69
|
6762 if (__pyx_v_zero) {
|
|
jpayne@69
|
6763 } else {
|
|
jpayne@69
|
6764 __pyx_t_2 = __pyx_v_zero;
|
|
jpayne@69
|
6765 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
6766 }
|
|
jpayne@69
|
6767 __pyx_t_3 = (((PyObject *)__pyx_v_op) != Py_None);
|
|
jpayne@69
|
6768 __pyx_t_2 = __pyx_t_3;
|
|
jpayne@69
|
6769 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
6770 if (__pyx_t_2) {
|
|
jpayne@69
|
6771
|
|
jpayne@69
|
6772 /* "array.pxd":147
|
|
jpayne@69
|
6773 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
|
|
jpayne@69
|
6774 * if zero and op is not None:
|
|
jpayne@69
|
6775 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6776 * return op
|
|
jpayne@69
|
6777 *
|
|
jpayne@69
|
6778 */
|
|
jpayne@69
|
6779 (void)(memset(__pyx_v_op->data.as_chars, 0, (__pyx_v_length * __pyx_v_op->ob_descr->itemsize)));
|
|
jpayne@69
|
6780
|
|
jpayne@69
|
6781 /* "array.pxd":146
|
|
jpayne@69
|
6782 * if zero is true, new array will be initialized with zeroes."""
|
|
jpayne@69
|
6783 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
|
|
jpayne@69
|
6784 * if zero and op is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6785 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
6786 * return op
|
|
jpayne@69
|
6787 */
|
|
jpayne@69
|
6788 }
|
|
jpayne@69
|
6789
|
|
jpayne@69
|
6790 /* "array.pxd":148
|
|
jpayne@69
|
6791 * if zero and op is not None:
|
|
jpayne@69
|
6792 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
6793 * return op # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6794 *
|
|
jpayne@69
|
6795 * cdef inline array copy(array self):
|
|
jpayne@69
|
6796 */
|
|
jpayne@69
|
6797 __Pyx_XDECREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
6798 __Pyx_INCREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
6799 __pyx_r = __pyx_v_op;
|
|
jpayne@69
|
6800 goto __pyx_L0;
|
|
jpayne@69
|
6801
|
|
jpayne@69
|
6802 /* "array.pxd":141
|
|
jpayne@69
|
6803 *
|
|
jpayne@69
|
6804 *
|
|
jpayne@69
|
6805 * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6806 * """ fast creation of a new array, given a template array.
|
|
jpayne@69
|
6807 * type will be same as template.
|
|
jpayne@69
|
6808 */
|
|
jpayne@69
|
6809
|
|
jpayne@69
|
6810 /* function exit code */
|
|
jpayne@69
|
6811 __pyx_L1_error:;
|
|
jpayne@69
|
6812 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
6813 __Pyx_AddTraceback("cpython.array.clone", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6814 __pyx_r = 0;
|
|
jpayne@69
|
6815 __pyx_L0:;
|
|
jpayne@69
|
6816 __Pyx_XDECREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
6817 __Pyx_XGIVEREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
6818 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
6819 return __pyx_r;
|
|
jpayne@69
|
6820 }
|
|
jpayne@69
|
6821
|
|
jpayne@69
|
6822 /* "array.pxd":150
|
|
jpayne@69
|
6823 * return op
|
|
jpayne@69
|
6824 *
|
|
jpayne@69
|
6825 * cdef inline array copy(array self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6826 * """ make a copy of an array. """
|
|
jpayne@69
|
6827 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
6828 */
|
|
jpayne@69
|
6829
|
|
jpayne@69
|
6830 static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_copy(arrayobject *__pyx_v_self) {
|
|
jpayne@69
|
6831 arrayobject *__pyx_v_op = 0;
|
|
jpayne@69
|
6832 arrayobject *__pyx_r = NULL;
|
|
jpayne@69
|
6833 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
6834 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
6835 int __pyx_lineno = 0;
|
|
jpayne@69
|
6836 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6837 int __pyx_clineno = 0;
|
|
jpayne@69
|
6838 __Pyx_RefNannySetupContext("copy", 1);
|
|
jpayne@69
|
6839
|
|
jpayne@69
|
6840 /* "array.pxd":152
|
|
jpayne@69
|
6841 * cdef inline array copy(array self):
|
|
jpayne@69
|
6842 * """ make a copy of an array. """
|
|
jpayne@69
|
6843 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6844 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize)
|
|
jpayne@69
|
6845 * return op
|
|
jpayne@69
|
6846 */
|
|
jpayne@69
|
6847 __pyx_t_1 = ((PyObject *)newarrayobject(Py_TYPE(((PyObject *)__pyx_v_self)), Py_SIZE(((PyObject *)__pyx_v_self)), __pyx_v_self->ob_descr)); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 152, __pyx_L1_error)
|
|
jpayne@69
|
6848 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
6849 __pyx_v_op = ((arrayobject *)__pyx_t_1);
|
|
jpayne@69
|
6850 __pyx_t_1 = 0;
|
|
jpayne@69
|
6851
|
|
jpayne@69
|
6852 /* "array.pxd":153
|
|
jpayne@69
|
6853 * """ make a copy of an array. """
|
|
jpayne@69
|
6854 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
6855 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6856 * return op
|
|
jpayne@69
|
6857 *
|
|
jpayne@69
|
6858 */
|
|
jpayne@69
|
6859 (void)(memcpy(__pyx_v_op->data.as_chars, __pyx_v_self->data.as_chars, (Py_SIZE(((PyObject *)__pyx_v_op)) * __pyx_v_op->ob_descr->itemsize)));
|
|
jpayne@69
|
6860
|
|
jpayne@69
|
6861 /* "array.pxd":154
|
|
jpayne@69
|
6862 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
6863 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize)
|
|
jpayne@69
|
6864 * return op # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6865 *
|
|
jpayne@69
|
6866 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1:
|
|
jpayne@69
|
6867 */
|
|
jpayne@69
|
6868 __Pyx_XDECREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
6869 __Pyx_INCREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
6870 __pyx_r = __pyx_v_op;
|
|
jpayne@69
|
6871 goto __pyx_L0;
|
|
jpayne@69
|
6872
|
|
jpayne@69
|
6873 /* "array.pxd":150
|
|
jpayne@69
|
6874 * return op
|
|
jpayne@69
|
6875 *
|
|
jpayne@69
|
6876 * cdef inline array copy(array self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6877 * """ make a copy of an array. """
|
|
jpayne@69
|
6878 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
6879 */
|
|
jpayne@69
|
6880
|
|
jpayne@69
|
6881 /* function exit code */
|
|
jpayne@69
|
6882 __pyx_L1_error:;
|
|
jpayne@69
|
6883 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
6884 __Pyx_AddTraceback("cpython.array.copy", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6885 __pyx_r = 0;
|
|
jpayne@69
|
6886 __pyx_L0:;
|
|
jpayne@69
|
6887 __Pyx_XDECREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
6888 __Pyx_XGIVEREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
6889 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
6890 return __pyx_r;
|
|
jpayne@69
|
6891 }
|
|
jpayne@69
|
6892
|
|
jpayne@69
|
6893 /* "array.pxd":156
|
|
jpayne@69
|
6894 * return op
|
|
jpayne@69
|
6895 *
|
|
jpayne@69
|
6896 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6897 * """ efficient appending of new stuff of same type
|
|
jpayne@69
|
6898 * (e.g. of same array type)
|
|
jpayne@69
|
6899 */
|
|
jpayne@69
|
6900
|
|
jpayne@69
|
6901 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *__pyx_v_self, char *__pyx_v_stuff, Py_ssize_t __pyx_v_n) {
|
|
jpayne@69
|
6902 Py_ssize_t __pyx_v_itemsize;
|
|
jpayne@69
|
6903 Py_ssize_t __pyx_v_origsize;
|
|
jpayne@69
|
6904 int __pyx_r;
|
|
jpayne@69
|
6905 int __pyx_t_1;
|
|
jpayne@69
|
6906 int __pyx_lineno = 0;
|
|
jpayne@69
|
6907 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6908 int __pyx_clineno = 0;
|
|
jpayne@69
|
6909
|
|
jpayne@69
|
6910 /* "array.pxd":160
|
|
jpayne@69
|
6911 * (e.g. of same array type)
|
|
jpayne@69
|
6912 * n: number of elements (not number of bytes!) """
|
|
jpayne@69
|
6913 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6914 * cdef Py_ssize_t origsize = Py_SIZE(self)
|
|
jpayne@69
|
6915 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
6916 */
|
|
jpayne@69
|
6917 __pyx_t_1 = __pyx_v_self->ob_descr->itemsize;
|
|
jpayne@69
|
6918 __pyx_v_itemsize = __pyx_t_1;
|
|
jpayne@69
|
6919
|
|
jpayne@69
|
6920 /* "array.pxd":161
|
|
jpayne@69
|
6921 * n: number of elements (not number of bytes!) """
|
|
jpayne@69
|
6922 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize
|
|
jpayne@69
|
6923 * cdef Py_ssize_t origsize = Py_SIZE(self) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6924 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
6925 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
|
|
jpayne@69
|
6926 */
|
|
jpayne@69
|
6927 __pyx_v_origsize = Py_SIZE(((PyObject *)__pyx_v_self));
|
|
jpayne@69
|
6928
|
|
jpayne@69
|
6929 /* "array.pxd":162
|
|
jpayne@69
|
6930 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize
|
|
jpayne@69
|
6931 * cdef Py_ssize_t origsize = Py_SIZE(self)
|
|
jpayne@69
|
6932 * resize_smart(self, origsize + n) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6933 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
|
|
jpayne@69
|
6934 * return 0
|
|
jpayne@69
|
6935 */
|
|
jpayne@69
|
6936 __pyx_t_1 = resize_smart(__pyx_v_self, (__pyx_v_origsize + __pyx_v_n)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(3, 162, __pyx_L1_error)
|
|
jpayne@69
|
6937
|
|
jpayne@69
|
6938 /* "array.pxd":163
|
|
jpayne@69
|
6939 * cdef Py_ssize_t origsize = Py_SIZE(self)
|
|
jpayne@69
|
6940 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
6941 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6942 * return 0
|
|
jpayne@69
|
6943 *
|
|
jpayne@69
|
6944 */
|
|
jpayne@69
|
6945 (void)(memcpy((__pyx_v_self->data.as_chars + (__pyx_v_origsize * __pyx_v_itemsize)), __pyx_v_stuff, (__pyx_v_n * __pyx_v_itemsize)));
|
|
jpayne@69
|
6946
|
|
jpayne@69
|
6947 /* "array.pxd":164
|
|
jpayne@69
|
6948 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
6949 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
|
|
jpayne@69
|
6950 * return 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6951 *
|
|
jpayne@69
|
6952 * cdef inline int extend(array self, array other) except -1:
|
|
jpayne@69
|
6953 */
|
|
jpayne@69
|
6954 __pyx_r = 0;
|
|
jpayne@69
|
6955 goto __pyx_L0;
|
|
jpayne@69
|
6956
|
|
jpayne@69
|
6957 /* "array.pxd":156
|
|
jpayne@69
|
6958 * return op
|
|
jpayne@69
|
6959 *
|
|
jpayne@69
|
6960 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6961 * """ efficient appending of new stuff of same type
|
|
jpayne@69
|
6962 * (e.g. of same array type)
|
|
jpayne@69
|
6963 */
|
|
jpayne@69
|
6964
|
|
jpayne@69
|
6965 /* function exit code */
|
|
jpayne@69
|
6966 __pyx_L1_error:;
|
|
jpayne@69
|
6967 __Pyx_AddTraceback("cpython.array.extend_buffer", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6968 __pyx_r = -1;
|
|
jpayne@69
|
6969 __pyx_L0:;
|
|
jpayne@69
|
6970 return __pyx_r;
|
|
jpayne@69
|
6971 }
|
|
jpayne@69
|
6972
|
|
jpayne@69
|
6973 /* "array.pxd":166
|
|
jpayne@69
|
6974 * return 0
|
|
jpayne@69
|
6975 *
|
|
jpayne@69
|
6976 * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6977 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
6978 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
6979 */
|
|
jpayne@69
|
6980
|
|
jpayne@69
|
6981 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend(arrayobject *__pyx_v_self, arrayobject *__pyx_v_other) {
|
|
jpayne@69
|
6982 int __pyx_r;
|
|
jpayne@69
|
6983 int __pyx_t_1;
|
|
jpayne@69
|
6984 int __pyx_t_2;
|
|
jpayne@69
|
6985 int __pyx_lineno = 0;
|
|
jpayne@69
|
6986 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6987 int __pyx_clineno = 0;
|
|
jpayne@69
|
6988
|
|
jpayne@69
|
6989 /* "array.pxd":168
|
|
jpayne@69
|
6990 * cdef inline int extend(array self, array other) except -1:
|
|
jpayne@69
|
6991 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
6992 * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6993 * PyErr_BadArgument()
|
|
jpayne@69
|
6994 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
6995 */
|
|
jpayne@69
|
6996 __pyx_t_1 = (__pyx_v_self->ob_descr->typecode != __pyx_v_other->ob_descr->typecode);
|
|
jpayne@69
|
6997 if (__pyx_t_1) {
|
|
jpayne@69
|
6998
|
|
jpayne@69
|
6999 /* "array.pxd":169
|
|
jpayne@69
|
7000 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
7001 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
7002 * PyErr_BadArgument() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7003 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
7004 *
|
|
jpayne@69
|
7005 */
|
|
jpayne@69
|
7006 __pyx_t_2 = PyErr_BadArgument(); if (unlikely(__pyx_t_2 == ((int)0))) __PYX_ERR(3, 169, __pyx_L1_error)
|
|
jpayne@69
|
7007
|
|
jpayne@69
|
7008 /* "array.pxd":168
|
|
jpayne@69
|
7009 * cdef inline int extend(array self, array other) except -1:
|
|
jpayne@69
|
7010 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
7011 * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7012 * PyErr_BadArgument()
|
|
jpayne@69
|
7013 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
7014 */
|
|
jpayne@69
|
7015 }
|
|
jpayne@69
|
7016
|
|
jpayne@69
|
7017 /* "array.pxd":170
|
|
jpayne@69
|
7018 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
7019 * PyErr_BadArgument()
|
|
jpayne@69
|
7020 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7021 *
|
|
jpayne@69
|
7022 * cdef inline void zero(array self) noexcept:
|
|
jpayne@69
|
7023 */
|
|
jpayne@69
|
7024 __pyx_t_2 = __pyx_f_7cpython_5array_extend_buffer(__pyx_v_self, __pyx_v_other->data.as_chars, Py_SIZE(((PyObject *)__pyx_v_other))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(3, 170, __pyx_L1_error)
|
|
jpayne@69
|
7025 __pyx_r = __pyx_t_2;
|
|
jpayne@69
|
7026 goto __pyx_L0;
|
|
jpayne@69
|
7027
|
|
jpayne@69
|
7028 /* "array.pxd":166
|
|
jpayne@69
|
7029 * return 0
|
|
jpayne@69
|
7030 *
|
|
jpayne@69
|
7031 * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7032 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
7033 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
7034 */
|
|
jpayne@69
|
7035
|
|
jpayne@69
|
7036 /* function exit code */
|
|
jpayne@69
|
7037 __pyx_L1_error:;
|
|
jpayne@69
|
7038 __Pyx_AddTraceback("cpython.array.extend", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7039 __pyx_r = -1;
|
|
jpayne@69
|
7040 __pyx_L0:;
|
|
jpayne@69
|
7041 return __pyx_r;
|
|
jpayne@69
|
7042 }
|
|
jpayne@69
|
7043
|
|
jpayne@69
|
7044 /* "array.pxd":172
|
|
jpayne@69
|
7045 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
7046 *
|
|
jpayne@69
|
7047 * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7048 * """ set all elements of array to zero. """
|
|
jpayne@69
|
7049 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize)
|
|
jpayne@69
|
7050 */
|
|
jpayne@69
|
7051
|
|
jpayne@69
|
7052 static CYTHON_INLINE void __pyx_f_7cpython_5array_zero(arrayobject *__pyx_v_self) {
|
|
jpayne@69
|
7053
|
|
jpayne@69
|
7054 /* "array.pxd":174
|
|
jpayne@69
|
7055 * cdef inline void zero(array self) noexcept:
|
|
jpayne@69
|
7056 * """ set all elements of array to zero. """
|
|
jpayne@69
|
7057 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7058 */
|
|
jpayne@69
|
7059 (void)(memset(__pyx_v_self->data.as_chars, 0, (Py_SIZE(((PyObject *)__pyx_v_self)) * __pyx_v_self->ob_descr->itemsize)));
|
|
jpayne@69
|
7060
|
|
jpayne@69
|
7061 /* "array.pxd":172
|
|
jpayne@69
|
7062 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
7063 *
|
|
jpayne@69
|
7064 * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7065 * """ set all elements of array to zero. """
|
|
jpayne@69
|
7066 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize)
|
|
jpayne@69
|
7067 */
|
|
jpayne@69
|
7068
|
|
jpayne@69
|
7069 /* function exit code */
|
|
jpayne@69
|
7070 }
|
|
jpayne@69
|
7071
|
|
jpayne@69
|
7072 /* "pysam/libctabix.pyx":84
|
|
jpayne@69
|
7073 * cdef class Parser:
|
|
jpayne@69
|
7074 *
|
|
jpayne@69
|
7075 * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7076 * self.encoding = encoding
|
|
jpayne@69
|
7077 *
|
|
jpayne@69
|
7078 */
|
|
jpayne@69
|
7079
|
|
jpayne@69
|
7080 /* Python wrapper */
|
|
jpayne@69
|
7081 static int __pyx_pw_5pysam_9libctabix_6Parser_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
7082 static int __pyx_pw_5pysam_9libctabix_6Parser_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
7083 PyObject *__pyx_v_encoding = 0;
|
|
jpayne@69
|
7084 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
7085 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
7086 PyObject* values[1] = {0};
|
|
jpayne@69
|
7087 int __pyx_lineno = 0;
|
|
jpayne@69
|
7088 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7089 int __pyx_clineno = 0;
|
|
jpayne@69
|
7090 int __pyx_r;
|
|
jpayne@69
|
7091 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7092 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
|
|
jpayne@69
|
7093 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
7094 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
7095 #else
|
|
jpayne@69
|
7096 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
7097 #endif
|
|
jpayne@69
|
7098 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
7099 {
|
|
jpayne@69
|
7100 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_encoding,0};
|
|
jpayne@69
|
7101 values[0] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii));
|
|
jpayne@69
|
7102 if (__pyx_kwds) {
|
|
jpayne@69
|
7103 Py_ssize_t kw_args;
|
|
jpayne@69
|
7104 switch (__pyx_nargs) {
|
|
jpayne@69
|
7105 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
7106 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7107 case 0: break;
|
|
jpayne@69
|
7108 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7109 }
|
|
jpayne@69
|
7110 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
7111 switch (__pyx_nargs) {
|
|
jpayne@69
|
7112 case 0:
|
|
jpayne@69
|
7113 if (kw_args > 0) {
|
|
jpayne@69
|
7114 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding);
|
|
jpayne@69
|
7115 if (value) { values[0] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
7116 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 84, __pyx_L3_error)
|
|
jpayne@69
|
7117 }
|
|
jpayne@69
|
7118 }
|
|
jpayne@69
|
7119 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
7120 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
7121 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 84, __pyx_L3_error)
|
|
jpayne@69
|
7122 }
|
|
jpayne@69
|
7123 } else {
|
|
jpayne@69
|
7124 switch (__pyx_nargs) {
|
|
jpayne@69
|
7125 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
7126 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7127 case 0: break;
|
|
jpayne@69
|
7128 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7129 }
|
|
jpayne@69
|
7130 }
|
|
jpayne@69
|
7131 __pyx_v_encoding = values[0];
|
|
jpayne@69
|
7132 }
|
|
jpayne@69
|
7133 goto __pyx_L6_skip;
|
|
jpayne@69
|
7134 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
7135 __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 84, __pyx_L3_error)
|
|
jpayne@69
|
7136 __pyx_L6_skip:;
|
|
jpayne@69
|
7137 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
7138 __pyx_L3_error:;
|
|
jpayne@69
|
7139 {
|
|
jpayne@69
|
7140 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
7141 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
7142 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
7143 }
|
|
jpayne@69
|
7144 }
|
|
jpayne@69
|
7145 __Pyx_AddTraceback("pysam.libctabix.Parser.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7146 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7147 return -1;
|
|
jpayne@69
|
7148 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
7149 __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser___init__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v_encoding);
|
|
jpayne@69
|
7150
|
|
jpayne@69
|
7151 /* function exit code */
|
|
jpayne@69
|
7152 {
|
|
jpayne@69
|
7153 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
7154 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
7155 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
7156 }
|
|
jpayne@69
|
7157 }
|
|
jpayne@69
|
7158 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7159 return __pyx_r;
|
|
jpayne@69
|
7160 }
|
|
jpayne@69
|
7161
|
|
jpayne@69
|
7162 static int __pyx_pf_5pysam_9libctabix_6Parser___init__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding) {
|
|
jpayne@69
|
7163 int __pyx_r;
|
|
jpayne@69
|
7164 __Pyx_TraceDeclarations
|
|
jpayne@69
|
7165 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7166 int __pyx_lineno = 0;
|
|
jpayne@69
|
7167 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7168 int __pyx_clineno = 0;
|
|
jpayne@69
|
7169 __Pyx_RefNannySetupContext("__init__", 1);
|
|
jpayne@69
|
7170 __Pyx_TraceCall("__init__", __pyx_f[0], 84, 0, __PYX_ERR(0, 84, __pyx_L1_error));
|
|
jpayne@69
|
7171
|
|
jpayne@69
|
7172 /* "pysam/libctabix.pyx":85
|
|
jpayne@69
|
7173 *
|
|
jpayne@69
|
7174 * def __init__(self, encoding="ascii"):
|
|
jpayne@69
|
7175 * self.encoding = encoding # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7176 *
|
|
jpayne@69
|
7177 * def set_encoding(self, encoding):
|
|
jpayne@69
|
7178 */
|
|
jpayne@69
|
7179 __Pyx_INCREF(__pyx_v_encoding);
|
|
jpayne@69
|
7180 __Pyx_GIVEREF(__pyx_v_encoding);
|
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jpayne@69
|
7181 __Pyx_GOTREF(__pyx_v_self->encoding);
|
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jpayne@69
|
7182 __Pyx_DECREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
7183 __pyx_v_self->encoding = __pyx_v_encoding;
|
|
jpayne@69
|
7184
|
|
jpayne@69
|
7185 /* "pysam/libctabix.pyx":84
|
|
jpayne@69
|
7186 * cdef class Parser:
|
|
jpayne@69
|
7187 *
|
|
jpayne@69
|
7188 * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7189 * self.encoding = encoding
|
|
jpayne@69
|
7190 *
|
|
jpayne@69
|
7191 */
|
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jpayne@69
|
7192
|
|
jpayne@69
|
7193 /* function exit code */
|
|
jpayne@69
|
7194 __pyx_r = 0;
|
|
jpayne@69
|
7195 goto __pyx_L0;
|
|
jpayne@69
|
7196 __pyx_L1_error:;
|
|
jpayne@69
|
7197 __Pyx_AddTraceback("pysam.libctabix.Parser.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
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jpayne@69
|
7198 __pyx_r = -1;
|
|
jpayne@69
|
7199 __pyx_L0:;
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jpayne@69
|
7200 __Pyx_TraceReturn(Py_None, 0);
|
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jpayne@69
|
7201 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
7202 return __pyx_r;
|
|
jpayne@69
|
7203 }
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|
jpayne@69
|
7204
|
|
jpayne@69
|
7205 /* "pysam/libctabix.pyx":87
|
|
jpayne@69
|
7206 * self.encoding = encoding
|
|
jpayne@69
|
7207 *
|
|
jpayne@69
|
7208 * def set_encoding(self, encoding): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7209 * self.encoding = encoding
|
|
jpayne@69
|
7210 *
|
|
jpayne@69
|
7211 */
|
|
jpayne@69
|
7212
|
|
jpayne@69
|
7213 /* Python wrapper */
|
|
jpayne@69
|
7214 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7215 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7216 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7217 #else
|
|
jpayne@69
|
7218 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7219 #endif
|
|
jpayne@69
|
7220 ); /*proto*/
|
|
jpayne@69
|
7221 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_2set_encoding, "Parser.set_encoding(self, encoding)");
|
|
jpayne@69
|
7222 static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_3set_encoding = {"set_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_2set_encoding};
|
|
jpayne@69
|
7223 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7224 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7225 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7226 #else
|
|
jpayne@69
|
7227 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7228 #endif
|
|
jpayne@69
|
7229 ) {
|
|
jpayne@69
|
7230 PyObject *__pyx_v_encoding = 0;
|
|
jpayne@69
|
7231 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7232 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
7233 #endif
|
|
jpayne@69
|
7234 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
7235 PyObject* values[1] = {0};
|
|
jpayne@69
|
7236 int __pyx_lineno = 0;
|
|
jpayne@69
|
7237 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7238 int __pyx_clineno = 0;
|
|
jpayne@69
|
7239 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
7240 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7241 __Pyx_RefNannySetupContext("set_encoding (wrapper)", 0);
|
|
jpayne@69
|
7242 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7243 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
7244 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
7245 #else
|
|
jpayne@69
|
7246 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
7247 #endif
|
|
jpayne@69
|
7248 #endif
|
|
jpayne@69
|
7249 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
7250 {
|
|
jpayne@69
|
7251 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_encoding,0};
|
|
jpayne@69
|
7252 if (__pyx_kwds) {
|
|
jpayne@69
|
7253 Py_ssize_t kw_args;
|
|
jpayne@69
|
7254 switch (__pyx_nargs) {
|
|
jpayne@69
|
7255 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
7256 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7257 case 0: break;
|
|
jpayne@69
|
7258 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7259 }
|
|
jpayne@69
|
7260 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
7261 switch (__pyx_nargs) {
|
|
jpayne@69
|
7262 case 0:
|
|
jpayne@69
|
7263 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding)) != 0)) {
|
|
jpayne@69
|
7264 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
7265 kw_args--;
|
|
jpayne@69
|
7266 }
|
|
jpayne@69
|
7267 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 87, __pyx_L3_error)
|
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jpayne@69
|
7268 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7269 }
|
|
jpayne@69
|
7270 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
7271 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
7272 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "set_encoding") < 0)) __PYX_ERR(0, 87, __pyx_L3_error)
|
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jpayne@69
|
7273 }
|
|
jpayne@69
|
7274 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
7275 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7276 } else {
|
|
jpayne@69
|
7277 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
7278 }
|
|
jpayne@69
|
7279 __pyx_v_encoding = values[0];
|
|
jpayne@69
|
7280 }
|
|
jpayne@69
|
7281 goto __pyx_L6_skip;
|
|
jpayne@69
|
7282 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
7283 __Pyx_RaiseArgtupleInvalid("set_encoding", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 87, __pyx_L3_error)
|
|
jpayne@69
|
7284 __pyx_L6_skip:;
|
|
jpayne@69
|
7285 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
7286 __pyx_L3_error:;
|
|
jpayne@69
|
7287 {
|
|
jpayne@69
|
7288 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
7289 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
7290 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
7291 }
|
|
jpayne@69
|
7292 }
|
|
jpayne@69
|
7293 __Pyx_AddTraceback("pysam.libctabix.Parser.set_encoding", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7294 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7295 return NULL;
|
|
jpayne@69
|
7296 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
7297 __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_2set_encoding(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v_encoding);
|
|
jpayne@69
|
7298
|
|
jpayne@69
|
7299 /* function exit code */
|
|
jpayne@69
|
7300 {
|
|
jpayne@69
|
7301 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
7302 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
7303 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
7304 }
|
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jpayne@69
|
7305 }
|
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jpayne@69
|
7306 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
7307 return __pyx_r;
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jpayne@69
|
7308 }
|
|
jpayne@69
|
7309
|
|
jpayne@69
|
7310 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_2set_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding) {
|
|
jpayne@69
|
7311 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
7312 __Pyx_TraceDeclarations
|
|
jpayne@69
|
7313 __Pyx_RefNannyDeclarations
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jpayne@69
|
7314 int __pyx_lineno = 0;
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jpayne@69
|
7315 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7316 int __pyx_clineno = 0;
|
|
jpayne@69
|
7317 __Pyx_TraceFrameInit(__pyx_codeobj_)
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jpayne@69
|
7318 __Pyx_RefNannySetupContext("set_encoding", 1);
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jpayne@69
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7319 __Pyx_TraceCall("set_encoding", __pyx_f[0], 87, 0, __PYX_ERR(0, 87, __pyx_L1_error));
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jpayne@69
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7320
|
|
jpayne@69
|
7321 /* "pysam/libctabix.pyx":88
|
|
jpayne@69
|
7322 *
|
|
jpayne@69
|
7323 * def set_encoding(self, encoding):
|
|
jpayne@69
|
7324 * self.encoding = encoding # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7325 *
|
|
jpayne@69
|
7326 * def get_encoding(self):
|
|
jpayne@69
|
7327 */
|
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jpayne@69
|
7328 __Pyx_INCREF(__pyx_v_encoding);
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jpayne@69
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7329 __Pyx_GIVEREF(__pyx_v_encoding);
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jpayne@69
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7330 __Pyx_GOTREF(__pyx_v_self->encoding);
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jpayne@69
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7331 __Pyx_DECREF(__pyx_v_self->encoding);
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jpayne@69
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7332 __pyx_v_self->encoding = __pyx_v_encoding;
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jpayne@69
|
7333
|
|
jpayne@69
|
7334 /* "pysam/libctabix.pyx":87
|
|
jpayne@69
|
7335 * self.encoding = encoding
|
|
jpayne@69
|
7336 *
|
|
jpayne@69
|
7337 * def set_encoding(self, encoding): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7338 * self.encoding = encoding
|
|
jpayne@69
|
7339 *
|
|
jpayne@69
|
7340 */
|
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jpayne@69
|
7341
|
|
jpayne@69
|
7342 /* function exit code */
|
|
jpayne@69
|
7343 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
7344 goto __pyx_L0;
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jpayne@69
|
7345 __pyx_L1_error:;
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|
jpayne@69
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7346 __Pyx_AddTraceback("pysam.libctabix.Parser.set_encoding", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
|
7347 __pyx_r = NULL;
|
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jpayne@69
|
7348 __pyx_L0:;
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jpayne@69
|
7349 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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7350 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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7351 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
7352 return __pyx_r;
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jpayne@69
|
7353 }
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jpayne@69
|
7354
|
|
jpayne@69
|
7355 /* "pysam/libctabix.pyx":90
|
|
jpayne@69
|
7356 * self.encoding = encoding
|
|
jpayne@69
|
7357 *
|
|
jpayne@69
|
7358 * def get_encoding(self): # <<<<<<<<<<<<<<
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|
jpayne@69
|
7359 * return self.encoding
|
|
jpayne@69
|
7360 *
|
|
jpayne@69
|
7361 */
|
|
jpayne@69
|
7362
|
|
jpayne@69
|
7363 /* Python wrapper */
|
|
jpayne@69
|
7364 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7365 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7366 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7367 #else
|
|
jpayne@69
|
7368 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
|
7369 #endif
|
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jpayne@69
|
7370 ); /*proto*/
|
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jpayne@69
|
7371 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_4get_encoding, "Parser.get_encoding(self)");
|
|
jpayne@69
|
7372 static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_5get_encoding = {"get_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_4get_encoding};
|
|
jpayne@69
|
7373 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7374 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7375 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7376 #else
|
|
jpayne@69
|
7377 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7378 #endif
|
|
jpayne@69
|
7379 ) {
|
|
jpayne@69
|
7380 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7381 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
7382 #endif
|
|
jpayne@69
|
7383 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
7384 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
7385 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7386 __Pyx_RefNannySetupContext("get_encoding (wrapper)", 0);
|
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jpayne@69
|
7387 #if !CYTHON_METH_FASTCALL
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|
jpayne@69
|
7388 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
7389 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
7390 #else
|
|
jpayne@69
|
7391 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
7392 #endif
|
|
jpayne@69
|
7393 #endif
|
|
jpayne@69
|
7394 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
7395 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
7396 __Pyx_RaiseArgtupleInvalid("get_encoding", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
7397 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "get_encoding", 0))) return NULL;
|
|
jpayne@69
|
7398 __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_4get_encoding(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self));
|
|
jpayne@69
|
7399
|
|
jpayne@69
|
7400 /* function exit code */
|
|
jpayne@69
|
7401 __Pyx_RefNannyFinishContext();
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jpayne@69
|
7402 return __pyx_r;
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jpayne@69
|
7403 }
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|
jpayne@69
|
7404
|
|
jpayne@69
|
7405 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_4get_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self) {
|
|
jpayne@69
|
7406 PyObject *__pyx_r = NULL;
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jpayne@69
|
7407 __Pyx_TraceDeclarations
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jpayne@69
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7408 __Pyx_RefNannyDeclarations
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jpayne@69
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7409 int __pyx_lineno = 0;
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jpayne@69
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7410 const char *__pyx_filename = NULL;
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jpayne@69
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7411 int __pyx_clineno = 0;
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jpayne@69
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7412 __Pyx_TraceFrameInit(__pyx_codeobj__2)
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jpayne@69
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jpayne@69
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7414 __Pyx_TraceCall("get_encoding", __pyx_f[0], 90, 0, __PYX_ERR(0, 90, __pyx_L1_error));
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jpayne@69
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7415
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jpayne@69
|
7416 /* "pysam/libctabix.pyx":91
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|
jpayne@69
|
7417 *
|
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jpayne@69
|
7418 * def get_encoding(self):
|
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jpayne@69
|
7419 * return self.encoding # <<<<<<<<<<<<<<
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jpayne@69
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7420 *
|
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jpayne@69
|
7421 * cdef parse(self, char * buffer, int length):
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jpayne@69
|
7422 */
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jpayne@69
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7423 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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7424 __Pyx_INCREF(__pyx_v_self->encoding);
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jpayne@69
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7425 __pyx_r = __pyx_v_self->encoding;
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jpayne@69
|
7426 goto __pyx_L0;
|
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jpayne@69
|
7427
|
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jpayne@69
|
7428 /* "pysam/libctabix.pyx":90
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jpayne@69
|
7429 * self.encoding = encoding
|
|
jpayne@69
|
7430 *
|
|
jpayne@69
|
7431 * def get_encoding(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7432 * return self.encoding
|
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jpayne@69
|
7433 *
|
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jpayne@69
|
7434 */
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jpayne@69
|
7435
|
|
jpayne@69
|
7436 /* function exit code */
|
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jpayne@69
|
7437 __pyx_L1_error:;
|
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jpayne@69
|
7438 __Pyx_AddTraceback("pysam.libctabix.Parser.get_encoding", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
|
7439 __pyx_r = NULL;
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jpayne@69
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7440 __pyx_L0:;
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jpayne@69
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7441 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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7442 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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7443 __Pyx_RefNannyFinishContext();
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jpayne@69
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7444 return __pyx_r;
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jpayne@69
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7445 }
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jpayne@69
|
7446
|
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jpayne@69
|
7447 /* "pysam/libctabix.pyx":93
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|
jpayne@69
|
7448 * return self.encoding
|
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jpayne@69
|
7449 *
|
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jpayne@69
|
7450 * cdef parse(self, char * buffer, int length): # <<<<<<<<<<<<<<
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jpayne@69
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7451 * raise NotImplementedError(
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jpayne@69
|
7452 * 'parse method of %s not implemented' % str(self))
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jpayne@69
|
7453 */
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jpayne@69
|
7454
|
|
jpayne@69
|
7455 static PyObject *__pyx_f_5pysam_9libctabix_6Parser_parse(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, CYTHON_UNUSED char *__pyx_v_buffer, CYTHON_UNUSED int __pyx_v_length) {
|
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jpayne@69
|
7456 PyObject *__pyx_r = NULL;
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jpayne@69
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7457 __Pyx_TraceDeclarations
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jpayne@69
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7458 __Pyx_RefNannyDeclarations
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jpayne@69
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7459 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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7460 PyObject *__pyx_t_2 = NULL;
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jpayne@69
|
7461 int __pyx_lineno = 0;
|
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jpayne@69
|
7462 const char *__pyx_filename = NULL;
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jpayne@69
|
7463 int __pyx_clineno = 0;
|
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jpayne@69
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7464 __Pyx_RefNannySetupContext("parse", 1);
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jpayne@69
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7465 __Pyx_TraceCall("parse", __pyx_f[0], 93, 0, __PYX_ERR(0, 93, __pyx_L1_error));
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jpayne@69
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7466
|
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jpayne@69
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7467 /* "pysam/libctabix.pyx":95
|
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jpayne@69
|
7468 * cdef parse(self, char * buffer, int length):
|
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jpayne@69
|
7469 * raise NotImplementedError(
|
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jpayne@69
|
7470 * 'parse method of %s not implemented' % str(self)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7471 *
|
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jpayne@69
|
7472 * def __call__(self, char * buffer, int length):
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jpayne@69
|
7473 */
|
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jpayne@69
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7474 __pyx_t_1 = __Pyx_PyObject_Unicode(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 95, __pyx_L1_error)
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jpayne@69
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7475 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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7476 __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_parse_method_of_s_not_implemente, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 95, __pyx_L1_error)
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jpayne@69
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7477 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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7478 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
|
7479
|
|
jpayne@69
|
7480 /* "pysam/libctabix.pyx":94
|
|
jpayne@69
|
7481 *
|
|
jpayne@69
|
7482 * cdef parse(self, char * buffer, int length):
|
|
jpayne@69
|
7483 * raise NotImplementedError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7484 * 'parse method of %s not implemented' % str(self))
|
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jpayne@69
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7485 *
|
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jpayne@69
|
7486 */
|
|
jpayne@69
|
7487 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_NotImplementedError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 94, __pyx_L1_error)
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7488 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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7489 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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|
jpayne@69
|
7490 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
7491 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
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jpayne@69
|
7492 __PYX_ERR(0, 94, __pyx_L1_error)
|
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jpayne@69
|
7493
|
|
jpayne@69
|
7494 /* "pysam/libctabix.pyx":93
|
|
jpayne@69
|
7495 * return self.encoding
|
|
jpayne@69
|
7496 *
|
|
jpayne@69
|
7497 * cdef parse(self, char * buffer, int length): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7498 * raise NotImplementedError(
|
|
jpayne@69
|
7499 * 'parse method of %s not implemented' % str(self))
|
|
jpayne@69
|
7500 */
|
|
jpayne@69
|
7501
|
|
jpayne@69
|
7502 /* function exit code */
|
|
jpayne@69
|
7503 __pyx_L1_error:;
|
|
jpayne@69
|
7504 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
7505 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
7506 __Pyx_AddTraceback("pysam.libctabix.Parser.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7507 __pyx_r = 0;
|
|
jpayne@69
|
7508 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
7509 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
7510 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7511 return __pyx_r;
|
|
jpayne@69
|
7512 }
|
|
jpayne@69
|
7513
|
|
jpayne@69
|
7514 /* "pysam/libctabix.pyx":97
|
|
jpayne@69
|
7515 * 'parse method of %s not implemented' % str(self))
|
|
jpayne@69
|
7516 *
|
|
jpayne@69
|
7517 * def __call__(self, char * buffer, int length): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7518 * return self.parse(buffer, length)
|
|
jpayne@69
|
7519 *
|
|
jpayne@69
|
7520 */
|
|
jpayne@69
|
7521
|
|
jpayne@69
|
7522 /* Python wrapper */
|
|
jpayne@69
|
7523 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_7__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
7524 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_7__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
7525 char *__pyx_v_buffer;
|
|
jpayne@69
|
7526 int __pyx_v_length;
|
|
jpayne@69
|
7527 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
7528 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
7529 PyObject* values[2] = {0,0};
|
|
jpayne@69
|
7530 int __pyx_lineno = 0;
|
|
jpayne@69
|
7531 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7532 int __pyx_clineno = 0;
|
|
jpayne@69
|
7533 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
7534 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7535 __Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
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jpayne@69
|
7536 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
7537 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
7538 #else
|
|
jpayne@69
|
7539 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
7540 #endif
|
|
jpayne@69
|
7541 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
7542 {
|
|
jpayne@69
|
7543 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_buffer,&__pyx_n_s_length,0};
|
|
jpayne@69
|
7544 if (__pyx_kwds) {
|
|
jpayne@69
|
7545 Py_ssize_t kw_args;
|
|
jpayne@69
|
7546 switch (__pyx_nargs) {
|
|
jpayne@69
|
7547 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
7548 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7549 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
7550 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7551 case 0: break;
|
|
jpayne@69
|
7552 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7553 }
|
|
jpayne@69
|
7554 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
7555 switch (__pyx_nargs) {
|
|
jpayne@69
|
7556 case 0:
|
|
jpayne@69
|
7557 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buffer)) != 0)) {
|
|
jpayne@69
|
7558 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
|
|
jpayne@69
|
7559 kw_args--;
|
|
jpayne@69
|
7560 }
|
|
jpayne@69
|
7561 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error)
|
|
jpayne@69
|
7562 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7563 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7564 case 1:
|
|
jpayne@69
|
7565 if (likely((values[1] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_length)) != 0)) {
|
|
jpayne@69
|
7566 (void)__Pyx_Arg_NewRef_VARARGS(values[1]);
|
|
jpayne@69
|
7567 kw_args--;
|
|
jpayne@69
|
7568 }
|
|
jpayne@69
|
7569 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error)
|
|
jpayne@69
|
7570 else {
|
|
jpayne@69
|
7571 __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); __PYX_ERR(0, 97, __pyx_L3_error)
|
|
jpayne@69
|
7572 }
|
|
jpayne@69
|
7573 }
|
|
jpayne@69
|
7574 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
7575 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
7576 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__call__") < 0)) __PYX_ERR(0, 97, __pyx_L3_error)
|
|
jpayne@69
|
7577 }
|
|
jpayne@69
|
7578 } else if (unlikely(__pyx_nargs != 2)) {
|
|
jpayne@69
|
7579 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7580 } else {
|
|
jpayne@69
|
7581 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
7582 values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
7583 }
|
|
jpayne@69
|
7584 __pyx_v_buffer = __Pyx_PyObject_AsWritableString(values[0]); if (unlikely((!__pyx_v_buffer) && PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error)
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jpayne@69
|
7585 __pyx_v_length = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_length == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error)
|
|
jpayne@69
|
7586 }
|
|
jpayne@69
|
7587 goto __pyx_L6_skip;
|
|
jpayne@69
|
7588 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
7589 __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 97, __pyx_L3_error)
|
|
jpayne@69
|
7590 __pyx_L6_skip:;
|
|
jpayne@69
|
7591 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
7592 __pyx_L3_error:;
|
|
jpayne@69
|
7593 {
|
|
jpayne@69
|
7594 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
7595 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
7596 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
7597 }
|
|
jpayne@69
|
7598 }
|
|
jpayne@69
|
7599 __Pyx_AddTraceback("pysam.libctabix.Parser.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7600 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7601 return NULL;
|
|
jpayne@69
|
7602 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
7603 __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_6__call__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v_buffer, __pyx_v_length);
|
|
jpayne@69
|
7604
|
|
jpayne@69
|
7605 /* function exit code */
|
|
jpayne@69
|
7606 {
|
|
jpayne@69
|
7607 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
7608 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
7609 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
7610 }
|
|
jpayne@69
|
7611 }
|
|
jpayne@69
|
7612 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7613 return __pyx_r;
|
|
jpayne@69
|
7614 }
|
|
jpayne@69
|
7615
|
|
jpayne@69
|
7616 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_6__call__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length) {
|
|
jpayne@69
|
7617 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
7618 __Pyx_TraceDeclarations
|
|
jpayne@69
|
7619 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7620 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
7621 int __pyx_lineno = 0;
|
|
jpayne@69
|
7622 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7623 int __pyx_clineno = 0;
|
|
jpayne@69
|
7624 __Pyx_RefNannySetupContext("__call__", 1);
|
|
jpayne@69
|
7625 __Pyx_TraceCall("__call__", __pyx_f[0], 97, 0, __PYX_ERR(0, 97, __pyx_L1_error));
|
|
jpayne@69
|
7626
|
|
jpayne@69
|
7627 /* "pysam/libctabix.pyx":98
|
|
jpayne@69
|
7628 *
|
|
jpayne@69
|
7629 * def __call__(self, char * buffer, int length):
|
|
jpayne@69
|
7630 * return self.parse(buffer, length) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7631 *
|
|
jpayne@69
|
7632 *
|
|
jpayne@69
|
7633 */
|
|
jpayne@69
|
7634 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
7635 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->__pyx_vtab)->parse(__pyx_v_self, __pyx_v_buffer, __pyx_v_length); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 98, __pyx_L1_error)
|
|
jpayne@69
|
7636 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
7637 __pyx_r = __pyx_t_1;
|
|
jpayne@69
|
7638 __pyx_t_1 = 0;
|
|
jpayne@69
|
7639 goto __pyx_L0;
|
|
jpayne@69
|
7640
|
|
jpayne@69
|
7641 /* "pysam/libctabix.pyx":97
|
|
jpayne@69
|
7642 * 'parse method of %s not implemented' % str(self))
|
|
jpayne@69
|
7643 *
|
|
jpayne@69
|
7644 * def __call__(self, char * buffer, int length): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7645 * return self.parse(buffer, length)
|
|
jpayne@69
|
7646 *
|
|
jpayne@69
|
7647 */
|
|
jpayne@69
|
7648
|
|
jpayne@69
|
7649 /* function exit code */
|
|
jpayne@69
|
7650 __pyx_L1_error:;
|
|
jpayne@69
|
7651 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
|
7652 __Pyx_AddTraceback("pysam.libctabix.Parser.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7653 __pyx_r = NULL;
|
|
jpayne@69
|
7654 __pyx_L0:;
|
|
jpayne@69
|
7655 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
7656 __Pyx_TraceReturn(__pyx_r, 0);
|
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jpayne@69
|
7657 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7658 return __pyx_r;
|
|
jpayne@69
|
7659 }
|
|
jpayne@69
|
7660
|
|
jpayne@69
|
7661 /* "(tree fragment)":1
|
|
jpayne@69
|
7662 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7663 * cdef tuple state
|
|
jpayne@69
|
7664 * cdef object _dict
|
|
jpayne@69
|
7665 */
|
|
jpayne@69
|
7666
|
|
jpayne@69
|
7667 /* Python wrapper */
|
|
jpayne@69
|
7668 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7669 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7670 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7671 #else
|
|
jpayne@69
|
7672 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7673 #endif
|
|
jpayne@69
|
7674 ); /*proto*/
|
|
jpayne@69
|
7675 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_8__reduce_cython__, "Parser.__reduce_cython__(self)");
|
|
jpayne@69
|
7676 static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_8__reduce_cython__};
|
|
jpayne@69
|
7677 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7678 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7679 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7680 #else
|
|
jpayne@69
|
7681 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7682 #endif
|
|
jpayne@69
|
7683 ) {
|
|
jpayne@69
|
7684 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7685 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
7686 #endif
|
|
jpayne@69
|
7687 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
7688 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
7689 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7690 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
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jpayne@69
|
7691 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7692 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
7693 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
7694 #else
|
|
jpayne@69
|
7695 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
7696 #endif
|
|
jpayne@69
|
7697 #endif
|
|
jpayne@69
|
7698 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
7699 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
7700 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
7701 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
7702 __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self));
|
|
jpayne@69
|
7703
|
|
jpayne@69
|
7704 /* function exit code */
|
|
jpayne@69
|
7705 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
7706 return __pyx_r;
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jpayne@69
|
7707 }
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jpayne@69
|
7708
|
|
jpayne@69
|
7709 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_8__reduce_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self) {
|
|
jpayne@69
|
7710 PyObject *__pyx_v_state = 0;
|
|
jpayne@69
|
7711 PyObject *__pyx_v__dict = 0;
|
|
jpayne@69
|
7712 int __pyx_v_use_setstate;
|
|
jpayne@69
|
7713 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
7714 __Pyx_TraceDeclarations
|
|
jpayne@69
|
7715 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
7716 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
7717 int __pyx_t_2;
|
|
jpayne@69
|
7718 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
7719 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
7720 int __pyx_lineno = 0;
|
|
jpayne@69
|
7721 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7722 int __pyx_clineno = 0;
|
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jpayne@69
|
7723 __Pyx_TraceFrameInit(__pyx_codeobj__3)
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jpayne@69
|
7724 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
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jpayne@69
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7725 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
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jpayne@69
|
7726
|
|
jpayne@69
|
7727 /* "(tree fragment)":5
|
|
jpayne@69
|
7728 * cdef object _dict
|
|
jpayne@69
|
7729 * cdef bint use_setstate
|
|
jpayne@69
|
7730 * state = (self.encoding,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7731 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
7732 * if _dict is not None:
|
|
jpayne@69
|
7733 */
|
|
jpayne@69
|
7734 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
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jpayne@69
|
7735 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
7736 __Pyx_INCREF(__pyx_v_self->encoding);
|
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jpayne@69
|
7737 __Pyx_GIVEREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
7738 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
|
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jpayne@69
|
7739 __pyx_v_state = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
7740 __pyx_t_1 = 0;
|
|
jpayne@69
|
7741
|
|
jpayne@69
|
7742 /* "(tree fragment)":6
|
|
jpayne@69
|
7743 * cdef bint use_setstate
|
|
jpayne@69
|
7744 * state = (self.encoding,)
|
|
jpayne@69
|
7745 * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7746 * if _dict is not None:
|
|
jpayne@69
|
7747 * state += (_dict,)
|
|
jpayne@69
|
7748 */
|
|
jpayne@69
|
7749 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
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jpayne@69
|
7750 __Pyx_GOTREF(__pyx_t_1);
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|
jpayne@69
|
7751 __pyx_v__dict = __pyx_t_1;
|
|
jpayne@69
|
7752 __pyx_t_1 = 0;
|
|
jpayne@69
|
7753
|
|
jpayne@69
|
7754 /* "(tree fragment)":7
|
|
jpayne@69
|
7755 * state = (self.encoding,)
|
|
jpayne@69
|
7756 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
7757 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7758 * state += (_dict,)
|
|
jpayne@69
|
7759 * use_setstate = True
|
|
jpayne@69
|
7760 */
|
|
jpayne@69
|
7761 __pyx_t_2 = (__pyx_v__dict != Py_None);
|
|
jpayne@69
|
7762 if (__pyx_t_2) {
|
|
jpayne@69
|
7763
|
|
jpayne@69
|
7764 /* "(tree fragment)":8
|
|
jpayne@69
|
7765 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
7766 * if _dict is not None:
|
|
jpayne@69
|
7767 * state += (_dict,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7768 * use_setstate = True
|
|
jpayne@69
|
7769 * else:
|
|
jpayne@69
|
7770 */
|
|
jpayne@69
|
7771 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
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|
jpayne@69
|
7772 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
7773 __Pyx_INCREF(__pyx_v__dict);
|
|
jpayne@69
|
7774 __Pyx_GIVEREF(__pyx_v__dict);
|
|
jpayne@69
|
7775 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
|
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jpayne@69
|
7776 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
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jpayne@69
|
7777 __Pyx_GOTREF(__pyx_t_3);
|
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jpayne@69
|
7778 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
7779 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
7780 __pyx_t_3 = 0;
|
|
jpayne@69
|
7781
|
|
jpayne@69
|
7782 /* "(tree fragment)":9
|
|
jpayne@69
|
7783 * if _dict is not None:
|
|
jpayne@69
|
7784 * state += (_dict,)
|
|
jpayne@69
|
7785 * use_setstate = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7786 * else:
|
|
jpayne@69
|
7787 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
7788 */
|
|
jpayne@69
|
7789 __pyx_v_use_setstate = 1;
|
|
jpayne@69
|
7790
|
|
jpayne@69
|
7791 /* "(tree fragment)":7
|
|
jpayne@69
|
7792 * state = (self.encoding,)
|
|
jpayne@69
|
7793 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
7794 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7795 * state += (_dict,)
|
|
jpayne@69
|
7796 * use_setstate = True
|
|
jpayne@69
|
7797 */
|
|
jpayne@69
|
7798 goto __pyx_L3;
|
|
jpayne@69
|
7799 }
|
|
jpayne@69
|
7800
|
|
jpayne@69
|
7801 /* "(tree fragment)":11
|
|
jpayne@69
|
7802 * use_setstate = True
|
|
jpayne@69
|
7803 * else:
|
|
jpayne@69
|
7804 * use_setstate = self.encoding is not None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7805 * if use_setstate:
|
|
jpayne@69
|
7806 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
7807 */
|
|
jpayne@69
|
7808 /*else*/ {
|
|
jpayne@69
|
7809 __pyx_t_2 = (__pyx_v_self->encoding != Py_None);
|
|
jpayne@69
|
7810 __pyx_v_use_setstate = __pyx_t_2;
|
|
jpayne@69
|
7811 }
|
|
jpayne@69
|
7812 __pyx_L3:;
|
|
jpayne@69
|
7813
|
|
jpayne@69
|
7814 /* "(tree fragment)":12
|
|
jpayne@69
|
7815 * else:
|
|
jpayne@69
|
7816 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
7817 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7818 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
7819 * else:
|
|
jpayne@69
|
7820 */
|
|
jpayne@69
|
7821 if (__pyx_v_use_setstate) {
|
|
jpayne@69
|
7822
|
|
jpayne@69
|
7823 /* "(tree fragment)":13
|
|
jpayne@69
|
7824 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
7825 * if use_setstate:
|
|
jpayne@69
|
7826 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7827 * else:
|
|
jpayne@69
|
7828 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
7829 */
|
|
jpayne@69
|
7830 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
7831 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_Parser); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
7832 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
7833 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
7834 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
7835 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
7836 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
7837 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
7838 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
7839 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
7840 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
7841 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
7842 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
7843 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
7844 __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
7845 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
7846 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
7847 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
7848 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
7849 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
7850 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
7851 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
7852 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
7853 __pyx_t_3 = 0;
|
|
jpayne@69
|
7854 __pyx_t_1 = 0;
|
|
jpayne@69
|
7855 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
7856 __pyx_t_4 = 0;
|
|
jpayne@69
|
7857 goto __pyx_L0;
|
|
jpayne@69
|
7858
|
|
jpayne@69
|
7859 /* "(tree fragment)":12
|
|
jpayne@69
|
7860 * else:
|
|
jpayne@69
|
7861 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
7862 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7863 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
7864 * else:
|
|
jpayne@69
|
7865 */
|
|
jpayne@69
|
7866 }
|
|
jpayne@69
|
7867
|
|
jpayne@69
|
7868 /* "(tree fragment)":15
|
|
jpayne@69
|
7869 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
7870 * else:
|
|
jpayne@69
|
7871 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7872 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
7873 * __pyx_unpickle_Parser__set_state(self, __pyx_state)
|
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jpayne@69
|
7874 */
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jpayne@69
|
7875 /*else*/ {
|
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jpayne@69
|
7876 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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7877 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_Parser); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error)
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jpayne@69
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7878 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
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7879 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
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jpayne@69
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7880 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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7881 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
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jpayne@69
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7882 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
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jpayne@69
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7883 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
|
7884 __Pyx_INCREF(__pyx_int_243541226);
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jpayne@69
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7885 __Pyx_GIVEREF(__pyx_int_243541226);
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jpayne@69
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7886 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
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7887 __Pyx_INCREF(__pyx_v_state);
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jpayne@69
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7888 __Pyx_GIVEREF(__pyx_v_state);
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jpayne@69
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7889 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
|
7890 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
|
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jpayne@69
|
7891 __Pyx_GOTREF(__pyx_t_3);
|
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jpayne@69
|
7892 __Pyx_GIVEREF(__pyx_t_4);
|
|
jpayne@69
|
7893 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error);
|
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jpayne@69
|
7894 __Pyx_GIVEREF(__pyx_t_1);
|
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jpayne@69
|
7895 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
|
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jpayne@69
|
7896 __pyx_t_4 = 0;
|
|
jpayne@69
|
7897 __pyx_t_1 = 0;
|
|
jpayne@69
|
7898 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
7899 __pyx_t_3 = 0;
|
|
jpayne@69
|
7900 goto __pyx_L0;
|
|
jpayne@69
|
7901 }
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|
jpayne@69
|
7902
|
|
jpayne@69
|
7903 /* "(tree fragment)":1
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|
jpayne@69
|
7904 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
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|
jpayne@69
|
7905 * cdef tuple state
|
|
jpayne@69
|
7906 * cdef object _dict
|
|
jpayne@69
|
7907 */
|
|
jpayne@69
|
7908
|
|
jpayne@69
|
7909 /* function exit code */
|
|
jpayne@69
|
7910 __pyx_L1_error:;
|
|
jpayne@69
|
7911 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
7912 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
7913 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
7914 __Pyx_AddTraceback("pysam.libctabix.Parser.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7915 __pyx_r = NULL;
|
|
jpayne@69
|
7916 __pyx_L0:;
|
|
jpayne@69
|
7917 __Pyx_XDECREF(__pyx_v_state);
|
|
jpayne@69
|
7918 __Pyx_XDECREF(__pyx_v__dict);
|
|
jpayne@69
|
7919 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
7920 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
7921 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
7922 return __pyx_r;
|
|
jpayne@69
|
7923 }
|
|
jpayne@69
|
7924
|
|
jpayne@69
|
7925 /* "(tree fragment)":16
|
|
jpayne@69
|
7926 * else:
|
|
jpayne@69
|
7927 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
7928 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7929 * __pyx_unpickle_Parser__set_state(self, __pyx_state)
|
|
jpayne@69
|
7930 */
|
|
jpayne@69
|
7931
|
|
jpayne@69
|
7932 /* Python wrapper */
|
|
jpayne@69
|
7933 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7934 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7935 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7936 #else
|
|
jpayne@69
|
7937 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7938 #endif
|
|
jpayne@69
|
7939 ); /*proto*/
|
|
jpayne@69
|
7940 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_10__setstate_cython__, "Parser.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
7941 static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_10__setstate_cython__};
|
|
jpayne@69
|
7942 static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
7943 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7944 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
7945 #else
|
|
jpayne@69
|
7946 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
7947 #endif
|
|
jpayne@69
|
7948 ) {
|
|
jpayne@69
|
7949 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
7950 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7951 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
7952 #endif
|
|
jpayne@69
|
7953 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
7954 PyObject* values[1] = {0};
|
|
jpayne@69
|
7955 int __pyx_lineno = 0;
|
|
jpayne@69
|
7956 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
7957 int __pyx_clineno = 0;
|
|
jpayne@69
|
7958 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
7959 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
7960 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
7961 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
7962 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
7963 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
7964 #else
|
|
jpayne@69
|
7965 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
7966 #endif
|
|
jpayne@69
|
7967 #endif
|
|
jpayne@69
|
7968 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
7969 {
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|
jpayne@69
|
7970 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
7971 if (__pyx_kwds) {
|
|
jpayne@69
|
7972 Py_ssize_t kw_args;
|
|
jpayne@69
|
7973 switch (__pyx_nargs) {
|
|
jpayne@69
|
7974 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
7975 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
7976 case 0: break;
|
|
jpayne@69
|
7977 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
7978 }
|
|
jpayne@69
|
7979 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
7980 switch (__pyx_nargs) {
|
|
jpayne@69
|
7981 case 0:
|
|
jpayne@69
|
7982 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
7983 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
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jpayne@69
|
7984 kw_args--;
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jpayne@69
|
7985 }
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jpayne@69
|
7986 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
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jpayne@69
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7987 else goto __pyx_L5_argtuple_error;
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jpayne@69
|
7988 }
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|
jpayne@69
|
7989 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
7990 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
7991 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
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jpayne@69
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7992 }
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jpayne@69
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7993 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
7994 goto __pyx_L5_argtuple_error;
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jpayne@69
|
7995 } else {
|
|
jpayne@69
|
7996 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
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jpayne@69
|
7997 }
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jpayne@69
|
7998 __pyx_v___pyx_state = values[0];
|
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jpayne@69
|
7999 }
|
|
jpayne@69
|
8000 goto __pyx_L6_skip;
|
|
jpayne@69
|
8001 __pyx_L5_argtuple_error:;
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jpayne@69
|
8002 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
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jpayne@69
|
8003 __pyx_L6_skip:;
|
|
jpayne@69
|
8004 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
8005 __pyx_L3_error:;
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jpayne@69
|
8006 {
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|
jpayne@69
|
8007 Py_ssize_t __pyx_temp;
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jpayne@69
|
8008 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8009 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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|
jpayne@69
|
8010 }
|
|
jpayne@69
|
8011 }
|
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jpayne@69
|
8012 __Pyx_AddTraceback("pysam.libctabix.Parser.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8013 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8014 return NULL;
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jpayne@69
|
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|
jpayne@69
|
8016 __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
8017
|
|
jpayne@69
|
8018 /* function exit code */
|
|
jpayne@69
|
8019 {
|
|
jpayne@69
|
8020 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8021 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8022 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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jpayne@69
|
8023 }
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jpayne@69
|
8024 }
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jpayne@69
|
8025 __Pyx_RefNannyFinishContext();
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jpayne@69
|
8026 return __pyx_r;
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jpayne@69
|
8027 }
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jpayne@69
|
8028
|
|
jpayne@69
|
8029 static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_10__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
8030 PyObject *__pyx_r = NULL;
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jpayne@69
|
8031 __Pyx_TraceDeclarations
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|
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|
|
jpayne@69
|
8035 const char *__pyx_filename = NULL;
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jpayne@69
|
8036 int __pyx_clineno = 0;
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8037 __Pyx_TraceFrameInit(__pyx_codeobj__4)
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jpayne@69
|
8040
|
|
jpayne@69
|
8041 /* "(tree fragment)":17
|
|
jpayne@69
|
8042 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8043 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
8044 * __pyx_unpickle_Parser__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8045 */
|
|
jpayne@69
|
8046 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
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jpayne@69
|
8047 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
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8048 __Pyx_GOTREF(__pyx_t_1);
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8049 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
|
8050
|
|
jpayne@69
|
8051 /* "(tree fragment)":16
|
|
jpayne@69
|
8052 * else:
|
|
jpayne@69
|
8053 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8054 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
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|
jpayne@69
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jpayne@69
|
8056 */
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|
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jpayne@69
|
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|
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|
8071
|
|
jpayne@69
|
8072 /* "pysam/libctabix.pyx":106
|
|
jpayne@69
|
8073 * A field in a row is accessed by numeric index.
|
|
jpayne@69
|
8074 * '''
|
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jpayne@69
|
8075 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
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|
jpayne@69
|
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|
|
jpayne@69
|
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jpayne@69
|
8078 */
|
|
jpayne@69
|
8079
|
|
jpayne@69
|
8080 static PyObject *__pyx_f_5pysam_9libctabix_7asTuple_parse(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) {
|
|
jpayne@69
|
8081 struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *__pyx_v_r = 0;
|
|
jpayne@69
|
8082 PyObject *__pyx_r = NULL;
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jpayne@69
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jpayne@69
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|
|
jpayne@69
|
8093 * cdef parse(self, char * buffer, int len):
|
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jpayne@69
|
8094 * cdef ctabixproxies.TupleProxy r
|
|
jpayne@69
|
8095 * r = ctabixproxies.TupleProxy(self.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8096 * # need to copy - there were some
|
|
jpayne@69
|
8097 * # persistence issues with "present"
|
|
jpayne@69
|
8098 */
|
|
jpayne@69
|
8099 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_TupleProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 108, __pyx_L1_error)
|
|
jpayne@69
|
8100 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8101 __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_t_1);
|
|
jpayne@69
|
8102 __pyx_t_1 = 0;
|
|
jpayne@69
|
8103
|
|
jpayne@69
|
8104 /* "pysam/libctabix.pyx":111
|
|
jpayne@69
|
8105 * # need to copy - there were some
|
|
jpayne@69
|
8106 * # persistence issues with "present"
|
|
jpayne@69
|
8107 * r.copy(buffer, len) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8108 * return r
|
|
jpayne@69
|
8109 *
|
|
jpayne@69
|
8110 */
|
|
jpayne@69
|
8111 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r->__pyx_vtab)->copy(__pyx_v_r, __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 111, __pyx_L1_error)
|
|
jpayne@69
|
8112 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8113 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
8114
|
|
jpayne@69
|
8115 /* "pysam/libctabix.pyx":112
|
|
jpayne@69
|
8116 * # persistence issues with "present"
|
|
jpayne@69
|
8117 * r.copy(buffer, len)
|
|
jpayne@69
|
8118 * return r # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8119 *
|
|
jpayne@69
|
8120 *
|
|
jpayne@69
|
8121 */
|
|
jpayne@69
|
8122 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
8123 __Pyx_INCREF((PyObject *)__pyx_v_r);
|
|
jpayne@69
|
8124 __pyx_r = ((PyObject *)__pyx_v_r);
|
|
jpayne@69
|
8125 goto __pyx_L0;
|
|
jpayne@69
|
8126
|
|
jpayne@69
|
8127 /* "pysam/libctabix.pyx":106
|
|
jpayne@69
|
8128 * A field in a row is accessed by numeric index.
|
|
jpayne@69
|
8129 * '''
|
|
jpayne@69
|
8130 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8131 * cdef ctabixproxies.TupleProxy r
|
|
jpayne@69
|
8132 * r = ctabixproxies.TupleProxy(self.encoding)
|
|
jpayne@69
|
8133 */
|
|
jpayne@69
|
8134
|
|
jpayne@69
|
8135 /* function exit code */
|
|
jpayne@69
|
8136 __pyx_L1_error:;
|
|
jpayne@69
|
8137 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
8138 __Pyx_AddTraceback("pysam.libctabix.asTuple.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8139 __pyx_r = 0;
|
|
jpayne@69
|
8140 __pyx_L0:;
|
|
jpayne@69
|
8141 __Pyx_XDECREF((PyObject *)__pyx_v_r);
|
|
jpayne@69
|
8142 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
8143 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
8144 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8145 return __pyx_r;
|
|
jpayne@69
|
8146 }
|
|
jpayne@69
|
8147
|
|
jpayne@69
|
8148 /* "(tree fragment)":1
|
|
jpayne@69
|
8149 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8150 * cdef tuple state
|
|
jpayne@69
|
8151 * cdef object _dict
|
|
jpayne@69
|
8152 */
|
|
jpayne@69
|
8153
|
|
jpayne@69
|
8154 /* Python wrapper */
|
|
jpayne@69
|
8155 static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8156 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8157 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8158 #else
|
|
jpayne@69
|
8159 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8160 #endif
|
|
jpayne@69
|
8161 ); /*proto*/
|
|
jpayne@69
|
8162 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_7asTuple___reduce_cython__, "asTuple.__reduce_cython__(self)");
|
|
jpayne@69
|
8163 static PyMethodDef __pyx_mdef_5pysam_9libctabix_7asTuple_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple___reduce_cython__};
|
|
jpayne@69
|
8164 static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8165 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8166 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8167 #else
|
|
jpayne@69
|
8168 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8169 #endif
|
|
jpayne@69
|
8170 ) {
|
|
jpayne@69
|
8171 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8172 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
8173 #endif
|
|
jpayne@69
|
8174 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
8175 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
8176 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
8177 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
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jpayne@69
|
8178 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8179 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
8180 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
8181 #else
|
|
jpayne@69
|
8182 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
8183 #endif
|
|
jpayne@69
|
8184 #endif
|
|
jpayne@69
|
8185 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
8186 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
8187 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
8188 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
8189 __pyx_r = __pyx_pf_5pysam_9libctabix_7asTuple___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asTuple *)__pyx_v_self));
|
|
jpayne@69
|
8190
|
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jpayne@69
|
8191 /* function exit code */
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jpayne@69
|
8192 __Pyx_RefNannyFinishContext();
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jpayne@69
|
8193 return __pyx_r;
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jpayne@69
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8194 }
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jpayne@69
|
8195
|
|
jpayne@69
|
8196 static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self) {
|
|
jpayne@69
|
8197 PyObject *__pyx_v_state = 0;
|
|
jpayne@69
|
8198 PyObject *__pyx_v__dict = 0;
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|
jpayne@69
|
8199 int __pyx_v_use_setstate;
|
|
jpayne@69
|
8200 PyObject *__pyx_r = NULL;
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jpayne@69
|
8201 __Pyx_TraceDeclarations
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jpayne@69
|
8202 __Pyx_RefNannyDeclarations
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jpayne@69
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8203 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
8204 int __pyx_t_2;
|
|
jpayne@69
|
8205 PyObject *__pyx_t_3 = NULL;
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|
jpayne@69
|
8206 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
8207 int __pyx_lineno = 0;
|
|
jpayne@69
|
8208 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
8209 int __pyx_clineno = 0;
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jpayne@69
|
8210 __Pyx_TraceFrameInit(__pyx_codeobj__5)
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jpayne@69
|
8211 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
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jpayne@69
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8212 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
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jpayne@69
|
8213
|
|
jpayne@69
|
8214 /* "(tree fragment)":5
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|
jpayne@69
|
8215 * cdef object _dict
|
|
jpayne@69
|
8216 * cdef bint use_setstate
|
|
jpayne@69
|
8217 * state = (self.encoding,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8218 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8219 * if _dict is not None:
|
|
jpayne@69
|
8220 */
|
|
jpayne@69
|
8221 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
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jpayne@69
|
8222 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
8223 __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding);
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jpayne@69
|
8224 __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding);
|
|
jpayne@69
|
8225 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
|
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jpayne@69
|
8226 __pyx_v_state = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
8227 __pyx_t_1 = 0;
|
|
jpayne@69
|
8228
|
|
jpayne@69
|
8229 /* "(tree fragment)":6
|
|
jpayne@69
|
8230 * cdef bint use_setstate
|
|
jpayne@69
|
8231 * state = (self.encoding,)
|
|
jpayne@69
|
8232 * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8233 * if _dict is not None:
|
|
jpayne@69
|
8234 * state += (_dict,)
|
|
jpayne@69
|
8235 */
|
|
jpayne@69
|
8236 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
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jpayne@69
|
8237 __Pyx_GOTREF(__pyx_t_1);
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|
jpayne@69
|
8238 __pyx_v__dict = __pyx_t_1;
|
|
jpayne@69
|
8239 __pyx_t_1 = 0;
|
|
jpayne@69
|
8240
|
|
jpayne@69
|
8241 /* "(tree fragment)":7
|
|
jpayne@69
|
8242 * state = (self.encoding,)
|
|
jpayne@69
|
8243 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8244 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8245 * state += (_dict,)
|
|
jpayne@69
|
8246 * use_setstate = True
|
|
jpayne@69
|
8247 */
|
|
jpayne@69
|
8248 __pyx_t_2 = (__pyx_v__dict != Py_None);
|
|
jpayne@69
|
8249 if (__pyx_t_2) {
|
|
jpayne@69
|
8250
|
|
jpayne@69
|
8251 /* "(tree fragment)":8
|
|
jpayne@69
|
8252 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8253 * if _dict is not None:
|
|
jpayne@69
|
8254 * state += (_dict,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8255 * use_setstate = True
|
|
jpayne@69
|
8256 * else:
|
|
jpayne@69
|
8257 */
|
|
jpayne@69
|
8258 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
8259 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8260 __Pyx_INCREF(__pyx_v__dict);
|
|
jpayne@69
|
8261 __Pyx_GIVEREF(__pyx_v__dict);
|
|
jpayne@69
|
8262 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
|
|
jpayne@69
|
8263 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
8264 __Pyx_GOTREF(__pyx_t_3);
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|
jpayne@69
|
8265 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
8266 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
8267 __pyx_t_3 = 0;
|
|
jpayne@69
|
8268
|
|
jpayne@69
|
8269 /* "(tree fragment)":9
|
|
jpayne@69
|
8270 * if _dict is not None:
|
|
jpayne@69
|
8271 * state += (_dict,)
|
|
jpayne@69
|
8272 * use_setstate = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8273 * else:
|
|
jpayne@69
|
8274 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8275 */
|
|
jpayne@69
|
8276 __pyx_v_use_setstate = 1;
|
|
jpayne@69
|
8277
|
|
jpayne@69
|
8278 /* "(tree fragment)":7
|
|
jpayne@69
|
8279 * state = (self.encoding,)
|
|
jpayne@69
|
8280 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8281 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8282 * state += (_dict,)
|
|
jpayne@69
|
8283 * use_setstate = True
|
|
jpayne@69
|
8284 */
|
|
jpayne@69
|
8285 goto __pyx_L3;
|
|
jpayne@69
|
8286 }
|
|
jpayne@69
|
8287
|
|
jpayne@69
|
8288 /* "(tree fragment)":11
|
|
jpayne@69
|
8289 * use_setstate = True
|
|
jpayne@69
|
8290 * else:
|
|
jpayne@69
|
8291 * use_setstate = self.encoding is not None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8292 * if use_setstate:
|
|
jpayne@69
|
8293 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8294 */
|
|
jpayne@69
|
8295 /*else*/ {
|
|
jpayne@69
|
8296 __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None);
|
|
jpayne@69
|
8297 __pyx_v_use_setstate = __pyx_t_2;
|
|
jpayne@69
|
8298 }
|
|
jpayne@69
|
8299 __pyx_L3:;
|
|
jpayne@69
|
8300
|
|
jpayne@69
|
8301 /* "(tree fragment)":12
|
|
jpayne@69
|
8302 * else:
|
|
jpayne@69
|
8303 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8304 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8305 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8306 * else:
|
|
jpayne@69
|
8307 */
|
|
jpayne@69
|
8308 if (__pyx_v_use_setstate) {
|
|
jpayne@69
|
8309
|
|
jpayne@69
|
8310 /* "(tree fragment)":13
|
|
jpayne@69
|
8311 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8312 * if use_setstate:
|
|
jpayne@69
|
8313 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8314 * else:
|
|
jpayne@69
|
8315 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8316 */
|
|
jpayne@69
|
8317 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
8318 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asTuple); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
8319 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
8320 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
8321 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8322 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
8323 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
8324 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
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jpayne@69
|
8325 __Pyx_INCREF(__pyx_int_243541226);
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jpayne@69
|
8326 __Pyx_GIVEREF(__pyx_int_243541226);
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jpayne@69
|
8327 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error);
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jpayne@69
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8328 __Pyx_INCREF(Py_None);
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jpayne@69
|
8329 __Pyx_GIVEREF(Py_None);
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jpayne@69
|
8330 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
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jpayne@69
|
8331 __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error)
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jpayne@69
|
8332 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
|
8333 __Pyx_GIVEREF(__pyx_t_3);
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jpayne@69
|
8334 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
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jpayne@69
|
8335 __Pyx_GIVEREF(__pyx_t_1);
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jpayne@69
|
8336 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
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jpayne@69
|
8337 __Pyx_INCREF(__pyx_v_state);
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jpayne@69
|
8338 __Pyx_GIVEREF(__pyx_v_state);
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jpayne@69
|
8339 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
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jpayne@69
|
8340 __pyx_t_3 = 0;
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|
jpayne@69
|
8341 __pyx_t_1 = 0;
|
|
jpayne@69
|
8342 __pyx_r = __pyx_t_4;
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|
jpayne@69
|
8343 __pyx_t_4 = 0;
|
|
jpayne@69
|
8344 goto __pyx_L0;
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|
jpayne@69
|
8345
|
|
jpayne@69
|
8346 /* "(tree fragment)":12
|
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jpayne@69
|
8347 * else:
|
|
jpayne@69
|
8348 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8349 * if use_setstate: # <<<<<<<<<<<<<<
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|
jpayne@69
|
8350 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8351 * else:
|
|
jpayne@69
|
8352 */
|
|
jpayne@69
|
8353 }
|
|
jpayne@69
|
8354
|
|
jpayne@69
|
8355 /* "(tree fragment)":15
|
|
jpayne@69
|
8356 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8357 * else:
|
|
jpayne@69
|
8358 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8359 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
8360 * __pyx_unpickle_asTuple__set_state(self, __pyx_state)
|
|
jpayne@69
|
8361 */
|
|
jpayne@69
|
8362 /*else*/ {
|
|
jpayne@69
|
8363 __Pyx_XDECREF(__pyx_r);
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jpayne@69
|
8364 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asTuple); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error)
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jpayne@69
|
8365 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
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8366 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
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jpayne@69
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8367 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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8368 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
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jpayne@69
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8369 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
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jpayne@69
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8370 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
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8371 __Pyx_INCREF(__pyx_int_243541226);
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jpayne@69
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8372 __Pyx_GIVEREF(__pyx_int_243541226);
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jpayne@69
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8373 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
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8374 __Pyx_INCREF(__pyx_v_state);
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jpayne@69
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8375 __Pyx_GIVEREF(__pyx_v_state);
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jpayne@69
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8376 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
|
8377 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
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jpayne@69
|
8378 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
8379 __Pyx_GIVEREF(__pyx_t_4);
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jpayne@69
|
8380 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
|
8381 __Pyx_GIVEREF(__pyx_t_1);
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jpayne@69
|
8382 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
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jpayne@69
|
8383 __pyx_t_4 = 0;
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jpayne@69
|
8384 __pyx_t_1 = 0;
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jpayne@69
|
8385 __pyx_r = __pyx_t_3;
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jpayne@69
|
8386 __pyx_t_3 = 0;
|
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jpayne@69
|
8387 goto __pyx_L0;
|
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jpayne@69
|
8388 }
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jpayne@69
|
8389
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jpayne@69
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8390 /* "(tree fragment)":1
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jpayne@69
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8391 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
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jpayne@69
|
8392 * cdef tuple state
|
|
jpayne@69
|
8393 * cdef object _dict
|
|
jpayne@69
|
8394 */
|
|
jpayne@69
|
8395
|
|
jpayne@69
|
8396 /* function exit code */
|
|
jpayne@69
|
8397 __pyx_L1_error:;
|
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jpayne@69
|
8398 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
8399 __Pyx_XDECREF(__pyx_t_3);
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jpayne@69
|
8400 __Pyx_XDECREF(__pyx_t_4);
|
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jpayne@69
|
8401 __Pyx_AddTraceback("pysam.libctabix.asTuple.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8402 __pyx_r = NULL;
|
|
jpayne@69
|
8403 __pyx_L0:;
|
|
jpayne@69
|
8404 __Pyx_XDECREF(__pyx_v_state);
|
|
jpayne@69
|
8405 __Pyx_XDECREF(__pyx_v__dict);
|
|
jpayne@69
|
8406 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
8407 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
8408 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8409 return __pyx_r;
|
|
jpayne@69
|
8410 }
|
|
jpayne@69
|
8411
|
|
jpayne@69
|
8412 /* "(tree fragment)":16
|
|
jpayne@69
|
8413 * else:
|
|
jpayne@69
|
8414 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8415 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8416 * __pyx_unpickle_asTuple__set_state(self, __pyx_state)
|
|
jpayne@69
|
8417 */
|
|
jpayne@69
|
8418
|
|
jpayne@69
|
8419 /* Python wrapper */
|
|
jpayne@69
|
8420 static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8421 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8422 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8423 #else
|
|
jpayne@69
|
8424 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8425 #endif
|
|
jpayne@69
|
8426 ); /*proto*/
|
|
jpayne@69
|
8427 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_7asTuple_2__setstate_cython__, "asTuple.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
8428 static PyMethodDef __pyx_mdef_5pysam_9libctabix_7asTuple_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple_2__setstate_cython__};
|
|
jpayne@69
|
8429 static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8430 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8431 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8432 #else
|
|
jpayne@69
|
8433 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8434 #endif
|
|
jpayne@69
|
8435 ) {
|
|
jpayne@69
|
8436 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
8437 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8438 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
8439 #endif
|
|
jpayne@69
|
8440 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
8441 PyObject* values[1] = {0};
|
|
jpayne@69
|
8442 int __pyx_lineno = 0;
|
|
jpayne@69
|
8443 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
8444 int __pyx_clineno = 0;
|
|
jpayne@69
|
8445 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
8446 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
8447 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
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jpayne@69
|
8448 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8449 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
8450 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
8451 #else
|
|
jpayne@69
|
8452 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
8453 #endif
|
|
jpayne@69
|
8454 #endif
|
|
jpayne@69
|
8455 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
8456 {
|
|
jpayne@69
|
8457 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
8458 if (__pyx_kwds) {
|
|
jpayne@69
|
8459 Py_ssize_t kw_args;
|
|
jpayne@69
|
8460 switch (__pyx_nargs) {
|
|
jpayne@69
|
8461 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8462 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8463 case 0: break;
|
|
jpayne@69
|
8464 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8465 }
|
|
jpayne@69
|
8466 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
8467 switch (__pyx_nargs) {
|
|
jpayne@69
|
8468 case 0:
|
|
jpayne@69
|
8469 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
8470 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
8471 kw_args--;
|
|
jpayne@69
|
8472 }
|
|
jpayne@69
|
8473 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
8474 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8475 }
|
|
jpayne@69
|
8476 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
8477 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
8478 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
8479 }
|
|
jpayne@69
|
8480 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
8481 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8482 } else {
|
|
jpayne@69
|
8483 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8484 }
|
|
jpayne@69
|
8485 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
8486 }
|
|
jpayne@69
|
8487 goto __pyx_L6_skip;
|
|
jpayne@69
|
8488 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
8489 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
8490 __pyx_L6_skip:;
|
|
jpayne@69
|
8491 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
8492 __pyx_L3_error:;
|
|
jpayne@69
|
8493 {
|
|
jpayne@69
|
8494 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8495 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8496 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8497 }
|
|
jpayne@69
|
8498 }
|
|
jpayne@69
|
8499 __Pyx_AddTraceback("pysam.libctabix.asTuple.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8500 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8501 return NULL;
|
|
jpayne@69
|
8502 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
8503 __pyx_r = __pyx_pf_5pysam_9libctabix_7asTuple_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asTuple *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
8504
|
|
jpayne@69
|
8505 /* function exit code */
|
|
jpayne@69
|
8506 {
|
|
jpayne@69
|
8507 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8508 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8509 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8510 }
|
|
jpayne@69
|
8511 }
|
|
jpayne@69
|
8512 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
8513 return __pyx_r;
|
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jpayne@69
|
8514 }
|
|
jpayne@69
|
8515
|
|
jpayne@69
|
8516 static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
8517 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
8518 __Pyx_TraceDeclarations
|
|
jpayne@69
|
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|
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jpayne@69
|
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|
|
jpayne@69
|
8522 const char *__pyx_filename = NULL;
|
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jpayne@69
|
8523 int __pyx_clineno = 0;
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jpayne@69
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8524 __Pyx_TraceFrameInit(__pyx_codeobj__6)
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8526 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error));
|
|
jpayne@69
|
8527
|
|
jpayne@69
|
8528 /* "(tree fragment)":17
|
|
jpayne@69
|
8529 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8530 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
8531 * __pyx_unpickle_asTuple__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8532 */
|
|
jpayne@69
|
8533 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
|
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jpayne@69
|
8534 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
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jpayne@69
|
8535 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
8536 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
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jpayne@69
|
8537
|
|
jpayne@69
|
8538 /* "(tree fragment)":16
|
|
jpayne@69
|
8539 * else:
|
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jpayne@69
|
8540 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8541 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8542 * __pyx_unpickle_asTuple__set_state(self, __pyx_state)
|
|
jpayne@69
|
8543 */
|
|
jpayne@69
|
8544
|
|
jpayne@69
|
8545 /* function exit code */
|
|
jpayne@69
|
8546 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
8547 goto __pyx_L0;
|
|
jpayne@69
|
8548 __pyx_L1_error:;
|
|
jpayne@69
|
8549 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
8550 __Pyx_AddTraceback("pysam.libctabix.asTuple.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8551 __pyx_r = NULL;
|
|
jpayne@69
|
8552 __pyx_L0:;
|
|
jpayne@69
|
8553 __Pyx_XGIVEREF(__pyx_r);
|
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jpayne@69
|
8554 __Pyx_TraceReturn(__pyx_r, 0);
|
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jpayne@69
|
8555 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8556 return __pyx_r;
|
|
jpayne@69
|
8557 }
|
|
jpayne@69
|
8558
|
|
jpayne@69
|
8559 /* "pysam/libctabix.pyx":144
|
|
jpayne@69
|
8560 *
|
|
jpayne@69
|
8561 * '''
|
|
jpayne@69
|
8562 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8563 * cdef ctabixproxies.GFF3Proxy r
|
|
jpayne@69
|
8564 * r = ctabixproxies.GFF3Proxy(self.encoding)
|
|
jpayne@69
|
8565 */
|
|
jpayne@69
|
8566
|
|
jpayne@69
|
8567 static PyObject *__pyx_f_5pysam_9libctabix_6asGFF3_parse(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) {
|
|
jpayne@69
|
8568 struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy *__pyx_v_r = 0;
|
|
jpayne@69
|
8569 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
8570 __Pyx_TraceDeclarations
|
|
jpayne@69
|
8571 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
8572 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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8573 int __pyx_lineno = 0;
|
|
jpayne@69
|
8574 const char *__pyx_filename = NULL;
|
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jpayne@69
|
8575 int __pyx_clineno = 0;
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jpayne@69
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8576 __Pyx_RefNannySetupContext("parse", 1);
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jpayne@69
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8577 __Pyx_TraceCall("parse", __pyx_f[0], 144, 0, __PYX_ERR(0, 144, __pyx_L1_error));
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jpayne@69
|
8578
|
|
jpayne@69
|
8579 /* "pysam/libctabix.pyx":146
|
|
jpayne@69
|
8580 * cdef parse(self, char * buffer, int len):
|
|
jpayne@69
|
8581 * cdef ctabixproxies.GFF3Proxy r
|
|
jpayne@69
|
8582 * r = ctabixproxies.GFF3Proxy(self.encoding) # <<<<<<<<<<<<<<
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|
jpayne@69
|
8583 * r.copy(buffer, len)
|
|
jpayne@69
|
8584 * return r
|
|
jpayne@69
|
8585 */
|
|
jpayne@69
|
8586 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 146, __pyx_L1_error)
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jpayne@69
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8587 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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8588 __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy *)__pyx_t_1);
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jpayne@69
|
8589 __pyx_t_1 = 0;
|
|
jpayne@69
|
8590
|
|
jpayne@69
|
8591 /* "pysam/libctabix.pyx":147
|
|
jpayne@69
|
8592 * cdef ctabixproxies.GFF3Proxy r
|
|
jpayne@69
|
8593 * r = ctabixproxies.GFF3Proxy(self.encoding)
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|
jpayne@69
|
8594 * r.copy(buffer, len) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8595 * return r
|
|
jpayne@69
|
8596 *
|
|
jpayne@69
|
8597 */
|
|
jpayne@69
|
8598 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 147, __pyx_L1_error)
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jpayne@69
|
8599 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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8600 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
|
8601
|
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jpayne@69
|
8602 /* "pysam/libctabix.pyx":148
|
|
jpayne@69
|
8603 * r = ctabixproxies.GFF3Proxy(self.encoding)
|
|
jpayne@69
|
8604 * r.copy(buffer, len)
|
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jpayne@69
|
8605 * return r # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8606 *
|
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jpayne@69
|
8607 *
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jpayne@69
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8608 */
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jpayne@69
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8609 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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8610 __Pyx_INCREF((PyObject *)__pyx_v_r);
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jpayne@69
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8611 __pyx_r = ((PyObject *)__pyx_v_r);
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jpayne@69
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8612 goto __pyx_L0;
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jpayne@69
|
8613
|
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jpayne@69
|
8614 /* "pysam/libctabix.pyx":144
|
|
jpayne@69
|
8615 *
|
|
jpayne@69
|
8616 * '''
|
|
jpayne@69
|
8617 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
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|
jpayne@69
|
8618 * cdef ctabixproxies.GFF3Proxy r
|
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jpayne@69
|
8619 * r = ctabixproxies.GFF3Proxy(self.encoding)
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jpayne@69
|
8620 */
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jpayne@69
|
8621
|
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jpayne@69
|
8622 /* function exit code */
|
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jpayne@69
|
8623 __pyx_L1_error:;
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jpayne@69
|
8624 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
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8625 __Pyx_AddTraceback("pysam.libctabix.asGFF3.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
|
8626 __pyx_r = 0;
|
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jpayne@69
|
8627 __pyx_L0:;
|
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jpayne@69
|
8628 __Pyx_XDECREF((PyObject *)__pyx_v_r);
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jpayne@69
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8629 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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8630 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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8631 __Pyx_RefNannyFinishContext();
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jpayne@69
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8632 return __pyx_r;
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jpayne@69
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8633 }
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jpayne@69
|
8634
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jpayne@69
|
8635 /* "(tree fragment)":1
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jpayne@69
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8636 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
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jpayne@69
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8637 * cdef tuple state
|
|
jpayne@69
|
8638 * cdef object _dict
|
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jpayne@69
|
8639 */
|
|
jpayne@69
|
8640
|
|
jpayne@69
|
8641 /* Python wrapper */
|
|
jpayne@69
|
8642 static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__(PyObject *__pyx_v_self,
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jpayne@69
|
8643 #if CYTHON_METH_FASTCALL
|
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jpayne@69
|
8644 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8645 #else
|
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jpayne@69
|
8646 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
|
8647 #endif
|
|
jpayne@69
|
8648 ); /*proto*/
|
|
jpayne@69
|
8649 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6asGFF3___reduce_cython__, "asGFF3.__reduce_cython__(self)");
|
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jpayne@69
|
8650 static PyMethodDef __pyx_mdef_5pysam_9libctabix_6asGFF3_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3___reduce_cython__};
|
|
jpayne@69
|
8651 static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8652 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8653 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8654 #else
|
|
jpayne@69
|
8655 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8656 #endif
|
|
jpayne@69
|
8657 ) {
|
|
jpayne@69
|
8658 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8659 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
8660 #endif
|
|
jpayne@69
|
8661 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
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jpayne@69
|
8662 PyObject *__pyx_r = 0;
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jpayne@69
|
8663 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
8664 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
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jpayne@69
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jpayne@69
|
8666 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
8667 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
8668 #else
|
|
jpayne@69
|
8669 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
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jpayne@69
|
8670 #endif
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jpayne@69
|
8671 #endif
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jpayne@69
|
8672 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
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jpayne@69
|
8673 if (unlikely(__pyx_nargs > 0)) {
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jpayne@69
|
8674 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
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jpayne@69
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8675 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
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jpayne@69
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8676 __pyx_r = __pyx_pf_5pysam_9libctabix_6asGFF3___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)__pyx_v_self));
|
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jpayne@69
|
8677
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jpayne@69
|
8678 /* function exit code */
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jpayne@69
|
8679 __Pyx_RefNannyFinishContext();
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jpayne@69
|
8680 return __pyx_r;
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jpayne@69
|
8681 }
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jpayne@69
|
8682
|
|
jpayne@69
|
8683 static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self) {
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jpayne@69
|
8684 PyObject *__pyx_v_state = 0;
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|
jpayne@69
|
8685 PyObject *__pyx_v__dict = 0;
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|
jpayne@69
|
8686 int __pyx_v_use_setstate;
|
|
jpayne@69
|
8687 PyObject *__pyx_r = NULL;
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jpayne@69
|
8688 __Pyx_TraceDeclarations
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jpayne@69
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8689 __Pyx_RefNannyDeclarations
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jpayne@69
|
8690 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
8691 int __pyx_t_2;
|
|
jpayne@69
|
8692 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
8693 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
8694 int __pyx_lineno = 0;
|
|
jpayne@69
|
8695 const char *__pyx_filename = NULL;
|
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jpayne@69
|
8696 int __pyx_clineno = 0;
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jpayne@69
|
8697 __Pyx_TraceFrameInit(__pyx_codeobj__7)
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jpayne@69
|
8698 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
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jpayne@69
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8699 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
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jpayne@69
|
8700
|
|
jpayne@69
|
8701 /* "(tree fragment)":5
|
|
jpayne@69
|
8702 * cdef object _dict
|
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jpayne@69
|
8703 * cdef bint use_setstate
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jpayne@69
|
8704 * state = (self.encoding,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8705 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8706 * if _dict is not None:
|
|
jpayne@69
|
8707 */
|
|
jpayne@69
|
8708 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
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jpayne@69
|
8709 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
8710 __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding);
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jpayne@69
|
8711 __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding);
|
|
jpayne@69
|
8712 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
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jpayne@69
|
8713 __pyx_v_state = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
8714 __pyx_t_1 = 0;
|
|
jpayne@69
|
8715
|
|
jpayne@69
|
8716 /* "(tree fragment)":6
|
|
jpayne@69
|
8717 * cdef bint use_setstate
|
|
jpayne@69
|
8718 * state = (self.encoding,)
|
|
jpayne@69
|
8719 * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8720 * if _dict is not None:
|
|
jpayne@69
|
8721 * state += (_dict,)
|
|
jpayne@69
|
8722 */
|
|
jpayne@69
|
8723 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
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jpayne@69
|
8724 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8725 __pyx_v__dict = __pyx_t_1;
|
|
jpayne@69
|
8726 __pyx_t_1 = 0;
|
|
jpayne@69
|
8727
|
|
jpayne@69
|
8728 /* "(tree fragment)":7
|
|
jpayne@69
|
8729 * state = (self.encoding,)
|
|
jpayne@69
|
8730 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8731 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8732 * state += (_dict,)
|
|
jpayne@69
|
8733 * use_setstate = True
|
|
jpayne@69
|
8734 */
|
|
jpayne@69
|
8735 __pyx_t_2 = (__pyx_v__dict != Py_None);
|
|
jpayne@69
|
8736 if (__pyx_t_2) {
|
|
jpayne@69
|
8737
|
|
jpayne@69
|
8738 /* "(tree fragment)":8
|
|
jpayne@69
|
8739 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8740 * if _dict is not None:
|
|
jpayne@69
|
8741 * state += (_dict,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8742 * use_setstate = True
|
|
jpayne@69
|
8743 * else:
|
|
jpayne@69
|
8744 */
|
|
jpayne@69
|
8745 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
8746 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8747 __Pyx_INCREF(__pyx_v__dict);
|
|
jpayne@69
|
8748 __Pyx_GIVEREF(__pyx_v__dict);
|
|
jpayne@69
|
8749 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
|
|
jpayne@69
|
8750 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
|
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jpayne@69
|
8751 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
8752 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
8753 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
8754 __pyx_t_3 = 0;
|
|
jpayne@69
|
8755
|
|
jpayne@69
|
8756 /* "(tree fragment)":9
|
|
jpayne@69
|
8757 * if _dict is not None:
|
|
jpayne@69
|
8758 * state += (_dict,)
|
|
jpayne@69
|
8759 * use_setstate = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8760 * else:
|
|
jpayne@69
|
8761 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8762 */
|
|
jpayne@69
|
8763 __pyx_v_use_setstate = 1;
|
|
jpayne@69
|
8764
|
|
jpayne@69
|
8765 /* "(tree fragment)":7
|
|
jpayne@69
|
8766 * state = (self.encoding,)
|
|
jpayne@69
|
8767 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
8768 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8769 * state += (_dict,)
|
|
jpayne@69
|
8770 * use_setstate = True
|
|
jpayne@69
|
8771 */
|
|
jpayne@69
|
8772 goto __pyx_L3;
|
|
jpayne@69
|
8773 }
|
|
jpayne@69
|
8774
|
|
jpayne@69
|
8775 /* "(tree fragment)":11
|
|
jpayne@69
|
8776 * use_setstate = True
|
|
jpayne@69
|
8777 * else:
|
|
jpayne@69
|
8778 * use_setstate = self.encoding is not None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8779 * if use_setstate:
|
|
jpayne@69
|
8780 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8781 */
|
|
jpayne@69
|
8782 /*else*/ {
|
|
jpayne@69
|
8783 __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None);
|
|
jpayne@69
|
8784 __pyx_v_use_setstate = __pyx_t_2;
|
|
jpayne@69
|
8785 }
|
|
jpayne@69
|
8786 __pyx_L3:;
|
|
jpayne@69
|
8787
|
|
jpayne@69
|
8788 /* "(tree fragment)":12
|
|
jpayne@69
|
8789 * else:
|
|
jpayne@69
|
8790 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8791 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8792 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8793 * else:
|
|
jpayne@69
|
8794 */
|
|
jpayne@69
|
8795 if (__pyx_v_use_setstate) {
|
|
jpayne@69
|
8796
|
|
jpayne@69
|
8797 /* "(tree fragment)":13
|
|
jpayne@69
|
8798 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8799 * if use_setstate:
|
|
jpayne@69
|
8800 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8801 * else:
|
|
jpayne@69
|
8802 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8803 */
|
|
jpayne@69
|
8804 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
8805 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asGFF3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
8806 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
8807 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
8808 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8809 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
8810 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
8811 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
8812 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
8813 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
8814 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
8815 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
8816 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
8817 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
8818 __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
8819 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
8820 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
8821 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
8822 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
8823 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
8824 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
8825 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
8826 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
8827 __pyx_t_3 = 0;
|
|
jpayne@69
|
8828 __pyx_t_1 = 0;
|
|
jpayne@69
|
8829 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
8830 __pyx_t_4 = 0;
|
|
jpayne@69
|
8831 goto __pyx_L0;
|
|
jpayne@69
|
8832
|
|
jpayne@69
|
8833 /* "(tree fragment)":12
|
|
jpayne@69
|
8834 * else:
|
|
jpayne@69
|
8835 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
8836 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8837 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8838 * else:
|
|
jpayne@69
|
8839 */
|
|
jpayne@69
|
8840 }
|
|
jpayne@69
|
8841
|
|
jpayne@69
|
8842 /* "(tree fragment)":15
|
|
jpayne@69
|
8843 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
8844 * else:
|
|
jpayne@69
|
8845 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8846 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
8847 * __pyx_unpickle_asGFF3__set_state(self, __pyx_state)
|
|
jpayne@69
|
8848 */
|
|
jpayne@69
|
8849 /*else*/ {
|
|
jpayne@69
|
8850 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
8851 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asGFF3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
8852 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
8853 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
8854 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8855 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
8856 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
8857 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
8858 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
8859 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
8860 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
8861 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
8862 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
8863 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
8864 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
8865 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
8866 __Pyx_GIVEREF(__pyx_t_4);
|
|
jpayne@69
|
8867 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
8868 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
8869 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
8870 __pyx_t_4 = 0;
|
|
jpayne@69
|
8871 __pyx_t_1 = 0;
|
|
jpayne@69
|
8872 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
8873 __pyx_t_3 = 0;
|
|
jpayne@69
|
8874 goto __pyx_L0;
|
|
jpayne@69
|
8875 }
|
|
jpayne@69
|
8876
|
|
jpayne@69
|
8877 /* "(tree fragment)":1
|
|
jpayne@69
|
8878 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8879 * cdef tuple state
|
|
jpayne@69
|
8880 * cdef object _dict
|
|
jpayne@69
|
8881 */
|
|
jpayne@69
|
8882
|
|
jpayne@69
|
8883 /* function exit code */
|
|
jpayne@69
|
8884 __pyx_L1_error:;
|
|
jpayne@69
|
8885 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
8886 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
8887 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
8888 __Pyx_AddTraceback("pysam.libctabix.asGFF3.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8889 __pyx_r = NULL;
|
|
jpayne@69
|
8890 __pyx_L0:;
|
|
jpayne@69
|
8891 __Pyx_XDECREF(__pyx_v_state);
|
|
jpayne@69
|
8892 __Pyx_XDECREF(__pyx_v__dict);
|
|
jpayne@69
|
8893 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
8894 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
8895 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8896 return __pyx_r;
|
|
jpayne@69
|
8897 }
|
|
jpayne@69
|
8898
|
|
jpayne@69
|
8899 /* "(tree fragment)":16
|
|
jpayne@69
|
8900 * else:
|
|
jpayne@69
|
8901 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
8902 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8903 * __pyx_unpickle_asGFF3__set_state(self, __pyx_state)
|
|
jpayne@69
|
8904 */
|
|
jpayne@69
|
8905
|
|
jpayne@69
|
8906 /* Python wrapper */
|
|
jpayne@69
|
8907 static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8908 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8909 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8910 #else
|
|
jpayne@69
|
8911 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8912 #endif
|
|
jpayne@69
|
8913 ); /*proto*/
|
|
jpayne@69
|
8914 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6asGFF3_2__setstate_cython__, "asGFF3.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
8915 static PyMethodDef __pyx_mdef_5pysam_9libctabix_6asGFF3_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3_2__setstate_cython__};
|
|
jpayne@69
|
8916 static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
8917 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8918 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8919 #else
|
|
jpayne@69
|
8920 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8921 #endif
|
|
jpayne@69
|
8922 ) {
|
|
jpayne@69
|
8923 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
8924 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8925 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
8926 #endif
|
|
jpayne@69
|
8927 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
8928 PyObject* values[1] = {0};
|
|
jpayne@69
|
8929 int __pyx_lineno = 0;
|
|
jpayne@69
|
8930 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
8931 int __pyx_clineno = 0;
|
|
jpayne@69
|
8932 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
8933 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
8934 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
8935 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8936 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
8937 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
8938 #else
|
|
jpayne@69
|
8939 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
8940 #endif
|
|
jpayne@69
|
8941 #endif
|
|
jpayne@69
|
8942 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
8943 {
|
|
jpayne@69
|
8944 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
8945 if (__pyx_kwds) {
|
|
jpayne@69
|
8946 Py_ssize_t kw_args;
|
|
jpayne@69
|
8947 switch (__pyx_nargs) {
|
|
jpayne@69
|
8948 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8949 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8950 case 0: break;
|
|
jpayne@69
|
8951 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8952 }
|
|
jpayne@69
|
8953 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
8954 switch (__pyx_nargs) {
|
|
jpayne@69
|
8955 case 0:
|
|
jpayne@69
|
8956 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
8957 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
8958 kw_args--;
|
|
jpayne@69
|
8959 }
|
|
jpayne@69
|
8960 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
8961 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8962 }
|
|
jpayne@69
|
8963 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
8964 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
8965 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
8966 }
|
|
jpayne@69
|
8967 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
8968 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8969 } else {
|
|
jpayne@69
|
8970 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8971 }
|
|
jpayne@69
|
8972 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
8973 }
|
|
jpayne@69
|
8974 goto __pyx_L6_skip;
|
|
jpayne@69
|
8975 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
8976 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
8977 __pyx_L6_skip:;
|
|
jpayne@69
|
8978 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
8979 __pyx_L3_error:;
|
|
jpayne@69
|
8980 {
|
|
jpayne@69
|
8981 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8982 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8983 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8984 }
|
|
jpayne@69
|
8985 }
|
|
jpayne@69
|
8986 __Pyx_AddTraceback("pysam.libctabix.asGFF3.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8987 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8988 return NULL;
|
|
jpayne@69
|
8989 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
8990 __pyx_r = __pyx_pf_5pysam_9libctabix_6asGFF3_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
8991
|
|
jpayne@69
|
8992 /* function exit code */
|
|
jpayne@69
|
8993 {
|
|
jpayne@69
|
8994 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8995 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8996 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8997 }
|
|
jpayne@69
|
8998 }
|
|
jpayne@69
|
8999 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
9000 return __pyx_r;
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jpayne@69
|
9001 }
|
|
jpayne@69
|
9002
|
|
jpayne@69
|
9003 static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
9004 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
9005 __Pyx_TraceDeclarations
|
|
jpayne@69
|
9006 __Pyx_RefNannyDeclarations
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jpayne@69
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9007 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
9008 int __pyx_lineno = 0;
|
|
jpayne@69
|
9009 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9010 int __pyx_clineno = 0;
|
|
jpayne@69
|
9011 __Pyx_TraceFrameInit(__pyx_codeobj__8)
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jpayne@69
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9012 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
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jpayne@69
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9013 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error));
|
|
jpayne@69
|
9014
|
|
jpayne@69
|
9015 /* "(tree fragment)":17
|
|
jpayne@69
|
9016 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9017 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
9018 * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9019 */
|
|
jpayne@69
|
9020 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
|
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jpayne@69
|
9021 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
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jpayne@69
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9022 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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9023 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
|
9024
|
|
jpayne@69
|
9025 /* "(tree fragment)":16
|
|
jpayne@69
|
9026 * else:
|
|
jpayne@69
|
9027 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9028 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9029 * __pyx_unpickle_asGFF3__set_state(self, __pyx_state)
|
|
jpayne@69
|
9030 */
|
|
jpayne@69
|
9031
|
|
jpayne@69
|
9032 /* function exit code */
|
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jpayne@69
|
9033 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
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|
jpayne@69
|
9034 goto __pyx_L0;
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|
jpayne@69
|
9035 __pyx_L1_error:;
|
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jpayne@69
|
9036 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
|
9037 __Pyx_AddTraceback("pysam.libctabix.asGFF3.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9038 __pyx_r = NULL;
|
|
jpayne@69
|
9039 __pyx_L0:;
|
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jpayne@69
|
9040 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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9041 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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9042 __Pyx_RefNannyFinishContext();
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jpayne@69
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9043 return __pyx_r;
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jpayne@69
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9044 }
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jpayne@69
|
9045
|
|
jpayne@69
|
9046 /* "pysam/libctabix.pyx":191
|
|
jpayne@69
|
9047 *
|
|
jpayne@69
|
9048 * '''
|
|
jpayne@69
|
9049 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9050 * cdef ctabixproxies.GTFProxy r
|
|
jpayne@69
|
9051 * r = ctabixproxies.GTFProxy(self.encoding)
|
|
jpayne@69
|
9052 */
|
|
jpayne@69
|
9053
|
|
jpayne@69
|
9054 static PyObject *__pyx_f_5pysam_9libctabix_5asGTF_parse(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) {
|
|
jpayne@69
|
9055 struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy *__pyx_v_r = 0;
|
|
jpayne@69
|
9056 PyObject *__pyx_r = NULL;
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jpayne@69
|
9057 __Pyx_TraceDeclarations
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jpayne@69
|
9058 __Pyx_RefNannyDeclarations
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jpayne@69
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9059 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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9060 int __pyx_lineno = 0;
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jpayne@69
|
9061 const char *__pyx_filename = NULL;
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jpayne@69
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9062 int __pyx_clineno = 0;
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jpayne@69
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9063 __Pyx_RefNannySetupContext("parse", 1);
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jpayne@69
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9064 __Pyx_TraceCall("parse", __pyx_f[0], 191, 0, __PYX_ERR(0, 191, __pyx_L1_error));
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jpayne@69
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9065
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jpayne@69
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9066 /* "pysam/libctabix.pyx":193
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|
jpayne@69
|
9067 * cdef parse(self, char * buffer, int len):
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jpayne@69
|
9068 * cdef ctabixproxies.GTFProxy r
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jpayne@69
|
9069 * r = ctabixproxies.GTFProxy(self.encoding) # <<<<<<<<<<<<<<
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jpayne@69
|
9070 * r.copy(buffer, len)
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jpayne@69
|
9071 * return r
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jpayne@69
|
9072 */
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jpayne@69
|
9073 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_GTFProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 193, __pyx_L1_error)
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jpayne@69
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9074 __Pyx_GOTREF(__pyx_t_1);
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9075 __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy *)__pyx_t_1);
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jpayne@69
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9076 __pyx_t_1 = 0;
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jpayne@69
|
9077
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jpayne@69
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9078 /* "pysam/libctabix.pyx":194
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jpayne@69
|
9079 * cdef ctabixproxies.GTFProxy r
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jpayne@69
|
9080 * r = ctabixproxies.GTFProxy(self.encoding)
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jpayne@69
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9081 * r.copy(buffer, len) # <<<<<<<<<<<<<<
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jpayne@69
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9082 * return r
|
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jpayne@69
|
9083 *
|
|
jpayne@69
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9084 */
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jpayne@69
|
9085 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 194, __pyx_L1_error)
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jpayne@69
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9086 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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9087 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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9088
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jpayne@69
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9089 /* "pysam/libctabix.pyx":195
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jpayne@69
|
9090 * r = ctabixproxies.GTFProxy(self.encoding)
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jpayne@69
|
9091 * r.copy(buffer, len)
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jpayne@69
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9092 * return r # <<<<<<<<<<<<<<
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jpayne@69
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9093 *
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jpayne@69
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9094 *
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jpayne@69
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9095 */
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jpayne@69
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9096 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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9097 __Pyx_INCREF((PyObject *)__pyx_v_r);
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jpayne@69
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9098 __pyx_r = ((PyObject *)__pyx_v_r);
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jpayne@69
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9099 goto __pyx_L0;
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jpayne@69
|
9100
|
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jpayne@69
|
9101 /* "pysam/libctabix.pyx":191
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jpayne@69
|
9102 *
|
|
jpayne@69
|
9103 * '''
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jpayne@69
|
9104 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
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jpayne@69
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9105 * cdef ctabixproxies.GTFProxy r
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jpayne@69
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9106 * r = ctabixproxies.GTFProxy(self.encoding)
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jpayne@69
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9107 */
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jpayne@69
|
9108
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jpayne@69
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jpayne@69
|
9110 __pyx_L1_error:;
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jpayne@69
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jpayne@69
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jpayne@69
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9114 __pyx_L0:;
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jpayne@69
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9115 __Pyx_XDECREF((PyObject *)__pyx_v_r);
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jpayne@69
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9116 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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9117 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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9118 __Pyx_RefNannyFinishContext();
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jpayne@69
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9119 return __pyx_r;
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jpayne@69
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9120 }
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jpayne@69
|
9121
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jpayne@69
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9122 /* "(tree fragment)":1
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jpayne@69
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9123 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
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jpayne@69
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9124 * cdef tuple state
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jpayne@69
|
9125 * cdef object _dict
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jpayne@69
|
9126 */
|
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jpayne@69
|
9127
|
|
jpayne@69
|
9128 /* Python wrapper */
|
|
jpayne@69
|
9129 static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__(PyObject *__pyx_v_self,
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jpayne@69
|
9130 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9131 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
|
9132 #else
|
|
jpayne@69
|
9133 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
|
9134 #endif
|
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jpayne@69
|
9135 ); /*proto*/
|
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jpayne@69
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9136 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asGTF___reduce_cython__, "asGTF.__reduce_cython__(self)");
|
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jpayne@69
|
9137 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asGTF_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF___reduce_cython__};
|
|
jpayne@69
|
9138 static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9139 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9140 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
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jpayne@69
|
9141 #else
|
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jpayne@69
|
9142 PyObject *__pyx_args, PyObject *__pyx_kwds
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jpayne@69
|
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|
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jpayne@69
|
9144 ) {
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|
jpayne@69
|
9145 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9146 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
9147 #endif
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|
jpayne@69
|
9148 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
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jpayne@69
|
9149 PyObject *__pyx_r = 0;
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jpayne@69
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9150 __Pyx_RefNannyDeclarations
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jpayne@69
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jpayne@69
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9153 #if CYTHON_ASSUME_SAFE_MACROS
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|
jpayne@69
|
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|
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jpayne@69
|
9155 #else
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jpayne@69
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9156 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
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jpayne@69
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9157 #endif
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jpayne@69
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9158 #endif
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9159 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
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9163 __pyx_r = __pyx_pf_5pysam_9libctabix_5asGTF___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asGTF *)__pyx_v_self));
|
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jpayne@69
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9164
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jpayne@69
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9165 /* function exit code */
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jpayne@69
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9166 __Pyx_RefNannyFinishContext();
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jpayne@69
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jpayne@69
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jpayne@69
|
9169
|
|
jpayne@69
|
9170 static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self) {
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jpayne@69
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9171 PyObject *__pyx_v_state = 0;
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jpayne@69
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9172 PyObject *__pyx_v__dict = 0;
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jpayne@69
|
9173 int __pyx_v_use_setstate;
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jpayne@69
|
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jpayne@69
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|
|
jpayne@69
|
9179 PyObject *__pyx_t_3 = NULL;
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|
jpayne@69
|
9180 PyObject *__pyx_t_4 = NULL;
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jpayne@69
|
9181 int __pyx_lineno = 0;
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jpayne@69
|
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jpayne@69
|
9183 int __pyx_clineno = 0;
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jpayne@69
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jpayne@69
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9186 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
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jpayne@69
|
9187
|
|
jpayne@69
|
9188 /* "(tree fragment)":5
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|
jpayne@69
|
9189 * cdef object _dict
|
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jpayne@69
|
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jpayne@69
|
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jpayne@69
|
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|
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|
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jpayne@69
|
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jpayne@69
|
9195 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
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jpayne@69
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9199 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
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9200 __pyx_v_state = ((PyObject*)__pyx_t_1);
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jpayne@69
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9201 __pyx_t_1 = 0;
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
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|
|
jpayne@69
|
9208 * state += (_dict,)
|
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jpayne@69
|
9209 */
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jpayne@69
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9210 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
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jpayne@69
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9211 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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jpayne@69
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9214
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jpayne@69
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9215 /* "(tree fragment)":7
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jpayne@69
|
9216 * state = (self.encoding,)
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jpayne@69
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9217 * _dict = getattr(self, '__dict__', None)
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jpayne@69
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9218 * if _dict is not None: # <<<<<<<<<<<<<<
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jpayne@69
|
9219 * state += (_dict,)
|
|
jpayne@69
|
9220 * use_setstate = True
|
|
jpayne@69
|
9221 */
|
|
jpayne@69
|
9222 __pyx_t_2 = (__pyx_v__dict != Py_None);
|
|
jpayne@69
|
9223 if (__pyx_t_2) {
|
|
jpayne@69
|
9224
|
|
jpayne@69
|
9225 /* "(tree fragment)":8
|
|
jpayne@69
|
9226 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
9227 * if _dict is not None:
|
|
jpayne@69
|
9228 * state += (_dict,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9229 * use_setstate = True
|
|
jpayne@69
|
9230 * else:
|
|
jpayne@69
|
9231 */
|
|
jpayne@69
|
9232 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
9233 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9234 __Pyx_INCREF(__pyx_v__dict);
|
|
jpayne@69
|
9235 __Pyx_GIVEREF(__pyx_v__dict);
|
|
jpayne@69
|
9236 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
|
|
jpayne@69
|
9237 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
9238 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
9239 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9240 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
9241 __pyx_t_3 = 0;
|
|
jpayne@69
|
9242
|
|
jpayne@69
|
9243 /* "(tree fragment)":9
|
|
jpayne@69
|
9244 * if _dict is not None:
|
|
jpayne@69
|
9245 * state += (_dict,)
|
|
jpayne@69
|
9246 * use_setstate = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9247 * else:
|
|
jpayne@69
|
9248 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9249 */
|
|
jpayne@69
|
9250 __pyx_v_use_setstate = 1;
|
|
jpayne@69
|
9251
|
|
jpayne@69
|
9252 /* "(tree fragment)":7
|
|
jpayne@69
|
9253 * state = (self.encoding,)
|
|
jpayne@69
|
9254 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
9255 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9256 * state += (_dict,)
|
|
jpayne@69
|
9257 * use_setstate = True
|
|
jpayne@69
|
9258 */
|
|
jpayne@69
|
9259 goto __pyx_L3;
|
|
jpayne@69
|
9260 }
|
|
jpayne@69
|
9261
|
|
jpayne@69
|
9262 /* "(tree fragment)":11
|
|
jpayne@69
|
9263 * use_setstate = True
|
|
jpayne@69
|
9264 * else:
|
|
jpayne@69
|
9265 * use_setstate = self.encoding is not None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9266 * if use_setstate:
|
|
jpayne@69
|
9267 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9268 */
|
|
jpayne@69
|
9269 /*else*/ {
|
|
jpayne@69
|
9270 __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None);
|
|
jpayne@69
|
9271 __pyx_v_use_setstate = __pyx_t_2;
|
|
jpayne@69
|
9272 }
|
|
jpayne@69
|
9273 __pyx_L3:;
|
|
jpayne@69
|
9274
|
|
jpayne@69
|
9275 /* "(tree fragment)":12
|
|
jpayne@69
|
9276 * else:
|
|
jpayne@69
|
9277 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9278 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9279 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9280 * else:
|
|
jpayne@69
|
9281 */
|
|
jpayne@69
|
9282 if (__pyx_v_use_setstate) {
|
|
jpayne@69
|
9283
|
|
jpayne@69
|
9284 /* "(tree fragment)":13
|
|
jpayne@69
|
9285 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9286 * if use_setstate:
|
|
jpayne@69
|
9287 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9288 * else:
|
|
jpayne@69
|
9289 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9290 */
|
|
jpayne@69
|
9291 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
9292 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asGTF); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
9293 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
9294 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
9295 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9296 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9297 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9298 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9299 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
9300 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
9301 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9302 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
9303 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
9304 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9305 __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
9306 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
9307 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
9308 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9309 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
9310 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9311 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
9312 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
9313 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9314 __pyx_t_3 = 0;
|
|
jpayne@69
|
9315 __pyx_t_1 = 0;
|
|
jpayne@69
|
9316 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
9317 __pyx_t_4 = 0;
|
|
jpayne@69
|
9318 goto __pyx_L0;
|
|
jpayne@69
|
9319
|
|
jpayne@69
|
9320 /* "(tree fragment)":12
|
|
jpayne@69
|
9321 * else:
|
|
jpayne@69
|
9322 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9323 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9324 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9325 * else:
|
|
jpayne@69
|
9326 */
|
|
jpayne@69
|
9327 }
|
|
jpayne@69
|
9328
|
|
jpayne@69
|
9329 /* "(tree fragment)":15
|
|
jpayne@69
|
9330 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9331 * else:
|
|
jpayne@69
|
9332 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9333 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
9334 * __pyx_unpickle_asGTF__set_state(self, __pyx_state)
|
|
jpayne@69
|
9335 */
|
|
jpayne@69
|
9336 /*else*/ {
|
|
jpayne@69
|
9337 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
9338 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asGTF); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
9339 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
9340 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
9341 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9342 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9343 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9344 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9345 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
9346 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
9347 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9348 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
9349 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
9350 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9351 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
9352 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
9353 __Pyx_GIVEREF(__pyx_t_4);
|
|
jpayne@69
|
9354 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9355 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
9356 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9357 __pyx_t_4 = 0;
|
|
jpayne@69
|
9358 __pyx_t_1 = 0;
|
|
jpayne@69
|
9359 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
9360 __pyx_t_3 = 0;
|
|
jpayne@69
|
9361 goto __pyx_L0;
|
|
jpayne@69
|
9362 }
|
|
jpayne@69
|
9363
|
|
jpayne@69
|
9364 /* "(tree fragment)":1
|
|
jpayne@69
|
9365 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9366 * cdef tuple state
|
|
jpayne@69
|
9367 * cdef object _dict
|
|
jpayne@69
|
9368 */
|
|
jpayne@69
|
9369
|
|
jpayne@69
|
9370 /* function exit code */
|
|
jpayne@69
|
9371 __pyx_L1_error:;
|
|
jpayne@69
|
9372 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
9373 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
9374 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
9375 __Pyx_AddTraceback("pysam.libctabix.asGTF.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9376 __pyx_r = NULL;
|
|
jpayne@69
|
9377 __pyx_L0:;
|
|
jpayne@69
|
9378 __Pyx_XDECREF(__pyx_v_state);
|
|
jpayne@69
|
9379 __Pyx_XDECREF(__pyx_v__dict);
|
|
jpayne@69
|
9380 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
9381 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
9382 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9383 return __pyx_r;
|
|
jpayne@69
|
9384 }
|
|
jpayne@69
|
9385
|
|
jpayne@69
|
9386 /* "(tree fragment)":16
|
|
jpayne@69
|
9387 * else:
|
|
jpayne@69
|
9388 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9389 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9390 * __pyx_unpickle_asGTF__set_state(self, __pyx_state)
|
|
jpayne@69
|
9391 */
|
|
jpayne@69
|
9392
|
|
jpayne@69
|
9393 /* Python wrapper */
|
|
jpayne@69
|
9394 static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9395 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9396 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9397 #else
|
|
jpayne@69
|
9398 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9399 #endif
|
|
jpayne@69
|
9400 ); /*proto*/
|
|
jpayne@69
|
9401 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asGTF_2__setstate_cython__, "asGTF.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
9402 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asGTF_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF_2__setstate_cython__};
|
|
jpayne@69
|
9403 static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9404 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9405 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9406 #else
|
|
jpayne@69
|
9407 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9408 #endif
|
|
jpayne@69
|
9409 ) {
|
|
jpayne@69
|
9410 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
9411 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9412 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
9413 #endif
|
|
jpayne@69
|
9414 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
9415 PyObject* values[1] = {0};
|
|
jpayne@69
|
9416 int __pyx_lineno = 0;
|
|
jpayne@69
|
9417 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9418 int __pyx_clineno = 0;
|
|
jpayne@69
|
9419 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
9420 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
9421 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
9422 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9423 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
9424 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
9425 #else
|
|
jpayne@69
|
9426 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
9427 #endif
|
|
jpayne@69
|
9428 #endif
|
|
jpayne@69
|
9429 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
9430 {
|
|
jpayne@69
|
9431 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
9432 if (__pyx_kwds) {
|
|
jpayne@69
|
9433 Py_ssize_t kw_args;
|
|
jpayne@69
|
9434 switch (__pyx_nargs) {
|
|
jpayne@69
|
9435 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
9436 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
9437 case 0: break;
|
|
jpayne@69
|
9438 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9439 }
|
|
jpayne@69
|
9440 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
9441 switch (__pyx_nargs) {
|
|
jpayne@69
|
9442 case 0:
|
|
jpayne@69
|
9443 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
9444 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
9445 kw_args--;
|
|
jpayne@69
|
9446 }
|
|
jpayne@69
|
9447 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
9448 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9449 }
|
|
jpayne@69
|
9450 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
9451 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
9452 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
9453 }
|
|
jpayne@69
|
9454 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
9455 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9456 } else {
|
|
jpayne@69
|
9457 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
9458 }
|
|
jpayne@69
|
9459 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
9460 }
|
|
jpayne@69
|
9461 goto __pyx_L6_skip;
|
|
jpayne@69
|
9462 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
9463 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
9464 __pyx_L6_skip:;
|
|
jpayne@69
|
9465 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
9466 __pyx_L3_error:;
|
|
jpayne@69
|
9467 {
|
|
jpayne@69
|
9468 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
9469 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
9470 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
9471 }
|
|
jpayne@69
|
9472 }
|
|
jpayne@69
|
9473 __Pyx_AddTraceback("pysam.libctabix.asGTF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9474 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9475 return NULL;
|
|
jpayne@69
|
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|
|
jpayne@69
|
9477 __pyx_r = __pyx_pf_5pysam_9libctabix_5asGTF_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asGTF *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
9478
|
|
jpayne@69
|
9479 /* function exit code */
|
|
jpayne@69
|
9480 {
|
|
jpayne@69
|
9481 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
9482 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
9483 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
9484 }
|
|
jpayne@69
|
9485 }
|
|
jpayne@69
|
9486 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9487 return __pyx_r;
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jpayne@69
|
9488 }
|
|
jpayne@69
|
9489
|
|
jpayne@69
|
9490 static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
9491 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
9492 __Pyx_TraceDeclarations
|
|
jpayne@69
|
9493 __Pyx_RefNannyDeclarations
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jpayne@69
|
9494 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
9495 int __pyx_lineno = 0;
|
|
jpayne@69
|
9496 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9497 int __pyx_clineno = 0;
|
|
jpayne@69
|
9498 __Pyx_TraceFrameInit(__pyx_codeobj__10)
|
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jpayne@69
|
9499 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
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jpayne@69
|
9500 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error));
|
|
jpayne@69
|
9501
|
|
jpayne@69
|
9502 /* "(tree fragment)":17
|
|
jpayne@69
|
9503 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9504 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
9505 * __pyx_unpickle_asGTF__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9506 */
|
|
jpayne@69
|
9507 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
|
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jpayne@69
|
9508 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
|
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jpayne@69
|
9509 __Pyx_GOTREF(__pyx_t_1);
|
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jpayne@69
|
9510 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
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jpayne@69
|
9511
|
|
jpayne@69
|
9512 /* "(tree fragment)":16
|
|
jpayne@69
|
9513 * else:
|
|
jpayne@69
|
9514 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9515 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9516 * __pyx_unpickle_asGTF__set_state(self, __pyx_state)
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jpayne@69
|
9517 */
|
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jpayne@69
|
9518
|
|
jpayne@69
|
9519 /* function exit code */
|
|
jpayne@69
|
9520 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
9521 goto __pyx_L0;
|
|
jpayne@69
|
9522 __pyx_L1_error:;
|
|
jpayne@69
|
9523 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
9524 __Pyx_AddTraceback("pysam.libctabix.asGTF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9525 __pyx_r = NULL;
|
|
jpayne@69
|
9526 __pyx_L0:;
|
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jpayne@69
|
9527 __Pyx_XGIVEREF(__pyx_r);
|
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jpayne@69
|
9528 __Pyx_TraceReturn(__pyx_r, 0);
|
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jpayne@69
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9529 __Pyx_RefNannyFinishContext();
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jpayne@69
|
9530 return __pyx_r;
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jpayne@69
|
9531 }
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jpayne@69
|
9532
|
|
jpayne@69
|
9533 /* "pysam/libctabix.pyx":239
|
|
jpayne@69
|
9534 *
|
|
jpayne@69
|
9535 * '''
|
|
jpayne@69
|
9536 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9537 * cdef ctabixproxies.BedProxy r
|
|
jpayne@69
|
9538 * r = ctabixproxies.BedProxy(self.encoding)
|
|
jpayne@69
|
9539 */
|
|
jpayne@69
|
9540
|
|
jpayne@69
|
9541 static PyObject *__pyx_f_5pysam_9libctabix_5asBed_parse(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) {
|
|
jpayne@69
|
9542 struct __pyx_obj_5pysam_16libctabixproxies_BedProxy *__pyx_v_r = 0;
|
|
jpayne@69
|
9543 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
9544 __Pyx_TraceDeclarations
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jpayne@69
|
9545 __Pyx_RefNannyDeclarations
|
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jpayne@69
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9546 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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9547 int __pyx_lineno = 0;
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|
jpayne@69
|
9548 const char *__pyx_filename = NULL;
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jpayne@69
|
9549 int __pyx_clineno = 0;
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jpayne@69
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jpayne@69
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9551 __Pyx_TraceCall("parse", __pyx_f[0], 239, 0, __PYX_ERR(0, 239, __pyx_L1_error));
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jpayne@69
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9552
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jpayne@69
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9553 /* "pysam/libctabix.pyx":241
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|
jpayne@69
|
9554 * cdef parse(self, char * buffer, int len):
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jpayne@69
|
9555 * cdef ctabixproxies.BedProxy r
|
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jpayne@69
|
9556 * r = ctabixproxies.BedProxy(self.encoding) # <<<<<<<<<<<<<<
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jpayne@69
|
9557 * r.copy(buffer, len)
|
|
jpayne@69
|
9558 * return r
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jpayne@69
|
9559 */
|
|
jpayne@69
|
9560 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_BedProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 241, __pyx_L1_error)
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jpayne@69
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jpayne@69
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9562 __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_BedProxy *)__pyx_t_1);
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jpayne@69
|
9563 __pyx_t_1 = 0;
|
|
jpayne@69
|
9564
|
|
jpayne@69
|
9565 /* "pysam/libctabix.pyx":242
|
|
jpayne@69
|
9566 * cdef ctabixproxies.BedProxy r
|
|
jpayne@69
|
9567 * r = ctabixproxies.BedProxy(self.encoding)
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jpayne@69
|
9568 * r.copy(buffer, len) # <<<<<<<<<<<<<<
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jpayne@69
|
9569 * return r
|
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jpayne@69
|
9570 *
|
|
jpayne@69
|
9571 */
|
|
jpayne@69
|
9572 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 242, __pyx_L1_error)
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jpayne@69
|
9573 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
9574 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
|
9575
|
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jpayne@69
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9576 /* "pysam/libctabix.pyx":243
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|
jpayne@69
|
9577 * r = ctabixproxies.BedProxy(self.encoding)
|
|
jpayne@69
|
9578 * r.copy(buffer, len)
|
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jpayne@69
|
9579 * return r # <<<<<<<<<<<<<<
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jpayne@69
|
9580 *
|
|
jpayne@69
|
9581 *
|
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jpayne@69
|
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jpayne@69
|
9583 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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9584 __Pyx_INCREF((PyObject *)__pyx_v_r);
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jpayne@69
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9585 __pyx_r = ((PyObject *)__pyx_v_r);
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jpayne@69
|
9586 goto __pyx_L0;
|
|
jpayne@69
|
9587
|
|
jpayne@69
|
9588 /* "pysam/libctabix.pyx":239
|
|
jpayne@69
|
9589 *
|
|
jpayne@69
|
9590 * '''
|
|
jpayne@69
|
9591 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
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|
jpayne@69
|
9592 * cdef ctabixproxies.BedProxy r
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jpayne@69
|
9593 * r = ctabixproxies.BedProxy(self.encoding)
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jpayne@69
|
9594 */
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jpayne@69
|
9595
|
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jpayne@69
|
9596 /* function exit code */
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jpayne@69
|
9597 __pyx_L1_error:;
|
|
jpayne@69
|
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|
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jpayne@69
|
9599 __Pyx_AddTraceback("pysam.libctabix.asBed.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9600 __pyx_r = 0;
|
|
jpayne@69
|
9601 __pyx_L0:;
|
|
jpayne@69
|
9602 __Pyx_XDECREF((PyObject *)__pyx_v_r);
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jpayne@69
|
9603 __Pyx_XGIVEREF(__pyx_r);
|
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jpayne@69
|
9604 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
|
9605 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
9606 return __pyx_r;
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jpayne@69
|
9607 }
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jpayne@69
|
9608
|
|
jpayne@69
|
9609 /* "(tree fragment)":1
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jpayne@69
|
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jpayne@69
|
9611 * cdef tuple state
|
|
jpayne@69
|
9612 * cdef object _dict
|
|
jpayne@69
|
9613 */
|
|
jpayne@69
|
9614
|
|
jpayne@69
|
9615 /* Python wrapper */
|
|
jpayne@69
|
9616 static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9617 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9618 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9619 #else
|
|
jpayne@69
|
9620 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9621 #endif
|
|
jpayne@69
|
9622 ); /*proto*/
|
|
jpayne@69
|
9623 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asBed___reduce_cython__, "asBed.__reduce_cython__(self)");
|
|
jpayne@69
|
9624 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asBed_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed___reduce_cython__};
|
|
jpayne@69
|
9625 static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9626 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9627 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9628 #else
|
|
jpayne@69
|
9629 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9630 #endif
|
|
jpayne@69
|
9631 ) {
|
|
jpayne@69
|
9632 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9633 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
9634 #endif
|
|
jpayne@69
|
9635 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
9636 PyObject *__pyx_r = 0;
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|
jpayne@69
|
9637 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
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jpayne@69
|
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|
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jpayne@69
|
9640 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
9641 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
9642 #else
|
|
jpayne@69
|
9643 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
9644 #endif
|
|
jpayne@69
|
9645 #endif
|
|
jpayne@69
|
9646 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
9647 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
9648 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
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jpayne@69
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9649 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
9650 __pyx_r = __pyx_pf_5pysam_9libctabix_5asBed___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asBed *)__pyx_v_self));
|
|
jpayne@69
|
9651
|
|
jpayne@69
|
9652 /* function exit code */
|
|
jpayne@69
|
9653 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
9654 return __pyx_r;
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jpayne@69
|
9655 }
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jpayne@69
|
9656
|
|
jpayne@69
|
9657 static PyObject *__pyx_pf_5pysam_9libctabix_5asBed___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self) {
|
|
jpayne@69
|
9658 PyObject *__pyx_v_state = 0;
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|
jpayne@69
|
9659 PyObject *__pyx_v__dict = 0;
|
|
jpayne@69
|
9660 int __pyx_v_use_setstate;
|
|
jpayne@69
|
9661 PyObject *__pyx_r = NULL;
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jpayne@69
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9662 __Pyx_TraceDeclarations
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jpayne@69
|
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jpayne@69
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9664 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
9665 int __pyx_t_2;
|
|
jpayne@69
|
9666 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
9667 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
9668 int __pyx_lineno = 0;
|
|
jpayne@69
|
9669 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9670 int __pyx_clineno = 0;
|
|
jpayne@69
|
9671 __Pyx_TraceFrameInit(__pyx_codeobj__11)
|
|
jpayne@69
|
9672 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
9673 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
9674
|
|
jpayne@69
|
9675 /* "(tree fragment)":5
|
|
jpayne@69
|
9676 * cdef object _dict
|
|
jpayne@69
|
9677 * cdef bint use_setstate
|
|
jpayne@69
|
9678 * state = (self.encoding,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9679 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
9680 * if _dict is not None:
|
|
jpayne@69
|
9681 */
|
|
jpayne@69
|
9682 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
9683 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9684 __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding);
|
|
jpayne@69
|
9685 __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding);
|
|
jpayne@69
|
9686 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
9687 __pyx_v_state = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
9688 __pyx_t_1 = 0;
|
|
jpayne@69
|
9689
|
|
jpayne@69
|
9690 /* "(tree fragment)":6
|
|
jpayne@69
|
9691 * cdef bint use_setstate
|
|
jpayne@69
|
9692 * state = (self.encoding,)
|
|
jpayne@69
|
9693 * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9694 * if _dict is not None:
|
|
jpayne@69
|
9695 * state += (_dict,)
|
|
jpayne@69
|
9696 */
|
|
jpayne@69
|
9697 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
9698 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9699 __pyx_v__dict = __pyx_t_1;
|
|
jpayne@69
|
9700 __pyx_t_1 = 0;
|
|
jpayne@69
|
9701
|
|
jpayne@69
|
9702 /* "(tree fragment)":7
|
|
jpayne@69
|
9703 * state = (self.encoding,)
|
|
jpayne@69
|
9704 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
9705 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9706 * state += (_dict,)
|
|
jpayne@69
|
9707 * use_setstate = True
|
|
jpayne@69
|
9708 */
|
|
jpayne@69
|
9709 __pyx_t_2 = (__pyx_v__dict != Py_None);
|
|
jpayne@69
|
9710 if (__pyx_t_2) {
|
|
jpayne@69
|
9711
|
|
jpayne@69
|
9712 /* "(tree fragment)":8
|
|
jpayne@69
|
9713 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
9714 * if _dict is not None:
|
|
jpayne@69
|
9715 * state += (_dict,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9716 * use_setstate = True
|
|
jpayne@69
|
9717 * else:
|
|
jpayne@69
|
9718 */
|
|
jpayne@69
|
9719 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
9720 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9721 __Pyx_INCREF(__pyx_v__dict);
|
|
jpayne@69
|
9722 __Pyx_GIVEREF(__pyx_v__dict);
|
|
jpayne@69
|
9723 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
|
|
jpayne@69
|
9724 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
9725 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
9726 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9727 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
9728 __pyx_t_3 = 0;
|
|
jpayne@69
|
9729
|
|
jpayne@69
|
9730 /* "(tree fragment)":9
|
|
jpayne@69
|
9731 * if _dict is not None:
|
|
jpayne@69
|
9732 * state += (_dict,)
|
|
jpayne@69
|
9733 * use_setstate = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9734 * else:
|
|
jpayne@69
|
9735 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9736 */
|
|
jpayne@69
|
9737 __pyx_v_use_setstate = 1;
|
|
jpayne@69
|
9738
|
|
jpayne@69
|
9739 /* "(tree fragment)":7
|
|
jpayne@69
|
9740 * state = (self.encoding,)
|
|
jpayne@69
|
9741 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
9742 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9743 * state += (_dict,)
|
|
jpayne@69
|
9744 * use_setstate = True
|
|
jpayne@69
|
9745 */
|
|
jpayne@69
|
9746 goto __pyx_L3;
|
|
jpayne@69
|
9747 }
|
|
jpayne@69
|
9748
|
|
jpayne@69
|
9749 /* "(tree fragment)":11
|
|
jpayne@69
|
9750 * use_setstate = True
|
|
jpayne@69
|
9751 * else:
|
|
jpayne@69
|
9752 * use_setstate = self.encoding is not None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9753 * if use_setstate:
|
|
jpayne@69
|
9754 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9755 */
|
|
jpayne@69
|
9756 /*else*/ {
|
|
jpayne@69
|
9757 __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None);
|
|
jpayne@69
|
9758 __pyx_v_use_setstate = __pyx_t_2;
|
|
jpayne@69
|
9759 }
|
|
jpayne@69
|
9760 __pyx_L3:;
|
|
jpayne@69
|
9761
|
|
jpayne@69
|
9762 /* "(tree fragment)":12
|
|
jpayne@69
|
9763 * else:
|
|
jpayne@69
|
9764 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9765 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9766 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9767 * else:
|
|
jpayne@69
|
9768 */
|
|
jpayne@69
|
9769 if (__pyx_v_use_setstate) {
|
|
jpayne@69
|
9770
|
|
jpayne@69
|
9771 /* "(tree fragment)":13
|
|
jpayne@69
|
9772 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9773 * if use_setstate:
|
|
jpayne@69
|
9774 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9775 * else:
|
|
jpayne@69
|
9776 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9777 */
|
|
jpayne@69
|
9778 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
9779 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asBed); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
9780 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
9781 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
9782 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9783 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9784 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9785 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9786 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
9787 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
9788 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9789 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
9790 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
9791 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9792 __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
9793 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
9794 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
9795 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9796 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
9797 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9798 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
9799 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
9800 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
9801 __pyx_t_3 = 0;
|
|
jpayne@69
|
9802 __pyx_t_1 = 0;
|
|
jpayne@69
|
9803 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
9804 __pyx_t_4 = 0;
|
|
jpayne@69
|
9805 goto __pyx_L0;
|
|
jpayne@69
|
9806
|
|
jpayne@69
|
9807 /* "(tree fragment)":12
|
|
jpayne@69
|
9808 * else:
|
|
jpayne@69
|
9809 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
9810 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9811 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9812 * else:
|
|
jpayne@69
|
9813 */
|
|
jpayne@69
|
9814 }
|
|
jpayne@69
|
9815
|
|
jpayne@69
|
9816 /* "(tree fragment)":15
|
|
jpayne@69
|
9817 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
9818 * else:
|
|
jpayne@69
|
9819 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9820 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
9821 * __pyx_unpickle_asBed__set_state(self, __pyx_state)
|
|
jpayne@69
|
9822 */
|
|
jpayne@69
|
9823 /*else*/ {
|
|
jpayne@69
|
9824 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
9825 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asBed); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
9826 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
9827 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
9828 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9829 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9830 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
9831 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9832 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
9833 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
9834 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9835 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
9836 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
9837 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9838 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
9839 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
9840 __Pyx_GIVEREF(__pyx_t_4);
|
|
jpayne@69
|
9841 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9842 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
9843 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
9844 __pyx_t_4 = 0;
|
|
jpayne@69
|
9845 __pyx_t_1 = 0;
|
|
jpayne@69
|
9846 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
9847 __pyx_t_3 = 0;
|
|
jpayne@69
|
9848 goto __pyx_L0;
|
|
jpayne@69
|
9849 }
|
|
jpayne@69
|
9850
|
|
jpayne@69
|
9851 /* "(tree fragment)":1
|
|
jpayne@69
|
9852 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9853 * cdef tuple state
|
|
jpayne@69
|
9854 * cdef object _dict
|
|
jpayne@69
|
9855 */
|
|
jpayne@69
|
9856
|
|
jpayne@69
|
9857 /* function exit code */
|
|
jpayne@69
|
9858 __pyx_L1_error:;
|
|
jpayne@69
|
9859 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
9860 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
9861 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
9862 __Pyx_AddTraceback("pysam.libctabix.asBed.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9863 __pyx_r = NULL;
|
|
jpayne@69
|
9864 __pyx_L0:;
|
|
jpayne@69
|
9865 __Pyx_XDECREF(__pyx_v_state);
|
|
jpayne@69
|
9866 __Pyx_XDECREF(__pyx_v__dict);
|
|
jpayne@69
|
9867 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
9868 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
9869 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9870 return __pyx_r;
|
|
jpayne@69
|
9871 }
|
|
jpayne@69
|
9872
|
|
jpayne@69
|
9873 /* "(tree fragment)":16
|
|
jpayne@69
|
9874 * else:
|
|
jpayne@69
|
9875 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9876 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9877 * __pyx_unpickle_asBed__set_state(self, __pyx_state)
|
|
jpayne@69
|
9878 */
|
|
jpayne@69
|
9879
|
|
jpayne@69
|
9880 /* Python wrapper */
|
|
jpayne@69
|
9881 static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9882 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9883 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9884 #else
|
|
jpayne@69
|
9885 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9886 #endif
|
|
jpayne@69
|
9887 ); /*proto*/
|
|
jpayne@69
|
9888 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asBed_2__setstate_cython__, "asBed.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
9889 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asBed_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed_2__setstate_cython__};
|
|
jpayne@69
|
9890 static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
9891 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9892 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9893 #else
|
|
jpayne@69
|
9894 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9895 #endif
|
|
jpayne@69
|
9896 ) {
|
|
jpayne@69
|
9897 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
9898 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9899 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
9900 #endif
|
|
jpayne@69
|
9901 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
9902 PyObject* values[1] = {0};
|
|
jpayne@69
|
9903 int __pyx_lineno = 0;
|
|
jpayne@69
|
9904 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9905 int __pyx_clineno = 0;
|
|
jpayne@69
|
9906 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
9907 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
9908 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
9909 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9910 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
9911 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
9912 #else
|
|
jpayne@69
|
9913 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
9914 #endif
|
|
jpayne@69
|
9915 #endif
|
|
jpayne@69
|
9916 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
9917 {
|
|
jpayne@69
|
9918 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
9919 if (__pyx_kwds) {
|
|
jpayne@69
|
9920 Py_ssize_t kw_args;
|
|
jpayne@69
|
9921 switch (__pyx_nargs) {
|
|
jpayne@69
|
9922 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
9923 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
9924 case 0: break;
|
|
jpayne@69
|
9925 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9926 }
|
|
jpayne@69
|
9927 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
9928 switch (__pyx_nargs) {
|
|
jpayne@69
|
9929 case 0:
|
|
jpayne@69
|
9930 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
9931 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
9932 kw_args--;
|
|
jpayne@69
|
9933 }
|
|
jpayne@69
|
9934 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
9935 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9936 }
|
|
jpayne@69
|
9937 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
9938 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
9939 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
9940 }
|
|
jpayne@69
|
9941 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
9942 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9943 } else {
|
|
jpayne@69
|
9944 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
9945 }
|
|
jpayne@69
|
9946 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
9947 }
|
|
jpayne@69
|
9948 goto __pyx_L6_skip;
|
|
jpayne@69
|
9949 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
9950 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
9951 __pyx_L6_skip:;
|
|
jpayne@69
|
9952 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
9953 __pyx_L3_error:;
|
|
jpayne@69
|
9954 {
|
|
jpayne@69
|
9955 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
9956 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
9957 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
9958 }
|
|
jpayne@69
|
9959 }
|
|
jpayne@69
|
9960 __Pyx_AddTraceback("pysam.libctabix.asBed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9961 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9962 return NULL;
|
|
jpayne@69
|
9963 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
9964 __pyx_r = __pyx_pf_5pysam_9libctabix_5asBed_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asBed *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
9965
|
|
jpayne@69
|
9966 /* function exit code */
|
|
jpayne@69
|
9967 {
|
|
jpayne@69
|
9968 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
9969 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
9970 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
9971 }
|
|
jpayne@69
|
9972 }
|
|
jpayne@69
|
9973 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9974 return __pyx_r;
|
|
jpayne@69
|
9975 }
|
|
jpayne@69
|
9976
|
|
jpayne@69
|
9977 static PyObject *__pyx_pf_5pysam_9libctabix_5asBed_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
9978 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
9979 __Pyx_TraceDeclarations
|
|
jpayne@69
|
9980 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
9981 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
9982 int __pyx_lineno = 0;
|
|
jpayne@69
|
9983 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9984 int __pyx_clineno = 0;
|
|
jpayne@69
|
9985 __Pyx_TraceFrameInit(__pyx_codeobj__12)
|
|
jpayne@69
|
9986 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
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jpayne@69
|
9987 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error));
|
|
jpayne@69
|
9988
|
|
jpayne@69
|
9989 /* "(tree fragment)":17
|
|
jpayne@69
|
9990 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
9991 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
9992 * __pyx_unpickle_asBed__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9993 */
|
|
jpayne@69
|
9994 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
|
|
jpayne@69
|
9995 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
|
|
jpayne@69
|
9996 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9997 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9998
|
|
jpayne@69
|
9999 /* "(tree fragment)":16
|
|
jpayne@69
|
10000 * else:
|
|
jpayne@69
|
10001 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
10002 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10003 * __pyx_unpickle_asBed__set_state(self, __pyx_state)
|
|
jpayne@69
|
10004 */
|
|
jpayne@69
|
10005
|
|
jpayne@69
|
10006 /* function exit code */
|
|
jpayne@69
|
10007 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
10008 goto __pyx_L0;
|
|
jpayne@69
|
10009 __pyx_L1_error:;
|
|
jpayne@69
|
10010 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
10011 __Pyx_AddTraceback("pysam.libctabix.asBed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10012 __pyx_r = NULL;
|
|
jpayne@69
|
10013 __pyx_L0:;
|
|
jpayne@69
|
10014 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
10015 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
10016 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10017 return __pyx_r;
|
|
jpayne@69
|
10018 }
|
|
jpayne@69
|
10019
|
|
jpayne@69
|
10020 /* "pysam/libctabix.pyx":280
|
|
jpayne@69
|
10021 *
|
|
jpayne@69
|
10022 * '''
|
|
jpayne@69
|
10023 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10024 * cdef ctabixproxies.VCFProxy r
|
|
jpayne@69
|
10025 * r = ctabixproxies.VCFProxy(self.encoding)
|
|
jpayne@69
|
10026 */
|
|
jpayne@69
|
10027
|
|
jpayne@69
|
10028 static PyObject *__pyx_f_5pysam_9libctabix_5asVCF_parse(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) {
|
|
jpayne@69
|
10029 struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy *__pyx_v_r = 0;
|
|
jpayne@69
|
10030 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
10031 __Pyx_TraceDeclarations
|
|
jpayne@69
|
10032 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10033 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
10034 int __pyx_lineno = 0;
|
|
jpayne@69
|
10035 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
10036 int __pyx_clineno = 0;
|
|
jpayne@69
|
10037 __Pyx_RefNannySetupContext("parse", 1);
|
|
jpayne@69
|
10038 __Pyx_TraceCall("parse", __pyx_f[0], 280, 0, __PYX_ERR(0, 280, __pyx_L1_error));
|
|
jpayne@69
|
10039
|
|
jpayne@69
|
10040 /* "pysam/libctabix.pyx":282
|
|
jpayne@69
|
10041 * cdef parse(self, char * buffer, int len):
|
|
jpayne@69
|
10042 * cdef ctabixproxies.VCFProxy r
|
|
jpayne@69
|
10043 * r = ctabixproxies.VCFProxy(self.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10044 * r.copy(buffer, len)
|
|
jpayne@69
|
10045 * return r
|
|
jpayne@69
|
10046 */
|
|
jpayne@69
|
10047 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_VCFProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 282, __pyx_L1_error)
|
|
jpayne@69
|
10048 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10049 __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy *)__pyx_t_1);
|
|
jpayne@69
|
10050 __pyx_t_1 = 0;
|
|
jpayne@69
|
10051
|
|
jpayne@69
|
10052 /* "pysam/libctabix.pyx":283
|
|
jpayne@69
|
10053 * cdef ctabixproxies.VCFProxy r
|
|
jpayne@69
|
10054 * r = ctabixproxies.VCFProxy(self.encoding)
|
|
jpayne@69
|
10055 * r.copy(buffer, len) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10056 * return r
|
|
jpayne@69
|
10057 *
|
|
jpayne@69
|
10058 */
|
|
jpayne@69
|
10059 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 283, __pyx_L1_error)
|
|
jpayne@69
|
10060 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10061 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
10062
|
|
jpayne@69
|
10063 /* "pysam/libctabix.pyx":284
|
|
jpayne@69
|
10064 * r = ctabixproxies.VCFProxy(self.encoding)
|
|
jpayne@69
|
10065 * r.copy(buffer, len)
|
|
jpayne@69
|
10066 * return r # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10067 *
|
|
jpayne@69
|
10068 *
|
|
jpayne@69
|
10069 */
|
|
jpayne@69
|
10070 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
10071 __Pyx_INCREF((PyObject *)__pyx_v_r);
|
|
jpayne@69
|
10072 __pyx_r = ((PyObject *)__pyx_v_r);
|
|
jpayne@69
|
10073 goto __pyx_L0;
|
|
jpayne@69
|
10074
|
|
jpayne@69
|
10075 /* "pysam/libctabix.pyx":280
|
|
jpayne@69
|
10076 *
|
|
jpayne@69
|
10077 * '''
|
|
jpayne@69
|
10078 * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10079 * cdef ctabixproxies.VCFProxy r
|
|
jpayne@69
|
10080 * r = ctabixproxies.VCFProxy(self.encoding)
|
|
jpayne@69
|
10081 */
|
|
jpayne@69
|
10082
|
|
jpayne@69
|
10083 /* function exit code */
|
|
jpayne@69
|
10084 __pyx_L1_error:;
|
|
jpayne@69
|
10085 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
10086 __Pyx_AddTraceback("pysam.libctabix.asVCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10087 __pyx_r = 0;
|
|
jpayne@69
|
10088 __pyx_L0:;
|
|
jpayne@69
|
10089 __Pyx_XDECREF((PyObject *)__pyx_v_r);
|
|
jpayne@69
|
10090 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
10091 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
10092 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10093 return __pyx_r;
|
|
jpayne@69
|
10094 }
|
|
jpayne@69
|
10095
|
|
jpayne@69
|
10096 /* "(tree fragment)":1
|
|
jpayne@69
|
10097 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10098 * cdef tuple state
|
|
jpayne@69
|
10099 * cdef object _dict
|
|
jpayne@69
|
10100 */
|
|
jpayne@69
|
10101
|
|
jpayne@69
|
10102 /* Python wrapper */
|
|
jpayne@69
|
10103 static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
10104 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10105 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
10106 #else
|
|
jpayne@69
|
10107 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
10108 #endif
|
|
jpayne@69
|
10109 ); /*proto*/
|
|
jpayne@69
|
10110 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asVCF___reduce_cython__, "asVCF.__reduce_cython__(self)");
|
|
jpayne@69
|
10111 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asVCF_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF___reduce_cython__};
|
|
jpayne@69
|
10112 static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
10113 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10114 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
10115 #else
|
|
jpayne@69
|
10116 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
10117 #endif
|
|
jpayne@69
|
10118 ) {
|
|
jpayne@69
|
10119 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10120 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
10121 #endif
|
|
jpayne@69
|
10122 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
10123 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
10124 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10125 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
10126 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10127 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
10128 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
10129 #else
|
|
jpayne@69
|
10130 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
10131 #endif
|
|
jpayne@69
|
10132 #endif
|
|
jpayne@69
|
10133 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
10134 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
10135 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
10136 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
10137 __pyx_r = __pyx_pf_5pysam_9libctabix_5asVCF___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asVCF *)__pyx_v_self));
|
|
jpayne@69
|
10138
|
|
jpayne@69
|
10139 /* function exit code */
|
|
jpayne@69
|
10140 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10141 return __pyx_r;
|
|
jpayne@69
|
10142 }
|
|
jpayne@69
|
10143
|
|
jpayne@69
|
10144 static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self) {
|
|
jpayne@69
|
10145 PyObject *__pyx_v_state = 0;
|
|
jpayne@69
|
10146 PyObject *__pyx_v__dict = 0;
|
|
jpayne@69
|
10147 int __pyx_v_use_setstate;
|
|
jpayne@69
|
10148 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
10149 __Pyx_TraceDeclarations
|
|
jpayne@69
|
10150 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10151 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
10152 int __pyx_t_2;
|
|
jpayne@69
|
10153 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
10154 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
10155 int __pyx_lineno = 0;
|
|
jpayne@69
|
10156 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
10157 int __pyx_clineno = 0;
|
|
jpayne@69
|
10158 __Pyx_TraceFrameInit(__pyx_codeobj__13)
|
|
jpayne@69
|
10159 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
10160 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
10161
|
|
jpayne@69
|
10162 /* "(tree fragment)":5
|
|
jpayne@69
|
10163 * cdef object _dict
|
|
jpayne@69
|
10164 * cdef bint use_setstate
|
|
jpayne@69
|
10165 * state = (self.encoding,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10166 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
10167 * if _dict is not None:
|
|
jpayne@69
|
10168 */
|
|
jpayne@69
|
10169 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
10170 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10171 __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding);
|
|
jpayne@69
|
10172 __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding);
|
|
jpayne@69
|
10173 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
10174 __pyx_v_state = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
10175 __pyx_t_1 = 0;
|
|
jpayne@69
|
10176
|
|
jpayne@69
|
10177 /* "(tree fragment)":6
|
|
jpayne@69
|
10178 * cdef bint use_setstate
|
|
jpayne@69
|
10179 * state = (self.encoding,)
|
|
jpayne@69
|
10180 * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10181 * if _dict is not None:
|
|
jpayne@69
|
10182 * state += (_dict,)
|
|
jpayne@69
|
10183 */
|
|
jpayne@69
|
10184 __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
10185 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10186 __pyx_v__dict = __pyx_t_1;
|
|
jpayne@69
|
10187 __pyx_t_1 = 0;
|
|
jpayne@69
|
10188
|
|
jpayne@69
|
10189 /* "(tree fragment)":7
|
|
jpayne@69
|
10190 * state = (self.encoding,)
|
|
jpayne@69
|
10191 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
10192 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10193 * state += (_dict,)
|
|
jpayne@69
|
10194 * use_setstate = True
|
|
jpayne@69
|
10195 */
|
|
jpayne@69
|
10196 __pyx_t_2 = (__pyx_v__dict != Py_None);
|
|
jpayne@69
|
10197 if (__pyx_t_2) {
|
|
jpayne@69
|
10198
|
|
jpayne@69
|
10199 /* "(tree fragment)":8
|
|
jpayne@69
|
10200 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
10201 * if _dict is not None:
|
|
jpayne@69
|
10202 * state += (_dict,) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10203 * use_setstate = True
|
|
jpayne@69
|
10204 * else:
|
|
jpayne@69
|
10205 */
|
|
jpayne@69
|
10206 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
10207 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10208 __Pyx_INCREF(__pyx_v__dict);
|
|
jpayne@69
|
10209 __Pyx_GIVEREF(__pyx_v__dict);
|
|
jpayne@69
|
10210 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error);
|
|
jpayne@69
|
10211 __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error)
|
|
jpayne@69
|
10212 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10213 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
10214 __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
10215 __pyx_t_3 = 0;
|
|
jpayne@69
|
10216
|
|
jpayne@69
|
10217 /* "(tree fragment)":9
|
|
jpayne@69
|
10218 * if _dict is not None:
|
|
jpayne@69
|
10219 * state += (_dict,)
|
|
jpayne@69
|
10220 * use_setstate = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10221 * else:
|
|
jpayne@69
|
10222 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
10223 */
|
|
jpayne@69
|
10224 __pyx_v_use_setstate = 1;
|
|
jpayne@69
|
10225
|
|
jpayne@69
|
10226 /* "(tree fragment)":7
|
|
jpayne@69
|
10227 * state = (self.encoding,)
|
|
jpayne@69
|
10228 * _dict = getattr(self, '__dict__', None)
|
|
jpayne@69
|
10229 * if _dict is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10230 * state += (_dict,)
|
|
jpayne@69
|
10231 * use_setstate = True
|
|
jpayne@69
|
10232 */
|
|
jpayne@69
|
10233 goto __pyx_L3;
|
|
jpayne@69
|
10234 }
|
|
jpayne@69
|
10235
|
|
jpayne@69
|
10236 /* "(tree fragment)":11
|
|
jpayne@69
|
10237 * use_setstate = True
|
|
jpayne@69
|
10238 * else:
|
|
jpayne@69
|
10239 * use_setstate = self.encoding is not None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10240 * if use_setstate:
|
|
jpayne@69
|
10241 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
10242 */
|
|
jpayne@69
|
10243 /*else*/ {
|
|
jpayne@69
|
10244 __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None);
|
|
jpayne@69
|
10245 __pyx_v_use_setstate = __pyx_t_2;
|
|
jpayne@69
|
10246 }
|
|
jpayne@69
|
10247 __pyx_L3:;
|
|
jpayne@69
|
10248
|
|
jpayne@69
|
10249 /* "(tree fragment)":12
|
|
jpayne@69
|
10250 * else:
|
|
jpayne@69
|
10251 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
10252 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10253 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
10254 * else:
|
|
jpayne@69
|
10255 */
|
|
jpayne@69
|
10256 if (__pyx_v_use_setstate) {
|
|
jpayne@69
|
10257
|
|
jpayne@69
|
10258 /* "(tree fragment)":13
|
|
jpayne@69
|
10259 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
10260 * if use_setstate:
|
|
jpayne@69
|
10261 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10262 * else:
|
|
jpayne@69
|
10263 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
10264 */
|
|
jpayne@69
|
10265 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
10266 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asVCF); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
10267 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10268 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
10269 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10270 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
10271 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
10272 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
10273 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
10274 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
10275 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
10276 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
10277 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
10278 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
10279 __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
10280 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
10281 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
10282 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
10283 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
10284 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
10285 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
10286 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
10287 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error);
|
|
jpayne@69
|
10288 __pyx_t_3 = 0;
|
|
jpayne@69
|
10289 __pyx_t_1 = 0;
|
|
jpayne@69
|
10290 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
10291 __pyx_t_4 = 0;
|
|
jpayne@69
|
10292 goto __pyx_L0;
|
|
jpayne@69
|
10293
|
|
jpayne@69
|
10294 /* "(tree fragment)":12
|
|
jpayne@69
|
10295 * else:
|
|
jpayne@69
|
10296 * use_setstate = self.encoding is not None
|
|
jpayne@69
|
10297 * if use_setstate: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10298 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
10299 * else:
|
|
jpayne@69
|
10300 */
|
|
jpayne@69
|
10301 }
|
|
jpayne@69
|
10302
|
|
jpayne@69
|
10303 /* "(tree fragment)":15
|
|
jpayne@69
|
10304 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state
|
|
jpayne@69
|
10305 * else:
|
|
jpayne@69
|
10306 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10307 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
10308 * __pyx_unpickle_asVCF__set_state(self, __pyx_state)
|
|
jpayne@69
|
10309 */
|
|
jpayne@69
|
10310 /*else*/ {
|
|
jpayne@69
|
10311 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
10312 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asVCF); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
10313 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
10314 __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
10315 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10316 __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
10317 __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))));
|
|
jpayne@69
|
10318 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
10319 __Pyx_INCREF(__pyx_int_243541226);
|
|
jpayne@69
|
10320 __Pyx_GIVEREF(__pyx_int_243541226);
|
|
jpayne@69
|
10321 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
10322 __Pyx_INCREF(__pyx_v_state);
|
|
jpayne@69
|
10323 __Pyx_GIVEREF(__pyx_v_state);
|
|
jpayne@69
|
10324 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
10325 __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error)
|
|
jpayne@69
|
10326 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10327 __Pyx_GIVEREF(__pyx_t_4);
|
|
jpayne@69
|
10328 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
10329 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
10330 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error);
|
|
jpayne@69
|
10331 __pyx_t_4 = 0;
|
|
jpayne@69
|
10332 __pyx_t_1 = 0;
|
|
jpayne@69
|
10333 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
10334 __pyx_t_3 = 0;
|
|
jpayne@69
|
10335 goto __pyx_L0;
|
|
jpayne@69
|
10336 }
|
|
jpayne@69
|
10337
|
|
jpayne@69
|
10338 /* "(tree fragment)":1
|
|
jpayne@69
|
10339 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10340 * cdef tuple state
|
|
jpayne@69
|
10341 * cdef object _dict
|
|
jpayne@69
|
10342 */
|
|
jpayne@69
|
10343
|
|
jpayne@69
|
10344 /* function exit code */
|
|
jpayne@69
|
10345 __pyx_L1_error:;
|
|
jpayne@69
|
10346 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
10347 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
10348 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
10349 __Pyx_AddTraceback("pysam.libctabix.asVCF.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10350 __pyx_r = NULL;
|
|
jpayne@69
|
10351 __pyx_L0:;
|
|
jpayne@69
|
10352 __Pyx_XDECREF(__pyx_v_state);
|
|
jpayne@69
|
10353 __Pyx_XDECREF(__pyx_v__dict);
|
|
jpayne@69
|
10354 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
10355 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
10356 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10357 return __pyx_r;
|
|
jpayne@69
|
10358 }
|
|
jpayne@69
|
10359
|
|
jpayne@69
|
10360 /* "(tree fragment)":16
|
|
jpayne@69
|
10361 * else:
|
|
jpayne@69
|
10362 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
10363 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10364 * __pyx_unpickle_asVCF__set_state(self, __pyx_state)
|
|
jpayne@69
|
10365 */
|
|
jpayne@69
|
10366
|
|
jpayne@69
|
10367 /* Python wrapper */
|
|
jpayne@69
|
10368 static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
10369 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10370 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
10371 #else
|
|
jpayne@69
|
10372 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
10373 #endif
|
|
jpayne@69
|
10374 ); /*proto*/
|
|
jpayne@69
|
10375 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asVCF_2__setstate_cython__, "asVCF.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
10376 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asVCF_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF_2__setstate_cython__};
|
|
jpayne@69
|
10377 static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
10378 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10379 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
10380 #else
|
|
jpayne@69
|
10381 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
10382 #endif
|
|
jpayne@69
|
10383 ) {
|
|
jpayne@69
|
10384 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
10385 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10386 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
10387 #endif
|
|
jpayne@69
|
10388 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
10389 PyObject* values[1] = {0};
|
|
jpayne@69
|
10390 int __pyx_lineno = 0;
|
|
jpayne@69
|
10391 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
10392 int __pyx_clineno = 0;
|
|
jpayne@69
|
10393 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
10394 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10395 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
10396 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10397 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
10398 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
10399 #else
|
|
jpayne@69
|
10400 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
10401 #endif
|
|
jpayne@69
|
10402 #endif
|
|
jpayne@69
|
10403 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
10404 {
|
|
jpayne@69
|
10405 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
10406 if (__pyx_kwds) {
|
|
jpayne@69
|
10407 Py_ssize_t kw_args;
|
|
jpayne@69
|
10408 switch (__pyx_nargs) {
|
|
jpayne@69
|
10409 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
10410 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10411 case 0: break;
|
|
jpayne@69
|
10412 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10413 }
|
|
jpayne@69
|
10414 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
10415 switch (__pyx_nargs) {
|
|
jpayne@69
|
10416 case 0:
|
|
jpayne@69
|
10417 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
10418 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
10419 kw_args--;
|
|
jpayne@69
|
10420 }
|
|
jpayne@69
|
10421 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
10422 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10423 }
|
|
jpayne@69
|
10424 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
10425 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
10426 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
10427 }
|
|
jpayne@69
|
10428 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
10429 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10430 } else {
|
|
jpayne@69
|
10431 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
10432 }
|
|
jpayne@69
|
10433 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
10434 }
|
|
jpayne@69
|
10435 goto __pyx_L6_skip;
|
|
jpayne@69
|
10436 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
10437 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error)
|
|
jpayne@69
|
10438 __pyx_L6_skip:;
|
|
jpayne@69
|
10439 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
10440 __pyx_L3_error:;
|
|
jpayne@69
|
10441 {
|
|
jpayne@69
|
10442 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
10443 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
10444 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
10445 }
|
|
jpayne@69
|
10446 }
|
|
jpayne@69
|
10447 __Pyx_AddTraceback("pysam.libctabix.asVCF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10448 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10449 return NULL;
|
|
jpayne@69
|
10450 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
10451 __pyx_r = __pyx_pf_5pysam_9libctabix_5asVCF_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asVCF *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
10452
|
|
jpayne@69
|
10453 /* function exit code */
|
|
jpayne@69
|
10454 {
|
|
jpayne@69
|
10455 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
10456 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
10457 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
10458 }
|
|
jpayne@69
|
10459 }
|
|
jpayne@69
|
10460 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
10461 return __pyx_r;
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jpayne@69
|
10462 }
|
|
jpayne@69
|
10463
|
|
jpayne@69
|
10464 static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
10465 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
10466 __Pyx_TraceDeclarations
|
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jpayne@69
|
10467 __Pyx_RefNannyDeclarations
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jpayne@69
|
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jpayne@69
|
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|
|
jpayne@69
|
10470 const char *__pyx_filename = NULL;
|
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jpayne@69
|
10471 int __pyx_clineno = 0;
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jpayne@69
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10472 __Pyx_TraceFrameInit(__pyx_codeobj__14)
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jpayne@69
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10473 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
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jpayne@69
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10474 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error));
|
|
jpayne@69
|
10475
|
|
jpayne@69
|
10476 /* "(tree fragment)":17
|
|
jpayne@69
|
10477 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
10478 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
10479 * __pyx_unpickle_asVCF__set_state(self, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10480 */
|
|
jpayne@69
|
10481 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error)
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jpayne@69
|
10482 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error)
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jpayne@69
|
10483 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
10484 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
10485
|
|
jpayne@69
|
10486 /* "(tree fragment)":16
|
|
jpayne@69
|
10487 * else:
|
|
jpayne@69
|
10488 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
10489 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10490 * __pyx_unpickle_asVCF__set_state(self, __pyx_state)
|
|
jpayne@69
|
10491 */
|
|
jpayne@69
|
10492
|
|
jpayne@69
|
10493 /* function exit code */
|
|
jpayne@69
|
10494 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
10495 goto __pyx_L0;
|
|
jpayne@69
|
10496 __pyx_L1_error:;
|
|
jpayne@69
|
10497 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
10498 __Pyx_AddTraceback("pysam.libctabix.asVCF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10499 __pyx_r = NULL;
|
|
jpayne@69
|
10500 __pyx_L0:;
|
|
jpayne@69
|
10501 __Pyx_XGIVEREF(__pyx_r);
|
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jpayne@69
|
10502 __Pyx_TraceReturn(__pyx_r, 0);
|
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jpayne@69
|
10503 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
10504 return __pyx_r;
|
|
jpayne@69
|
10505 }
|
|
jpayne@69
|
10506
|
|
jpayne@69
|
10507 /* "pysam/libctabix.pyx":334
|
|
jpayne@69
|
10508 * if file could not be opened
|
|
jpayne@69
|
10509 * """
|
|
jpayne@69
|
10510 * def __cinit__(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10511 * filename,
|
|
jpayne@69
|
10512 * mode='r',
|
|
jpayne@69
|
10513 */
|
|
jpayne@69
|
10514
|
|
jpayne@69
|
10515 /* Python wrapper */
|
|
jpayne@69
|
10516 static int __pyx_pw_5pysam_9libctabix_9TabixFile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
10517 static int __pyx_pw_5pysam_9libctabix_9TabixFile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
10518 PyObject *__pyx_v_filename = 0;
|
|
jpayne@69
|
10519 PyObject *__pyx_v_mode = 0;
|
|
jpayne@69
|
10520 PyObject *__pyx_v_parser = 0;
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|
jpayne@69
|
10521 PyObject *__pyx_v_index = 0;
|
|
jpayne@69
|
10522 PyObject *__pyx_v_encoding = 0;
|
|
jpayne@69
|
10523 PyObject *__pyx_v_threads = 0;
|
|
jpayne@69
|
10524 PyObject *__pyx_v_args = 0;
|
|
jpayne@69
|
10525 PyObject *__pyx_v_kwargs = 0;
|
|
jpayne@69
|
10526 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
10527 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
10528 PyObject* values[6] = {0,0,0,0,0,0};
|
|
jpayne@69
|
10529 int __pyx_lineno = 0;
|
|
jpayne@69
|
10530 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
10531 int __pyx_clineno = 0;
|
|
jpayne@69
|
10532 int __pyx_r;
|
|
jpayne@69
|
10533 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10534 __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
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jpayne@69
|
10535 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
10536 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
10537 #else
|
|
jpayne@69
|
10538 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
10539 #endif
|
|
jpayne@69
|
10540 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
10541 __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
|
|
jpayne@69
|
10542 __Pyx_GOTREF(__pyx_v_kwargs);
|
|
jpayne@69
|
10543 __pyx_v_args = __Pyx_ArgsSlice_VARARGS(__pyx_args, 6, __pyx_nargs);
|
|
jpayne@69
|
10544 if (unlikely(!__pyx_v_args)) {
|
|
jpayne@69
|
10545 __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
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jpayne@69
|
10546 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10547 return -1;
|
|
jpayne@69
|
10548 }
|
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jpayne@69
|
10549 __Pyx_GOTREF(__pyx_v_args);
|
|
jpayne@69
|
10550 {
|
|
jpayne@69
|
10551 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_mode,&__pyx_n_s_parser,&__pyx_n_s_index,&__pyx_n_s_encoding,&__pyx_n_s_threads,0};
|
|
jpayne@69
|
10552 values[1] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_r));
|
|
jpayne@69
|
10553
|
|
jpayne@69
|
10554 /* "pysam/libctabix.pyx":337
|
|
jpayne@69
|
10555 * filename,
|
|
jpayne@69
|
10556 * mode='r',
|
|
jpayne@69
|
10557 * parser=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10558 * index=None,
|
|
jpayne@69
|
10559 * encoding="ascii",
|
|
jpayne@69
|
10560 */
|
|
jpayne@69
|
10561 values[2] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)Py_None));
|
|
jpayne@69
|
10562
|
|
jpayne@69
|
10563 /* "pysam/libctabix.pyx":338
|
|
jpayne@69
|
10564 * mode='r',
|
|
jpayne@69
|
10565 * parser=None,
|
|
jpayne@69
|
10566 * index=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10567 * encoding="ascii",
|
|
jpayne@69
|
10568 * threads=1,
|
|
jpayne@69
|
10569 */
|
|
jpayne@69
|
10570 values[3] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)Py_None));
|
|
jpayne@69
|
10571 values[4] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii));
|
|
jpayne@69
|
10572 values[5] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_int_1));
|
|
jpayne@69
|
10573 if (__pyx_kwds) {
|
|
jpayne@69
|
10574 Py_ssize_t kw_args;
|
|
jpayne@69
|
10575 switch (__pyx_nargs) {
|
|
jpayne@69
|
10576 default:
|
|
jpayne@69
|
10577 case 6: values[5] = __Pyx_Arg_VARARGS(__pyx_args, 5);
|
|
jpayne@69
|
10578 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10579 case 5: values[4] = __Pyx_Arg_VARARGS(__pyx_args, 4);
|
|
jpayne@69
|
10580 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10581 case 4: values[3] = __Pyx_Arg_VARARGS(__pyx_args, 3);
|
|
jpayne@69
|
10582 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10583 case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2);
|
|
jpayne@69
|
10584 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10585 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
10586 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10587 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
10588 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10589 case 0: break;
|
|
jpayne@69
|
10590 }
|
|
jpayne@69
|
10591 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
10592 switch (__pyx_nargs) {
|
|
jpayne@69
|
10593 case 0:
|
|
jpayne@69
|
10594 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) {
|
|
jpayne@69
|
10595 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
|
|
jpayne@69
|
10596 kw_args--;
|
|
jpayne@69
|
10597 }
|
|
jpayne@69
|
10598 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10599 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10600 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10601 case 1:
|
|
jpayne@69
|
10602 if (kw_args > 0) {
|
|
jpayne@69
|
10603 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_mode);
|
|
jpayne@69
|
10604 if (value) { values[1] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
10605 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10606 }
|
|
jpayne@69
|
10607 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10608 case 2:
|
|
jpayne@69
|
10609 if (kw_args > 0) {
|
|
jpayne@69
|
10610 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser);
|
|
jpayne@69
|
10611 if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
10612 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10613 }
|
|
jpayne@69
|
10614 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10615 case 3:
|
|
jpayne@69
|
10616 if (kw_args > 0) {
|
|
jpayne@69
|
10617 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_index);
|
|
jpayne@69
|
10618 if (value) { values[3] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
10619 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10620 }
|
|
jpayne@69
|
10621 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10622 case 4:
|
|
jpayne@69
|
10623 if (kw_args > 0) {
|
|
jpayne@69
|
10624 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding);
|
|
jpayne@69
|
10625 if (value) { values[4] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
10626 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10627 }
|
|
jpayne@69
|
10628 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10629 case 5:
|
|
jpayne@69
|
10630 if (kw_args > 0) {
|
|
jpayne@69
|
10631 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_threads);
|
|
jpayne@69
|
10632 if (value) { values[5] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
10633 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10634 }
|
|
jpayne@69
|
10635 }
|
|
jpayne@69
|
10636 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
10637 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
10638 const Py_ssize_t used_pos_args = (kwd_pos_args < 6) ? kwd_pos_args : 6;
|
|
jpayne@69
|
10639 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, __pyx_v_kwargs, values + 0, used_pos_args, "__cinit__") < 0)) __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10640 }
|
|
jpayne@69
|
10641 } else {
|
|
jpayne@69
|
10642 switch (__pyx_nargs) {
|
|
jpayne@69
|
10643 default:
|
|
jpayne@69
|
10644 case 6: values[5] = __Pyx_Arg_VARARGS(__pyx_args, 5);
|
|
jpayne@69
|
10645 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10646 case 5: values[4] = __Pyx_Arg_VARARGS(__pyx_args, 4);
|
|
jpayne@69
|
10647 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10648 case 4: values[3] = __Pyx_Arg_VARARGS(__pyx_args, 3);
|
|
jpayne@69
|
10649 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10650 case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2);
|
|
jpayne@69
|
10651 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10652 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
10653 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10654 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
10655 break;
|
|
jpayne@69
|
10656 case 0:
|
|
jpayne@69
|
10657 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10658 }
|
|
jpayne@69
|
10659 }
|
|
jpayne@69
|
10660 __pyx_v_filename = values[0];
|
|
jpayne@69
|
10661 __pyx_v_mode = values[1];
|
|
jpayne@69
|
10662 __pyx_v_parser = values[2];
|
|
jpayne@69
|
10663 __pyx_v_index = values[3];
|
|
jpayne@69
|
10664 __pyx_v_encoding = values[4];
|
|
jpayne@69
|
10665 __pyx_v_threads = values[5];
|
|
jpayne@69
|
10666 }
|
|
jpayne@69
|
10667 goto __pyx_L6_skip;
|
|
jpayne@69
|
10668 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
10669 __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 6, __pyx_nargs); __PYX_ERR(0, 334, __pyx_L3_error)
|
|
jpayne@69
|
10670 __pyx_L6_skip:;
|
|
jpayne@69
|
10671 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
10672 __pyx_L3_error:;
|
|
jpayne@69
|
10673 {
|
|
jpayne@69
|
10674 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
10675 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
10676 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
10677 }
|
|
jpayne@69
|
10678 }
|
|
jpayne@69
|
10679 __Pyx_DECREF(__pyx_v_args); __pyx_v_args = 0;
|
|
jpayne@69
|
10680 __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
|
|
jpayne@69
|
10681 __Pyx_AddTraceback("pysam.libctabix.TabixFile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10682 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10683 return -1;
|
|
jpayne@69
|
10684 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
10685 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile___cinit__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_parser, __pyx_v_index, __pyx_v_encoding, __pyx_v_threads, __pyx_v_args, __pyx_v_kwargs);
|
|
jpayne@69
|
10686
|
|
jpayne@69
|
10687 /* "pysam/libctabix.pyx":334
|
|
jpayne@69
|
10688 * if file could not be opened
|
|
jpayne@69
|
10689 * """
|
|
jpayne@69
|
10690 * def __cinit__(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10691 * filename,
|
|
jpayne@69
|
10692 * mode='r',
|
|
jpayne@69
|
10693 */
|
|
jpayne@69
|
10694
|
|
jpayne@69
|
10695 /* function exit code */
|
|
jpayne@69
|
10696 __Pyx_DECREF(__pyx_v_args);
|
|
jpayne@69
|
10697 __Pyx_DECREF(__pyx_v_kwargs);
|
|
jpayne@69
|
10698 {
|
|
jpayne@69
|
10699 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
10700 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
10701 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
10702 }
|
|
jpayne@69
|
10703 }
|
|
jpayne@69
|
10704 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10705 return __pyx_r;
|
|
jpayne@69
|
10706 }
|
|
jpayne@69
|
10707
|
|
jpayne@69
|
10708 static int __pyx_pf_5pysam_9libctabix_9TabixFile___cinit__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_parser, PyObject *__pyx_v_index, PyObject *__pyx_v_encoding, PyObject *__pyx_v_threads, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
|
|
jpayne@69
|
10709 int __pyx_r;
|
|
jpayne@69
|
10710 __Pyx_TraceDeclarations
|
|
jpayne@69
|
10711 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10712 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
10713 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
10714 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
10715 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
10716 int __pyx_lineno = 0;
|
|
jpayne@69
|
10717 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
10718 int __pyx_clineno = 0;
|
|
jpayne@69
|
10719 __Pyx_RefNannySetupContext("__cinit__", 1);
|
|
jpayne@69
|
10720 __Pyx_TraceCall("__cinit__", __pyx_f[0], 334, 0, __PYX_ERR(0, 334, __pyx_L1_error));
|
|
jpayne@69
|
10721
|
|
jpayne@69
|
10722 /* "pysam/libctabix.pyx":344
|
|
jpayne@69
|
10723 * **kwargs ):
|
|
jpayne@69
|
10724 *
|
|
jpayne@69
|
10725 * self.htsfile = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10726 * self.is_remote = False
|
|
jpayne@69
|
10727 * self.is_stream = False
|
|
jpayne@69
|
10728 */
|
|
jpayne@69
|
10729 __pyx_v_self->__pyx_base.htsfile = NULL;
|
|
jpayne@69
|
10730
|
|
jpayne@69
|
10731 /* "pysam/libctabix.pyx":345
|
|
jpayne@69
|
10732 *
|
|
jpayne@69
|
10733 * self.htsfile = NULL
|
|
jpayne@69
|
10734 * self.is_remote = False # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10735 * self.is_stream = False
|
|
jpayne@69
|
10736 * self.parser = parser
|
|
jpayne@69
|
10737 */
|
|
jpayne@69
|
10738 __pyx_v_self->__pyx_base.is_remote = 0;
|
|
jpayne@69
|
10739
|
|
jpayne@69
|
10740 /* "pysam/libctabix.pyx":346
|
|
jpayne@69
|
10741 * self.htsfile = NULL
|
|
jpayne@69
|
10742 * self.is_remote = False
|
|
jpayne@69
|
10743 * self.is_stream = False # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10744 * self.parser = parser
|
|
jpayne@69
|
10745 * self.threads = threads
|
|
jpayne@69
|
10746 */
|
|
jpayne@69
|
10747 __pyx_v_self->__pyx_base.is_stream = 0;
|
|
jpayne@69
|
10748
|
|
jpayne@69
|
10749 /* "pysam/libctabix.pyx":347
|
|
jpayne@69
|
10750 * self.is_remote = False
|
|
jpayne@69
|
10751 * self.is_stream = False
|
|
jpayne@69
|
10752 * self.parser = parser # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10753 * self.threads = threads
|
|
jpayne@69
|
10754 * self._open(filename, mode, index, *args, **kwargs)
|
|
jpayne@69
|
10755 */
|
|
jpayne@69
|
10756 if (!(likely(((__pyx_v_parser) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_parser, __pyx_ptype_5pysam_9libctabix_Parser))))) __PYX_ERR(0, 347, __pyx_L1_error)
|
|
jpayne@69
|
10757 __pyx_t_1 = __pyx_v_parser;
|
|
jpayne@69
|
10758 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
10759 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
10760 __Pyx_GOTREF((PyObject *)__pyx_v_self->parser);
|
|
jpayne@69
|
10761 __Pyx_DECREF((PyObject *)__pyx_v_self->parser);
|
|
jpayne@69
|
10762 __pyx_v_self->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_t_1);
|
|
jpayne@69
|
10763 __pyx_t_1 = 0;
|
|
jpayne@69
|
10764
|
|
jpayne@69
|
10765 /* "pysam/libctabix.pyx":348
|
|
jpayne@69
|
10766 * self.is_stream = False
|
|
jpayne@69
|
10767 * self.parser = parser
|
|
jpayne@69
|
10768 * self.threads = threads # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10769 * self._open(filename, mode, index, *args, **kwargs)
|
|
jpayne@69
|
10770 * self.encoding = encoding
|
|
jpayne@69
|
10771 */
|
|
jpayne@69
|
10772 __Pyx_INCREF(__pyx_v_threads);
|
|
jpayne@69
|
10773 __Pyx_GIVEREF(__pyx_v_threads);
|
|
jpayne@69
|
10774 __Pyx_GOTREF(__pyx_v_self->__pyx_base.threads);
|
|
jpayne@69
|
10775 __Pyx_DECREF(__pyx_v_self->__pyx_base.threads);
|
|
jpayne@69
|
10776 __pyx_v_self->__pyx_base.threads = __pyx_v_threads;
|
|
jpayne@69
|
10777
|
|
jpayne@69
|
10778 /* "pysam/libctabix.pyx":349
|
|
jpayne@69
|
10779 * self.parser = parser
|
|
jpayne@69
|
10780 * self.threads = threads
|
|
jpayne@69
|
10781 * self._open(filename, mode, index, *args, **kwargs) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10782 * self.encoding = encoding
|
|
jpayne@69
|
10783 *
|
|
jpayne@69
|
10784 */
|
|
jpayne@69
|
10785 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 349, __pyx_L1_error)
|
|
jpayne@69
|
10786 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
10787 __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 349, __pyx_L1_error)
|
|
jpayne@69
|
10788 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
10789 __Pyx_INCREF(__pyx_v_filename);
|
|
jpayne@69
|
10790 __Pyx_GIVEREF(__pyx_v_filename);
|
|
jpayne@69
|
10791 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_filename)) __PYX_ERR(0, 349, __pyx_L1_error);
|
|
jpayne@69
|
10792 __Pyx_INCREF(__pyx_v_mode);
|
|
jpayne@69
|
10793 __Pyx_GIVEREF(__pyx_v_mode);
|
|
jpayne@69
|
10794 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_mode)) __PYX_ERR(0, 349, __pyx_L1_error);
|
|
jpayne@69
|
10795 __Pyx_INCREF(__pyx_v_index);
|
|
jpayne@69
|
10796 __Pyx_GIVEREF(__pyx_v_index);
|
|
jpayne@69
|
10797 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_index)) __PYX_ERR(0, 349, __pyx_L1_error);
|
|
jpayne@69
|
10798 __pyx_t_3 = PyNumber_Add(__pyx_t_2, __pyx_v_args); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 349, __pyx_L1_error)
|
|
jpayne@69
|
10799 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10800 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
10801 __pyx_t_2 = PyDict_Copy(__pyx_v_kwargs); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 349, __pyx_L1_error)
|
|
jpayne@69
|
10802 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
10803 __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 349, __pyx_L1_error)
|
|
jpayne@69
|
10804 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
10805 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
10806 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10807 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
10808 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
10809
|
|
jpayne@69
|
10810 /* "pysam/libctabix.pyx":350
|
|
jpayne@69
|
10811 * self.threads = threads
|
|
jpayne@69
|
10812 * self._open(filename, mode, index, *args, **kwargs)
|
|
jpayne@69
|
10813 * self.encoding = encoding # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10814 *
|
|
jpayne@69
|
10815 * def _open( self,
|
|
jpayne@69
|
10816 */
|
|
jpayne@69
|
10817 __Pyx_INCREF(__pyx_v_encoding);
|
|
jpayne@69
|
10818 __Pyx_GIVEREF(__pyx_v_encoding);
|
|
jpayne@69
|
10819 __Pyx_GOTREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
10820 __Pyx_DECREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
10821 __pyx_v_self->encoding = __pyx_v_encoding;
|
|
jpayne@69
|
10822
|
|
jpayne@69
|
10823 /* "pysam/libctabix.pyx":334
|
|
jpayne@69
|
10824 * if file could not be opened
|
|
jpayne@69
|
10825 * """
|
|
jpayne@69
|
10826 * def __cinit__(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10827 * filename,
|
|
jpayne@69
|
10828 * mode='r',
|
|
jpayne@69
|
10829 */
|
|
jpayne@69
|
10830
|
|
jpayne@69
|
10831 /* function exit code */
|
|
jpayne@69
|
10832 __pyx_r = 0;
|
|
jpayne@69
|
10833 goto __pyx_L0;
|
|
jpayne@69
|
10834 __pyx_L1_error:;
|
|
jpayne@69
|
10835 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
10836 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
10837 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
10838 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
10839 __Pyx_AddTraceback("pysam.libctabix.TabixFile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10840 __pyx_r = -1;
|
|
jpayne@69
|
10841 __pyx_L0:;
|
|
jpayne@69
|
10842 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
10843 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10844 return __pyx_r;
|
|
jpayne@69
|
10845 }
|
|
jpayne@69
|
10846
|
|
jpayne@69
|
10847 /* "pysam/libctabix.pyx":352
|
|
jpayne@69
|
10848 * self.encoding = encoding
|
|
jpayne@69
|
10849 *
|
|
jpayne@69
|
10850 * def _open( self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10851 * filename,
|
|
jpayne@69
|
10852 * mode='r',
|
|
jpayne@69
|
10853 */
|
|
jpayne@69
|
10854
|
|
jpayne@69
|
10855 /* Python wrapper */
|
|
jpayne@69
|
10856 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_3_open(PyObject *__pyx_v_self,
|
|
jpayne@69
|
10857 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10858 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
10859 #else
|
|
jpayne@69
|
10860 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
10861 #endif
|
|
jpayne@69
|
10862 ); /*proto*/
|
|
jpayne@69
|
10863 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_2_open, "TabixFile._open(self, filename, mode=u'r', index=None, threads=1)\nopen a :term:`tabix file` for reading.");
|
|
jpayne@69
|
10864 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_3_open = {"_open", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_3_open, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_2_open};
|
|
jpayne@69
|
10865 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_3_open(PyObject *__pyx_v_self,
|
|
jpayne@69
|
10866 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10867 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
10868 #else
|
|
jpayne@69
|
10869 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
10870 #endif
|
|
jpayne@69
|
10871 ) {
|
|
jpayne@69
|
10872 PyObject *__pyx_v_filename = 0;
|
|
jpayne@69
|
10873 PyObject *__pyx_v_mode = 0;
|
|
jpayne@69
|
10874 PyObject *__pyx_v_index = 0;
|
|
jpayne@69
|
10875 PyObject *__pyx_v_threads = 0;
|
|
jpayne@69
|
10876 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10877 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
10878 #endif
|
|
jpayne@69
|
10879 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
10880 PyObject* values[4] = {0,0,0,0};
|
|
jpayne@69
|
10881 int __pyx_lineno = 0;
|
|
jpayne@69
|
10882 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
10883 int __pyx_clineno = 0;
|
|
jpayne@69
|
10884 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
10885 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
10886 __Pyx_RefNannySetupContext("_open (wrapper)", 0);
|
|
jpayne@69
|
10887 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
10888 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
10889 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
10890 #else
|
|
jpayne@69
|
10891 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
10892 #endif
|
|
jpayne@69
|
10893 #endif
|
|
jpayne@69
|
10894 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
10895 {
|
|
jpayne@69
|
10896 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_mode,&__pyx_n_s_index,&__pyx_n_s_threads,0};
|
|
jpayne@69
|
10897 values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)__pyx_n_u_r));
|
|
jpayne@69
|
10898
|
|
jpayne@69
|
10899 /* "pysam/libctabix.pyx":355
|
|
jpayne@69
|
10900 * filename,
|
|
jpayne@69
|
10901 * mode='r',
|
|
jpayne@69
|
10902 * index=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10903 * threads=1,
|
|
jpayne@69
|
10904 * ):
|
|
jpayne@69
|
10905 */
|
|
jpayne@69
|
10906 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
10907 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)__pyx_int_1));
|
|
jpayne@69
|
10908 if (__pyx_kwds) {
|
|
jpayne@69
|
10909 Py_ssize_t kw_args;
|
|
jpayne@69
|
10910 switch (__pyx_nargs) {
|
|
jpayne@69
|
10911 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
10912 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10913 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
10914 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10915 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
10916 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10917 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
10918 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10919 case 0: break;
|
|
jpayne@69
|
10920 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10921 }
|
|
jpayne@69
|
10922 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
10923 switch (__pyx_nargs) {
|
|
jpayne@69
|
10924 case 0:
|
|
jpayne@69
|
10925 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) {
|
|
jpayne@69
|
10926 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
10927 kw_args--;
|
|
jpayne@69
|
10928 }
|
|
jpayne@69
|
10929 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error)
|
|
jpayne@69
|
10930 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10931 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10932 case 1:
|
|
jpayne@69
|
10933 if (kw_args > 0) {
|
|
jpayne@69
|
10934 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_mode);
|
|
jpayne@69
|
10935 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
10936 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error)
|
|
jpayne@69
|
10937 }
|
|
jpayne@69
|
10938 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10939 case 2:
|
|
jpayne@69
|
10940 if (kw_args > 0) {
|
|
jpayne@69
|
10941 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_index);
|
|
jpayne@69
|
10942 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
10943 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error)
|
|
jpayne@69
|
10944 }
|
|
jpayne@69
|
10945 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10946 case 3:
|
|
jpayne@69
|
10947 if (kw_args > 0) {
|
|
jpayne@69
|
10948 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_threads);
|
|
jpayne@69
|
10949 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
10950 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error)
|
|
jpayne@69
|
10951 }
|
|
jpayne@69
|
10952 }
|
|
jpayne@69
|
10953 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
10954 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
10955 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_open") < 0)) __PYX_ERR(0, 352, __pyx_L3_error)
|
|
jpayne@69
|
10956 }
|
|
jpayne@69
|
10957 } else {
|
|
jpayne@69
|
10958 switch (__pyx_nargs) {
|
|
jpayne@69
|
10959 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
10960 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10961 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
10962 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10963 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
10964 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
10965 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
10966 break;
|
|
jpayne@69
|
10967 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
10968 }
|
|
jpayne@69
|
10969 }
|
|
jpayne@69
|
10970 __pyx_v_filename = values[0];
|
|
jpayne@69
|
10971 __pyx_v_mode = values[1];
|
|
jpayne@69
|
10972 __pyx_v_index = values[2];
|
|
jpayne@69
|
10973 __pyx_v_threads = values[3];
|
|
jpayne@69
|
10974 }
|
|
jpayne@69
|
10975 goto __pyx_L6_skip;
|
|
jpayne@69
|
10976 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
10977 __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 4, __pyx_nargs); __PYX_ERR(0, 352, __pyx_L3_error)
|
|
jpayne@69
|
10978 __pyx_L6_skip:;
|
|
jpayne@69
|
10979 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
10980 __pyx_L3_error:;
|
|
jpayne@69
|
10981 {
|
|
jpayne@69
|
10982 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
10983 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
10984 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
10985 }
|
|
jpayne@69
|
10986 }
|
|
jpayne@69
|
10987 __Pyx_AddTraceback("pysam.libctabix.TabixFile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
10988 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
10989 return NULL;
|
|
jpayne@69
|
10990 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
10991 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_2_open(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_index, __pyx_v_threads);
|
|
jpayne@69
|
10992
|
|
jpayne@69
|
10993 /* "pysam/libctabix.pyx":352
|
|
jpayne@69
|
10994 * self.encoding = encoding
|
|
jpayne@69
|
10995 *
|
|
jpayne@69
|
10996 * def _open( self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10997 * filename,
|
|
jpayne@69
|
10998 * mode='r',
|
|
jpayne@69
|
10999 */
|
|
jpayne@69
|
11000
|
|
jpayne@69
|
11001 /* function exit code */
|
|
jpayne@69
|
11002 {
|
|
jpayne@69
|
11003 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
11004 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
11005 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
11006 }
|
|
jpayne@69
|
11007 }
|
|
jpayne@69
|
11008 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11009 return __pyx_r;
|
|
jpayne@69
|
11010 }
|
|
jpayne@69
|
11011
|
|
jpayne@69
|
11012 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_2_open(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_index, PyObject *__pyx_v_threads) {
|
|
jpayne@69
|
11013 PyObject *__pyx_v_filename_index = NULL;
|
|
jpayne@69
|
11014 char *__pyx_v_cfilename;
|
|
jpayne@69
|
11015 char *__pyx_v_cfilename_index;
|
|
jpayne@69
|
11016 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
11017 __Pyx_TraceDeclarations
|
|
jpayne@69
|
11018 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
11019 int __pyx_t_1;
|
|
jpayne@69
|
11020 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
11021 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
11022 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
11023 unsigned int __pyx_t_5;
|
|
jpayne@69
|
11024 char const *__pyx_t_6;
|
|
jpayne@69
|
11025 int __pyx_t_7;
|
|
jpayne@69
|
11026 char *__pyx_t_8;
|
|
jpayne@69
|
11027 int64_t __pyx_t_9;
|
|
jpayne@69
|
11028 int __pyx_lineno = 0;
|
|
jpayne@69
|
11029 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
11030 int __pyx_clineno = 0;
|
|
jpayne@69
|
11031 __Pyx_TraceFrameInit(__pyx_codeobj__15)
|
|
jpayne@69
|
11032 __Pyx_RefNannySetupContext("_open", 1);
|
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jpayne@69
|
11033 __Pyx_TraceCall("_open", __pyx_f[0], 352, 0, __PYX_ERR(0, 352, __pyx_L1_error));
|
|
jpayne@69
|
11034
|
|
jpayne@69
|
11035 /* "pysam/libctabix.pyx":360
|
|
jpayne@69
|
11036 * '''open a :term:`tabix file` for reading.'''
|
|
jpayne@69
|
11037 *
|
|
jpayne@69
|
11038 * if mode != 'r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11039 * raise ValueError("invalid file opening mode `%s`" % mode)
|
|
jpayne@69
|
11040 *
|
|
jpayne@69
|
11041 */
|
|
jpayne@69
|
11042 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_mode, __pyx_n_u_r, Py_NE)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 360, __pyx_L1_error)
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jpayne@69
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11043 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
11044
|
|
jpayne@69
|
11045 /* "pysam/libctabix.pyx":361
|
|
jpayne@69
|
11046 *
|
|
jpayne@69
|
11047 * if mode != 'r':
|
|
jpayne@69
|
11048 * raise ValueError("invalid file opening mode `%s`" % mode) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11049 *
|
|
jpayne@69
|
11050 * if self.htsfile != NULL:
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|
jpayne@69
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11051 */
|
|
jpayne@69
|
11052 __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_invalid_file_opening_mode_s, __pyx_v_mode); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 361, __pyx_L1_error)
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jpayne@69
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11053 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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11054 __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 361, __pyx_L1_error)
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jpayne@69
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11055 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
11056 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
|
11057 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
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11058 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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jpayne@69
|
11059 __PYX_ERR(0, 361, __pyx_L1_error)
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jpayne@69
|
11060
|
|
jpayne@69
|
11061 /* "pysam/libctabix.pyx":360
|
|
jpayne@69
|
11062 * '''open a :term:`tabix file` for reading.'''
|
|
jpayne@69
|
11063 *
|
|
jpayne@69
|
11064 * if mode != 'r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11065 * raise ValueError("invalid file opening mode `%s`" % mode)
|
|
jpayne@69
|
11066 *
|
|
jpayne@69
|
11067 */
|
|
jpayne@69
|
11068 }
|
|
jpayne@69
|
11069
|
|
jpayne@69
|
11070 /* "pysam/libctabix.pyx":363
|
|
jpayne@69
|
11071 * raise ValueError("invalid file opening mode `%s`" % mode)
|
|
jpayne@69
|
11072 *
|
|
jpayne@69
|
11073 * if self.htsfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11074 * self.close()
|
|
jpayne@69
|
11075 * self.htsfile = NULL
|
|
jpayne@69
|
11076 */
|
|
jpayne@69
|
11077 __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile != NULL);
|
|
jpayne@69
|
11078 if (__pyx_t_1) {
|
|
jpayne@69
|
11079
|
|
jpayne@69
|
11080 /* "pysam/libctabix.pyx":364
|
|
jpayne@69
|
11081 *
|
|
jpayne@69
|
11082 * if self.htsfile != NULL:
|
|
jpayne@69
|
11083 * self.close() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11084 * self.htsfile = NULL
|
|
jpayne@69
|
11085 * self.threads=threads
|
|
jpayne@69
|
11086 */
|
|
jpayne@69
|
11087 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 364, __pyx_L1_error)
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jpayne@69
|
11088 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
|
11089 __pyx_t_4 = NULL;
|
|
jpayne@69
|
11090 __pyx_t_5 = 0;
|
|
jpayne@69
|
11091 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
11092 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
11093 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
11094 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
11095 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
11096 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
11097 __Pyx_INCREF(function);
|
|
jpayne@69
|
11098 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
11099 __pyx_t_5 = 1;
|
|
jpayne@69
|
11100 }
|
|
jpayne@69
|
11101 }
|
|
jpayne@69
|
11102 #endif
|
|
jpayne@69
|
11103 {
|
|
jpayne@69
|
11104 PyObject *__pyx_callargs[2] = {__pyx_t_4, NULL};
|
|
jpayne@69
|
11105 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5);
|
|
jpayne@69
|
11106 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
11107 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 364, __pyx_L1_error)
|
|
jpayne@69
|
11108 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11109 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11110 }
|
|
jpayne@69
|
11111 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11112
|
|
jpayne@69
|
11113 /* "pysam/libctabix.pyx":363
|
|
jpayne@69
|
11114 * raise ValueError("invalid file opening mode `%s`" % mode)
|
|
jpayne@69
|
11115 *
|
|
jpayne@69
|
11116 * if self.htsfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11117 * self.close()
|
|
jpayne@69
|
11118 * self.htsfile = NULL
|
|
jpayne@69
|
11119 */
|
|
jpayne@69
|
11120 }
|
|
jpayne@69
|
11121
|
|
jpayne@69
|
11122 /* "pysam/libctabix.pyx":365
|
|
jpayne@69
|
11123 * if self.htsfile != NULL:
|
|
jpayne@69
|
11124 * self.close()
|
|
jpayne@69
|
11125 * self.htsfile = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11126 * self.threads=threads
|
|
jpayne@69
|
11127 *
|
|
jpayne@69
|
11128 */
|
|
jpayne@69
|
11129 __pyx_v_self->__pyx_base.htsfile = NULL;
|
|
jpayne@69
|
11130
|
|
jpayne@69
|
11131 /* "pysam/libctabix.pyx":366
|
|
jpayne@69
|
11132 * self.close()
|
|
jpayne@69
|
11133 * self.htsfile = NULL
|
|
jpayne@69
|
11134 * self.threads=threads # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11135 *
|
|
jpayne@69
|
11136 * filename_index = index or (filename + ".tbi")
|
|
jpayne@69
|
11137 */
|
|
jpayne@69
|
11138 __Pyx_INCREF(__pyx_v_threads);
|
|
jpayne@69
|
11139 __Pyx_GIVEREF(__pyx_v_threads);
|
|
jpayne@69
|
11140 __Pyx_GOTREF(__pyx_v_self->__pyx_base.threads);
|
|
jpayne@69
|
11141 __Pyx_DECREF(__pyx_v_self->__pyx_base.threads);
|
|
jpayne@69
|
11142 __pyx_v_self->__pyx_base.threads = __pyx_v_threads;
|
|
jpayne@69
|
11143
|
|
jpayne@69
|
11144 /* "pysam/libctabix.pyx":368
|
|
jpayne@69
|
11145 * self.threads=threads
|
|
jpayne@69
|
11146 *
|
|
jpayne@69
|
11147 * filename_index = index or (filename + ".tbi") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11148 * # encode all the strings to pass to tabix
|
|
jpayne@69
|
11149 * self.filename = encode_filename(filename)
|
|
jpayne@69
|
11150 */
|
|
jpayne@69
|
11151 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_index); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 368, __pyx_L1_error)
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jpayne@69
|
11152 if (!__pyx_t_1) {
|
|
jpayne@69
|
11153 } else {
|
|
jpayne@69
|
11154 __Pyx_INCREF(__pyx_v_index);
|
|
jpayne@69
|
11155 __pyx_t_3 = __pyx_v_index;
|
|
jpayne@69
|
11156 goto __pyx_L5_bool_binop_done;
|
|
jpayne@69
|
11157 }
|
|
jpayne@69
|
11158 __pyx_t_2 = PyNumber_Add(__pyx_v_filename, __pyx_kp_u_tbi); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 368, __pyx_L1_error)
|
|
jpayne@69
|
11159 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11160 __Pyx_INCREF(__pyx_t_2);
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|
jpayne@69
|
11161 __pyx_t_3 = __pyx_t_2;
|
|
jpayne@69
|
11162 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11163 __pyx_L5_bool_binop_done:;
|
|
jpayne@69
|
11164 __pyx_v_filename_index = __pyx_t_3;
|
|
jpayne@69
|
11165 __pyx_t_3 = 0;
|
|
jpayne@69
|
11166
|
|
jpayne@69
|
11167 /* "pysam/libctabix.pyx":370
|
|
jpayne@69
|
11168 * filename_index = index or (filename + ".tbi")
|
|
jpayne@69
|
11169 * # encode all the strings to pass to tabix
|
|
jpayne@69
|
11170 * self.filename = encode_filename(filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11171 * self.filename_index = encode_filename(filename_index)
|
|
jpayne@69
|
11172 *
|
|
jpayne@69
|
11173 */
|
|
jpayne@69
|
11174 __pyx_t_3 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 370, __pyx_L1_error)
|
|
jpayne@69
|
11175 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11176 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
11177 __Pyx_GOTREF(__pyx_v_self->__pyx_base.filename);
|
|
jpayne@69
|
11178 __Pyx_DECREF(__pyx_v_self->__pyx_base.filename);
|
|
jpayne@69
|
11179 __pyx_v_self->__pyx_base.filename = __pyx_t_3;
|
|
jpayne@69
|
11180 __pyx_t_3 = 0;
|
|
jpayne@69
|
11181
|
|
jpayne@69
|
11182 /* "pysam/libctabix.pyx":371
|
|
jpayne@69
|
11183 * # encode all the strings to pass to tabix
|
|
jpayne@69
|
11184 * self.filename = encode_filename(filename)
|
|
jpayne@69
|
11185 * self.filename_index = encode_filename(filename_index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11186 *
|
|
jpayne@69
|
11187 * self.is_stream = self.filename == b'-'
|
|
jpayne@69
|
11188 */
|
|
jpayne@69
|
11189 __pyx_t_3 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename_index); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 371, __pyx_L1_error)
|
|
jpayne@69
|
11190 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11191 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
11192 __Pyx_GOTREF(__pyx_v_self->filename_index);
|
|
jpayne@69
|
11193 __Pyx_DECREF(__pyx_v_self->filename_index);
|
|
jpayne@69
|
11194 __pyx_v_self->filename_index = __pyx_t_3;
|
|
jpayne@69
|
11195 __pyx_t_3 = 0;
|
|
jpayne@69
|
11196
|
|
jpayne@69
|
11197 /* "pysam/libctabix.pyx":373
|
|
jpayne@69
|
11198 * self.filename_index = encode_filename(filename_index)
|
|
jpayne@69
|
11199 *
|
|
jpayne@69
|
11200 * self.is_stream = self.filename == b'-' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11201 * self.is_remote = hisremote(self.filename)
|
|
jpayne@69
|
11202 *
|
|
jpayne@69
|
11203 */
|
|
jpayne@69
|
11204 __pyx_t_3 = PyObject_RichCompare(__pyx_v_self->__pyx_base.filename, __pyx_kp_b__16, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 373, __pyx_L1_error)
|
|
jpayne@69
|
11205 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 373, __pyx_L1_error)
|
|
jpayne@69
|
11206 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11207 __pyx_v_self->__pyx_base.is_stream = __pyx_t_1;
|
|
jpayne@69
|
11208
|
|
jpayne@69
|
11209 /* "pysam/libctabix.pyx":374
|
|
jpayne@69
|
11210 *
|
|
jpayne@69
|
11211 * self.is_stream = self.filename == b'-'
|
|
jpayne@69
|
11212 * self.is_remote = hisremote(self.filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11213 *
|
|
jpayne@69
|
11214 * if not self.is_remote:
|
|
jpayne@69
|
11215 */
|
|
jpayne@69
|
11216 __pyx_t_6 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.filename); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) __PYX_ERR(0, 374, __pyx_L1_error)
|
|
jpayne@69
|
11217 __pyx_v_self->__pyx_base.is_remote = hisremote(__pyx_t_6);
|
|
jpayne@69
|
11218
|
|
jpayne@69
|
11219 /* "pysam/libctabix.pyx":376
|
|
jpayne@69
|
11220 * self.is_remote = hisremote(self.filename)
|
|
jpayne@69
|
11221 *
|
|
jpayne@69
|
11222 * if not self.is_remote: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11223 * if not os.path.exists(filename):
|
|
jpayne@69
|
11224 * raise IOError("file `%s` not found" % filename)
|
|
jpayne@69
|
11225 */
|
|
jpayne@69
|
11226 __pyx_t_1 = (!__pyx_v_self->__pyx_base.is_remote);
|
|
jpayne@69
|
11227 if (__pyx_t_1) {
|
|
jpayne@69
|
11228
|
|
jpayne@69
|
11229 /* "pysam/libctabix.pyx":377
|
|
jpayne@69
|
11230 *
|
|
jpayne@69
|
11231 * if not self.is_remote:
|
|
jpayne@69
|
11232 * if not os.path.exists(filename): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11233 * raise IOError("file `%s` not found" % filename)
|
|
jpayne@69
|
11234 *
|
|
jpayne@69
|
11235 */
|
|
jpayne@69
|
11236 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_os); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 377, __pyx_L1_error)
|
|
jpayne@69
|
11237 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11238 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_path); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 377, __pyx_L1_error)
|
|
jpayne@69
|
11239 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
11240 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11241 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 377, __pyx_L1_error)
|
|
jpayne@69
|
11242 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11243 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
11244 __pyx_t_4 = NULL;
|
|
jpayne@69
|
11245 __pyx_t_5 = 0;
|
|
jpayne@69
|
11246 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
11247 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
11248 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
11249 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
11250 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
11251 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
11252 __Pyx_INCREF(function);
|
|
jpayne@69
|
11253 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
11254 __pyx_t_5 = 1;
|
|
jpayne@69
|
11255 }
|
|
jpayne@69
|
11256 }
|
|
jpayne@69
|
11257 #endif
|
|
jpayne@69
|
11258 {
|
|
jpayne@69
|
11259 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v_filename};
|
|
jpayne@69
|
11260 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
11261 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
11262 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 377, __pyx_L1_error)
|
|
jpayne@69
|
11263 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11264 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11265 }
|
|
jpayne@69
|
11266 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 377, __pyx_L1_error)
|
|
jpayne@69
|
11267 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11268 __pyx_t_7 = (!__pyx_t_1);
|
|
jpayne@69
|
11269 if (unlikely(__pyx_t_7)) {
|
|
jpayne@69
|
11270
|
|
jpayne@69
|
11271 /* "pysam/libctabix.pyx":378
|
|
jpayne@69
|
11272 * if not self.is_remote:
|
|
jpayne@69
|
11273 * if not os.path.exists(filename):
|
|
jpayne@69
|
11274 * raise IOError("file `%s` not found" % filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11275 *
|
|
jpayne@69
|
11276 * if not os.path.exists(filename_index):
|
|
jpayne@69
|
11277 */
|
|
jpayne@69
|
11278 __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_file_s_not_found, __pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 378, __pyx_L1_error)
|
|
jpayne@69
|
11279 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11280 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 378, __pyx_L1_error)
|
|
jpayne@69
|
11281 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11282 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11283 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
11284 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11285 __PYX_ERR(0, 378, __pyx_L1_error)
|
|
jpayne@69
|
11286
|
|
jpayne@69
|
11287 /* "pysam/libctabix.pyx":377
|
|
jpayne@69
|
11288 *
|
|
jpayne@69
|
11289 * if not self.is_remote:
|
|
jpayne@69
|
11290 * if not os.path.exists(filename): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11291 * raise IOError("file `%s` not found" % filename)
|
|
jpayne@69
|
11292 *
|
|
jpayne@69
|
11293 */
|
|
jpayne@69
|
11294 }
|
|
jpayne@69
|
11295
|
|
jpayne@69
|
11296 /* "pysam/libctabix.pyx":380
|
|
jpayne@69
|
11297 * raise IOError("file `%s` not found" % filename)
|
|
jpayne@69
|
11298 *
|
|
jpayne@69
|
11299 * if not os.path.exists(filename_index): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11300 * raise IOError("index `%s` not found" % filename_index)
|
|
jpayne@69
|
11301 *
|
|
jpayne@69
|
11302 */
|
|
jpayne@69
|
11303 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_os); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 380, __pyx_L1_error)
|
|
jpayne@69
|
11304 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11305 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_path); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 380, __pyx_L1_error)
|
|
jpayne@69
|
11306 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
11307 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11308 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_exists); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 380, __pyx_L1_error)
|
|
jpayne@69
|
11309 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11310 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
11311 __pyx_t_4 = NULL;
|
|
jpayne@69
|
11312 __pyx_t_5 = 0;
|
|
jpayne@69
|
11313 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
11314 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
11315 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
11316 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
11317 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
11318 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
11319 __Pyx_INCREF(function);
|
|
jpayne@69
|
11320 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
11321 __pyx_t_5 = 1;
|
|
jpayne@69
|
11322 }
|
|
jpayne@69
|
11323 }
|
|
jpayne@69
|
11324 #endif
|
|
jpayne@69
|
11325 {
|
|
jpayne@69
|
11326 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v_filename_index};
|
|
jpayne@69
|
11327 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
11328 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
11329 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 380, __pyx_L1_error)
|
|
jpayne@69
|
11330 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11331 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11332 }
|
|
jpayne@69
|
11333 __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 380, __pyx_L1_error)
|
|
jpayne@69
|
11334 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11335 __pyx_t_1 = (!__pyx_t_7);
|
|
jpayne@69
|
11336 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
11337
|
|
jpayne@69
|
11338 /* "pysam/libctabix.pyx":381
|
|
jpayne@69
|
11339 *
|
|
jpayne@69
|
11340 * if not os.path.exists(filename_index):
|
|
jpayne@69
|
11341 * raise IOError("index `%s` not found" % filename_index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11342 *
|
|
jpayne@69
|
11343 * # open file
|
|
jpayne@69
|
11344 */
|
|
jpayne@69
|
11345 __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_index_s_not_found, __pyx_v_filename_index); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 381, __pyx_L1_error)
|
|
jpayne@69
|
11346 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11347 __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 381, __pyx_L1_error)
|
|
jpayne@69
|
11348 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11349 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11350 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
11351 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11352 __PYX_ERR(0, 381, __pyx_L1_error)
|
|
jpayne@69
|
11353
|
|
jpayne@69
|
11354 /* "pysam/libctabix.pyx":380
|
|
jpayne@69
|
11355 * raise IOError("file `%s` not found" % filename)
|
|
jpayne@69
|
11356 *
|
|
jpayne@69
|
11357 * if not os.path.exists(filename_index): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11358 * raise IOError("index `%s` not found" % filename_index)
|
|
jpayne@69
|
11359 *
|
|
jpayne@69
|
11360 */
|
|
jpayne@69
|
11361 }
|
|
jpayne@69
|
11362
|
|
jpayne@69
|
11363 /* "pysam/libctabix.pyx":376
|
|
jpayne@69
|
11364 * self.is_remote = hisremote(self.filename)
|
|
jpayne@69
|
11365 *
|
|
jpayne@69
|
11366 * if not self.is_remote: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11367 * if not os.path.exists(filename):
|
|
jpayne@69
|
11368 * raise IOError("file `%s` not found" % filename)
|
|
jpayne@69
|
11369 */
|
|
jpayne@69
|
11370 }
|
|
jpayne@69
|
11371
|
|
jpayne@69
|
11372 /* "pysam/libctabix.pyx":384
|
|
jpayne@69
|
11373 *
|
|
jpayne@69
|
11374 * # open file
|
|
jpayne@69
|
11375 * cdef char *cfilename = self.filename # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11376 * cdef char *cfilename_index = self.filename_index
|
|
jpayne@69
|
11377 * with nogil:
|
|
jpayne@69
|
11378 */
|
|
jpayne@69
|
11379 __pyx_t_8 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.filename); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 384, __pyx_L1_error)
|
|
jpayne@69
|
11380 __pyx_v_cfilename = __pyx_t_8;
|
|
jpayne@69
|
11381
|
|
jpayne@69
|
11382 /* "pysam/libctabix.pyx":385
|
|
jpayne@69
|
11383 * # open file
|
|
jpayne@69
|
11384 * cdef char *cfilename = self.filename
|
|
jpayne@69
|
11385 * cdef char *cfilename_index = self.filename_index # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11386 * with nogil:
|
|
jpayne@69
|
11387 * self.htsfile = hts_open(cfilename, 'r')
|
|
jpayne@69
|
11388 */
|
|
jpayne@69
|
11389 __pyx_t_8 = __Pyx_PyObject_AsWritableString(__pyx_v_self->filename_index); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 385, __pyx_L1_error)
|
|
jpayne@69
|
11390 __pyx_v_cfilename_index = __pyx_t_8;
|
|
jpayne@69
|
11391
|
|
jpayne@69
|
11392 /* "pysam/libctabix.pyx":386
|
|
jpayne@69
|
11393 * cdef char *cfilename = self.filename
|
|
jpayne@69
|
11394 * cdef char *cfilename_index = self.filename_index
|
|
jpayne@69
|
11395 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11396 * self.htsfile = hts_open(cfilename, 'r')
|
|
jpayne@69
|
11397 *
|
|
jpayne@69
|
11398 */
|
|
jpayne@69
|
11399 {
|
|
jpayne@69
|
11400 #ifdef WITH_THREAD
|
|
jpayne@69
|
11401 PyThreadState *_save;
|
|
jpayne@69
|
11402 _save = NULL;
|
|
jpayne@69
|
11403 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
11404 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
11405 #endif
|
|
jpayne@69
|
11406 /*try:*/ {
|
|
jpayne@69
|
11407
|
|
jpayne@69
|
11408 /* "pysam/libctabix.pyx":387
|
|
jpayne@69
|
11409 * cdef char *cfilename_index = self.filename_index
|
|
jpayne@69
|
11410 * with nogil:
|
|
jpayne@69
|
11411 * self.htsfile = hts_open(cfilename, 'r') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11412 *
|
|
jpayne@69
|
11413 * if self.htsfile == NULL:
|
|
jpayne@69
|
11414 */
|
|
jpayne@69
|
11415 __pyx_v_self->__pyx_base.htsfile = hts_open(__pyx_v_cfilename, ((char const *)"r"));
|
|
jpayne@69
|
11416 }
|
|
jpayne@69
|
11417
|
|
jpayne@69
|
11418 /* "pysam/libctabix.pyx":386
|
|
jpayne@69
|
11419 * cdef char *cfilename = self.filename
|
|
jpayne@69
|
11420 * cdef char *cfilename_index = self.filename_index
|
|
jpayne@69
|
11421 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11422 * self.htsfile = hts_open(cfilename, 'r')
|
|
jpayne@69
|
11423 *
|
|
jpayne@69
|
11424 */
|
|
jpayne@69
|
11425 /*finally:*/ {
|
|
jpayne@69
|
11426 /*normal exit:*/{
|
|
jpayne@69
|
11427 #ifdef WITH_THREAD
|
|
jpayne@69
|
11428 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
11429 Py_BLOCK_THREADS
|
|
jpayne@69
|
11430 #endif
|
|
jpayne@69
|
11431 goto __pyx_L12;
|
|
jpayne@69
|
11432 }
|
|
jpayne@69
|
11433 __pyx_L12:;
|
|
jpayne@69
|
11434 }
|
|
jpayne@69
|
11435 }
|
|
jpayne@69
|
11436
|
|
jpayne@69
|
11437 /* "pysam/libctabix.pyx":389
|
|
jpayne@69
|
11438 * self.htsfile = hts_open(cfilename, 'r')
|
|
jpayne@69
|
11439 *
|
|
jpayne@69
|
11440 * if self.htsfile == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11441 * raise IOError("could not open file `%s`" % filename)
|
|
jpayne@69
|
11442 *
|
|
jpayne@69
|
11443 */
|
|
jpayne@69
|
11444 __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile == NULL);
|
|
jpayne@69
|
11445 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
11446
|
|
jpayne@69
|
11447 /* "pysam/libctabix.pyx":390
|
|
jpayne@69
|
11448 *
|
|
jpayne@69
|
11449 * if self.htsfile == NULL:
|
|
jpayne@69
|
11450 * raise IOError("could not open file `%s`" % filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11451 *
|
|
jpayne@69
|
11452 * #if self.htsfile.format.category != region_list:
|
|
jpayne@69
|
11453 */
|
|
jpayne@69
|
11454 __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_file_s, __pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 390, __pyx_L1_error)
|
|
jpayne@69
|
11455 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11456 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 390, __pyx_L1_error)
|
|
jpayne@69
|
11457 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11458 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11459 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
11460 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11461 __PYX_ERR(0, 390, __pyx_L1_error)
|
|
jpayne@69
|
11462
|
|
jpayne@69
|
11463 /* "pysam/libctabix.pyx":389
|
|
jpayne@69
|
11464 * self.htsfile = hts_open(cfilename, 'r')
|
|
jpayne@69
|
11465 *
|
|
jpayne@69
|
11466 * if self.htsfile == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11467 * raise IOError("could not open file `%s`" % filename)
|
|
jpayne@69
|
11468 *
|
|
jpayne@69
|
11469 */
|
|
jpayne@69
|
11470 }
|
|
jpayne@69
|
11471
|
|
jpayne@69
|
11472 /* "pysam/libctabix.pyx":395
|
|
jpayne@69
|
11473 * # raise ValueError("file does not contain region data")
|
|
jpayne@69
|
11474 *
|
|
jpayne@69
|
11475 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11476 * self.index = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
11477 *
|
|
jpayne@69
|
11478 */
|
|
jpayne@69
|
11479 {
|
|
jpayne@69
|
11480 #ifdef WITH_THREAD
|
|
jpayne@69
|
11481 PyThreadState *_save;
|
|
jpayne@69
|
11482 _save = NULL;
|
|
jpayne@69
|
11483 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
11484 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
11485 #endif
|
|
jpayne@69
|
11486 /*try:*/ {
|
|
jpayne@69
|
11487
|
|
jpayne@69
|
11488 /* "pysam/libctabix.pyx":396
|
|
jpayne@69
|
11489 *
|
|
jpayne@69
|
11490 * with nogil:
|
|
jpayne@69
|
11491 * self.index = tbx_index_load2(cfilename, cfilename_index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11492 *
|
|
jpayne@69
|
11493 * if self.index == NULL:
|
|
jpayne@69
|
11494 */
|
|
jpayne@69
|
11495 __pyx_v_self->index = tbx_index_load2(__pyx_v_cfilename, __pyx_v_cfilename_index);
|
|
jpayne@69
|
11496 }
|
|
jpayne@69
|
11497
|
|
jpayne@69
|
11498 /* "pysam/libctabix.pyx":395
|
|
jpayne@69
|
11499 * # raise ValueError("file does not contain region data")
|
|
jpayne@69
|
11500 *
|
|
jpayne@69
|
11501 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11502 * self.index = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
11503 *
|
|
jpayne@69
|
11504 */
|
|
jpayne@69
|
11505 /*finally:*/ {
|
|
jpayne@69
|
11506 /*normal exit:*/{
|
|
jpayne@69
|
11507 #ifdef WITH_THREAD
|
|
jpayne@69
|
11508 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
11509 Py_BLOCK_THREADS
|
|
jpayne@69
|
11510 #endif
|
|
jpayne@69
|
11511 goto __pyx_L16;
|
|
jpayne@69
|
11512 }
|
|
jpayne@69
|
11513 __pyx_L16:;
|
|
jpayne@69
|
11514 }
|
|
jpayne@69
|
11515 }
|
|
jpayne@69
|
11516
|
|
jpayne@69
|
11517 /* "pysam/libctabix.pyx":398
|
|
jpayne@69
|
11518 * self.index = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
11519 *
|
|
jpayne@69
|
11520 * if self.index == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11521 * raise IOError("could not open index for `%s`" % filename)
|
|
jpayne@69
|
11522 *
|
|
jpayne@69
|
11523 */
|
|
jpayne@69
|
11524 __pyx_t_1 = (__pyx_v_self->index == NULL);
|
|
jpayne@69
|
11525 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
11526
|
|
jpayne@69
|
11527 /* "pysam/libctabix.pyx":399
|
|
jpayne@69
|
11528 *
|
|
jpayne@69
|
11529 * if self.index == NULL:
|
|
jpayne@69
|
11530 * raise IOError("could not open index for `%s`" % filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11531 *
|
|
jpayne@69
|
11532 * if not self.is_stream:
|
|
jpayne@69
|
11533 */
|
|
jpayne@69
|
11534 __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_index_for_s, __pyx_v_filename); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 399, __pyx_L1_error)
|
|
jpayne@69
|
11535 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11536 __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 399, __pyx_L1_error)
|
|
jpayne@69
|
11537 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11538 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11539 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
11540 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11541 __PYX_ERR(0, 399, __pyx_L1_error)
|
|
jpayne@69
|
11542
|
|
jpayne@69
|
11543 /* "pysam/libctabix.pyx":398
|
|
jpayne@69
|
11544 * self.index = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
11545 *
|
|
jpayne@69
|
11546 * if self.index == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11547 * raise IOError("could not open index for `%s`" % filename)
|
|
jpayne@69
|
11548 *
|
|
jpayne@69
|
11549 */
|
|
jpayne@69
|
11550 }
|
|
jpayne@69
|
11551
|
|
jpayne@69
|
11552 /* "pysam/libctabix.pyx":401
|
|
jpayne@69
|
11553 * raise IOError("could not open index for `%s`" % filename)
|
|
jpayne@69
|
11554 *
|
|
jpayne@69
|
11555 * if not self.is_stream: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11556 * self.start_offset = self.tell()
|
|
jpayne@69
|
11557 *
|
|
jpayne@69
|
11558 */
|
|
jpayne@69
|
11559 __pyx_t_1 = (!__pyx_v_self->__pyx_base.is_stream);
|
|
jpayne@69
|
11560 if (__pyx_t_1) {
|
|
jpayne@69
|
11561
|
|
jpayne@69
|
11562 /* "pysam/libctabix.pyx":402
|
|
jpayne@69
|
11563 *
|
|
jpayne@69
|
11564 * if not self.is_stream:
|
|
jpayne@69
|
11565 * self.start_offset = self.tell() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11566 *
|
|
jpayne@69
|
11567 * def _dup(self):
|
|
jpayne@69
|
11568 */
|
|
jpayne@69
|
11569 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_tell); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 402, __pyx_L1_error)
|
|
jpayne@69
|
11570 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11571 __pyx_t_4 = NULL;
|
|
jpayne@69
|
11572 __pyx_t_5 = 0;
|
|
jpayne@69
|
11573 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
11574 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
11575 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
11576 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
11577 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
11578 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
11579 __Pyx_INCREF(function);
|
|
jpayne@69
|
11580 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
11581 __pyx_t_5 = 1;
|
|
jpayne@69
|
11582 }
|
|
jpayne@69
|
11583 }
|
|
jpayne@69
|
11584 #endif
|
|
jpayne@69
|
11585 {
|
|
jpayne@69
|
11586 PyObject *__pyx_callargs[2] = {__pyx_t_4, NULL};
|
|
jpayne@69
|
11587 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5);
|
|
jpayne@69
|
11588 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
11589 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 402, __pyx_L1_error)
|
|
jpayne@69
|
11590 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11591 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11592 }
|
|
jpayne@69
|
11593 __pyx_t_9 = __Pyx_PyInt_As_int64_t(__pyx_t_3); if (unlikely((__pyx_t_9 == ((int64_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 402, __pyx_L1_error)
|
|
jpayne@69
|
11594 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11595 __pyx_v_self->__pyx_base.start_offset = __pyx_t_9;
|
|
jpayne@69
|
11596
|
|
jpayne@69
|
11597 /* "pysam/libctabix.pyx":401
|
|
jpayne@69
|
11598 * raise IOError("could not open index for `%s`" % filename)
|
|
jpayne@69
|
11599 *
|
|
jpayne@69
|
11600 * if not self.is_stream: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11601 * self.start_offset = self.tell()
|
|
jpayne@69
|
11602 *
|
|
jpayne@69
|
11603 */
|
|
jpayne@69
|
11604 }
|
|
jpayne@69
|
11605
|
|
jpayne@69
|
11606 /* "pysam/libctabix.pyx":352
|
|
jpayne@69
|
11607 * self.encoding = encoding
|
|
jpayne@69
|
11608 *
|
|
jpayne@69
|
11609 * def _open( self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11610 * filename,
|
|
jpayne@69
|
11611 * mode='r',
|
|
jpayne@69
|
11612 */
|
|
jpayne@69
|
11613
|
|
jpayne@69
|
11614 /* function exit code */
|
|
jpayne@69
|
11615 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
11616 goto __pyx_L0;
|
|
jpayne@69
|
11617 __pyx_L1_error:;
|
|
jpayne@69
|
11618 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
11619 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
11620 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
11621 __Pyx_AddTraceback("pysam.libctabix.TabixFile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
11622 __pyx_r = NULL;
|
|
jpayne@69
|
11623 __pyx_L0:;
|
|
jpayne@69
|
11624 __Pyx_XDECREF(__pyx_v_filename_index);
|
|
jpayne@69
|
11625 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
11626 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
11627 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11628 return __pyx_r;
|
|
jpayne@69
|
11629 }
|
|
jpayne@69
|
11630
|
|
jpayne@69
|
11631 /* "pysam/libctabix.pyx":404
|
|
jpayne@69
|
11632 * self.start_offset = self.tell()
|
|
jpayne@69
|
11633 *
|
|
jpayne@69
|
11634 * def _dup(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11635 * '''return a copy of this tabix file.
|
|
jpayne@69
|
11636 *
|
|
jpayne@69
|
11637 */
|
|
jpayne@69
|
11638
|
|
jpayne@69
|
11639 /* Python wrapper */
|
|
jpayne@69
|
11640 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup(PyObject *__pyx_v_self,
|
|
jpayne@69
|
11641 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11642 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
11643 #else
|
|
jpayne@69
|
11644 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
11645 #endif
|
|
jpayne@69
|
11646 ); /*proto*/
|
|
jpayne@69
|
11647 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_4_dup, "TabixFile._dup(self)\nreturn a copy of this tabix file.\n \n The file is being re-opened.\n ");
|
|
jpayne@69
|
11648 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_5_dup = {"_dup", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_4_dup};
|
|
jpayne@69
|
11649 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup(PyObject *__pyx_v_self,
|
|
jpayne@69
|
11650 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11651 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
11652 #else
|
|
jpayne@69
|
11653 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
11654 #endif
|
|
jpayne@69
|
11655 ) {
|
|
jpayne@69
|
11656 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11657 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
11658 #endif
|
|
jpayne@69
|
11659 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
11660 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
11661 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
11662 __Pyx_RefNannySetupContext("_dup (wrapper)", 0);
|
|
jpayne@69
|
11663 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11664 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
11665 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
11666 #else
|
|
jpayne@69
|
11667 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
11668 #endif
|
|
jpayne@69
|
11669 #endif
|
|
jpayne@69
|
11670 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
11671 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
11672 __Pyx_RaiseArgtupleInvalid("_dup", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
11673 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "_dup", 0))) return NULL;
|
|
jpayne@69
|
11674 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_4_dup(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
11675
|
|
jpayne@69
|
11676 /* function exit code */
|
|
jpayne@69
|
11677 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11678 return __pyx_r;
|
|
jpayne@69
|
11679 }
|
|
jpayne@69
|
11680
|
|
jpayne@69
|
11681 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_4_dup(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
11682 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
11683 __Pyx_TraceDeclarations
|
|
jpayne@69
|
11684 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
11685 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
11686 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
11687 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
11688 int __pyx_lineno = 0;
|
|
jpayne@69
|
11689 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
11690 int __pyx_clineno = 0;
|
|
jpayne@69
|
11691 __Pyx_TraceFrameInit(__pyx_codeobj__17)
|
|
jpayne@69
|
11692 __Pyx_RefNannySetupContext("_dup", 1);
|
|
jpayne@69
|
11693 __Pyx_TraceCall("_dup", __pyx_f[0], 404, 0, __PYX_ERR(0, 404, __pyx_L1_error));
|
|
jpayne@69
|
11694
|
|
jpayne@69
|
11695 /* "pysam/libctabix.pyx":409
|
|
jpayne@69
|
11696 * The file is being re-opened.
|
|
jpayne@69
|
11697 * '''
|
|
jpayne@69
|
11698 * return TabixFile(self.filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11699 * mode="r",
|
|
jpayne@69
|
11700 * threads=self.threads,
|
|
jpayne@69
|
11701 */
|
|
jpayne@69
|
11702 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
11703 __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 409, __pyx_L1_error)
|
|
jpayne@69
|
11704 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
11705 __Pyx_INCREF(__pyx_v_self->__pyx_base.filename);
|
|
jpayne@69
|
11706 __Pyx_GIVEREF(__pyx_v_self->__pyx_base.filename);
|
|
jpayne@69
|
11707 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.filename)) __PYX_ERR(0, 409, __pyx_L1_error);
|
|
jpayne@69
|
11708
|
|
jpayne@69
|
11709 /* "pysam/libctabix.pyx":410
|
|
jpayne@69
|
11710 * '''
|
|
jpayne@69
|
11711 * return TabixFile(self.filename,
|
|
jpayne@69
|
11712 * mode="r", # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11713 * threads=self.threads,
|
|
jpayne@69
|
11714 * parser=self.parser,
|
|
jpayne@69
|
11715 */
|
|
jpayne@69
|
11716 __pyx_t_2 = __Pyx_PyDict_NewPresized(5); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 410, __pyx_L1_error)
|
|
jpayne@69
|
11717 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
11718 if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_mode, __pyx_n_u_r) < 0) __PYX_ERR(0, 410, __pyx_L1_error)
|
|
jpayne@69
|
11719
|
|
jpayne@69
|
11720 /* "pysam/libctabix.pyx":411
|
|
jpayne@69
|
11721 * return TabixFile(self.filename,
|
|
jpayne@69
|
11722 * mode="r",
|
|
jpayne@69
|
11723 * threads=self.threads, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11724 * parser=self.parser,
|
|
jpayne@69
|
11725 * index=self.filename_index,
|
|
jpayne@69
|
11726 */
|
|
jpayne@69
|
11727 if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_threads, __pyx_v_self->__pyx_base.threads) < 0) __PYX_ERR(0, 410, __pyx_L1_error)
|
|
jpayne@69
|
11728
|
|
jpayne@69
|
11729 /* "pysam/libctabix.pyx":412
|
|
jpayne@69
|
11730 * mode="r",
|
|
jpayne@69
|
11731 * threads=self.threads,
|
|
jpayne@69
|
11732 * parser=self.parser, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11733 * index=self.filename_index,
|
|
jpayne@69
|
11734 * encoding=self.encoding)
|
|
jpayne@69
|
11735 */
|
|
jpayne@69
|
11736 if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_parser, ((PyObject *)__pyx_v_self->parser)) < 0) __PYX_ERR(0, 410, __pyx_L1_error)
|
|
jpayne@69
|
11737
|
|
jpayne@69
|
11738 /* "pysam/libctabix.pyx":413
|
|
jpayne@69
|
11739 * threads=self.threads,
|
|
jpayne@69
|
11740 * parser=self.parser,
|
|
jpayne@69
|
11741 * index=self.filename_index, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11742 * encoding=self.encoding)
|
|
jpayne@69
|
11743 *
|
|
jpayne@69
|
11744 */
|
|
jpayne@69
|
11745 if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_index, __pyx_v_self->filename_index) < 0) __PYX_ERR(0, 410, __pyx_L1_error)
|
|
jpayne@69
|
11746
|
|
jpayne@69
|
11747 /* "pysam/libctabix.pyx":414
|
|
jpayne@69
|
11748 * parser=self.parser,
|
|
jpayne@69
|
11749 * index=self.filename_index,
|
|
jpayne@69
|
11750 * encoding=self.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11751 *
|
|
jpayne@69
|
11752 * def fetch(self,
|
|
jpayne@69
|
11753 */
|
|
jpayne@69
|
11754 if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_encoding, __pyx_v_self->encoding) < 0) __PYX_ERR(0, 410, __pyx_L1_error)
|
|
jpayne@69
|
11755
|
|
jpayne@69
|
11756 /* "pysam/libctabix.pyx":409
|
|
jpayne@69
|
11757 * The file is being re-opened.
|
|
jpayne@69
|
11758 * '''
|
|
jpayne@69
|
11759 * return TabixFile(self.filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11760 * mode="r",
|
|
jpayne@69
|
11761 * threads=self.threads,
|
|
jpayne@69
|
11762 */
|
|
jpayne@69
|
11763 __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile), __pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 409, __pyx_L1_error)
|
|
jpayne@69
|
11764 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11765 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
11766 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
11767 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
11768 __pyx_t_3 = 0;
|
|
jpayne@69
|
11769 goto __pyx_L0;
|
|
jpayne@69
|
11770
|
|
jpayne@69
|
11771 /* "pysam/libctabix.pyx":404
|
|
jpayne@69
|
11772 * self.start_offset = self.tell()
|
|
jpayne@69
|
11773 *
|
|
jpayne@69
|
11774 * def _dup(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11775 * '''return a copy of this tabix file.
|
|
jpayne@69
|
11776 *
|
|
jpayne@69
|
11777 */
|
|
jpayne@69
|
11778
|
|
jpayne@69
|
11779 /* function exit code */
|
|
jpayne@69
|
11780 __pyx_L1_error:;
|
|
jpayne@69
|
11781 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
11782 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
11783 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
11784 __Pyx_AddTraceback("pysam.libctabix.TabixFile._dup", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
11785 __pyx_r = NULL;
|
|
jpayne@69
|
11786 __pyx_L0:;
|
|
jpayne@69
|
11787 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
11788 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
11789 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11790 return __pyx_r;
|
|
jpayne@69
|
11791 }
|
|
jpayne@69
|
11792
|
|
jpayne@69
|
11793 /* "pysam/libctabix.pyx":416
|
|
jpayne@69
|
11794 * encoding=self.encoding)
|
|
jpayne@69
|
11795 *
|
|
jpayne@69
|
11796 * def fetch(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11797 * reference=None,
|
|
jpayne@69
|
11798 * start=None,
|
|
jpayne@69
|
11799 */
|
|
jpayne@69
|
11800
|
|
jpayne@69
|
11801 /* Python wrapper */
|
|
jpayne@69
|
11802 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch(PyObject *__pyx_v_self,
|
|
jpayne@69
|
11803 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11804 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
11805 #else
|
|
jpayne@69
|
11806 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
11807 #endif
|
|
jpayne@69
|
11808 ); /*proto*/
|
|
jpayne@69
|
11809 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_6fetch, "TabixFile.fetch(self, reference=None, start=None, end=None, region=None, parser=None, multiple_iterators=False)\nfetch one or more rows in a :term:`region` using 0-based\n indexing. The region is specified by :term:`reference`,\n *start* and *end*. Alternatively, a samtools :term:`region`\n string can be supplied.\n\n Without *reference* or *region* all entries will be fetched. \n \n If only *reference* is set, all reads matching on *reference*\n will be fetched.\n\n If *parser* is None, the default parser will be used for\n parsing.\n \n Set *multiple_iterators* to true if you will be using multiple\n iterators on the same file at the same time. The iterator\n returned will receive its own copy of a filehandle to the file\n effectively re-opening the file. Re-opening a file creates\n some overhead, so beware.\n\n ");
|
|
jpayne@69
|
11810 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_7fetch = {"fetch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_6fetch};
|
|
jpayne@69
|
11811 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch(PyObject *__pyx_v_self,
|
|
jpayne@69
|
11812 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11813 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
11814 #else
|
|
jpayne@69
|
11815 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
11816 #endif
|
|
jpayne@69
|
11817 ) {
|
|
jpayne@69
|
11818 PyObject *__pyx_v_reference = 0;
|
|
jpayne@69
|
11819 PyObject *__pyx_v_start = 0;
|
|
jpayne@69
|
11820 PyObject *__pyx_v_end = 0;
|
|
jpayne@69
|
11821 PyObject *__pyx_v_region = 0;
|
|
jpayne@69
|
11822 PyObject *__pyx_v_parser = 0;
|
|
jpayne@69
|
11823 PyObject *__pyx_v_multiple_iterators = 0;
|
|
jpayne@69
|
11824 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11825 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
11826 #endif
|
|
jpayne@69
|
11827 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
11828 PyObject* values[6] = {0,0,0,0,0,0};
|
|
jpayne@69
|
11829 int __pyx_lineno = 0;
|
|
jpayne@69
|
11830 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
11831 int __pyx_clineno = 0;
|
|
jpayne@69
|
11832 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
11833 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
11834 __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
|
|
jpayne@69
|
11835 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
11836 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
11837 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
11838 #else
|
|
jpayne@69
|
11839 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
11840 #endif
|
|
jpayne@69
|
11841 #endif
|
|
jpayne@69
|
11842 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
11843 {
|
|
jpayne@69
|
11844 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_reference,&__pyx_n_s_start,&__pyx_n_s_end,&__pyx_n_s_region,&__pyx_n_s_parser,&__pyx_n_s_multiple_iterators,0};
|
|
jpayne@69
|
11845
|
|
jpayne@69
|
11846 /* "pysam/libctabix.pyx":417
|
|
jpayne@69
|
11847 *
|
|
jpayne@69
|
11848 * def fetch(self,
|
|
jpayne@69
|
11849 * reference=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11850 * start=None,
|
|
jpayne@69
|
11851 * end=None,
|
|
jpayne@69
|
11852 */
|
|
jpayne@69
|
11853 values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
11854
|
|
jpayne@69
|
11855 /* "pysam/libctabix.pyx":418
|
|
jpayne@69
|
11856 * def fetch(self,
|
|
jpayne@69
|
11857 * reference=None,
|
|
jpayne@69
|
11858 * start=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11859 * end=None,
|
|
jpayne@69
|
11860 * region=None,
|
|
jpayne@69
|
11861 */
|
|
jpayne@69
|
11862 values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
11863
|
|
jpayne@69
|
11864 /* "pysam/libctabix.pyx":419
|
|
jpayne@69
|
11865 * reference=None,
|
|
jpayne@69
|
11866 * start=None,
|
|
jpayne@69
|
11867 * end=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11868 * region=None,
|
|
jpayne@69
|
11869 * parser=None,
|
|
jpayne@69
|
11870 */
|
|
jpayne@69
|
11871 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
11872
|
|
jpayne@69
|
11873 /* "pysam/libctabix.pyx":420
|
|
jpayne@69
|
11874 * start=None,
|
|
jpayne@69
|
11875 * end=None,
|
|
jpayne@69
|
11876 * region=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11877 * parser=None,
|
|
jpayne@69
|
11878 * multiple_iterators=False):
|
|
jpayne@69
|
11879 */
|
|
jpayne@69
|
11880 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
11881
|
|
jpayne@69
|
11882 /* "pysam/libctabix.pyx":421
|
|
jpayne@69
|
11883 * end=None,
|
|
jpayne@69
|
11884 * region=None,
|
|
jpayne@69
|
11885 * parser=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11886 * multiple_iterators=False):
|
|
jpayne@69
|
11887 * '''fetch one or more rows in a :term:`region` using 0-based
|
|
jpayne@69
|
11888 */
|
|
jpayne@69
|
11889 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
11890
|
|
jpayne@69
|
11891 /* "pysam/libctabix.pyx":422
|
|
jpayne@69
|
11892 * region=None,
|
|
jpayne@69
|
11893 * parser=None,
|
|
jpayne@69
|
11894 * multiple_iterators=False): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11895 * '''fetch one or more rows in a :term:`region` using 0-based
|
|
jpayne@69
|
11896 * indexing. The region is specified by :term:`reference`,
|
|
jpayne@69
|
11897 */
|
|
jpayne@69
|
11898 values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_False));
|
|
jpayne@69
|
11899 if (__pyx_kwds) {
|
|
jpayne@69
|
11900 Py_ssize_t kw_args;
|
|
jpayne@69
|
11901 switch (__pyx_nargs) {
|
|
jpayne@69
|
11902 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
11903 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11904 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
11905 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11906 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
11907 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11908 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
11909 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11910 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
11911 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11912 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
11913 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11914 case 0: break;
|
|
jpayne@69
|
11915 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
11916 }
|
|
jpayne@69
|
11917 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
11918 switch (__pyx_nargs) {
|
|
jpayne@69
|
11919 case 0:
|
|
jpayne@69
|
11920 if (kw_args > 0) {
|
|
jpayne@69
|
11921 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_reference);
|
|
jpayne@69
|
11922 if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
11923 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11924 }
|
|
jpayne@69
|
11925 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11926 case 1:
|
|
jpayne@69
|
11927 if (kw_args > 0) {
|
|
jpayne@69
|
11928 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start);
|
|
jpayne@69
|
11929 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
11930 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11931 }
|
|
jpayne@69
|
11932 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11933 case 2:
|
|
jpayne@69
|
11934 if (kw_args > 0) {
|
|
jpayne@69
|
11935 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end);
|
|
jpayne@69
|
11936 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
11937 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11938 }
|
|
jpayne@69
|
11939 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11940 case 3:
|
|
jpayne@69
|
11941 if (kw_args > 0) {
|
|
jpayne@69
|
11942 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_region);
|
|
jpayne@69
|
11943 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
11944 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11945 }
|
|
jpayne@69
|
11946 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11947 case 4:
|
|
jpayne@69
|
11948 if (kw_args > 0) {
|
|
jpayne@69
|
11949 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser);
|
|
jpayne@69
|
11950 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
11951 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11952 }
|
|
jpayne@69
|
11953 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11954 case 5:
|
|
jpayne@69
|
11955 if (kw_args > 0) {
|
|
jpayne@69
|
11956 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_multiple_iterators);
|
|
jpayne@69
|
11957 if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
11958 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11959 }
|
|
jpayne@69
|
11960 }
|
|
jpayne@69
|
11961 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
11962 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
11963 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "fetch") < 0)) __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11964 }
|
|
jpayne@69
|
11965 } else {
|
|
jpayne@69
|
11966 switch (__pyx_nargs) {
|
|
jpayne@69
|
11967 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
11968 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11969 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
11970 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11971 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
11972 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11973 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
11974 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11975 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
11976 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11977 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
11978 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
11979 case 0: break;
|
|
jpayne@69
|
11980 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
11981 }
|
|
jpayne@69
|
11982 }
|
|
jpayne@69
|
11983 __pyx_v_reference = values[0];
|
|
jpayne@69
|
11984 __pyx_v_start = values[1];
|
|
jpayne@69
|
11985 __pyx_v_end = values[2];
|
|
jpayne@69
|
11986 __pyx_v_region = values[3];
|
|
jpayne@69
|
11987 __pyx_v_parser = values[4];
|
|
jpayne@69
|
11988 __pyx_v_multiple_iterators = values[5];
|
|
jpayne@69
|
11989 }
|
|
jpayne@69
|
11990 goto __pyx_L6_skip;
|
|
jpayne@69
|
11991 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
11992 __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, __pyx_nargs); __PYX_ERR(0, 416, __pyx_L3_error)
|
|
jpayne@69
|
11993 __pyx_L6_skip:;
|
|
jpayne@69
|
11994 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
11995 __pyx_L3_error:;
|
|
jpayne@69
|
11996 {
|
|
jpayne@69
|
11997 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
11998 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
11999 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
12000 }
|
|
jpayne@69
|
12001 }
|
|
jpayne@69
|
12002 __Pyx_AddTraceback("pysam.libctabix.TabixFile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
12003 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
12004 return NULL;
|
|
jpayne@69
|
12005 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
12006 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_6fetch(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_parser, __pyx_v_multiple_iterators);
|
|
jpayne@69
|
12007
|
|
jpayne@69
|
12008 /* "pysam/libctabix.pyx":416
|
|
jpayne@69
|
12009 * encoding=self.encoding)
|
|
jpayne@69
|
12010 *
|
|
jpayne@69
|
12011 * def fetch(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12012 * reference=None,
|
|
jpayne@69
|
12013 * start=None,
|
|
jpayne@69
|
12014 */
|
|
jpayne@69
|
12015
|
|
jpayne@69
|
12016 /* function exit code */
|
|
jpayne@69
|
12017 {
|
|
jpayne@69
|
12018 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
12019 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
12020 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
12021 }
|
|
jpayne@69
|
12022 }
|
|
jpayne@69
|
12023 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
12024 return __pyx_r;
|
|
jpayne@69
|
12025 }
|
|
jpayne@69
|
12026
|
|
jpayne@69
|
12027 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6fetch(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser, PyObject *__pyx_v_multiple_iterators) {
|
|
jpayne@69
|
12028 hts_itr_t *__pyx_v_itr;
|
|
jpayne@69
|
12029 char *__pyx_v_cstr;
|
|
jpayne@69
|
12030 struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_fileobj = 0;
|
|
jpayne@69
|
12031 PyObject *__pyx_v_s = NULL;
|
|
jpayne@69
|
12032 struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_a = 0;
|
|
jpayne@69
|
12033 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
12034 __Pyx_TraceDeclarations
|
|
jpayne@69
|
12035 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
12036 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
12037 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
12038 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
12039 unsigned int __pyx_t_4;
|
|
jpayne@69
|
12040 int __pyx_t_5;
|
|
jpayne@69
|
12041 int __pyx_t_6;
|
|
jpayne@69
|
12042 struct __pyx_opt_args_5pysam_9libcutils_force_bytes __pyx_t_7;
|
|
jpayne@69
|
12043 char *__pyx_t_8;
|
|
jpayne@69
|
12044 Py_ssize_t __pyx_t_9;
|
|
jpayne@69
|
12045 int __pyx_lineno = 0;
|
|
jpayne@69
|
12046 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
12047 int __pyx_clineno = 0;
|
|
jpayne@69
|
12048 __Pyx_TraceFrameInit(__pyx_codeobj__18)
|
|
jpayne@69
|
12049 __Pyx_RefNannySetupContext("fetch", 0);
|
|
jpayne@69
|
12050 __Pyx_TraceCall("fetch", __pyx_f[0], 416, 0, __PYX_ERR(0, 416, __pyx_L1_error));
|
|
jpayne@69
|
12051 __Pyx_INCREF(__pyx_v_start);
|
|
jpayne@69
|
12052 __Pyx_INCREF(__pyx_v_region);
|
|
jpayne@69
|
12053 __Pyx_INCREF(__pyx_v_parser);
|
|
jpayne@69
|
12054
|
|
jpayne@69
|
12055 /* "pysam/libctabix.pyx":443
|
|
jpayne@69
|
12056 *
|
|
jpayne@69
|
12057 * '''
|
|
jpayne@69
|
12058 * if not self.is_open(): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12059 * raise ValueError("I/O operation on closed file")
|
|
jpayne@69
|
12060 *
|
|
jpayne@69
|
12061 */
|
|
jpayne@69
|
12062 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_is_open); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 443, __pyx_L1_error)
|
|
jpayne@69
|
12063 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12064 __pyx_t_3 = NULL;
|
|
jpayne@69
|
12065 __pyx_t_4 = 0;
|
|
jpayne@69
|
12066 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
12067 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
12068 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
12069 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
12070 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
12071 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
12072 __Pyx_INCREF(function);
|
|
jpayne@69
|
12073 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
12074 __pyx_t_4 = 1;
|
|
jpayne@69
|
12075 }
|
|
jpayne@69
|
12076 }
|
|
jpayne@69
|
12077 #endif
|
|
jpayne@69
|
12078 {
|
|
jpayne@69
|
12079 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
|
|
jpayne@69
|
12080 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
|
|
jpayne@69
|
12081 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12082 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 443, __pyx_L1_error)
|
|
jpayne@69
|
12083 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12084 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12085 }
|
|
jpayne@69
|
12086 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 443, __pyx_L1_error)
|
|
jpayne@69
|
12087 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12088 __pyx_t_6 = (!__pyx_t_5);
|
|
jpayne@69
|
12089 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
12090
|
|
jpayne@69
|
12091 /* "pysam/libctabix.pyx":444
|
|
jpayne@69
|
12092 * '''
|
|
jpayne@69
|
12093 * if not self.is_open():
|
|
jpayne@69
|
12094 * raise ValueError("I/O operation on closed file") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12095 *
|
|
jpayne@69
|
12096 * # convert coordinates to region string, which is one-based
|
|
jpayne@69
|
12097 */
|
|
jpayne@69
|
12098 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 444, __pyx_L1_error)
|
|
jpayne@69
|
12099 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12100 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
12101 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12102 __PYX_ERR(0, 444, __pyx_L1_error)
|
|
jpayne@69
|
12103
|
|
jpayne@69
|
12104 /* "pysam/libctabix.pyx":443
|
|
jpayne@69
|
12105 *
|
|
jpayne@69
|
12106 * '''
|
|
jpayne@69
|
12107 * if not self.is_open(): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12108 * raise ValueError("I/O operation on closed file")
|
|
jpayne@69
|
12109 *
|
|
jpayne@69
|
12110 */
|
|
jpayne@69
|
12111 }
|
|
jpayne@69
|
12112
|
|
jpayne@69
|
12113 /* "pysam/libctabix.pyx":447
|
|
jpayne@69
|
12114 *
|
|
jpayne@69
|
12115 * # convert coordinates to region string, which is one-based
|
|
jpayne@69
|
12116 * if reference: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12117 * if end is not None:
|
|
jpayne@69
|
12118 * if end < 0:
|
|
jpayne@69
|
12119 */
|
|
jpayne@69
|
12120 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 447, __pyx_L1_error)
|
|
jpayne@69
|
12121 if (__pyx_t_6) {
|
|
jpayne@69
|
12122
|
|
jpayne@69
|
12123 /* "pysam/libctabix.pyx":448
|
|
jpayne@69
|
12124 * # convert coordinates to region string, which is one-based
|
|
jpayne@69
|
12125 * if reference:
|
|
jpayne@69
|
12126 * if end is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12127 * if end < 0:
|
|
jpayne@69
|
12128 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12129 */
|
|
jpayne@69
|
12130 __pyx_t_6 = (__pyx_v_end != Py_None);
|
|
jpayne@69
|
12131 if (__pyx_t_6) {
|
|
jpayne@69
|
12132
|
|
jpayne@69
|
12133 /* "pysam/libctabix.pyx":449
|
|
jpayne@69
|
12134 * if reference:
|
|
jpayne@69
|
12135 * if end is not None:
|
|
jpayne@69
|
12136 * if end < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12137 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12138 * if start is None:
|
|
jpayne@69
|
12139 */
|
|
jpayne@69
|
12140 __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 449, __pyx_L1_error)
|
|
jpayne@69
|
12141 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 449, __pyx_L1_error)
|
|
jpayne@69
|
12142 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12143 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
12144
|
|
jpayne@69
|
12145 /* "pysam/libctabix.pyx":450
|
|
jpayne@69
|
12146 * if end is not None:
|
|
jpayne@69
|
12147 * if end < 0:
|
|
jpayne@69
|
12148 * raise ValueError("end out of range (%i)" % end) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12149 * if start is None:
|
|
jpayne@69
|
12150 * start = 0
|
|
jpayne@69
|
12151 */
|
|
jpayne@69
|
12152 __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_end_out_of_range_i, __pyx_v_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 450, __pyx_L1_error)
|
|
jpayne@69
|
12153 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12154 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 450, __pyx_L1_error)
|
|
jpayne@69
|
12155 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12156 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12157 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
12158 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12159 __PYX_ERR(0, 450, __pyx_L1_error)
|
|
jpayne@69
|
12160
|
|
jpayne@69
|
12161 /* "pysam/libctabix.pyx":449
|
|
jpayne@69
|
12162 * if reference:
|
|
jpayne@69
|
12163 * if end is not None:
|
|
jpayne@69
|
12164 * if end < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12165 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12166 * if start is None:
|
|
jpayne@69
|
12167 */
|
|
jpayne@69
|
12168 }
|
|
jpayne@69
|
12169
|
|
jpayne@69
|
12170 /* "pysam/libctabix.pyx":451
|
|
jpayne@69
|
12171 * if end < 0:
|
|
jpayne@69
|
12172 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12173 * if start is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12174 * start = 0
|
|
jpayne@69
|
12175 *
|
|
jpayne@69
|
12176 */
|
|
jpayne@69
|
12177 __pyx_t_6 = (__pyx_v_start == Py_None);
|
|
jpayne@69
|
12178 if (__pyx_t_6) {
|
|
jpayne@69
|
12179
|
|
jpayne@69
|
12180 /* "pysam/libctabix.pyx":452
|
|
jpayne@69
|
12181 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12182 * if start is None:
|
|
jpayne@69
|
12183 * start = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12184 *
|
|
jpayne@69
|
12185 * if start < 0:
|
|
jpayne@69
|
12186 */
|
|
jpayne@69
|
12187 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
12188 __Pyx_DECREF_SET(__pyx_v_start, __pyx_int_0);
|
|
jpayne@69
|
12189
|
|
jpayne@69
|
12190 /* "pysam/libctabix.pyx":451
|
|
jpayne@69
|
12191 * if end < 0:
|
|
jpayne@69
|
12192 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12193 * if start is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12194 * start = 0
|
|
jpayne@69
|
12195 *
|
|
jpayne@69
|
12196 */
|
|
jpayne@69
|
12197 }
|
|
jpayne@69
|
12198
|
|
jpayne@69
|
12199 /* "pysam/libctabix.pyx":454
|
|
jpayne@69
|
12200 * start = 0
|
|
jpayne@69
|
12201 *
|
|
jpayne@69
|
12202 * if start < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12203 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12204 * elif start > end:
|
|
jpayne@69
|
12205 */
|
|
jpayne@69
|
12206 __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 454, __pyx_L1_error)
|
|
jpayne@69
|
12207 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 454, __pyx_L1_error)
|
|
jpayne@69
|
12208 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12209 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
12210
|
|
jpayne@69
|
12211 /* "pysam/libctabix.pyx":455
|
|
jpayne@69
|
12212 *
|
|
jpayne@69
|
12213 * if start < 0:
|
|
jpayne@69
|
12214 * raise ValueError("start out of range (%i)" % end) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12215 * elif start > end:
|
|
jpayne@69
|
12216 * raise ValueError(
|
|
jpayne@69
|
12217 */
|
|
jpayne@69
|
12218 __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_start_out_of_range_i, __pyx_v_end); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 455, __pyx_L1_error)
|
|
jpayne@69
|
12219 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12220 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 455, __pyx_L1_error)
|
|
jpayne@69
|
12221 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12222 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12223 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
12224 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12225 __PYX_ERR(0, 455, __pyx_L1_error)
|
|
jpayne@69
|
12226
|
|
jpayne@69
|
12227 /* "pysam/libctabix.pyx":454
|
|
jpayne@69
|
12228 * start = 0
|
|
jpayne@69
|
12229 *
|
|
jpayne@69
|
12230 * if start < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12231 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12232 * elif start > end:
|
|
jpayne@69
|
12233 */
|
|
jpayne@69
|
12234 }
|
|
jpayne@69
|
12235
|
|
jpayne@69
|
12236 /* "pysam/libctabix.pyx":456
|
|
jpayne@69
|
12237 * if start < 0:
|
|
jpayne@69
|
12238 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12239 * elif start > end: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12240 * raise ValueError(
|
|
jpayne@69
|
12241 * 'start (%i) >= end (%i)' % (start, end))
|
|
jpayne@69
|
12242 */
|
|
jpayne@69
|
12243 __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 456, __pyx_L1_error)
|
|
jpayne@69
|
12244 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 456, __pyx_L1_error)
|
|
jpayne@69
|
12245 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12246 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
12247
|
|
jpayne@69
|
12248 /* "pysam/libctabix.pyx":458
|
|
jpayne@69
|
12249 * elif start > end:
|
|
jpayne@69
|
12250 * raise ValueError(
|
|
jpayne@69
|
12251 * 'start (%i) >= end (%i)' % (start, end)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12252 * elif start == end:
|
|
jpayne@69
|
12253 * return EmptyIterator()
|
|
jpayne@69
|
12254 */
|
|
jpayne@69
|
12255 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 458, __pyx_L1_error)
|
|
jpayne@69
|
12256 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12257 __Pyx_INCREF(__pyx_v_start);
|
|
jpayne@69
|
12258 __Pyx_GIVEREF(__pyx_v_start);
|
|
jpayne@69
|
12259 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_start)) __PYX_ERR(0, 458, __pyx_L1_error);
|
|
jpayne@69
|
12260 __Pyx_INCREF(__pyx_v_end);
|
|
jpayne@69
|
12261 __Pyx_GIVEREF(__pyx_v_end);
|
|
jpayne@69
|
12262 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_end)) __PYX_ERR(0, 458, __pyx_L1_error);
|
|
jpayne@69
|
12263 __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_start_i_end_i, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 458, __pyx_L1_error)
|
|
jpayne@69
|
12264 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12265 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12266
|
|
jpayne@69
|
12267 /* "pysam/libctabix.pyx":457
|
|
jpayne@69
|
12268 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12269 * elif start > end:
|
|
jpayne@69
|
12270 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12271 * 'start (%i) >= end (%i)' % (start, end))
|
|
jpayne@69
|
12272 * elif start == end:
|
|
jpayne@69
|
12273 */
|
|
jpayne@69
|
12274 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 457, __pyx_L1_error)
|
|
jpayne@69
|
12275 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12276 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12277 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
12278 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12279 __PYX_ERR(0, 457, __pyx_L1_error)
|
|
jpayne@69
|
12280
|
|
jpayne@69
|
12281 /* "pysam/libctabix.pyx":456
|
|
jpayne@69
|
12282 * if start < 0:
|
|
jpayne@69
|
12283 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12284 * elif start > end: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12285 * raise ValueError(
|
|
jpayne@69
|
12286 * 'start (%i) >= end (%i)' % (start, end))
|
|
jpayne@69
|
12287 */
|
|
jpayne@69
|
12288 }
|
|
jpayne@69
|
12289
|
|
jpayne@69
|
12290 /* "pysam/libctabix.pyx":459
|
|
jpayne@69
|
12291 * raise ValueError(
|
|
jpayne@69
|
12292 * 'start (%i) >= end (%i)' % (start, end))
|
|
jpayne@69
|
12293 * elif start == end: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12294 * return EmptyIterator()
|
|
jpayne@69
|
12295 * else:
|
|
jpayne@69
|
12296 */
|
|
jpayne@69
|
12297 __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 459, __pyx_L1_error)
|
|
jpayne@69
|
12298 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 459, __pyx_L1_error)
|
|
jpayne@69
|
12299 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12300 if (__pyx_t_6) {
|
|
jpayne@69
|
12301
|
|
jpayne@69
|
12302 /* "pysam/libctabix.pyx":460
|
|
jpayne@69
|
12303 * 'start (%i) >= end (%i)' % (start, end))
|
|
jpayne@69
|
12304 * elif start == end:
|
|
jpayne@69
|
12305 * return EmptyIterator() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12306 * else:
|
|
jpayne@69
|
12307 * region = '%s:%i-%i' % (reference, start + 1, end)
|
|
jpayne@69
|
12308 */
|
|
jpayne@69
|
12309 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
12310 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_EmptyIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 460, __pyx_L1_error)
|
|
jpayne@69
|
12311 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12312 __pyx_t_3 = NULL;
|
|
jpayne@69
|
12313 __pyx_t_4 = 0;
|
|
jpayne@69
|
12314 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
12315 if (unlikely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
12316 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
12317 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
12318 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
12319 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
12320 __Pyx_INCREF(function);
|
|
jpayne@69
|
12321 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
12322 __pyx_t_4 = 1;
|
|
jpayne@69
|
12323 }
|
|
jpayne@69
|
12324 }
|
|
jpayne@69
|
12325 #endif
|
|
jpayne@69
|
12326 {
|
|
jpayne@69
|
12327 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
|
|
jpayne@69
|
12328 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
|
|
jpayne@69
|
12329 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12330 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 460, __pyx_L1_error)
|
|
jpayne@69
|
12331 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12332 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12333 }
|
|
jpayne@69
|
12334 __pyx_r = __pyx_t_1;
|
|
jpayne@69
|
12335 __pyx_t_1 = 0;
|
|
jpayne@69
|
12336 goto __pyx_L0;
|
|
jpayne@69
|
12337
|
|
jpayne@69
|
12338 /* "pysam/libctabix.pyx":459
|
|
jpayne@69
|
12339 * raise ValueError(
|
|
jpayne@69
|
12340 * 'start (%i) >= end (%i)' % (start, end))
|
|
jpayne@69
|
12341 * elif start == end: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12342 * return EmptyIterator()
|
|
jpayne@69
|
12343 * else:
|
|
jpayne@69
|
12344 */
|
|
jpayne@69
|
12345 }
|
|
jpayne@69
|
12346
|
|
jpayne@69
|
12347 /* "pysam/libctabix.pyx":462
|
|
jpayne@69
|
12348 * return EmptyIterator()
|
|
jpayne@69
|
12349 * else:
|
|
jpayne@69
|
12350 * region = '%s:%i-%i' % (reference, start + 1, end) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12351 * elif start is not None:
|
|
jpayne@69
|
12352 * if start < 0:
|
|
jpayne@69
|
12353 */
|
|
jpayne@69
|
12354 /*else*/ {
|
|
jpayne@69
|
12355 __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_start, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error)
|
|
jpayne@69
|
12356 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12357 __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 462, __pyx_L1_error)
|
|
jpayne@69
|
12358 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12359 __Pyx_INCREF(__pyx_v_reference);
|
|
jpayne@69
|
12360 __Pyx_GIVEREF(__pyx_v_reference);
|
|
jpayne@69
|
12361 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference)) __PYX_ERR(0, 462, __pyx_L1_error);
|
|
jpayne@69
|
12362 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
12363 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error);
|
|
jpayne@69
|
12364 __Pyx_INCREF(__pyx_v_end);
|
|
jpayne@69
|
12365 __Pyx_GIVEREF(__pyx_v_end);
|
|
jpayne@69
|
12366 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end)) __PYX_ERR(0, 462, __pyx_L1_error);
|
|
jpayne@69
|
12367 __pyx_t_1 = 0;
|
|
jpayne@69
|
12368 __pyx_t_1 = PyUnicode_Format(__pyx_kp_u_s_i_i, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error)
|
|
jpayne@69
|
12369 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12370 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12371 __Pyx_DECREF_SET(__pyx_v_region, __pyx_t_1);
|
|
jpayne@69
|
12372 __pyx_t_1 = 0;
|
|
jpayne@69
|
12373 }
|
|
jpayne@69
|
12374
|
|
jpayne@69
|
12375 /* "pysam/libctabix.pyx":448
|
|
jpayne@69
|
12376 * # convert coordinates to region string, which is one-based
|
|
jpayne@69
|
12377 * if reference:
|
|
jpayne@69
|
12378 * if end is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12379 * if end < 0:
|
|
jpayne@69
|
12380 * raise ValueError("end out of range (%i)" % end)
|
|
jpayne@69
|
12381 */
|
|
jpayne@69
|
12382 goto __pyx_L5;
|
|
jpayne@69
|
12383 }
|
|
jpayne@69
|
12384
|
|
jpayne@69
|
12385 /* "pysam/libctabix.pyx":463
|
|
jpayne@69
|
12386 * else:
|
|
jpayne@69
|
12387 * region = '%s:%i-%i' % (reference, start + 1, end)
|
|
jpayne@69
|
12388 * elif start is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12389 * if start < 0:
|
|
jpayne@69
|
12390 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12391 */
|
|
jpayne@69
|
12392 __pyx_t_6 = (__pyx_v_start != Py_None);
|
|
jpayne@69
|
12393 if (__pyx_t_6) {
|
|
jpayne@69
|
12394
|
|
jpayne@69
|
12395 /* "pysam/libctabix.pyx":464
|
|
jpayne@69
|
12396 * region = '%s:%i-%i' % (reference, start + 1, end)
|
|
jpayne@69
|
12397 * elif start is not None:
|
|
jpayne@69
|
12398 * if start < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12399 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12400 * region = '%s:%i' % (reference, start + 1)
|
|
jpayne@69
|
12401 */
|
|
jpayne@69
|
12402 __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 464, __pyx_L1_error)
|
|
jpayne@69
|
12403 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 464, __pyx_L1_error)
|
|
jpayne@69
|
12404 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12405 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
12406
|
|
jpayne@69
|
12407 /* "pysam/libctabix.pyx":465
|
|
jpayne@69
|
12408 * elif start is not None:
|
|
jpayne@69
|
12409 * if start < 0:
|
|
jpayne@69
|
12410 * raise ValueError("start out of range (%i)" % end) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12411 * region = '%s:%i' % (reference, start + 1)
|
|
jpayne@69
|
12412 * else:
|
|
jpayne@69
|
12413 */
|
|
jpayne@69
|
12414 __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_start_out_of_range_i, __pyx_v_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 465, __pyx_L1_error)
|
|
jpayne@69
|
12415 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12416 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 465, __pyx_L1_error)
|
|
jpayne@69
|
12417 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12418 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12419 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
12420 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12421 __PYX_ERR(0, 465, __pyx_L1_error)
|
|
jpayne@69
|
12422
|
|
jpayne@69
|
12423 /* "pysam/libctabix.pyx":464
|
|
jpayne@69
|
12424 * region = '%s:%i-%i' % (reference, start + 1, end)
|
|
jpayne@69
|
12425 * elif start is not None:
|
|
jpayne@69
|
12426 * if start < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12427 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12428 * region = '%s:%i' % (reference, start + 1)
|
|
jpayne@69
|
12429 */
|
|
jpayne@69
|
12430 }
|
|
jpayne@69
|
12431
|
|
jpayne@69
|
12432 /* "pysam/libctabix.pyx":466
|
|
jpayne@69
|
12433 * if start < 0:
|
|
jpayne@69
|
12434 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12435 * region = '%s:%i' % (reference, start + 1) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12436 * else:
|
|
jpayne@69
|
12437 * region = reference
|
|
jpayne@69
|
12438 */
|
|
jpayne@69
|
12439 __pyx_t_2 = __Pyx_PyInt_AddObjC(__pyx_v_start, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 466, __pyx_L1_error)
|
|
jpayne@69
|
12440 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12441 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 466, __pyx_L1_error)
|
|
jpayne@69
|
12442 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12443 __Pyx_INCREF(__pyx_v_reference);
|
|
jpayne@69
|
12444 __Pyx_GIVEREF(__pyx_v_reference);
|
|
jpayne@69
|
12445 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference)) __PYX_ERR(0, 466, __pyx_L1_error);
|
|
jpayne@69
|
12446 __Pyx_GIVEREF(__pyx_t_2);
|
|
jpayne@69
|
12447 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2)) __PYX_ERR(0, 466, __pyx_L1_error);
|
|
jpayne@69
|
12448 __pyx_t_2 = 0;
|
|
jpayne@69
|
12449 __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_s_i, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 466, __pyx_L1_error)
|
|
jpayne@69
|
12450 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12451 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12452 __Pyx_DECREF_SET(__pyx_v_region, __pyx_t_2);
|
|
jpayne@69
|
12453 __pyx_t_2 = 0;
|
|
jpayne@69
|
12454
|
|
jpayne@69
|
12455 /* "pysam/libctabix.pyx":463
|
|
jpayne@69
|
12456 * else:
|
|
jpayne@69
|
12457 * region = '%s:%i-%i' % (reference, start + 1, end)
|
|
jpayne@69
|
12458 * elif start is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12459 * if start < 0:
|
|
jpayne@69
|
12460 * raise ValueError("start out of range (%i)" % end)
|
|
jpayne@69
|
12461 */
|
|
jpayne@69
|
12462 goto __pyx_L5;
|
|
jpayne@69
|
12463 }
|
|
jpayne@69
|
12464
|
|
jpayne@69
|
12465 /* "pysam/libctabix.pyx":468
|
|
jpayne@69
|
12466 * region = '%s:%i' % (reference, start + 1)
|
|
jpayne@69
|
12467 * else:
|
|
jpayne@69
|
12468 * region = reference # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12469 *
|
|
jpayne@69
|
12470 * # get iterator
|
|
jpayne@69
|
12471 */
|
|
jpayne@69
|
12472 /*else*/ {
|
|
jpayne@69
|
12473 __Pyx_INCREF(__pyx_v_reference);
|
|
jpayne@69
|
12474 __Pyx_DECREF_SET(__pyx_v_region, __pyx_v_reference);
|
|
jpayne@69
|
12475 }
|
|
jpayne@69
|
12476 __pyx_L5:;
|
|
jpayne@69
|
12477
|
|
jpayne@69
|
12478 /* "pysam/libctabix.pyx":447
|
|
jpayne@69
|
12479 *
|
|
jpayne@69
|
12480 * # convert coordinates to region string, which is one-based
|
|
jpayne@69
|
12481 * if reference: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12482 * if end is not None:
|
|
jpayne@69
|
12483 * if end < 0:
|
|
jpayne@69
|
12484 */
|
|
jpayne@69
|
12485 }
|
|
jpayne@69
|
12486
|
|
jpayne@69
|
12487 /* "pysam/libctabix.pyx":476
|
|
jpayne@69
|
12488 *
|
|
jpayne@69
|
12489 * # reopen the same file if necessary
|
|
jpayne@69
|
12490 * if multiple_iterators: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12491 * fileobj = self._dup()
|
|
jpayne@69
|
12492 * else:
|
|
jpayne@69
|
12493 */
|
|
jpayne@69
|
12494 __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_multiple_iterators); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 476, __pyx_L1_error)
|
|
jpayne@69
|
12495 if (__pyx_t_6) {
|
|
jpayne@69
|
12496
|
|
jpayne@69
|
12497 /* "pysam/libctabix.pyx":477
|
|
jpayne@69
|
12498 * # reopen the same file if necessary
|
|
jpayne@69
|
12499 * if multiple_iterators:
|
|
jpayne@69
|
12500 * fileobj = self._dup() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12501 * else:
|
|
jpayne@69
|
12502 * fileobj = self
|
|
jpayne@69
|
12503 */
|
|
jpayne@69
|
12504 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dup); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 477, __pyx_L1_error)
|
|
jpayne@69
|
12505 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12506 __pyx_t_3 = NULL;
|
|
jpayne@69
|
12507 __pyx_t_4 = 0;
|
|
jpayne@69
|
12508 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
12509 if (likely(PyMethod_Check(__pyx_t_1))) {
|
|
jpayne@69
|
12510 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1);
|
|
jpayne@69
|
12511 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
12512 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
|
|
jpayne@69
|
12513 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
12514 __Pyx_INCREF(function);
|
|
jpayne@69
|
12515 __Pyx_DECREF_SET(__pyx_t_1, function);
|
|
jpayne@69
|
12516 __pyx_t_4 = 1;
|
|
jpayne@69
|
12517 }
|
|
jpayne@69
|
12518 }
|
|
jpayne@69
|
12519 #endif
|
|
jpayne@69
|
12520 {
|
|
jpayne@69
|
12521 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
|
|
jpayne@69
|
12522 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
|
|
jpayne@69
|
12523 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12524 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 477, __pyx_L1_error)
|
|
jpayne@69
|
12525 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12526 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12527 }
|
|
jpayne@69
|
12528 if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5pysam_9libctabix_TabixFile))))) __PYX_ERR(0, 477, __pyx_L1_error)
|
|
jpayne@69
|
12529 __pyx_v_fileobj = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_t_2);
|
|
jpayne@69
|
12530 __pyx_t_2 = 0;
|
|
jpayne@69
|
12531
|
|
jpayne@69
|
12532 /* "pysam/libctabix.pyx":476
|
|
jpayne@69
|
12533 *
|
|
jpayne@69
|
12534 * # reopen the same file if necessary
|
|
jpayne@69
|
12535 * if multiple_iterators: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12536 * fileobj = self._dup()
|
|
jpayne@69
|
12537 * else:
|
|
jpayne@69
|
12538 */
|
|
jpayne@69
|
12539 goto __pyx_L10;
|
|
jpayne@69
|
12540 }
|
|
jpayne@69
|
12541
|
|
jpayne@69
|
12542 /* "pysam/libctabix.pyx":479
|
|
jpayne@69
|
12543 * fileobj = self._dup()
|
|
jpayne@69
|
12544 * else:
|
|
jpayne@69
|
12545 * fileobj = self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12546 *
|
|
jpayne@69
|
12547 * if region is None:
|
|
jpayne@69
|
12548 */
|
|
jpayne@69
|
12549 /*else*/ {
|
|
jpayne@69
|
12550 __Pyx_INCREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
12551 __pyx_v_fileobj = __pyx_v_self;
|
|
jpayne@69
|
12552 }
|
|
jpayne@69
|
12553 __pyx_L10:;
|
|
jpayne@69
|
12554
|
|
jpayne@69
|
12555 /* "pysam/libctabix.pyx":481
|
|
jpayne@69
|
12556 * fileobj = self
|
|
jpayne@69
|
12557 *
|
|
jpayne@69
|
12558 * if region is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12559 * # without region or reference - iterate from start
|
|
jpayne@69
|
12560 * with nogil:
|
|
jpayne@69
|
12561 */
|
|
jpayne@69
|
12562 __pyx_t_6 = (__pyx_v_region == Py_None);
|
|
jpayne@69
|
12563 if (__pyx_t_6) {
|
|
jpayne@69
|
12564
|
|
jpayne@69
|
12565 /* "pysam/libctabix.pyx":483
|
|
jpayne@69
|
12566 * if region is None:
|
|
jpayne@69
|
12567 * # without region or reference - iterate from start
|
|
jpayne@69
|
12568 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12569 * itr = tbx_itr_queryi(fileobj.index,
|
|
jpayne@69
|
12570 * HTS_IDX_START,
|
|
jpayne@69
|
12571 */
|
|
jpayne@69
|
12572 {
|
|
jpayne@69
|
12573 #ifdef WITH_THREAD
|
|
jpayne@69
|
12574 PyThreadState *_save;
|
|
jpayne@69
|
12575 _save = NULL;
|
|
jpayne@69
|
12576 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
12577 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
12578 #endif
|
|
jpayne@69
|
12579 /*try:*/ {
|
|
jpayne@69
|
12580
|
|
jpayne@69
|
12581 /* "pysam/libctabix.pyx":484
|
|
jpayne@69
|
12582 * # without region or reference - iterate from start
|
|
jpayne@69
|
12583 * with nogil:
|
|
jpayne@69
|
12584 * itr = tbx_itr_queryi(fileobj.index, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12585 * HTS_IDX_START,
|
|
jpayne@69
|
12586 * 0,
|
|
jpayne@69
|
12587 */
|
|
jpayne@69
|
12588 __pyx_v_itr = tbx_itr_queryi(__pyx_v_fileobj->index, HTS_IDX_START, 0, 0);
|
|
jpayne@69
|
12589 }
|
|
jpayne@69
|
12590
|
|
jpayne@69
|
12591 /* "pysam/libctabix.pyx":483
|
|
jpayne@69
|
12592 * if region is None:
|
|
jpayne@69
|
12593 * # without region or reference - iterate from start
|
|
jpayne@69
|
12594 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12595 * itr = tbx_itr_queryi(fileobj.index,
|
|
jpayne@69
|
12596 * HTS_IDX_START,
|
|
jpayne@69
|
12597 */
|
|
jpayne@69
|
12598 /*finally:*/ {
|
|
jpayne@69
|
12599 /*normal exit:*/{
|
|
jpayne@69
|
12600 #ifdef WITH_THREAD
|
|
jpayne@69
|
12601 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
12602 Py_BLOCK_THREADS
|
|
jpayne@69
|
12603 #endif
|
|
jpayne@69
|
12604 goto __pyx_L14;
|
|
jpayne@69
|
12605 }
|
|
jpayne@69
|
12606 __pyx_L14:;
|
|
jpayne@69
|
12607 }
|
|
jpayne@69
|
12608 }
|
|
jpayne@69
|
12609
|
|
jpayne@69
|
12610 /* "pysam/libctabix.pyx":481
|
|
jpayne@69
|
12611 * fileobj = self
|
|
jpayne@69
|
12612 *
|
|
jpayne@69
|
12613 * if region is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12614 * # without region or reference - iterate from start
|
|
jpayne@69
|
12615 * with nogil:
|
|
jpayne@69
|
12616 */
|
|
jpayne@69
|
12617 goto __pyx_L11;
|
|
jpayne@69
|
12618 }
|
|
jpayne@69
|
12619
|
|
jpayne@69
|
12620 /* "pysam/libctabix.pyx":489
|
|
jpayne@69
|
12621 * 0)
|
|
jpayne@69
|
12622 * else:
|
|
jpayne@69
|
12623 * s = force_bytes(region, encoding=fileobj.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12624 * cstr = s
|
|
jpayne@69
|
12625 * with nogil:
|
|
jpayne@69
|
12626 */
|
|
jpayne@69
|
12627 /*else*/ {
|
|
jpayne@69
|
12628 __pyx_t_2 = __pyx_v_fileobj->encoding;
|
|
jpayne@69
|
12629 __Pyx_INCREF(__pyx_t_2);
|
|
jpayne@69
|
12630 __pyx_t_7.__pyx_n = 1;
|
|
jpayne@69
|
12631 __pyx_t_7.encoding = __pyx_t_2;
|
|
jpayne@69
|
12632 __pyx_t_1 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_region, &__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 489, __pyx_L1_error)
|
|
jpayne@69
|
12633 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12634 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12635 __pyx_v_s = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
12636 __pyx_t_1 = 0;
|
|
jpayne@69
|
12637
|
|
jpayne@69
|
12638 /* "pysam/libctabix.pyx":490
|
|
jpayne@69
|
12639 * else:
|
|
jpayne@69
|
12640 * s = force_bytes(region, encoding=fileobj.encoding)
|
|
jpayne@69
|
12641 * cstr = s # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12642 * with nogil:
|
|
jpayne@69
|
12643 * itr = tbx_itr_querys(fileobj.index, cstr)
|
|
jpayne@69
|
12644 */
|
|
jpayne@69
|
12645 if (unlikely(__pyx_v_s == Py_None)) {
|
|
jpayne@69
|
12646 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
12647 __PYX_ERR(0, 490, __pyx_L1_error)
|
|
jpayne@69
|
12648 }
|
|
jpayne@69
|
12649 __pyx_t_8 = __Pyx_PyBytes_AsWritableString(__pyx_v_s); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 490, __pyx_L1_error)
|
|
jpayne@69
|
12650 __pyx_v_cstr = __pyx_t_8;
|
|
jpayne@69
|
12651
|
|
jpayne@69
|
12652 /* "pysam/libctabix.pyx":491
|
|
jpayne@69
|
12653 * s = force_bytes(region, encoding=fileobj.encoding)
|
|
jpayne@69
|
12654 * cstr = s
|
|
jpayne@69
|
12655 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12656 * itr = tbx_itr_querys(fileobj.index, cstr)
|
|
jpayne@69
|
12657 *
|
|
jpayne@69
|
12658 */
|
|
jpayne@69
|
12659 {
|
|
jpayne@69
|
12660 #ifdef WITH_THREAD
|
|
jpayne@69
|
12661 PyThreadState *_save;
|
|
jpayne@69
|
12662 _save = NULL;
|
|
jpayne@69
|
12663 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
12664 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
12665 #endif
|
|
jpayne@69
|
12666 /*try:*/ {
|
|
jpayne@69
|
12667
|
|
jpayne@69
|
12668 /* "pysam/libctabix.pyx":492
|
|
jpayne@69
|
12669 * cstr = s
|
|
jpayne@69
|
12670 * with nogil:
|
|
jpayne@69
|
12671 * itr = tbx_itr_querys(fileobj.index, cstr) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12672 *
|
|
jpayne@69
|
12673 * if itr == NULL:
|
|
jpayne@69
|
12674 */
|
|
jpayne@69
|
12675 __pyx_v_itr = tbx_itr_querys(__pyx_v_fileobj->index, __pyx_v_cstr);
|
|
jpayne@69
|
12676 }
|
|
jpayne@69
|
12677
|
|
jpayne@69
|
12678 /* "pysam/libctabix.pyx":491
|
|
jpayne@69
|
12679 * s = force_bytes(region, encoding=fileobj.encoding)
|
|
jpayne@69
|
12680 * cstr = s
|
|
jpayne@69
|
12681 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12682 * itr = tbx_itr_querys(fileobj.index, cstr)
|
|
jpayne@69
|
12683 *
|
|
jpayne@69
|
12684 */
|
|
jpayne@69
|
12685 /*finally:*/ {
|
|
jpayne@69
|
12686 /*normal exit:*/{
|
|
jpayne@69
|
12687 #ifdef WITH_THREAD
|
|
jpayne@69
|
12688 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
12689 Py_BLOCK_THREADS
|
|
jpayne@69
|
12690 #endif
|
|
jpayne@69
|
12691 goto __pyx_L17;
|
|
jpayne@69
|
12692 }
|
|
jpayne@69
|
12693 __pyx_L17:;
|
|
jpayne@69
|
12694 }
|
|
jpayne@69
|
12695 }
|
|
jpayne@69
|
12696 }
|
|
jpayne@69
|
12697 __pyx_L11:;
|
|
jpayne@69
|
12698
|
|
jpayne@69
|
12699 /* "pysam/libctabix.pyx":494
|
|
jpayne@69
|
12700 * itr = tbx_itr_querys(fileobj.index, cstr)
|
|
jpayne@69
|
12701 *
|
|
jpayne@69
|
12702 * if itr == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12703 * if region is None:
|
|
jpayne@69
|
12704 * if len(self.contigs) > 0:
|
|
jpayne@69
|
12705 */
|
|
jpayne@69
|
12706 __pyx_t_6 = (__pyx_v_itr == NULL);
|
|
jpayne@69
|
12707 if (__pyx_t_6) {
|
|
jpayne@69
|
12708
|
|
jpayne@69
|
12709 /* "pysam/libctabix.pyx":495
|
|
jpayne@69
|
12710 *
|
|
jpayne@69
|
12711 * if itr == NULL:
|
|
jpayne@69
|
12712 * if region is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12713 * if len(self.contigs) > 0:
|
|
jpayne@69
|
12714 * # when accessing a tabix file created prior tabix 1.0
|
|
jpayne@69
|
12715 */
|
|
jpayne@69
|
12716 __pyx_t_6 = (__pyx_v_region == Py_None);
|
|
jpayne@69
|
12717 if (likely(__pyx_t_6)) {
|
|
jpayne@69
|
12718
|
|
jpayne@69
|
12719 /* "pysam/libctabix.pyx":496
|
|
jpayne@69
|
12720 * if itr == NULL:
|
|
jpayne@69
|
12721 * if region is None:
|
|
jpayne@69
|
12722 * if len(self.contigs) > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12723 * # when accessing a tabix file created prior tabix 1.0
|
|
jpayne@69
|
12724 * # the full-file iterator is empty.
|
|
jpayne@69
|
12725 */
|
|
jpayne@69
|
12726 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_contigs); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 496, __pyx_L1_error)
|
|
jpayne@69
|
12727 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12728 __pyx_t_9 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 496, __pyx_L1_error)
|
|
jpayne@69
|
12729 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12730 __pyx_t_6 = (__pyx_t_9 > 0);
|
|
jpayne@69
|
12731 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
12732
|
|
jpayne@69
|
12733 /* "pysam/libctabix.pyx":499
|
|
jpayne@69
|
12734 * # when accessing a tabix file created prior tabix 1.0
|
|
jpayne@69
|
12735 * # the full-file iterator is empty.
|
|
jpayne@69
|
12736 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12737 * "could not create iterator, possible "
|
|
jpayne@69
|
12738 * "tabix version mismatch")
|
|
jpayne@69
|
12739 */
|
|
jpayne@69
|
12740 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 499, __pyx_L1_error)
|
|
jpayne@69
|
12741 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12742 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
12743 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12744 __PYX_ERR(0, 499, __pyx_L1_error)
|
|
jpayne@69
|
12745
|
|
jpayne@69
|
12746 /* "pysam/libctabix.pyx":496
|
|
jpayne@69
|
12747 * if itr == NULL:
|
|
jpayne@69
|
12748 * if region is None:
|
|
jpayne@69
|
12749 * if len(self.contigs) > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12750 * # when accessing a tabix file created prior tabix 1.0
|
|
jpayne@69
|
12751 * # the full-file iterator is empty.
|
|
jpayne@69
|
12752 */
|
|
jpayne@69
|
12753 }
|
|
jpayne@69
|
12754
|
|
jpayne@69
|
12755 /* "pysam/libctabix.pyx":505
|
|
jpayne@69
|
12756 * # possible reason is that the file is empty -
|
|
jpayne@69
|
12757 * # return an empty iterator
|
|
jpayne@69
|
12758 * return EmptyIterator() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12759 * else:
|
|
jpayne@69
|
12760 * raise ValueError(
|
|
jpayne@69
|
12761 */
|
|
jpayne@69
|
12762 /*else*/ {
|
|
jpayne@69
|
12763 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
12764 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_EmptyIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 505, __pyx_L1_error)
|
|
jpayne@69
|
12765 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12766 __pyx_t_3 = NULL;
|
|
jpayne@69
|
12767 __pyx_t_4 = 0;
|
|
jpayne@69
|
12768 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
12769 if (unlikely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
12770 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
12771 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
12772 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
12773 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
12774 __Pyx_INCREF(function);
|
|
jpayne@69
|
12775 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
12776 __pyx_t_4 = 1;
|
|
jpayne@69
|
12777 }
|
|
jpayne@69
|
12778 }
|
|
jpayne@69
|
12779 #endif
|
|
jpayne@69
|
12780 {
|
|
jpayne@69
|
12781 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
|
|
jpayne@69
|
12782 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
|
|
jpayne@69
|
12783 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12784 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 505, __pyx_L1_error)
|
|
jpayne@69
|
12785 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12786 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12787 }
|
|
jpayne@69
|
12788 __pyx_r = __pyx_t_1;
|
|
jpayne@69
|
12789 __pyx_t_1 = 0;
|
|
jpayne@69
|
12790 goto __pyx_L0;
|
|
jpayne@69
|
12791 }
|
|
jpayne@69
|
12792
|
|
jpayne@69
|
12793 /* "pysam/libctabix.pyx":495
|
|
jpayne@69
|
12794 *
|
|
jpayne@69
|
12795 * if itr == NULL:
|
|
jpayne@69
|
12796 * if region is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12797 * if len(self.contigs) > 0:
|
|
jpayne@69
|
12798 * # when accessing a tabix file created prior tabix 1.0
|
|
jpayne@69
|
12799 */
|
|
jpayne@69
|
12800 }
|
|
jpayne@69
|
12801
|
|
jpayne@69
|
12802 /* "pysam/libctabix.pyx":507
|
|
jpayne@69
|
12803 * return EmptyIterator()
|
|
jpayne@69
|
12804 * else:
|
|
jpayne@69
|
12805 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12806 * "could not create iterator for region '%s'" %
|
|
jpayne@69
|
12807 * region)
|
|
jpayne@69
|
12808 */
|
|
jpayne@69
|
12809 /*else*/ {
|
|
jpayne@69
|
12810
|
|
jpayne@69
|
12811 /* "pysam/libctabix.pyx":508
|
|
jpayne@69
|
12812 * else:
|
|
jpayne@69
|
12813 * raise ValueError(
|
|
jpayne@69
|
12814 * "could not create iterator for region '%s'" % # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12815 * region)
|
|
jpayne@69
|
12816 *
|
|
jpayne@69
|
12817 */
|
|
jpayne@69
|
12818 __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_create_iterator_for_re, __pyx_v_region); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 508, __pyx_L1_error)
|
|
jpayne@69
|
12819 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12820
|
|
jpayne@69
|
12821 /* "pysam/libctabix.pyx":507
|
|
jpayne@69
|
12822 * return EmptyIterator()
|
|
jpayne@69
|
12823 * else:
|
|
jpayne@69
|
12824 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12825 * "could not create iterator for region '%s'" %
|
|
jpayne@69
|
12826 * region)
|
|
jpayne@69
|
12827 */
|
|
jpayne@69
|
12828 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 507, __pyx_L1_error)
|
|
jpayne@69
|
12829 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12830 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12831 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
12832 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12833 __PYX_ERR(0, 507, __pyx_L1_error)
|
|
jpayne@69
|
12834 }
|
|
jpayne@69
|
12835
|
|
jpayne@69
|
12836 /* "pysam/libctabix.pyx":494
|
|
jpayne@69
|
12837 * itr = tbx_itr_querys(fileobj.index, cstr)
|
|
jpayne@69
|
12838 *
|
|
jpayne@69
|
12839 * if itr == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12840 * if region is None:
|
|
jpayne@69
|
12841 * if len(self.contigs) > 0:
|
|
jpayne@69
|
12842 */
|
|
jpayne@69
|
12843 }
|
|
jpayne@69
|
12844
|
|
jpayne@69
|
12845 /* "pysam/libctabix.pyx":512
|
|
jpayne@69
|
12846 *
|
|
jpayne@69
|
12847 * # use default parser if no parser is specified
|
|
jpayne@69
|
12848 * if parser is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12849 * parser = fileobj.parser
|
|
jpayne@69
|
12850 *
|
|
jpayne@69
|
12851 */
|
|
jpayne@69
|
12852 __pyx_t_6 = (__pyx_v_parser == Py_None);
|
|
jpayne@69
|
12853 if (__pyx_t_6) {
|
|
jpayne@69
|
12854
|
|
jpayne@69
|
12855 /* "pysam/libctabix.pyx":513
|
|
jpayne@69
|
12856 * # use default parser if no parser is specified
|
|
jpayne@69
|
12857 * if parser is None:
|
|
jpayne@69
|
12858 * parser = fileobj.parser # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12859 *
|
|
jpayne@69
|
12860 * cdef TabixIterator a
|
|
jpayne@69
|
12861 */
|
|
jpayne@69
|
12862 __pyx_t_2 = ((PyObject *)__pyx_v_fileobj->parser);
|
|
jpayne@69
|
12863 __Pyx_INCREF(__pyx_t_2);
|
|
jpayne@69
|
12864 __Pyx_DECREF_SET(__pyx_v_parser, __pyx_t_2);
|
|
jpayne@69
|
12865 __pyx_t_2 = 0;
|
|
jpayne@69
|
12866
|
|
jpayne@69
|
12867 /* "pysam/libctabix.pyx":512
|
|
jpayne@69
|
12868 *
|
|
jpayne@69
|
12869 * # use default parser if no parser is specified
|
|
jpayne@69
|
12870 * if parser is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12871 * parser = fileobj.parser
|
|
jpayne@69
|
12872 *
|
|
jpayne@69
|
12873 */
|
|
jpayne@69
|
12874 }
|
|
jpayne@69
|
12875
|
|
jpayne@69
|
12876 /* "pysam/libctabix.pyx":516
|
|
jpayne@69
|
12877 *
|
|
jpayne@69
|
12878 * cdef TabixIterator a
|
|
jpayne@69
|
12879 * if parser is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12880 * a = TabixIterator(encoding=fileobj.encoding)
|
|
jpayne@69
|
12881 * else:
|
|
jpayne@69
|
12882 */
|
|
jpayne@69
|
12883 __pyx_t_6 = (__pyx_v_parser == Py_None);
|
|
jpayne@69
|
12884 if (__pyx_t_6) {
|
|
jpayne@69
|
12885
|
|
jpayne@69
|
12886 /* "pysam/libctabix.pyx":517
|
|
jpayne@69
|
12887 * cdef TabixIterator a
|
|
jpayne@69
|
12888 * if parser is None:
|
|
jpayne@69
|
12889 * a = TabixIterator(encoding=fileobj.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12890 * else:
|
|
jpayne@69
|
12891 * parser.set_encoding(fileobj.encoding)
|
|
jpayne@69
|
12892 */
|
|
jpayne@69
|
12893 __pyx_t_2 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 517, __pyx_L1_error)
|
|
jpayne@69
|
12894 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12895 if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_encoding, __pyx_v_fileobj->encoding) < 0) __PYX_ERR(0, 517, __pyx_L1_error)
|
|
jpayne@69
|
12896 __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIterator), __pyx_empty_tuple, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 517, __pyx_L1_error)
|
|
jpayne@69
|
12897 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12898 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12899 __pyx_v_a = ((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_t_1);
|
|
jpayne@69
|
12900 __pyx_t_1 = 0;
|
|
jpayne@69
|
12901
|
|
jpayne@69
|
12902 /* "pysam/libctabix.pyx":516
|
|
jpayne@69
|
12903 *
|
|
jpayne@69
|
12904 * cdef TabixIterator a
|
|
jpayne@69
|
12905 * if parser is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12906 * a = TabixIterator(encoding=fileobj.encoding)
|
|
jpayne@69
|
12907 * else:
|
|
jpayne@69
|
12908 */
|
|
jpayne@69
|
12909 goto __pyx_L22;
|
|
jpayne@69
|
12910 }
|
|
jpayne@69
|
12911
|
|
jpayne@69
|
12912 /* "pysam/libctabix.pyx":519
|
|
jpayne@69
|
12913 * a = TabixIterator(encoding=fileobj.encoding)
|
|
jpayne@69
|
12914 * else:
|
|
jpayne@69
|
12915 * parser.set_encoding(fileobj.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12916 * a = TabixIteratorParsed(parser)
|
|
jpayne@69
|
12917 *
|
|
jpayne@69
|
12918 */
|
|
jpayne@69
|
12919 /*else*/ {
|
|
jpayne@69
|
12920 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_parser, __pyx_n_s_set_encoding); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 519, __pyx_L1_error)
|
|
jpayne@69
|
12921 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12922 __pyx_t_3 = NULL;
|
|
jpayne@69
|
12923 __pyx_t_4 = 0;
|
|
jpayne@69
|
12924 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
12925 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
12926 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
12927 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
12928 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
12929 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
12930 __Pyx_INCREF(function);
|
|
jpayne@69
|
12931 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
12932 __pyx_t_4 = 1;
|
|
jpayne@69
|
12933 }
|
|
jpayne@69
|
12934 }
|
|
jpayne@69
|
12935 #endif
|
|
jpayne@69
|
12936 {
|
|
jpayne@69
|
12937 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_fileobj->encoding};
|
|
jpayne@69
|
12938 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
|
|
jpayne@69
|
12939 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12940 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 519, __pyx_L1_error)
|
|
jpayne@69
|
12941 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12942 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12943 }
|
|
jpayne@69
|
12944 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
12945
|
|
jpayne@69
|
12946 /* "pysam/libctabix.pyx":520
|
|
jpayne@69
|
12947 * else:
|
|
jpayne@69
|
12948 * parser.set_encoding(fileobj.encoding)
|
|
jpayne@69
|
12949 * a = TabixIteratorParsed(parser) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12950 *
|
|
jpayne@69
|
12951 * a.tabixfile = fileobj
|
|
jpayne@69
|
12952 */
|
|
jpayne@69
|
12953 __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed), __pyx_v_parser); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 520, __pyx_L1_error)
|
|
jpayne@69
|
12954 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
12955 __pyx_v_a = ((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_t_1);
|
|
jpayne@69
|
12956 __pyx_t_1 = 0;
|
|
jpayne@69
|
12957 }
|
|
jpayne@69
|
12958 __pyx_L22:;
|
|
jpayne@69
|
12959
|
|
jpayne@69
|
12960 /* "pysam/libctabix.pyx":522
|
|
jpayne@69
|
12961 * a = TabixIteratorParsed(parser)
|
|
jpayne@69
|
12962 *
|
|
jpayne@69
|
12963 * a.tabixfile = fileobj # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12964 * a.iterator = itr
|
|
jpayne@69
|
12965 *
|
|
jpayne@69
|
12966 */
|
|
jpayne@69
|
12967 __Pyx_INCREF((PyObject *)__pyx_v_fileobj);
|
|
jpayne@69
|
12968 __Pyx_GIVEREF((PyObject *)__pyx_v_fileobj);
|
|
jpayne@69
|
12969 __Pyx_GOTREF((PyObject *)__pyx_v_a->tabixfile);
|
|
jpayne@69
|
12970 __Pyx_DECREF((PyObject *)__pyx_v_a->tabixfile);
|
|
jpayne@69
|
12971 __pyx_v_a->tabixfile = __pyx_v_fileobj;
|
|
jpayne@69
|
12972
|
|
jpayne@69
|
12973 /* "pysam/libctabix.pyx":523
|
|
jpayne@69
|
12974 *
|
|
jpayne@69
|
12975 * a.tabixfile = fileobj
|
|
jpayne@69
|
12976 * a.iterator = itr # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12977 *
|
|
jpayne@69
|
12978 * return a
|
|
jpayne@69
|
12979 */
|
|
jpayne@69
|
12980 __pyx_v_a->iterator = __pyx_v_itr;
|
|
jpayne@69
|
12981
|
|
jpayne@69
|
12982 /* "pysam/libctabix.pyx":525
|
|
jpayne@69
|
12983 * a.iterator = itr
|
|
jpayne@69
|
12984 *
|
|
jpayne@69
|
12985 * return a # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12986 *
|
|
jpayne@69
|
12987 * ###############################################################
|
|
jpayne@69
|
12988 */
|
|
jpayne@69
|
12989 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
12990 __Pyx_INCREF((PyObject *)__pyx_v_a);
|
|
jpayne@69
|
12991 __pyx_r = ((PyObject *)__pyx_v_a);
|
|
jpayne@69
|
12992 goto __pyx_L0;
|
|
jpayne@69
|
12993
|
|
jpayne@69
|
12994 /* "pysam/libctabix.pyx":416
|
|
jpayne@69
|
12995 * encoding=self.encoding)
|
|
jpayne@69
|
12996 *
|
|
jpayne@69
|
12997 * def fetch(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12998 * reference=None,
|
|
jpayne@69
|
12999 * start=None,
|
|
jpayne@69
|
13000 */
|
|
jpayne@69
|
13001
|
|
jpayne@69
|
13002 /* function exit code */
|
|
jpayne@69
|
13003 __pyx_L1_error:;
|
|
jpayne@69
|
13004 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
13005 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
13006 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
13007 __Pyx_AddTraceback("pysam.libctabix.TabixFile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
13008 __pyx_r = NULL;
|
|
jpayne@69
|
13009 __pyx_L0:;
|
|
jpayne@69
|
13010 __Pyx_XDECREF((PyObject *)__pyx_v_fileobj);
|
|
jpayne@69
|
13011 __Pyx_XDECREF(__pyx_v_s);
|
|
jpayne@69
|
13012 __Pyx_XDECREF((PyObject *)__pyx_v_a);
|
|
jpayne@69
|
13013 __Pyx_XDECREF(__pyx_v_start);
|
|
jpayne@69
|
13014 __Pyx_XDECREF(__pyx_v_region);
|
|
jpayne@69
|
13015 __Pyx_XDECREF(__pyx_v_parser);
|
|
jpayne@69
|
13016 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
13017 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
13018 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13019 return __pyx_r;
|
|
jpayne@69
|
13020 }
|
|
jpayne@69
|
13021
|
|
jpayne@69
|
13022 /* "pysam/libctabix.pyx":543
|
|
jpayne@69
|
13023 * '''
|
|
jpayne@69
|
13024 *
|
|
jpayne@69
|
13025 * def __get__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13026 *
|
|
jpayne@69
|
13027 * cdef char *cfilename = self.filename
|
|
jpayne@69
|
13028 */
|
|
jpayne@69
|
13029
|
|
jpayne@69
|
13030 /* Python wrapper */
|
|
jpayne@69
|
13031 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
13032 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_6header_1__get__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
13033 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
13034 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
13035 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13036 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
|
|
jpayne@69
|
13037 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
13038 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_6header___get__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
13039
|
|
jpayne@69
|
13040 /* function exit code */
|
|
jpayne@69
|
13041 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13042 return __pyx_r;
|
|
jpayne@69
|
13043 }
|
|
jpayne@69
|
13044
|
|
jpayne@69
|
13045 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6header___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
13046 char *__pyx_v_cfilename;
|
|
jpayne@69
|
13047 char *__pyx_v_cfilename_index;
|
|
jpayne@69
|
13048 kstring_t __pyx_v_buffer;
|
|
jpayne@69
|
13049 htsFile *__pyx_v_fp;
|
|
jpayne@69
|
13050 int __pyx_v_KS_SEP_LINE;
|
|
jpayne@69
|
13051 tbx_t *__pyx_v_tbx;
|
|
jpayne@69
|
13052 PyObject *__pyx_v_lines = NULL;
|
|
jpayne@69
|
13053 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
13054 __Pyx_TraceDeclarations
|
|
jpayne@69
|
13055 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13056 char *__pyx_t_1;
|
|
jpayne@69
|
13057 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
13058 int __pyx_t_3;
|
|
jpayne@69
|
13059 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
13060 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
13061 unsigned int __pyx_t_6;
|
|
jpayne@69
|
13062 int __pyx_t_7;
|
|
jpayne@69
|
13063 struct __pyx_opt_args_5pysam_9libcutils_force_str __pyx_t_8;
|
|
jpayne@69
|
13064 int __pyx_t_9;
|
|
jpayne@69
|
13065 int __pyx_lineno = 0;
|
|
jpayne@69
|
13066 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
13067 int __pyx_clineno = 0;
|
|
jpayne@69
|
13068 __Pyx_RefNannySetupContext("__get__", 1);
|
|
jpayne@69
|
13069 __Pyx_TraceCall("__get__", __pyx_f[0], 543, 0, __PYX_ERR(0, 543, __pyx_L1_error));
|
|
jpayne@69
|
13070
|
|
jpayne@69
|
13071 /* "pysam/libctabix.pyx":545
|
|
jpayne@69
|
13072 * def __get__(self):
|
|
jpayne@69
|
13073 *
|
|
jpayne@69
|
13074 * cdef char *cfilename = self.filename # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13075 * cdef char *cfilename_index = self.filename_index
|
|
jpayne@69
|
13076 *
|
|
jpayne@69
|
13077 */
|
|
jpayne@69
|
13078 __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.filename); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 545, __pyx_L1_error)
|
|
jpayne@69
|
13079 __pyx_v_cfilename = __pyx_t_1;
|
|
jpayne@69
|
13080
|
|
jpayne@69
|
13081 /* "pysam/libctabix.pyx":546
|
|
jpayne@69
|
13082 *
|
|
jpayne@69
|
13083 * cdef char *cfilename = self.filename
|
|
jpayne@69
|
13084 * cdef char *cfilename_index = self.filename_index # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13085 *
|
|
jpayne@69
|
13086 * cdef kstring_t buffer
|
|
jpayne@69
|
13087 */
|
|
jpayne@69
|
13088 __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->filename_index); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 546, __pyx_L1_error)
|
|
jpayne@69
|
13089 __pyx_v_cfilename_index = __pyx_t_1;
|
|
jpayne@69
|
13090
|
|
jpayne@69
|
13091 /* "pysam/libctabix.pyx":549
|
|
jpayne@69
|
13092 *
|
|
jpayne@69
|
13093 * cdef kstring_t buffer
|
|
jpayne@69
|
13094 * buffer.l = buffer.m = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13095 * buffer.s = NULL
|
|
jpayne@69
|
13096 *
|
|
jpayne@69
|
13097 */
|
|
jpayne@69
|
13098 __pyx_v_buffer.l = 0;
|
|
jpayne@69
|
13099 __pyx_v_buffer.m = 0;
|
|
jpayne@69
|
13100
|
|
jpayne@69
|
13101 /* "pysam/libctabix.pyx":550
|
|
jpayne@69
|
13102 * cdef kstring_t buffer
|
|
jpayne@69
|
13103 * buffer.l = buffer.m = 0
|
|
jpayne@69
|
13104 * buffer.s = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13105 *
|
|
jpayne@69
|
13106 * cdef htsFile * fp = NULL
|
|
jpayne@69
|
13107 */
|
|
jpayne@69
|
13108 __pyx_v_buffer.s = NULL;
|
|
jpayne@69
|
13109
|
|
jpayne@69
|
13110 /* "pysam/libctabix.pyx":552
|
|
jpayne@69
|
13111 * buffer.s = NULL
|
|
jpayne@69
|
13112 *
|
|
jpayne@69
|
13113 * cdef htsFile * fp = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13114 * cdef int KS_SEP_LINE = 2
|
|
jpayne@69
|
13115 * cdef tbx_t * tbx = NULL
|
|
jpayne@69
|
13116 */
|
|
jpayne@69
|
13117 __pyx_v_fp = NULL;
|
|
jpayne@69
|
13118
|
|
jpayne@69
|
13119 /* "pysam/libctabix.pyx":553
|
|
jpayne@69
|
13120 *
|
|
jpayne@69
|
13121 * cdef htsFile * fp = NULL
|
|
jpayne@69
|
13122 * cdef int KS_SEP_LINE = 2 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13123 * cdef tbx_t * tbx = NULL
|
|
jpayne@69
|
13124 * lines = []
|
|
jpayne@69
|
13125 */
|
|
jpayne@69
|
13126 __pyx_v_KS_SEP_LINE = 2;
|
|
jpayne@69
|
13127
|
|
jpayne@69
|
13128 /* "pysam/libctabix.pyx":554
|
|
jpayne@69
|
13129 * cdef htsFile * fp = NULL
|
|
jpayne@69
|
13130 * cdef int KS_SEP_LINE = 2
|
|
jpayne@69
|
13131 * cdef tbx_t * tbx = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13132 * lines = []
|
|
jpayne@69
|
13133 * with nogil:
|
|
jpayne@69
|
13134 */
|
|
jpayne@69
|
13135 __pyx_v_tbx = NULL;
|
|
jpayne@69
|
13136
|
|
jpayne@69
|
13137 /* "pysam/libctabix.pyx":555
|
|
jpayne@69
|
13138 * cdef int KS_SEP_LINE = 2
|
|
jpayne@69
|
13139 * cdef tbx_t * tbx = NULL
|
|
jpayne@69
|
13140 * lines = [] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13141 * with nogil:
|
|
jpayne@69
|
13142 * fp = hts_open(cfilename, 'r')
|
|
jpayne@69
|
13143 */
|
|
jpayne@69
|
13144 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 555, __pyx_L1_error)
|
|
jpayne@69
|
13145 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
13146 __pyx_v_lines = ((PyObject*)__pyx_t_2);
|
|
jpayne@69
|
13147 __pyx_t_2 = 0;
|
|
jpayne@69
|
13148
|
|
jpayne@69
|
13149 /* "pysam/libctabix.pyx":556
|
|
jpayne@69
|
13150 * cdef tbx_t * tbx = NULL
|
|
jpayne@69
|
13151 * lines = []
|
|
jpayne@69
|
13152 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13153 * fp = hts_open(cfilename, 'r')
|
|
jpayne@69
|
13154 *
|
|
jpayne@69
|
13155 */
|
|
jpayne@69
|
13156 {
|
|
jpayne@69
|
13157 #ifdef WITH_THREAD
|
|
jpayne@69
|
13158 PyThreadState *_save;
|
|
jpayne@69
|
13159 _save = NULL;
|
|
jpayne@69
|
13160 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
13161 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
13162 #endif
|
|
jpayne@69
|
13163 /*try:*/ {
|
|
jpayne@69
|
13164
|
|
jpayne@69
|
13165 /* "pysam/libctabix.pyx":557
|
|
jpayne@69
|
13166 * lines = []
|
|
jpayne@69
|
13167 * with nogil:
|
|
jpayne@69
|
13168 * fp = hts_open(cfilename, 'r') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13169 *
|
|
jpayne@69
|
13170 * if fp == NULL:
|
|
jpayne@69
|
13171 */
|
|
jpayne@69
|
13172 __pyx_v_fp = hts_open(__pyx_v_cfilename, ((char const *)"r"));
|
|
jpayne@69
|
13173 }
|
|
jpayne@69
|
13174
|
|
jpayne@69
|
13175 /* "pysam/libctabix.pyx":556
|
|
jpayne@69
|
13176 * cdef tbx_t * tbx = NULL
|
|
jpayne@69
|
13177 * lines = []
|
|
jpayne@69
|
13178 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13179 * fp = hts_open(cfilename, 'r')
|
|
jpayne@69
|
13180 *
|
|
jpayne@69
|
13181 */
|
|
jpayne@69
|
13182 /*finally:*/ {
|
|
jpayne@69
|
13183 /*normal exit:*/{
|
|
jpayne@69
|
13184 #ifdef WITH_THREAD
|
|
jpayne@69
|
13185 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
13186 Py_BLOCK_THREADS
|
|
jpayne@69
|
13187 #endif
|
|
jpayne@69
|
13188 goto __pyx_L5;
|
|
jpayne@69
|
13189 }
|
|
jpayne@69
|
13190 __pyx_L5:;
|
|
jpayne@69
|
13191 }
|
|
jpayne@69
|
13192 }
|
|
jpayne@69
|
13193
|
|
jpayne@69
|
13194 /* "pysam/libctabix.pyx":559
|
|
jpayne@69
|
13195 * fp = hts_open(cfilename, 'r')
|
|
jpayne@69
|
13196 *
|
|
jpayne@69
|
13197 * if fp == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13198 * raise OSError("could not open {} for reading header".format(self.filename))
|
|
jpayne@69
|
13199 *
|
|
jpayne@69
|
13200 */
|
|
jpayne@69
|
13201 __pyx_t_3 = (__pyx_v_fp == NULL);
|
|
jpayne@69
|
13202 if (unlikely(__pyx_t_3)) {
|
|
jpayne@69
|
13203
|
|
jpayne@69
|
13204 /* "pysam/libctabix.pyx":560
|
|
jpayne@69
|
13205 *
|
|
jpayne@69
|
13206 * if fp == NULL:
|
|
jpayne@69
|
13207 * raise OSError("could not open {} for reading header".format(self.filename)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13208 *
|
|
jpayne@69
|
13209 * with nogil:
|
|
jpayne@69
|
13210 */
|
|
jpayne@69
|
13211 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_could_not_open_for_reading_heade, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 560, __pyx_L1_error)
|
|
jpayne@69
|
13212 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
13213 __pyx_t_5 = NULL;
|
|
jpayne@69
|
13214 __pyx_t_6 = 0;
|
|
jpayne@69
|
13215 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
13216 if (likely(PyMethod_Check(__pyx_t_4))) {
|
|
jpayne@69
|
13217 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4);
|
|
jpayne@69
|
13218 if (likely(__pyx_t_5)) {
|
|
jpayne@69
|
13219 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
|
|
jpayne@69
|
13220 __Pyx_INCREF(__pyx_t_5);
|
|
jpayne@69
|
13221 __Pyx_INCREF(function);
|
|
jpayne@69
|
13222 __Pyx_DECREF_SET(__pyx_t_4, function);
|
|
jpayne@69
|
13223 __pyx_t_6 = 1;
|
|
jpayne@69
|
13224 }
|
|
jpayne@69
|
13225 }
|
|
jpayne@69
|
13226 #endif
|
|
jpayne@69
|
13227 {
|
|
jpayne@69
|
13228 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_self->__pyx_base.filename};
|
|
jpayne@69
|
13229 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6);
|
|
jpayne@69
|
13230 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
13231 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 560, __pyx_L1_error)
|
|
jpayne@69
|
13232 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
13233 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
13234 }
|
|
jpayne@69
|
13235 __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_OSError, __pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 560, __pyx_L1_error)
|
|
jpayne@69
|
13236 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
13237 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
13238 __Pyx_Raise(__pyx_t_4, 0, 0, 0);
|
|
jpayne@69
|
13239 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
13240 __PYX_ERR(0, 560, __pyx_L1_error)
|
|
jpayne@69
|
13241
|
|
jpayne@69
|
13242 /* "pysam/libctabix.pyx":559
|
|
jpayne@69
|
13243 * fp = hts_open(cfilename, 'r')
|
|
jpayne@69
|
13244 *
|
|
jpayne@69
|
13245 * if fp == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13246 * raise OSError("could not open {} for reading header".format(self.filename))
|
|
jpayne@69
|
13247 *
|
|
jpayne@69
|
13248 */
|
|
jpayne@69
|
13249 }
|
|
jpayne@69
|
13250
|
|
jpayne@69
|
13251 /* "pysam/libctabix.pyx":562
|
|
jpayne@69
|
13252 * raise OSError("could not open {} for reading header".format(self.filename))
|
|
jpayne@69
|
13253 *
|
|
jpayne@69
|
13254 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13255 * tbx = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
13256 *
|
|
jpayne@69
|
13257 */
|
|
jpayne@69
|
13258 {
|
|
jpayne@69
|
13259 #ifdef WITH_THREAD
|
|
jpayne@69
|
13260 PyThreadState *_save;
|
|
jpayne@69
|
13261 _save = NULL;
|
|
jpayne@69
|
13262 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
13263 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
13264 #endif
|
|
jpayne@69
|
13265 /*try:*/ {
|
|
jpayne@69
|
13266
|
|
jpayne@69
|
13267 /* "pysam/libctabix.pyx":563
|
|
jpayne@69
|
13268 *
|
|
jpayne@69
|
13269 * with nogil:
|
|
jpayne@69
|
13270 * tbx = tbx_index_load2(cfilename, cfilename_index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13271 *
|
|
jpayne@69
|
13272 * if tbx == NULL:
|
|
jpayne@69
|
13273 */
|
|
jpayne@69
|
13274 __pyx_v_tbx = tbx_index_load2(__pyx_v_cfilename, __pyx_v_cfilename_index);
|
|
jpayne@69
|
13275 }
|
|
jpayne@69
|
13276
|
|
jpayne@69
|
13277 /* "pysam/libctabix.pyx":562
|
|
jpayne@69
|
13278 * raise OSError("could not open {} for reading header".format(self.filename))
|
|
jpayne@69
|
13279 *
|
|
jpayne@69
|
13280 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13281 * tbx = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
13282 *
|
|
jpayne@69
|
13283 */
|
|
jpayne@69
|
13284 /*finally:*/ {
|
|
jpayne@69
|
13285 /*normal exit:*/{
|
|
jpayne@69
|
13286 #ifdef WITH_THREAD
|
|
jpayne@69
|
13287 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
13288 Py_BLOCK_THREADS
|
|
jpayne@69
|
13289 #endif
|
|
jpayne@69
|
13290 goto __pyx_L9;
|
|
jpayne@69
|
13291 }
|
|
jpayne@69
|
13292 __pyx_L9:;
|
|
jpayne@69
|
13293 }
|
|
jpayne@69
|
13294 }
|
|
jpayne@69
|
13295
|
|
jpayne@69
|
13296 /* "pysam/libctabix.pyx":565
|
|
jpayne@69
|
13297 * tbx = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
13298 *
|
|
jpayne@69
|
13299 * if tbx == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13300 * raise OSError("could not load .tbi/.csi index of {}".format(self.filename))
|
|
jpayne@69
|
13301 *
|
|
jpayne@69
|
13302 */
|
|
jpayne@69
|
13303 __pyx_t_3 = (__pyx_v_tbx == NULL);
|
|
jpayne@69
|
13304 if (unlikely(__pyx_t_3)) {
|
|
jpayne@69
|
13305
|
|
jpayne@69
|
13306 /* "pysam/libctabix.pyx":566
|
|
jpayne@69
|
13307 *
|
|
jpayne@69
|
13308 * if tbx == NULL:
|
|
jpayne@69
|
13309 * raise OSError("could not load .tbi/.csi index of {}".format(self.filename)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13310 *
|
|
jpayne@69
|
13311 * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0:
|
|
jpayne@69
|
13312 */
|
|
jpayne@69
|
13313 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_could_not_load_tbi_csi_index_of, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 566, __pyx_L1_error)
|
|
jpayne@69
|
13314 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
13315 __pyx_t_5 = NULL;
|
|
jpayne@69
|
13316 __pyx_t_6 = 0;
|
|
jpayne@69
|
13317 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
13318 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
13319 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
13320 if (likely(__pyx_t_5)) {
|
|
jpayne@69
|
13321 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
13322 __Pyx_INCREF(__pyx_t_5);
|
|
jpayne@69
|
13323 __Pyx_INCREF(function);
|
|
jpayne@69
|
13324 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
13325 __pyx_t_6 = 1;
|
|
jpayne@69
|
13326 }
|
|
jpayne@69
|
13327 }
|
|
jpayne@69
|
13328 #endif
|
|
jpayne@69
|
13329 {
|
|
jpayne@69
|
13330 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_self->__pyx_base.filename};
|
|
jpayne@69
|
13331 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6);
|
|
jpayne@69
|
13332 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
13333 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 566, __pyx_L1_error)
|
|
jpayne@69
|
13334 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
13335 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
13336 }
|
|
jpayne@69
|
13337 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_OSError, __pyx_t_4); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 566, __pyx_L1_error)
|
|
jpayne@69
|
13338 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
13339 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
13340 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
13341 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
13342 __PYX_ERR(0, 566, __pyx_L1_error)
|
|
jpayne@69
|
13343
|
|
jpayne@69
|
13344 /* "pysam/libctabix.pyx":565
|
|
jpayne@69
|
13345 * tbx = tbx_index_load2(cfilename, cfilename_index)
|
|
jpayne@69
|
13346 *
|
|
jpayne@69
|
13347 * if tbx == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13348 * raise OSError("could not load .tbi/.csi index of {}".format(self.filename))
|
|
jpayne@69
|
13349 *
|
|
jpayne@69
|
13350 */
|
|
jpayne@69
|
13351 }
|
|
jpayne@69
|
13352
|
|
jpayne@69
|
13353 /* "pysam/libctabix.pyx":568
|
|
jpayne@69
|
13354 * raise OSError("could not load .tbi/.csi index of {}".format(self.filename))
|
|
jpayne@69
|
13355 *
|
|
jpayne@69
|
13356 * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13357 * if not buffer.l or buffer.s[0] != tbx.conf.meta_char:
|
|
jpayne@69
|
13358 * break
|
|
jpayne@69
|
13359 */
|
|
jpayne@69
|
13360 while (1) {
|
|
jpayne@69
|
13361 __pyx_t_3 = (hts_getline(__pyx_v_fp, __pyx_v_KS_SEP_LINE, (&__pyx_v_buffer)) >= 0);
|
|
jpayne@69
|
13362 if (!__pyx_t_3) break;
|
|
jpayne@69
|
13363
|
|
jpayne@69
|
13364 /* "pysam/libctabix.pyx":569
|
|
jpayne@69
|
13365 *
|
|
jpayne@69
|
13366 * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0:
|
|
jpayne@69
|
13367 * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13368 * break
|
|
jpayne@69
|
13369 * lines.append(force_str(buffer.s, self.encoding))
|
|
jpayne@69
|
13370 */
|
|
jpayne@69
|
13371 __pyx_t_7 = (!(__pyx_v_buffer.l != 0));
|
|
jpayne@69
|
13372 if (!__pyx_t_7) {
|
|
jpayne@69
|
13373 } else {
|
|
jpayne@69
|
13374 __pyx_t_3 = __pyx_t_7;
|
|
jpayne@69
|
13375 goto __pyx_L14_bool_binop_done;
|
|
jpayne@69
|
13376 }
|
|
jpayne@69
|
13377 __pyx_t_7 = ((__pyx_v_buffer.s[0]) != __pyx_v_tbx->conf.meta_char);
|
|
jpayne@69
|
13378 __pyx_t_3 = __pyx_t_7;
|
|
jpayne@69
|
13379 __pyx_L14_bool_binop_done:;
|
|
jpayne@69
|
13380 if (__pyx_t_3) {
|
|
jpayne@69
|
13381
|
|
jpayne@69
|
13382 /* "pysam/libctabix.pyx":570
|
|
jpayne@69
|
13383 * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0:
|
|
jpayne@69
|
13384 * if not buffer.l or buffer.s[0] != tbx.conf.meta_char:
|
|
jpayne@69
|
13385 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13386 * lines.append(force_str(buffer.s, self.encoding))
|
|
jpayne@69
|
13387 *
|
|
jpayne@69
|
13388 */
|
|
jpayne@69
|
13389 goto __pyx_L12_break;
|
|
jpayne@69
|
13390
|
|
jpayne@69
|
13391 /* "pysam/libctabix.pyx":569
|
|
jpayne@69
|
13392 *
|
|
jpayne@69
|
13393 * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0:
|
|
jpayne@69
|
13394 * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13395 * break
|
|
jpayne@69
|
13396 * lines.append(force_str(buffer.s, self.encoding))
|
|
jpayne@69
|
13397 */
|
|
jpayne@69
|
13398 }
|
|
jpayne@69
|
13399
|
|
jpayne@69
|
13400 /* "pysam/libctabix.pyx":571
|
|
jpayne@69
|
13401 * if not buffer.l or buffer.s[0] != tbx.conf.meta_char:
|
|
jpayne@69
|
13402 * break
|
|
jpayne@69
|
13403 * lines.append(force_str(buffer.s, self.encoding)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13404 *
|
|
jpayne@69
|
13405 * with nogil:
|
|
jpayne@69
|
13406 */
|
|
jpayne@69
|
13407 __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_buffer.s); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 571, __pyx_L1_error)
|
|
jpayne@69
|
13408 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
13409 __pyx_t_4 = __pyx_v_self->encoding;
|
|
jpayne@69
|
13410 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
13411 __pyx_t_8.__pyx_n = 1;
|
|
jpayne@69
|
13412 __pyx_t_8.encoding = __pyx_t_4;
|
|
jpayne@69
|
13413 __pyx_t_5 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_2, &__pyx_t_8); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 571, __pyx_L1_error)
|
|
jpayne@69
|
13414 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
13415 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
13416 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
13417 __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_lines, __pyx_t_5); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 571, __pyx_L1_error)
|
|
jpayne@69
|
13418 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
13419 }
|
|
jpayne@69
|
13420 __pyx_L12_break:;
|
|
jpayne@69
|
13421
|
|
jpayne@69
|
13422 /* "pysam/libctabix.pyx":573
|
|
jpayne@69
|
13423 * lines.append(force_str(buffer.s, self.encoding))
|
|
jpayne@69
|
13424 *
|
|
jpayne@69
|
13425 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13426 * hts_close(fp)
|
|
jpayne@69
|
13427 * free(buffer.s)
|
|
jpayne@69
|
13428 */
|
|
jpayne@69
|
13429 {
|
|
jpayne@69
|
13430 #ifdef WITH_THREAD
|
|
jpayne@69
|
13431 PyThreadState *_save;
|
|
jpayne@69
|
13432 _save = NULL;
|
|
jpayne@69
|
13433 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
13434 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
13435 #endif
|
|
jpayne@69
|
13436 /*try:*/ {
|
|
jpayne@69
|
13437
|
|
jpayne@69
|
13438 /* "pysam/libctabix.pyx":574
|
|
jpayne@69
|
13439 *
|
|
jpayne@69
|
13440 * with nogil:
|
|
jpayne@69
|
13441 * hts_close(fp) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13442 * free(buffer.s)
|
|
jpayne@69
|
13443 *
|
|
jpayne@69
|
13444 */
|
|
jpayne@69
|
13445 (void)(hts_close(__pyx_v_fp));
|
|
jpayne@69
|
13446
|
|
jpayne@69
|
13447 /* "pysam/libctabix.pyx":575
|
|
jpayne@69
|
13448 * with nogil:
|
|
jpayne@69
|
13449 * hts_close(fp)
|
|
jpayne@69
|
13450 * free(buffer.s) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13451 *
|
|
jpayne@69
|
13452 * return lines
|
|
jpayne@69
|
13453 */
|
|
jpayne@69
|
13454 free(__pyx_v_buffer.s);
|
|
jpayne@69
|
13455 }
|
|
jpayne@69
|
13456
|
|
jpayne@69
|
13457 /* "pysam/libctabix.pyx":573
|
|
jpayne@69
|
13458 * lines.append(force_str(buffer.s, self.encoding))
|
|
jpayne@69
|
13459 *
|
|
jpayne@69
|
13460 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13461 * hts_close(fp)
|
|
jpayne@69
|
13462 * free(buffer.s)
|
|
jpayne@69
|
13463 */
|
|
jpayne@69
|
13464 /*finally:*/ {
|
|
jpayne@69
|
13465 /*normal exit:*/{
|
|
jpayne@69
|
13466 #ifdef WITH_THREAD
|
|
jpayne@69
|
13467 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
13468 Py_BLOCK_THREADS
|
|
jpayne@69
|
13469 #endif
|
|
jpayne@69
|
13470 goto __pyx_L18;
|
|
jpayne@69
|
13471 }
|
|
jpayne@69
|
13472 __pyx_L18:;
|
|
jpayne@69
|
13473 }
|
|
jpayne@69
|
13474 }
|
|
jpayne@69
|
13475
|
|
jpayne@69
|
13476 /* "pysam/libctabix.pyx":577
|
|
jpayne@69
|
13477 * free(buffer.s)
|
|
jpayne@69
|
13478 *
|
|
jpayne@69
|
13479 * return lines # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13480 *
|
|
jpayne@69
|
13481 * property contigs:
|
|
jpayne@69
|
13482 */
|
|
jpayne@69
|
13483 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
13484 __Pyx_INCREF(__pyx_v_lines);
|
|
jpayne@69
|
13485 __pyx_r = __pyx_v_lines;
|
|
jpayne@69
|
13486 goto __pyx_L0;
|
|
jpayne@69
|
13487
|
|
jpayne@69
|
13488 /* "pysam/libctabix.pyx":543
|
|
jpayne@69
|
13489 * '''
|
|
jpayne@69
|
13490 *
|
|
jpayne@69
|
13491 * def __get__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13492 *
|
|
jpayne@69
|
13493 * cdef char *cfilename = self.filename
|
|
jpayne@69
|
13494 */
|
|
jpayne@69
|
13495
|
|
jpayne@69
|
13496 /* function exit code */
|
|
jpayne@69
|
13497 __pyx_L1_error:;
|
|
jpayne@69
|
13498 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
13499 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
13500 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
13501 __Pyx_AddTraceback("pysam.libctabix.TabixFile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
13502 __pyx_r = NULL;
|
|
jpayne@69
|
13503 __pyx_L0:;
|
|
jpayne@69
|
13504 __Pyx_XDECREF(__pyx_v_lines);
|
|
jpayne@69
|
13505 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
13506 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
13507 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13508 return __pyx_r;
|
|
jpayne@69
|
13509 }
|
|
jpayne@69
|
13510
|
|
jpayne@69
|
13511 /* "pysam/libctabix.pyx":581
|
|
jpayne@69
|
13512 * property contigs:
|
|
jpayne@69
|
13513 * '''list of chromosome names'''
|
|
jpayne@69
|
13514 * def __get__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13515 * cdef const char ** sequences
|
|
jpayne@69
|
13516 * cdef int nsequences
|
|
jpayne@69
|
13517 */
|
|
jpayne@69
|
13518
|
|
jpayne@69
|
13519 /* Python wrapper */
|
|
jpayne@69
|
13520 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7contigs_1__get__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
13521 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7contigs_1__get__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
13522 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
13523 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
13524 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13525 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
|
|
jpayne@69
|
13526 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
13527 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
13528
|
|
jpayne@69
|
13529 /* function exit code */
|
|
jpayne@69
|
13530 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13531 return __pyx_r;
|
|
jpayne@69
|
13532 }
|
|
jpayne@69
|
13533
|
|
jpayne@69
|
13534 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
13535 char const **__pyx_v_sequences;
|
|
jpayne@69
|
13536 int __pyx_v_nsequences;
|
|
jpayne@69
|
13537 int __pyx_v_x;
|
|
jpayne@69
|
13538 PyObject *__pyx_v_result = NULL;
|
|
jpayne@69
|
13539 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
13540 __Pyx_TraceDeclarations
|
|
jpayne@69
|
13541 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13542 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
13543 int __pyx_t_2;
|
|
jpayne@69
|
13544 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
13545 int __pyx_t_4;
|
|
jpayne@69
|
13546 int __pyx_lineno = 0;
|
|
jpayne@69
|
13547 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
13548 int __pyx_clineno = 0;
|
|
jpayne@69
|
13549 __Pyx_RefNannySetupContext("__get__", 1);
|
|
jpayne@69
|
13550 __Pyx_TraceCall("__get__", __pyx_f[0], 581, 0, __PYX_ERR(0, 581, __pyx_L1_error));
|
|
jpayne@69
|
13551
|
|
jpayne@69
|
13552 /* "pysam/libctabix.pyx":585
|
|
jpayne@69
|
13553 * cdef int nsequences
|
|
jpayne@69
|
13554 *
|
|
jpayne@69
|
13555 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13556 * sequences = tbx_seqnames(self.index, &nsequences)
|
|
jpayne@69
|
13557 * cdef int x
|
|
jpayne@69
|
13558 */
|
|
jpayne@69
|
13559 {
|
|
jpayne@69
|
13560 #ifdef WITH_THREAD
|
|
jpayne@69
|
13561 PyThreadState *_save;
|
|
jpayne@69
|
13562 _save = NULL;
|
|
jpayne@69
|
13563 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
13564 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
13565 #endif
|
|
jpayne@69
|
13566 /*try:*/ {
|
|
jpayne@69
|
13567
|
|
jpayne@69
|
13568 /* "pysam/libctabix.pyx":586
|
|
jpayne@69
|
13569 *
|
|
jpayne@69
|
13570 * with nogil:
|
|
jpayne@69
|
13571 * sequences = tbx_seqnames(self.index, &nsequences) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13572 * cdef int x
|
|
jpayne@69
|
13573 * result = []
|
|
jpayne@69
|
13574 */
|
|
jpayne@69
|
13575 __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
|
|
jpayne@69
|
13576 }
|
|
jpayne@69
|
13577
|
|
jpayne@69
|
13578 /* "pysam/libctabix.pyx":585
|
|
jpayne@69
|
13579 * cdef int nsequences
|
|
jpayne@69
|
13580 *
|
|
jpayne@69
|
13581 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13582 * sequences = tbx_seqnames(self.index, &nsequences)
|
|
jpayne@69
|
13583 * cdef int x
|
|
jpayne@69
|
13584 */
|
|
jpayne@69
|
13585 /*finally:*/ {
|
|
jpayne@69
|
13586 /*normal exit:*/{
|
|
jpayne@69
|
13587 #ifdef WITH_THREAD
|
|
jpayne@69
|
13588 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
13589 Py_BLOCK_THREADS
|
|
jpayne@69
|
13590 #endif
|
|
jpayne@69
|
13591 goto __pyx_L5;
|
|
jpayne@69
|
13592 }
|
|
jpayne@69
|
13593 __pyx_L5:;
|
|
jpayne@69
|
13594 }
|
|
jpayne@69
|
13595 }
|
|
jpayne@69
|
13596
|
|
jpayne@69
|
13597 /* "pysam/libctabix.pyx":588
|
|
jpayne@69
|
13598 * sequences = tbx_seqnames(self.index, &nsequences)
|
|
jpayne@69
|
13599 * cdef int x
|
|
jpayne@69
|
13600 * result = [] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13601 * for x from 0 <= x < nsequences:
|
|
jpayne@69
|
13602 * result.append(force_str(sequences[x]))
|
|
jpayne@69
|
13603 */
|
|
jpayne@69
|
13604 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 588, __pyx_L1_error)
|
|
jpayne@69
|
13605 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
13606 __pyx_v_result = ((PyObject*)__pyx_t_1);
|
|
jpayne@69
|
13607 __pyx_t_1 = 0;
|
|
jpayne@69
|
13608
|
|
jpayne@69
|
13609 /* "pysam/libctabix.pyx":589
|
|
jpayne@69
|
13610 * cdef int x
|
|
jpayne@69
|
13611 * result = []
|
|
jpayne@69
|
13612 * for x from 0 <= x < nsequences: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13613 * result.append(force_str(sequences[x]))
|
|
jpayne@69
|
13614 *
|
|
jpayne@69
|
13615 */
|
|
jpayne@69
|
13616 __pyx_t_2 = __pyx_v_nsequences;
|
|
jpayne@69
|
13617 for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) {
|
|
jpayne@69
|
13618
|
|
jpayne@69
|
13619 /* "pysam/libctabix.pyx":590
|
|
jpayne@69
|
13620 * result = []
|
|
jpayne@69
|
13621 * for x from 0 <= x < nsequences:
|
|
jpayne@69
|
13622 * result.append(force_str(sequences[x])) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13623 *
|
|
jpayne@69
|
13624 * # htslib instructions:
|
|
jpayne@69
|
13625 */
|
|
jpayne@69
|
13626 __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_sequences[__pyx_v_x])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 590, __pyx_L1_error)
|
|
jpayne@69
|
13627 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
13628 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 590, __pyx_L1_error)
|
|
jpayne@69
|
13629 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
13630 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
13631 __pyx_t_4 = __Pyx_PyList_Append(__pyx_v_result, __pyx_t_3); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 590, __pyx_L1_error)
|
|
jpayne@69
|
13632 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
13633 }
|
|
jpayne@69
|
13634
|
|
jpayne@69
|
13635 /* "pysam/libctabix.pyx":594
|
|
jpayne@69
|
13636 * # htslib instructions:
|
|
jpayne@69
|
13637 * # only free container, not the sequences themselves
|
|
jpayne@69
|
13638 * free(sequences) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13639 *
|
|
jpayne@69
|
13640 * return result
|
|
jpayne@69
|
13641 */
|
|
jpayne@69
|
13642 free(__pyx_v_sequences);
|
|
jpayne@69
|
13643
|
|
jpayne@69
|
13644 /* "pysam/libctabix.pyx":596
|
|
jpayne@69
|
13645 * free(sequences)
|
|
jpayne@69
|
13646 *
|
|
jpayne@69
|
13647 * return result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13648 *
|
|
jpayne@69
|
13649 * def close(self):
|
|
jpayne@69
|
13650 */
|
|
jpayne@69
|
13651 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
13652 __Pyx_INCREF(__pyx_v_result);
|
|
jpayne@69
|
13653 __pyx_r = __pyx_v_result;
|
|
jpayne@69
|
13654 goto __pyx_L0;
|
|
jpayne@69
|
13655
|
|
jpayne@69
|
13656 /* "pysam/libctabix.pyx":581
|
|
jpayne@69
|
13657 * property contigs:
|
|
jpayne@69
|
13658 * '''list of chromosome names'''
|
|
jpayne@69
|
13659 * def __get__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13660 * cdef const char ** sequences
|
|
jpayne@69
|
13661 * cdef int nsequences
|
|
jpayne@69
|
13662 */
|
|
jpayne@69
|
13663
|
|
jpayne@69
|
13664 /* function exit code */
|
|
jpayne@69
|
13665 __pyx_L1_error:;
|
|
jpayne@69
|
13666 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
13667 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
13668 __Pyx_AddTraceback("pysam.libctabix.TabixFile.contigs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
13669 __pyx_r = NULL;
|
|
jpayne@69
|
13670 __pyx_L0:;
|
|
jpayne@69
|
13671 __Pyx_XDECREF(__pyx_v_result);
|
|
jpayne@69
|
13672 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
13673 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
13674 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13675 return __pyx_r;
|
|
jpayne@69
|
13676 }
|
|
jpayne@69
|
13677
|
|
jpayne@69
|
13678 /* "pysam/libctabix.pyx":598
|
|
jpayne@69
|
13679 * return result
|
|
jpayne@69
|
13680 *
|
|
jpayne@69
|
13681 * def close(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13682 * '''
|
|
jpayne@69
|
13683 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
13684 */
|
|
jpayne@69
|
13685
|
|
jpayne@69
|
13686 /* Python wrapper */
|
|
jpayne@69
|
13687 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_9close(PyObject *__pyx_v_self,
|
|
jpayne@69
|
13688 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
13689 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
13690 #else
|
|
jpayne@69
|
13691 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
13692 #endif
|
|
jpayne@69
|
13693 ); /*proto*/
|
|
jpayne@69
|
13694 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_8close, "TabixFile.close(self)\n\n closes the :class:`pysam.TabixFile`.");
|
|
jpayne@69
|
13695 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_9close = {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_9close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_8close};
|
|
jpayne@69
|
13696 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_9close(PyObject *__pyx_v_self,
|
|
jpayne@69
|
13697 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
13698 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
13699 #else
|
|
jpayne@69
|
13700 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
13701 #endif
|
|
jpayne@69
|
13702 ) {
|
|
jpayne@69
|
13703 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
13704 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
13705 #endif
|
|
jpayne@69
|
13706 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
13707 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
13708 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13709 __Pyx_RefNannySetupContext("close (wrapper)", 0);
|
|
jpayne@69
|
13710 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
13711 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
13712 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
13713 #else
|
|
jpayne@69
|
13714 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
13715 #endif
|
|
jpayne@69
|
13716 #endif
|
|
jpayne@69
|
13717 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
13718 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
13719 __Pyx_RaiseArgtupleInvalid("close", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
13720 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "close", 0))) return NULL;
|
|
jpayne@69
|
13721 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_8close(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
13722
|
|
jpayne@69
|
13723 /* function exit code */
|
|
jpayne@69
|
13724 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13725 return __pyx_r;
|
|
jpayne@69
|
13726 }
|
|
jpayne@69
|
13727
|
|
jpayne@69
|
13728 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_8close(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
13729 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
13730 __Pyx_TraceDeclarations
|
|
jpayne@69
|
13731 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13732 int __pyx_t_1;
|
|
jpayne@69
|
13733 int __pyx_lineno = 0;
|
|
jpayne@69
|
13734 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
13735 int __pyx_clineno = 0;
|
|
jpayne@69
|
13736 __Pyx_TraceFrameInit(__pyx_codeobj__21)
|
|
jpayne@69
|
13737 __Pyx_RefNannySetupContext("close", 1);
|
|
jpayne@69
|
13738 __Pyx_TraceCall("close", __pyx_f[0], 598, 0, __PYX_ERR(0, 598, __pyx_L1_error));
|
|
jpayne@69
|
13739
|
|
jpayne@69
|
13740 /* "pysam/libctabix.pyx":601
|
|
jpayne@69
|
13741 * '''
|
|
jpayne@69
|
13742 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
13743 * if self.htsfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13744 * hts_close(self.htsfile)
|
|
jpayne@69
|
13745 * self.htsfile = NULL
|
|
jpayne@69
|
13746 */
|
|
jpayne@69
|
13747 __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile != NULL);
|
|
jpayne@69
|
13748 if (__pyx_t_1) {
|
|
jpayne@69
|
13749
|
|
jpayne@69
|
13750 /* "pysam/libctabix.pyx":602
|
|
jpayne@69
|
13751 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
13752 * if self.htsfile != NULL:
|
|
jpayne@69
|
13753 * hts_close(self.htsfile) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13754 * self.htsfile = NULL
|
|
jpayne@69
|
13755 * if self.index != NULL:
|
|
jpayne@69
|
13756 */
|
|
jpayne@69
|
13757 (void)(hts_close(__pyx_v_self->__pyx_base.htsfile));
|
|
jpayne@69
|
13758
|
|
jpayne@69
|
13759 /* "pysam/libctabix.pyx":603
|
|
jpayne@69
|
13760 * if self.htsfile != NULL:
|
|
jpayne@69
|
13761 * hts_close(self.htsfile)
|
|
jpayne@69
|
13762 * self.htsfile = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13763 * if self.index != NULL:
|
|
jpayne@69
|
13764 * tbx_destroy(self.index)
|
|
jpayne@69
|
13765 */
|
|
jpayne@69
|
13766 __pyx_v_self->__pyx_base.htsfile = NULL;
|
|
jpayne@69
|
13767
|
|
jpayne@69
|
13768 /* "pysam/libctabix.pyx":601
|
|
jpayne@69
|
13769 * '''
|
|
jpayne@69
|
13770 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
13771 * if self.htsfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13772 * hts_close(self.htsfile)
|
|
jpayne@69
|
13773 * self.htsfile = NULL
|
|
jpayne@69
|
13774 */
|
|
jpayne@69
|
13775 }
|
|
jpayne@69
|
13776
|
|
jpayne@69
|
13777 /* "pysam/libctabix.pyx":604
|
|
jpayne@69
|
13778 * hts_close(self.htsfile)
|
|
jpayne@69
|
13779 * self.htsfile = NULL
|
|
jpayne@69
|
13780 * if self.index != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13781 * tbx_destroy(self.index)
|
|
jpayne@69
|
13782 * self.index = NULL
|
|
jpayne@69
|
13783 */
|
|
jpayne@69
|
13784 __pyx_t_1 = (__pyx_v_self->index != NULL);
|
|
jpayne@69
|
13785 if (__pyx_t_1) {
|
|
jpayne@69
|
13786
|
|
jpayne@69
|
13787 /* "pysam/libctabix.pyx":605
|
|
jpayne@69
|
13788 * self.htsfile = NULL
|
|
jpayne@69
|
13789 * if self.index != NULL:
|
|
jpayne@69
|
13790 * tbx_destroy(self.index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13791 * self.index = NULL
|
|
jpayne@69
|
13792 *
|
|
jpayne@69
|
13793 */
|
|
jpayne@69
|
13794 tbx_destroy(__pyx_v_self->index);
|
|
jpayne@69
|
13795
|
|
jpayne@69
|
13796 /* "pysam/libctabix.pyx":606
|
|
jpayne@69
|
13797 * if self.index != NULL:
|
|
jpayne@69
|
13798 * tbx_destroy(self.index)
|
|
jpayne@69
|
13799 * self.index = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13800 *
|
|
jpayne@69
|
13801 * def __dealloc__( self ):
|
|
jpayne@69
|
13802 */
|
|
jpayne@69
|
13803 __pyx_v_self->index = NULL;
|
|
jpayne@69
|
13804
|
|
jpayne@69
|
13805 /* "pysam/libctabix.pyx":604
|
|
jpayne@69
|
13806 * hts_close(self.htsfile)
|
|
jpayne@69
|
13807 * self.htsfile = NULL
|
|
jpayne@69
|
13808 * if self.index != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13809 * tbx_destroy(self.index)
|
|
jpayne@69
|
13810 * self.index = NULL
|
|
jpayne@69
|
13811 */
|
|
jpayne@69
|
13812 }
|
|
jpayne@69
|
13813
|
|
jpayne@69
|
13814 /* "pysam/libctabix.pyx":598
|
|
jpayne@69
|
13815 * return result
|
|
jpayne@69
|
13816 *
|
|
jpayne@69
|
13817 * def close(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13818 * '''
|
|
jpayne@69
|
13819 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
13820 */
|
|
jpayne@69
|
13821
|
|
jpayne@69
|
13822 /* function exit code */
|
|
jpayne@69
|
13823 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
13824 goto __pyx_L0;
|
|
jpayne@69
|
13825 __pyx_L1_error:;
|
|
jpayne@69
|
13826 __Pyx_AddTraceback("pysam.libctabix.TabixFile.close", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
13827 __pyx_r = NULL;
|
|
jpayne@69
|
13828 __pyx_L0:;
|
|
jpayne@69
|
13829 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
13830 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
13831 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13832 return __pyx_r;
|
|
jpayne@69
|
13833 }
|
|
jpayne@69
|
13834
|
|
jpayne@69
|
13835 /* "pysam/libctabix.pyx":608
|
|
jpayne@69
|
13836 * self.index = NULL
|
|
jpayne@69
|
13837 *
|
|
jpayne@69
|
13838 * def __dealloc__( self ): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13839 * # remember: dealloc cannot call other python methods
|
|
jpayne@69
|
13840 * # note: no doc string
|
|
jpayne@69
|
13841 */
|
|
jpayne@69
|
13842
|
|
jpayne@69
|
13843 /* Python wrapper */
|
|
jpayne@69
|
13844 static void __pyx_pw_5pysam_9libctabix_9TabixFile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
13845 static void __pyx_pw_5pysam_9libctabix_9TabixFile_11__dealloc__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
13846 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
13847 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13848 __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
|
|
jpayne@69
|
13849 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
13850 __pyx_pf_5pysam_9libctabix_9TabixFile_10__dealloc__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
13851
|
|
jpayne@69
|
13852 /* function exit code */
|
|
jpayne@69
|
13853 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13854 }
|
|
jpayne@69
|
13855
|
|
jpayne@69
|
13856 static void __pyx_pf_5pysam_9libctabix_9TabixFile_10__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
13857 __Pyx_TraceDeclarations
|
|
jpayne@69
|
13858 int __pyx_t_1;
|
|
jpayne@69
|
13859 int __pyx_lineno = 0;
|
|
jpayne@69
|
13860 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
13861 int __pyx_clineno = 0;
|
|
jpayne@69
|
13862 __Pyx_TraceCall("__dealloc__", __pyx_f[0], 608, 0, __PYX_ERR(0, 608, __pyx_L1_error));
|
|
jpayne@69
|
13863
|
|
jpayne@69
|
13864 /* "pysam/libctabix.pyx":612
|
|
jpayne@69
|
13865 * # note: no doc string
|
|
jpayne@69
|
13866 * # note: __del__ is not called.
|
|
jpayne@69
|
13867 * if self.htsfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13868 * hts_close(self.htsfile)
|
|
jpayne@69
|
13869 * self.htsfile = NULL
|
|
jpayne@69
|
13870 */
|
|
jpayne@69
|
13871 __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile != NULL);
|
|
jpayne@69
|
13872 if (__pyx_t_1) {
|
|
jpayne@69
|
13873
|
|
jpayne@69
|
13874 /* "pysam/libctabix.pyx":613
|
|
jpayne@69
|
13875 * # note: __del__ is not called.
|
|
jpayne@69
|
13876 * if self.htsfile != NULL:
|
|
jpayne@69
|
13877 * hts_close(self.htsfile) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13878 * self.htsfile = NULL
|
|
jpayne@69
|
13879 * if self.index != NULL:
|
|
jpayne@69
|
13880 */
|
|
jpayne@69
|
13881 (void)(hts_close(__pyx_v_self->__pyx_base.htsfile));
|
|
jpayne@69
|
13882
|
|
jpayne@69
|
13883 /* "pysam/libctabix.pyx":614
|
|
jpayne@69
|
13884 * if self.htsfile != NULL:
|
|
jpayne@69
|
13885 * hts_close(self.htsfile)
|
|
jpayne@69
|
13886 * self.htsfile = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13887 * if self.index != NULL:
|
|
jpayne@69
|
13888 * tbx_destroy(self.index)
|
|
jpayne@69
|
13889 */
|
|
jpayne@69
|
13890 __pyx_v_self->__pyx_base.htsfile = NULL;
|
|
jpayne@69
|
13891
|
|
jpayne@69
|
13892 /* "pysam/libctabix.pyx":612
|
|
jpayne@69
|
13893 * # note: no doc string
|
|
jpayne@69
|
13894 * # note: __del__ is not called.
|
|
jpayne@69
|
13895 * if self.htsfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13896 * hts_close(self.htsfile)
|
|
jpayne@69
|
13897 * self.htsfile = NULL
|
|
jpayne@69
|
13898 */
|
|
jpayne@69
|
13899 }
|
|
jpayne@69
|
13900
|
|
jpayne@69
|
13901 /* "pysam/libctabix.pyx":615
|
|
jpayne@69
|
13902 * hts_close(self.htsfile)
|
|
jpayne@69
|
13903 * self.htsfile = NULL
|
|
jpayne@69
|
13904 * if self.index != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13905 * tbx_destroy(self.index)
|
|
jpayne@69
|
13906 *
|
|
jpayne@69
|
13907 */
|
|
jpayne@69
|
13908 __pyx_t_1 = (__pyx_v_self->index != NULL);
|
|
jpayne@69
|
13909 if (__pyx_t_1) {
|
|
jpayne@69
|
13910
|
|
jpayne@69
|
13911 /* "pysam/libctabix.pyx":616
|
|
jpayne@69
|
13912 * self.htsfile = NULL
|
|
jpayne@69
|
13913 * if self.index != NULL:
|
|
jpayne@69
|
13914 * tbx_destroy(self.index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13915 *
|
|
jpayne@69
|
13916 *
|
|
jpayne@69
|
13917 */
|
|
jpayne@69
|
13918 tbx_destroy(__pyx_v_self->index);
|
|
jpayne@69
|
13919
|
|
jpayne@69
|
13920 /* "pysam/libctabix.pyx":615
|
|
jpayne@69
|
13921 * hts_close(self.htsfile)
|
|
jpayne@69
|
13922 * self.htsfile = NULL
|
|
jpayne@69
|
13923 * if self.index != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13924 * tbx_destroy(self.index)
|
|
jpayne@69
|
13925 *
|
|
jpayne@69
|
13926 */
|
|
jpayne@69
|
13927 }
|
|
jpayne@69
|
13928
|
|
jpayne@69
|
13929 /* "pysam/libctabix.pyx":608
|
|
jpayne@69
|
13930 * self.index = NULL
|
|
jpayne@69
|
13931 *
|
|
jpayne@69
|
13932 * def __dealloc__( self ): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13933 * # remember: dealloc cannot call other python methods
|
|
jpayne@69
|
13934 * # note: no doc string
|
|
jpayne@69
|
13935 */
|
|
jpayne@69
|
13936
|
|
jpayne@69
|
13937 /* function exit code */
|
|
jpayne@69
|
13938 goto __pyx_L0;
|
|
jpayne@69
|
13939 __pyx_L1_error:;
|
|
jpayne@69
|
13940 __Pyx_WriteUnraisable("pysam.libctabix.TabixFile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
|
|
jpayne@69
|
13941 __pyx_L0:;
|
|
jpayne@69
|
13942 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
13943 }
|
|
jpayne@69
|
13944
|
|
jpayne@69
|
13945 /* "pysam/libctabix.pxd":65
|
|
jpayne@69
|
13946 * cdef tbx_t * index
|
|
jpayne@69
|
13947 *
|
|
jpayne@69
|
13948 * cdef readonly object filename_index # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13949 *
|
|
jpayne@69
|
13950 * cdef Parser parser
|
|
jpayne@69
|
13951 */
|
|
jpayne@69
|
13952
|
|
jpayne@69
|
13953 /* Python wrapper */
|
|
jpayne@69
|
13954 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_14filename_index_1__get__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
13955 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_14filename_index_1__get__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
13956 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
13957 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
13958 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13959 __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
|
|
jpayne@69
|
13960 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
13961 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_14filename_index___get__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
13962
|
|
jpayne@69
|
13963 /* function exit code */
|
|
jpayne@69
|
13964 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13965 return __pyx_r;
|
|
jpayne@69
|
13966 }
|
|
jpayne@69
|
13967
|
|
jpayne@69
|
13968 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14filename_index___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
13969 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
13970 __Pyx_TraceDeclarations
|
|
jpayne@69
|
13971 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
13972 int __pyx_lineno = 0;
|
|
jpayne@69
|
13973 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
13974 int __pyx_clineno = 0;
|
|
jpayne@69
|
13975 __Pyx_RefNannySetupContext("__get__", 1);
|
|
jpayne@69
|
13976 __Pyx_TraceCall("__get__", __pyx_f[4], 65, 0, __PYX_ERR(4, 65, __pyx_L1_error));
|
|
jpayne@69
|
13977 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
13978 __Pyx_INCREF(__pyx_v_self->filename_index);
|
|
jpayne@69
|
13979 __pyx_r = __pyx_v_self->filename_index;
|
|
jpayne@69
|
13980 goto __pyx_L0;
|
|
jpayne@69
|
13981
|
|
jpayne@69
|
13982 /* function exit code */
|
|
jpayne@69
|
13983 __pyx_L1_error:;
|
|
jpayne@69
|
13984 __Pyx_AddTraceback("pysam.libctabix.TabixFile.filename_index.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
13985 __pyx_r = NULL;
|
|
jpayne@69
|
13986 __pyx_L0:;
|
|
jpayne@69
|
13987 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
13988 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
13989 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
13990 return __pyx_r;
|
|
jpayne@69
|
13991 }
|
|
jpayne@69
|
13992
|
|
jpayne@69
|
13993 /* "(tree fragment)":1
|
|
jpayne@69
|
13994 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
13995 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
13996 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
13997 */
|
|
jpayne@69
|
13998
|
|
jpayne@69
|
13999 /* Python wrapper */
|
|
jpayne@69
|
14000 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14001 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14002 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14003 #else
|
|
jpayne@69
|
14004 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14005 #endif
|
|
jpayne@69
|
14006 ); /*proto*/
|
|
jpayne@69
|
14007 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_12__reduce_cython__, "TabixFile.__reduce_cython__(self)");
|
|
jpayne@69
|
14008 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_13__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_12__reduce_cython__};
|
|
jpayne@69
|
14009 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14010 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14011 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14012 #else
|
|
jpayne@69
|
14013 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14014 #endif
|
|
jpayne@69
|
14015 ) {
|
|
jpayne@69
|
14016 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14017 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
14018 #endif
|
|
jpayne@69
|
14019 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14020 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
14021 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14022 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
14023 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14024 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
14025 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
14026 #else
|
|
jpayne@69
|
14027 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
14028 #endif
|
|
jpayne@69
|
14029 #endif
|
|
jpayne@69
|
14030 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14031 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
14032 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
14033 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
14034 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_12__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self));
|
|
jpayne@69
|
14035
|
|
jpayne@69
|
14036 /* function exit code */
|
|
jpayne@69
|
14037 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14038 return __pyx_r;
|
|
jpayne@69
|
14039 }
|
|
jpayne@69
|
14040
|
|
jpayne@69
|
14041 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_12__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) {
|
|
jpayne@69
|
14042 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
14043 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14044 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14045 int __pyx_lineno = 0;
|
|
jpayne@69
|
14046 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14047 int __pyx_clineno = 0;
|
|
jpayne@69
|
14048 __Pyx_TraceFrameInit(__pyx_codeobj__22)
|
|
jpayne@69
|
14049 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
14050 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
14051
|
|
jpayne@69
|
14052 /* "(tree fragment)":2
|
|
jpayne@69
|
14053 * def __reduce_cython__(self):
|
|
jpayne@69
|
14054 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14055 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
14056 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14057 */
|
|
jpayne@69
|
14058 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
|
|
jpayne@69
|
14059 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
14060
|
|
jpayne@69
|
14061 /* "(tree fragment)":1
|
|
jpayne@69
|
14062 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14063 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14064 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
14065 */
|
|
jpayne@69
|
14066
|
|
jpayne@69
|
14067 /* function exit code */
|
|
jpayne@69
|
14068 __pyx_L1_error:;
|
|
jpayne@69
|
14069 __Pyx_AddTraceback("pysam.libctabix.TabixFile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14070 __pyx_r = NULL;
|
|
jpayne@69
|
14071 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
14072 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
14073 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14074 return __pyx_r;
|
|
jpayne@69
|
14075 }
|
|
jpayne@69
|
14076
|
|
jpayne@69
|
14077 /* "(tree fragment)":3
|
|
jpayne@69
|
14078 * def __reduce_cython__(self):
|
|
jpayne@69
|
14079 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14080 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14081 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14082 */
|
|
jpayne@69
|
14083
|
|
jpayne@69
|
14084 /* Python wrapper */
|
|
jpayne@69
|
14085 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14086 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14087 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14088 #else
|
|
jpayne@69
|
14089 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14090 #endif
|
|
jpayne@69
|
14091 ); /*proto*/
|
|
jpayne@69
|
14092 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_14__setstate_cython__, "TabixFile.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
14093 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_15__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_14__setstate_cython__};
|
|
jpayne@69
|
14094 static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14095 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14096 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14097 #else
|
|
jpayne@69
|
14098 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14099 #endif
|
|
jpayne@69
|
14100 ) {
|
|
jpayne@69
|
14101 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
14102 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14103 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
14104 #endif
|
|
jpayne@69
|
14105 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14106 PyObject* values[1] = {0};
|
|
jpayne@69
|
14107 int __pyx_lineno = 0;
|
|
jpayne@69
|
14108 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14109 int __pyx_clineno = 0;
|
|
jpayne@69
|
14110 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
14111 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14112 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
14113 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14114 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
14115 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
14116 #else
|
|
jpayne@69
|
14117 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
14118 #endif
|
|
jpayne@69
|
14119 #endif
|
|
jpayne@69
|
14120 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14121 {
|
|
jpayne@69
|
14122 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
14123 if (__pyx_kwds) {
|
|
jpayne@69
|
14124 Py_ssize_t kw_args;
|
|
jpayne@69
|
14125 switch (__pyx_nargs) {
|
|
jpayne@69
|
14126 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
14127 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14128 case 0: break;
|
|
jpayne@69
|
14129 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
14130 }
|
|
jpayne@69
|
14131 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
14132 switch (__pyx_nargs) {
|
|
jpayne@69
|
14133 case 0:
|
|
jpayne@69
|
14134 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
14135 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
14136 kw_args--;
|
|
jpayne@69
|
14137 }
|
|
jpayne@69
|
14138 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
14139 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
14140 }
|
|
jpayne@69
|
14141 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
14142 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
14143 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
14144 }
|
|
jpayne@69
|
14145 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
14146 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
14147 } else {
|
|
jpayne@69
|
14148 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
14149 }
|
|
jpayne@69
|
14150 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
14151 }
|
|
jpayne@69
|
14152 goto __pyx_L6_skip;
|
|
jpayne@69
|
14153 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
14154 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
14155 __pyx_L6_skip:;
|
|
jpayne@69
|
14156 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
14157 __pyx_L3_error:;
|
|
jpayne@69
|
14158 {
|
|
jpayne@69
|
14159 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
14160 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
14161 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
14162 }
|
|
jpayne@69
|
14163 }
|
|
jpayne@69
|
14164 __Pyx_AddTraceback("pysam.libctabix.TabixFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14165 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14166 return NULL;
|
|
jpayne@69
|
14167 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
14168 __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_14__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
14169
|
|
jpayne@69
|
14170 /* function exit code */
|
|
jpayne@69
|
14171 {
|
|
jpayne@69
|
14172 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
14173 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
14174 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
14175 }
|
|
jpayne@69
|
14176 }
|
|
jpayne@69
|
14177 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14178 return __pyx_r;
|
|
jpayne@69
|
14179 }
|
|
jpayne@69
|
14180
|
|
jpayne@69
|
14181 static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
14182 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
14183 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14184 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14185 int __pyx_lineno = 0;
|
|
jpayne@69
|
14186 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14187 int __pyx_clineno = 0;
|
|
jpayne@69
|
14188 __Pyx_TraceFrameInit(__pyx_codeobj__23)
|
|
jpayne@69
|
14189 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
14190 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
14191
|
|
jpayne@69
|
14192 /* "(tree fragment)":4
|
|
jpayne@69
|
14193 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14194 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
14195 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14196 */
|
|
jpayne@69
|
14197 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
|
|
jpayne@69
|
14198 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
14199
|
|
jpayne@69
|
14200 /* "(tree fragment)":3
|
|
jpayne@69
|
14201 * def __reduce_cython__(self):
|
|
jpayne@69
|
14202 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14203 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14204 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
14205 */
|
|
jpayne@69
|
14206
|
|
jpayne@69
|
14207 /* function exit code */
|
|
jpayne@69
|
14208 __pyx_L1_error:;
|
|
jpayne@69
|
14209 __Pyx_AddTraceback("pysam.libctabix.TabixFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14210 __pyx_r = NULL;
|
|
jpayne@69
|
14211 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
14212 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
14213 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14214 return __pyx_r;
|
|
jpayne@69
|
14215 }
|
|
jpayne@69
|
14216
|
|
jpayne@69
|
14217 /* "pysam/libctabix.pyx":624
|
|
jpayne@69
|
14218 * """
|
|
jpayne@69
|
14219 *
|
|
jpayne@69
|
14220 * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14221 * self.encoding = encoding
|
|
jpayne@69
|
14222 *
|
|
jpayne@69
|
14223 */
|
|
jpayne@69
|
14224
|
|
jpayne@69
|
14225 /* Python wrapper */
|
|
jpayne@69
|
14226 static int __pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
14227 static int __pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
14228 PyObject *__pyx_v_encoding = 0;
|
|
jpayne@69
|
14229 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
14230 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14231 PyObject* values[1] = {0};
|
|
jpayne@69
|
14232 int __pyx_lineno = 0;
|
|
jpayne@69
|
14233 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14234 int __pyx_clineno = 0;
|
|
jpayne@69
|
14235 int __pyx_r;
|
|
jpayne@69
|
14236 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14237 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
|
|
jpayne@69
|
14238 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
14239 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
14240 #else
|
|
jpayne@69
|
14241 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
14242 #endif
|
|
jpayne@69
|
14243 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14244 {
|
|
jpayne@69
|
14245 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_encoding,0};
|
|
jpayne@69
|
14246 values[0] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii));
|
|
jpayne@69
|
14247 if (__pyx_kwds) {
|
|
jpayne@69
|
14248 Py_ssize_t kw_args;
|
|
jpayne@69
|
14249 switch (__pyx_nargs) {
|
|
jpayne@69
|
14250 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
14251 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14252 case 0: break;
|
|
jpayne@69
|
14253 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
14254 }
|
|
jpayne@69
|
14255 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
14256 switch (__pyx_nargs) {
|
|
jpayne@69
|
14257 case 0:
|
|
jpayne@69
|
14258 if (kw_args > 0) {
|
|
jpayne@69
|
14259 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding);
|
|
jpayne@69
|
14260 if (value) { values[0] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
14261 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 624, __pyx_L3_error)
|
|
jpayne@69
|
14262 }
|
|
jpayne@69
|
14263 }
|
|
jpayne@69
|
14264 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
14265 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
14266 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 624, __pyx_L3_error)
|
|
jpayne@69
|
14267 }
|
|
jpayne@69
|
14268 } else {
|
|
jpayne@69
|
14269 switch (__pyx_nargs) {
|
|
jpayne@69
|
14270 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
14271 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14272 case 0: break;
|
|
jpayne@69
|
14273 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
14274 }
|
|
jpayne@69
|
14275 }
|
|
jpayne@69
|
14276 __pyx_v_encoding = values[0];
|
|
jpayne@69
|
14277 }
|
|
jpayne@69
|
14278 goto __pyx_L6_skip;
|
|
jpayne@69
|
14279 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
14280 __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 624, __pyx_L3_error)
|
|
jpayne@69
|
14281 __pyx_L6_skip:;
|
|
jpayne@69
|
14282 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
14283 __pyx_L3_error:;
|
|
jpayne@69
|
14284 {
|
|
jpayne@69
|
14285 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
14286 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
14287 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
14288 }
|
|
jpayne@69
|
14289 }
|
|
jpayne@69
|
14290 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14291 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14292 return -1;
|
|
jpayne@69
|
14293 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
14294 __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator___init__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self), __pyx_v_encoding);
|
|
jpayne@69
|
14295
|
|
jpayne@69
|
14296 /* function exit code */
|
|
jpayne@69
|
14297 {
|
|
jpayne@69
|
14298 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
14299 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
14300 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
14301 }
|
|
jpayne@69
|
14302 }
|
|
jpayne@69
|
14303 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14304 return __pyx_r;
|
|
jpayne@69
|
14305 }
|
|
jpayne@69
|
14306
|
|
jpayne@69
|
14307 static int __pyx_pf_5pysam_9libctabix_13TabixIterator___init__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, PyObject *__pyx_v_encoding) {
|
|
jpayne@69
|
14308 int __pyx_r;
|
|
jpayne@69
|
14309 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14310 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14311 int __pyx_lineno = 0;
|
|
jpayne@69
|
14312 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14313 int __pyx_clineno = 0;
|
|
jpayne@69
|
14314 __Pyx_RefNannySetupContext("__init__", 1);
|
|
jpayne@69
|
14315 __Pyx_TraceCall("__init__", __pyx_f[0], 624, 0, __PYX_ERR(0, 624, __pyx_L1_error));
|
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jpayne@69
|
14316
|
|
jpayne@69
|
14317 /* "pysam/libctabix.pyx":625
|
|
jpayne@69
|
14318 *
|
|
jpayne@69
|
14319 * def __init__(self, encoding="ascii"):
|
|
jpayne@69
|
14320 * self.encoding = encoding # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14321 *
|
|
jpayne@69
|
14322 * def __iter__(self):
|
|
jpayne@69
|
14323 */
|
|
jpayne@69
|
14324 __Pyx_INCREF(__pyx_v_encoding);
|
|
jpayne@69
|
14325 __Pyx_GIVEREF(__pyx_v_encoding);
|
|
jpayne@69
|
14326 __Pyx_GOTREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
14327 __Pyx_DECREF(__pyx_v_self->encoding);
|
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jpayne@69
|
14328 __pyx_v_self->encoding = __pyx_v_encoding;
|
|
jpayne@69
|
14329
|
|
jpayne@69
|
14330 /* "pysam/libctabix.pyx":624
|
|
jpayne@69
|
14331 * """
|
|
jpayne@69
|
14332 *
|
|
jpayne@69
|
14333 * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14334 * self.encoding = encoding
|
|
jpayne@69
|
14335 *
|
|
jpayne@69
|
14336 */
|
|
jpayne@69
|
14337
|
|
jpayne@69
|
14338 /* function exit code */
|
|
jpayne@69
|
14339 __pyx_r = 0;
|
|
jpayne@69
|
14340 goto __pyx_L0;
|
|
jpayne@69
|
14341 __pyx_L1_error:;
|
|
jpayne@69
|
14342 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
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jpayne@69
|
14343 __pyx_r = -1;
|
|
jpayne@69
|
14344 __pyx_L0:;
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jpayne@69
|
14345 __Pyx_TraceReturn(Py_None, 0);
|
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jpayne@69
|
14346 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
14347 return __pyx_r;
|
|
jpayne@69
|
14348 }
|
|
jpayne@69
|
14349
|
|
jpayne@69
|
14350 /* "pysam/libctabix.pyx":627
|
|
jpayne@69
|
14351 * self.encoding = encoding
|
|
jpayne@69
|
14352 *
|
|
jpayne@69
|
14353 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14354 * self.buffer.s = NULL
|
|
jpayne@69
|
14355 * self.buffer.l = 0
|
|
jpayne@69
|
14356 */
|
|
jpayne@69
|
14357
|
|
jpayne@69
|
14358 /* Python wrapper */
|
|
jpayne@69
|
14359 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
14360 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
14361 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14362 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
14363 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14364 __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
|
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jpayne@69
|
14365 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14366 __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_2__iter__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self));
|
|
jpayne@69
|
14367
|
|
jpayne@69
|
14368 /* function exit code */
|
|
jpayne@69
|
14369 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14370 return __pyx_r;
|
|
jpayne@69
|
14371 }
|
|
jpayne@69
|
14372
|
|
jpayne@69
|
14373 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) {
|
|
jpayne@69
|
14374 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
14375 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14376 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14377 int __pyx_lineno = 0;
|
|
jpayne@69
|
14378 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14379 int __pyx_clineno = 0;
|
|
jpayne@69
|
14380 __Pyx_RefNannySetupContext("__iter__", 1);
|
|
jpayne@69
|
14381 __Pyx_TraceCall("__iter__", __pyx_f[0], 627, 0, __PYX_ERR(0, 627, __pyx_L1_error));
|
|
jpayne@69
|
14382
|
|
jpayne@69
|
14383 /* "pysam/libctabix.pyx":628
|
|
jpayne@69
|
14384 *
|
|
jpayne@69
|
14385 * def __iter__(self):
|
|
jpayne@69
|
14386 * self.buffer.s = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14387 * self.buffer.l = 0
|
|
jpayne@69
|
14388 * self.buffer.m = 0
|
|
jpayne@69
|
14389 */
|
|
jpayne@69
|
14390 __pyx_v_self->buffer.s = NULL;
|
|
jpayne@69
|
14391
|
|
jpayne@69
|
14392 /* "pysam/libctabix.pyx":629
|
|
jpayne@69
|
14393 * def __iter__(self):
|
|
jpayne@69
|
14394 * self.buffer.s = NULL
|
|
jpayne@69
|
14395 * self.buffer.l = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14396 * self.buffer.m = 0
|
|
jpayne@69
|
14397 *
|
|
jpayne@69
|
14398 */
|
|
jpayne@69
|
14399 __pyx_v_self->buffer.l = 0;
|
|
jpayne@69
|
14400
|
|
jpayne@69
|
14401 /* "pysam/libctabix.pyx":630
|
|
jpayne@69
|
14402 * self.buffer.s = NULL
|
|
jpayne@69
|
14403 * self.buffer.l = 0
|
|
jpayne@69
|
14404 * self.buffer.m = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14405 *
|
|
jpayne@69
|
14406 * return self
|
|
jpayne@69
|
14407 */
|
|
jpayne@69
|
14408 __pyx_v_self->buffer.m = 0;
|
|
jpayne@69
|
14409
|
|
jpayne@69
|
14410 /* "pysam/libctabix.pyx":632
|
|
jpayne@69
|
14411 * self.buffer.m = 0
|
|
jpayne@69
|
14412 *
|
|
jpayne@69
|
14413 * return self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14414 *
|
|
jpayne@69
|
14415 * cdef int __cnext__(self):
|
|
jpayne@69
|
14416 */
|
|
jpayne@69
|
14417 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
14418 __Pyx_INCREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
14419 __pyx_r = ((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
14420 goto __pyx_L0;
|
|
jpayne@69
|
14421
|
|
jpayne@69
|
14422 /* "pysam/libctabix.pyx":627
|
|
jpayne@69
|
14423 * self.encoding = encoding
|
|
jpayne@69
|
14424 *
|
|
jpayne@69
|
14425 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14426 * self.buffer.s = NULL
|
|
jpayne@69
|
14427 * self.buffer.l = 0
|
|
jpayne@69
|
14428 */
|
|
jpayne@69
|
14429
|
|
jpayne@69
|
14430 /* function exit code */
|
|
jpayne@69
|
14431 __pyx_L1_error:;
|
|
jpayne@69
|
14432 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14433 __pyx_r = NULL;
|
|
jpayne@69
|
14434 __pyx_L0:;
|
|
jpayne@69
|
14435 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
14436 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
14437 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14438 return __pyx_r;
|
|
jpayne@69
|
14439 }
|
|
jpayne@69
|
14440
|
|
jpayne@69
|
14441 /* "pysam/libctabix.pyx":634
|
|
jpayne@69
|
14442 * return self
|
|
jpayne@69
|
14443 *
|
|
jpayne@69
|
14444 * cdef int __cnext__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14445 * '''iterate to next element.
|
|
jpayne@69
|
14446 *
|
|
jpayne@69
|
14447 */
|
|
jpayne@69
|
14448
|
|
jpayne@69
|
14449 static int __pyx_f_5pysam_9libctabix_13TabixIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) {
|
|
jpayne@69
|
14450 int __pyx_v_retval;
|
|
jpayne@69
|
14451 int __pyx_r;
|
|
jpayne@69
|
14452 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14453 int __pyx_t_1;
|
|
jpayne@69
|
14454 int __pyx_lineno = 0;
|
|
jpayne@69
|
14455 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14456 int __pyx_clineno = 0;
|
|
jpayne@69
|
14457 __Pyx_TraceCall("__cnext__", __pyx_f[0], 634, 0, __PYX_ERR(0, 634, __pyx_L1_error));
|
|
jpayne@69
|
14458
|
|
jpayne@69
|
14459 /* "pysam/libctabix.pyx":640
|
|
jpayne@69
|
14460 * was called.
|
|
jpayne@69
|
14461 * '''
|
|
jpayne@69
|
14462 * if self.tabixfile.htsfile == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14463 * return -5
|
|
jpayne@69
|
14464 *
|
|
jpayne@69
|
14465 */
|
|
jpayne@69
|
14466 __pyx_t_1 = (__pyx_v_self->tabixfile->__pyx_base.htsfile == NULL);
|
|
jpayne@69
|
14467 if (__pyx_t_1) {
|
|
jpayne@69
|
14468
|
|
jpayne@69
|
14469 /* "pysam/libctabix.pyx":641
|
|
jpayne@69
|
14470 * '''
|
|
jpayne@69
|
14471 * if self.tabixfile.htsfile == NULL:
|
|
jpayne@69
|
14472 * return -5 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14473 *
|
|
jpayne@69
|
14474 * cdef int retval
|
|
jpayne@69
|
14475 */
|
|
jpayne@69
|
14476 __pyx_r = -5;
|
|
jpayne@69
|
14477 goto __pyx_L0;
|
|
jpayne@69
|
14478
|
|
jpayne@69
|
14479 /* "pysam/libctabix.pyx":640
|
|
jpayne@69
|
14480 * was called.
|
|
jpayne@69
|
14481 * '''
|
|
jpayne@69
|
14482 * if self.tabixfile.htsfile == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14483 * return -5
|
|
jpayne@69
|
14484 *
|
|
jpayne@69
|
14485 */
|
|
jpayne@69
|
14486 }
|
|
jpayne@69
|
14487
|
|
jpayne@69
|
14488 /* "pysam/libctabix.pyx":645
|
|
jpayne@69
|
14489 * cdef int retval
|
|
jpayne@69
|
14490 *
|
|
jpayne@69
|
14491 * while 1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14492 * with nogil:
|
|
jpayne@69
|
14493 * retval = tbx_itr_next(
|
|
jpayne@69
|
14494 */
|
|
jpayne@69
|
14495 while (1) {
|
|
jpayne@69
|
14496
|
|
jpayne@69
|
14497 /* "pysam/libctabix.pyx":646
|
|
jpayne@69
|
14498 *
|
|
jpayne@69
|
14499 * while 1:
|
|
jpayne@69
|
14500 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14501 * retval = tbx_itr_next(
|
|
jpayne@69
|
14502 * self.tabixfile.htsfile,
|
|
jpayne@69
|
14503 */
|
|
jpayne@69
|
14504 {
|
|
jpayne@69
|
14505 #ifdef WITH_THREAD
|
|
jpayne@69
|
14506 PyThreadState *_save;
|
|
jpayne@69
|
14507 _save = NULL;
|
|
jpayne@69
|
14508 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
14509 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
14510 #endif
|
|
jpayne@69
|
14511 /*try:*/ {
|
|
jpayne@69
|
14512
|
|
jpayne@69
|
14513 /* "pysam/libctabix.pyx":647
|
|
jpayne@69
|
14514 * while 1:
|
|
jpayne@69
|
14515 * with nogil:
|
|
jpayne@69
|
14516 * retval = tbx_itr_next( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14517 * self.tabixfile.htsfile,
|
|
jpayne@69
|
14518 * self.tabixfile.index,
|
|
jpayne@69
|
14519 */
|
|
jpayne@69
|
14520 __pyx_v_retval = tbx_itr_next(__pyx_v_self->tabixfile->__pyx_base.htsfile, __pyx_v_self->tabixfile->index, __pyx_v_self->iterator, (&__pyx_v_self->buffer));
|
|
jpayne@69
|
14521 }
|
|
jpayne@69
|
14522
|
|
jpayne@69
|
14523 /* "pysam/libctabix.pyx":646
|
|
jpayne@69
|
14524 *
|
|
jpayne@69
|
14525 * while 1:
|
|
jpayne@69
|
14526 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14527 * retval = tbx_itr_next(
|
|
jpayne@69
|
14528 * self.tabixfile.htsfile,
|
|
jpayne@69
|
14529 */
|
|
jpayne@69
|
14530 /*finally:*/ {
|
|
jpayne@69
|
14531 /*normal exit:*/{
|
|
jpayne@69
|
14532 #ifdef WITH_THREAD
|
|
jpayne@69
|
14533 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
14534 Py_BLOCK_THREADS
|
|
jpayne@69
|
14535 #endif
|
|
jpayne@69
|
14536 goto __pyx_L10;
|
|
jpayne@69
|
14537 }
|
|
jpayne@69
|
14538 __pyx_L10:;
|
|
jpayne@69
|
14539 }
|
|
jpayne@69
|
14540 }
|
|
jpayne@69
|
14541
|
|
jpayne@69
|
14542 /* "pysam/libctabix.pyx":653
|
|
jpayne@69
|
14543 * &self.buffer)
|
|
jpayne@69
|
14544 *
|
|
jpayne@69
|
14545 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14546 * break
|
|
jpayne@69
|
14547 *
|
|
jpayne@69
|
14548 */
|
|
jpayne@69
|
14549 __pyx_t_1 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
14550 if (__pyx_t_1) {
|
|
jpayne@69
|
14551
|
|
jpayne@69
|
14552 /* "pysam/libctabix.pyx":654
|
|
jpayne@69
|
14553 *
|
|
jpayne@69
|
14554 * if retval < 0:
|
|
jpayne@69
|
14555 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14556 *
|
|
jpayne@69
|
14557 * if self.buffer.s[0] != b'#':
|
|
jpayne@69
|
14558 */
|
|
jpayne@69
|
14559 goto __pyx_L5_break;
|
|
jpayne@69
|
14560
|
|
jpayne@69
|
14561 /* "pysam/libctabix.pyx":653
|
|
jpayne@69
|
14562 * &self.buffer)
|
|
jpayne@69
|
14563 *
|
|
jpayne@69
|
14564 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14565 * break
|
|
jpayne@69
|
14566 *
|
|
jpayne@69
|
14567 */
|
|
jpayne@69
|
14568 }
|
|
jpayne@69
|
14569
|
|
jpayne@69
|
14570 /* "pysam/libctabix.pyx":656
|
|
jpayne@69
|
14571 * break
|
|
jpayne@69
|
14572 *
|
|
jpayne@69
|
14573 * if self.buffer.s[0] != b'#': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14574 * break
|
|
jpayne@69
|
14575 *
|
|
jpayne@69
|
14576 */
|
|
jpayne@69
|
14577 __pyx_t_1 = ((__pyx_v_self->buffer.s[0]) != '#');
|
|
jpayne@69
|
14578 if (__pyx_t_1) {
|
|
jpayne@69
|
14579
|
|
jpayne@69
|
14580 /* "pysam/libctabix.pyx":657
|
|
jpayne@69
|
14581 *
|
|
jpayne@69
|
14582 * if self.buffer.s[0] != b'#':
|
|
jpayne@69
|
14583 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14584 *
|
|
jpayne@69
|
14585 * return retval
|
|
jpayne@69
|
14586 */
|
|
jpayne@69
|
14587 goto __pyx_L5_break;
|
|
jpayne@69
|
14588
|
|
jpayne@69
|
14589 /* "pysam/libctabix.pyx":656
|
|
jpayne@69
|
14590 * break
|
|
jpayne@69
|
14591 *
|
|
jpayne@69
|
14592 * if self.buffer.s[0] != b'#': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14593 * break
|
|
jpayne@69
|
14594 *
|
|
jpayne@69
|
14595 */
|
|
jpayne@69
|
14596 }
|
|
jpayne@69
|
14597 }
|
|
jpayne@69
|
14598 __pyx_L5_break:;
|
|
jpayne@69
|
14599
|
|
jpayne@69
|
14600 /* "pysam/libctabix.pyx":659
|
|
jpayne@69
|
14601 * break
|
|
jpayne@69
|
14602 *
|
|
jpayne@69
|
14603 * return retval # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14604 *
|
|
jpayne@69
|
14605 * def __next__(self):
|
|
jpayne@69
|
14606 */
|
|
jpayne@69
|
14607 __pyx_r = __pyx_v_retval;
|
|
jpayne@69
|
14608 goto __pyx_L0;
|
|
jpayne@69
|
14609
|
|
jpayne@69
|
14610 /* "pysam/libctabix.pyx":634
|
|
jpayne@69
|
14611 * return self
|
|
jpayne@69
|
14612 *
|
|
jpayne@69
|
14613 * cdef int __cnext__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14614 * '''iterate to next element.
|
|
jpayne@69
|
14615 *
|
|
jpayne@69
|
14616 */
|
|
jpayne@69
|
14617
|
|
jpayne@69
|
14618 /* function exit code */
|
|
jpayne@69
|
14619 __pyx_L1_error:;
|
|
jpayne@69
|
14620 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14621 __pyx_r = 0;
|
|
jpayne@69
|
14622 __pyx_L0:;
|
|
jpayne@69
|
14623 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
14624 return __pyx_r;
|
|
jpayne@69
|
14625 }
|
|
jpayne@69
|
14626
|
|
jpayne@69
|
14627 /* "pysam/libctabix.pyx":661
|
|
jpayne@69
|
14628 * return retval
|
|
jpayne@69
|
14629 *
|
|
jpayne@69
|
14630 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14631 * """python version of next().
|
|
jpayne@69
|
14632 *
|
|
jpayne@69
|
14633 */
|
|
jpayne@69
|
14634
|
|
jpayne@69
|
14635 /* Python wrapper */
|
|
jpayne@69
|
14636 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
14637 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13TabixIterator_4__next__, "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ");
|
|
jpayne@69
|
14638 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
14639 struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__;
|
|
jpayne@69
|
14640 #endif
|
|
jpayne@69
|
14641 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
14642 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14643 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
14644 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14645 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
|
|
jpayne@69
|
14646 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14647 __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_4__next__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self));
|
|
jpayne@69
|
14648
|
|
jpayne@69
|
14649 /* function exit code */
|
|
jpayne@69
|
14650 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14651 return __pyx_r;
|
|
jpayne@69
|
14652 }
|
|
jpayne@69
|
14653
|
|
jpayne@69
|
14654 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) {
|
|
jpayne@69
|
14655 int __pyx_v_retval;
|
|
jpayne@69
|
14656 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
14657 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14658 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14659 int __pyx_error_without_exception = 0; /* StopIteration */
|
|
jpayne@69
|
14660 int __pyx_t_1;
|
|
jpayne@69
|
14661 int __pyx_t_2;
|
|
jpayne@69
|
14662 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
14663 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
14664 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str __pyx_t_5;
|
|
jpayne@69
|
14665 int __pyx_lineno = 0;
|
|
jpayne@69
|
14666 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14667 int __pyx_clineno = 0;
|
|
jpayne@69
|
14668 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
14669 __Pyx_TraceCall("__next__", __pyx_f[0], 661, 0, __PYX_ERR(0, 661, __pyx_L1_error));
|
|
jpayne@69
|
14670
|
|
jpayne@69
|
14671 /* "pysam/libctabix.pyx":667
|
|
jpayne@69
|
14672 * """
|
|
jpayne@69
|
14673 *
|
|
jpayne@69
|
14674 * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14675 * if retval == -5:
|
|
jpayne@69
|
14676 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
14677 */
|
|
jpayne@69
|
14678 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 667, __pyx_L1_error)
|
|
jpayne@69
|
14679 __pyx_v_retval = __pyx_t_1;
|
|
jpayne@69
|
14680
|
|
jpayne@69
|
14681 /* "pysam/libctabix.pyx":668
|
|
jpayne@69
|
14682 *
|
|
jpayne@69
|
14683 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
14684 * if retval == -5: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14685 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
14686 * elif retval < 0:
|
|
jpayne@69
|
14687 */
|
|
jpayne@69
|
14688 __pyx_t_2 = (__pyx_v_retval == -5L);
|
|
jpayne@69
|
14689 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
14690
|
|
jpayne@69
|
14691 /* "pysam/libctabix.pyx":669
|
|
jpayne@69
|
14692 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
14693 * if retval == -5:
|
|
jpayne@69
|
14694 * raise IOError("iteration on closed file") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14695 * elif retval < 0:
|
|
jpayne@69
|
14696 * raise StopIteration
|
|
jpayne@69
|
14697 */
|
|
jpayne@69
|
14698 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 669, __pyx_L1_error)
|
|
jpayne@69
|
14699 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
14700 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
14701 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
14702 __PYX_ERR(0, 669, __pyx_L1_error)
|
|
jpayne@69
|
14703
|
|
jpayne@69
|
14704 /* "pysam/libctabix.pyx":668
|
|
jpayne@69
|
14705 *
|
|
jpayne@69
|
14706 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
14707 * if retval == -5: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14708 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
14709 * elif retval < 0:
|
|
jpayne@69
|
14710 */
|
|
jpayne@69
|
14711 }
|
|
jpayne@69
|
14712
|
|
jpayne@69
|
14713 /* "pysam/libctabix.pyx":670
|
|
jpayne@69
|
14714 * if retval == -5:
|
|
jpayne@69
|
14715 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
14716 * elif retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14717 * raise StopIteration
|
|
jpayne@69
|
14718 *
|
|
jpayne@69
|
14719 */
|
|
jpayne@69
|
14720 __pyx_t_2 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
14721 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
14722
|
|
jpayne@69
|
14723 /* "pysam/libctabix.pyx":671
|
|
jpayne@69
|
14724 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
14725 * elif retval < 0:
|
|
jpayne@69
|
14726 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14727 *
|
|
jpayne@69
|
14728 * return charptr_to_str(self.buffer.s, self.encoding)
|
|
jpayne@69
|
14729 */
|
|
jpayne@69
|
14730 __pyx_error_without_exception = 1;
|
|
jpayne@69
|
14731 goto __pyx_L1_error;;
|
|
jpayne@69
|
14732
|
|
jpayne@69
|
14733 /* "pysam/libctabix.pyx":670
|
|
jpayne@69
|
14734 * if retval == -5:
|
|
jpayne@69
|
14735 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
14736 * elif retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14737 * raise StopIteration
|
|
jpayne@69
|
14738 *
|
|
jpayne@69
|
14739 */
|
|
jpayne@69
|
14740 }
|
|
jpayne@69
|
14741
|
|
jpayne@69
|
14742 /* "pysam/libctabix.pyx":673
|
|
jpayne@69
|
14743 * raise StopIteration
|
|
jpayne@69
|
14744 *
|
|
jpayne@69
|
14745 * return charptr_to_str(self.buffer.s, self.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14746 *
|
|
jpayne@69
|
14747 * def __dealloc__(self):
|
|
jpayne@69
|
14748 */
|
|
jpayne@69
|
14749 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
14750 __pyx_t_3 = __pyx_v_self->encoding;
|
|
jpayne@69
|
14751 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
14752 __pyx_t_5.__pyx_n = 1;
|
|
jpayne@69
|
14753 __pyx_t_5.encoding = __pyx_t_3;
|
|
jpayne@69
|
14754 __pyx_t_4 = __pyx_f_5pysam_9libcutils_charptr_to_str(__pyx_v_self->buffer.s, &__pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 673, __pyx_L1_error)
|
|
jpayne@69
|
14755 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
14756 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
14757 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
14758 __pyx_t_4 = 0;
|
|
jpayne@69
|
14759 goto __pyx_L0;
|
|
jpayne@69
|
14760
|
|
jpayne@69
|
14761 /* "pysam/libctabix.pyx":661
|
|
jpayne@69
|
14762 * return retval
|
|
jpayne@69
|
14763 *
|
|
jpayne@69
|
14764 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14765 * """python version of next().
|
|
jpayne@69
|
14766 *
|
|
jpayne@69
|
14767 */
|
|
jpayne@69
|
14768
|
|
jpayne@69
|
14769 /* function exit code */
|
|
jpayne@69
|
14770 __pyx_L1_error:;
|
|
jpayne@69
|
14771 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
14772 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
14773 if (!__pyx_error_without_exception) {
|
|
jpayne@69
|
14774 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14775 }
|
|
jpayne@69
|
14776 __pyx_r = NULL;
|
|
jpayne@69
|
14777 __pyx_L0:;
|
|
jpayne@69
|
14778 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
14779 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
14780 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14781 return __pyx_r;
|
|
jpayne@69
|
14782 }
|
|
jpayne@69
|
14783
|
|
jpayne@69
|
14784 /* "pysam/libctabix.pyx":675
|
|
jpayne@69
|
14785 * return charptr_to_str(self.buffer.s, self.encoding)
|
|
jpayne@69
|
14786 *
|
|
jpayne@69
|
14787 * def __dealloc__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14788 * if <void*>self.iterator != NULL:
|
|
jpayne@69
|
14789 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14790 */
|
|
jpayne@69
|
14791
|
|
jpayne@69
|
14792 /* Python wrapper */
|
|
jpayne@69
|
14793 static void __pyx_pw_5pysam_9libctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
14794 static void __pyx_pw_5pysam_9libctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
14795 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14796 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14797 __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
|
|
jpayne@69
|
14798 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14799 __pyx_pf_5pysam_9libctabix_13TabixIterator_6__dealloc__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self));
|
|
jpayne@69
|
14800
|
|
jpayne@69
|
14801 /* function exit code */
|
|
jpayne@69
|
14802 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14803 }
|
|
jpayne@69
|
14804
|
|
jpayne@69
|
14805 static void __pyx_pf_5pysam_9libctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) {
|
|
jpayne@69
|
14806 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14807 int __pyx_t_1;
|
|
jpayne@69
|
14808 int __pyx_lineno = 0;
|
|
jpayne@69
|
14809 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14810 int __pyx_clineno = 0;
|
|
jpayne@69
|
14811 __Pyx_TraceCall("__dealloc__", __pyx_f[0], 675, 0, __PYX_ERR(0, 675, __pyx_L1_error));
|
|
jpayne@69
|
14812
|
|
jpayne@69
|
14813 /* "pysam/libctabix.pyx":676
|
|
jpayne@69
|
14814 *
|
|
jpayne@69
|
14815 * def __dealloc__(self):
|
|
jpayne@69
|
14816 * if <void*>self.iterator != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14817 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14818 * if self.buffer.s != NULL:
|
|
jpayne@69
|
14819 */
|
|
jpayne@69
|
14820 __pyx_t_1 = (((void *)__pyx_v_self->iterator) != NULL);
|
|
jpayne@69
|
14821 if (__pyx_t_1) {
|
|
jpayne@69
|
14822
|
|
jpayne@69
|
14823 /* "pysam/libctabix.pyx":677
|
|
jpayne@69
|
14824 * def __dealloc__(self):
|
|
jpayne@69
|
14825 * if <void*>self.iterator != NULL:
|
|
jpayne@69
|
14826 * tbx_itr_destroy(self.iterator) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14827 * if self.buffer.s != NULL:
|
|
jpayne@69
|
14828 * free(self.buffer.s)
|
|
jpayne@69
|
14829 */
|
|
jpayne@69
|
14830 tbx_itr_destroy(__pyx_v_self->iterator);
|
|
jpayne@69
|
14831
|
|
jpayne@69
|
14832 /* "pysam/libctabix.pyx":676
|
|
jpayne@69
|
14833 *
|
|
jpayne@69
|
14834 * def __dealloc__(self):
|
|
jpayne@69
|
14835 * if <void*>self.iterator != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14836 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14837 * if self.buffer.s != NULL:
|
|
jpayne@69
|
14838 */
|
|
jpayne@69
|
14839 }
|
|
jpayne@69
|
14840
|
|
jpayne@69
|
14841 /* "pysam/libctabix.pyx":678
|
|
jpayne@69
|
14842 * if <void*>self.iterator != NULL:
|
|
jpayne@69
|
14843 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14844 * if self.buffer.s != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14845 * free(self.buffer.s)
|
|
jpayne@69
|
14846 *
|
|
jpayne@69
|
14847 */
|
|
jpayne@69
|
14848 __pyx_t_1 = (__pyx_v_self->buffer.s != NULL);
|
|
jpayne@69
|
14849 if (__pyx_t_1) {
|
|
jpayne@69
|
14850
|
|
jpayne@69
|
14851 /* "pysam/libctabix.pyx":679
|
|
jpayne@69
|
14852 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14853 * if self.buffer.s != NULL:
|
|
jpayne@69
|
14854 * free(self.buffer.s) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14855 *
|
|
jpayne@69
|
14856 *
|
|
jpayne@69
|
14857 */
|
|
jpayne@69
|
14858 free(__pyx_v_self->buffer.s);
|
|
jpayne@69
|
14859
|
|
jpayne@69
|
14860 /* "pysam/libctabix.pyx":678
|
|
jpayne@69
|
14861 * if <void*>self.iterator != NULL:
|
|
jpayne@69
|
14862 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14863 * if self.buffer.s != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14864 * free(self.buffer.s)
|
|
jpayne@69
|
14865 *
|
|
jpayne@69
|
14866 */
|
|
jpayne@69
|
14867 }
|
|
jpayne@69
|
14868
|
|
jpayne@69
|
14869 /* "pysam/libctabix.pyx":675
|
|
jpayne@69
|
14870 * return charptr_to_str(self.buffer.s, self.encoding)
|
|
jpayne@69
|
14871 *
|
|
jpayne@69
|
14872 * def __dealloc__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14873 * if <void*>self.iterator != NULL:
|
|
jpayne@69
|
14874 * tbx_itr_destroy(self.iterator)
|
|
jpayne@69
|
14875 */
|
|
jpayne@69
|
14876
|
|
jpayne@69
|
14877 /* function exit code */
|
|
jpayne@69
|
14878 goto __pyx_L0;
|
|
jpayne@69
|
14879 __pyx_L1_error:;
|
|
jpayne@69
|
14880 __Pyx_WriteUnraisable("pysam.libctabix.TabixIterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
|
|
jpayne@69
|
14881 __pyx_L0:;
|
|
jpayne@69
|
14882 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
14883 }
|
|
jpayne@69
|
14884
|
|
jpayne@69
|
14885 /* "(tree fragment)":1
|
|
jpayne@69
|
14886 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14887 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
14888 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
14889 */
|
|
jpayne@69
|
14890
|
|
jpayne@69
|
14891 /* Python wrapper */
|
|
jpayne@69
|
14892 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14893 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14894 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14895 #else
|
|
jpayne@69
|
14896 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14897 #endif
|
|
jpayne@69
|
14898 ); /*proto*/
|
|
jpayne@69
|
14899 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13TabixIterator_8__reduce_cython__, "TabixIterator.__reduce_cython__(self)");
|
|
jpayne@69
|
14900 static PyMethodDef __pyx_mdef_5pysam_9libctabix_13TabixIterator_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_8__reduce_cython__};
|
|
jpayne@69
|
14901 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14902 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14903 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14904 #else
|
|
jpayne@69
|
14905 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14906 #endif
|
|
jpayne@69
|
14907 ) {
|
|
jpayne@69
|
14908 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14909 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
14910 #endif
|
|
jpayne@69
|
14911 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14912 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
14913 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14914 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
14915 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14916 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
14917 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
14918 #else
|
|
jpayne@69
|
14919 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
14920 #endif
|
|
jpayne@69
|
14921 #endif
|
|
jpayne@69
|
14922 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
14923 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
14924 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
14925 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
14926 __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self));
|
|
jpayne@69
|
14927
|
|
jpayne@69
|
14928 /* function exit code */
|
|
jpayne@69
|
14929 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14930 return __pyx_r;
|
|
jpayne@69
|
14931 }
|
|
jpayne@69
|
14932
|
|
jpayne@69
|
14933 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) {
|
|
jpayne@69
|
14934 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
14935 __Pyx_TraceDeclarations
|
|
jpayne@69
|
14936 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
14937 int __pyx_lineno = 0;
|
|
jpayne@69
|
14938 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
14939 int __pyx_clineno = 0;
|
|
jpayne@69
|
14940 __Pyx_TraceFrameInit(__pyx_codeobj__25)
|
|
jpayne@69
|
14941 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
14942 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
14943
|
|
jpayne@69
|
14944 /* "(tree fragment)":2
|
|
jpayne@69
|
14945 * def __reduce_cython__(self):
|
|
jpayne@69
|
14946 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14947 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
14948 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
14949 */
|
|
jpayne@69
|
14950 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0);
|
|
jpayne@69
|
14951 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
14952
|
|
jpayne@69
|
14953 /* "(tree fragment)":1
|
|
jpayne@69
|
14954 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14955 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
14956 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
14957 */
|
|
jpayne@69
|
14958
|
|
jpayne@69
|
14959 /* function exit code */
|
|
jpayne@69
|
14960 __pyx_L1_error:;
|
|
jpayne@69
|
14961 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
14962 __pyx_r = NULL;
|
|
jpayne@69
|
14963 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
14964 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
14965 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
14966 return __pyx_r;
|
|
jpayne@69
|
14967 }
|
|
jpayne@69
|
14968
|
|
jpayne@69
|
14969 /* "(tree fragment)":3
|
|
jpayne@69
|
14970 * def __reduce_cython__(self):
|
|
jpayne@69
|
14971 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
14972 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
14973 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
14974 */
|
|
jpayne@69
|
14975
|
|
jpayne@69
|
14976 /* Python wrapper */
|
|
jpayne@69
|
14977 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14978 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14979 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14980 #else
|
|
jpayne@69
|
14981 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14982 #endif
|
|
jpayne@69
|
14983 ); /*proto*/
|
|
jpayne@69
|
14984 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13TabixIterator_10__setstate_cython__, "TabixIterator.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
14985 static PyMethodDef __pyx_mdef_5pysam_9libctabix_13TabixIterator_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_10__setstate_cython__};
|
|
jpayne@69
|
14986 static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
14987 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14988 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
14989 #else
|
|
jpayne@69
|
14990 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
14991 #endif
|
|
jpayne@69
|
14992 ) {
|
|
jpayne@69
|
14993 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
14994 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14995 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
14996 #endif
|
|
jpayne@69
|
14997 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
14998 PyObject* values[1] = {0};
|
|
jpayne@69
|
14999 int __pyx_lineno = 0;
|
|
jpayne@69
|
15000 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15001 int __pyx_clineno = 0;
|
|
jpayne@69
|
15002 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
15003 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15004 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
15005 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15006 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15007 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
15008 #else
|
|
jpayne@69
|
15009 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
15010 #endif
|
|
jpayne@69
|
15011 #endif
|
|
jpayne@69
|
15012 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
15013 {
|
|
jpayne@69
|
15014 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
15015 if (__pyx_kwds) {
|
|
jpayne@69
|
15016 Py_ssize_t kw_args;
|
|
jpayne@69
|
15017 switch (__pyx_nargs) {
|
|
jpayne@69
|
15018 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15019 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
15020 case 0: break;
|
|
jpayne@69
|
15021 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15022 }
|
|
jpayne@69
|
15023 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
15024 switch (__pyx_nargs) {
|
|
jpayne@69
|
15025 case 0:
|
|
jpayne@69
|
15026 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
15027 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
15028 kw_args--;
|
|
jpayne@69
|
15029 }
|
|
jpayne@69
|
15030 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
15031 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15032 }
|
|
jpayne@69
|
15033 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
15034 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
15035 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
15036 }
|
|
jpayne@69
|
15037 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
15038 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15039 } else {
|
|
jpayne@69
|
15040 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15041 }
|
|
jpayne@69
|
15042 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
15043 }
|
|
jpayne@69
|
15044 goto __pyx_L6_skip;
|
|
jpayne@69
|
15045 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
15046 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
15047 __pyx_L6_skip:;
|
|
jpayne@69
|
15048 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
15049 __pyx_L3_error:;
|
|
jpayne@69
|
15050 {
|
|
jpayne@69
|
15051 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15052 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15053 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15054 }
|
|
jpayne@69
|
15055 }
|
|
jpayne@69
|
15056 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15057 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15058 return NULL;
|
|
jpayne@69
|
15059 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
15060 __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
15061
|
|
jpayne@69
|
15062 /* function exit code */
|
|
jpayne@69
|
15063 {
|
|
jpayne@69
|
15064 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15065 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15066 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15067 }
|
|
jpayne@69
|
15068 }
|
|
jpayne@69
|
15069 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15070 return __pyx_r;
|
|
jpayne@69
|
15071 }
|
|
jpayne@69
|
15072
|
|
jpayne@69
|
15073 static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
15074 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
15075 __Pyx_TraceDeclarations
|
|
jpayne@69
|
15076 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15077 int __pyx_lineno = 0;
|
|
jpayne@69
|
15078 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15079 int __pyx_clineno = 0;
|
|
jpayne@69
|
15080 __Pyx_TraceFrameInit(__pyx_codeobj__26)
|
|
jpayne@69
|
15081 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
15082 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
15083
|
|
jpayne@69
|
15084 /* "(tree fragment)":4
|
|
jpayne@69
|
15085 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15086 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
15087 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15088 */
|
|
jpayne@69
|
15089 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0);
|
|
jpayne@69
|
15090 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
15091
|
|
jpayne@69
|
15092 /* "(tree fragment)":3
|
|
jpayne@69
|
15093 * def __reduce_cython__(self):
|
|
jpayne@69
|
15094 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15095 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15096 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15097 */
|
|
jpayne@69
|
15098
|
|
jpayne@69
|
15099 /* function exit code */
|
|
jpayne@69
|
15100 __pyx_L1_error:;
|
|
jpayne@69
|
15101 __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15102 __pyx_r = NULL;
|
|
jpayne@69
|
15103 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
15104 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
15105 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15106 return __pyx_r;
|
|
jpayne@69
|
15107 }
|
|
jpayne@69
|
15108
|
|
jpayne@69
|
15109 /* "pysam/libctabix.pyx":685
|
|
jpayne@69
|
15110 * '''empty iterator'''
|
|
jpayne@69
|
15111 *
|
|
jpayne@69
|
15112 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15113 * return self
|
|
jpayne@69
|
15114 *
|
|
jpayne@69
|
15115 */
|
|
jpayne@69
|
15116
|
|
jpayne@69
|
15117 /* Python wrapper */
|
|
jpayne@69
|
15118 static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_1__iter__(PyObject *__pyx_self,
|
|
jpayne@69
|
15119 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15120 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15121 #else
|
|
jpayne@69
|
15122 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15123 #endif
|
|
jpayne@69
|
15124 ); /*proto*/
|
|
jpayne@69
|
15125 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13EmptyIterator___iter__, "EmptyIterator.__iter__(self)");
|
|
jpayne@69
|
15126 static PyMethodDef __pyx_mdef_5pysam_9libctabix_13EmptyIterator_1__iter__ = {"__iter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13EmptyIterator_1__iter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13EmptyIterator___iter__};
|
|
jpayne@69
|
15127 static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_1__iter__(PyObject *__pyx_self,
|
|
jpayne@69
|
15128 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15129 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15130 #else
|
|
jpayne@69
|
15131 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15132 #endif
|
|
jpayne@69
|
15133 ) {
|
|
jpayne@69
|
15134 PyObject *__pyx_v_self = 0;
|
|
jpayne@69
|
15135 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15136 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
15137 #endif
|
|
jpayne@69
|
15138 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
15139 PyObject* values[1] = {0};
|
|
jpayne@69
|
15140 int __pyx_lineno = 0;
|
|
jpayne@69
|
15141 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15142 int __pyx_clineno = 0;
|
|
jpayne@69
|
15143 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
15144 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15145 __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
|
|
jpayne@69
|
15146 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15147 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15148 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
15149 #else
|
|
jpayne@69
|
15150 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
15151 #endif
|
|
jpayne@69
|
15152 #endif
|
|
jpayne@69
|
15153 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
15154 {
|
|
jpayne@69
|
15155 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
|
|
jpayne@69
|
15156 if (__pyx_kwds) {
|
|
jpayne@69
|
15157 Py_ssize_t kw_args;
|
|
jpayne@69
|
15158 switch (__pyx_nargs) {
|
|
jpayne@69
|
15159 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15160 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
15161 case 0: break;
|
|
jpayne@69
|
15162 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15163 }
|
|
jpayne@69
|
15164 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
15165 switch (__pyx_nargs) {
|
|
jpayne@69
|
15166 case 0:
|
|
jpayne@69
|
15167 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
|
|
jpayne@69
|
15168 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
15169 kw_args--;
|
|
jpayne@69
|
15170 }
|
|
jpayne@69
|
15171 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 685, __pyx_L3_error)
|
|
jpayne@69
|
15172 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15173 }
|
|
jpayne@69
|
15174 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
15175 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
15176 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__iter__") < 0)) __PYX_ERR(0, 685, __pyx_L3_error)
|
|
jpayne@69
|
15177 }
|
|
jpayne@69
|
15178 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
15179 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15180 } else {
|
|
jpayne@69
|
15181 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15182 }
|
|
jpayne@69
|
15183 __pyx_v_self = values[0];
|
|
jpayne@69
|
15184 }
|
|
jpayne@69
|
15185 goto __pyx_L6_skip;
|
|
jpayne@69
|
15186 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
15187 __Pyx_RaiseArgtupleInvalid("__iter__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 685, __pyx_L3_error)
|
|
jpayne@69
|
15188 __pyx_L6_skip:;
|
|
jpayne@69
|
15189 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
15190 __pyx_L3_error:;
|
|
jpayne@69
|
15191 {
|
|
jpayne@69
|
15192 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15193 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15194 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15195 }
|
|
jpayne@69
|
15196 }
|
|
jpayne@69
|
15197 __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15198 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15199 return NULL;
|
|
jpayne@69
|
15200 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
15201 __pyx_r = __pyx_pf_5pysam_9libctabix_13EmptyIterator___iter__(__pyx_self, __pyx_v_self);
|
|
jpayne@69
|
15202
|
|
jpayne@69
|
15203 /* function exit code */
|
|
jpayne@69
|
15204 {
|
|
jpayne@69
|
15205 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15206 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15207 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15208 }
|
|
jpayne@69
|
15209 }
|
|
jpayne@69
|
15210 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15211 return __pyx_r;
|
|
jpayne@69
|
15212 }
|
|
jpayne@69
|
15213
|
|
jpayne@69
|
15214 static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator___iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
|
|
jpayne@69
|
15215 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
15216 __Pyx_TraceDeclarations
|
|
jpayne@69
|
15217 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15218 int __pyx_lineno = 0;
|
|
jpayne@69
|
15219 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15220 int __pyx_clineno = 0;
|
|
jpayne@69
|
15221 __Pyx_TraceFrameInit(__pyx_codeobj__27)
|
|
jpayne@69
|
15222 __Pyx_RefNannySetupContext("__iter__", 1);
|
|
jpayne@69
|
15223 __Pyx_TraceCall("__iter__", __pyx_f[0], 685, 0, __PYX_ERR(0, 685, __pyx_L1_error));
|
|
jpayne@69
|
15224
|
|
jpayne@69
|
15225 /* "pysam/libctabix.pyx":686
|
|
jpayne@69
|
15226 *
|
|
jpayne@69
|
15227 * def __iter__(self):
|
|
jpayne@69
|
15228 * return self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15229 *
|
|
jpayne@69
|
15230 * def __next__(self):
|
|
jpayne@69
|
15231 */
|
|
jpayne@69
|
15232 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
15233 __Pyx_INCREF(__pyx_v_self);
|
|
jpayne@69
|
15234 __pyx_r = __pyx_v_self;
|
|
jpayne@69
|
15235 goto __pyx_L0;
|
|
jpayne@69
|
15236
|
|
jpayne@69
|
15237 /* "pysam/libctabix.pyx":685
|
|
jpayne@69
|
15238 * '''empty iterator'''
|
|
jpayne@69
|
15239 *
|
|
jpayne@69
|
15240 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15241 * return self
|
|
jpayne@69
|
15242 *
|
|
jpayne@69
|
15243 */
|
|
jpayne@69
|
15244
|
|
jpayne@69
|
15245 /* function exit code */
|
|
jpayne@69
|
15246 __pyx_L1_error:;
|
|
jpayne@69
|
15247 __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15248 __pyx_r = NULL;
|
|
jpayne@69
|
15249 __pyx_L0:;
|
|
jpayne@69
|
15250 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
15251 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
15252 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15253 return __pyx_r;
|
|
jpayne@69
|
15254 }
|
|
jpayne@69
|
15255
|
|
jpayne@69
|
15256 /* "pysam/libctabix.pyx":688
|
|
jpayne@69
|
15257 * return self
|
|
jpayne@69
|
15258 *
|
|
jpayne@69
|
15259 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15260 * raise StopIteration()
|
|
jpayne@69
|
15261 *
|
|
jpayne@69
|
15262 */
|
|
jpayne@69
|
15263
|
|
jpayne@69
|
15264 /* Python wrapper */
|
|
jpayne@69
|
15265 static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_3__next__(PyObject *__pyx_self,
|
|
jpayne@69
|
15266 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15267 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15268 #else
|
|
jpayne@69
|
15269 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15270 #endif
|
|
jpayne@69
|
15271 ); /*proto*/
|
|
jpayne@69
|
15272 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13EmptyIterator_2__next__, "EmptyIterator.__next__(self)");
|
|
jpayne@69
|
15273 static PyMethodDef __pyx_mdef_5pysam_9libctabix_13EmptyIterator_3__next__ = {"__next__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13EmptyIterator_3__next__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13EmptyIterator_2__next__};
|
|
jpayne@69
|
15274 static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_3__next__(PyObject *__pyx_self,
|
|
jpayne@69
|
15275 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15276 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15277 #else
|
|
jpayne@69
|
15278 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15279 #endif
|
|
jpayne@69
|
15280 ) {
|
|
jpayne@69
|
15281 CYTHON_UNUSED PyObject *__pyx_v_self = 0;
|
|
jpayne@69
|
15282 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15283 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
15284 #endif
|
|
jpayne@69
|
15285 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
15286 PyObject* values[1] = {0};
|
|
jpayne@69
|
15287 int __pyx_lineno = 0;
|
|
jpayne@69
|
15288 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15289 int __pyx_clineno = 0;
|
|
jpayne@69
|
15290 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
15291 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15292 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
|
|
jpayne@69
|
15293 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15294 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15295 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
15296 #else
|
|
jpayne@69
|
15297 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
15298 #endif
|
|
jpayne@69
|
15299 #endif
|
|
jpayne@69
|
15300 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
15301 {
|
|
jpayne@69
|
15302 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
|
|
jpayne@69
|
15303 if (__pyx_kwds) {
|
|
jpayne@69
|
15304 Py_ssize_t kw_args;
|
|
jpayne@69
|
15305 switch (__pyx_nargs) {
|
|
jpayne@69
|
15306 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15307 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
15308 case 0: break;
|
|
jpayne@69
|
15309 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15310 }
|
|
jpayne@69
|
15311 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
15312 switch (__pyx_nargs) {
|
|
jpayne@69
|
15313 case 0:
|
|
jpayne@69
|
15314 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
|
|
jpayne@69
|
15315 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
15316 kw_args--;
|
|
jpayne@69
|
15317 }
|
|
jpayne@69
|
15318 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 688, __pyx_L3_error)
|
|
jpayne@69
|
15319 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15320 }
|
|
jpayne@69
|
15321 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
15322 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
15323 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__next__") < 0)) __PYX_ERR(0, 688, __pyx_L3_error)
|
|
jpayne@69
|
15324 }
|
|
jpayne@69
|
15325 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
15326 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15327 } else {
|
|
jpayne@69
|
15328 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15329 }
|
|
jpayne@69
|
15330 __pyx_v_self = values[0];
|
|
jpayne@69
|
15331 }
|
|
jpayne@69
|
15332 goto __pyx_L6_skip;
|
|
jpayne@69
|
15333 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
15334 __Pyx_RaiseArgtupleInvalid("__next__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 688, __pyx_L3_error)
|
|
jpayne@69
|
15335 __pyx_L6_skip:;
|
|
jpayne@69
|
15336 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
15337 __pyx_L3_error:;
|
|
jpayne@69
|
15338 {
|
|
jpayne@69
|
15339 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15340 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15341 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15342 }
|
|
jpayne@69
|
15343 }
|
|
jpayne@69
|
15344 __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15345 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15346 return NULL;
|
|
jpayne@69
|
15347 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
15348 __pyx_r = __pyx_pf_5pysam_9libctabix_13EmptyIterator_2__next__(__pyx_self, __pyx_v_self);
|
|
jpayne@69
|
15349
|
|
jpayne@69
|
15350 /* function exit code */
|
|
jpayne@69
|
15351 {
|
|
jpayne@69
|
15352 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15353 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15354 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15355 }
|
|
jpayne@69
|
15356 }
|
|
jpayne@69
|
15357 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15358 return __pyx_r;
|
|
jpayne@69
|
15359 }
|
|
jpayne@69
|
15360
|
|
jpayne@69
|
15361 static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator_2__next__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
|
|
jpayne@69
|
15362 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
15363 __Pyx_TraceDeclarations
|
|
jpayne@69
|
15364 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15365 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
15366 int __pyx_lineno = 0;
|
|
jpayne@69
|
15367 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15368 int __pyx_clineno = 0;
|
|
jpayne@69
|
15369 __Pyx_TraceFrameInit(__pyx_codeobj__28)
|
|
jpayne@69
|
15370 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
15371 __Pyx_TraceCall("__next__", __pyx_f[0], 688, 0, __PYX_ERR(0, 688, __pyx_L1_error));
|
|
jpayne@69
|
15372
|
|
jpayne@69
|
15373 /* "pysam/libctabix.pyx":689
|
|
jpayne@69
|
15374 *
|
|
jpayne@69
|
15375 * def __next__(self):
|
|
jpayne@69
|
15376 * raise StopIteration() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15377 *
|
|
jpayne@69
|
15378 *
|
|
jpayne@69
|
15379 */
|
|
jpayne@69
|
15380 __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_builtin_StopIteration); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 689, __pyx_L1_error)
|
|
jpayne@69
|
15381 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
15382 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
15383 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
15384 __PYX_ERR(0, 689, __pyx_L1_error)
|
|
jpayne@69
|
15385
|
|
jpayne@69
|
15386 /* "pysam/libctabix.pyx":688
|
|
jpayne@69
|
15387 * return self
|
|
jpayne@69
|
15388 *
|
|
jpayne@69
|
15389 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15390 * raise StopIteration()
|
|
jpayne@69
|
15391 *
|
|
jpayne@69
|
15392 */
|
|
jpayne@69
|
15393
|
|
jpayne@69
|
15394 /* function exit code */
|
|
jpayne@69
|
15395 __pyx_L1_error:;
|
|
jpayne@69
|
15396 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
15397 __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15398 __pyx_r = NULL;
|
|
jpayne@69
|
15399 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
15400 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
15401 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15402 return __pyx_r;
|
|
jpayne@69
|
15403 }
|
|
jpayne@69
|
15404
|
|
jpayne@69
|
15405 /* "pysam/libctabix.pyx":700
|
|
jpayne@69
|
15406 * """
|
|
jpayne@69
|
15407 *
|
|
jpayne@69
|
15408 * def __init__(self, Parser parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15409 * super().__init__()
|
|
jpayne@69
|
15410 * self.parser = parser
|
|
jpayne@69
|
15411 */
|
|
jpayne@69
|
15412
|
|
jpayne@69
|
15413 /* Python wrapper */
|
|
jpayne@69
|
15414 static int __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
15415 static int __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
15416 struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser = 0;
|
|
jpayne@69
|
15417 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
15418 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
15419 PyObject* values[1] = {0};
|
|
jpayne@69
|
15420 int __pyx_lineno = 0;
|
|
jpayne@69
|
15421 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15422 int __pyx_clineno = 0;
|
|
jpayne@69
|
15423 int __pyx_r;
|
|
jpayne@69
|
15424 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15425 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
|
|
jpayne@69
|
15426 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15427 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
15428 #else
|
|
jpayne@69
|
15429 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
15430 #endif
|
|
jpayne@69
|
15431 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
15432 {
|
|
jpayne@69
|
15433 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_parser,0};
|
|
jpayne@69
|
15434 if (__pyx_kwds) {
|
|
jpayne@69
|
15435 Py_ssize_t kw_args;
|
|
jpayne@69
|
15436 switch (__pyx_nargs) {
|
|
jpayne@69
|
15437 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
15438 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
15439 case 0: break;
|
|
jpayne@69
|
15440 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15441 }
|
|
jpayne@69
|
15442 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
15443 switch (__pyx_nargs) {
|
|
jpayne@69
|
15444 case 0:
|
|
jpayne@69
|
15445 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) {
|
|
jpayne@69
|
15446 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
|
|
jpayne@69
|
15447 kw_args--;
|
|
jpayne@69
|
15448 }
|
|
jpayne@69
|
15449 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 700, __pyx_L3_error)
|
|
jpayne@69
|
15450 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15451 }
|
|
jpayne@69
|
15452 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
15453 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
15454 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 700, __pyx_L3_error)
|
|
jpayne@69
|
15455 }
|
|
jpayne@69
|
15456 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
15457 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15458 } else {
|
|
jpayne@69
|
15459 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
15460 }
|
|
jpayne@69
|
15461 __pyx_v_parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)values[0]);
|
|
jpayne@69
|
15462 }
|
|
jpayne@69
|
15463 goto __pyx_L6_skip;
|
|
jpayne@69
|
15464 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
15465 __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 700, __pyx_L3_error)
|
|
jpayne@69
|
15466 __pyx_L6_skip:;
|
|
jpayne@69
|
15467 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
15468 __pyx_L3_error:;
|
|
jpayne@69
|
15469 {
|
|
jpayne@69
|
15470 Py_ssize_t __pyx_temp;
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|
jpayne@69
|
15471 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15472 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
15473 }
|
|
jpayne@69
|
15474 }
|
|
jpayne@69
|
15475 __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
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jpayne@69
|
15476 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
15477 return -1;
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jpayne@69
|
15478 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
15479 if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_5pysam_9libctabix_Parser, 1, "parser", 0))) __PYX_ERR(0, 700, __pyx_L1_error)
|
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jpayne@69
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15480 __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed___init__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self), __pyx_v_parser);
|
|
jpayne@69
|
15481
|
|
jpayne@69
|
15482 /* function exit code */
|
|
jpayne@69
|
15483 goto __pyx_L0;
|
|
jpayne@69
|
15484 __pyx_L1_error:;
|
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jpayne@69
|
15485 __pyx_r = -1;
|
|
jpayne@69
|
15486 __pyx_L0:;
|
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jpayne@69
|
15487 {
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jpayne@69
|
15488 Py_ssize_t __pyx_temp;
|
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jpayne@69
|
15489 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
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jpayne@69
|
15490 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
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jpayne@69
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15491 }
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jpayne@69
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15492 }
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jpayne@69
|
15493 __Pyx_RefNannyFinishContext();
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jpayne@69
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15494 return __pyx_r;
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jpayne@69
|
15495 }
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jpayne@69
|
15496
|
|
jpayne@69
|
15497 static int __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser) {
|
|
jpayne@69
|
15498 int __pyx_r;
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jpayne@69
|
15499 __Pyx_TraceDeclarations
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jpayne@69
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15500 __Pyx_RefNannyDeclarations
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jpayne@69
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15501 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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15502 PyObject *__pyx_t_2 = NULL;
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jpayne@69
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15503 PyObject *__pyx_t_3 = NULL;
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jpayne@69
|
15504 unsigned int __pyx_t_4;
|
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jpayne@69
|
15505 int __pyx_lineno = 0;
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jpayne@69
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15506 const char *__pyx_filename = NULL;
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jpayne@69
|
15507 int __pyx_clineno = 0;
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jpayne@69
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15508 __Pyx_RefNannySetupContext("__init__", 1);
|
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jpayne@69
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15509 __Pyx_TraceCall("__init__", __pyx_f[0], 700, 0, __PYX_ERR(0, 700, __pyx_L1_error));
|
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jpayne@69
|
15510
|
|
jpayne@69
|
15511 /* "pysam/libctabix.pyx":701
|
|
jpayne@69
|
15512 *
|
|
jpayne@69
|
15513 * def __init__(self, Parser parser):
|
|
jpayne@69
|
15514 * super().__init__() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15515 * self.parser = parser
|
|
jpayne@69
|
15516 *
|
|
jpayne@69
|
15517 */
|
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jpayne@69
|
15518 __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 701, __pyx_L1_error)
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jpayne@69
|
15519 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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15521 __Pyx_GIVEREF((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed);
|
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jpayne@69
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15522 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed))) __PYX_ERR(0, 701, __pyx_L1_error);
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jpayne@69
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15523 __Pyx_INCREF((PyObject *)__pyx_v_self);
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jpayne@69
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15524 __Pyx_GIVEREF((PyObject *)__pyx_v_self);
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jpayne@69
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15525 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_self))) __PYX_ERR(0, 701, __pyx_L1_error);
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jpayne@69
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15526 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_super, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 701, __pyx_L1_error)
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jpayne@69
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jpayne@69
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15529 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_init); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 701, __pyx_L1_error)
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jpayne@69
|
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|
15532 __pyx_t_3 = NULL;
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jpayne@69
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15533 __pyx_t_4 = 0;
|
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jpayne@69
|
15534 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
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jpayne@69
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|
|
jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
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15543 }
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jpayne@69
|
15544 }
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|
jpayne@69
|
15545 #endif
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jpayne@69
|
15546 {
|
|
jpayne@69
|
15547 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
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jpayne@69
|
15548 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
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jpayne@69
|
15549 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
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jpayne@69
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jpayne@69
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jpayne@69
|
15553 }
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jpayne@69
|
15554 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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15555
|
|
jpayne@69
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15556 /* "pysam/libctabix.pyx":702
|
|
jpayne@69
|
15557 * def __init__(self, Parser parser):
|
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jpayne@69
|
15558 * super().__init__()
|
|
jpayne@69
|
15559 * self.parser = parser # <<<<<<<<<<<<<<
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|
jpayne@69
|
15560 *
|
|
jpayne@69
|
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|
|
jpayne@69
|
15562 */
|
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jpayne@69
|
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jpayne@69
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jpayne@69
|
15565 __Pyx_GOTREF((PyObject *)__pyx_v_self->parser);
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jpayne@69
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15566 __Pyx_DECREF((PyObject *)__pyx_v_self->parser);
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jpayne@69
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jpayne@69
|
15568
|
|
jpayne@69
|
15569 /* "pysam/libctabix.pyx":700
|
|
jpayne@69
|
15570 * """
|
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jpayne@69
|
15571 *
|
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jpayne@69
|
15572 * def __init__(self, Parser parser): # <<<<<<<<<<<<<<
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jpayne@69
|
15573 * super().__init__()
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jpayne@69
|
15574 * self.parser = parser
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jpayne@69
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15575 */
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15576
|
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jpayne@69
|
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jpayne@69
|
15578 __pyx_r = 0;
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jpayne@69
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15579 goto __pyx_L0;
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jpayne@69
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jpayne@69
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15581 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
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15582 __Pyx_XDECREF(__pyx_t_2);
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jpayne@69
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15583 __Pyx_XDECREF(__pyx_t_3);
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jpayne@69
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jpayne@69
|
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jpayne@69
|
15586 __pyx_L0:;
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jpayne@69
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jpayne@69
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jpayne@69
|
15591
|
|
jpayne@69
|
15592 /* "pysam/libctabix.pyx":704
|
|
jpayne@69
|
15593 * self.parser = parser
|
|
jpayne@69
|
15594 *
|
|
jpayne@69
|
15595 * def __next__(self): # <<<<<<<<<<<<<<
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|
jpayne@69
|
15596 * """python version of next().
|
|
jpayne@69
|
15597 *
|
|
jpayne@69
|
15598 */
|
|
jpayne@69
|
15599
|
|
jpayne@69
|
15600 /* Python wrapper */
|
|
jpayne@69
|
15601 static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(PyObject *__pyx_v_self); /*proto*/
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|
jpayne@69
|
15602 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_2__next__, "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ");
|
|
jpayne@69
|
15603 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
15604 struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__;
|
|
jpayne@69
|
15605 #endif
|
|
jpayne@69
|
15606 static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
15607 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
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|
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jpayne@69
|
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|
|
jpayne@69
|
15613
|
|
jpayne@69
|
15614 /* function exit code */
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jpayne@69
|
15615 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
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jpayne@69
|
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jpayne@69
|
15618
|
|
jpayne@69
|
15619 static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self) {
|
|
jpayne@69
|
15620 int __pyx_v_retval;
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jpayne@69
|
15621 PyObject *__pyx_r = NULL;
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|
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jpayne@69
|
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jpayne@69
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jpayne@69
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15633
|
|
jpayne@69
|
15634 /* "pysam/libctabix.pyx":710
|
|
jpayne@69
|
15635 * """
|
|
jpayne@69
|
15636 *
|
|
jpayne@69
|
15637 * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<<
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jpayne@69
|
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|
jpayne@69
|
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|
jpayne@69
|
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|
jpayne@69
|
15643
|
|
jpayne@69
|
15644 /* "pysam/libctabix.pyx":711
|
|
jpayne@69
|
15645 *
|
|
jpayne@69
|
15646 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
15647 * if retval == -5: # <<<<<<<<<<<<<<
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|
jpayne@69
|
15648 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
15649 * elif retval < 0:
|
|
jpayne@69
|
15650 */
|
|
jpayne@69
|
15651 __pyx_t_2 = (__pyx_v_retval == -5L);
|
|
jpayne@69
|
15652 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
15653
|
|
jpayne@69
|
15654 /* "pysam/libctabix.pyx":712
|
|
jpayne@69
|
15655 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
15656 * if retval == -5:
|
|
jpayne@69
|
15657 * raise IOError("iteration on closed file") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15658 * elif retval < 0:
|
|
jpayne@69
|
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|
|
jpayne@69
|
15660 */
|
|
jpayne@69
|
15661 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 712, __pyx_L1_error)
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jpayne@69
|
15662 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
15663 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
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jpayne@69
|
15664 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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jpayne@69
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jpayne@69
|
15666
|
|
jpayne@69
|
15667 /* "pysam/libctabix.pyx":711
|
|
jpayne@69
|
15668 *
|
|
jpayne@69
|
15669 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
15670 * if retval == -5: # <<<<<<<<<<<<<<
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|
jpayne@69
|
15671 * raise IOError("iteration on closed file")
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|
jpayne@69
|
15672 * elif retval < 0:
|
|
jpayne@69
|
15673 */
|
|
jpayne@69
|
15674 }
|
|
jpayne@69
|
15675
|
|
jpayne@69
|
15676 /* "pysam/libctabix.pyx":713
|
|
jpayne@69
|
15677 * if retval == -5:
|
|
jpayne@69
|
15678 * raise IOError("iteration on closed file")
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|
jpayne@69
|
15679 * elif retval < 0: # <<<<<<<<<<<<<<
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|
jpayne@69
|
15680 * raise StopIteration
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|
jpayne@69
|
15681 *
|
|
jpayne@69
|
15682 */
|
|
jpayne@69
|
15683 __pyx_t_2 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
15684 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
15685
|
|
jpayne@69
|
15686 /* "pysam/libctabix.pyx":714
|
|
jpayne@69
|
15687 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
15688 * elif retval < 0:
|
|
jpayne@69
|
15689 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15690 *
|
|
jpayne@69
|
15691 * return self.parser.parse(self.buffer.s,
|
|
jpayne@69
|
15692 */
|
|
jpayne@69
|
15693 __pyx_error_without_exception = 1;
|
|
jpayne@69
|
15694 goto __pyx_L1_error;;
|
|
jpayne@69
|
15695
|
|
jpayne@69
|
15696 /* "pysam/libctabix.pyx":713
|
|
jpayne@69
|
15697 * if retval == -5:
|
|
jpayne@69
|
15698 * raise IOError("iteration on closed file")
|
|
jpayne@69
|
15699 * elif retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15700 * raise StopIteration
|
|
jpayne@69
|
15701 *
|
|
jpayne@69
|
15702 */
|
|
jpayne@69
|
15703 }
|
|
jpayne@69
|
15704
|
|
jpayne@69
|
15705 /* "pysam/libctabix.pyx":716
|
|
jpayne@69
|
15706 * raise StopIteration
|
|
jpayne@69
|
15707 *
|
|
jpayne@69
|
15708 * return self.parser.parse(self.buffer.s, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15709 * self.buffer.l)
|
|
jpayne@69
|
15710 *
|
|
jpayne@69
|
15711 */
|
|
jpayne@69
|
15712 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
15713
|
|
jpayne@69
|
15714 /* "pysam/libctabix.pyx":717
|
|
jpayne@69
|
15715 *
|
|
jpayne@69
|
15716 * return self.parser.parse(self.buffer.s,
|
|
jpayne@69
|
15717 * self.buffer.l) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15718 *
|
|
jpayne@69
|
15719 *
|
|
jpayne@69
|
15720 */
|
|
jpayne@69
|
15721 __pyx_t_3 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->parser->__pyx_vtab)->parse(__pyx_v_self->parser, __pyx_v_self->__pyx_base.buffer.s, __pyx_v_self->__pyx_base.buffer.l); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 716, __pyx_L1_error)
|
|
jpayne@69
|
15722 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
15723 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
15724 __pyx_t_3 = 0;
|
|
jpayne@69
|
15725 goto __pyx_L0;
|
|
jpayne@69
|
15726
|
|
jpayne@69
|
15727 /* "pysam/libctabix.pyx":704
|
|
jpayne@69
|
15728 * self.parser = parser
|
|
jpayne@69
|
15729 *
|
|
jpayne@69
|
15730 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15731 * """python version of next().
|
|
jpayne@69
|
15732 *
|
|
jpayne@69
|
15733 */
|
|
jpayne@69
|
15734
|
|
jpayne@69
|
15735 /* function exit code */
|
|
jpayne@69
|
15736 __pyx_L1_error:;
|
|
jpayne@69
|
15737 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
15738 if (!__pyx_error_without_exception) {
|
|
jpayne@69
|
15739 __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15740 }
|
|
jpayne@69
|
15741 __pyx_r = NULL;
|
|
jpayne@69
|
15742 __pyx_L0:;
|
|
jpayne@69
|
15743 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
15744 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
15745 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15746 return __pyx_r;
|
|
jpayne@69
|
15747 }
|
|
jpayne@69
|
15748
|
|
jpayne@69
|
15749 /* "(tree fragment)":1
|
|
jpayne@69
|
15750 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15751 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15752 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
15753 */
|
|
jpayne@69
|
15754
|
|
jpayne@69
|
15755 /* Python wrapper */
|
|
jpayne@69
|
15756 static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
15757 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15758 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15759 #else
|
|
jpayne@69
|
15760 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15761 #endif
|
|
jpayne@69
|
15762 ); /*proto*/
|
|
jpayne@69
|
15763 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__, "TabixIteratorParsed.__reduce_cython__(self)");
|
|
jpayne@69
|
15764 static PyMethodDef __pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__};
|
|
jpayne@69
|
15765 static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
15766 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15767 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15768 #else
|
|
jpayne@69
|
15769 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15770 #endif
|
|
jpayne@69
|
15771 ) {
|
|
jpayne@69
|
15772 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15773 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
15774 #endif
|
|
jpayne@69
|
15775 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
15776 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
15777 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15778 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
15779 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15780 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15781 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
15782 #else
|
|
jpayne@69
|
15783 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
15784 #endif
|
|
jpayne@69
|
15785 #endif
|
|
jpayne@69
|
15786 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
15787 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
15788 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
15789 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
15790 __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self));
|
|
jpayne@69
|
15791
|
|
jpayne@69
|
15792 /* function exit code */
|
|
jpayne@69
|
15793 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15794 return __pyx_r;
|
|
jpayne@69
|
15795 }
|
|
jpayne@69
|
15796
|
|
jpayne@69
|
15797 static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self) {
|
|
jpayne@69
|
15798 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
15799 __Pyx_TraceDeclarations
|
|
jpayne@69
|
15800 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15801 int __pyx_lineno = 0;
|
|
jpayne@69
|
15802 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15803 int __pyx_clineno = 0;
|
|
jpayne@69
|
15804 __Pyx_TraceFrameInit(__pyx_codeobj__29)
|
|
jpayne@69
|
15805 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
15806 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
15807
|
|
jpayne@69
|
15808 /* "(tree fragment)":2
|
|
jpayne@69
|
15809 * def __reduce_cython__(self):
|
|
jpayne@69
|
15810 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15811 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
15812 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15813 */
|
|
jpayne@69
|
15814 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0);
|
|
jpayne@69
|
15815 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
15816
|
|
jpayne@69
|
15817 /* "(tree fragment)":1
|
|
jpayne@69
|
15818 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15819 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15820 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
15821 */
|
|
jpayne@69
|
15822
|
|
jpayne@69
|
15823 /* function exit code */
|
|
jpayne@69
|
15824 __pyx_L1_error:;
|
|
jpayne@69
|
15825 __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15826 __pyx_r = NULL;
|
|
jpayne@69
|
15827 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
15828 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
15829 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15830 return __pyx_r;
|
|
jpayne@69
|
15831 }
|
|
jpayne@69
|
15832
|
|
jpayne@69
|
15833 /* "(tree fragment)":3
|
|
jpayne@69
|
15834 * def __reduce_cython__(self):
|
|
jpayne@69
|
15835 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15836 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15837 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15838 */
|
|
jpayne@69
|
15839
|
|
jpayne@69
|
15840 /* Python wrapper */
|
|
jpayne@69
|
15841 static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
15842 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15843 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15844 #else
|
|
jpayne@69
|
15845 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15846 #endif
|
|
jpayne@69
|
15847 ); /*proto*/
|
|
jpayne@69
|
15848 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__, "TabixIteratorParsed.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
15849 static PyMethodDef __pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__};
|
|
jpayne@69
|
15850 static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
15851 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15852 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
15853 #else
|
|
jpayne@69
|
15854 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
15855 #endif
|
|
jpayne@69
|
15856 ) {
|
|
jpayne@69
|
15857 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
15858 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15859 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
15860 #endif
|
|
jpayne@69
|
15861 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
15862 PyObject* values[1] = {0};
|
|
jpayne@69
|
15863 int __pyx_lineno = 0;
|
|
jpayne@69
|
15864 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15865 int __pyx_clineno = 0;
|
|
jpayne@69
|
15866 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
15867 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15868 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
15869 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15870 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15871 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
15872 #else
|
|
jpayne@69
|
15873 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
15874 #endif
|
|
jpayne@69
|
15875 #endif
|
|
jpayne@69
|
15876 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
15877 {
|
|
jpayne@69
|
15878 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
15879 if (__pyx_kwds) {
|
|
jpayne@69
|
15880 Py_ssize_t kw_args;
|
|
jpayne@69
|
15881 switch (__pyx_nargs) {
|
|
jpayne@69
|
15882 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15883 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
15884 case 0: break;
|
|
jpayne@69
|
15885 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15886 }
|
|
jpayne@69
|
15887 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
15888 switch (__pyx_nargs) {
|
|
jpayne@69
|
15889 case 0:
|
|
jpayne@69
|
15890 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
15891 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
15892 kw_args--;
|
|
jpayne@69
|
15893 }
|
|
jpayne@69
|
15894 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
15895 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15896 }
|
|
jpayne@69
|
15897 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
15898 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
15899 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
15900 }
|
|
jpayne@69
|
15901 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
15902 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
15903 } else {
|
|
jpayne@69
|
15904 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
15905 }
|
|
jpayne@69
|
15906 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
15907 }
|
|
jpayne@69
|
15908 goto __pyx_L6_skip;
|
|
jpayne@69
|
15909 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
15910 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
15911 __pyx_L6_skip:;
|
|
jpayne@69
|
15912 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
15913 __pyx_L3_error:;
|
|
jpayne@69
|
15914 {
|
|
jpayne@69
|
15915 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15916 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15917 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15918 }
|
|
jpayne@69
|
15919 }
|
|
jpayne@69
|
15920 __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15921 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15922 return NULL;
|
|
jpayne@69
|
15923 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
15924 __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
15925
|
|
jpayne@69
|
15926 /* function exit code */
|
|
jpayne@69
|
15927 {
|
|
jpayne@69
|
15928 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
15929 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
15930 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
15931 }
|
|
jpayne@69
|
15932 }
|
|
jpayne@69
|
15933 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15934 return __pyx_r;
|
|
jpayne@69
|
15935 }
|
|
jpayne@69
|
15936
|
|
jpayne@69
|
15937 static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
15938 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
15939 __Pyx_TraceDeclarations
|
|
jpayne@69
|
15940 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15941 int __pyx_lineno = 0;
|
|
jpayne@69
|
15942 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15943 int __pyx_clineno = 0;
|
|
jpayne@69
|
15944 __Pyx_TraceFrameInit(__pyx_codeobj__30)
|
|
jpayne@69
|
15945 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
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jpayne@69
|
15946 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
15947
|
|
jpayne@69
|
15948 /* "(tree fragment)":4
|
|
jpayne@69
|
15949 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15950 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
15951 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15952 */
|
|
jpayne@69
|
15953 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0);
|
|
jpayne@69
|
15954 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
15955
|
|
jpayne@69
|
15956 /* "(tree fragment)":3
|
|
jpayne@69
|
15957 * def __reduce_cython__(self):
|
|
jpayne@69
|
15958 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15959 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15960 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
15961 */
|
|
jpayne@69
|
15962
|
|
jpayne@69
|
15963 /* function exit code */
|
|
jpayne@69
|
15964 __pyx_L1_error:;
|
|
jpayne@69
|
15965 __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
15966 __pyx_r = NULL;
|
|
jpayne@69
|
15967 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
15968 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
15969 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
15970 return __pyx_r;
|
|
jpayne@69
|
15971 }
|
|
jpayne@69
|
15972
|
|
jpayne@69
|
15973 /* "pysam/libctabix.pyx":721
|
|
jpayne@69
|
15974 *
|
|
jpayne@69
|
15975 * cdef class GZIterator:
|
|
jpayne@69
|
15976 * def __init__(self, filename, int buffer_size=65536, encoding="ascii"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
15977 * '''iterate line-by-line through gzip (or bgzip)
|
|
jpayne@69
|
15978 * compressed file.
|
|
jpayne@69
|
15979 */
|
|
jpayne@69
|
15980
|
|
jpayne@69
|
15981 /* Python wrapper */
|
|
jpayne@69
|
15982 static int __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
15983 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator___init__, "iterate line-by-line through gzip (or bgzip)\n compressed file.\n ");
|
|
jpayne@69
|
15984 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
15985 struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__;
|
|
jpayne@69
|
15986 #endif
|
|
jpayne@69
|
15987 static int __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
15988 PyObject *__pyx_v_filename = 0;
|
|
jpayne@69
|
15989 int __pyx_v_buffer_size;
|
|
jpayne@69
|
15990 PyObject *__pyx_v_encoding = 0;
|
|
jpayne@69
|
15991 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
15992 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
15993 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
15994 int __pyx_lineno = 0;
|
|
jpayne@69
|
15995 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
15996 int __pyx_clineno = 0;
|
|
jpayne@69
|
15997 int __pyx_r;
|
|
jpayne@69
|
15998 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
15999 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
|
|
jpayne@69
|
16000 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
16001 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
16002 #else
|
|
jpayne@69
|
16003 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
16004 #endif
|
|
jpayne@69
|
16005 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
16006 {
|
|
jpayne@69
|
16007 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_buffer_size,&__pyx_n_s_encoding,0};
|
|
jpayne@69
|
16008 values[2] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii));
|
|
jpayne@69
|
16009 if (__pyx_kwds) {
|
|
jpayne@69
|
16010 Py_ssize_t kw_args;
|
|
jpayne@69
|
16011 switch (__pyx_nargs) {
|
|
jpayne@69
|
16012 case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2);
|
|
jpayne@69
|
16013 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16014 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
16015 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16016 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
16017 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16018 case 0: break;
|
|
jpayne@69
|
16019 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
16020 }
|
|
jpayne@69
|
16021 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
16022 switch (__pyx_nargs) {
|
|
jpayne@69
|
16023 case 0:
|
|
jpayne@69
|
16024 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) {
|
|
jpayne@69
|
16025 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
|
|
jpayne@69
|
16026 kw_args--;
|
|
jpayne@69
|
16027 }
|
|
jpayne@69
|
16028 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error)
|
|
jpayne@69
|
16029 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
16030 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16031 case 1:
|
|
jpayne@69
|
16032 if (kw_args > 0) {
|
|
jpayne@69
|
16033 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buffer_size);
|
|
jpayne@69
|
16034 if (value) { values[1] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
16035 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error)
|
|
jpayne@69
|
16036 }
|
|
jpayne@69
|
16037 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16038 case 2:
|
|
jpayne@69
|
16039 if (kw_args > 0) {
|
|
jpayne@69
|
16040 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding);
|
|
jpayne@69
|
16041 if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
16042 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error)
|
|
jpayne@69
|
16043 }
|
|
jpayne@69
|
16044 }
|
|
jpayne@69
|
16045 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
16046 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
16047 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 721, __pyx_L3_error)
|
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jpayne@69
|
16048 }
|
|
jpayne@69
|
16049 } else {
|
|
jpayne@69
|
16050 switch (__pyx_nargs) {
|
|
jpayne@69
|
16051 case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2);
|
|
jpayne@69
|
16052 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16053 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
16054 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16055 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
16056 break;
|
|
jpayne@69
|
16057 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
16058 }
|
|
jpayne@69
|
16059 }
|
|
jpayne@69
|
16060 __pyx_v_filename = values[0];
|
|
jpayne@69
|
16061 if (values[1]) {
|
|
jpayne@69
|
16062 __pyx_v_buffer_size = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_buffer_size == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error)
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jpayne@69
|
16063 } else {
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jpayne@69
|
16064 __pyx_v_buffer_size = ((int)0x10000);
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|
jpayne@69
|
16065 }
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jpayne@69
|
16066 __pyx_v_encoding = values[2];
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jpayne@69
|
16067 }
|
|
jpayne@69
|
16068 goto __pyx_L6_skip;
|
|
jpayne@69
|
16069 __pyx_L5_argtuple_error:;
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|
jpayne@69
|
16070 __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 3, __pyx_nargs); __PYX_ERR(0, 721, __pyx_L3_error)
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jpayne@69
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16071 __pyx_L6_skip:;
|
|
jpayne@69
|
16072 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
16073 __pyx_L3_error:;
|
|
jpayne@69
|
16074 {
|
|
jpayne@69
|
16075 Py_ssize_t __pyx_temp;
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jpayne@69
|
16076 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
16077 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
16078 }
|
|
jpayne@69
|
16079 }
|
|
jpayne@69
|
16080 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16081 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16082 return -1;
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jpayne@69
|
16083 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
16084 __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator___init__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self), __pyx_v_filename, __pyx_v_buffer_size, __pyx_v_encoding);
|
|
jpayne@69
|
16085
|
|
jpayne@69
|
16086 /* function exit code */
|
|
jpayne@69
|
16087 {
|
|
jpayne@69
|
16088 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
16089 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
16090 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
16091 }
|
|
jpayne@69
|
16092 }
|
|
jpayne@69
|
16093 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16094 return __pyx_r;
|
|
jpayne@69
|
16095 }
|
|
jpayne@69
|
16096
|
|
jpayne@69
|
16097 static int __pyx_pf_5pysam_9libctabix_10GZIterator___init__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, PyObject *__pyx_v_filename, int __pyx_v_buffer_size, PyObject *__pyx_v_encoding) {
|
|
jpayne@69
|
16098 char *__pyx_v_cfilename;
|
|
jpayne@69
|
16099 int __pyx_r;
|
|
jpayne@69
|
16100 __Pyx_TraceDeclarations
|
|
jpayne@69
|
16101 __Pyx_RefNannyDeclarations
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jpayne@69
|
16102 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
16103 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
16104 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
16105 unsigned int __pyx_t_4;
|
|
jpayne@69
|
16106 int __pyx_t_5;
|
|
jpayne@69
|
16107 int __pyx_t_6;
|
|
jpayne@69
|
16108 char *__pyx_t_7;
|
|
jpayne@69
|
16109 int __pyx_lineno = 0;
|
|
jpayne@69
|
16110 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16111 int __pyx_clineno = 0;
|
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jpayne@69
|
16112 __Pyx_RefNannySetupContext("__init__", 0);
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jpayne@69
|
16113 __Pyx_TraceCall("__init__", __pyx_f[0], 721, 0, __PYX_ERR(0, 721, __pyx_L1_error));
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jpayne@69
|
16114 __Pyx_INCREF(__pyx_v_filename);
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jpayne@69
|
16115
|
|
jpayne@69
|
16116 /* "pysam/libctabix.pyx":725
|
|
jpayne@69
|
16117 * compressed file.
|
|
jpayne@69
|
16118 * '''
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jpayne@69
|
16119 * if not os.path.exists(filename): # <<<<<<<<<<<<<<
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|
jpayne@69
|
16120 * raise IOError("No such file or directory: %s" % filename)
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|
jpayne@69
|
16121 *
|
|
jpayne@69
|
16122 */
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jpayne@69
|
16123 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_os); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 725, __pyx_L1_error)
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jpayne@69
|
16124 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
|
16125 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_path); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 725, __pyx_L1_error)
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jpayne@69
|
16126 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
16127 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
|
16128 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 725, __pyx_L1_error)
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jpayne@69
|
16129 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
|
16130 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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|
jpayne@69
|
16131 __pyx_t_3 = NULL;
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|
jpayne@69
|
16132 __pyx_t_4 = 0;
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|
jpayne@69
|
16133 #if CYTHON_UNPACK_METHODS
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|
jpayne@69
|
16134 if (likely(PyMethod_Check(__pyx_t_2))) {
|
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jpayne@69
|
16135 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
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|
jpayne@69
|
16136 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
16137 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
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jpayne@69
|
16138 __Pyx_INCREF(__pyx_t_3);
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jpayne@69
|
16139 __Pyx_INCREF(function);
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jpayne@69
|
16140 __Pyx_DECREF_SET(__pyx_t_2, function);
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jpayne@69
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16141 __pyx_t_4 = 1;
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|
jpayne@69
|
16142 }
|
|
jpayne@69
|
16143 }
|
|
jpayne@69
|
16144 #endif
|
|
jpayne@69
|
16145 {
|
|
jpayne@69
|
16146 PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_filename};
|
|
jpayne@69
|
16147 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4);
|
|
jpayne@69
|
16148 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
16149 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 725, __pyx_L1_error)
|
|
jpayne@69
|
16150 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
16151 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
16152 }
|
|
jpayne@69
|
16153 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 725, __pyx_L1_error)
|
|
jpayne@69
|
16154 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
16155 __pyx_t_6 = (!__pyx_t_5);
|
|
jpayne@69
|
16156 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
16157
|
|
jpayne@69
|
16158 /* "pysam/libctabix.pyx":726
|
|
jpayne@69
|
16159 * '''
|
|
jpayne@69
|
16160 * if not os.path.exists(filename):
|
|
jpayne@69
|
16161 * raise IOError("No such file or directory: %s" % filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16162 *
|
|
jpayne@69
|
16163 * filename = encode_filename(filename)
|
|
jpayne@69
|
16164 */
|
|
jpayne@69
|
16165 __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_No_such_file_or_directory_s, __pyx_v_filename); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 726, __pyx_L1_error)
|
|
jpayne@69
|
16166 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
16167 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 726, __pyx_L1_error)
|
|
jpayne@69
|
16168 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
16169 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
16170 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
16171 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
16172 __PYX_ERR(0, 726, __pyx_L1_error)
|
|
jpayne@69
|
16173
|
|
jpayne@69
|
16174 /* "pysam/libctabix.pyx":725
|
|
jpayne@69
|
16175 * compressed file.
|
|
jpayne@69
|
16176 * '''
|
|
jpayne@69
|
16177 * if not os.path.exists(filename): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16178 * raise IOError("No such file or directory: %s" % filename)
|
|
jpayne@69
|
16179 *
|
|
jpayne@69
|
16180 */
|
|
jpayne@69
|
16181 }
|
|
jpayne@69
|
16182
|
|
jpayne@69
|
16183 /* "pysam/libctabix.pyx":728
|
|
jpayne@69
|
16184 * raise IOError("No such file or directory: %s" % filename)
|
|
jpayne@69
|
16185 *
|
|
jpayne@69
|
16186 * filename = encode_filename(filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16187 * cdef char *cfilename = filename
|
|
jpayne@69
|
16188 * with nogil:
|
|
jpayne@69
|
16189 */
|
|
jpayne@69
|
16190 __pyx_t_2 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 728, __pyx_L1_error)
|
|
jpayne@69
|
16191 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
16192 __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_2);
|
|
jpayne@69
|
16193 __pyx_t_2 = 0;
|
|
jpayne@69
|
16194
|
|
jpayne@69
|
16195 /* "pysam/libctabix.pyx":729
|
|
jpayne@69
|
16196 *
|
|
jpayne@69
|
16197 * filename = encode_filename(filename)
|
|
jpayne@69
|
16198 * cdef char *cfilename = filename # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16199 * with nogil:
|
|
jpayne@69
|
16200 * self.gzipfile = bgzf_open(cfilename, "r")
|
|
jpayne@69
|
16201 */
|
|
jpayne@69
|
16202 __pyx_t_7 = __Pyx_PyObject_AsWritableString(__pyx_v_filename); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) __PYX_ERR(0, 729, __pyx_L1_error)
|
|
jpayne@69
|
16203 __pyx_v_cfilename = __pyx_t_7;
|
|
jpayne@69
|
16204
|
|
jpayne@69
|
16205 /* "pysam/libctabix.pyx":730
|
|
jpayne@69
|
16206 * filename = encode_filename(filename)
|
|
jpayne@69
|
16207 * cdef char *cfilename = filename
|
|
jpayne@69
|
16208 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16209 * self.gzipfile = bgzf_open(cfilename, "r")
|
|
jpayne@69
|
16210 * self._filename = filename
|
|
jpayne@69
|
16211 */
|
|
jpayne@69
|
16212 {
|
|
jpayne@69
|
16213 #ifdef WITH_THREAD
|
|
jpayne@69
|
16214 PyThreadState *_save;
|
|
jpayne@69
|
16215 _save = NULL;
|
|
jpayne@69
|
16216 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
16217 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
16218 #endif
|
|
jpayne@69
|
16219 /*try:*/ {
|
|
jpayne@69
|
16220
|
|
jpayne@69
|
16221 /* "pysam/libctabix.pyx":731
|
|
jpayne@69
|
16222 * cdef char *cfilename = filename
|
|
jpayne@69
|
16223 * with nogil:
|
|
jpayne@69
|
16224 * self.gzipfile = bgzf_open(cfilename, "r") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16225 * self._filename = filename
|
|
jpayne@69
|
16226 * self.kstream = ks_init(self.gzipfile)
|
|
jpayne@69
|
16227 */
|
|
jpayne@69
|
16228 __pyx_v_self->gzipfile = bgzf_open(__pyx_v_cfilename, ((char const *)"r"));
|
|
jpayne@69
|
16229 }
|
|
jpayne@69
|
16230
|
|
jpayne@69
|
16231 /* "pysam/libctabix.pyx":730
|
|
jpayne@69
|
16232 * filename = encode_filename(filename)
|
|
jpayne@69
|
16233 * cdef char *cfilename = filename
|
|
jpayne@69
|
16234 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16235 * self.gzipfile = bgzf_open(cfilename, "r")
|
|
jpayne@69
|
16236 * self._filename = filename
|
|
jpayne@69
|
16237 */
|
|
jpayne@69
|
16238 /*finally:*/ {
|
|
jpayne@69
|
16239 /*normal exit:*/{
|
|
jpayne@69
|
16240 #ifdef WITH_THREAD
|
|
jpayne@69
|
16241 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
16242 Py_BLOCK_THREADS
|
|
jpayne@69
|
16243 #endif
|
|
jpayne@69
|
16244 goto __pyx_L6;
|
|
jpayne@69
|
16245 }
|
|
jpayne@69
|
16246 __pyx_L6:;
|
|
jpayne@69
|
16247 }
|
|
jpayne@69
|
16248 }
|
|
jpayne@69
|
16249
|
|
jpayne@69
|
16250 /* "pysam/libctabix.pyx":732
|
|
jpayne@69
|
16251 * with nogil:
|
|
jpayne@69
|
16252 * self.gzipfile = bgzf_open(cfilename, "r")
|
|
jpayne@69
|
16253 * self._filename = filename # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16254 * self.kstream = ks_init(self.gzipfile)
|
|
jpayne@69
|
16255 * self.encoding = encoding
|
|
jpayne@69
|
16256 */
|
|
jpayne@69
|
16257 __Pyx_INCREF(__pyx_v_filename);
|
|
jpayne@69
|
16258 __Pyx_GIVEREF(__pyx_v_filename);
|
|
jpayne@69
|
16259 __Pyx_GOTREF(__pyx_v_self->_filename);
|
|
jpayne@69
|
16260 __Pyx_DECREF(__pyx_v_self->_filename);
|
|
jpayne@69
|
16261 __pyx_v_self->_filename = __pyx_v_filename;
|
|
jpayne@69
|
16262
|
|
jpayne@69
|
16263 /* "pysam/libctabix.pyx":733
|
|
jpayne@69
|
16264 * self.gzipfile = bgzf_open(cfilename, "r")
|
|
jpayne@69
|
16265 * self._filename = filename
|
|
jpayne@69
|
16266 * self.kstream = ks_init(self.gzipfile) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16267 * self.encoding = encoding
|
|
jpayne@69
|
16268 *
|
|
jpayne@69
|
16269 */
|
|
jpayne@69
|
16270 __pyx_v_self->kstream = ks_init(__pyx_v_self->gzipfile);
|
|
jpayne@69
|
16271
|
|
jpayne@69
|
16272 /* "pysam/libctabix.pyx":734
|
|
jpayne@69
|
16273 * self._filename = filename
|
|
jpayne@69
|
16274 * self.kstream = ks_init(self.gzipfile)
|
|
jpayne@69
|
16275 * self.encoding = encoding # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16276 *
|
|
jpayne@69
|
16277 * self.buffer.l = 0
|
|
jpayne@69
|
16278 */
|
|
jpayne@69
|
16279 __Pyx_INCREF(__pyx_v_encoding);
|
|
jpayne@69
|
16280 __Pyx_GIVEREF(__pyx_v_encoding);
|
|
jpayne@69
|
16281 __Pyx_GOTREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
16282 __Pyx_DECREF(__pyx_v_self->encoding);
|
|
jpayne@69
|
16283 __pyx_v_self->encoding = __pyx_v_encoding;
|
|
jpayne@69
|
16284
|
|
jpayne@69
|
16285 /* "pysam/libctabix.pyx":736
|
|
jpayne@69
|
16286 * self.encoding = encoding
|
|
jpayne@69
|
16287 *
|
|
jpayne@69
|
16288 * self.buffer.l = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16289 * self.buffer.m = 0
|
|
jpayne@69
|
16290 * self.buffer.s = <char*>malloc(buffer_size)
|
|
jpayne@69
|
16291 */
|
|
jpayne@69
|
16292 __pyx_v_self->buffer.l = 0;
|
|
jpayne@69
|
16293
|
|
jpayne@69
|
16294 /* "pysam/libctabix.pyx":737
|
|
jpayne@69
|
16295 *
|
|
jpayne@69
|
16296 * self.buffer.l = 0
|
|
jpayne@69
|
16297 * self.buffer.m = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16298 * self.buffer.s = <char*>malloc(buffer_size)
|
|
jpayne@69
|
16299 *
|
|
jpayne@69
|
16300 */
|
|
jpayne@69
|
16301 __pyx_v_self->buffer.m = 0;
|
|
jpayne@69
|
16302
|
|
jpayne@69
|
16303 /* "pysam/libctabix.pyx":738
|
|
jpayne@69
|
16304 * self.buffer.l = 0
|
|
jpayne@69
|
16305 * self.buffer.m = 0
|
|
jpayne@69
|
16306 * self.buffer.s = <char*>malloc(buffer_size) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16307 *
|
|
jpayne@69
|
16308 * def __dealloc__(self):
|
|
jpayne@69
|
16309 */
|
|
jpayne@69
|
16310 __pyx_v_self->buffer.s = ((char *)malloc(__pyx_v_buffer_size));
|
|
jpayne@69
|
16311
|
|
jpayne@69
|
16312 /* "pysam/libctabix.pyx":721
|
|
jpayne@69
|
16313 *
|
|
jpayne@69
|
16314 * cdef class GZIterator:
|
|
jpayne@69
|
16315 * def __init__(self, filename, int buffer_size=65536, encoding="ascii"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16316 * '''iterate line-by-line through gzip (or bgzip)
|
|
jpayne@69
|
16317 * compressed file.
|
|
jpayne@69
|
16318 */
|
|
jpayne@69
|
16319
|
|
jpayne@69
|
16320 /* function exit code */
|
|
jpayne@69
|
16321 __pyx_r = 0;
|
|
jpayne@69
|
16322 goto __pyx_L0;
|
|
jpayne@69
|
16323 __pyx_L1_error:;
|
|
jpayne@69
|
16324 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
16325 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
16326 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
16327 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16328 __pyx_r = -1;
|
|
jpayne@69
|
16329 __pyx_L0:;
|
|
jpayne@69
|
16330 __Pyx_XDECREF(__pyx_v_filename);
|
|
jpayne@69
|
16331 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
16332 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16333 return __pyx_r;
|
|
jpayne@69
|
16334 }
|
|
jpayne@69
|
16335
|
|
jpayne@69
|
16336 /* "pysam/libctabix.pyx":740
|
|
jpayne@69
|
16337 * self.buffer.s = <char*>malloc(buffer_size)
|
|
jpayne@69
|
16338 *
|
|
jpayne@69
|
16339 * def __dealloc__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16340 * '''close file.'''
|
|
jpayne@69
|
16341 * if self.gzipfile != NULL:
|
|
jpayne@69
|
16342 */
|
|
jpayne@69
|
16343
|
|
jpayne@69
|
16344 /* Python wrapper */
|
|
jpayne@69
|
16345 static void __pyx_pw_5pysam_9libctabix_10GZIterator_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
16346 static void __pyx_pw_5pysam_9libctabix_10GZIterator_3__dealloc__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
16347 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
16348 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16349 __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
|
|
jpayne@69
|
16350 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
16351 __pyx_pf_5pysam_9libctabix_10GZIterator_2__dealloc__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self));
|
|
jpayne@69
|
16352
|
|
jpayne@69
|
16353 /* function exit code */
|
|
jpayne@69
|
16354 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16355 }
|
|
jpayne@69
|
16356
|
|
jpayne@69
|
16357 static void __pyx_pf_5pysam_9libctabix_10GZIterator_2__dealloc__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) {
|
|
jpayne@69
|
16358 __Pyx_TraceDeclarations
|
|
jpayne@69
|
16359 int __pyx_t_1;
|
|
jpayne@69
|
16360 int __pyx_lineno = 0;
|
|
jpayne@69
|
16361 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16362 int __pyx_clineno = 0;
|
|
jpayne@69
|
16363 __Pyx_TraceCall("__dealloc__", __pyx_f[0], 740, 0, __PYX_ERR(0, 740, __pyx_L1_error));
|
|
jpayne@69
|
16364
|
|
jpayne@69
|
16365 /* "pysam/libctabix.pyx":742
|
|
jpayne@69
|
16366 * def __dealloc__(self):
|
|
jpayne@69
|
16367 * '''close file.'''
|
|
jpayne@69
|
16368 * if self.gzipfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16369 * bgzf_close(self.gzipfile)
|
|
jpayne@69
|
16370 * self.gzipfile = NULL
|
|
jpayne@69
|
16371 */
|
|
jpayne@69
|
16372 __pyx_t_1 = (__pyx_v_self->gzipfile != NULL);
|
|
jpayne@69
|
16373 if (__pyx_t_1) {
|
|
jpayne@69
|
16374
|
|
jpayne@69
|
16375 /* "pysam/libctabix.pyx":743
|
|
jpayne@69
|
16376 * '''close file.'''
|
|
jpayne@69
|
16377 * if self.gzipfile != NULL:
|
|
jpayne@69
|
16378 * bgzf_close(self.gzipfile) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16379 * self.gzipfile = NULL
|
|
jpayne@69
|
16380 * if self.buffer.s != NULL:
|
|
jpayne@69
|
16381 */
|
|
jpayne@69
|
16382 (void)(bgzf_close(__pyx_v_self->gzipfile));
|
|
jpayne@69
|
16383
|
|
jpayne@69
|
16384 /* "pysam/libctabix.pyx":744
|
|
jpayne@69
|
16385 * if self.gzipfile != NULL:
|
|
jpayne@69
|
16386 * bgzf_close(self.gzipfile)
|
|
jpayne@69
|
16387 * self.gzipfile = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16388 * if self.buffer.s != NULL:
|
|
jpayne@69
|
16389 * free(self.buffer.s)
|
|
jpayne@69
|
16390 */
|
|
jpayne@69
|
16391 __pyx_v_self->gzipfile = NULL;
|
|
jpayne@69
|
16392
|
|
jpayne@69
|
16393 /* "pysam/libctabix.pyx":742
|
|
jpayne@69
|
16394 * def __dealloc__(self):
|
|
jpayne@69
|
16395 * '''close file.'''
|
|
jpayne@69
|
16396 * if self.gzipfile != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16397 * bgzf_close(self.gzipfile)
|
|
jpayne@69
|
16398 * self.gzipfile = NULL
|
|
jpayne@69
|
16399 */
|
|
jpayne@69
|
16400 }
|
|
jpayne@69
|
16401
|
|
jpayne@69
|
16402 /* "pysam/libctabix.pyx":745
|
|
jpayne@69
|
16403 * bgzf_close(self.gzipfile)
|
|
jpayne@69
|
16404 * self.gzipfile = NULL
|
|
jpayne@69
|
16405 * if self.buffer.s != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16406 * free(self.buffer.s)
|
|
jpayne@69
|
16407 * if self.kstream != NULL:
|
|
jpayne@69
|
16408 */
|
|
jpayne@69
|
16409 __pyx_t_1 = (__pyx_v_self->buffer.s != NULL);
|
|
jpayne@69
|
16410 if (__pyx_t_1) {
|
|
jpayne@69
|
16411
|
|
jpayne@69
|
16412 /* "pysam/libctabix.pyx":746
|
|
jpayne@69
|
16413 * self.gzipfile = NULL
|
|
jpayne@69
|
16414 * if self.buffer.s != NULL:
|
|
jpayne@69
|
16415 * free(self.buffer.s) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16416 * if self.kstream != NULL:
|
|
jpayne@69
|
16417 * ks_destroy(self.kstream)
|
|
jpayne@69
|
16418 */
|
|
jpayne@69
|
16419 free(__pyx_v_self->buffer.s);
|
|
jpayne@69
|
16420
|
|
jpayne@69
|
16421 /* "pysam/libctabix.pyx":745
|
|
jpayne@69
|
16422 * bgzf_close(self.gzipfile)
|
|
jpayne@69
|
16423 * self.gzipfile = NULL
|
|
jpayne@69
|
16424 * if self.buffer.s != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16425 * free(self.buffer.s)
|
|
jpayne@69
|
16426 * if self.kstream != NULL:
|
|
jpayne@69
|
16427 */
|
|
jpayne@69
|
16428 }
|
|
jpayne@69
|
16429
|
|
jpayne@69
|
16430 /* "pysam/libctabix.pyx":747
|
|
jpayne@69
|
16431 * if self.buffer.s != NULL:
|
|
jpayne@69
|
16432 * free(self.buffer.s)
|
|
jpayne@69
|
16433 * if self.kstream != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16434 * ks_destroy(self.kstream)
|
|
jpayne@69
|
16435 *
|
|
jpayne@69
|
16436 */
|
|
jpayne@69
|
16437 __pyx_t_1 = (__pyx_v_self->kstream != NULL);
|
|
jpayne@69
|
16438 if (__pyx_t_1) {
|
|
jpayne@69
|
16439
|
|
jpayne@69
|
16440 /* "pysam/libctabix.pyx":748
|
|
jpayne@69
|
16441 * free(self.buffer.s)
|
|
jpayne@69
|
16442 * if self.kstream != NULL:
|
|
jpayne@69
|
16443 * ks_destroy(self.kstream) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16444 *
|
|
jpayne@69
|
16445 * def __iter__(self):
|
|
jpayne@69
|
16446 */
|
|
jpayne@69
|
16447 ks_destroy(__pyx_v_self->kstream);
|
|
jpayne@69
|
16448
|
|
jpayne@69
|
16449 /* "pysam/libctabix.pyx":747
|
|
jpayne@69
|
16450 * if self.buffer.s != NULL:
|
|
jpayne@69
|
16451 * free(self.buffer.s)
|
|
jpayne@69
|
16452 * if self.kstream != NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16453 * ks_destroy(self.kstream)
|
|
jpayne@69
|
16454 *
|
|
jpayne@69
|
16455 */
|
|
jpayne@69
|
16456 }
|
|
jpayne@69
|
16457
|
|
jpayne@69
|
16458 /* "pysam/libctabix.pyx":740
|
|
jpayne@69
|
16459 * self.buffer.s = <char*>malloc(buffer_size)
|
|
jpayne@69
|
16460 *
|
|
jpayne@69
|
16461 * def __dealloc__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16462 * '''close file.'''
|
|
jpayne@69
|
16463 * if self.gzipfile != NULL:
|
|
jpayne@69
|
16464 */
|
|
jpayne@69
|
16465
|
|
jpayne@69
|
16466 /* function exit code */
|
|
jpayne@69
|
16467 goto __pyx_L0;
|
|
jpayne@69
|
16468 __pyx_L1_error:;
|
|
jpayne@69
|
16469 __Pyx_WriteUnraisable("pysam.libctabix.GZIterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
|
|
jpayne@69
|
16470 __pyx_L0:;
|
|
jpayne@69
|
16471 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
16472 }
|
|
jpayne@69
|
16473
|
|
jpayne@69
|
16474 /* "pysam/libctabix.pyx":750
|
|
jpayne@69
|
16475 * ks_destroy(self.kstream)
|
|
jpayne@69
|
16476 *
|
|
jpayne@69
|
16477 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16478 * return self
|
|
jpayne@69
|
16479 *
|
|
jpayne@69
|
16480 */
|
|
jpayne@69
|
16481
|
|
jpayne@69
|
16482 /* Python wrapper */
|
|
jpayne@69
|
16483 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
16484 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
16485 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
16486 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
16487 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16488 __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
|
|
jpayne@69
|
16489 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
16490 __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_4__iter__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self));
|
|
jpayne@69
|
16491
|
|
jpayne@69
|
16492 /* function exit code */
|
|
jpayne@69
|
16493 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16494 return __pyx_r;
|
|
jpayne@69
|
16495 }
|
|
jpayne@69
|
16496
|
|
jpayne@69
|
16497 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_4__iter__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) {
|
|
jpayne@69
|
16498 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
16499 __Pyx_TraceDeclarations
|
|
jpayne@69
|
16500 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16501 int __pyx_lineno = 0;
|
|
jpayne@69
|
16502 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16503 int __pyx_clineno = 0;
|
|
jpayne@69
|
16504 __Pyx_RefNannySetupContext("__iter__", 1);
|
|
jpayne@69
|
16505 __Pyx_TraceCall("__iter__", __pyx_f[0], 750, 0, __PYX_ERR(0, 750, __pyx_L1_error));
|
|
jpayne@69
|
16506
|
|
jpayne@69
|
16507 /* "pysam/libctabix.pyx":751
|
|
jpayne@69
|
16508 *
|
|
jpayne@69
|
16509 * def __iter__(self):
|
|
jpayne@69
|
16510 * return self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16511 *
|
|
jpayne@69
|
16512 * cdef int __cnext__(self):
|
|
jpayne@69
|
16513 */
|
|
jpayne@69
|
16514 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
16515 __Pyx_INCREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
16516 __pyx_r = ((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
16517 goto __pyx_L0;
|
|
jpayne@69
|
16518
|
|
jpayne@69
|
16519 /* "pysam/libctabix.pyx":750
|
|
jpayne@69
|
16520 * ks_destroy(self.kstream)
|
|
jpayne@69
|
16521 *
|
|
jpayne@69
|
16522 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16523 * return self
|
|
jpayne@69
|
16524 *
|
|
jpayne@69
|
16525 */
|
|
jpayne@69
|
16526
|
|
jpayne@69
|
16527 /* function exit code */
|
|
jpayne@69
|
16528 __pyx_L1_error:;
|
|
jpayne@69
|
16529 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16530 __pyx_r = NULL;
|
|
jpayne@69
|
16531 __pyx_L0:;
|
|
jpayne@69
|
16532 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
16533 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
16534 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16535 return __pyx_r;
|
|
jpayne@69
|
16536 }
|
|
jpayne@69
|
16537
|
|
jpayne@69
|
16538 /* "pysam/libctabix.pyx":753
|
|
jpayne@69
|
16539 * return self
|
|
jpayne@69
|
16540 *
|
|
jpayne@69
|
16541 * cdef int __cnext__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16542 * cdef int dret = 0
|
|
jpayne@69
|
16543 * cdef int retval = 0
|
|
jpayne@69
|
16544 */
|
|
jpayne@69
|
16545
|
|
jpayne@69
|
16546 static int __pyx_f_5pysam_9libctabix_10GZIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) {
|
|
jpayne@69
|
16547 int __pyx_v_dret;
|
|
jpayne@69
|
16548 int __pyx_v_retval;
|
|
jpayne@69
|
16549 int __pyx_r;
|
|
jpayne@69
|
16550 __Pyx_TraceDeclarations
|
|
jpayne@69
|
16551 int __pyx_t_1;
|
|
jpayne@69
|
16552 int __pyx_lineno = 0;
|
|
jpayne@69
|
16553 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16554 int __pyx_clineno = 0;
|
|
jpayne@69
|
16555 __Pyx_TraceCall("__cnext__", __pyx_f[0], 753, 0, __PYX_ERR(0, 753, __pyx_L1_error));
|
|
jpayne@69
|
16556
|
|
jpayne@69
|
16557 /* "pysam/libctabix.pyx":754
|
|
jpayne@69
|
16558 *
|
|
jpayne@69
|
16559 * cdef int __cnext__(self):
|
|
jpayne@69
|
16560 * cdef int dret = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16561 * cdef int retval = 0
|
|
jpayne@69
|
16562 * while 1:
|
|
jpayne@69
|
16563 */
|
|
jpayne@69
|
16564 __pyx_v_dret = 0;
|
|
jpayne@69
|
16565
|
|
jpayne@69
|
16566 /* "pysam/libctabix.pyx":755
|
|
jpayne@69
|
16567 * cdef int __cnext__(self):
|
|
jpayne@69
|
16568 * cdef int dret = 0
|
|
jpayne@69
|
16569 * cdef int retval = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16570 * while 1:
|
|
jpayne@69
|
16571 * with nogil:
|
|
jpayne@69
|
16572 */
|
|
jpayne@69
|
16573 __pyx_v_retval = 0;
|
|
jpayne@69
|
16574
|
|
jpayne@69
|
16575 /* "pysam/libctabix.pyx":756
|
|
jpayne@69
|
16576 * cdef int dret = 0
|
|
jpayne@69
|
16577 * cdef int retval = 0
|
|
jpayne@69
|
16578 * while 1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16579 * with nogil:
|
|
jpayne@69
|
16580 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
16581 */
|
|
jpayne@69
|
16582 while (1) {
|
|
jpayne@69
|
16583
|
|
jpayne@69
|
16584 /* "pysam/libctabix.pyx":757
|
|
jpayne@69
|
16585 * cdef int retval = 0
|
|
jpayne@69
|
16586 * while 1:
|
|
jpayne@69
|
16587 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16588 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
16589 *
|
|
jpayne@69
|
16590 */
|
|
jpayne@69
|
16591 {
|
|
jpayne@69
|
16592 #ifdef WITH_THREAD
|
|
jpayne@69
|
16593 PyThreadState *_save;
|
|
jpayne@69
|
16594 _save = NULL;
|
|
jpayne@69
|
16595 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
16596 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
16597 #endif
|
|
jpayne@69
|
16598 /*try:*/ {
|
|
jpayne@69
|
16599
|
|
jpayne@69
|
16600 /* "pysam/libctabix.pyx":758
|
|
jpayne@69
|
16601 * while 1:
|
|
jpayne@69
|
16602 * with nogil:
|
|
jpayne@69
|
16603 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16604 *
|
|
jpayne@69
|
16605 * if retval < 0:
|
|
jpayne@69
|
16606 */
|
|
jpayne@69
|
16607 __pyx_v_retval = ks_getuntil(__pyx_v_self->kstream, '\n', (&__pyx_v_self->buffer), (&__pyx_v_dret));
|
|
jpayne@69
|
16608 }
|
|
jpayne@69
|
16609
|
|
jpayne@69
|
16610 /* "pysam/libctabix.pyx":757
|
|
jpayne@69
|
16611 * cdef int retval = 0
|
|
jpayne@69
|
16612 * while 1:
|
|
jpayne@69
|
16613 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16614 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
16615 *
|
|
jpayne@69
|
16616 */
|
|
jpayne@69
|
16617 /*finally:*/ {
|
|
jpayne@69
|
16618 /*normal exit:*/{
|
|
jpayne@69
|
16619 #ifdef WITH_THREAD
|
|
jpayne@69
|
16620 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
16621 Py_BLOCK_THREADS
|
|
jpayne@69
|
16622 #endif
|
|
jpayne@69
|
16623 goto __pyx_L9;
|
|
jpayne@69
|
16624 }
|
|
jpayne@69
|
16625 __pyx_L9:;
|
|
jpayne@69
|
16626 }
|
|
jpayne@69
|
16627 }
|
|
jpayne@69
|
16628
|
|
jpayne@69
|
16629 /* "pysam/libctabix.pyx":760
|
|
jpayne@69
|
16630 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
16631 *
|
|
jpayne@69
|
16632 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16633 * break
|
|
jpayne@69
|
16634 *
|
|
jpayne@69
|
16635 */
|
|
jpayne@69
|
16636 __pyx_t_1 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
16637 if (__pyx_t_1) {
|
|
jpayne@69
|
16638
|
|
jpayne@69
|
16639 /* "pysam/libctabix.pyx":761
|
|
jpayne@69
|
16640 *
|
|
jpayne@69
|
16641 * if retval < 0:
|
|
jpayne@69
|
16642 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16643 *
|
|
jpayne@69
|
16644 * return dret
|
|
jpayne@69
|
16645 */
|
|
jpayne@69
|
16646 goto __pyx_L4_break;
|
|
jpayne@69
|
16647
|
|
jpayne@69
|
16648 /* "pysam/libctabix.pyx":760
|
|
jpayne@69
|
16649 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
16650 *
|
|
jpayne@69
|
16651 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16652 * break
|
|
jpayne@69
|
16653 *
|
|
jpayne@69
|
16654 */
|
|
jpayne@69
|
16655 }
|
|
jpayne@69
|
16656
|
|
jpayne@69
|
16657 /* "pysam/libctabix.pyx":763
|
|
jpayne@69
|
16658 * break
|
|
jpayne@69
|
16659 *
|
|
jpayne@69
|
16660 * return dret # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16661 * return -1
|
|
jpayne@69
|
16662 *
|
|
jpayne@69
|
16663 */
|
|
jpayne@69
|
16664 __pyx_r = __pyx_v_dret;
|
|
jpayne@69
|
16665 goto __pyx_L0;
|
|
jpayne@69
|
16666 }
|
|
jpayne@69
|
16667 __pyx_L4_break:;
|
|
jpayne@69
|
16668
|
|
jpayne@69
|
16669 /* "pysam/libctabix.pyx":764
|
|
jpayne@69
|
16670 *
|
|
jpayne@69
|
16671 * return dret
|
|
jpayne@69
|
16672 * return -1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16673 *
|
|
jpayne@69
|
16674 * def __next__(self):
|
|
jpayne@69
|
16675 */
|
|
jpayne@69
|
16676 __pyx_r = -1;
|
|
jpayne@69
|
16677 goto __pyx_L0;
|
|
jpayne@69
|
16678
|
|
jpayne@69
|
16679 /* "pysam/libctabix.pyx":753
|
|
jpayne@69
|
16680 * return self
|
|
jpayne@69
|
16681 *
|
|
jpayne@69
|
16682 * cdef int __cnext__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16683 * cdef int dret = 0
|
|
jpayne@69
|
16684 * cdef int retval = 0
|
|
jpayne@69
|
16685 */
|
|
jpayne@69
|
16686
|
|
jpayne@69
|
16687 /* function exit code */
|
|
jpayne@69
|
16688 __pyx_L1_error:;
|
|
jpayne@69
|
16689 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16690 __pyx_r = 0;
|
|
jpayne@69
|
16691 __pyx_L0:;
|
|
jpayne@69
|
16692 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
16693 return __pyx_r;
|
|
jpayne@69
|
16694 }
|
|
jpayne@69
|
16695
|
|
jpayne@69
|
16696 /* "pysam/libctabix.pyx":766
|
|
jpayne@69
|
16697 * return -1
|
|
jpayne@69
|
16698 *
|
|
jpayne@69
|
16699 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16700 * """python version of next().
|
|
jpayne@69
|
16701 * """
|
|
jpayne@69
|
16702 */
|
|
jpayne@69
|
16703
|
|
jpayne@69
|
16704 /* Python wrapper */
|
|
jpayne@69
|
16705 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
16706 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator_6__next__, "python version of next().\n ");
|
|
jpayne@69
|
16707 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
16708 struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__;
|
|
jpayne@69
|
16709 #endif
|
|
jpayne@69
|
16710 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
16711 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
16712 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
16713 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16714 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
|
|
jpayne@69
|
16715 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
16716 __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_6__next__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self));
|
|
jpayne@69
|
16717
|
|
jpayne@69
|
16718 /* function exit code */
|
|
jpayne@69
|
16719 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16720 return __pyx_r;
|
|
jpayne@69
|
16721 }
|
|
jpayne@69
|
16722
|
|
jpayne@69
|
16723 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_6__next__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) {
|
|
jpayne@69
|
16724 int __pyx_v_retval;
|
|
jpayne@69
|
16725 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
16726 __Pyx_TraceDeclarations
|
|
jpayne@69
|
16727 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16728 int __pyx_error_without_exception = 0; /* StopIteration */
|
|
jpayne@69
|
16729 int __pyx_t_1;
|
|
jpayne@69
|
16730 int __pyx_t_2;
|
|
jpayne@69
|
16731 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
16732 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
16733 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
16734 struct __pyx_opt_args_5pysam_9libcutils_force_str __pyx_t_6;
|
|
jpayne@69
|
16735 int __pyx_lineno = 0;
|
|
jpayne@69
|
16736 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16737 int __pyx_clineno = 0;
|
|
jpayne@69
|
16738 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
16739 __Pyx_TraceCall("__next__", __pyx_f[0], 766, 0, __PYX_ERR(0, 766, __pyx_L1_error));
|
|
jpayne@69
|
16740
|
|
jpayne@69
|
16741 /* "pysam/libctabix.pyx":769
|
|
jpayne@69
|
16742 * """python version of next().
|
|
jpayne@69
|
16743 * """
|
|
jpayne@69
|
16744 * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16745 * if retval < 0:
|
|
jpayne@69
|
16746 * raise StopIteration
|
|
jpayne@69
|
16747 */
|
|
jpayne@69
|
16748 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 769, __pyx_L1_error)
|
|
jpayne@69
|
16749 __pyx_v_retval = __pyx_t_1;
|
|
jpayne@69
|
16750
|
|
jpayne@69
|
16751 /* "pysam/libctabix.pyx":770
|
|
jpayne@69
|
16752 * """
|
|
jpayne@69
|
16753 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
16754 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16755 * raise StopIteration
|
|
jpayne@69
|
16756 * return force_str(self.buffer.s, self.encoding)
|
|
jpayne@69
|
16757 */
|
|
jpayne@69
|
16758 __pyx_t_2 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
16759 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
16760
|
|
jpayne@69
|
16761 /* "pysam/libctabix.pyx":771
|
|
jpayne@69
|
16762 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
16763 * if retval < 0:
|
|
jpayne@69
|
16764 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16765 * return force_str(self.buffer.s, self.encoding)
|
|
jpayne@69
|
16766 *
|
|
jpayne@69
|
16767 */
|
|
jpayne@69
|
16768 __pyx_error_without_exception = 1;
|
|
jpayne@69
|
16769 goto __pyx_L1_error;;
|
|
jpayne@69
|
16770
|
|
jpayne@69
|
16771 /* "pysam/libctabix.pyx":770
|
|
jpayne@69
|
16772 * """
|
|
jpayne@69
|
16773 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
16774 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16775 * raise StopIteration
|
|
jpayne@69
|
16776 * return force_str(self.buffer.s, self.encoding)
|
|
jpayne@69
|
16777 */
|
|
jpayne@69
|
16778 }
|
|
jpayne@69
|
16779
|
|
jpayne@69
|
16780 /* "pysam/libctabix.pyx":772
|
|
jpayne@69
|
16781 * if retval < 0:
|
|
jpayne@69
|
16782 * raise StopIteration
|
|
jpayne@69
|
16783 * return force_str(self.buffer.s, self.encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16784 *
|
|
jpayne@69
|
16785 *
|
|
jpayne@69
|
16786 */
|
|
jpayne@69
|
16787 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
16788 __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_self->buffer.s); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 772, __pyx_L1_error)
|
|
jpayne@69
|
16789 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
16790 __pyx_t_4 = __pyx_v_self->encoding;
|
|
jpayne@69
|
16791 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
16792 __pyx_t_6.__pyx_n = 1;
|
|
jpayne@69
|
16793 __pyx_t_6.encoding = __pyx_t_4;
|
|
jpayne@69
|
16794 __pyx_t_5 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_3, &__pyx_t_6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 772, __pyx_L1_error)
|
|
jpayne@69
|
16795 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
16796 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
16797 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
16798 __pyx_r = __pyx_t_5;
|
|
jpayne@69
|
16799 __pyx_t_5 = 0;
|
|
jpayne@69
|
16800 goto __pyx_L0;
|
|
jpayne@69
|
16801
|
|
jpayne@69
|
16802 /* "pysam/libctabix.pyx":766
|
|
jpayne@69
|
16803 * return -1
|
|
jpayne@69
|
16804 *
|
|
jpayne@69
|
16805 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16806 * """python version of next().
|
|
jpayne@69
|
16807 * """
|
|
jpayne@69
|
16808 */
|
|
jpayne@69
|
16809
|
|
jpayne@69
|
16810 /* function exit code */
|
|
jpayne@69
|
16811 __pyx_L1_error:;
|
|
jpayne@69
|
16812 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
16813 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
16814 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
16815 if (!__pyx_error_without_exception) {
|
|
jpayne@69
|
16816 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16817 }
|
|
jpayne@69
|
16818 __pyx_r = NULL;
|
|
jpayne@69
|
16819 __pyx_L0:;
|
|
jpayne@69
|
16820 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
16821 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
16822 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16823 return __pyx_r;
|
|
jpayne@69
|
16824 }
|
|
jpayne@69
|
16825
|
|
jpayne@69
|
16826 /* "(tree fragment)":1
|
|
jpayne@69
|
16827 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16828 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
16829 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
16830 */
|
|
jpayne@69
|
16831
|
|
jpayne@69
|
16832 /* Python wrapper */
|
|
jpayne@69
|
16833 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
16834 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16835 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
16836 #else
|
|
jpayne@69
|
16837 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
16838 #endif
|
|
jpayne@69
|
16839 ); /*proto*/
|
|
jpayne@69
|
16840 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator_8__reduce_cython__, "GZIterator.__reduce_cython__(self)");
|
|
jpayne@69
|
16841 static PyMethodDef __pyx_mdef_5pysam_9libctabix_10GZIterator_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_8__reduce_cython__};
|
|
jpayne@69
|
16842 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
16843 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16844 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
16845 #else
|
|
jpayne@69
|
16846 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
16847 #endif
|
|
jpayne@69
|
16848 ) {
|
|
jpayne@69
|
16849 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16850 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
16851 #endif
|
|
jpayne@69
|
16852 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
16853 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
16854 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16855 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
16856 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16857 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
16858 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
16859 #else
|
|
jpayne@69
|
16860 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
16861 #endif
|
|
jpayne@69
|
16862 #endif
|
|
jpayne@69
|
16863 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
16864 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
16865 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
16866 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
16867 __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self));
|
|
jpayne@69
|
16868
|
|
jpayne@69
|
16869 /* function exit code */
|
|
jpayne@69
|
16870 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16871 return __pyx_r;
|
|
jpayne@69
|
16872 }
|
|
jpayne@69
|
16873
|
|
jpayne@69
|
16874 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) {
|
|
jpayne@69
|
16875 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
16876 __Pyx_TraceDeclarations
|
|
jpayne@69
|
16877 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16878 int __pyx_lineno = 0;
|
|
jpayne@69
|
16879 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16880 int __pyx_clineno = 0;
|
|
jpayne@69
|
16881 __Pyx_TraceFrameInit(__pyx_codeobj__31)
|
|
jpayne@69
|
16882 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
16883 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
16884
|
|
jpayne@69
|
16885 /* "(tree fragment)":2
|
|
jpayne@69
|
16886 * def __reduce_cython__(self):
|
|
jpayne@69
|
16887 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16888 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
16889 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
16890 */
|
|
jpayne@69
|
16891 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0);
|
|
jpayne@69
|
16892 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
16893
|
|
jpayne@69
|
16894 /* "(tree fragment)":1
|
|
jpayne@69
|
16895 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16896 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
16897 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
16898 */
|
|
jpayne@69
|
16899
|
|
jpayne@69
|
16900 /* function exit code */
|
|
jpayne@69
|
16901 __pyx_L1_error:;
|
|
jpayne@69
|
16902 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16903 __pyx_r = NULL;
|
|
jpayne@69
|
16904 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
16905 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
16906 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16907 return __pyx_r;
|
|
jpayne@69
|
16908 }
|
|
jpayne@69
|
16909
|
|
jpayne@69
|
16910 /* "(tree fragment)":3
|
|
jpayne@69
|
16911 * def __reduce_cython__(self):
|
|
jpayne@69
|
16912 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
16913 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
16914 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
16915 */
|
|
jpayne@69
|
16916
|
|
jpayne@69
|
16917 /* Python wrapper */
|
|
jpayne@69
|
16918 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
16919 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16920 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
16921 #else
|
|
jpayne@69
|
16922 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
16923 #endif
|
|
jpayne@69
|
16924 ); /*proto*/
|
|
jpayne@69
|
16925 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator_10__setstate_cython__, "GZIterator.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
16926 static PyMethodDef __pyx_mdef_5pysam_9libctabix_10GZIterator_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_10__setstate_cython__};
|
|
jpayne@69
|
16927 static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
16928 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16929 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
16930 #else
|
|
jpayne@69
|
16931 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
16932 #endif
|
|
jpayne@69
|
16933 ) {
|
|
jpayne@69
|
16934 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
16935 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16936 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
16937 #endif
|
|
jpayne@69
|
16938 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
16939 PyObject* values[1] = {0};
|
|
jpayne@69
|
16940 int __pyx_lineno = 0;
|
|
jpayne@69
|
16941 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
16942 int __pyx_clineno = 0;
|
|
jpayne@69
|
16943 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
16944 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
16945 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
16946 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
16947 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
16948 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
16949 #else
|
|
jpayne@69
|
16950 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
16951 #endif
|
|
jpayne@69
|
16952 #endif
|
|
jpayne@69
|
16953 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
16954 {
|
|
jpayne@69
|
16955 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
16956 if (__pyx_kwds) {
|
|
jpayne@69
|
16957 Py_ssize_t kw_args;
|
|
jpayne@69
|
16958 switch (__pyx_nargs) {
|
|
jpayne@69
|
16959 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
16960 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
16961 case 0: break;
|
|
jpayne@69
|
16962 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
16963 }
|
|
jpayne@69
|
16964 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
16965 switch (__pyx_nargs) {
|
|
jpayne@69
|
16966 case 0:
|
|
jpayne@69
|
16967 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
16968 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
16969 kw_args--;
|
|
jpayne@69
|
16970 }
|
|
jpayne@69
|
16971 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
16972 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
16973 }
|
|
jpayne@69
|
16974 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
16975 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
16976 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
16977 }
|
|
jpayne@69
|
16978 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
16979 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
16980 } else {
|
|
jpayne@69
|
16981 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
16982 }
|
|
jpayne@69
|
16983 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
16984 }
|
|
jpayne@69
|
16985 goto __pyx_L6_skip;
|
|
jpayne@69
|
16986 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
16987 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
16988 __pyx_L6_skip:;
|
|
jpayne@69
|
16989 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
16990 __pyx_L3_error:;
|
|
jpayne@69
|
16991 {
|
|
jpayne@69
|
16992 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
16993 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
16994 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
16995 }
|
|
jpayne@69
|
16996 }
|
|
jpayne@69
|
16997 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
16998 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
16999 return NULL;
|
|
jpayne@69
|
17000 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
17001 __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
17002
|
|
jpayne@69
|
17003 /* function exit code */
|
|
jpayne@69
|
17004 {
|
|
jpayne@69
|
17005 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17006 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17007 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
17008 }
|
|
jpayne@69
|
17009 }
|
|
jpayne@69
|
17010 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17011 return __pyx_r;
|
|
jpayne@69
|
17012 }
|
|
jpayne@69
|
17013
|
|
jpayne@69
|
17014 static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
17015 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17016 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17017 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17018 int __pyx_lineno = 0;
|
|
jpayne@69
|
17019 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17020 int __pyx_clineno = 0;
|
|
jpayne@69
|
17021 __Pyx_TraceFrameInit(__pyx_codeobj__32)
|
|
jpayne@69
|
17022 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
17023 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
17024
|
|
jpayne@69
|
17025 /* "(tree fragment)":4
|
|
jpayne@69
|
17026 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17027 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17028 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17029 */
|
|
jpayne@69
|
17030 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0);
|
|
jpayne@69
|
17031 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
17032
|
|
jpayne@69
|
17033 /* "(tree fragment)":3
|
|
jpayne@69
|
17034 * def __reduce_cython__(self):
|
|
jpayne@69
|
17035 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17036 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17037 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17038 */
|
|
jpayne@69
|
17039
|
|
jpayne@69
|
17040 /* function exit code */
|
|
jpayne@69
|
17041 __pyx_L1_error:;
|
|
jpayne@69
|
17042 __Pyx_AddTraceback("pysam.libctabix.GZIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17043 __pyx_r = NULL;
|
|
jpayne@69
|
17044 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17045 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17046 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17047 return __pyx_r;
|
|
jpayne@69
|
17048 }
|
|
jpayne@69
|
17049
|
|
jpayne@69
|
17050 /* "pysam/libctabix.pyx":780
|
|
jpayne@69
|
17051 * '''
|
|
jpayne@69
|
17052 *
|
|
jpayne@69
|
17053 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17054 * """python version of next().
|
|
jpayne@69
|
17055 * """
|
|
jpayne@69
|
17056 */
|
|
jpayne@69
|
17057
|
|
jpayne@69
|
17058 /* Python wrapper */
|
|
jpayne@69
|
17059 static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
17060 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14GZIteratorHead___next__, "python version of next().\n ");
|
|
jpayne@69
|
17061 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
17062 struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__;
|
|
jpayne@69
|
17063 #endif
|
|
jpayne@69
|
17064 static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
17065 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17066 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17067 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17068 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
|
|
jpayne@69
|
17069 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17070 __pyx_r = __pyx_pf_5pysam_9libctabix_14GZIteratorHead___next__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self));
|
|
jpayne@69
|
17071
|
|
jpayne@69
|
17072 /* function exit code */
|
|
jpayne@69
|
17073 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17074 return __pyx_r;
|
|
jpayne@69
|
17075 }
|
|
jpayne@69
|
17076
|
|
jpayne@69
|
17077 static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead___next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self) {
|
|
jpayne@69
|
17078 int __pyx_v_retval;
|
|
jpayne@69
|
17079 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17080 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17081 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17082 int __pyx_error_without_exception = 0; /* StopIteration */
|
|
jpayne@69
|
17083 int __pyx_t_1;
|
|
jpayne@69
|
17084 int __pyx_t_2;
|
|
jpayne@69
|
17085 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
17086 int __pyx_lineno = 0;
|
|
jpayne@69
|
17087 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17088 int __pyx_clineno = 0;
|
|
jpayne@69
|
17089 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
17090 __Pyx_TraceCall("__next__", __pyx_f[0], 780, 0, __PYX_ERR(0, 780, __pyx_L1_error));
|
|
jpayne@69
|
17091
|
|
jpayne@69
|
17092 /* "pysam/libctabix.pyx":783
|
|
jpayne@69
|
17093 * """python version of next().
|
|
jpayne@69
|
17094 * """
|
|
jpayne@69
|
17095 * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17096 * if retval < 0:
|
|
jpayne@69
|
17097 * raise StopIteration
|
|
jpayne@69
|
17098 */
|
|
jpayne@69
|
17099 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.__pyx___cnext__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 783, __pyx_L1_error)
|
|
jpayne@69
|
17100 __pyx_v_retval = __pyx_t_1;
|
|
jpayne@69
|
17101
|
|
jpayne@69
|
17102 /* "pysam/libctabix.pyx":784
|
|
jpayne@69
|
17103 * """
|
|
jpayne@69
|
17104 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
17105 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17106 * raise StopIteration
|
|
jpayne@69
|
17107 * if self.buffer.s[0] == b'#':
|
|
jpayne@69
|
17108 */
|
|
jpayne@69
|
17109 __pyx_t_2 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
17110 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
17111
|
|
jpayne@69
|
17112 /* "pysam/libctabix.pyx":785
|
|
jpayne@69
|
17113 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
17114 * if retval < 0:
|
|
jpayne@69
|
17115 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17116 * if self.buffer.s[0] == b'#':
|
|
jpayne@69
|
17117 * return self.buffer.s
|
|
jpayne@69
|
17118 */
|
|
jpayne@69
|
17119 __pyx_error_without_exception = 1;
|
|
jpayne@69
|
17120 goto __pyx_L1_error;;
|
|
jpayne@69
|
17121
|
|
jpayne@69
|
17122 /* "pysam/libctabix.pyx":784
|
|
jpayne@69
|
17123 * """
|
|
jpayne@69
|
17124 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
17125 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17126 * raise StopIteration
|
|
jpayne@69
|
17127 * if self.buffer.s[0] == b'#':
|
|
jpayne@69
|
17128 */
|
|
jpayne@69
|
17129 }
|
|
jpayne@69
|
17130
|
|
jpayne@69
|
17131 /* "pysam/libctabix.pyx":786
|
|
jpayne@69
|
17132 * if retval < 0:
|
|
jpayne@69
|
17133 * raise StopIteration
|
|
jpayne@69
|
17134 * if self.buffer.s[0] == b'#': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17135 * return self.buffer.s
|
|
jpayne@69
|
17136 * else:
|
|
jpayne@69
|
17137 */
|
|
jpayne@69
|
17138 __pyx_t_2 = ((__pyx_v_self->__pyx_base.buffer.s[0]) == '#');
|
|
jpayne@69
|
17139 if (likely(__pyx_t_2)) {
|
|
jpayne@69
|
17140
|
|
jpayne@69
|
17141 /* "pysam/libctabix.pyx":787
|
|
jpayne@69
|
17142 * raise StopIteration
|
|
jpayne@69
|
17143 * if self.buffer.s[0] == b'#':
|
|
jpayne@69
|
17144 * return self.buffer.s # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17145 * else:
|
|
jpayne@69
|
17146 * raise StopIteration
|
|
jpayne@69
|
17147 */
|
|
jpayne@69
|
17148 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
17149 __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_self->__pyx_base.buffer.s); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 787, __pyx_L1_error)
|
|
jpayne@69
|
17150 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
17151 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
17152 __pyx_t_3 = 0;
|
|
jpayne@69
|
17153 goto __pyx_L0;
|
|
jpayne@69
|
17154
|
|
jpayne@69
|
17155 /* "pysam/libctabix.pyx":786
|
|
jpayne@69
|
17156 * if retval < 0:
|
|
jpayne@69
|
17157 * raise StopIteration
|
|
jpayne@69
|
17158 * if self.buffer.s[0] == b'#': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17159 * return self.buffer.s
|
|
jpayne@69
|
17160 * else:
|
|
jpayne@69
|
17161 */
|
|
jpayne@69
|
17162 }
|
|
jpayne@69
|
17163
|
|
jpayne@69
|
17164 /* "pysam/libctabix.pyx":789
|
|
jpayne@69
|
17165 * return self.buffer.s
|
|
jpayne@69
|
17166 * else:
|
|
jpayne@69
|
17167 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17168 *
|
|
jpayne@69
|
17169 *
|
|
jpayne@69
|
17170 */
|
|
jpayne@69
|
17171 /*else*/ {
|
|
jpayne@69
|
17172 __pyx_error_without_exception = 1;
|
|
jpayne@69
|
17173 goto __pyx_L1_error;;
|
|
jpayne@69
|
17174 }
|
|
jpayne@69
|
17175
|
|
jpayne@69
|
17176 /* "pysam/libctabix.pyx":780
|
|
jpayne@69
|
17177 * '''
|
|
jpayne@69
|
17178 *
|
|
jpayne@69
|
17179 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17180 * """python version of next().
|
|
jpayne@69
|
17181 * """
|
|
jpayne@69
|
17182 */
|
|
jpayne@69
|
17183
|
|
jpayne@69
|
17184 /* function exit code */
|
|
jpayne@69
|
17185 __pyx_L1_error:;
|
|
jpayne@69
|
17186 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
17187 if (!__pyx_error_without_exception) {
|
|
jpayne@69
|
17188 __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17189 }
|
|
jpayne@69
|
17190 __pyx_r = NULL;
|
|
jpayne@69
|
17191 __pyx_L0:;
|
|
jpayne@69
|
17192 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17193 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17194 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17195 return __pyx_r;
|
|
jpayne@69
|
17196 }
|
|
jpayne@69
|
17197
|
|
jpayne@69
|
17198 /* "(tree fragment)":1
|
|
jpayne@69
|
17199 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17200 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17201 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17202 */
|
|
jpayne@69
|
17203
|
|
jpayne@69
|
17204 /* Python wrapper */
|
|
jpayne@69
|
17205 static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17206 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17207 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17208 #else
|
|
jpayne@69
|
17209 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17210 #endif
|
|
jpayne@69
|
17211 ); /*proto*/
|
|
jpayne@69
|
17212 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__, "GZIteratorHead.__reduce_cython__(self)");
|
|
jpayne@69
|
17213 static PyMethodDef __pyx_mdef_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__};
|
|
jpayne@69
|
17214 static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17215 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17216 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17217 #else
|
|
jpayne@69
|
17218 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17219 #endif
|
|
jpayne@69
|
17220 ) {
|
|
jpayne@69
|
17221 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17222 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
17223 #endif
|
|
jpayne@69
|
17224 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17225 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17226 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17227 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
17228 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17229 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
17230 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
17231 #else
|
|
jpayne@69
|
17232 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
17233 #endif
|
|
jpayne@69
|
17234 #endif
|
|
jpayne@69
|
17235 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17236 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
17237 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
17238 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
17239 __pyx_r = __pyx_pf_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self));
|
|
jpayne@69
|
17240
|
|
jpayne@69
|
17241 /* function exit code */
|
|
jpayne@69
|
17242 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17243 return __pyx_r;
|
|
jpayne@69
|
17244 }
|
|
jpayne@69
|
17245
|
|
jpayne@69
|
17246 static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self) {
|
|
jpayne@69
|
17247 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17248 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17249 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17250 int __pyx_lineno = 0;
|
|
jpayne@69
|
17251 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17252 int __pyx_clineno = 0;
|
|
jpayne@69
|
17253 __Pyx_TraceFrameInit(__pyx_codeobj__33)
|
|
jpayne@69
|
17254 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
17255 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
17256
|
|
jpayne@69
|
17257 /* "(tree fragment)":2
|
|
jpayne@69
|
17258 * def __reduce_cython__(self):
|
|
jpayne@69
|
17259 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17260 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17261 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17262 */
|
|
jpayne@69
|
17263 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0);
|
|
jpayne@69
|
17264 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
17265
|
|
jpayne@69
|
17266 /* "(tree fragment)":1
|
|
jpayne@69
|
17267 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17268 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17269 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17270 */
|
|
jpayne@69
|
17271
|
|
jpayne@69
|
17272 /* function exit code */
|
|
jpayne@69
|
17273 __pyx_L1_error:;
|
|
jpayne@69
|
17274 __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17275 __pyx_r = NULL;
|
|
jpayne@69
|
17276 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17277 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17278 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17279 return __pyx_r;
|
|
jpayne@69
|
17280 }
|
|
jpayne@69
|
17281
|
|
jpayne@69
|
17282 /* "(tree fragment)":3
|
|
jpayne@69
|
17283 * def __reduce_cython__(self):
|
|
jpayne@69
|
17284 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17285 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17286 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17287 */
|
|
jpayne@69
|
17288
|
|
jpayne@69
|
17289 /* Python wrapper */
|
|
jpayne@69
|
17290 static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17291 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17292 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17293 #else
|
|
jpayne@69
|
17294 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17295 #endif
|
|
jpayne@69
|
17296 ); /*proto*/
|
|
jpayne@69
|
17297 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__, "GZIteratorHead.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
17298 static PyMethodDef __pyx_mdef_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__};
|
|
jpayne@69
|
17299 static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17300 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17301 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17302 #else
|
|
jpayne@69
|
17303 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17304 #endif
|
|
jpayne@69
|
17305 ) {
|
|
jpayne@69
|
17306 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
17307 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17308 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
17309 #endif
|
|
jpayne@69
|
17310 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17311 PyObject* values[1] = {0};
|
|
jpayne@69
|
17312 int __pyx_lineno = 0;
|
|
jpayne@69
|
17313 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17314 int __pyx_clineno = 0;
|
|
jpayne@69
|
17315 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17316 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17317 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
17318 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17319 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
17320 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
17321 #else
|
|
jpayne@69
|
17322 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
17323 #endif
|
|
jpayne@69
|
17324 #endif
|
|
jpayne@69
|
17325 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17326 {
|
|
jpayne@69
|
17327 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
17328 if (__pyx_kwds) {
|
|
jpayne@69
|
17329 Py_ssize_t kw_args;
|
|
jpayne@69
|
17330 switch (__pyx_nargs) {
|
|
jpayne@69
|
17331 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
17332 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17333 case 0: break;
|
|
jpayne@69
|
17334 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17335 }
|
|
jpayne@69
|
17336 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
17337 switch (__pyx_nargs) {
|
|
jpayne@69
|
17338 case 0:
|
|
jpayne@69
|
17339 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
17340 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
17341 kw_args--;
|
|
jpayne@69
|
17342 }
|
|
jpayne@69
|
17343 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
17344 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17345 }
|
|
jpayne@69
|
17346 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
17347 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
17348 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
17349 }
|
|
jpayne@69
|
17350 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
17351 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17352 } else {
|
|
jpayne@69
|
17353 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
17354 }
|
|
jpayne@69
|
17355 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
17356 }
|
|
jpayne@69
|
17357 goto __pyx_L6_skip;
|
|
jpayne@69
|
17358 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
17359 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
17360 __pyx_L6_skip:;
|
|
jpayne@69
|
17361 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
17362 __pyx_L3_error:;
|
|
jpayne@69
|
17363 {
|
|
jpayne@69
|
17364 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17365 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17366 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
17367 }
|
|
jpayne@69
|
17368 }
|
|
jpayne@69
|
17369 __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17370 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17371 return NULL;
|
|
jpayne@69
|
17372 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
17373 __pyx_r = __pyx_pf_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
17374
|
|
jpayne@69
|
17375 /* function exit code */
|
|
jpayne@69
|
17376 {
|
|
jpayne@69
|
17377 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17378 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17379 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
17380 }
|
|
jpayne@69
|
17381 }
|
|
jpayne@69
|
17382 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17383 return __pyx_r;
|
|
jpayne@69
|
17384 }
|
|
jpayne@69
|
17385
|
|
jpayne@69
|
17386 static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
17387 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17388 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17389 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17390 int __pyx_lineno = 0;
|
|
jpayne@69
|
17391 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17392 int __pyx_clineno = 0;
|
|
jpayne@69
|
17393 __Pyx_TraceFrameInit(__pyx_codeobj__34)
|
|
jpayne@69
|
17394 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
17395 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
17396
|
|
jpayne@69
|
17397 /* "(tree fragment)":4
|
|
jpayne@69
|
17398 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17399 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17400 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17401 */
|
|
jpayne@69
|
17402 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0);
|
|
jpayne@69
|
17403 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
17404
|
|
jpayne@69
|
17405 /* "(tree fragment)":3
|
|
jpayne@69
|
17406 * def __reduce_cython__(self):
|
|
jpayne@69
|
17407 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17408 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17409 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17410 */
|
|
jpayne@69
|
17411
|
|
jpayne@69
|
17412 /* function exit code */
|
|
jpayne@69
|
17413 __pyx_L1_error:;
|
|
jpayne@69
|
17414 __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17415 __pyx_r = NULL;
|
|
jpayne@69
|
17416 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17417 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17418 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17419 return __pyx_r;
|
|
jpayne@69
|
17420 }
|
|
jpayne@69
|
17421
|
|
jpayne@69
|
17422 /* "pysam/libctabix.pyx":797
|
|
jpayne@69
|
17423 * '''
|
|
jpayne@69
|
17424 *
|
|
jpayne@69
|
17425 * def __init__(self, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17426 * self.parser = parser
|
|
jpayne@69
|
17427 *
|
|
jpayne@69
|
17428 */
|
|
jpayne@69
|
17429
|
|
jpayne@69
|
17430 /* Python wrapper */
|
|
jpayne@69
|
17431 static int __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
17432 static int __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
17433 PyObject *__pyx_v_parser = 0;
|
|
jpayne@69
|
17434 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
17435 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17436 PyObject* values[1] = {0};
|
|
jpayne@69
|
17437 int __pyx_lineno = 0;
|
|
jpayne@69
|
17438 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17439 int __pyx_clineno = 0;
|
|
jpayne@69
|
17440 int __pyx_r;
|
|
jpayne@69
|
17441 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17442 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
|
|
jpayne@69
|
17443 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
17444 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
17445 #else
|
|
jpayne@69
|
17446 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
17447 #endif
|
|
jpayne@69
|
17448 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17449 {
|
|
jpayne@69
|
17450 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_parser,0};
|
|
jpayne@69
|
17451 if (__pyx_kwds) {
|
|
jpayne@69
|
17452 Py_ssize_t kw_args;
|
|
jpayne@69
|
17453 switch (__pyx_nargs) {
|
|
jpayne@69
|
17454 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
17455 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17456 case 0: break;
|
|
jpayne@69
|
17457 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17458 }
|
|
jpayne@69
|
17459 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
17460 switch (__pyx_nargs) {
|
|
jpayne@69
|
17461 case 0:
|
|
jpayne@69
|
17462 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) {
|
|
jpayne@69
|
17463 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
|
|
jpayne@69
|
17464 kw_args--;
|
|
jpayne@69
|
17465 }
|
|
jpayne@69
|
17466 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 797, __pyx_L3_error)
|
|
jpayne@69
|
17467 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17468 }
|
|
jpayne@69
|
17469 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
17470 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
17471 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 797, __pyx_L3_error)
|
|
jpayne@69
|
17472 }
|
|
jpayne@69
|
17473 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
17474 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17475 } else {
|
|
jpayne@69
|
17476 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
17477 }
|
|
jpayne@69
|
17478 __pyx_v_parser = values[0];
|
|
jpayne@69
|
17479 }
|
|
jpayne@69
|
17480 goto __pyx_L6_skip;
|
|
jpayne@69
|
17481 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
17482 __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 797, __pyx_L3_error)
|
|
jpayne@69
|
17483 __pyx_L6_skip:;
|
|
jpayne@69
|
17484 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
17485 __pyx_L3_error:;
|
|
jpayne@69
|
17486 {
|
|
jpayne@69
|
17487 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17488 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17489 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
17490 }
|
|
jpayne@69
|
17491 }
|
|
jpayne@69
|
17492 __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17493 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17494 return -1;
|
|
jpayne@69
|
17495 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
17496 __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed___init__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self), __pyx_v_parser);
|
|
jpayne@69
|
17497
|
|
jpayne@69
|
17498 /* function exit code */
|
|
jpayne@69
|
17499 {
|
|
jpayne@69
|
17500 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17501 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17502 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
17503 }
|
|
jpayne@69
|
17504 }
|
|
jpayne@69
|
17505 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17506 return __pyx_r;
|
|
jpayne@69
|
17507 }
|
|
jpayne@69
|
17508
|
|
jpayne@69
|
17509 static int __pyx_pf_5pysam_9libctabix_16GZIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, PyObject *__pyx_v_parser) {
|
|
jpayne@69
|
17510 int __pyx_r;
|
|
jpayne@69
|
17511 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17512 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17513 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
17514 int __pyx_lineno = 0;
|
|
jpayne@69
|
17515 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17516 int __pyx_clineno = 0;
|
|
jpayne@69
|
17517 __Pyx_RefNannySetupContext("__init__", 1);
|
|
jpayne@69
|
17518 __Pyx_TraceCall("__init__", __pyx_f[0], 797, 0, __PYX_ERR(0, 797, __pyx_L1_error));
|
|
jpayne@69
|
17519
|
|
jpayne@69
|
17520 /* "pysam/libctabix.pyx":798
|
|
jpayne@69
|
17521 *
|
|
jpayne@69
|
17522 * def __init__(self, parser):
|
|
jpayne@69
|
17523 * self.parser = parser # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17524 *
|
|
jpayne@69
|
17525 * def __next__(self):
|
|
jpayne@69
|
17526 */
|
|
jpayne@69
|
17527 if (!(likely(((__pyx_v_parser) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_parser, __pyx_ptype_5pysam_9libctabix_Parser))))) __PYX_ERR(0, 798, __pyx_L1_error)
|
|
jpayne@69
|
17528 __pyx_t_1 = __pyx_v_parser;
|
|
jpayne@69
|
17529 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
17530 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
17531 __Pyx_GOTREF((PyObject *)__pyx_v_self->parser);
|
|
jpayne@69
|
17532 __Pyx_DECREF((PyObject *)__pyx_v_self->parser);
|
|
jpayne@69
|
17533 __pyx_v_self->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_t_1);
|
|
jpayne@69
|
17534 __pyx_t_1 = 0;
|
|
jpayne@69
|
17535
|
|
jpayne@69
|
17536 /* "pysam/libctabix.pyx":797
|
|
jpayne@69
|
17537 * '''
|
|
jpayne@69
|
17538 *
|
|
jpayne@69
|
17539 * def __init__(self, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17540 * self.parser = parser
|
|
jpayne@69
|
17541 *
|
|
jpayne@69
|
17542 */
|
|
jpayne@69
|
17543
|
|
jpayne@69
|
17544 /* function exit code */
|
|
jpayne@69
|
17545 __pyx_r = 0;
|
|
jpayne@69
|
17546 goto __pyx_L0;
|
|
jpayne@69
|
17547 __pyx_L1_error:;
|
|
jpayne@69
|
17548 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
17549 __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17550 __pyx_r = -1;
|
|
jpayne@69
|
17551 __pyx_L0:;
|
|
jpayne@69
|
17552 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
17553 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17554 return __pyx_r;
|
|
jpayne@69
|
17555 }
|
|
jpayne@69
|
17556
|
|
jpayne@69
|
17557 /* "pysam/libctabix.pyx":800
|
|
jpayne@69
|
17558 * self.parser = parser
|
|
jpayne@69
|
17559 *
|
|
jpayne@69
|
17560 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17561 * """python version of next().
|
|
jpayne@69
|
17562 * """
|
|
jpayne@69
|
17563 */
|
|
jpayne@69
|
17564
|
|
jpayne@69
|
17565 /* Python wrapper */
|
|
jpayne@69
|
17566 static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
17567 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16GZIteratorParsed_2__next__, "python version of next().\n ");
|
|
jpayne@69
|
17568 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
17569 struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__;
|
|
jpayne@69
|
17570 #endif
|
|
jpayne@69
|
17571 static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
17572 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17573 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17574 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17575 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
|
|
jpayne@69
|
17576 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17577 __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed_2__next__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self));
|
|
jpayne@69
|
17578
|
|
jpayne@69
|
17579 /* function exit code */
|
|
jpayne@69
|
17580 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17581 return __pyx_r;
|
|
jpayne@69
|
17582 }
|
|
jpayne@69
|
17583
|
|
jpayne@69
|
17584 static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self) {
|
|
jpayne@69
|
17585 int __pyx_v_retval;
|
|
jpayne@69
|
17586 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17587 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17588 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17589 int __pyx_error_without_exception = 0; /* StopIteration */
|
|
jpayne@69
|
17590 int __pyx_t_1;
|
|
jpayne@69
|
17591 int __pyx_t_2;
|
|
jpayne@69
|
17592 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
17593 int __pyx_lineno = 0;
|
|
jpayne@69
|
17594 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17595 int __pyx_clineno = 0;
|
|
jpayne@69
|
17596 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
17597 __Pyx_TraceCall("__next__", __pyx_f[0], 800, 0, __PYX_ERR(0, 800, __pyx_L1_error));
|
|
jpayne@69
|
17598
|
|
jpayne@69
|
17599 /* "pysam/libctabix.pyx":803
|
|
jpayne@69
|
17600 * """python version of next().
|
|
jpayne@69
|
17601 * """
|
|
jpayne@69
|
17602 * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17603 * if retval < 0:
|
|
jpayne@69
|
17604 * raise StopIteration
|
|
jpayne@69
|
17605 */
|
|
jpayne@69
|
17606 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.__pyx___cnext__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 803, __pyx_L1_error)
|
|
jpayne@69
|
17607 __pyx_v_retval = __pyx_t_1;
|
|
jpayne@69
|
17608
|
|
jpayne@69
|
17609 /* "pysam/libctabix.pyx":804
|
|
jpayne@69
|
17610 * """
|
|
jpayne@69
|
17611 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
17612 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17613 * raise StopIteration
|
|
jpayne@69
|
17614 *
|
|
jpayne@69
|
17615 */
|
|
jpayne@69
|
17616 __pyx_t_2 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
17617 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
17618
|
|
jpayne@69
|
17619 /* "pysam/libctabix.pyx":805
|
|
jpayne@69
|
17620 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
17621 * if retval < 0:
|
|
jpayne@69
|
17622 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17623 *
|
|
jpayne@69
|
17624 * return self.parser.parse(self.buffer.s,
|
|
jpayne@69
|
17625 */
|
|
jpayne@69
|
17626 __pyx_error_without_exception = 1;
|
|
jpayne@69
|
17627 goto __pyx_L1_error;;
|
|
jpayne@69
|
17628
|
|
jpayne@69
|
17629 /* "pysam/libctabix.pyx":804
|
|
jpayne@69
|
17630 * """
|
|
jpayne@69
|
17631 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
17632 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17633 * raise StopIteration
|
|
jpayne@69
|
17634 *
|
|
jpayne@69
|
17635 */
|
|
jpayne@69
|
17636 }
|
|
jpayne@69
|
17637
|
|
jpayne@69
|
17638 /* "pysam/libctabix.pyx":807
|
|
jpayne@69
|
17639 * raise StopIteration
|
|
jpayne@69
|
17640 *
|
|
jpayne@69
|
17641 * return self.parser.parse(self.buffer.s, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17642 * self.buffer.l)
|
|
jpayne@69
|
17643 *
|
|
jpayne@69
|
17644 */
|
|
jpayne@69
|
17645 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
17646
|
|
jpayne@69
|
17647 /* "pysam/libctabix.pyx":808
|
|
jpayne@69
|
17648 *
|
|
jpayne@69
|
17649 * return self.parser.parse(self.buffer.s,
|
|
jpayne@69
|
17650 * self.buffer.l) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17651 *
|
|
jpayne@69
|
17652 *
|
|
jpayne@69
|
17653 */
|
|
jpayne@69
|
17654 __pyx_t_3 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->parser->__pyx_vtab)->parse(__pyx_v_self->parser, __pyx_v_self->__pyx_base.buffer.s, __pyx_v_self->__pyx_base.buffer.l); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 807, __pyx_L1_error)
|
|
jpayne@69
|
17655 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
17656 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
17657 __pyx_t_3 = 0;
|
|
jpayne@69
|
17658 goto __pyx_L0;
|
|
jpayne@69
|
17659
|
|
jpayne@69
|
17660 /* "pysam/libctabix.pyx":800
|
|
jpayne@69
|
17661 * self.parser = parser
|
|
jpayne@69
|
17662 *
|
|
jpayne@69
|
17663 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17664 * """python version of next().
|
|
jpayne@69
|
17665 * """
|
|
jpayne@69
|
17666 */
|
|
jpayne@69
|
17667
|
|
jpayne@69
|
17668 /* function exit code */
|
|
jpayne@69
|
17669 __pyx_L1_error:;
|
|
jpayne@69
|
17670 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
17671 if (!__pyx_error_without_exception) {
|
|
jpayne@69
|
17672 __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17673 }
|
|
jpayne@69
|
17674 __pyx_r = NULL;
|
|
jpayne@69
|
17675 __pyx_L0:;
|
|
jpayne@69
|
17676 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17677 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17678 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17679 return __pyx_r;
|
|
jpayne@69
|
17680 }
|
|
jpayne@69
|
17681
|
|
jpayne@69
|
17682 /* "(tree fragment)":1
|
|
jpayne@69
|
17683 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17684 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17685 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17686 */
|
|
jpayne@69
|
17687
|
|
jpayne@69
|
17688 /* Python wrapper */
|
|
jpayne@69
|
17689 static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17690 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17691 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17692 #else
|
|
jpayne@69
|
17693 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17694 #endif
|
|
jpayne@69
|
17695 ); /*proto*/
|
|
jpayne@69
|
17696 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__, "GZIteratorParsed.__reduce_cython__(self)");
|
|
jpayne@69
|
17697 static PyMethodDef __pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__};
|
|
jpayne@69
|
17698 static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17699 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17700 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17701 #else
|
|
jpayne@69
|
17702 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17703 #endif
|
|
jpayne@69
|
17704 ) {
|
|
jpayne@69
|
17705 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17706 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
17707 #endif
|
|
jpayne@69
|
17708 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17709 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17710 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17711 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
|
jpayne@69
|
17712 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17713 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
17714 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
17715 #else
|
|
jpayne@69
|
17716 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
17717 #endif
|
|
jpayne@69
|
17718 #endif
|
|
jpayne@69
|
17719 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17720 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
17721 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
17722 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
17723 __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self));
|
|
jpayne@69
|
17724
|
|
jpayne@69
|
17725 /* function exit code */
|
|
jpayne@69
|
17726 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17727 return __pyx_r;
|
|
jpayne@69
|
17728 }
|
|
jpayne@69
|
17729
|
|
jpayne@69
|
17730 static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self) {
|
|
jpayne@69
|
17731 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17732 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17733 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17734 int __pyx_lineno = 0;
|
|
jpayne@69
|
17735 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17736 int __pyx_clineno = 0;
|
|
jpayne@69
|
17737 __Pyx_TraceFrameInit(__pyx_codeobj__35)
|
|
jpayne@69
|
17738 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
17739 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
17740
|
|
jpayne@69
|
17741 /* "(tree fragment)":2
|
|
jpayne@69
|
17742 * def __reduce_cython__(self):
|
|
jpayne@69
|
17743 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17744 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17745 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17746 */
|
|
jpayne@69
|
17747 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0);
|
|
jpayne@69
|
17748 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
17749
|
|
jpayne@69
|
17750 /* "(tree fragment)":1
|
|
jpayne@69
|
17751 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17752 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17753 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17754 */
|
|
jpayne@69
|
17755
|
|
jpayne@69
|
17756 /* function exit code */
|
|
jpayne@69
|
17757 __pyx_L1_error:;
|
|
jpayne@69
|
17758 __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17759 __pyx_r = NULL;
|
|
jpayne@69
|
17760 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17761 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17762 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17763 return __pyx_r;
|
|
jpayne@69
|
17764 }
|
|
jpayne@69
|
17765
|
|
jpayne@69
|
17766 /* "(tree fragment)":3
|
|
jpayne@69
|
17767 * def __reduce_cython__(self):
|
|
jpayne@69
|
17768 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17769 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17770 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17771 */
|
|
jpayne@69
|
17772
|
|
jpayne@69
|
17773 /* Python wrapper */
|
|
jpayne@69
|
17774 static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17775 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17776 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17777 #else
|
|
jpayne@69
|
17778 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17779 #endif
|
|
jpayne@69
|
17780 ); /*proto*/
|
|
jpayne@69
|
17781 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__, "GZIteratorParsed.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
17782 static PyMethodDef __pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__};
|
|
jpayne@69
|
17783 static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
17784 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17785 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17786 #else
|
|
jpayne@69
|
17787 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17788 #endif
|
|
jpayne@69
|
17789 ) {
|
|
jpayne@69
|
17790 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
17791 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17792 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
17793 #endif
|
|
jpayne@69
|
17794 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17795 PyObject* values[1] = {0};
|
|
jpayne@69
|
17796 int __pyx_lineno = 0;
|
|
jpayne@69
|
17797 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17798 int __pyx_clineno = 0;
|
|
jpayne@69
|
17799 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17800 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17801 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
17802 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17803 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
17804 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
17805 #else
|
|
jpayne@69
|
17806 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
17807 #endif
|
|
jpayne@69
|
17808 #endif
|
|
jpayne@69
|
17809 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17810 {
|
|
jpayne@69
|
17811 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
17812 if (__pyx_kwds) {
|
|
jpayne@69
|
17813 Py_ssize_t kw_args;
|
|
jpayne@69
|
17814 switch (__pyx_nargs) {
|
|
jpayne@69
|
17815 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
17816 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17817 case 0: break;
|
|
jpayne@69
|
17818 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17819 }
|
|
jpayne@69
|
17820 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
17821 switch (__pyx_nargs) {
|
|
jpayne@69
|
17822 case 0:
|
|
jpayne@69
|
17823 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
17824 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
17825 kw_args--;
|
|
jpayne@69
|
17826 }
|
|
jpayne@69
|
17827 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
17828 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17829 }
|
|
jpayne@69
|
17830 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
17831 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
17832 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
17833 }
|
|
jpayne@69
|
17834 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
17835 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17836 } else {
|
|
jpayne@69
|
17837 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
17838 }
|
|
jpayne@69
|
17839 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
17840 }
|
|
jpayne@69
|
17841 goto __pyx_L6_skip;
|
|
jpayne@69
|
17842 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
17843 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
17844 __pyx_L6_skip:;
|
|
jpayne@69
|
17845 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
17846 __pyx_L3_error:;
|
|
jpayne@69
|
17847 {
|
|
jpayne@69
|
17848 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17849 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17850 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
17851 }
|
|
jpayne@69
|
17852 }
|
|
jpayne@69
|
17853 __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17854 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17855 return NULL;
|
|
jpayne@69
|
17856 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
17857 __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
17858
|
|
jpayne@69
|
17859 /* function exit code */
|
|
jpayne@69
|
17860 {
|
|
jpayne@69
|
17861 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
17862 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
17863 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
17864 }
|
|
jpayne@69
|
17865 }
|
|
jpayne@69
|
17866 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17867 return __pyx_r;
|
|
jpayne@69
|
17868 }
|
|
jpayne@69
|
17869
|
|
jpayne@69
|
17870 static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
17871 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
17872 __Pyx_TraceDeclarations
|
|
jpayne@69
|
17873 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17874 int __pyx_lineno = 0;
|
|
jpayne@69
|
17875 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17876 int __pyx_clineno = 0;
|
|
jpayne@69
|
17877 __Pyx_TraceFrameInit(__pyx_codeobj__36)
|
|
jpayne@69
|
17878 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
17879 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
17880
|
|
jpayne@69
|
17881 /* "(tree fragment)":4
|
|
jpayne@69
|
17882 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17883 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
17884 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17885 */
|
|
jpayne@69
|
17886 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0);
|
|
jpayne@69
|
17887 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
17888
|
|
jpayne@69
|
17889 /* "(tree fragment)":3
|
|
jpayne@69
|
17890 * def __reduce_cython__(self):
|
|
jpayne@69
|
17891 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17892 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17893 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
17894 */
|
|
jpayne@69
|
17895
|
|
jpayne@69
|
17896 /* function exit code */
|
|
jpayne@69
|
17897 __pyx_L1_error:;
|
|
jpayne@69
|
17898 __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
17899 __pyx_r = NULL;
|
|
jpayne@69
|
17900 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
17901 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
17902 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
17903 return __pyx_r;
|
|
jpayne@69
|
17904 }
|
|
jpayne@69
|
17905
|
|
jpayne@69
|
17906 /* "pysam/libctabix.pyx":811
|
|
jpayne@69
|
17907 *
|
|
jpayne@69
|
17908 *
|
|
jpayne@69
|
17909 * def tabix_compress(filename_in, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17910 * filename_out,
|
|
jpayne@69
|
17911 * force=False):
|
|
jpayne@69
|
17912 */
|
|
jpayne@69
|
17913
|
|
jpayne@69
|
17914 /* Python wrapper */
|
|
jpayne@69
|
17915 static PyObject *__pyx_pw_5pysam_9libctabix_1tabix_compress(PyObject *__pyx_self,
|
|
jpayne@69
|
17916 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17917 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17918 #else
|
|
jpayne@69
|
17919 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17920 #endif
|
|
jpayne@69
|
17921 ); /*proto*/
|
|
jpayne@69
|
17922 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_tabix_compress, "tabix_compress(filename_in, filename_out, force=False)\ncompress *filename_in* writing the output to *filename_out*.\n \n Raise an IOError if *filename_out* already exists, unless *force*\n is set.\n ");
|
|
jpayne@69
|
17923 static PyMethodDef __pyx_mdef_5pysam_9libctabix_1tabix_compress = {"tabix_compress", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_1tabix_compress, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_tabix_compress};
|
|
jpayne@69
|
17924 static PyObject *__pyx_pw_5pysam_9libctabix_1tabix_compress(PyObject *__pyx_self,
|
|
jpayne@69
|
17925 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17926 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
17927 #else
|
|
jpayne@69
|
17928 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
17929 #endif
|
|
jpayne@69
|
17930 ) {
|
|
jpayne@69
|
17931 PyObject *__pyx_v_filename_in = 0;
|
|
jpayne@69
|
17932 PyObject *__pyx_v_filename_out = 0;
|
|
jpayne@69
|
17933 PyObject *__pyx_v_force = 0;
|
|
jpayne@69
|
17934 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17935 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
17936 #endif
|
|
jpayne@69
|
17937 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
17938 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
17939 int __pyx_lineno = 0;
|
|
jpayne@69
|
17940 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
17941 int __pyx_clineno = 0;
|
|
jpayne@69
|
17942 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
17943 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
17944 __Pyx_RefNannySetupContext("tabix_compress (wrapper)", 0);
|
|
jpayne@69
|
17945 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
17946 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
17947 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
17948 #else
|
|
jpayne@69
|
17949 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
17950 #endif
|
|
jpayne@69
|
17951 #endif
|
|
jpayne@69
|
17952 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
17953 {
|
|
jpayne@69
|
17954 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename_in,&__pyx_n_s_filename_out,&__pyx_n_s_force,0};
|
|
jpayne@69
|
17955
|
|
jpayne@69
|
17956 /* "pysam/libctabix.pyx":813
|
|
jpayne@69
|
17957 * def tabix_compress(filename_in,
|
|
jpayne@69
|
17958 * filename_out,
|
|
jpayne@69
|
17959 * force=False): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
17960 * '''compress *filename_in* writing the output to *filename_out*.
|
|
jpayne@69
|
17961 *
|
|
jpayne@69
|
17962 */
|
|
jpayne@69
|
17963 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
|
|
jpayne@69
|
17964 if (__pyx_kwds) {
|
|
jpayne@69
|
17965 Py_ssize_t kw_args;
|
|
jpayne@69
|
17966 switch (__pyx_nargs) {
|
|
jpayne@69
|
17967 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
17968 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17969 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
17970 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17971 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
17972 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17973 case 0: break;
|
|
jpayne@69
|
17974 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17975 }
|
|
jpayne@69
|
17976 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
17977 switch (__pyx_nargs) {
|
|
jpayne@69
|
17978 case 0:
|
|
jpayne@69
|
17979 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename_in)) != 0)) {
|
|
jpayne@69
|
17980 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
17981 kw_args--;
|
|
jpayne@69
|
17982 }
|
|
jpayne@69
|
17983 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 811, __pyx_L3_error)
|
|
jpayne@69
|
17984 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
17985 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17986 case 1:
|
|
jpayne@69
|
17987 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename_out)) != 0)) {
|
|
jpayne@69
|
17988 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
17989 kw_args--;
|
|
jpayne@69
|
17990 }
|
|
jpayne@69
|
17991 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 811, __pyx_L3_error)
|
|
jpayne@69
|
17992 else {
|
|
jpayne@69
|
17993 __Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, 1); __PYX_ERR(0, 811, __pyx_L3_error)
|
|
jpayne@69
|
17994 }
|
|
jpayne@69
|
17995 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
17996 case 2:
|
|
jpayne@69
|
17997 if (kw_args > 0) {
|
|
jpayne@69
|
17998 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_force);
|
|
jpayne@69
|
17999 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18000 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 811, __pyx_L3_error)
|
|
jpayne@69
|
18001 }
|
|
jpayne@69
|
18002 }
|
|
jpayne@69
|
18003 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
18004 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
18005 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "tabix_compress") < 0)) __PYX_ERR(0, 811, __pyx_L3_error)
|
|
jpayne@69
|
18006 }
|
|
jpayne@69
|
18007 } else {
|
|
jpayne@69
|
18008 switch (__pyx_nargs) {
|
|
jpayne@69
|
18009 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
18010 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18011 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
18012 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
18013 break;
|
|
jpayne@69
|
18014 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
18015 }
|
|
jpayne@69
|
18016 }
|
|
jpayne@69
|
18017 __pyx_v_filename_in = values[0];
|
|
jpayne@69
|
18018 __pyx_v_filename_out = values[1];
|
|
jpayne@69
|
18019 __pyx_v_force = values[2];
|
|
jpayne@69
|
18020 }
|
|
jpayne@69
|
18021 goto __pyx_L6_skip;
|
|
jpayne@69
|
18022 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
18023 __Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 811, __pyx_L3_error)
|
|
jpayne@69
|
18024 __pyx_L6_skip:;
|
|
jpayne@69
|
18025 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
18026 __pyx_L3_error:;
|
|
jpayne@69
|
18027 {
|
|
jpayne@69
|
18028 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
18029 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
18030 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
18031 }
|
|
jpayne@69
|
18032 }
|
|
jpayne@69
|
18033 __Pyx_AddTraceback("pysam.libctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
18034 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
18035 return NULL;
|
|
jpayne@69
|
18036 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
18037 __pyx_r = __pyx_pf_5pysam_9libctabix_tabix_compress(__pyx_self, __pyx_v_filename_in, __pyx_v_filename_out, __pyx_v_force);
|
|
jpayne@69
|
18038
|
|
jpayne@69
|
18039 /* "pysam/libctabix.pyx":811
|
|
jpayne@69
|
18040 *
|
|
jpayne@69
|
18041 *
|
|
jpayne@69
|
18042 * def tabix_compress(filename_in, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18043 * filename_out,
|
|
jpayne@69
|
18044 * force=False):
|
|
jpayne@69
|
18045 */
|
|
jpayne@69
|
18046
|
|
jpayne@69
|
18047 /* function exit code */
|
|
jpayne@69
|
18048 {
|
|
jpayne@69
|
18049 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
18050 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
18051 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
18052 }
|
|
jpayne@69
|
18053 }
|
|
jpayne@69
|
18054 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
18055 return __pyx_r;
|
|
jpayne@69
|
18056 }
|
|
jpayne@69
|
18057
|
|
jpayne@69
|
18058 static PyObject *__pyx_pf_5pysam_9libctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force) {
|
|
jpayne@69
|
18059 int __pyx_v_WINDOW_SIZE;
|
|
jpayne@69
|
18060 int __pyx_v_c;
|
|
jpayne@69
|
18061 int __pyx_v_r;
|
|
jpayne@69
|
18062 void *__pyx_v_buffer;
|
|
jpayne@69
|
18063 BGZF *__pyx_v_fp;
|
|
jpayne@69
|
18064 int __pyx_v_fd_src;
|
|
jpayne@69
|
18065 int __pyx_v_is_empty;
|
|
jpayne@69
|
18066 int __pyx_v_O_RDONLY;
|
|
jpayne@69
|
18067 PyObject *__pyx_v_fn = NULL;
|
|
jpayne@69
|
18068 char *__pyx_v_cfn;
|
|
jpayne@69
|
18069 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
18070 __Pyx_TraceDeclarations
|
|
jpayne@69
|
18071 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
18072 int __pyx_t_1;
|
|
jpayne@69
|
18073 int __pyx_t_2;
|
|
jpayne@69
|
18074 int __pyx_t_3;
|
|
jpayne@69
|
18075 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
18076 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
18077 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
18078 unsigned int __pyx_t_7;
|
|
jpayne@69
|
18079 int __pyx_t_8;
|
|
jpayne@69
|
18080 char *__pyx_t_9;
|
|
jpayne@69
|
18081 int __pyx_lineno = 0;
|
|
jpayne@69
|
18082 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
18083 int __pyx_clineno = 0;
|
|
jpayne@69
|
18084 __Pyx_TraceFrameInit(__pyx_codeobj__37)
|
|
jpayne@69
|
18085 __Pyx_RefNannySetupContext("tabix_compress", 1);
|
|
jpayne@69
|
18086 __Pyx_TraceCall("tabix_compress", __pyx_f[0], 811, 0, __PYX_ERR(0, 811, __pyx_L1_error));
|
|
jpayne@69
|
18087
|
|
jpayne@69
|
18088 /* "pysam/libctabix.pyx":820
|
|
jpayne@69
|
18089 * '''
|
|
jpayne@69
|
18090 *
|
|
jpayne@69
|
18091 * if not force and os.path.exists(filename_out): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18092 * raise IOError(
|
|
jpayne@69
|
18093 * "Filename '%s' already exists, use *force* to "
|
|
jpayne@69
|
18094 */
|
|
jpayne@69
|
18095 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_force); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 820, __pyx_L1_error)
|
|
jpayne@69
|
18096 __pyx_t_3 = (!__pyx_t_2);
|
|
jpayne@69
|
18097 if (__pyx_t_3) {
|
|
jpayne@69
|
18098 } else {
|
|
jpayne@69
|
18099 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
18100 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
18101 }
|
|
jpayne@69
|
18102 __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_os); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 820, __pyx_L1_error)
|
|
jpayne@69
|
18103 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18104 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_path); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 820, __pyx_L1_error)
|
|
jpayne@69
|
18105 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
18106 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18107 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_exists); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 820, __pyx_L1_error)
|
|
jpayne@69
|
18108 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18109 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
18110 __pyx_t_6 = NULL;
|
|
jpayne@69
|
18111 __pyx_t_7 = 0;
|
|
jpayne@69
|
18112 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
18113 if (likely(PyMethod_Check(__pyx_t_5))) {
|
|
jpayne@69
|
18114 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5);
|
|
jpayne@69
|
18115 if (likely(__pyx_t_6)) {
|
|
jpayne@69
|
18116 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
|
|
jpayne@69
|
18117 __Pyx_INCREF(__pyx_t_6);
|
|
jpayne@69
|
18118 __Pyx_INCREF(function);
|
|
jpayne@69
|
18119 __Pyx_DECREF_SET(__pyx_t_5, function);
|
|
jpayne@69
|
18120 __pyx_t_7 = 1;
|
|
jpayne@69
|
18121 }
|
|
jpayne@69
|
18122 }
|
|
jpayne@69
|
18123 #endif
|
|
jpayne@69
|
18124 {
|
|
jpayne@69
|
18125 PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_v_filename_out};
|
|
jpayne@69
|
18126 __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_7, 1+__pyx_t_7);
|
|
jpayne@69
|
18127 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
18128 if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 820, __pyx_L1_error)
|
|
jpayne@69
|
18129 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18130 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18131 }
|
|
jpayne@69
|
18132 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 820, __pyx_L1_error)
|
|
jpayne@69
|
18133 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18134 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
18135 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
18136 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
18137
|
|
jpayne@69
|
18138 /* "pysam/libctabix.pyx":823
|
|
jpayne@69
|
18139 * raise IOError(
|
|
jpayne@69
|
18140 * "Filename '%s' already exists, use *force* to "
|
|
jpayne@69
|
18141 * "overwrite" % filename_out) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18142 *
|
|
jpayne@69
|
18143 * cdef int WINDOW_SIZE
|
|
jpayne@69
|
18144 */
|
|
jpayne@69
|
18145 __pyx_t_4 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Filename_s_already_exists_use_fo, __pyx_v_filename_out); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 823, __pyx_L1_error)
|
|
jpayne@69
|
18146 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18147
|
|
jpayne@69
|
18148 /* "pysam/libctabix.pyx":821
|
|
jpayne@69
|
18149 *
|
|
jpayne@69
|
18150 * if not force and os.path.exists(filename_out):
|
|
jpayne@69
|
18151 * raise IOError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18152 * "Filename '%s' already exists, use *force* to "
|
|
jpayne@69
|
18153 * "overwrite" % filename_out)
|
|
jpayne@69
|
18154 */
|
|
jpayne@69
|
18155 __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 821, __pyx_L1_error)
|
|
jpayne@69
|
18156 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18157 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18158 __Pyx_Raise(__pyx_t_5, 0, 0, 0);
|
|
jpayne@69
|
18159 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18160 __PYX_ERR(0, 821, __pyx_L1_error)
|
|
jpayne@69
|
18161
|
|
jpayne@69
|
18162 /* "pysam/libctabix.pyx":820
|
|
jpayne@69
|
18163 * '''
|
|
jpayne@69
|
18164 *
|
|
jpayne@69
|
18165 * if not force and os.path.exists(filename_out): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18166 * raise IOError(
|
|
jpayne@69
|
18167 * "Filename '%s' already exists, use *force* to "
|
|
jpayne@69
|
18168 */
|
|
jpayne@69
|
18169 }
|
|
jpayne@69
|
18170
|
|
jpayne@69
|
18171 /* "pysam/libctabix.pyx":830
|
|
jpayne@69
|
18172 * cdef BGZF * fp
|
|
jpayne@69
|
18173 * cdef int fd_src
|
|
jpayne@69
|
18174 * cdef bint is_empty = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18175 * cdef int O_RDONLY
|
|
jpayne@69
|
18176 * O_RDONLY = os.O_RDONLY
|
|
jpayne@69
|
18177 */
|
|
jpayne@69
|
18178 __pyx_v_is_empty = 1;
|
|
jpayne@69
|
18179
|
|
jpayne@69
|
18180 /* "pysam/libctabix.pyx":832
|
|
jpayne@69
|
18181 * cdef bint is_empty = True
|
|
jpayne@69
|
18182 * cdef int O_RDONLY
|
|
jpayne@69
|
18183 * O_RDONLY = os.O_RDONLY # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18184 *
|
|
jpayne@69
|
18185 * WINDOW_SIZE = 64 * 1024
|
|
jpayne@69
|
18186 */
|
|
jpayne@69
|
18187 __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_os); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 832, __pyx_L1_error)
|
|
jpayne@69
|
18188 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18189 __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_O_RDONLY); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 832, __pyx_L1_error)
|
|
jpayne@69
|
18190 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18191 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18192 __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 832, __pyx_L1_error)
|
|
jpayne@69
|
18193 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18194 __pyx_v_O_RDONLY = __pyx_t_8;
|
|
jpayne@69
|
18195
|
|
jpayne@69
|
18196 /* "pysam/libctabix.pyx":834
|
|
jpayne@69
|
18197 * O_RDONLY = os.O_RDONLY
|
|
jpayne@69
|
18198 *
|
|
jpayne@69
|
18199 * WINDOW_SIZE = 64 * 1024 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18200 *
|
|
jpayne@69
|
18201 * fn = encode_filename(filename_out)
|
|
jpayne@69
|
18202 */
|
|
jpayne@69
|
18203 __pyx_v_WINDOW_SIZE = 0x10000;
|
|
jpayne@69
|
18204
|
|
jpayne@69
|
18205 /* "pysam/libctabix.pyx":836
|
|
jpayne@69
|
18206 * WINDOW_SIZE = 64 * 1024
|
|
jpayne@69
|
18207 *
|
|
jpayne@69
|
18208 * fn = encode_filename(filename_out) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18209 * cdef char *cfn = fn
|
|
jpayne@69
|
18210 * with nogil:
|
|
jpayne@69
|
18211 */
|
|
jpayne@69
|
18212 __pyx_t_4 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename_out); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 836, __pyx_L1_error)
|
|
jpayne@69
|
18213 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18214 __pyx_v_fn = ((PyObject*)__pyx_t_4);
|
|
jpayne@69
|
18215 __pyx_t_4 = 0;
|
|
jpayne@69
|
18216
|
|
jpayne@69
|
18217 /* "pysam/libctabix.pyx":837
|
|
jpayne@69
|
18218 *
|
|
jpayne@69
|
18219 * fn = encode_filename(filename_out)
|
|
jpayne@69
|
18220 * cdef char *cfn = fn # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18221 * with nogil:
|
|
jpayne@69
|
18222 * fp = bgzf_open(cfn, "w")
|
|
jpayne@69
|
18223 */
|
|
jpayne@69
|
18224 if (unlikely(__pyx_v_fn == Py_None)) {
|
|
jpayne@69
|
18225 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
18226 __PYX_ERR(0, 837, __pyx_L1_error)
|
|
jpayne@69
|
18227 }
|
|
jpayne@69
|
18228 __pyx_t_9 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_9) && PyErr_Occurred())) __PYX_ERR(0, 837, __pyx_L1_error)
|
|
jpayne@69
|
18229 __pyx_v_cfn = __pyx_t_9;
|
|
jpayne@69
|
18230
|
|
jpayne@69
|
18231 /* "pysam/libctabix.pyx":838
|
|
jpayne@69
|
18232 * fn = encode_filename(filename_out)
|
|
jpayne@69
|
18233 * cdef char *cfn = fn
|
|
jpayne@69
|
18234 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18235 * fp = bgzf_open(cfn, "w")
|
|
jpayne@69
|
18236 * if fp == NULL:
|
|
jpayne@69
|
18237 */
|
|
jpayne@69
|
18238 {
|
|
jpayne@69
|
18239 #ifdef WITH_THREAD
|
|
jpayne@69
|
18240 PyThreadState *_save;
|
|
jpayne@69
|
18241 _save = NULL;
|
|
jpayne@69
|
18242 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
18243 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
18244 #endif
|
|
jpayne@69
|
18245 /*try:*/ {
|
|
jpayne@69
|
18246
|
|
jpayne@69
|
18247 /* "pysam/libctabix.pyx":839
|
|
jpayne@69
|
18248 * cdef char *cfn = fn
|
|
jpayne@69
|
18249 * with nogil:
|
|
jpayne@69
|
18250 * fp = bgzf_open(cfn, "w") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18251 * if fp == NULL:
|
|
jpayne@69
|
18252 * raise IOError("could not open '%s' for writing" % filename_out)
|
|
jpayne@69
|
18253 */
|
|
jpayne@69
|
18254 __pyx_v_fp = bgzf_open(__pyx_v_cfn, ((char const *)"w"));
|
|
jpayne@69
|
18255 }
|
|
jpayne@69
|
18256
|
|
jpayne@69
|
18257 /* "pysam/libctabix.pyx":838
|
|
jpayne@69
|
18258 * fn = encode_filename(filename_out)
|
|
jpayne@69
|
18259 * cdef char *cfn = fn
|
|
jpayne@69
|
18260 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18261 * fp = bgzf_open(cfn, "w")
|
|
jpayne@69
|
18262 * if fp == NULL:
|
|
jpayne@69
|
18263 */
|
|
jpayne@69
|
18264 /*finally:*/ {
|
|
jpayne@69
|
18265 /*normal exit:*/{
|
|
jpayne@69
|
18266 #ifdef WITH_THREAD
|
|
jpayne@69
|
18267 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
18268 Py_BLOCK_THREADS
|
|
jpayne@69
|
18269 #endif
|
|
jpayne@69
|
18270 goto __pyx_L8;
|
|
jpayne@69
|
18271 }
|
|
jpayne@69
|
18272 __pyx_L8:;
|
|
jpayne@69
|
18273 }
|
|
jpayne@69
|
18274 }
|
|
jpayne@69
|
18275
|
|
jpayne@69
|
18276 /* "pysam/libctabix.pyx":840
|
|
jpayne@69
|
18277 * with nogil:
|
|
jpayne@69
|
18278 * fp = bgzf_open(cfn, "w")
|
|
jpayne@69
|
18279 * if fp == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18280 * raise IOError("could not open '%s' for writing" % filename_out)
|
|
jpayne@69
|
18281 *
|
|
jpayne@69
|
18282 */
|
|
jpayne@69
|
18283 __pyx_t_1 = (__pyx_v_fp == NULL);
|
|
jpayne@69
|
18284 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
18285
|
|
jpayne@69
|
18286 /* "pysam/libctabix.pyx":841
|
|
jpayne@69
|
18287 * fp = bgzf_open(cfn, "w")
|
|
jpayne@69
|
18288 * if fp == NULL:
|
|
jpayne@69
|
18289 * raise IOError("could not open '%s' for writing" % filename_out) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18290 *
|
|
jpayne@69
|
18291 * fn = encode_filename(filename_in)
|
|
jpayne@69
|
18292 */
|
|
jpayne@69
|
18293 __pyx_t_4 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_s_for_writing, __pyx_v_filename_out); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 841, __pyx_L1_error)
|
|
jpayne@69
|
18294 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18295 __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 841, __pyx_L1_error)
|
|
jpayne@69
|
18296 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18297 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18298 __Pyx_Raise(__pyx_t_5, 0, 0, 0);
|
|
jpayne@69
|
18299 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18300 __PYX_ERR(0, 841, __pyx_L1_error)
|
|
jpayne@69
|
18301
|
|
jpayne@69
|
18302 /* "pysam/libctabix.pyx":840
|
|
jpayne@69
|
18303 * with nogil:
|
|
jpayne@69
|
18304 * fp = bgzf_open(cfn, "w")
|
|
jpayne@69
|
18305 * if fp == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18306 * raise IOError("could not open '%s' for writing" % filename_out)
|
|
jpayne@69
|
18307 *
|
|
jpayne@69
|
18308 */
|
|
jpayne@69
|
18309 }
|
|
jpayne@69
|
18310
|
|
jpayne@69
|
18311 /* "pysam/libctabix.pyx":843
|
|
jpayne@69
|
18312 * raise IOError("could not open '%s' for writing" % filename_out)
|
|
jpayne@69
|
18313 *
|
|
jpayne@69
|
18314 * fn = encode_filename(filename_in) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18315 * fd_src = open(fn, O_RDONLY)
|
|
jpayne@69
|
18316 * if fd_src == 0:
|
|
jpayne@69
|
18317 */
|
|
jpayne@69
|
18318 __pyx_t_5 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename_in); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 843, __pyx_L1_error)
|
|
jpayne@69
|
18319 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18320 __Pyx_DECREF_SET(__pyx_v_fn, ((PyObject*)__pyx_t_5));
|
|
jpayne@69
|
18321 __pyx_t_5 = 0;
|
|
jpayne@69
|
18322
|
|
jpayne@69
|
18323 /* "pysam/libctabix.pyx":844
|
|
jpayne@69
|
18324 *
|
|
jpayne@69
|
18325 * fn = encode_filename(filename_in)
|
|
jpayne@69
|
18326 * fd_src = open(fn, O_RDONLY) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18327 * if fd_src == 0:
|
|
jpayne@69
|
18328 * raise IOError("could not open '%s' for reading" % filename_in)
|
|
jpayne@69
|
18329 */
|
|
jpayne@69
|
18330 if (unlikely(__pyx_v_fn == Py_None)) {
|
|
jpayne@69
|
18331 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
18332 __PYX_ERR(0, 844, __pyx_L1_error)
|
|
jpayne@69
|
18333 }
|
|
jpayne@69
|
18334 __pyx_t_9 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_9) && PyErr_Occurred())) __PYX_ERR(0, 844, __pyx_L1_error)
|
|
jpayne@69
|
18335 __pyx_v_fd_src = open(__pyx_t_9, __pyx_v_O_RDONLY);
|
|
jpayne@69
|
18336
|
|
jpayne@69
|
18337 /* "pysam/libctabix.pyx":845
|
|
jpayne@69
|
18338 * fn = encode_filename(filename_in)
|
|
jpayne@69
|
18339 * fd_src = open(fn, O_RDONLY)
|
|
jpayne@69
|
18340 * if fd_src == 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18341 * raise IOError("could not open '%s' for reading" % filename_in)
|
|
jpayne@69
|
18342 *
|
|
jpayne@69
|
18343 */
|
|
jpayne@69
|
18344 __pyx_t_1 = (__pyx_v_fd_src == 0);
|
|
jpayne@69
|
18345 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
18346
|
|
jpayne@69
|
18347 /* "pysam/libctabix.pyx":846
|
|
jpayne@69
|
18348 * fd_src = open(fn, O_RDONLY)
|
|
jpayne@69
|
18349 * if fd_src == 0:
|
|
jpayne@69
|
18350 * raise IOError("could not open '%s' for reading" % filename_in) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18351 *
|
|
jpayne@69
|
18352 * buffer = malloc(WINDOW_SIZE)
|
|
jpayne@69
|
18353 */
|
|
jpayne@69
|
18354 __pyx_t_5 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_s_for_reading, __pyx_v_filename_in); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 846, __pyx_L1_error)
|
|
jpayne@69
|
18355 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18356 __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 846, __pyx_L1_error)
|
|
jpayne@69
|
18357 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18358 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18359 __Pyx_Raise(__pyx_t_4, 0, 0, 0);
|
|
jpayne@69
|
18360 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18361 __PYX_ERR(0, 846, __pyx_L1_error)
|
|
jpayne@69
|
18362
|
|
jpayne@69
|
18363 /* "pysam/libctabix.pyx":845
|
|
jpayne@69
|
18364 * fn = encode_filename(filename_in)
|
|
jpayne@69
|
18365 * fd_src = open(fn, O_RDONLY)
|
|
jpayne@69
|
18366 * if fd_src == 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18367 * raise IOError("could not open '%s' for reading" % filename_in)
|
|
jpayne@69
|
18368 *
|
|
jpayne@69
|
18369 */
|
|
jpayne@69
|
18370 }
|
|
jpayne@69
|
18371
|
|
jpayne@69
|
18372 /* "pysam/libctabix.pyx":848
|
|
jpayne@69
|
18373 * raise IOError("could not open '%s' for reading" % filename_in)
|
|
jpayne@69
|
18374 *
|
|
jpayne@69
|
18375 * buffer = malloc(WINDOW_SIZE) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18376 * c = 1
|
|
jpayne@69
|
18377 *
|
|
jpayne@69
|
18378 */
|
|
jpayne@69
|
18379 __pyx_v_buffer = malloc(__pyx_v_WINDOW_SIZE);
|
|
jpayne@69
|
18380
|
|
jpayne@69
|
18381 /* "pysam/libctabix.pyx":849
|
|
jpayne@69
|
18382 *
|
|
jpayne@69
|
18383 * buffer = malloc(WINDOW_SIZE)
|
|
jpayne@69
|
18384 * c = 1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18385 *
|
|
jpayne@69
|
18386 * while c > 0:
|
|
jpayne@69
|
18387 */
|
|
jpayne@69
|
18388 __pyx_v_c = 1;
|
|
jpayne@69
|
18389
|
|
jpayne@69
|
18390 /* "pysam/libctabix.pyx":851
|
|
jpayne@69
|
18391 * c = 1
|
|
jpayne@69
|
18392 *
|
|
jpayne@69
|
18393 * while c > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18394 * with nogil:
|
|
jpayne@69
|
18395 * c = read(fd_src, buffer, WINDOW_SIZE)
|
|
jpayne@69
|
18396 */
|
|
jpayne@69
|
18397 while (1) {
|
|
jpayne@69
|
18398 __pyx_t_1 = (__pyx_v_c > 0);
|
|
jpayne@69
|
18399 if (!__pyx_t_1) break;
|
|
jpayne@69
|
18400
|
|
jpayne@69
|
18401 /* "pysam/libctabix.pyx":852
|
|
jpayne@69
|
18402 *
|
|
jpayne@69
|
18403 * while c > 0:
|
|
jpayne@69
|
18404 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18405 * c = read(fd_src, buffer, WINDOW_SIZE)
|
|
jpayne@69
|
18406 * if c > 0:
|
|
jpayne@69
|
18407 */
|
|
jpayne@69
|
18408 {
|
|
jpayne@69
|
18409 #ifdef WITH_THREAD
|
|
jpayne@69
|
18410 PyThreadState *_save;
|
|
jpayne@69
|
18411 _save = NULL;
|
|
jpayne@69
|
18412 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
18413 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
18414 #endif
|
|
jpayne@69
|
18415 /*try:*/ {
|
|
jpayne@69
|
18416
|
|
jpayne@69
|
18417 /* "pysam/libctabix.pyx":853
|
|
jpayne@69
|
18418 * while c > 0:
|
|
jpayne@69
|
18419 * with nogil:
|
|
jpayne@69
|
18420 * c = read(fd_src, buffer, WINDOW_SIZE) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18421 * if c > 0:
|
|
jpayne@69
|
18422 * is_empty = False
|
|
jpayne@69
|
18423 */
|
|
jpayne@69
|
18424 __pyx_v_c = read(__pyx_v_fd_src, __pyx_v_buffer, __pyx_v_WINDOW_SIZE);
|
|
jpayne@69
|
18425
|
|
jpayne@69
|
18426 /* "pysam/libctabix.pyx":854
|
|
jpayne@69
|
18427 * with nogil:
|
|
jpayne@69
|
18428 * c = read(fd_src, buffer, WINDOW_SIZE)
|
|
jpayne@69
|
18429 * if c > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18430 * is_empty = False
|
|
jpayne@69
|
18431 * r = bgzf_write(fp, buffer, c)
|
|
jpayne@69
|
18432 */
|
|
jpayne@69
|
18433 __pyx_t_1 = (__pyx_v_c > 0);
|
|
jpayne@69
|
18434 if (__pyx_t_1) {
|
|
jpayne@69
|
18435
|
|
jpayne@69
|
18436 /* "pysam/libctabix.pyx":855
|
|
jpayne@69
|
18437 * c = read(fd_src, buffer, WINDOW_SIZE)
|
|
jpayne@69
|
18438 * if c > 0:
|
|
jpayne@69
|
18439 * is_empty = False # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18440 * r = bgzf_write(fp, buffer, c)
|
|
jpayne@69
|
18441 * if r < 0:
|
|
jpayne@69
|
18442 */
|
|
jpayne@69
|
18443 __pyx_v_is_empty = 0;
|
|
jpayne@69
|
18444
|
|
jpayne@69
|
18445 /* "pysam/libctabix.pyx":854
|
|
jpayne@69
|
18446 * with nogil:
|
|
jpayne@69
|
18447 * c = read(fd_src, buffer, WINDOW_SIZE)
|
|
jpayne@69
|
18448 * if c > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18449 * is_empty = False
|
|
jpayne@69
|
18450 * r = bgzf_write(fp, buffer, c)
|
|
jpayne@69
|
18451 */
|
|
jpayne@69
|
18452 }
|
|
jpayne@69
|
18453
|
|
jpayne@69
|
18454 /* "pysam/libctabix.pyx":856
|
|
jpayne@69
|
18455 * if c > 0:
|
|
jpayne@69
|
18456 * is_empty = False
|
|
jpayne@69
|
18457 * r = bgzf_write(fp, buffer, c) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18458 * if r < 0:
|
|
jpayne@69
|
18459 * free(buffer)
|
|
jpayne@69
|
18460 */
|
|
jpayne@69
|
18461 __pyx_v_r = bgzf_write(__pyx_v_fp, __pyx_v_buffer, __pyx_v_c);
|
|
jpayne@69
|
18462 }
|
|
jpayne@69
|
18463
|
|
jpayne@69
|
18464 /* "pysam/libctabix.pyx":852
|
|
jpayne@69
|
18465 *
|
|
jpayne@69
|
18466 * while c > 0:
|
|
jpayne@69
|
18467 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18468 * c = read(fd_src, buffer, WINDOW_SIZE)
|
|
jpayne@69
|
18469 * if c > 0:
|
|
jpayne@69
|
18470 */
|
|
jpayne@69
|
18471 /*finally:*/ {
|
|
jpayne@69
|
18472 /*normal exit:*/{
|
|
jpayne@69
|
18473 #ifdef WITH_THREAD
|
|
jpayne@69
|
18474 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
18475 Py_BLOCK_THREADS
|
|
jpayne@69
|
18476 #endif
|
|
jpayne@69
|
18477 goto __pyx_L17;
|
|
jpayne@69
|
18478 }
|
|
jpayne@69
|
18479 __pyx_L17:;
|
|
jpayne@69
|
18480 }
|
|
jpayne@69
|
18481 }
|
|
jpayne@69
|
18482
|
|
jpayne@69
|
18483 /* "pysam/libctabix.pyx":857
|
|
jpayne@69
|
18484 * is_empty = False
|
|
jpayne@69
|
18485 * r = bgzf_write(fp, buffer, c)
|
|
jpayne@69
|
18486 * if r < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18487 * free(buffer)
|
|
jpayne@69
|
18488 * raise IOError("writing failed")
|
|
jpayne@69
|
18489 */
|
|
jpayne@69
|
18490 __pyx_t_1 = (__pyx_v_r < 0);
|
|
jpayne@69
|
18491 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
18492
|
|
jpayne@69
|
18493 /* "pysam/libctabix.pyx":858
|
|
jpayne@69
|
18494 * r = bgzf_write(fp, buffer, c)
|
|
jpayne@69
|
18495 * if r < 0:
|
|
jpayne@69
|
18496 * free(buffer) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18497 * raise IOError("writing failed")
|
|
jpayne@69
|
18498 *
|
|
jpayne@69
|
18499 */
|
|
jpayne@69
|
18500 free(__pyx_v_buffer);
|
|
jpayne@69
|
18501
|
|
jpayne@69
|
18502 /* "pysam/libctabix.pyx":859
|
|
jpayne@69
|
18503 * if r < 0:
|
|
jpayne@69
|
18504 * free(buffer)
|
|
jpayne@69
|
18505 * raise IOError("writing failed") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18506 *
|
|
jpayne@69
|
18507 * free(buffer)
|
|
jpayne@69
|
18508 */
|
|
jpayne@69
|
18509 __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__38, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 859, __pyx_L1_error)
|
|
jpayne@69
|
18510 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18511 __Pyx_Raise(__pyx_t_4, 0, 0, 0);
|
|
jpayne@69
|
18512 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18513 __PYX_ERR(0, 859, __pyx_L1_error)
|
|
jpayne@69
|
18514
|
|
jpayne@69
|
18515 /* "pysam/libctabix.pyx":857
|
|
jpayne@69
|
18516 * is_empty = False
|
|
jpayne@69
|
18517 * r = bgzf_write(fp, buffer, c)
|
|
jpayne@69
|
18518 * if r < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18519 * free(buffer)
|
|
jpayne@69
|
18520 * raise IOError("writing failed")
|
|
jpayne@69
|
18521 */
|
|
jpayne@69
|
18522 }
|
|
jpayne@69
|
18523 }
|
|
jpayne@69
|
18524
|
|
jpayne@69
|
18525 /* "pysam/libctabix.pyx":861
|
|
jpayne@69
|
18526 * raise IOError("writing failed")
|
|
jpayne@69
|
18527 *
|
|
jpayne@69
|
18528 * free(buffer) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18529 * r = bgzf_close(fp)
|
|
jpayne@69
|
18530 * if r < 0:
|
|
jpayne@69
|
18531 */
|
|
jpayne@69
|
18532 free(__pyx_v_buffer);
|
|
jpayne@69
|
18533
|
|
jpayne@69
|
18534 /* "pysam/libctabix.pyx":862
|
|
jpayne@69
|
18535 *
|
|
jpayne@69
|
18536 * free(buffer)
|
|
jpayne@69
|
18537 * r = bgzf_close(fp) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18538 * if r < 0:
|
|
jpayne@69
|
18539 * raise IOError("error %i when writing to file %s" % (r, filename_out))
|
|
jpayne@69
|
18540 */
|
|
jpayne@69
|
18541 __pyx_v_r = bgzf_close(__pyx_v_fp);
|
|
jpayne@69
|
18542
|
|
jpayne@69
|
18543 /* "pysam/libctabix.pyx":863
|
|
jpayne@69
|
18544 * free(buffer)
|
|
jpayne@69
|
18545 * r = bgzf_close(fp)
|
|
jpayne@69
|
18546 * if r < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18547 * raise IOError("error %i when writing to file %s" % (r, filename_out))
|
|
jpayne@69
|
18548 *
|
|
jpayne@69
|
18549 */
|
|
jpayne@69
|
18550 __pyx_t_1 = (__pyx_v_r < 0);
|
|
jpayne@69
|
18551 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
18552
|
|
jpayne@69
|
18553 /* "pysam/libctabix.pyx":864
|
|
jpayne@69
|
18554 * r = bgzf_close(fp)
|
|
jpayne@69
|
18555 * if r < 0:
|
|
jpayne@69
|
18556 * raise IOError("error %i when writing to file %s" % (r, filename_out)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18557 *
|
|
jpayne@69
|
18558 * r = close(fd_src)
|
|
jpayne@69
|
18559 */
|
|
jpayne@69
|
18560 __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_r); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 864, __pyx_L1_error)
|
|
jpayne@69
|
18561 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18562 __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 864, __pyx_L1_error)
|
|
jpayne@69
|
18563 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18564 __Pyx_GIVEREF(__pyx_t_4);
|
|
jpayne@69
|
18565 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4)) __PYX_ERR(0, 864, __pyx_L1_error);
|
|
jpayne@69
|
18566 __Pyx_INCREF(__pyx_v_filename_out);
|
|
jpayne@69
|
18567 __Pyx_GIVEREF(__pyx_v_filename_out);
|
|
jpayne@69
|
18568 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_filename_out)) __PYX_ERR(0, 864, __pyx_L1_error);
|
|
jpayne@69
|
18569 __pyx_t_4 = 0;
|
|
jpayne@69
|
18570 __pyx_t_4 = PyUnicode_Format(__pyx_kp_u_error_i_when_writing_to_file_s, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 864, __pyx_L1_error)
|
|
jpayne@69
|
18571 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18572 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18573 __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 864, __pyx_L1_error)
|
|
jpayne@69
|
18574 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18575 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18576 __Pyx_Raise(__pyx_t_5, 0, 0, 0);
|
|
jpayne@69
|
18577 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18578 __PYX_ERR(0, 864, __pyx_L1_error)
|
|
jpayne@69
|
18579
|
|
jpayne@69
|
18580 /* "pysam/libctabix.pyx":863
|
|
jpayne@69
|
18581 * free(buffer)
|
|
jpayne@69
|
18582 * r = bgzf_close(fp)
|
|
jpayne@69
|
18583 * if r < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18584 * raise IOError("error %i when writing to file %s" % (r, filename_out))
|
|
jpayne@69
|
18585 *
|
|
jpayne@69
|
18586 */
|
|
jpayne@69
|
18587 }
|
|
jpayne@69
|
18588
|
|
jpayne@69
|
18589 /* "pysam/libctabix.pyx":866
|
|
jpayne@69
|
18590 * raise IOError("error %i when writing to file %s" % (r, filename_out))
|
|
jpayne@69
|
18591 *
|
|
jpayne@69
|
18592 * r = close(fd_src) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18593 * # an empty file will return with -1, thus ignore this.
|
|
jpayne@69
|
18594 * if r < 0:
|
|
jpayne@69
|
18595 */
|
|
jpayne@69
|
18596 __pyx_v_r = close(__pyx_v_fd_src);
|
|
jpayne@69
|
18597
|
|
jpayne@69
|
18598 /* "pysam/libctabix.pyx":868
|
|
jpayne@69
|
18599 * r = close(fd_src)
|
|
jpayne@69
|
18600 * # an empty file will return with -1, thus ignore this.
|
|
jpayne@69
|
18601 * if r < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18602 * if not (r == -1 and is_empty):
|
|
jpayne@69
|
18603 * raise IOError("error %i when closing file %s" % (r, filename_in))
|
|
jpayne@69
|
18604 */
|
|
jpayne@69
|
18605 __pyx_t_1 = (__pyx_v_r < 0);
|
|
jpayne@69
|
18606 if (__pyx_t_1) {
|
|
jpayne@69
|
18607
|
|
jpayne@69
|
18608 /* "pysam/libctabix.pyx":869
|
|
jpayne@69
|
18609 * # an empty file will return with -1, thus ignore this.
|
|
jpayne@69
|
18610 * if r < 0:
|
|
jpayne@69
|
18611 * if not (r == -1 and is_empty): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18612 * raise IOError("error %i when closing file %s" % (r, filename_in))
|
|
jpayne@69
|
18613 *
|
|
jpayne@69
|
18614 */
|
|
jpayne@69
|
18615 __pyx_t_3 = (__pyx_v_r == -1L);
|
|
jpayne@69
|
18616 if (__pyx_t_3) {
|
|
jpayne@69
|
18617 } else {
|
|
jpayne@69
|
18618 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
18619 goto __pyx_L23_bool_binop_done;
|
|
jpayne@69
|
18620 }
|
|
jpayne@69
|
18621 __pyx_t_1 = __pyx_v_is_empty;
|
|
jpayne@69
|
18622 __pyx_L23_bool_binop_done:;
|
|
jpayne@69
|
18623 __pyx_t_3 = (!__pyx_t_1);
|
|
jpayne@69
|
18624 if (unlikely(__pyx_t_3)) {
|
|
jpayne@69
|
18625
|
|
jpayne@69
|
18626 /* "pysam/libctabix.pyx":870
|
|
jpayne@69
|
18627 * if r < 0:
|
|
jpayne@69
|
18628 * if not (r == -1 and is_empty):
|
|
jpayne@69
|
18629 * raise IOError("error %i when closing file %s" % (r, filename_in)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18630 *
|
|
jpayne@69
|
18631 *
|
|
jpayne@69
|
18632 */
|
|
jpayne@69
|
18633 __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_r); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error)
|
|
jpayne@69
|
18634 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18635 __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 870, __pyx_L1_error)
|
|
jpayne@69
|
18636 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18637 __Pyx_GIVEREF(__pyx_t_5);
|
|
jpayne@69
|
18638 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error);
|
|
jpayne@69
|
18639 __Pyx_INCREF(__pyx_v_filename_in);
|
|
jpayne@69
|
18640 __Pyx_GIVEREF(__pyx_v_filename_in);
|
|
jpayne@69
|
18641 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_filename_in)) __PYX_ERR(0, 870, __pyx_L1_error);
|
|
jpayne@69
|
18642 __pyx_t_5 = 0;
|
|
jpayne@69
|
18643 __pyx_t_5 = PyUnicode_Format(__pyx_kp_u_error_i_when_closing_file_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error)
|
|
jpayne@69
|
18644 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
18645 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18646 __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 870, __pyx_L1_error)
|
|
jpayne@69
|
18647 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
18648 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
18649 __Pyx_Raise(__pyx_t_4, 0, 0, 0);
|
|
jpayne@69
|
18650 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
18651 __PYX_ERR(0, 870, __pyx_L1_error)
|
|
jpayne@69
|
18652
|
|
jpayne@69
|
18653 /* "pysam/libctabix.pyx":869
|
|
jpayne@69
|
18654 * # an empty file will return with -1, thus ignore this.
|
|
jpayne@69
|
18655 * if r < 0:
|
|
jpayne@69
|
18656 * if not (r == -1 and is_empty): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18657 * raise IOError("error %i when closing file %s" % (r, filename_in))
|
|
jpayne@69
|
18658 *
|
|
jpayne@69
|
18659 */
|
|
jpayne@69
|
18660 }
|
|
jpayne@69
|
18661
|
|
jpayne@69
|
18662 /* "pysam/libctabix.pyx":868
|
|
jpayne@69
|
18663 * r = close(fd_src)
|
|
jpayne@69
|
18664 * # an empty file will return with -1, thus ignore this.
|
|
jpayne@69
|
18665 * if r < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18666 * if not (r == -1 and is_empty):
|
|
jpayne@69
|
18667 * raise IOError("error %i when closing file %s" % (r, filename_in))
|
|
jpayne@69
|
18668 */
|
|
jpayne@69
|
18669 }
|
|
jpayne@69
|
18670
|
|
jpayne@69
|
18671 /* "pysam/libctabix.pyx":811
|
|
jpayne@69
|
18672 *
|
|
jpayne@69
|
18673 *
|
|
jpayne@69
|
18674 * def tabix_compress(filename_in, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18675 * filename_out,
|
|
jpayne@69
|
18676 * force=False):
|
|
jpayne@69
|
18677 */
|
|
jpayne@69
|
18678
|
|
jpayne@69
|
18679 /* function exit code */
|
|
jpayne@69
|
18680 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
18681 goto __pyx_L0;
|
|
jpayne@69
|
18682 __pyx_L1_error:;
|
|
jpayne@69
|
18683 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
18684 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
18685 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
18686 __Pyx_AddTraceback("pysam.libctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
18687 __pyx_r = NULL;
|
|
jpayne@69
|
18688 __pyx_L0:;
|
|
jpayne@69
|
18689 __Pyx_XDECREF(__pyx_v_fn);
|
|
jpayne@69
|
18690 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
18691 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
18692 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
18693 return __pyx_r;
|
|
jpayne@69
|
18694 }
|
|
jpayne@69
|
18695
|
|
jpayne@69
|
18696 /* "pysam/libctabix.pyx":873
|
|
jpayne@69
|
18697 *
|
|
jpayne@69
|
18698 *
|
|
jpayne@69
|
18699 * def tabix_index(filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18700 * force=False,
|
|
jpayne@69
|
18701 * seq_col=None,
|
|
jpayne@69
|
18702 */
|
|
jpayne@69
|
18703
|
|
jpayne@69
|
18704 /* Python wrapper */
|
|
jpayne@69
|
18705 static PyObject *__pyx_pw_5pysam_9libctabix_3tabix_index(PyObject *__pyx_self,
|
|
jpayne@69
|
18706 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
18707 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
18708 #else
|
|
jpayne@69
|
18709 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
18710 #endif
|
|
jpayne@69
|
18711 ); /*proto*/
|
|
jpayne@69
|
18712 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_2tabix_index, "tabix_index(filename, force=False, seq_col=None, start_col=None, end_col=None, preset=None, meta_char=u'#', int line_skip=0, zerobased=False, int min_shift=-1, index=None, keep_original=False, csi=False)\nindex tab-separated *filename* using tabix.\n\n An existing index will not be overwritten unless *force* is set.\n\n The index will be built from coordinates in columns *seq_col*,\n *start_col* and *end_col*.\n\n The contents of *filename* have to be sorted by contig and\n position - the method does not check if the file is sorted.\n\n Column indices are 0-based. Note that this is different from the\n tabix command line utility where column indices start at 1.\n \n Coordinates in the file are assumed to be 1-based unless\n *zerobased* is set.\n\n If *preset* is provided, the column coordinates are taken from a\n preset. Valid values for preset are \"gff\", \"bed\", \"sam\", \"vcf\",\n psltbl\", \"pileup\".\n \n Lines beginning with *meta_char* and the first *line_skip* lines\n will be skipped.\n\n If *filename* is not detected as a gzip file it will be automatically\n compressed. The original file will be removed and only the compressed\n file will be retained.\n\n By default or when *min_shift* is 0, creates a TBI index. If *min_shift*\n is greater than zero and/or *csi* is True, creates a CSI index with a\n minimal interval size of 1<<*min_shift* (1<<14 if only *csi* is set).\n\n *index* controls the filename which should be used for creating the index.\n If not set, the default is to append ``.tbi`` to *filename*.\n\n When automatically compressing files, if *keep_original* is set the\n uncompressed file will not be deleted.\n\n returns the filename of the compressed data\n\n ");
|
|
jpayne@69
|
18713 static PyMethodDef __pyx_mdef_5pysam_9libctabix_3tabix_index = {"tabix_index", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_3tabix_index, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_2tabix_index};
|
|
jpayne@69
|
18714 static PyObject *__pyx_pw_5pysam_9libctabix_3tabix_index(PyObject *__pyx_self,
|
|
jpayne@69
|
18715 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
18716 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
18717 #else
|
|
jpayne@69
|
18718 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
18719 #endif
|
|
jpayne@69
|
18720 ) {
|
|
jpayne@69
|
18721 PyObject *__pyx_v_filename = 0;
|
|
jpayne@69
|
18722 PyObject *__pyx_v_force = 0;
|
|
jpayne@69
|
18723 PyObject *__pyx_v_seq_col = 0;
|
|
jpayne@69
|
18724 PyObject *__pyx_v_start_col = 0;
|
|
jpayne@69
|
18725 PyObject *__pyx_v_end_col = 0;
|
|
jpayne@69
|
18726 PyObject *__pyx_v_preset = 0;
|
|
jpayne@69
|
18727 PyObject *__pyx_v_meta_char = 0;
|
|
jpayne@69
|
18728 int __pyx_v_line_skip;
|
|
jpayne@69
|
18729 PyObject *__pyx_v_zerobased = 0;
|
|
jpayne@69
|
18730 int __pyx_v_min_shift;
|
|
jpayne@69
|
18731 PyObject *__pyx_v_index = 0;
|
|
jpayne@69
|
18732 PyObject *__pyx_v_keep_original = 0;
|
|
jpayne@69
|
18733 PyObject *__pyx_v_csi = 0;
|
|
jpayne@69
|
18734 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
18735 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
18736 #endif
|
|
jpayne@69
|
18737 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
18738 PyObject* values[13] = {0,0,0,0,0,0,0,0,0,0,0,0,0};
|
|
jpayne@69
|
18739 int __pyx_lineno = 0;
|
|
jpayne@69
|
18740 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
18741 int __pyx_clineno = 0;
|
|
jpayne@69
|
18742 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
18743 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
18744 __Pyx_RefNannySetupContext("tabix_index (wrapper)", 0);
|
|
jpayne@69
|
18745 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
18746 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
18747 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
18748 #else
|
|
jpayne@69
|
18749 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
18750 #endif
|
|
jpayne@69
|
18751 #endif
|
|
jpayne@69
|
18752 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
18753 {
|
|
jpayne@69
|
18754 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_force,&__pyx_n_s_seq_col,&__pyx_n_s_start_col,&__pyx_n_s_end_col,&__pyx_n_s_preset,&__pyx_n_s_meta_char,&__pyx_n_s_line_skip,&__pyx_n_s_zerobased,&__pyx_n_s_min_shift,&__pyx_n_s_index,&__pyx_n_s_keep_original,&__pyx_n_s_csi,0};
|
|
jpayne@69
|
18755
|
|
jpayne@69
|
18756 /* "pysam/libctabix.pyx":874
|
|
jpayne@69
|
18757 *
|
|
jpayne@69
|
18758 * def tabix_index(filename,
|
|
jpayne@69
|
18759 * force=False, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18760 * seq_col=None,
|
|
jpayne@69
|
18761 * start_col=None,
|
|
jpayne@69
|
18762 */
|
|
jpayne@69
|
18763 values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
|
|
jpayne@69
|
18764
|
|
jpayne@69
|
18765 /* "pysam/libctabix.pyx":875
|
|
jpayne@69
|
18766 * def tabix_index(filename,
|
|
jpayne@69
|
18767 * force=False,
|
|
jpayne@69
|
18768 * seq_col=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18769 * start_col=None,
|
|
jpayne@69
|
18770 * end_col=None,
|
|
jpayne@69
|
18771 */
|
|
jpayne@69
|
18772 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
18773
|
|
jpayne@69
|
18774 /* "pysam/libctabix.pyx":876
|
|
jpayne@69
|
18775 * force=False,
|
|
jpayne@69
|
18776 * seq_col=None,
|
|
jpayne@69
|
18777 * start_col=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18778 * end_col=None,
|
|
jpayne@69
|
18779 * preset=None,
|
|
jpayne@69
|
18780 */
|
|
jpayne@69
|
18781 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
18782
|
|
jpayne@69
|
18783 /* "pysam/libctabix.pyx":877
|
|
jpayne@69
|
18784 * seq_col=None,
|
|
jpayne@69
|
18785 * start_col=None,
|
|
jpayne@69
|
18786 * end_col=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18787 * preset=None,
|
|
jpayne@69
|
18788 * meta_char="#",
|
|
jpayne@69
|
18789 */
|
|
jpayne@69
|
18790 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
18791
|
|
jpayne@69
|
18792 /* "pysam/libctabix.pyx":878
|
|
jpayne@69
|
18793 * start_col=None,
|
|
jpayne@69
|
18794 * end_col=None,
|
|
jpayne@69
|
18795 * preset=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18796 * meta_char="#",
|
|
jpayne@69
|
18797 * int line_skip=0,
|
|
jpayne@69
|
18798 */
|
|
jpayne@69
|
18799 values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
18800 values[6] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject*)__pyx_kp_u__39)));
|
|
jpayne@69
|
18801
|
|
jpayne@69
|
18802 /* "pysam/libctabix.pyx":881
|
|
jpayne@69
|
18803 * meta_char="#",
|
|
jpayne@69
|
18804 * int line_skip=0,
|
|
jpayne@69
|
18805 * zerobased=False, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18806 * int min_shift=-1,
|
|
jpayne@69
|
18807 * index=None,
|
|
jpayne@69
|
18808 */
|
|
jpayne@69
|
18809 values[8] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
|
|
jpayne@69
|
18810
|
|
jpayne@69
|
18811 /* "pysam/libctabix.pyx":883
|
|
jpayne@69
|
18812 * zerobased=False,
|
|
jpayne@69
|
18813 * int min_shift=-1,
|
|
jpayne@69
|
18814 * index=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18815 * keep_original=False,
|
|
jpayne@69
|
18816 * csi=False,
|
|
jpayne@69
|
18817 */
|
|
jpayne@69
|
18818 values[10] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
18819
|
|
jpayne@69
|
18820 /* "pysam/libctabix.pyx":884
|
|
jpayne@69
|
18821 * int min_shift=-1,
|
|
jpayne@69
|
18822 * index=None,
|
|
jpayne@69
|
18823 * keep_original=False, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18824 * csi=False,
|
|
jpayne@69
|
18825 * ):
|
|
jpayne@69
|
18826 */
|
|
jpayne@69
|
18827 values[11] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
|
|
jpayne@69
|
18828
|
|
jpayne@69
|
18829 /* "pysam/libctabix.pyx":885
|
|
jpayne@69
|
18830 * index=None,
|
|
jpayne@69
|
18831 * keep_original=False,
|
|
jpayne@69
|
18832 * csi=False, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
18833 * ):
|
|
jpayne@69
|
18834 * '''index tab-separated *filename* using tabix.
|
|
jpayne@69
|
18835 */
|
|
jpayne@69
|
18836 values[12] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
|
|
jpayne@69
|
18837 if (__pyx_kwds) {
|
|
jpayne@69
|
18838 Py_ssize_t kw_args;
|
|
jpayne@69
|
18839 switch (__pyx_nargs) {
|
|
jpayne@69
|
18840 case 13: values[12] = __Pyx_Arg_FASTCALL(__pyx_args, 12);
|
|
jpayne@69
|
18841 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18842 case 12: values[11] = __Pyx_Arg_FASTCALL(__pyx_args, 11);
|
|
jpayne@69
|
18843 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18844 case 11: values[10] = __Pyx_Arg_FASTCALL(__pyx_args, 10);
|
|
jpayne@69
|
18845 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18846 case 10: values[9] = __Pyx_Arg_FASTCALL(__pyx_args, 9);
|
|
jpayne@69
|
18847 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18848 case 9: values[8] = __Pyx_Arg_FASTCALL(__pyx_args, 8);
|
|
jpayne@69
|
18849 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18850 case 8: values[7] = __Pyx_Arg_FASTCALL(__pyx_args, 7);
|
|
jpayne@69
|
18851 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18852 case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6);
|
|
jpayne@69
|
18853 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18854 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
18855 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18856 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
18857 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18858 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
18859 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18860 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
18861 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18862 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
18863 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18864 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
18865 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18866 case 0: break;
|
|
jpayne@69
|
18867 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
18868 }
|
|
jpayne@69
|
18869 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
18870 switch (__pyx_nargs) {
|
|
jpayne@69
|
18871 case 0:
|
|
jpayne@69
|
18872 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) {
|
|
jpayne@69
|
18873 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
18874 kw_args--;
|
|
jpayne@69
|
18875 }
|
|
jpayne@69
|
18876 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18877 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
18878 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18879 case 1:
|
|
jpayne@69
|
18880 if (kw_args > 0) {
|
|
jpayne@69
|
18881 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_force);
|
|
jpayne@69
|
18882 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18883 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18884 }
|
|
jpayne@69
|
18885 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18886 case 2:
|
|
jpayne@69
|
18887 if (kw_args > 0) {
|
|
jpayne@69
|
18888 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_seq_col);
|
|
jpayne@69
|
18889 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18890 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18891 }
|
|
jpayne@69
|
18892 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18893 case 3:
|
|
jpayne@69
|
18894 if (kw_args > 0) {
|
|
jpayne@69
|
18895 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start_col);
|
|
jpayne@69
|
18896 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18897 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18898 }
|
|
jpayne@69
|
18899 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18900 case 4:
|
|
jpayne@69
|
18901 if (kw_args > 0) {
|
|
jpayne@69
|
18902 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end_col);
|
|
jpayne@69
|
18903 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18904 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18905 }
|
|
jpayne@69
|
18906 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18907 case 5:
|
|
jpayne@69
|
18908 if (kw_args > 0) {
|
|
jpayne@69
|
18909 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_preset);
|
|
jpayne@69
|
18910 if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18911 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18912 }
|
|
jpayne@69
|
18913 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18914 case 6:
|
|
jpayne@69
|
18915 if (kw_args > 0) {
|
|
jpayne@69
|
18916 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_meta_char);
|
|
jpayne@69
|
18917 if (value) { values[6] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18918 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18919 }
|
|
jpayne@69
|
18920 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18921 case 7:
|
|
jpayne@69
|
18922 if (kw_args > 0) {
|
|
jpayne@69
|
18923 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line_skip);
|
|
jpayne@69
|
18924 if (value) { values[7] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18925 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18926 }
|
|
jpayne@69
|
18927 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18928 case 8:
|
|
jpayne@69
|
18929 if (kw_args > 0) {
|
|
jpayne@69
|
18930 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_zerobased);
|
|
jpayne@69
|
18931 if (value) { values[8] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18932 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18933 }
|
|
jpayne@69
|
18934 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18935 case 9:
|
|
jpayne@69
|
18936 if (kw_args > 0) {
|
|
jpayne@69
|
18937 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_min_shift);
|
|
jpayne@69
|
18938 if (value) { values[9] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18939 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18940 }
|
|
jpayne@69
|
18941 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18942 case 10:
|
|
jpayne@69
|
18943 if (kw_args > 0) {
|
|
jpayne@69
|
18944 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_index);
|
|
jpayne@69
|
18945 if (value) { values[10] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18946 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18947 }
|
|
jpayne@69
|
18948 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18949 case 11:
|
|
jpayne@69
|
18950 if (kw_args > 0) {
|
|
jpayne@69
|
18951 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_keep_original);
|
|
jpayne@69
|
18952 if (value) { values[11] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18953 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18954 }
|
|
jpayne@69
|
18955 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18956 case 12:
|
|
jpayne@69
|
18957 if (kw_args > 0) {
|
|
jpayne@69
|
18958 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_csi);
|
|
jpayne@69
|
18959 if (value) { values[12] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
18960 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18961 }
|
|
jpayne@69
|
18962 }
|
|
jpayne@69
|
18963 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
18964 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
18965 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "tabix_index") < 0)) __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
18966 }
|
|
jpayne@69
|
18967 } else {
|
|
jpayne@69
|
18968 switch (__pyx_nargs) {
|
|
jpayne@69
|
18969 case 13: values[12] = __Pyx_Arg_FASTCALL(__pyx_args, 12);
|
|
jpayne@69
|
18970 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18971 case 12: values[11] = __Pyx_Arg_FASTCALL(__pyx_args, 11);
|
|
jpayne@69
|
18972 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18973 case 11: values[10] = __Pyx_Arg_FASTCALL(__pyx_args, 10);
|
|
jpayne@69
|
18974 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18975 case 10: values[9] = __Pyx_Arg_FASTCALL(__pyx_args, 9);
|
|
jpayne@69
|
18976 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18977 case 9: values[8] = __Pyx_Arg_FASTCALL(__pyx_args, 8);
|
|
jpayne@69
|
18978 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18979 case 8: values[7] = __Pyx_Arg_FASTCALL(__pyx_args, 7);
|
|
jpayne@69
|
18980 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18981 case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6);
|
|
jpayne@69
|
18982 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18983 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
18984 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18985 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
18986 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18987 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
18988 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18989 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
18990 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18991 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
18992 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
18993 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
18994 break;
|
|
jpayne@69
|
18995 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
18996 }
|
|
jpayne@69
|
18997 }
|
|
jpayne@69
|
18998 __pyx_v_filename = values[0];
|
|
jpayne@69
|
18999 __pyx_v_force = values[1];
|
|
jpayne@69
|
19000 __pyx_v_seq_col = values[2];
|
|
jpayne@69
|
19001 __pyx_v_start_col = values[3];
|
|
jpayne@69
|
19002 __pyx_v_end_col = values[4];
|
|
jpayne@69
|
19003 __pyx_v_preset = values[5];
|
|
jpayne@69
|
19004 __pyx_v_meta_char = values[6];
|
|
jpayne@69
|
19005 if (values[7]) {
|
|
jpayne@69
|
19006 __pyx_v_line_skip = __Pyx_PyInt_As_int(values[7]); if (unlikely((__pyx_v_line_skip == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 880, __pyx_L3_error)
|
|
jpayne@69
|
19007 } else {
|
|
jpayne@69
|
19008 __pyx_v_line_skip = ((int)((int)0));
|
|
jpayne@69
|
19009 }
|
|
jpayne@69
|
19010 __pyx_v_zerobased = values[8];
|
|
jpayne@69
|
19011 if (values[9]) {
|
|
jpayne@69
|
19012 __pyx_v_min_shift = __Pyx_PyInt_As_int(values[9]); if (unlikely((__pyx_v_min_shift == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 882, __pyx_L3_error)
|
|
jpayne@69
|
19013 } else {
|
|
jpayne@69
|
19014 __pyx_v_min_shift = ((int)((int)-1));
|
|
jpayne@69
|
19015 }
|
|
jpayne@69
|
19016 __pyx_v_index = values[10];
|
|
jpayne@69
|
19017 __pyx_v_keep_original = values[11];
|
|
jpayne@69
|
19018 __pyx_v_csi = values[12];
|
|
jpayne@69
|
19019 }
|
|
jpayne@69
|
19020 goto __pyx_L6_skip;
|
|
jpayne@69
|
19021 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
19022 __Pyx_RaiseArgtupleInvalid("tabix_index", 0, 1, 13, __pyx_nargs); __PYX_ERR(0, 873, __pyx_L3_error)
|
|
jpayne@69
|
19023 __pyx_L6_skip:;
|
|
jpayne@69
|
19024 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
19025 __pyx_L3_error:;
|
|
jpayne@69
|
19026 {
|
|
jpayne@69
|
19027 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
19028 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
19029 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
19030 }
|
|
jpayne@69
|
19031 }
|
|
jpayne@69
|
19032 __Pyx_AddTraceback("pysam.libctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
19033 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
19034 return NULL;
|
|
jpayne@69
|
19035 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
19036 __pyx_r = __pyx_pf_5pysam_9libctabix_2tabix_index(__pyx_self, __pyx_v_filename, __pyx_v_force, __pyx_v_seq_col, __pyx_v_start_col, __pyx_v_end_col, __pyx_v_preset, __pyx_v_meta_char, __pyx_v_line_skip, __pyx_v_zerobased, __pyx_v_min_shift, __pyx_v_index, __pyx_v_keep_original, __pyx_v_csi);
|
|
jpayne@69
|
19037
|
|
jpayne@69
|
19038 /* "pysam/libctabix.pyx":873
|
|
jpayne@69
|
19039 *
|
|
jpayne@69
|
19040 *
|
|
jpayne@69
|
19041 * def tabix_index(filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19042 * force=False,
|
|
jpayne@69
|
19043 * seq_col=None,
|
|
jpayne@69
|
19044 */
|
|
jpayne@69
|
19045
|
|
jpayne@69
|
19046 /* function exit code */
|
|
jpayne@69
|
19047 {
|
|
jpayne@69
|
19048 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
19049 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
19050 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
19051 }
|
|
jpayne@69
|
19052 }
|
|
jpayne@69
|
19053 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
19054 return __pyx_r;
|
|
jpayne@69
|
19055 }
|
|
jpayne@69
|
19056
|
|
jpayne@69
|
19057 static PyObject *__pyx_pf_5pysam_9libctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, int __pyx_v_line_skip, PyObject *__pyx_v_zerobased, int __pyx_v_min_shift, PyObject *__pyx_v_index, PyObject *__pyx_v_keep_original, PyObject *__pyx_v_csi) {
|
|
jpayne@69
|
19058 PyObject *__pyx_v_fn = NULL;
|
|
jpayne@69
|
19059 char *__pyx_v_cfn;
|
|
jpayne@69
|
19060 htsFile *__pyx_v_fp;
|
|
jpayne@69
|
19061 htsFormat __pyx_v_fmt;
|
|
jpayne@69
|
19062 PyObject *__pyx_v_preset2conf = NULL;
|
|
jpayne@69
|
19063 PyObject *__pyx_v_conf_data = NULL;
|
|
jpayne@69
|
19064 tbx_conf_t __pyx_v_conf;
|
|
jpayne@69
|
19065 PyObject *__pyx_v_suffix = NULL;
|
|
jpayne@69
|
19066 PyObject *__pyx_v_fn_index = NULL;
|
|
jpayne@69
|
19067 char *__pyx_v_fnidx;
|
|
jpayne@69
|
19068 int __pyx_v_retval;
|
|
jpayne@69
|
19069 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
19070 __Pyx_TraceDeclarations
|
|
jpayne@69
|
19071 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
19072 int __pyx_t_1;
|
|
jpayne@69
|
19073 int __pyx_t_2;
|
|
jpayne@69
|
19074 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
19075 char *__pyx_t_4;
|
|
jpayne@69
|
19076 Py_ssize_t __pyx_t_5;
|
|
jpayne@69
|
19077 Py_UCS4 __pyx_t_6;
|
|
jpayne@69
|
19078 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
19079 PyObject *__pyx_t_8 = NULL;
|
|
jpayne@69
|
19080 PyObject *__pyx_t_9 = NULL;
|
|
jpayne@69
|
19081 unsigned int __pyx_t_10;
|
|
jpayne@69
|
19082 PyObject *__pyx_t_11 = NULL;
|
|
jpayne@69
|
19083 PyObject *__pyx_t_12 = NULL;
|
|
jpayne@69
|
19084 PyObject *__pyx_t_13 = NULL;
|
|
jpayne@69
|
19085 int __pyx_t_14;
|
|
jpayne@69
|
19086 PyObject *__pyx_t_15 = NULL;
|
|
jpayne@69
|
19087 PyObject *__pyx_t_16 = NULL;
|
|
jpayne@69
|
19088 long __pyx_t_17;
|
|
jpayne@69
|
19089 PyObject *__pyx_t_18 = NULL;
|
|
jpayne@69
|
19090 PyObject *(*__pyx_t_19)(PyObject *);
|
|
jpayne@69
|
19091 int32_t __pyx_t_20;
|
|
jpayne@69
|
19092 int32_t __pyx_t_21;
|
|
jpayne@69
|
19093 int32_t __pyx_t_22;
|
|
jpayne@69
|
19094 int32_t __pyx_t_23;
|
|
jpayne@69
|
19095 int32_t __pyx_t_24;
|
|
jpayne@69
|
19096 int32_t __pyx_t_25;
|
|
jpayne@69
|
19097 int __pyx_t_26;
|
|
jpayne@69
|
19098 int __pyx_lineno = 0;
|
|
jpayne@69
|
19099 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
19100 int __pyx_clineno = 0;
|
|
jpayne@69
|
19101 __Pyx_TraceFrameInit(__pyx_codeobj__40)
|
|
jpayne@69
|
19102 __Pyx_RefNannySetupContext("tabix_index", 0);
|
|
jpayne@69
|
19103 __Pyx_TraceCall("tabix_index", __pyx_f[0], 873, 0, __PYX_ERR(0, 873, __pyx_L1_error));
|
|
jpayne@69
|
19104 __Pyx_INCREF(__pyx_v_filename);
|
|
jpayne@69
|
19105 __Pyx_INCREF(__pyx_v_end_col);
|
|
jpayne@69
|
19106 __Pyx_INCREF(__pyx_v_preset);
|
|
jpayne@69
|
19107 __Pyx_INCREF(__pyx_v_index);
|
|
jpayne@69
|
19108 __Pyx_INCREF(__pyx_v_csi);
|
|
jpayne@69
|
19109
|
|
jpayne@69
|
19110 /* "pysam/libctabix.pyx":928
|
|
jpayne@69
|
19111 * '''
|
|
jpayne@69
|
19112 *
|
|
jpayne@69
|
19113 * if preset is None and \ # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19114 * (seq_col is None or start_col is None or end_col is None):
|
|
jpayne@69
|
19115 * raise ValueError(
|
|
jpayne@69
|
19116 */
|
|
jpayne@69
|
19117 __pyx_t_2 = (__pyx_v_preset == Py_None);
|
|
jpayne@69
|
19118 if (__pyx_t_2) {
|
|
jpayne@69
|
19119 } else {
|
|
jpayne@69
|
19120 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
19121 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
19122 }
|
|
jpayne@69
|
19123
|
|
jpayne@69
|
19124 /* "pysam/libctabix.pyx":929
|
|
jpayne@69
|
19125 *
|
|
jpayne@69
|
19126 * if preset is None and \
|
|
jpayne@69
|
19127 * (seq_col is None or start_col is None or end_col is None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19128 * raise ValueError(
|
|
jpayne@69
|
19129 * "neither preset nor seq_col,start_col and end_col given")
|
|
jpayne@69
|
19130 */
|
|
jpayne@69
|
19131 __pyx_t_2 = (__pyx_v_seq_col == Py_None);
|
|
jpayne@69
|
19132 if (!__pyx_t_2) {
|
|
jpayne@69
|
19133 } else {
|
|
jpayne@69
|
19134 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
19135 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
19136 }
|
|
jpayne@69
|
19137 __pyx_t_2 = (__pyx_v_start_col == Py_None);
|
|
jpayne@69
|
19138 if (!__pyx_t_2) {
|
|
jpayne@69
|
19139 } else {
|
|
jpayne@69
|
19140 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
19141 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
19142 }
|
|
jpayne@69
|
19143 __pyx_t_2 = (__pyx_v_end_col == Py_None);
|
|
jpayne@69
|
19144 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
19145 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
19146
|
|
jpayne@69
|
19147 /* "pysam/libctabix.pyx":928
|
|
jpayne@69
|
19148 * '''
|
|
jpayne@69
|
19149 *
|
|
jpayne@69
|
19150 * if preset is None and \ # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19151 * (seq_col is None or start_col is None or end_col is None):
|
|
jpayne@69
|
19152 * raise ValueError(
|
|
jpayne@69
|
19153 */
|
|
jpayne@69
|
19154 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
19155
|
|
jpayne@69
|
19156 /* "pysam/libctabix.pyx":930
|
|
jpayne@69
|
19157 * if preset is None and \
|
|
jpayne@69
|
19158 * (seq_col is None or start_col is None or end_col is None):
|
|
jpayne@69
|
19159 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19160 * "neither preset nor seq_col,start_col and end_col given")
|
|
jpayne@69
|
19161 *
|
|
jpayne@69
|
19162 */
|
|
jpayne@69
|
19163 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__41, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 930, __pyx_L1_error)
|
|
jpayne@69
|
19164 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19165 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
19166 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19167 __PYX_ERR(0, 930, __pyx_L1_error)
|
|
jpayne@69
|
19168
|
|
jpayne@69
|
19169 /* "pysam/libctabix.pyx":928
|
|
jpayne@69
|
19170 * '''
|
|
jpayne@69
|
19171 *
|
|
jpayne@69
|
19172 * if preset is None and \ # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19173 * (seq_col is None or start_col is None or end_col is None):
|
|
jpayne@69
|
19174 * raise ValueError(
|
|
jpayne@69
|
19175 */
|
|
jpayne@69
|
19176 }
|
|
jpayne@69
|
19177
|
|
jpayne@69
|
19178 /* "pysam/libctabix.pyx":933
|
|
jpayne@69
|
19179 * "neither preset nor seq_col,start_col and end_col given")
|
|
jpayne@69
|
19180 *
|
|
jpayne@69
|
19181 * fn = encode_filename(filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19182 * cdef char *cfn = fn
|
|
jpayne@69
|
19183 *
|
|
jpayne@69
|
19184 */
|
|
jpayne@69
|
19185 __pyx_t_3 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 933, __pyx_L1_error)
|
|
jpayne@69
|
19186 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19187 __pyx_v_fn = ((PyObject*)__pyx_t_3);
|
|
jpayne@69
|
19188 __pyx_t_3 = 0;
|
|
jpayne@69
|
19189
|
|
jpayne@69
|
19190 /* "pysam/libctabix.pyx":934
|
|
jpayne@69
|
19191 *
|
|
jpayne@69
|
19192 * fn = encode_filename(filename)
|
|
jpayne@69
|
19193 * cdef char *cfn = fn # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19194 *
|
|
jpayne@69
|
19195 * cdef htsFile *fp = hts_open(cfn, "r")
|
|
jpayne@69
|
19196 */
|
|
jpayne@69
|
19197 if (unlikely(__pyx_v_fn == Py_None)) {
|
|
jpayne@69
|
19198 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
19199 __PYX_ERR(0, 934, __pyx_L1_error)
|
|
jpayne@69
|
19200 }
|
|
jpayne@69
|
19201 __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 934, __pyx_L1_error)
|
|
jpayne@69
|
19202 __pyx_v_cfn = __pyx_t_4;
|
|
jpayne@69
|
19203
|
|
jpayne@69
|
19204 /* "pysam/libctabix.pyx":936
|
|
jpayne@69
|
19205 * cdef char *cfn = fn
|
|
jpayne@69
|
19206 *
|
|
jpayne@69
|
19207 * cdef htsFile *fp = hts_open(cfn, "r") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19208 * if fp == NULL:
|
|
jpayne@69
|
19209 * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno))))
|
|
jpayne@69
|
19210 */
|
|
jpayne@69
|
19211 __pyx_v_fp = hts_open(__pyx_v_cfn, ((char const *)"r"));
|
|
jpayne@69
|
19212
|
|
jpayne@69
|
19213 /* "pysam/libctabix.pyx":937
|
|
jpayne@69
|
19214 *
|
|
jpayne@69
|
19215 * cdef htsFile *fp = hts_open(cfn, "r")
|
|
jpayne@69
|
19216 * if fp == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19217 * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno))))
|
|
jpayne@69
|
19218 *
|
|
jpayne@69
|
19219 */
|
|
jpayne@69
|
19220 __pyx_t_1 = (__pyx_v_fp == NULL);
|
|
jpayne@69
|
19221 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
19222
|
|
jpayne@69
|
19223 /* "pysam/libctabix.pyx":938
|
|
jpayne@69
|
19224 * cdef htsFile *fp = hts_open(cfn, "r")
|
|
jpayne@69
|
19225 * if fp == NULL:
|
|
jpayne@69
|
19226 * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19227 *
|
|
jpayne@69
|
19228 * cdef htsFormat fmt = hts_get_format(fp)[0]
|
|
jpayne@69
|
19229 */
|
|
jpayne@69
|
19230 __pyx_t_3 = PyTuple_New(4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 938, __pyx_L1_error)
|
|
jpayne@69
|
19231 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19232 __pyx_t_5 = 0;
|
|
jpayne@69
|
19233 __pyx_t_6 = 127;
|
|
jpayne@69
|
19234 __Pyx_INCREF(__pyx_kp_u_Could_not_open_file);
|
|
jpayne@69
|
19235 __pyx_t_5 += 21;
|
|
jpayne@69
|
19236 __Pyx_GIVEREF(__pyx_kp_u_Could_not_open_file);
|
|
jpayne@69
|
19237 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_Could_not_open_file);
|
|
jpayne@69
|
19238 __pyx_t_7 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_filename), __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error)
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jpayne@69
|
19239 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19240 __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_6;
|
|
jpayne@69
|
19241 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7);
|
|
jpayne@69
|
19242 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
19243 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_7);
|
|
jpayne@69
|
19244 __pyx_t_7 = 0;
|
|
jpayne@69
|
19245 __Pyx_INCREF(__pyx_kp_u__42);
|
|
jpayne@69
|
19246 __pyx_t_5 += 3;
|
|
jpayne@69
|
19247 __Pyx_GIVEREF(__pyx_kp_u__42);
|
|
jpayne@69
|
19248 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u__42);
|
|
jpayne@69
|
19249 __pyx_t_7 = __Pyx_PyBytes_FromString(strerror(errno)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error)
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jpayne@69
|
19250 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19251 __pyx_t_8 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_7, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 938, __pyx_L1_error)
|
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jpayne@69
|
19252 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19253 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
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jpayne@69
|
19254 __pyx_t_7 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_8), __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error)
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jpayne@69
|
19255 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19256 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19257 __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_6;
|
|
jpayne@69
|
19258 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7);
|
|
jpayne@69
|
19259 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
19260 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_7);
|
|
jpayne@69
|
19261 __pyx_t_7 = 0;
|
|
jpayne@69
|
19262 __pyx_t_7 = __Pyx_PyUnicode_Join(__pyx_t_3, 4, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error)
|
|
jpayne@69
|
19263 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19264 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19265 __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 938, __pyx_L1_error)
|
|
jpayne@69
|
19266 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19267 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19268 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
19269 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19270 __PYX_ERR(0, 938, __pyx_L1_error)
|
|
jpayne@69
|
19271
|
|
jpayne@69
|
19272 /* "pysam/libctabix.pyx":937
|
|
jpayne@69
|
19273 *
|
|
jpayne@69
|
19274 * cdef htsFile *fp = hts_open(cfn, "r")
|
|
jpayne@69
|
19275 * if fp == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19276 * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno))))
|
|
jpayne@69
|
19277 *
|
|
jpayne@69
|
19278 */
|
|
jpayne@69
|
19279 }
|
|
jpayne@69
|
19280
|
|
jpayne@69
|
19281 /* "pysam/libctabix.pyx":940
|
|
jpayne@69
|
19282 * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno))))
|
|
jpayne@69
|
19283 *
|
|
jpayne@69
|
19284 * cdef htsFormat fmt = hts_get_format(fp)[0] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19285 * hts_close(fp)
|
|
jpayne@69
|
19286 *
|
|
jpayne@69
|
19287 */
|
|
jpayne@69
|
19288 __pyx_v_fmt = (hts_get_format(__pyx_v_fp)[0]);
|
|
jpayne@69
|
19289
|
|
jpayne@69
|
19290 /* "pysam/libctabix.pyx":941
|
|
jpayne@69
|
19291 *
|
|
jpayne@69
|
19292 * cdef htsFormat fmt = hts_get_format(fp)[0]
|
|
jpayne@69
|
19293 * hts_close(fp) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19294 *
|
|
jpayne@69
|
19295 * if fmt.compression == no_compression:
|
|
jpayne@69
|
19296 */
|
|
jpayne@69
|
19297 (void)(hts_close(__pyx_v_fp));
|
|
jpayne@69
|
19298
|
|
jpayne@69
|
19299 /* "pysam/libctabix.pyx":943
|
|
jpayne@69
|
19300 * hts_close(fp)
|
|
jpayne@69
|
19301 *
|
|
jpayne@69
|
19302 * if fmt.compression == no_compression: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19303 * tabix_compress(filename, filename + ".gz", force=force)
|
|
jpayne@69
|
19304 * if not keep_original:
|
|
jpayne@69
|
19305 */
|
|
jpayne@69
|
19306 __pyx_t_1 = (__pyx_v_fmt.compression == no_compression);
|
|
jpayne@69
|
19307 if (__pyx_t_1) {
|
|
jpayne@69
|
19308
|
|
jpayne@69
|
19309 /* "pysam/libctabix.pyx":944
|
|
jpayne@69
|
19310 *
|
|
jpayne@69
|
19311 * if fmt.compression == no_compression:
|
|
jpayne@69
|
19312 * tabix_compress(filename, filename + ".gz", force=force) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19313 * if not keep_original:
|
|
jpayne@69
|
19314 * os.unlink(filename)
|
|
jpayne@69
|
19315 */
|
|
jpayne@69
|
19316 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_tabix_compress); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 944, __pyx_L1_error)
|
|
jpayne@69
|
19317 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19318 __pyx_t_7 = PyNumber_Add(__pyx_v_filename, __pyx_kp_u_gz); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 944, __pyx_L1_error)
|
|
jpayne@69
|
19319 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19320 __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 944, __pyx_L1_error)
|
|
jpayne@69
|
19321 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19322 __Pyx_INCREF(__pyx_v_filename);
|
|
jpayne@69
|
19323 __Pyx_GIVEREF(__pyx_v_filename);
|
|
jpayne@69
|
19324 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_filename)) __PYX_ERR(0, 944, __pyx_L1_error);
|
|
jpayne@69
|
19325 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
19326 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7)) __PYX_ERR(0, 944, __pyx_L1_error);
|
|
jpayne@69
|
19327 __pyx_t_7 = 0;
|
|
jpayne@69
|
19328 __pyx_t_7 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 944, __pyx_L1_error)
|
|
jpayne@69
|
19329 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19330 if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_force, __pyx_v_force) < 0) __PYX_ERR(0, 944, __pyx_L1_error)
|
|
jpayne@69
|
19331 __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_8, __pyx_t_7); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 944, __pyx_L1_error)
|
|
jpayne@69
|
19332 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19333 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19334 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19335 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19336 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
19337
|
|
jpayne@69
|
19338 /* "pysam/libctabix.pyx":945
|
|
jpayne@69
|
19339 * if fmt.compression == no_compression:
|
|
jpayne@69
|
19340 * tabix_compress(filename, filename + ".gz", force=force)
|
|
jpayne@69
|
19341 * if not keep_original: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19342 * os.unlink(filename)
|
|
jpayne@69
|
19343 * filename += ".gz"
|
|
jpayne@69
|
19344 */
|
|
jpayne@69
|
19345 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_keep_original); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 945, __pyx_L1_error)
|
|
jpayne@69
|
19346 __pyx_t_2 = (!__pyx_t_1);
|
|
jpayne@69
|
19347 if (__pyx_t_2) {
|
|
jpayne@69
|
19348
|
|
jpayne@69
|
19349 /* "pysam/libctabix.pyx":946
|
|
jpayne@69
|
19350 * tabix_compress(filename, filename + ".gz", force=force)
|
|
jpayne@69
|
19351 * if not keep_original:
|
|
jpayne@69
|
19352 * os.unlink(filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19353 * filename += ".gz"
|
|
jpayne@69
|
19354 * fn = encode_filename(filename)
|
|
jpayne@69
|
19355 */
|
|
jpayne@69
|
19356 __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_os); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 946, __pyx_L1_error)
|
|
jpayne@69
|
19357 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19358 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_unlink); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 946, __pyx_L1_error)
|
|
jpayne@69
|
19359 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19360 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19361 __pyx_t_7 = NULL;
|
|
jpayne@69
|
19362 __pyx_t_10 = 0;
|
|
jpayne@69
|
19363 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
19364 if (unlikely(PyMethod_Check(__pyx_t_8))) {
|
|
jpayne@69
|
19365 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_8);
|
|
jpayne@69
|
19366 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
19367 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8);
|
|
jpayne@69
|
19368 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
19369 __Pyx_INCREF(function);
|
|
jpayne@69
|
19370 __Pyx_DECREF_SET(__pyx_t_8, function);
|
|
jpayne@69
|
19371 __pyx_t_10 = 1;
|
|
jpayne@69
|
19372 }
|
|
jpayne@69
|
19373 }
|
|
jpayne@69
|
19374 #endif
|
|
jpayne@69
|
19375 {
|
|
jpayne@69
|
19376 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_v_filename};
|
|
jpayne@69
|
19377 __pyx_t_9 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
|
|
jpayne@69
|
19378 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19379 if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 946, __pyx_L1_error)
|
|
jpayne@69
|
19380 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19381 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19382 }
|
|
jpayne@69
|
19383 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
19384
|
|
jpayne@69
|
19385 /* "pysam/libctabix.pyx":945
|
|
jpayne@69
|
19386 * if fmt.compression == no_compression:
|
|
jpayne@69
|
19387 * tabix_compress(filename, filename + ".gz", force=force)
|
|
jpayne@69
|
19388 * if not keep_original: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19389 * os.unlink(filename)
|
|
jpayne@69
|
19390 * filename += ".gz"
|
|
jpayne@69
|
19391 */
|
|
jpayne@69
|
19392 }
|
|
jpayne@69
|
19393
|
|
jpayne@69
|
19394 /* "pysam/libctabix.pyx":947
|
|
jpayne@69
|
19395 * if not keep_original:
|
|
jpayne@69
|
19396 * os.unlink(filename)
|
|
jpayne@69
|
19397 * filename += ".gz" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19398 * fn = encode_filename(filename)
|
|
jpayne@69
|
19399 * cfn = fn
|
|
jpayne@69
|
19400 */
|
|
jpayne@69
|
19401 __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_v_filename, __pyx_kp_u_gz); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 947, __pyx_L1_error)
|
|
jpayne@69
|
19402 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19403 __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_9);
|
|
jpayne@69
|
19404 __pyx_t_9 = 0;
|
|
jpayne@69
|
19405
|
|
jpayne@69
|
19406 /* "pysam/libctabix.pyx":948
|
|
jpayne@69
|
19407 * os.unlink(filename)
|
|
jpayne@69
|
19408 * filename += ".gz"
|
|
jpayne@69
|
19409 * fn = encode_filename(filename) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19410 * cfn = fn
|
|
jpayne@69
|
19411 *
|
|
jpayne@69
|
19412 */
|
|
jpayne@69
|
19413 __pyx_t_9 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 948, __pyx_L1_error)
|
|
jpayne@69
|
19414 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19415 __Pyx_DECREF_SET(__pyx_v_fn, ((PyObject*)__pyx_t_9));
|
|
jpayne@69
|
19416 __pyx_t_9 = 0;
|
|
jpayne@69
|
19417
|
|
jpayne@69
|
19418 /* "pysam/libctabix.pyx":949
|
|
jpayne@69
|
19419 * filename += ".gz"
|
|
jpayne@69
|
19420 * fn = encode_filename(filename)
|
|
jpayne@69
|
19421 * cfn = fn # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19422 *
|
|
jpayne@69
|
19423 * # columns (1-based):
|
|
jpayne@69
|
19424 */
|
|
jpayne@69
|
19425 if (unlikely(__pyx_v_fn == Py_None)) {
|
|
jpayne@69
|
19426 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
19427 __PYX_ERR(0, 949, __pyx_L1_error)
|
|
jpayne@69
|
19428 }
|
|
jpayne@69
|
19429 __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 949, __pyx_L1_error)
|
|
jpayne@69
|
19430 __pyx_v_cfn = __pyx_t_4;
|
|
jpayne@69
|
19431
|
|
jpayne@69
|
19432 /* "pysam/libctabix.pyx":943
|
|
jpayne@69
|
19433 * hts_close(fp)
|
|
jpayne@69
|
19434 *
|
|
jpayne@69
|
19435 * if fmt.compression == no_compression: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19436 * tabix_compress(filename, filename + ".gz", force=force)
|
|
jpayne@69
|
19437 * if not keep_original:
|
|
jpayne@69
|
19438 */
|
|
jpayne@69
|
19439 }
|
|
jpayne@69
|
19440
|
|
jpayne@69
|
19441 /* "pysam/libctabix.pyx":956
|
|
jpayne@69
|
19442 * # 0 is a missing column
|
|
jpayne@69
|
19443 * preset2conf = {
|
|
jpayne@69
|
19444 * 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0), # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19445 * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0),
|
|
jpayne@69
|
19446 * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0),
|
|
jpayne@69
|
19447 */
|
|
jpayne@69
|
19448 __pyx_t_9 = __Pyx_PyDict_NewPresized(5); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19449 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19450 __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_GENERIC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19451 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19452 __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19453 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19454 __Pyx_GIVEREF(__pyx_t_8);
|
|
jpayne@69
|
19455 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8)) __PYX_ERR(0, 956, __pyx_L1_error);
|
|
jpayne@69
|
19456 __Pyx_INCREF(__pyx_int_1);
|
|
jpayne@69
|
19457 __Pyx_GIVEREF(__pyx_int_1);
|
|
jpayne@69
|
19458 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_1)) __PYX_ERR(0, 956, __pyx_L1_error);
|
|
jpayne@69
|
19459 __Pyx_INCREF(__pyx_int_4);
|
|
jpayne@69
|
19460 __Pyx_GIVEREF(__pyx_int_4);
|
|
jpayne@69
|
19461 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_4)) __PYX_ERR(0, 956, __pyx_L1_error);
|
|
jpayne@69
|
19462 __Pyx_INCREF(__pyx_int_5);
|
|
jpayne@69
|
19463 __Pyx_GIVEREF(__pyx_int_5);
|
|
jpayne@69
|
19464 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_5)) __PYX_ERR(0, 956, __pyx_L1_error);
|
|
jpayne@69
|
19465 __Pyx_INCREF(__pyx_int_35);
|
|
jpayne@69
|
19466 __Pyx_GIVEREF(__pyx_int_35);
|
|
jpayne@69
|
19467 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_35)) __PYX_ERR(0, 956, __pyx_L1_error);
|
|
jpayne@69
|
19468 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19469 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19470 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_0)) __PYX_ERR(0, 956, __pyx_L1_error);
|
|
jpayne@69
|
19471 __pyx_t_8 = 0;
|
|
jpayne@69
|
19472 if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_gff, __pyx_t_7) < 0) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19473 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19474
|
|
jpayne@69
|
19475 /* "pysam/libctabix.pyx":957
|
|
jpayne@69
|
19476 * preset2conf = {
|
|
jpayne@69
|
19477 * 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0),
|
|
jpayne@69
|
19478 * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0), # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19479 * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0),
|
|
jpayne@69
|
19480 * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0),
|
|
jpayne@69
|
19481 */
|
|
jpayne@69
|
19482 __pyx_t_7 = __Pyx_PyInt_From_int32_t(TBX_UCSC); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 957, __pyx_L1_error)
|
|
jpayne@69
|
19483 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19484 __pyx_t_8 = PyTuple_New(6); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 957, __pyx_L1_error)
|
|
jpayne@69
|
19485 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19486 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
19487 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_7)) __PYX_ERR(0, 957, __pyx_L1_error);
|
|
jpayne@69
|
19488 __Pyx_INCREF(__pyx_int_1);
|
|
jpayne@69
|
19489 __Pyx_GIVEREF(__pyx_int_1);
|
|
jpayne@69
|
19490 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_int_1)) __PYX_ERR(0, 957, __pyx_L1_error);
|
|
jpayne@69
|
19491 __Pyx_INCREF(__pyx_int_2);
|
|
jpayne@69
|
19492 __Pyx_GIVEREF(__pyx_int_2);
|
|
jpayne@69
|
19493 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_int_2)) __PYX_ERR(0, 957, __pyx_L1_error);
|
|
jpayne@69
|
19494 __Pyx_INCREF(__pyx_int_3);
|
|
jpayne@69
|
19495 __Pyx_GIVEREF(__pyx_int_3);
|
|
jpayne@69
|
19496 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 3, __pyx_int_3)) __PYX_ERR(0, 957, __pyx_L1_error);
|
|
jpayne@69
|
19497 __Pyx_INCREF(__pyx_int_35);
|
|
jpayne@69
|
19498 __Pyx_GIVEREF(__pyx_int_35);
|
|
jpayne@69
|
19499 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 4, __pyx_int_35)) __PYX_ERR(0, 957, __pyx_L1_error);
|
|
jpayne@69
|
19500 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19501 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19502 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 5, __pyx_int_0)) __PYX_ERR(0, 957, __pyx_L1_error);
|
|
jpayne@69
|
19503 __pyx_t_7 = 0;
|
|
jpayne@69
|
19504 if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_bed, __pyx_t_8) < 0) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19505 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19506
|
|
jpayne@69
|
19507 /* "pysam/libctabix.pyx":958
|
|
jpayne@69
|
19508 * 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0),
|
|
jpayne@69
|
19509 * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0),
|
|
jpayne@69
|
19510 * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19511 * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0),
|
|
jpayne@69
|
19512 * 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0),
|
|
jpayne@69
|
19513 */
|
|
jpayne@69
|
19514 __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 958, __pyx_L1_error)
|
|
jpayne@69
|
19515 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19516 __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 958, __pyx_L1_error)
|
|
jpayne@69
|
19517 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19518 __Pyx_GIVEREF(__pyx_t_8);
|
|
jpayne@69
|
19519 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8)) __PYX_ERR(0, 958, __pyx_L1_error);
|
|
jpayne@69
|
19520 __Pyx_INCREF(__pyx_int_15);
|
|
jpayne@69
|
19521 __Pyx_GIVEREF(__pyx_int_15);
|
|
jpayne@69
|
19522 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_15)) __PYX_ERR(0, 958, __pyx_L1_error);
|
|
jpayne@69
|
19523 __Pyx_INCREF(__pyx_int_17);
|
|
jpayne@69
|
19524 __Pyx_GIVEREF(__pyx_int_17);
|
|
jpayne@69
|
19525 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_17)) __PYX_ERR(0, 958, __pyx_L1_error);
|
|
jpayne@69
|
19526 __Pyx_INCREF(__pyx_int_18);
|
|
jpayne@69
|
19527 __Pyx_GIVEREF(__pyx_int_18);
|
|
jpayne@69
|
19528 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_18)) __PYX_ERR(0, 958, __pyx_L1_error);
|
|
jpayne@69
|
19529 __Pyx_INCREF(__pyx_int_35);
|
|
jpayne@69
|
19530 __Pyx_GIVEREF(__pyx_int_35);
|
|
jpayne@69
|
19531 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_35)) __PYX_ERR(0, 958, __pyx_L1_error);
|
|
jpayne@69
|
19532 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19533 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19534 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_0)) __PYX_ERR(0, 958, __pyx_L1_error);
|
|
jpayne@69
|
19535 __pyx_t_8 = 0;
|
|
jpayne@69
|
19536 if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_psltbl, __pyx_t_7) < 0) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19537 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19538
|
|
jpayne@69
|
19539 /* "pysam/libctabix.pyx":959
|
|
jpayne@69
|
19540 * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0),
|
|
jpayne@69
|
19541 * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0),
|
|
jpayne@69
|
19542 * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0), # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19543 * 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0),
|
|
jpayne@69
|
19544 * }
|
|
jpayne@69
|
19545 */
|
|
jpayne@69
|
19546 __pyx_t_7 = __Pyx_PyInt_From_int32_t(TBX_SAM); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 959, __pyx_L1_error)
|
|
jpayne@69
|
19547 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19548 __pyx_t_8 = PyTuple_New(6); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 959, __pyx_L1_error)
|
|
jpayne@69
|
19549 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19550 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
19551 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_7)) __PYX_ERR(0, 959, __pyx_L1_error);
|
|
jpayne@69
|
19552 __Pyx_INCREF(__pyx_int_3);
|
|
jpayne@69
|
19553 __Pyx_GIVEREF(__pyx_int_3);
|
|
jpayne@69
|
19554 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_int_3)) __PYX_ERR(0, 959, __pyx_L1_error);
|
|
jpayne@69
|
19555 __Pyx_INCREF(__pyx_int_4);
|
|
jpayne@69
|
19556 __Pyx_GIVEREF(__pyx_int_4);
|
|
jpayne@69
|
19557 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_int_4)) __PYX_ERR(0, 959, __pyx_L1_error);
|
|
jpayne@69
|
19558 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19559 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19560 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 3, __pyx_int_0)) __PYX_ERR(0, 959, __pyx_L1_error);
|
|
jpayne@69
|
19561 __Pyx_INCREF(__pyx_int_64);
|
|
jpayne@69
|
19562 __Pyx_GIVEREF(__pyx_int_64);
|
|
jpayne@69
|
19563 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 4, __pyx_int_64)) __PYX_ERR(0, 959, __pyx_L1_error);
|
|
jpayne@69
|
19564 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19565 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19566 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 5, __pyx_int_0)) __PYX_ERR(0, 959, __pyx_L1_error);
|
|
jpayne@69
|
19567 __pyx_t_7 = 0;
|
|
jpayne@69
|
19568 if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_sam, __pyx_t_8) < 0) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19569 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19570
|
|
jpayne@69
|
19571 /* "pysam/libctabix.pyx":960
|
|
jpayne@69
|
19572 * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0),
|
|
jpayne@69
|
19573 * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0),
|
|
jpayne@69
|
19574 * 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0), # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19575 * }
|
|
jpayne@69
|
19576 *
|
|
jpayne@69
|
19577 */
|
|
jpayne@69
|
19578 __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_VCF); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 960, __pyx_L1_error)
|
|
jpayne@69
|
19579 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19580 __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 960, __pyx_L1_error)
|
|
jpayne@69
|
19581 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19582 __Pyx_GIVEREF(__pyx_t_8);
|
|
jpayne@69
|
19583 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8)) __PYX_ERR(0, 960, __pyx_L1_error);
|
|
jpayne@69
|
19584 __Pyx_INCREF(__pyx_int_1);
|
|
jpayne@69
|
19585 __Pyx_GIVEREF(__pyx_int_1);
|
|
jpayne@69
|
19586 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_1)) __PYX_ERR(0, 960, __pyx_L1_error);
|
|
jpayne@69
|
19587 __Pyx_INCREF(__pyx_int_2);
|
|
jpayne@69
|
19588 __Pyx_GIVEREF(__pyx_int_2);
|
|
jpayne@69
|
19589 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_2)) __PYX_ERR(0, 960, __pyx_L1_error);
|
|
jpayne@69
|
19590 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19591 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19592 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_0)) __PYX_ERR(0, 960, __pyx_L1_error);
|
|
jpayne@69
|
19593 __Pyx_INCREF(__pyx_int_35);
|
|
jpayne@69
|
19594 __Pyx_GIVEREF(__pyx_int_35);
|
|
jpayne@69
|
19595 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_35)) __PYX_ERR(0, 960, __pyx_L1_error);
|
|
jpayne@69
|
19596 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19597 __Pyx_GIVEREF(__pyx_int_0);
|
|
jpayne@69
|
19598 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_0)) __PYX_ERR(0, 960, __pyx_L1_error);
|
|
jpayne@69
|
19599 __pyx_t_8 = 0;
|
|
jpayne@69
|
19600 if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_vcf, __pyx_t_7) < 0) __PYX_ERR(0, 956, __pyx_L1_error)
|
|
jpayne@69
|
19601 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19602 __pyx_v_preset2conf = ((PyObject*)__pyx_t_9);
|
|
jpayne@69
|
19603 __pyx_t_9 = 0;
|
|
jpayne@69
|
19604
|
|
jpayne@69
|
19605 /* "pysam/libctabix.pyx":963
|
|
jpayne@69
|
19606 * }
|
|
jpayne@69
|
19607 *
|
|
jpayne@69
|
19608 * conf_data = None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19609 * if preset == "bcf" or fmt.format == bcf:
|
|
jpayne@69
|
19610 * csi = True
|
|
jpayne@69
|
19611 */
|
|
jpayne@69
|
19612 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
19613 __pyx_v_conf_data = Py_None;
|
|
jpayne@69
|
19614
|
|
jpayne@69
|
19615 /* "pysam/libctabix.pyx":964
|
|
jpayne@69
|
19616 *
|
|
jpayne@69
|
19617 * conf_data = None
|
|
jpayne@69
|
19618 * if preset == "bcf" or fmt.format == bcf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19619 * csi = True
|
|
jpayne@69
|
19620 * elif preset:
|
|
jpayne@69
|
19621 */
|
|
jpayne@69
|
19622 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_preset, __pyx_n_u_bcf, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 964, __pyx_L1_error)
|
|
jpayne@69
|
19623 if (!__pyx_t_1) {
|
|
jpayne@69
|
19624 } else {
|
|
jpayne@69
|
19625 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
19626 goto __pyx_L12_bool_binop_done;
|
|
jpayne@69
|
19627 }
|
|
jpayne@69
|
19628 __pyx_t_1 = (__pyx_v_fmt.format == bcf);
|
|
jpayne@69
|
19629 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
19630 __pyx_L12_bool_binop_done:;
|
|
jpayne@69
|
19631 if (__pyx_t_2) {
|
|
jpayne@69
|
19632
|
|
jpayne@69
|
19633 /* "pysam/libctabix.pyx":965
|
|
jpayne@69
|
19634 * conf_data = None
|
|
jpayne@69
|
19635 * if preset == "bcf" or fmt.format == bcf:
|
|
jpayne@69
|
19636 * csi = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19637 * elif preset:
|
|
jpayne@69
|
19638 * try:
|
|
jpayne@69
|
19639 */
|
|
jpayne@69
|
19640 __Pyx_INCREF(Py_True);
|
|
jpayne@69
|
19641 __Pyx_DECREF_SET(__pyx_v_csi, Py_True);
|
|
jpayne@69
|
19642
|
|
jpayne@69
|
19643 /* "pysam/libctabix.pyx":964
|
|
jpayne@69
|
19644 *
|
|
jpayne@69
|
19645 * conf_data = None
|
|
jpayne@69
|
19646 * if preset == "bcf" or fmt.format == bcf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19647 * csi = True
|
|
jpayne@69
|
19648 * elif preset:
|
|
jpayne@69
|
19649 */
|
|
jpayne@69
|
19650 goto __pyx_L11;
|
|
jpayne@69
|
19651 }
|
|
jpayne@69
|
19652
|
|
jpayne@69
|
19653 /* "pysam/libctabix.pyx":966
|
|
jpayne@69
|
19654 * if preset == "bcf" or fmt.format == bcf:
|
|
jpayne@69
|
19655 * csi = True
|
|
jpayne@69
|
19656 * elif preset: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19657 * try:
|
|
jpayne@69
|
19658 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19659 */
|
|
jpayne@69
|
19660 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_preset); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 966, __pyx_L1_error)
|
|
jpayne@69
|
19661 if (__pyx_t_2) {
|
|
jpayne@69
|
19662
|
|
jpayne@69
|
19663 /* "pysam/libctabix.pyx":967
|
|
jpayne@69
|
19664 * csi = True
|
|
jpayne@69
|
19665 * elif preset:
|
|
jpayne@69
|
19666 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19667 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19668 * except KeyError:
|
|
jpayne@69
|
19669 */
|
|
jpayne@69
|
19670 {
|
|
jpayne@69
|
19671 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
19672 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
19673 __Pyx_ExceptionSave(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13);
|
|
jpayne@69
|
19674 __Pyx_XGOTREF(__pyx_t_11);
|
|
jpayne@69
|
19675 __Pyx_XGOTREF(__pyx_t_12);
|
|
jpayne@69
|
19676 __Pyx_XGOTREF(__pyx_t_13);
|
|
jpayne@69
|
19677 /*try:*/ {
|
|
jpayne@69
|
19678
|
|
jpayne@69
|
19679 /* "pysam/libctabix.pyx":968
|
|
jpayne@69
|
19680 * elif preset:
|
|
jpayne@69
|
19681 * try:
|
|
jpayne@69
|
19682 * conf_data = preset2conf[preset] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19683 * except KeyError:
|
|
jpayne@69
|
19684 * raise KeyError(
|
|
jpayne@69
|
19685 */
|
|
jpayne@69
|
19686 __pyx_t_9 = __Pyx_PyDict_GetItem(__pyx_v_preset2conf, __pyx_v_preset); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 968, __pyx_L14_error)
|
|
jpayne@69
|
19687 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19688 __Pyx_DECREF_SET(__pyx_v_conf_data, __pyx_t_9);
|
|
jpayne@69
|
19689 __pyx_t_9 = 0;
|
|
jpayne@69
|
19690
|
|
jpayne@69
|
19691 /* "pysam/libctabix.pyx":967
|
|
jpayne@69
|
19692 * csi = True
|
|
jpayne@69
|
19693 * elif preset:
|
|
jpayne@69
|
19694 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19695 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19696 * except KeyError:
|
|
jpayne@69
|
19697 */
|
|
jpayne@69
|
19698 }
|
|
jpayne@69
|
19699 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
19700 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
19701 __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
|
|
jpayne@69
|
19702 goto __pyx_L19_try_end;
|
|
jpayne@69
|
19703 __pyx_L14_error:;
|
|
jpayne@69
|
19704 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19705 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
19706 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19707 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
19708
|
|
jpayne@69
|
19709 /* "pysam/libctabix.pyx":969
|
|
jpayne@69
|
19710 * try:
|
|
jpayne@69
|
19711 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19712 * except KeyError: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19713 * raise KeyError(
|
|
jpayne@69
|
19714 * "unknown preset '%s', valid presets are '%s'" %
|
|
jpayne@69
|
19715 */
|
|
jpayne@69
|
19716 __pyx_t_14 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError);
|
|
jpayne@69
|
19717 if (__pyx_t_14) {
|
|
jpayne@69
|
19718 __Pyx_AddTraceback("pysam.libctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
19719 if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_7, &__pyx_t_8) < 0) __PYX_ERR(0, 969, __pyx_L16_except_error)
|
|
jpayne@69
|
19720 __Pyx_XGOTREF(__pyx_t_9);
|
|
jpayne@69
|
19721 __Pyx_XGOTREF(__pyx_t_7);
|
|
jpayne@69
|
19722 __Pyx_XGOTREF(__pyx_t_8);
|
|
jpayne@69
|
19723
|
|
jpayne@69
|
19724 /* "pysam/libctabix.pyx":971
|
|
jpayne@69
|
19725 * except KeyError:
|
|
jpayne@69
|
19726 * raise KeyError(
|
|
jpayne@69
|
19727 * "unknown preset '%s', valid presets are '%s'" % # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19728 * (preset, ",".join(preset2conf.keys())))
|
|
jpayne@69
|
19729 * else:
|
|
jpayne@69
|
19730 */
|
|
jpayne@69
|
19731 __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 971, __pyx_L16_except_error)
|
|
jpayne@69
|
19732 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19733 __pyx_t_5 = 0;
|
|
jpayne@69
|
19734 __pyx_t_6 = 127;
|
|
jpayne@69
|
19735 __Pyx_INCREF(__pyx_kp_u_unknown_preset);
|
|
jpayne@69
|
19736 __pyx_t_5 += 16;
|
|
jpayne@69
|
19737 __Pyx_GIVEREF(__pyx_kp_u_unknown_preset);
|
|
jpayne@69
|
19738 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_unknown_preset);
|
|
jpayne@69
|
19739
|
|
jpayne@69
|
19740 /* "pysam/libctabix.pyx":972
|
|
jpayne@69
|
19741 * raise KeyError(
|
|
jpayne@69
|
19742 * "unknown preset '%s', valid presets are '%s'" %
|
|
jpayne@69
|
19743 * (preset, ",".join(preset2conf.keys()))) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19744 * else:
|
|
jpayne@69
|
19745 * if end_col is None:
|
|
jpayne@69
|
19746 */
|
|
jpayne@69
|
19747 __pyx_t_15 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_preset), __pyx_empty_unicode); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 972, __pyx_L16_except_error)
|
|
jpayne@69
|
19748 __Pyx_GOTREF(__pyx_t_15);
|
|
jpayne@69
|
19749 __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) : __pyx_t_6;
|
|
jpayne@69
|
19750 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_15);
|
|
jpayne@69
|
19751 __Pyx_GIVEREF(__pyx_t_15);
|
|
jpayne@69
|
19752 PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_15);
|
|
jpayne@69
|
19753 __pyx_t_15 = 0;
|
|
jpayne@69
|
19754 __Pyx_INCREF(__pyx_kp_u_valid_presets_are);
|
|
jpayne@69
|
19755 __pyx_t_5 += 22;
|
|
jpayne@69
|
19756 __Pyx_GIVEREF(__pyx_kp_u_valid_presets_are);
|
|
jpayne@69
|
19757 PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_valid_presets_are);
|
|
jpayne@69
|
19758 __pyx_t_15 = __Pyx_PyDict_Keys(__pyx_v_preset2conf); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 972, __pyx_L16_except_error)
|
|
jpayne@69
|
19759 __Pyx_GOTREF(__pyx_t_15);
|
|
jpayne@69
|
19760 __pyx_t_16 = PyUnicode_Join(__pyx_kp_u__43, __pyx_t_15); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 972, __pyx_L16_except_error)
|
|
jpayne@69
|
19761 __Pyx_GOTREF(__pyx_t_16);
|
|
jpayne@69
|
19762 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
|
|
jpayne@69
|
19763 __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_16) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_16) : __pyx_t_6;
|
|
jpayne@69
|
19764 __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_16);
|
|
jpayne@69
|
19765 __Pyx_GIVEREF(__pyx_t_16);
|
|
jpayne@69
|
19766 PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_16);
|
|
jpayne@69
|
19767 __pyx_t_16 = 0;
|
|
jpayne@69
|
19768 __Pyx_INCREF(__pyx_kp_u__44);
|
|
jpayne@69
|
19769 __pyx_t_5 += 1;
|
|
jpayne@69
|
19770 __Pyx_GIVEREF(__pyx_kp_u__44);
|
|
jpayne@69
|
19771 PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u__44);
|
|
jpayne@69
|
19772
|
|
jpayne@69
|
19773 /* "pysam/libctabix.pyx":971
|
|
jpayne@69
|
19774 * except KeyError:
|
|
jpayne@69
|
19775 * raise KeyError(
|
|
jpayne@69
|
19776 * "unknown preset '%s', valid presets are '%s'" % # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19777 * (preset, ",".join(preset2conf.keys())))
|
|
jpayne@69
|
19778 * else:
|
|
jpayne@69
|
19779 */
|
|
jpayne@69
|
19780 __pyx_t_16 = __Pyx_PyUnicode_Join(__pyx_t_3, 5, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 971, __pyx_L16_except_error)
|
|
jpayne@69
|
19781 __Pyx_GOTREF(__pyx_t_16);
|
|
jpayne@69
|
19782 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19783
|
|
jpayne@69
|
19784 /* "pysam/libctabix.pyx":970
|
|
jpayne@69
|
19785 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19786 * except KeyError:
|
|
jpayne@69
|
19787 * raise KeyError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19788 * "unknown preset '%s', valid presets are '%s'" %
|
|
jpayne@69
|
19789 * (preset, ",".join(preset2conf.keys())))
|
|
jpayne@69
|
19790 */
|
|
jpayne@69
|
19791 __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_KeyError, __pyx_t_16); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 970, __pyx_L16_except_error)
|
|
jpayne@69
|
19792 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19793 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
|
|
jpayne@69
|
19794 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
19795 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
19796 __PYX_ERR(0, 970, __pyx_L16_except_error)
|
|
jpayne@69
|
19797 }
|
|
jpayne@69
|
19798 goto __pyx_L16_except_error;
|
|
jpayne@69
|
19799
|
|
jpayne@69
|
19800 /* "pysam/libctabix.pyx":967
|
|
jpayne@69
|
19801 * csi = True
|
|
jpayne@69
|
19802 * elif preset:
|
|
jpayne@69
|
19803 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19804 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19805 * except KeyError:
|
|
jpayne@69
|
19806 */
|
|
jpayne@69
|
19807 __pyx_L16_except_error:;
|
|
jpayne@69
|
19808 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
19809 __Pyx_XGIVEREF(__pyx_t_12);
|
|
jpayne@69
|
19810 __Pyx_XGIVEREF(__pyx_t_13);
|
|
jpayne@69
|
19811 __Pyx_ExceptionReset(__pyx_t_11, __pyx_t_12, __pyx_t_13);
|
|
jpayne@69
|
19812 goto __pyx_L1_error;
|
|
jpayne@69
|
19813 __pyx_L19_try_end:;
|
|
jpayne@69
|
19814 }
|
|
jpayne@69
|
19815
|
|
jpayne@69
|
19816 /* "pysam/libctabix.pyx":966
|
|
jpayne@69
|
19817 * if preset == "bcf" or fmt.format == bcf:
|
|
jpayne@69
|
19818 * csi = True
|
|
jpayne@69
|
19819 * elif preset: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19820 * try:
|
|
jpayne@69
|
19821 * conf_data = preset2conf[preset]
|
|
jpayne@69
|
19822 */
|
|
jpayne@69
|
19823 goto __pyx_L11;
|
|
jpayne@69
|
19824 }
|
|
jpayne@69
|
19825
|
|
jpayne@69
|
19826 /* "pysam/libctabix.pyx":974
|
|
jpayne@69
|
19827 * (preset, ",".join(preset2conf.keys())))
|
|
jpayne@69
|
19828 * else:
|
|
jpayne@69
|
19829 * if end_col is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19830 * end_col = -1
|
|
jpayne@69
|
19831 *
|
|
jpayne@69
|
19832 */
|
|
jpayne@69
|
19833 /*else*/ {
|
|
jpayne@69
|
19834 __pyx_t_2 = (__pyx_v_end_col == Py_None);
|
|
jpayne@69
|
19835 if (__pyx_t_2) {
|
|
jpayne@69
|
19836
|
|
jpayne@69
|
19837 /* "pysam/libctabix.pyx":975
|
|
jpayne@69
|
19838 * else:
|
|
jpayne@69
|
19839 * if end_col is None:
|
|
jpayne@69
|
19840 * end_col = -1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19841 *
|
|
jpayne@69
|
19842 * preset = 0
|
|
jpayne@69
|
19843 */
|
|
jpayne@69
|
19844 __Pyx_INCREF(__pyx_int_neg_1);
|
|
jpayne@69
|
19845 __Pyx_DECREF_SET(__pyx_v_end_col, __pyx_int_neg_1);
|
|
jpayne@69
|
19846
|
|
jpayne@69
|
19847 /* "pysam/libctabix.pyx":974
|
|
jpayne@69
|
19848 * (preset, ",".join(preset2conf.keys())))
|
|
jpayne@69
|
19849 * else:
|
|
jpayne@69
|
19850 * if end_col is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19851 * end_col = -1
|
|
jpayne@69
|
19852 *
|
|
jpayne@69
|
19853 */
|
|
jpayne@69
|
19854 }
|
|
jpayne@69
|
19855
|
|
jpayne@69
|
19856 /* "pysam/libctabix.pyx":977
|
|
jpayne@69
|
19857 * end_col = -1
|
|
jpayne@69
|
19858 *
|
|
jpayne@69
|
19859 * preset = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19860 * # tabix internally works with 0-based coordinates and
|
|
jpayne@69
|
19861 * # open/closed intervals. When using a preset, conversion is
|
|
jpayne@69
|
19862 */
|
|
jpayne@69
|
19863 __Pyx_INCREF(__pyx_int_0);
|
|
jpayne@69
|
19864 __Pyx_DECREF_SET(__pyx_v_preset, __pyx_int_0);
|
|
jpayne@69
|
19865
|
|
jpayne@69
|
19866 /* "pysam/libctabix.pyx":984
|
|
jpayne@69
|
19867 * # from the start coordinate. To avoid doing this, set the
|
|
jpayne@69
|
19868 * # TI_FLAG_UCSC=0x10000 flag:
|
|
jpayne@69
|
19869 * if zerobased: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19870 * preset = preset | TBX_UCSC
|
|
jpayne@69
|
19871 *
|
|
jpayne@69
|
19872 */
|
|
jpayne@69
|
19873 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_zerobased); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 984, __pyx_L1_error)
|
|
jpayne@69
|
19874 if (__pyx_t_2) {
|
|
jpayne@69
|
19875
|
|
jpayne@69
|
19876 /* "pysam/libctabix.pyx":985
|
|
jpayne@69
|
19877 * # TI_FLAG_UCSC=0x10000 flag:
|
|
jpayne@69
|
19878 * if zerobased:
|
|
jpayne@69
|
19879 * preset = preset | TBX_UCSC # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19880 *
|
|
jpayne@69
|
19881 * conf_data = (preset, seq_col + 1, start_col + 1, end_col + 1, ord(meta_char), line_skip)
|
|
jpayne@69
|
19882 */
|
|
jpayne@69
|
19883 __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 985, __pyx_L1_error)
|
|
jpayne@69
|
19884 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19885 __pyx_t_7 = PyNumber_Or(__pyx_v_preset, __pyx_t_8); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 985, __pyx_L1_error)
|
|
jpayne@69
|
19886 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19887 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
19888 __Pyx_DECREF_SET(__pyx_v_preset, __pyx_t_7);
|
|
jpayne@69
|
19889 __pyx_t_7 = 0;
|
|
jpayne@69
|
19890
|
|
jpayne@69
|
19891 /* "pysam/libctabix.pyx":984
|
|
jpayne@69
|
19892 * # from the start coordinate. To avoid doing this, set the
|
|
jpayne@69
|
19893 * # TI_FLAG_UCSC=0x10000 flag:
|
|
jpayne@69
|
19894 * if zerobased: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19895 * preset = preset | TBX_UCSC
|
|
jpayne@69
|
19896 *
|
|
jpayne@69
|
19897 */
|
|
jpayne@69
|
19898 }
|
|
jpayne@69
|
19899
|
|
jpayne@69
|
19900 /* "pysam/libctabix.pyx":987
|
|
jpayne@69
|
19901 * preset = preset | TBX_UCSC
|
|
jpayne@69
|
19902 *
|
|
jpayne@69
|
19903 * conf_data = (preset, seq_col + 1, start_col + 1, end_col + 1, ord(meta_char), line_skip) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19904 *
|
|
jpayne@69
|
19905 * cdef tbx_conf_t conf
|
|
jpayne@69
|
19906 */
|
|
jpayne@69
|
19907 __pyx_t_7 = __Pyx_PyInt_AddObjC(__pyx_v_seq_col, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19908 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
19909 __pyx_t_8 = __Pyx_PyInt_AddObjC(__pyx_v_start_col, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19910 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
19911 __pyx_t_9 = __Pyx_PyInt_AddObjC(__pyx_v_end_col, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19912 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
19913 __pyx_t_17 = __Pyx_PyObject_Ord(__pyx_v_meta_char); if (unlikely(__pyx_t_17 == ((long)(long)(Py_UCS4)-1))) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19914 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_t_17); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19915 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
19916 __pyx_t_16 = __Pyx_PyInt_From_int(__pyx_v_line_skip); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19917 __Pyx_GOTREF(__pyx_t_16);
|
|
jpayne@69
|
19918 __pyx_t_15 = PyTuple_New(6); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 987, __pyx_L1_error)
|
|
jpayne@69
|
19919 __Pyx_GOTREF(__pyx_t_15);
|
|
jpayne@69
|
19920 __Pyx_INCREF(__pyx_v_preset);
|
|
jpayne@69
|
19921 __Pyx_GIVEREF(__pyx_v_preset);
|
|
jpayne@69
|
19922 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_preset)) __PYX_ERR(0, 987, __pyx_L1_error);
|
|
jpayne@69
|
19923 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
19924 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 1, __pyx_t_7)) __PYX_ERR(0, 987, __pyx_L1_error);
|
|
jpayne@69
|
19925 __Pyx_GIVEREF(__pyx_t_8);
|
|
jpayne@69
|
19926 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 2, __pyx_t_8)) __PYX_ERR(0, 987, __pyx_L1_error);
|
|
jpayne@69
|
19927 __Pyx_GIVEREF(__pyx_t_9);
|
|
jpayne@69
|
19928 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 3, __pyx_t_9)) __PYX_ERR(0, 987, __pyx_L1_error);
|
|
jpayne@69
|
19929 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
19930 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 4, __pyx_t_3)) __PYX_ERR(0, 987, __pyx_L1_error);
|
|
jpayne@69
|
19931 __Pyx_GIVEREF(__pyx_t_16);
|
|
jpayne@69
|
19932 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 5, __pyx_t_16)) __PYX_ERR(0, 987, __pyx_L1_error);
|
|
jpayne@69
|
19933 __pyx_t_7 = 0;
|
|
jpayne@69
|
19934 __pyx_t_8 = 0;
|
|
jpayne@69
|
19935 __pyx_t_9 = 0;
|
|
jpayne@69
|
19936 __pyx_t_3 = 0;
|
|
jpayne@69
|
19937 __pyx_t_16 = 0;
|
|
jpayne@69
|
19938 __Pyx_DECREF_SET(__pyx_v_conf_data, __pyx_t_15);
|
|
jpayne@69
|
19939 __pyx_t_15 = 0;
|
|
jpayne@69
|
19940 }
|
|
jpayne@69
|
19941 __pyx_L11:;
|
|
jpayne@69
|
19942
|
|
jpayne@69
|
19943 /* "pysam/libctabix.pyx":990
|
|
jpayne@69
|
19944 *
|
|
jpayne@69
|
19945 * cdef tbx_conf_t conf
|
|
jpayne@69
|
19946 * if conf_data: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19947 * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data
|
|
jpayne@69
|
19948 *
|
|
jpayne@69
|
19949 */
|
|
jpayne@69
|
19950 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_conf_data); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 990, __pyx_L1_error)
|
|
jpayne@69
|
19951 if (__pyx_t_2) {
|
|
jpayne@69
|
19952
|
|
jpayne@69
|
19953 /* "pysam/libctabix.pyx":991
|
|
jpayne@69
|
19954 * cdef tbx_conf_t conf
|
|
jpayne@69
|
19955 * if conf_data:
|
|
jpayne@69
|
19956 * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data # <<<<<<<<<<<<<<
|
|
jpayne@69
|
19957 *
|
|
jpayne@69
|
19958 * if csi or min_shift > 0:
|
|
jpayne@69
|
19959 */
|
|
jpayne@69
|
19960 if ((likely(PyTuple_CheckExact(__pyx_v_conf_data))) || (PyList_CheckExact(__pyx_v_conf_data))) {
|
|
jpayne@69
|
19961 PyObject* sequence = __pyx_v_conf_data;
|
|
jpayne@69
|
19962 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
|
|
jpayne@69
|
19963 if (unlikely(size != 6)) {
|
|
jpayne@69
|
19964 if (size > 6) __Pyx_RaiseTooManyValuesError(6);
|
|
jpayne@69
|
19965 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
|
|
jpayne@69
|
19966 __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
19967 }
|
|
jpayne@69
|
19968 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
19969 if (likely(PyTuple_CheckExact(sequence))) {
|
|
jpayne@69
|
19970 __pyx_t_15 = PyTuple_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
19971 __pyx_t_16 = PyTuple_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
19972 __pyx_t_3 = PyTuple_GET_ITEM(sequence, 2);
|
|
jpayne@69
|
19973 __pyx_t_9 = PyTuple_GET_ITEM(sequence, 3);
|
|
jpayne@69
|
19974 __pyx_t_8 = PyTuple_GET_ITEM(sequence, 4);
|
|
jpayne@69
|
19975 __pyx_t_7 = PyTuple_GET_ITEM(sequence, 5);
|
|
jpayne@69
|
19976 } else {
|
|
jpayne@69
|
19977 __pyx_t_15 = PyList_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
19978 __pyx_t_16 = PyList_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
19979 __pyx_t_3 = PyList_GET_ITEM(sequence, 2);
|
|
jpayne@69
|
19980 __pyx_t_9 = PyList_GET_ITEM(sequence, 3);
|
|
jpayne@69
|
19981 __pyx_t_8 = PyList_GET_ITEM(sequence, 4);
|
|
jpayne@69
|
19982 __pyx_t_7 = PyList_GET_ITEM(sequence, 5);
|
|
jpayne@69
|
19983 }
|
|
jpayne@69
|
19984 __Pyx_INCREF(__pyx_t_15);
|
|
jpayne@69
|
19985 __Pyx_INCREF(__pyx_t_16);
|
|
jpayne@69
|
19986 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
19987 __Pyx_INCREF(__pyx_t_9);
|
|
jpayne@69
|
19988 __Pyx_INCREF(__pyx_t_8);
|
|
jpayne@69
|
19989 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
19990 #else
|
|
jpayne@69
|
19991 {
|
|
jpayne@69
|
19992 Py_ssize_t i;
|
|
jpayne@69
|
19993 PyObject** temps[6] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_3,&__pyx_t_9,&__pyx_t_8,&__pyx_t_7};
|
|
jpayne@69
|
19994 for (i=0; i < 6; i++) {
|
|
jpayne@69
|
19995 PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
19996 __Pyx_GOTREF(item);
|
|
jpayne@69
|
19997 *(temps[i]) = item;
|
|
jpayne@69
|
19998 }
|
|
jpayne@69
|
19999 }
|
|
jpayne@69
|
20000 #endif
|
|
jpayne@69
|
20001 } else {
|
|
jpayne@69
|
20002 Py_ssize_t index = -1;
|
|
jpayne@69
|
20003 PyObject** temps[6] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_3,&__pyx_t_9,&__pyx_t_8,&__pyx_t_7};
|
|
jpayne@69
|
20004 __pyx_t_18 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20005 __Pyx_GOTREF(__pyx_t_18);
|
|
jpayne@69
|
20006 __pyx_t_19 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_18);
|
|
jpayne@69
|
20007 for (index=0; index < 6; index++) {
|
|
jpayne@69
|
20008 PyObject* item = __pyx_t_19(__pyx_t_18); if (unlikely(!item)) goto __pyx_L25_unpacking_failed;
|
|
jpayne@69
|
20009 __Pyx_GOTREF(item);
|
|
jpayne@69
|
20010 *(temps[index]) = item;
|
|
jpayne@69
|
20011 }
|
|
jpayne@69
|
20012 if (__Pyx_IternextUnpackEndCheck(__pyx_t_19(__pyx_t_18), 6) < 0) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20013 __pyx_t_19 = NULL;
|
|
jpayne@69
|
20014 __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
|
|
jpayne@69
|
20015 goto __pyx_L26_unpacking_done;
|
|
jpayne@69
|
20016 __pyx_L25_unpacking_failed:;
|
|
jpayne@69
|
20017 __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
|
|
jpayne@69
|
20018 __pyx_t_19 = NULL;
|
|
jpayne@69
|
20019 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
|
|
jpayne@69
|
20020 __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20021 __pyx_L26_unpacking_done:;
|
|
jpayne@69
|
20022 }
|
|
jpayne@69
|
20023 __pyx_t_20 = __Pyx_PyInt_As_int32_t(__pyx_t_15); if (unlikely((__pyx_t_20 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20024 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
|
|
jpayne@69
|
20025 __pyx_t_21 = __Pyx_PyInt_As_int32_t(__pyx_t_16); if (unlikely((__pyx_t_21 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20026 __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
|
|
jpayne@69
|
20027 __pyx_t_22 = __Pyx_PyInt_As_int32_t(__pyx_t_3); if (unlikely((__pyx_t_22 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20028 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
20029 __pyx_t_23 = __Pyx_PyInt_As_int32_t(__pyx_t_9); if (unlikely((__pyx_t_23 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20030 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
20031 __pyx_t_24 = __Pyx_PyInt_As_int32_t(__pyx_t_8); if (unlikely((__pyx_t_24 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20032 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
20033 __pyx_t_25 = __Pyx_PyInt_As_int32_t(__pyx_t_7); if (unlikely((__pyx_t_25 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error)
|
|
jpayne@69
|
20034 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
20035 __pyx_v_conf.preset = __pyx_t_20;
|
|
jpayne@69
|
20036 __pyx_v_conf.sc = __pyx_t_21;
|
|
jpayne@69
|
20037 __pyx_v_conf.bc = __pyx_t_22;
|
|
jpayne@69
|
20038 __pyx_v_conf.ec = __pyx_t_23;
|
|
jpayne@69
|
20039 __pyx_v_conf.meta_char = __pyx_t_24;
|
|
jpayne@69
|
20040 __pyx_v_conf.line_skip = __pyx_t_25;
|
|
jpayne@69
|
20041
|
|
jpayne@69
|
20042 /* "pysam/libctabix.pyx":990
|
|
jpayne@69
|
20043 *
|
|
jpayne@69
|
20044 * cdef tbx_conf_t conf
|
|
jpayne@69
|
20045 * if conf_data: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20046 * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data
|
|
jpayne@69
|
20047 *
|
|
jpayne@69
|
20048 */
|
|
jpayne@69
|
20049 }
|
|
jpayne@69
|
20050
|
|
jpayne@69
|
20051 /* "pysam/libctabix.pyx":993
|
|
jpayne@69
|
20052 * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data
|
|
jpayne@69
|
20053 *
|
|
jpayne@69
|
20054 * if csi or min_shift > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20055 * suffix = ".csi"
|
|
jpayne@69
|
20056 * if min_shift <= 0: min_shift = 14
|
|
jpayne@69
|
20057 */
|
|
jpayne@69
|
20058 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_csi); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 993, __pyx_L1_error)
|
|
jpayne@69
|
20059 if (!__pyx_t_1) {
|
|
jpayne@69
|
20060 } else {
|
|
jpayne@69
|
20061 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
20062 goto __pyx_L28_bool_binop_done;
|
|
jpayne@69
|
20063 }
|
|
jpayne@69
|
20064 __pyx_t_1 = (__pyx_v_min_shift > 0);
|
|
jpayne@69
|
20065 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
20066 __pyx_L28_bool_binop_done:;
|
|
jpayne@69
|
20067 if (__pyx_t_2) {
|
|
jpayne@69
|
20068
|
|
jpayne@69
|
20069 /* "pysam/libctabix.pyx":994
|
|
jpayne@69
|
20070 *
|
|
jpayne@69
|
20071 * if csi or min_shift > 0:
|
|
jpayne@69
|
20072 * suffix = ".csi" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20073 * if min_shift <= 0: min_shift = 14
|
|
jpayne@69
|
20074 * else:
|
|
jpayne@69
|
20075 */
|
|
jpayne@69
|
20076 __Pyx_INCREF(__pyx_kp_u_csi_2);
|
|
jpayne@69
|
20077 __pyx_v_suffix = __pyx_kp_u_csi_2;
|
|
jpayne@69
|
20078
|
|
jpayne@69
|
20079 /* "pysam/libctabix.pyx":995
|
|
jpayne@69
|
20080 * if csi or min_shift > 0:
|
|
jpayne@69
|
20081 * suffix = ".csi"
|
|
jpayne@69
|
20082 * if min_shift <= 0: min_shift = 14 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20083 * else:
|
|
jpayne@69
|
20084 * suffix = ".tbi"
|
|
jpayne@69
|
20085 */
|
|
jpayne@69
|
20086 __pyx_t_2 = (__pyx_v_min_shift <= 0);
|
|
jpayne@69
|
20087 if (__pyx_t_2) {
|
|
jpayne@69
|
20088 __pyx_v_min_shift = 14;
|
|
jpayne@69
|
20089 }
|
|
jpayne@69
|
20090
|
|
jpayne@69
|
20091 /* "pysam/libctabix.pyx":993
|
|
jpayne@69
|
20092 * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data
|
|
jpayne@69
|
20093 *
|
|
jpayne@69
|
20094 * if csi or min_shift > 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20095 * suffix = ".csi"
|
|
jpayne@69
|
20096 * if min_shift <= 0: min_shift = 14
|
|
jpayne@69
|
20097 */
|
|
jpayne@69
|
20098 goto __pyx_L27;
|
|
jpayne@69
|
20099 }
|
|
jpayne@69
|
20100
|
|
jpayne@69
|
20101 /* "pysam/libctabix.pyx":997
|
|
jpayne@69
|
20102 * if min_shift <= 0: min_shift = 14
|
|
jpayne@69
|
20103 * else:
|
|
jpayne@69
|
20104 * suffix = ".tbi" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20105 * min_shift = 0
|
|
jpayne@69
|
20106 *
|
|
jpayne@69
|
20107 */
|
|
jpayne@69
|
20108 /*else*/ {
|
|
jpayne@69
|
20109 __Pyx_INCREF(__pyx_kp_u_tbi);
|
|
jpayne@69
|
20110 __pyx_v_suffix = __pyx_kp_u_tbi;
|
|
jpayne@69
|
20111
|
|
jpayne@69
|
20112 /* "pysam/libctabix.pyx":998
|
|
jpayne@69
|
20113 * else:
|
|
jpayne@69
|
20114 * suffix = ".tbi"
|
|
jpayne@69
|
20115 * min_shift = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20116 *
|
|
jpayne@69
|
20117 * index = index or filename + suffix
|
|
jpayne@69
|
20118 */
|
|
jpayne@69
|
20119 __pyx_v_min_shift = 0;
|
|
jpayne@69
|
20120 }
|
|
jpayne@69
|
20121 __pyx_L27:;
|
|
jpayne@69
|
20122
|
|
jpayne@69
|
20123 /* "pysam/libctabix.pyx":1000
|
|
jpayne@69
|
20124 * min_shift = 0
|
|
jpayne@69
|
20125 *
|
|
jpayne@69
|
20126 * index = index or filename + suffix # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20127 * fn_index = encode_filename(index)
|
|
jpayne@69
|
20128 *
|
|
jpayne@69
|
20129 */
|
|
jpayne@69
|
20130 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_index); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 1000, __pyx_L1_error)
|
|
jpayne@69
|
20131 if (!__pyx_t_2) {
|
|
jpayne@69
|
20132 } else {
|
|
jpayne@69
|
20133 __Pyx_INCREF(__pyx_v_index);
|
|
jpayne@69
|
20134 __pyx_t_7 = __pyx_v_index;
|
|
jpayne@69
|
20135 goto __pyx_L31_bool_binop_done;
|
|
jpayne@69
|
20136 }
|
|
jpayne@69
|
20137 __pyx_t_8 = PyNumber_Add(__pyx_v_filename, __pyx_v_suffix); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1000, __pyx_L1_error)
|
|
jpayne@69
|
20138 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
20139 __Pyx_INCREF(__pyx_t_8);
|
|
jpayne@69
|
20140 __pyx_t_7 = __pyx_t_8;
|
|
jpayne@69
|
20141 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
20142 __pyx_L31_bool_binop_done:;
|
|
jpayne@69
|
20143 __Pyx_DECREF_SET(__pyx_v_index, __pyx_t_7);
|
|
jpayne@69
|
20144 __pyx_t_7 = 0;
|
|
jpayne@69
|
20145
|
|
jpayne@69
|
20146 /* "pysam/libctabix.pyx":1001
|
|
jpayne@69
|
20147 *
|
|
jpayne@69
|
20148 * index = index or filename + suffix
|
|
jpayne@69
|
20149 * fn_index = encode_filename(index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20150 *
|
|
jpayne@69
|
20151 * if not force and os.path.exists(index):
|
|
jpayne@69
|
20152 */
|
|
jpayne@69
|
20153 __pyx_t_7 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1001, __pyx_L1_error)
|
|
jpayne@69
|
20154 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
20155 __pyx_v_fn_index = ((PyObject*)__pyx_t_7);
|
|
jpayne@69
|
20156 __pyx_t_7 = 0;
|
|
jpayne@69
|
20157
|
|
jpayne@69
|
20158 /* "pysam/libctabix.pyx":1003
|
|
jpayne@69
|
20159 * fn_index = encode_filename(index)
|
|
jpayne@69
|
20160 *
|
|
jpayne@69
|
20161 * if not force and os.path.exists(index): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20162 * raise IOError(
|
|
jpayne@69
|
20163 * "filename '%s' already exists, use *force* to overwrite" % index)
|
|
jpayne@69
|
20164 */
|
|
jpayne@69
|
20165 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_force); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 1003, __pyx_L1_error)
|
|
jpayne@69
|
20166 __pyx_t_26 = (!__pyx_t_1);
|
|
jpayne@69
|
20167 if (__pyx_t_26) {
|
|
jpayne@69
|
20168 } else {
|
|
jpayne@69
|
20169 __pyx_t_2 = __pyx_t_26;
|
|
jpayne@69
|
20170 goto __pyx_L34_bool_binop_done;
|
|
jpayne@69
|
20171 }
|
|
jpayne@69
|
20172 __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_os); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1003, __pyx_L1_error)
|
|
jpayne@69
|
20173 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
20174 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_path); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 1003, __pyx_L1_error)
|
|
jpayne@69
|
20175 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
20176 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
20177 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_exists); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1003, __pyx_L1_error)
|
|
jpayne@69
|
20178 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
20179 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
20180 __pyx_t_9 = NULL;
|
|
jpayne@69
|
20181 __pyx_t_10 = 0;
|
|
jpayne@69
|
20182 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
20183 if (likely(PyMethod_Check(__pyx_t_8))) {
|
|
jpayne@69
|
20184 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_8);
|
|
jpayne@69
|
20185 if (likely(__pyx_t_9)) {
|
|
jpayne@69
|
20186 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8);
|
|
jpayne@69
|
20187 __Pyx_INCREF(__pyx_t_9);
|
|
jpayne@69
|
20188 __Pyx_INCREF(function);
|
|
jpayne@69
|
20189 __Pyx_DECREF_SET(__pyx_t_8, function);
|
|
jpayne@69
|
20190 __pyx_t_10 = 1;
|
|
jpayne@69
|
20191 }
|
|
jpayne@69
|
20192 }
|
|
jpayne@69
|
20193 #endif
|
|
jpayne@69
|
20194 {
|
|
jpayne@69
|
20195 PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_index};
|
|
jpayne@69
|
20196 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
|
|
jpayne@69
|
20197 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
20198 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1003, __pyx_L1_error)
|
|
jpayne@69
|
20199 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
20200 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
20201 }
|
|
jpayne@69
|
20202 __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 1003, __pyx_L1_error)
|
|
jpayne@69
|
20203 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
20204 __pyx_t_2 = __pyx_t_26;
|
|
jpayne@69
|
20205 __pyx_L34_bool_binop_done:;
|
|
jpayne@69
|
20206 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
20207
|
|
jpayne@69
|
20208 /* "pysam/libctabix.pyx":1005
|
|
jpayne@69
|
20209 * if not force and os.path.exists(index):
|
|
jpayne@69
|
20210 * raise IOError(
|
|
jpayne@69
|
20211 * "filename '%s' already exists, use *force* to overwrite" % index) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20212 *
|
|
jpayne@69
|
20213 * cdef char *fnidx = fn_index
|
|
jpayne@69
|
20214 */
|
|
jpayne@69
|
20215 __pyx_t_7 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_filename_s_already_exists_use_fo, __pyx_v_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1005, __pyx_L1_error)
|
|
jpayne@69
|
20216 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
20217
|
|
jpayne@69
|
20218 /* "pysam/libctabix.pyx":1004
|
|
jpayne@69
|
20219 *
|
|
jpayne@69
|
20220 * if not force and os.path.exists(index):
|
|
jpayne@69
|
20221 * raise IOError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20222 * "filename '%s' already exists, use *force* to overwrite" % index)
|
|
jpayne@69
|
20223 *
|
|
jpayne@69
|
20224 */
|
|
jpayne@69
|
20225 __pyx_t_8 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_7); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1004, __pyx_L1_error)
|
|
jpayne@69
|
20226 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
20227 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
20228 __Pyx_Raise(__pyx_t_8, 0, 0, 0);
|
|
jpayne@69
|
20229 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
20230 __PYX_ERR(0, 1004, __pyx_L1_error)
|
|
jpayne@69
|
20231
|
|
jpayne@69
|
20232 /* "pysam/libctabix.pyx":1003
|
|
jpayne@69
|
20233 * fn_index = encode_filename(index)
|
|
jpayne@69
|
20234 *
|
|
jpayne@69
|
20235 * if not force and os.path.exists(index): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20236 * raise IOError(
|
|
jpayne@69
|
20237 * "filename '%s' already exists, use *force* to overwrite" % index)
|
|
jpayne@69
|
20238 */
|
|
jpayne@69
|
20239 }
|
|
jpayne@69
|
20240
|
|
jpayne@69
|
20241 /* "pysam/libctabix.pyx":1007
|
|
jpayne@69
|
20242 * "filename '%s' already exists, use *force* to overwrite" % index)
|
|
jpayne@69
|
20243 *
|
|
jpayne@69
|
20244 * cdef char *fnidx = fn_index # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20245 * cdef int retval = 0
|
|
jpayne@69
|
20246 *
|
|
jpayne@69
|
20247 */
|
|
jpayne@69
|
20248 if (unlikely(__pyx_v_fn_index == Py_None)) {
|
|
jpayne@69
|
20249 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
20250 __PYX_ERR(0, 1007, __pyx_L1_error)
|
|
jpayne@69
|
20251 }
|
|
jpayne@69
|
20252 __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn_index); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 1007, __pyx_L1_error)
|
|
jpayne@69
|
20253 __pyx_v_fnidx = __pyx_t_4;
|
|
jpayne@69
|
20254
|
|
jpayne@69
|
20255 /* "pysam/libctabix.pyx":1008
|
|
jpayne@69
|
20256 *
|
|
jpayne@69
|
20257 * cdef char *fnidx = fn_index
|
|
jpayne@69
|
20258 * cdef int retval = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20259 *
|
|
jpayne@69
|
20260 * if csi and fmt.format == bcf:
|
|
jpayne@69
|
20261 */
|
|
jpayne@69
|
20262 __pyx_v_retval = 0;
|
|
jpayne@69
|
20263
|
|
jpayne@69
|
20264 /* "pysam/libctabix.pyx":1010
|
|
jpayne@69
|
20265 * cdef int retval = 0
|
|
jpayne@69
|
20266 *
|
|
jpayne@69
|
20267 * if csi and fmt.format == bcf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20268 * with nogil:
|
|
jpayne@69
|
20269 * retval = bcf_index_build2(cfn, fnidx, min_shift)
|
|
jpayne@69
|
20270 */
|
|
jpayne@69
|
20271 __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_v_csi); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 1010, __pyx_L1_error)
|
|
jpayne@69
|
20272 if (__pyx_t_26) {
|
|
jpayne@69
|
20273 } else {
|
|
jpayne@69
|
20274 __pyx_t_2 = __pyx_t_26;
|
|
jpayne@69
|
20275 goto __pyx_L37_bool_binop_done;
|
|
jpayne@69
|
20276 }
|
|
jpayne@69
|
20277 __pyx_t_26 = (__pyx_v_fmt.format == bcf);
|
|
jpayne@69
|
20278 __pyx_t_2 = __pyx_t_26;
|
|
jpayne@69
|
20279 __pyx_L37_bool_binop_done:;
|
|
jpayne@69
|
20280 if (__pyx_t_2) {
|
|
jpayne@69
|
20281
|
|
jpayne@69
|
20282 /* "pysam/libctabix.pyx":1011
|
|
jpayne@69
|
20283 *
|
|
jpayne@69
|
20284 * if csi and fmt.format == bcf:
|
|
jpayne@69
|
20285 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20286 * retval = bcf_index_build2(cfn, fnidx, min_shift)
|
|
jpayne@69
|
20287 * else:
|
|
jpayne@69
|
20288 */
|
|
jpayne@69
|
20289 {
|
|
jpayne@69
|
20290 #ifdef WITH_THREAD
|
|
jpayne@69
|
20291 PyThreadState *_save;
|
|
jpayne@69
|
20292 _save = NULL;
|
|
jpayne@69
|
20293 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
20294 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
20295 #endif
|
|
jpayne@69
|
20296 /*try:*/ {
|
|
jpayne@69
|
20297
|
|
jpayne@69
|
20298 /* "pysam/libctabix.pyx":1012
|
|
jpayne@69
|
20299 * if csi and fmt.format == bcf:
|
|
jpayne@69
|
20300 * with nogil:
|
|
jpayne@69
|
20301 * retval = bcf_index_build2(cfn, fnidx, min_shift) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20302 * else:
|
|
jpayne@69
|
20303 * with nogil:
|
|
jpayne@69
|
20304 */
|
|
jpayne@69
|
20305 __pyx_v_retval = bcf_index_build2(__pyx_v_cfn, __pyx_v_fnidx, __pyx_v_min_shift);
|
|
jpayne@69
|
20306 }
|
|
jpayne@69
|
20307
|
|
jpayne@69
|
20308 /* "pysam/libctabix.pyx":1011
|
|
jpayne@69
|
20309 *
|
|
jpayne@69
|
20310 * if csi and fmt.format == bcf:
|
|
jpayne@69
|
20311 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20312 * retval = bcf_index_build2(cfn, fnidx, min_shift)
|
|
jpayne@69
|
20313 * else:
|
|
jpayne@69
|
20314 */
|
|
jpayne@69
|
20315 /*finally:*/ {
|
|
jpayne@69
|
20316 /*normal exit:*/{
|
|
jpayne@69
|
20317 #ifdef WITH_THREAD
|
|
jpayne@69
|
20318 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
20319 Py_BLOCK_THREADS
|
|
jpayne@69
|
20320 #endif
|
|
jpayne@69
|
20321 goto __pyx_L41;
|
|
jpayne@69
|
20322 }
|
|
jpayne@69
|
20323 __pyx_L41:;
|
|
jpayne@69
|
20324 }
|
|
jpayne@69
|
20325 }
|
|
jpayne@69
|
20326
|
|
jpayne@69
|
20327 /* "pysam/libctabix.pyx":1010
|
|
jpayne@69
|
20328 * cdef int retval = 0
|
|
jpayne@69
|
20329 *
|
|
jpayne@69
|
20330 * if csi and fmt.format == bcf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20331 * with nogil:
|
|
jpayne@69
|
20332 * retval = bcf_index_build2(cfn, fnidx, min_shift)
|
|
jpayne@69
|
20333 */
|
|
jpayne@69
|
20334 goto __pyx_L36;
|
|
jpayne@69
|
20335 }
|
|
jpayne@69
|
20336
|
|
jpayne@69
|
20337 /* "pysam/libctabix.pyx":1014
|
|
jpayne@69
|
20338 * retval = bcf_index_build2(cfn, fnidx, min_shift)
|
|
jpayne@69
|
20339 * else:
|
|
jpayne@69
|
20340 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20341 * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf)
|
|
jpayne@69
|
20342 *
|
|
jpayne@69
|
20343 */
|
|
jpayne@69
|
20344 /*else*/ {
|
|
jpayne@69
|
20345 {
|
|
jpayne@69
|
20346 #ifdef WITH_THREAD
|
|
jpayne@69
|
20347 PyThreadState *_save;
|
|
jpayne@69
|
20348 _save = NULL;
|
|
jpayne@69
|
20349 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
20350 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
20351 #endif
|
|
jpayne@69
|
20352 /*try:*/ {
|
|
jpayne@69
|
20353
|
|
jpayne@69
|
20354 /* "pysam/libctabix.pyx":1015
|
|
jpayne@69
|
20355 * else:
|
|
jpayne@69
|
20356 * with nogil:
|
|
jpayne@69
|
20357 * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20358 *
|
|
jpayne@69
|
20359 * if retval != 0:
|
|
jpayne@69
|
20360 */
|
|
jpayne@69
|
20361 __pyx_v_retval = tbx_index_build2(__pyx_v_cfn, __pyx_v_fnidx, __pyx_v_min_shift, (&__pyx_v_conf));
|
|
jpayne@69
|
20362 }
|
|
jpayne@69
|
20363
|
|
jpayne@69
|
20364 /* "pysam/libctabix.pyx":1014
|
|
jpayne@69
|
20365 * retval = bcf_index_build2(cfn, fnidx, min_shift)
|
|
jpayne@69
|
20366 * else:
|
|
jpayne@69
|
20367 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20368 * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf)
|
|
jpayne@69
|
20369 *
|
|
jpayne@69
|
20370 */
|
|
jpayne@69
|
20371 /*finally:*/ {
|
|
jpayne@69
|
20372 /*normal exit:*/{
|
|
jpayne@69
|
20373 #ifdef WITH_THREAD
|
|
jpayne@69
|
20374 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
20375 Py_BLOCK_THREADS
|
|
jpayne@69
|
20376 #endif
|
|
jpayne@69
|
20377 goto __pyx_L44;
|
|
jpayne@69
|
20378 }
|
|
jpayne@69
|
20379 __pyx_L44:;
|
|
jpayne@69
|
20380 }
|
|
jpayne@69
|
20381 }
|
|
jpayne@69
|
20382 }
|
|
jpayne@69
|
20383 __pyx_L36:;
|
|
jpayne@69
|
20384
|
|
jpayne@69
|
20385 /* "pysam/libctabix.pyx":1017
|
|
jpayne@69
|
20386 * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf)
|
|
jpayne@69
|
20387 *
|
|
jpayne@69
|
20388 * if retval != 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20389 * raise OSError("building of index for {} failed".format(filename))
|
|
jpayne@69
|
20390 *
|
|
jpayne@69
|
20391 */
|
|
jpayne@69
|
20392 __pyx_t_2 = (__pyx_v_retval != 0);
|
|
jpayne@69
|
20393 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
20394
|
|
jpayne@69
|
20395 /* "pysam/libctabix.pyx":1018
|
|
jpayne@69
|
20396 *
|
|
jpayne@69
|
20397 * if retval != 0:
|
|
jpayne@69
|
20398 * raise OSError("building of index for {} failed".format(filename)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20399 *
|
|
jpayne@69
|
20400 * return filename
|
|
jpayne@69
|
20401 */
|
|
jpayne@69
|
20402 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_building_of_index_for_failed, __pyx_n_s_format); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1018, __pyx_L1_error)
|
|
jpayne@69
|
20403 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
20404 __pyx_t_9 = NULL;
|
|
jpayne@69
|
20405 __pyx_t_10 = 0;
|
|
jpayne@69
|
20406 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
20407 if (likely(PyMethod_Check(__pyx_t_7))) {
|
|
jpayne@69
|
20408 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_7);
|
|
jpayne@69
|
20409 if (likely(__pyx_t_9)) {
|
|
jpayne@69
|
20410 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
|
|
jpayne@69
|
20411 __Pyx_INCREF(__pyx_t_9);
|
|
jpayne@69
|
20412 __Pyx_INCREF(function);
|
|
jpayne@69
|
20413 __Pyx_DECREF_SET(__pyx_t_7, function);
|
|
jpayne@69
|
20414 __pyx_t_10 = 1;
|
|
jpayne@69
|
20415 }
|
|
jpayne@69
|
20416 }
|
|
jpayne@69
|
20417 #endif
|
|
jpayne@69
|
20418 {
|
|
jpayne@69
|
20419 PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_filename};
|
|
jpayne@69
|
20420 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10);
|
|
jpayne@69
|
20421 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
20422 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1018, __pyx_L1_error)
|
|
jpayne@69
|
20423 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
20424 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
20425 }
|
|
jpayne@69
|
20426 __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_builtin_OSError, __pyx_t_8); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1018, __pyx_L1_error)
|
|
jpayne@69
|
20427 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
20428 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
20429 __Pyx_Raise(__pyx_t_7, 0, 0, 0);
|
|
jpayne@69
|
20430 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
20431 __PYX_ERR(0, 1018, __pyx_L1_error)
|
|
jpayne@69
|
20432
|
|
jpayne@69
|
20433 /* "pysam/libctabix.pyx":1017
|
|
jpayne@69
|
20434 * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf)
|
|
jpayne@69
|
20435 *
|
|
jpayne@69
|
20436 * if retval != 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20437 * raise OSError("building of index for {} failed".format(filename))
|
|
jpayne@69
|
20438 *
|
|
jpayne@69
|
20439 */
|
|
jpayne@69
|
20440 }
|
|
jpayne@69
|
20441
|
|
jpayne@69
|
20442 /* "pysam/libctabix.pyx":1020
|
|
jpayne@69
|
20443 * raise OSError("building of index for {} failed".format(filename))
|
|
jpayne@69
|
20444 *
|
|
jpayne@69
|
20445 * return filename # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20446 *
|
|
jpayne@69
|
20447 * # #########################################################
|
|
jpayne@69
|
20448 */
|
|
jpayne@69
|
20449 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
20450 __Pyx_INCREF(__pyx_v_filename);
|
|
jpayne@69
|
20451 __pyx_r = __pyx_v_filename;
|
|
jpayne@69
|
20452 goto __pyx_L0;
|
|
jpayne@69
|
20453
|
|
jpayne@69
|
20454 /* "pysam/libctabix.pyx":873
|
|
jpayne@69
|
20455 *
|
|
jpayne@69
|
20456 *
|
|
jpayne@69
|
20457 * def tabix_index(filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20458 * force=False,
|
|
jpayne@69
|
20459 * seq_col=None,
|
|
jpayne@69
|
20460 */
|
|
jpayne@69
|
20461
|
|
jpayne@69
|
20462 /* function exit code */
|
|
jpayne@69
|
20463 __pyx_L1_error:;
|
|
jpayne@69
|
20464 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
20465 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
20466 __Pyx_XDECREF(__pyx_t_8);
|
|
jpayne@69
|
20467 __Pyx_XDECREF(__pyx_t_9);
|
|
jpayne@69
|
20468 __Pyx_XDECREF(__pyx_t_15);
|
|
jpayne@69
|
20469 __Pyx_XDECREF(__pyx_t_16);
|
|
jpayne@69
|
20470 __Pyx_XDECREF(__pyx_t_18);
|
|
jpayne@69
|
20471 __Pyx_AddTraceback("pysam.libctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
20472 __pyx_r = NULL;
|
|
jpayne@69
|
20473 __pyx_L0:;
|
|
jpayne@69
|
20474 __Pyx_XDECREF(__pyx_v_fn);
|
|
jpayne@69
|
20475 __Pyx_XDECREF(__pyx_v_preset2conf);
|
|
jpayne@69
|
20476 __Pyx_XDECREF(__pyx_v_conf_data);
|
|
jpayne@69
|
20477 __Pyx_XDECREF(__pyx_v_suffix);
|
|
jpayne@69
|
20478 __Pyx_XDECREF(__pyx_v_fn_index);
|
|
jpayne@69
|
20479 __Pyx_XDECREF(__pyx_v_filename);
|
|
jpayne@69
|
20480 __Pyx_XDECREF(__pyx_v_end_col);
|
|
jpayne@69
|
20481 __Pyx_XDECREF(__pyx_v_preset);
|
|
jpayne@69
|
20482 __Pyx_XDECREF(__pyx_v_index);
|
|
jpayne@69
|
20483 __Pyx_XDECREF(__pyx_v_csi);
|
|
jpayne@69
|
20484 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
20485 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
20486 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
20487 return __pyx_r;
|
|
jpayne@69
|
20488 }
|
|
jpayne@69
|
20489
|
|
jpayne@69
|
20490 /* "pysam/libctabix.pyx":1102
|
|
jpayne@69
|
20491 * '''
|
|
jpayne@69
|
20492 *
|
|
jpayne@69
|
20493 * def __cinit__(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20494 * infile,
|
|
jpayne@69
|
20495 * Parser parser,
|
|
jpayne@69
|
20496 */
|
|
jpayne@69
|
20497
|
|
jpayne@69
|
20498 /* Python wrapper */
|
|
jpayne@69
|
20499 static int __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
|
|
jpayne@69
|
20500 static int __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
|
|
jpayne@69
|
20501 PyObject *__pyx_v_infile = 0;
|
|
jpayne@69
|
20502 struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser = 0;
|
|
jpayne@69
|
20503 int __pyx_v_buffer_size;
|
|
jpayne@69
|
20504 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
20505 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
20506 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
20507 int __pyx_lineno = 0;
|
|
jpayne@69
|
20508 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
20509 int __pyx_clineno = 0;
|
|
jpayne@69
|
20510 int __pyx_r;
|
|
jpayne@69
|
20511 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
20512 __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
|
|
jpayne@69
|
20513 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
20514 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
20515 #else
|
|
jpayne@69
|
20516 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1;
|
|
jpayne@69
|
20517 #endif
|
|
jpayne@69
|
20518 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
20519 {
|
|
jpayne@69
|
20520 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_infile,&__pyx_n_s_parser,&__pyx_n_s_buffer_size,0};
|
|
jpayne@69
|
20521 if (__pyx_kwds) {
|
|
jpayne@69
|
20522 Py_ssize_t kw_args;
|
|
jpayne@69
|
20523 switch (__pyx_nargs) {
|
|
jpayne@69
|
20524 case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2);
|
|
jpayne@69
|
20525 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
20526 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
20527 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
20528 case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
20529 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
20530 case 0: break;
|
|
jpayne@69
|
20531 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
20532 }
|
|
jpayne@69
|
20533 kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds);
|
|
jpayne@69
|
20534 switch (__pyx_nargs) {
|
|
jpayne@69
|
20535 case 0:
|
|
jpayne@69
|
20536 if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_infile)) != 0)) {
|
|
jpayne@69
|
20537 (void)__Pyx_Arg_NewRef_VARARGS(values[0]);
|
|
jpayne@69
|
20538 kw_args--;
|
|
jpayne@69
|
20539 }
|
|
jpayne@69
|
20540 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1102, __pyx_L3_error)
|
|
jpayne@69
|
20541 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
20542 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
20543 case 1:
|
|
jpayne@69
|
20544 if (likely((values[1] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) {
|
|
jpayne@69
|
20545 (void)__Pyx_Arg_NewRef_VARARGS(values[1]);
|
|
jpayne@69
|
20546 kw_args--;
|
|
jpayne@69
|
20547 }
|
|
jpayne@69
|
20548 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1102, __pyx_L3_error)
|
|
jpayne@69
|
20549 else {
|
|
jpayne@69
|
20550 __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); __PYX_ERR(0, 1102, __pyx_L3_error)
|
|
jpayne@69
|
20551 }
|
|
jpayne@69
|
20552 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
20553 case 2:
|
|
jpayne@69
|
20554 if (kw_args > 0) {
|
|
jpayne@69
|
20555 PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buffer_size);
|
|
jpayne@69
|
20556 if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; }
|
|
jpayne@69
|
20557 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1102, __pyx_L3_error)
|
|
jpayne@69
|
20558 }
|
|
jpayne@69
|
20559 }
|
|
jpayne@69
|
20560 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
20561 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
20562 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__cinit__") < 0)) __PYX_ERR(0, 1102, __pyx_L3_error)
|
|
jpayne@69
|
20563 }
|
|
jpayne@69
|
20564 } else {
|
|
jpayne@69
|
20565 switch (__pyx_nargs) {
|
|
jpayne@69
|
20566 case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2);
|
|
jpayne@69
|
20567 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
20568 case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1);
|
|
jpayne@69
|
20569 values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0);
|
|
jpayne@69
|
20570 break;
|
|
jpayne@69
|
20571 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
20572 }
|
|
jpayne@69
|
20573 }
|
|
jpayne@69
|
20574 __pyx_v_infile = values[0];
|
|
jpayne@69
|
20575 __pyx_v_parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)values[1]);
|
|
jpayne@69
|
20576 if (values[2]) {
|
|
jpayne@69
|
20577 __pyx_v_buffer_size = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_buffer_size == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1105, __pyx_L3_error)
|
|
jpayne@69
|
20578 } else {
|
|
jpayne@69
|
20579 __pyx_v_buffer_size = ((int)0x10000);
|
|
jpayne@69
|
20580 }
|
|
jpayne@69
|
20581 }
|
|
jpayne@69
|
20582 goto __pyx_L6_skip;
|
|
jpayne@69
|
20583 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
20584 __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 1102, __pyx_L3_error)
|
|
jpayne@69
|
20585 __pyx_L6_skip:;
|
|
jpayne@69
|
20586 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
20587 __pyx_L3_error:;
|
|
jpayne@69
|
20588 {
|
|
jpayne@69
|
20589 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
20590 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
20591 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
|
|
jpayne@69
|
20592 }
|
|
jpayne@69
|
20593 }
|
|
jpayne@69
|
20594 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
20595 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
20596 return -1;
|
|
jpayne@69
|
20597 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
20598 if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_5pysam_9libctabix_Parser, 1, "parser", 0))) __PYX_ERR(0, 1104, __pyx_L1_error)
|
|
jpayne@69
|
20599 __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator___cinit__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_parser, __pyx_v_buffer_size);
|
|
jpayne@69
|
20600
|
|
jpayne@69
|
20601 /* function exit code */
|
|
jpayne@69
|
20602 goto __pyx_L0;
|
|
jpayne@69
|
20603 __pyx_L1_error:;
|
|
jpayne@69
|
20604 __pyx_r = -1;
|
|
jpayne@69
|
20605 __pyx_L0:;
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jpayne@69
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20606 {
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jpayne@69
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20607 Py_ssize_t __pyx_temp;
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jpayne@69
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20608 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
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jpayne@69
|
20609 __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]);
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jpayne@69
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20610 }
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jpayne@69
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20611 }
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jpayne@69
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20612 __Pyx_RefNannyFinishContext();
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jpayne@69
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20613 return __pyx_r;
|
|
jpayne@69
|
20614 }
|
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jpayne@69
|
20615
|
|
jpayne@69
|
20616 static int __pyx_pf_5pysam_9libctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size) {
|
|
jpayne@69
|
20617 int __pyx_v_fd;
|
|
jpayne@69
|
20618 int __pyx_r;
|
|
jpayne@69
|
20619 __Pyx_TraceDeclarations
|
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jpayne@69
|
20620 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
20621 PyObject *__pyx_t_1 = NULL;
|
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jpayne@69
|
20622 int __pyx_t_2;
|
|
jpayne@69
|
20623 int __pyx_t_3;
|
|
jpayne@69
|
20624 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
20625 int __pyx_lineno = 0;
|
|
jpayne@69
|
20626 const char *__pyx_filename = NULL;
|
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jpayne@69
|
20627 int __pyx_clineno = 0;
|
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jpayne@69
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20628 __Pyx_RefNannySetupContext("__cinit__", 1);
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jpayne@69
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20629 __Pyx_TraceCall("__cinit__", __pyx_f[0], 1102, 0, __PYX_ERR(0, 1102, __pyx_L1_error));
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jpayne@69
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20630
|
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jpayne@69
|
20631 /* "pysam/libctabix.pyx":1107
|
|
jpayne@69
|
20632 * int buffer_size=65536):
|
|
jpayne@69
|
20633 *
|
|
jpayne@69
|
20634 * if infile.closed: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20635 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20636 *
|
|
jpayne@69
|
20637 */
|
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jpayne@69
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20638 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_infile, __pyx_n_s_closed); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1107, __pyx_L1_error)
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jpayne@69
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20639 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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20640 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 1107, __pyx_L1_error)
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jpayne@69
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20641 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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20642 if (unlikely(__pyx_t_2)) {
|
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jpayne@69
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20643
|
|
jpayne@69
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20644 /* "pysam/libctabix.pyx":1108
|
|
jpayne@69
|
20645 *
|
|
jpayne@69
|
20646 * if infile.closed:
|
|
jpayne@69
|
20647 * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20648 *
|
|
jpayne@69
|
20649 * self.infile = infile
|
|
jpayne@69
|
20650 */
|
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jpayne@69
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20651 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1108, __pyx_L1_error)
|
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jpayne@69
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20652 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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20653 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
20654 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
20655 __PYX_ERR(0, 1108, __pyx_L1_error)
|
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jpayne@69
|
20656
|
|
jpayne@69
|
20657 /* "pysam/libctabix.pyx":1107
|
|
jpayne@69
|
20658 * int buffer_size=65536):
|
|
jpayne@69
|
20659 *
|
|
jpayne@69
|
20660 * if infile.closed: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20661 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20662 *
|
|
jpayne@69
|
20663 */
|
|
jpayne@69
|
20664 }
|
|
jpayne@69
|
20665
|
|
jpayne@69
|
20666 /* "pysam/libctabix.pyx":1110
|
|
jpayne@69
|
20667 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20668 *
|
|
jpayne@69
|
20669 * self.infile = infile # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20670 *
|
|
jpayne@69
|
20671 * cdef int fd = PyObject_AsFileDescriptor(infile)
|
|
jpayne@69
|
20672 */
|
|
jpayne@69
|
20673 __Pyx_INCREF(__pyx_v_infile);
|
|
jpayne@69
|
20674 __Pyx_GIVEREF(__pyx_v_infile);
|
|
jpayne@69
|
20675 __Pyx_GOTREF(__pyx_v_self->infile);
|
|
jpayne@69
|
20676 __Pyx_DECREF(__pyx_v_self->infile);
|
|
jpayne@69
|
20677 __pyx_v_self->infile = __pyx_v_infile;
|
|
jpayne@69
|
20678
|
|
jpayne@69
|
20679 /* "pysam/libctabix.pyx":1112
|
|
jpayne@69
|
20680 * self.infile = infile
|
|
jpayne@69
|
20681 *
|
|
jpayne@69
|
20682 * cdef int fd = PyObject_AsFileDescriptor(infile) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20683 * if fd == -1:
|
|
jpayne@69
|
20684 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20685 */
|
|
jpayne@69
|
20686 __pyx_t_3 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 1112, __pyx_L1_error)
|
|
jpayne@69
|
20687 __pyx_v_fd = __pyx_t_3;
|
|
jpayne@69
|
20688
|
|
jpayne@69
|
20689 /* "pysam/libctabix.pyx":1113
|
|
jpayne@69
|
20690 *
|
|
jpayne@69
|
20691 * cdef int fd = PyObject_AsFileDescriptor(infile)
|
|
jpayne@69
|
20692 * if fd == -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20693 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20694 *
|
|
jpayne@69
|
20695 */
|
|
jpayne@69
|
20696 __pyx_t_2 = (__pyx_v_fd == -1L);
|
|
jpayne@69
|
20697 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
20698
|
|
jpayne@69
|
20699 /* "pysam/libctabix.pyx":1114
|
|
jpayne@69
|
20700 * cdef int fd = PyObject_AsFileDescriptor(infile)
|
|
jpayne@69
|
20701 * if fd == -1:
|
|
jpayne@69
|
20702 * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20703 *
|
|
jpayne@69
|
20704 * self.duplicated_fd = dup(fd)
|
|
jpayne@69
|
20705 */
|
|
jpayne@69
|
20706 __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1114, __pyx_L1_error)
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jpayne@69
|
20707 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
20708 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
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jpayne@69
|
20709 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
|
20710 __PYX_ERR(0, 1114, __pyx_L1_error)
|
|
jpayne@69
|
20711
|
|
jpayne@69
|
20712 /* "pysam/libctabix.pyx":1113
|
|
jpayne@69
|
20713 *
|
|
jpayne@69
|
20714 * cdef int fd = PyObject_AsFileDescriptor(infile)
|
|
jpayne@69
|
20715 * if fd == -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20716 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20717 *
|
|
jpayne@69
|
20718 */
|
|
jpayne@69
|
20719 }
|
|
jpayne@69
|
20720
|
|
jpayne@69
|
20721 /* "pysam/libctabix.pyx":1116
|
|
jpayne@69
|
20722 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
20723 *
|
|
jpayne@69
|
20724 * self.duplicated_fd = dup(fd) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20725 *
|
|
jpayne@69
|
20726 * # From the manual:
|
|
jpayne@69
|
20727 */
|
|
jpayne@69
|
20728 __pyx_v_self->duplicated_fd = dup(__pyx_v_fd);
|
|
jpayne@69
|
20729
|
|
jpayne@69
|
20730 /* "pysam/libctabix.pyx":1123
|
|
jpayne@69
|
20731 * # When reading, this will be detected automatically by looking
|
|
jpayne@69
|
20732 * # for the magic two-byte gzip header.
|
|
jpayne@69
|
20733 * self.fh = bgzf_dopen(self.duplicated_fd, 'r') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20734 *
|
|
jpayne@69
|
20735 * if self.fh == NULL:
|
|
jpayne@69
|
20736 */
|
|
jpayne@69
|
20737 __pyx_v_self->fh = bgzf_dopen(__pyx_v_self->duplicated_fd, ((char const *)"r"));
|
|
jpayne@69
|
20738
|
|
jpayne@69
|
20739 /* "pysam/libctabix.pyx":1125
|
|
jpayne@69
|
20740 * self.fh = bgzf_dopen(self.duplicated_fd, 'r')
|
|
jpayne@69
|
20741 *
|
|
jpayne@69
|
20742 * if self.fh == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20743 * raise IOError('%s' % strerror(errno))
|
|
jpayne@69
|
20744 *
|
|
jpayne@69
|
20745 */
|
|
jpayne@69
|
20746 __pyx_t_2 = (__pyx_v_self->fh == NULL);
|
|
jpayne@69
|
20747 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
20748
|
|
jpayne@69
|
20749 /* "pysam/libctabix.pyx":1126
|
|
jpayne@69
|
20750 *
|
|
jpayne@69
|
20751 * if self.fh == NULL:
|
|
jpayne@69
|
20752 * raise IOError('%s' % strerror(errno)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20753 *
|
|
jpayne@69
|
20754 * self.kstream = ks_init(self.fh)
|
|
jpayne@69
|
20755 */
|
|
jpayne@69
|
20756 __pyx_t_1 = __Pyx_PyBytes_FromString(strerror(errno)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1126, __pyx_L1_error)
|
|
jpayne@69
|
20757 __Pyx_GOTREF(__pyx_t_1);
|
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jpayne@69
|
20758 __pyx_t_4 = PyUnicode_Format(__pyx_kp_u_s, __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1126, __pyx_L1_error)
|
|
jpayne@69
|
20759 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
20760 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
20761 __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1126, __pyx_L1_error)
|
|
jpayne@69
|
20762 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
20763 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
20764 __Pyx_Raise(__pyx_t_1, 0, 0, 0);
|
|
jpayne@69
|
20765 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
20766 __PYX_ERR(0, 1126, __pyx_L1_error)
|
|
jpayne@69
|
20767
|
|
jpayne@69
|
20768 /* "pysam/libctabix.pyx":1125
|
|
jpayne@69
|
20769 * self.fh = bgzf_dopen(self.duplicated_fd, 'r')
|
|
jpayne@69
|
20770 *
|
|
jpayne@69
|
20771 * if self.fh == NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20772 * raise IOError('%s' % strerror(errno))
|
|
jpayne@69
|
20773 *
|
|
jpayne@69
|
20774 */
|
|
jpayne@69
|
20775 }
|
|
jpayne@69
|
20776
|
|
jpayne@69
|
20777 /* "pysam/libctabix.pyx":1128
|
|
jpayne@69
|
20778 * raise IOError('%s' % strerror(errno))
|
|
jpayne@69
|
20779 *
|
|
jpayne@69
|
20780 * self.kstream = ks_init(self.fh) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20781 *
|
|
jpayne@69
|
20782 * self.buffer.s = <char*>malloc(buffer_size)
|
|
jpayne@69
|
20783 */
|
|
jpayne@69
|
20784 __pyx_v_self->kstream = ks_init(__pyx_v_self->fh);
|
|
jpayne@69
|
20785
|
|
jpayne@69
|
20786 /* "pysam/libctabix.pyx":1130
|
|
jpayne@69
|
20787 * self.kstream = ks_init(self.fh)
|
|
jpayne@69
|
20788 *
|
|
jpayne@69
|
20789 * self.buffer.s = <char*>malloc(buffer_size) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20790 * #if self.buffer == NULL:
|
|
jpayne@69
|
20791 * # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size)
|
|
jpayne@69
|
20792 */
|
|
jpayne@69
|
20793 __pyx_v_self->buffer.s = ((char *)malloc(__pyx_v_buffer_size));
|
|
jpayne@69
|
20794
|
|
jpayne@69
|
20795 /* "pysam/libctabix.pyx":1134
|
|
jpayne@69
|
20796 * # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size)
|
|
jpayne@69
|
20797 * #self.size = buffer_size
|
|
jpayne@69
|
20798 * self.parser = parser # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20799 *
|
|
jpayne@69
|
20800 * def __iter__(self):
|
|
jpayne@69
|
20801 */
|
|
jpayne@69
|
20802 __Pyx_INCREF((PyObject *)__pyx_v_parser);
|
|
jpayne@69
|
20803 __Pyx_GIVEREF((PyObject *)__pyx_v_parser);
|
|
jpayne@69
|
20804 __Pyx_GOTREF((PyObject *)__pyx_v_self->parser);
|
|
jpayne@69
|
20805 __Pyx_DECREF((PyObject *)__pyx_v_self->parser);
|
|
jpayne@69
|
20806 __pyx_v_self->parser = __pyx_v_parser;
|
|
jpayne@69
|
20807
|
|
jpayne@69
|
20808 /* "pysam/libctabix.pyx":1102
|
|
jpayne@69
|
20809 * '''
|
|
jpayne@69
|
20810 *
|
|
jpayne@69
|
20811 * def __cinit__(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20812 * infile,
|
|
jpayne@69
|
20813 * Parser parser,
|
|
jpayne@69
|
20814 */
|
|
jpayne@69
|
20815
|
|
jpayne@69
|
20816 /* function exit code */
|
|
jpayne@69
|
20817 __pyx_r = 0;
|
|
jpayne@69
|
20818 goto __pyx_L0;
|
|
jpayne@69
|
20819 __pyx_L1_error:;
|
|
jpayne@69
|
20820 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
20821 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
20822 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
20823 __pyx_r = -1;
|
|
jpayne@69
|
20824 __pyx_L0:;
|
|
jpayne@69
|
20825 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
20826 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
20827 return __pyx_r;
|
|
jpayne@69
|
20828 }
|
|
jpayne@69
|
20829
|
|
jpayne@69
|
20830 /* "pysam/libctabix.pyx":1136
|
|
jpayne@69
|
20831 * self.parser = parser
|
|
jpayne@69
|
20832 *
|
|
jpayne@69
|
20833 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20834 * return self
|
|
jpayne@69
|
20835 *
|
|
jpayne@69
|
20836 */
|
|
jpayne@69
|
20837
|
|
jpayne@69
|
20838 /* Python wrapper */
|
|
jpayne@69
|
20839 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
20840 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
20841 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
20842 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
20843 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
20844 __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
|
|
jpayne@69
|
20845 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
20846 __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_2__iter__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self));
|
|
jpayne@69
|
20847
|
|
jpayne@69
|
20848 /* function exit code */
|
|
jpayne@69
|
20849 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
20850 return __pyx_r;
|
|
jpayne@69
|
20851 }
|
|
jpayne@69
|
20852
|
|
jpayne@69
|
20853 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) {
|
|
jpayne@69
|
20854 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
20855 __Pyx_TraceDeclarations
|
|
jpayne@69
|
20856 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
20857 int __pyx_lineno = 0;
|
|
jpayne@69
|
20858 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
20859 int __pyx_clineno = 0;
|
|
jpayne@69
|
20860 __Pyx_RefNannySetupContext("__iter__", 1);
|
|
jpayne@69
|
20861 __Pyx_TraceCall("__iter__", __pyx_f[0], 1136, 0, __PYX_ERR(0, 1136, __pyx_L1_error));
|
|
jpayne@69
|
20862
|
|
jpayne@69
|
20863 /* "pysam/libctabix.pyx":1137
|
|
jpayne@69
|
20864 *
|
|
jpayne@69
|
20865 * def __iter__(self):
|
|
jpayne@69
|
20866 * return self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20867 *
|
|
jpayne@69
|
20868 * cdef __cnext__(self):
|
|
jpayne@69
|
20869 */
|
|
jpayne@69
|
20870 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
20871 __Pyx_INCREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
20872 __pyx_r = ((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
20873 goto __pyx_L0;
|
|
jpayne@69
|
20874
|
|
jpayne@69
|
20875 /* "pysam/libctabix.pyx":1136
|
|
jpayne@69
|
20876 * self.parser = parser
|
|
jpayne@69
|
20877 *
|
|
jpayne@69
|
20878 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20879 * return self
|
|
jpayne@69
|
20880 *
|
|
jpayne@69
|
20881 */
|
|
jpayne@69
|
20882
|
|
jpayne@69
|
20883 /* function exit code */
|
|
jpayne@69
|
20884 __pyx_L1_error:;
|
|
jpayne@69
|
20885 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
20886 __pyx_r = NULL;
|
|
jpayne@69
|
20887 __pyx_L0:;
|
|
jpayne@69
|
20888 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
20889 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
20890 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
20891 return __pyx_r;
|
|
jpayne@69
|
20892 }
|
|
jpayne@69
|
20893
|
|
jpayne@69
|
20894 /* "pysam/libctabix.pyx":1139
|
|
jpayne@69
|
20895 * return self
|
|
jpayne@69
|
20896 *
|
|
jpayne@69
|
20897 * cdef __cnext__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20898 *
|
|
jpayne@69
|
20899 * cdef char * b
|
|
jpayne@69
|
20900 */
|
|
jpayne@69
|
20901
|
|
jpayne@69
|
20902 static PyObject *__pyx_f_5pysam_9libctabix_19tabix_file_iterator___cnext__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) {
|
|
jpayne@69
|
20903 char *__pyx_v_b;
|
|
jpayne@69
|
20904 int __pyx_v_dret;
|
|
jpayne@69
|
20905 int __pyx_v_retval;
|
|
jpayne@69
|
20906 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
20907 __Pyx_TraceDeclarations
|
|
jpayne@69
|
20908 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
20909 int __pyx_t_1;
|
|
jpayne@69
|
20910 char *__pyx_t_2;
|
|
jpayne@69
|
20911 int __pyx_t_3;
|
|
jpayne@69
|
20912 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
20913 int __pyx_lineno = 0;
|
|
jpayne@69
|
20914 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
20915 int __pyx_clineno = 0;
|
|
jpayne@69
|
20916 __Pyx_RefNannySetupContext("__cnext__", 1);
|
|
jpayne@69
|
20917 __Pyx_TraceCall("__cnext__", __pyx_f[0], 1139, 0, __PYX_ERR(0, 1139, __pyx_L1_error));
|
|
jpayne@69
|
20918
|
|
jpayne@69
|
20919 /* "pysam/libctabix.pyx":1142
|
|
jpayne@69
|
20920 *
|
|
jpayne@69
|
20921 * cdef char * b
|
|
jpayne@69
|
20922 * cdef int dret = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20923 * cdef int retval = 0
|
|
jpayne@69
|
20924 * while 1:
|
|
jpayne@69
|
20925 */
|
|
jpayne@69
|
20926 __pyx_v_dret = 0;
|
|
jpayne@69
|
20927
|
|
jpayne@69
|
20928 /* "pysam/libctabix.pyx":1143
|
|
jpayne@69
|
20929 * cdef char * b
|
|
jpayne@69
|
20930 * cdef int dret = 0
|
|
jpayne@69
|
20931 * cdef int retval = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20932 * while 1:
|
|
jpayne@69
|
20933 * with nogil:
|
|
jpayne@69
|
20934 */
|
|
jpayne@69
|
20935 __pyx_v_retval = 0;
|
|
jpayne@69
|
20936
|
|
jpayne@69
|
20937 /* "pysam/libctabix.pyx":1144
|
|
jpayne@69
|
20938 * cdef int dret = 0
|
|
jpayne@69
|
20939 * cdef int retval = 0
|
|
jpayne@69
|
20940 * while 1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20941 * with nogil:
|
|
jpayne@69
|
20942 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
20943 */
|
|
jpayne@69
|
20944 while (1) {
|
|
jpayne@69
|
20945
|
|
jpayne@69
|
20946 /* "pysam/libctabix.pyx":1145
|
|
jpayne@69
|
20947 * cdef int retval = 0
|
|
jpayne@69
|
20948 * while 1:
|
|
jpayne@69
|
20949 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20950 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
20951 *
|
|
jpayne@69
|
20952 */
|
|
jpayne@69
|
20953 {
|
|
jpayne@69
|
20954 #ifdef WITH_THREAD
|
|
jpayne@69
|
20955 PyThreadState *_save;
|
|
jpayne@69
|
20956 _save = NULL;
|
|
jpayne@69
|
20957 Py_UNBLOCK_THREADS
|
|
jpayne@69
|
20958 __Pyx_FastGIL_Remember();
|
|
jpayne@69
|
20959 #endif
|
|
jpayne@69
|
20960 /*try:*/ {
|
|
jpayne@69
|
20961
|
|
jpayne@69
|
20962 /* "pysam/libctabix.pyx":1146
|
|
jpayne@69
|
20963 * while 1:
|
|
jpayne@69
|
20964 * with nogil:
|
|
jpayne@69
|
20965 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20966 *
|
|
jpayne@69
|
20967 * if retval < 0:
|
|
jpayne@69
|
20968 */
|
|
jpayne@69
|
20969 __pyx_v_retval = ks_getuntil(__pyx_v_self->kstream, '\n', (&__pyx_v_self->buffer), (&__pyx_v_dret));
|
|
jpayne@69
|
20970 }
|
|
jpayne@69
|
20971
|
|
jpayne@69
|
20972 /* "pysam/libctabix.pyx":1145
|
|
jpayne@69
|
20973 * cdef int retval = 0
|
|
jpayne@69
|
20974 * while 1:
|
|
jpayne@69
|
20975 * with nogil: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20976 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
20977 *
|
|
jpayne@69
|
20978 */
|
|
jpayne@69
|
20979 /*finally:*/ {
|
|
jpayne@69
|
20980 /*normal exit:*/{
|
|
jpayne@69
|
20981 #ifdef WITH_THREAD
|
|
jpayne@69
|
20982 __Pyx_FastGIL_Forget();
|
|
jpayne@69
|
20983 Py_BLOCK_THREADS
|
|
jpayne@69
|
20984 #endif
|
|
jpayne@69
|
20985 goto __pyx_L9;
|
|
jpayne@69
|
20986 }
|
|
jpayne@69
|
20987 __pyx_L9:;
|
|
jpayne@69
|
20988 }
|
|
jpayne@69
|
20989 }
|
|
jpayne@69
|
20990
|
|
jpayne@69
|
20991 /* "pysam/libctabix.pyx":1148
|
|
jpayne@69
|
20992 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
20993 *
|
|
jpayne@69
|
20994 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
20995 * break
|
|
jpayne@69
|
20996 * #raise IOError('gzip error: %s' % buildGzipError( self.fh ))
|
|
jpayne@69
|
20997 */
|
|
jpayne@69
|
20998 __pyx_t_1 = (__pyx_v_retval < 0);
|
|
jpayne@69
|
20999 if (__pyx_t_1) {
|
|
jpayne@69
|
21000
|
|
jpayne@69
|
21001 /* "pysam/libctabix.pyx":1149
|
|
jpayne@69
|
21002 *
|
|
jpayne@69
|
21003 * if retval < 0:
|
|
jpayne@69
|
21004 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21005 * #raise IOError('gzip error: %s' % buildGzipError( self.fh ))
|
|
jpayne@69
|
21006 *
|
|
jpayne@69
|
21007 */
|
|
jpayne@69
|
21008 goto __pyx_L4_break;
|
|
jpayne@69
|
21009
|
|
jpayne@69
|
21010 /* "pysam/libctabix.pyx":1148
|
|
jpayne@69
|
21011 * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret)
|
|
jpayne@69
|
21012 *
|
|
jpayne@69
|
21013 * if retval < 0: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21014 * break
|
|
jpayne@69
|
21015 * #raise IOError('gzip error: %s' % buildGzipError( self.fh ))
|
|
jpayne@69
|
21016 */
|
|
jpayne@69
|
21017 }
|
|
jpayne@69
|
21018
|
|
jpayne@69
|
21019 /* "pysam/libctabix.pyx":1152
|
|
jpayne@69
|
21020 * #raise IOError('gzip error: %s' % buildGzipError( self.fh ))
|
|
jpayne@69
|
21021 *
|
|
jpayne@69
|
21022 * b = self.buffer.s # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21023 *
|
|
jpayne@69
|
21024 * # skip comments
|
|
jpayne@69
|
21025 */
|
|
jpayne@69
|
21026 __pyx_t_2 = __pyx_v_self->buffer.s;
|
|
jpayne@69
|
21027 __pyx_v_b = __pyx_t_2;
|
|
jpayne@69
|
21028
|
|
jpayne@69
|
21029 /* "pysam/libctabix.pyx":1155
|
|
jpayne@69
|
21030 *
|
|
jpayne@69
|
21031 * # skip comments
|
|
jpayne@69
|
21032 * if (b[0] == b'#'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21033 * continue
|
|
jpayne@69
|
21034 *
|
|
jpayne@69
|
21035 */
|
|
jpayne@69
|
21036 __pyx_t_1 = ((__pyx_v_b[0]) == '#');
|
|
jpayne@69
|
21037 if (__pyx_t_1) {
|
|
jpayne@69
|
21038
|
|
jpayne@69
|
21039 /* "pysam/libctabix.pyx":1156
|
|
jpayne@69
|
21040 * # skip comments
|
|
jpayne@69
|
21041 * if (b[0] == b'#'):
|
|
jpayne@69
|
21042 * continue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21043 *
|
|
jpayne@69
|
21044 * # skip empty lines
|
|
jpayne@69
|
21045 */
|
|
jpayne@69
|
21046 goto __pyx_L3_continue;
|
|
jpayne@69
|
21047
|
|
jpayne@69
|
21048 /* "pysam/libctabix.pyx":1155
|
|
jpayne@69
|
21049 *
|
|
jpayne@69
|
21050 * # skip comments
|
|
jpayne@69
|
21051 * if (b[0] == b'#'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21052 * continue
|
|
jpayne@69
|
21053 *
|
|
jpayne@69
|
21054 */
|
|
jpayne@69
|
21055 }
|
|
jpayne@69
|
21056
|
|
jpayne@69
|
21057 /* "pysam/libctabix.pyx":1159
|
|
jpayne@69
|
21058 *
|
|
jpayne@69
|
21059 * # skip empty lines
|
|
jpayne@69
|
21060 * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21061 * continue
|
|
jpayne@69
|
21062 *
|
|
jpayne@69
|
21063 */
|
|
jpayne@69
|
21064 __pyx_t_3 = ((__pyx_v_b[0]) == '\x00');
|
|
jpayne@69
|
21065 if (!__pyx_t_3) {
|
|
jpayne@69
|
21066 } else {
|
|
jpayne@69
|
21067 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
21068 goto __pyx_L13_bool_binop_done;
|
|
jpayne@69
|
21069 }
|
|
jpayne@69
|
21070 __pyx_t_3 = ((__pyx_v_b[0]) == '\n');
|
|
jpayne@69
|
21071 if (!__pyx_t_3) {
|
|
jpayne@69
|
21072 } else {
|
|
jpayne@69
|
21073 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
21074 goto __pyx_L13_bool_binop_done;
|
|
jpayne@69
|
21075 }
|
|
jpayne@69
|
21076 __pyx_t_3 = ((__pyx_v_b[0]) == '\r');
|
|
jpayne@69
|
21077 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
21078 __pyx_L13_bool_binop_done:;
|
|
jpayne@69
|
21079 if (__pyx_t_1) {
|
|
jpayne@69
|
21080
|
|
jpayne@69
|
21081 /* "pysam/libctabix.pyx":1160
|
|
jpayne@69
|
21082 * # skip empty lines
|
|
jpayne@69
|
21083 * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r':
|
|
jpayne@69
|
21084 * continue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21085 *
|
|
jpayne@69
|
21086 * # gzgets terminates at \n, no need to test
|
|
jpayne@69
|
21087 */
|
|
jpayne@69
|
21088 goto __pyx_L3_continue;
|
|
jpayne@69
|
21089
|
|
jpayne@69
|
21090 /* "pysam/libctabix.pyx":1159
|
|
jpayne@69
|
21091 *
|
|
jpayne@69
|
21092 * # skip empty lines
|
|
jpayne@69
|
21093 * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21094 * continue
|
|
jpayne@69
|
21095 *
|
|
jpayne@69
|
21096 */
|
|
jpayne@69
|
21097 }
|
|
jpayne@69
|
21098
|
|
jpayne@69
|
21099 /* "pysam/libctabix.pyx":1165
|
|
jpayne@69
|
21100 *
|
|
jpayne@69
|
21101 * # parser creates a copy
|
|
jpayne@69
|
21102 * return self.parser.parse(b, self.buffer.l) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21103 *
|
|
jpayne@69
|
21104 * raise StopIteration
|
|
jpayne@69
|
21105 */
|
|
jpayne@69
|
21106 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
21107 __pyx_t_4 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->parser->__pyx_vtab)->parse(__pyx_v_self->parser, __pyx_v_b, __pyx_v_self->buffer.l); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1165, __pyx_L1_error)
|
|
jpayne@69
|
21108 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
21109 __pyx_r = __pyx_t_4;
|
|
jpayne@69
|
21110 __pyx_t_4 = 0;
|
|
jpayne@69
|
21111 goto __pyx_L0;
|
|
jpayne@69
|
21112 __pyx_L3_continue:;
|
|
jpayne@69
|
21113 }
|
|
jpayne@69
|
21114 __pyx_L4_break:;
|
|
jpayne@69
|
21115
|
|
jpayne@69
|
21116 /* "pysam/libctabix.pyx":1167
|
|
jpayne@69
|
21117 * return self.parser.parse(b, self.buffer.l)
|
|
jpayne@69
|
21118 *
|
|
jpayne@69
|
21119 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21120 *
|
|
jpayne@69
|
21121 * def __dealloc__(self):
|
|
jpayne@69
|
21122 */
|
|
jpayne@69
|
21123 __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
|
|
jpayne@69
|
21124 __PYX_ERR(0, 1167, __pyx_L1_error)
|
|
jpayne@69
|
21125
|
|
jpayne@69
|
21126 /* "pysam/libctabix.pyx":1139
|
|
jpayne@69
|
21127 * return self
|
|
jpayne@69
|
21128 *
|
|
jpayne@69
|
21129 * cdef __cnext__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21130 *
|
|
jpayne@69
|
21131 * cdef char * b
|
|
jpayne@69
|
21132 */
|
|
jpayne@69
|
21133
|
|
jpayne@69
|
21134 /* function exit code */
|
|
jpayne@69
|
21135 __pyx_L1_error:;
|
|
jpayne@69
|
21136 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
21137 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21138 __pyx_r = 0;
|
|
jpayne@69
|
21139 __pyx_L0:;
|
|
jpayne@69
|
21140 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
21141 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
21142 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21143 return __pyx_r;
|
|
jpayne@69
|
21144 }
|
|
jpayne@69
|
21145
|
|
jpayne@69
|
21146 /* "pysam/libctabix.pyx":1169
|
|
jpayne@69
|
21147 * raise StopIteration
|
|
jpayne@69
|
21148 *
|
|
jpayne@69
|
21149 * def __dealloc__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21150 * free(self.buffer.s)
|
|
jpayne@69
|
21151 * ks_destroy(self.kstream)
|
|
jpayne@69
|
21152 */
|
|
jpayne@69
|
21153
|
|
jpayne@69
|
21154 /* Python wrapper */
|
|
jpayne@69
|
21155 static void __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
21156 static void __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_5__dealloc__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
21157 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21158 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21159 __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
|
|
jpayne@69
|
21160 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21161 __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_4__dealloc__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self));
|
|
jpayne@69
|
21162
|
|
jpayne@69
|
21163 /* function exit code */
|
|
jpayne@69
|
21164 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21165 }
|
|
jpayne@69
|
21166
|
|
jpayne@69
|
21167 static void __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) {
|
|
jpayne@69
|
21168 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21169 int __pyx_lineno = 0;
|
|
jpayne@69
|
21170 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21171 int __pyx_clineno = 0;
|
|
jpayne@69
|
21172 __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1169, 0, __PYX_ERR(0, 1169, __pyx_L1_error));
|
|
jpayne@69
|
21173
|
|
jpayne@69
|
21174 /* "pysam/libctabix.pyx":1170
|
|
jpayne@69
|
21175 *
|
|
jpayne@69
|
21176 * def __dealloc__(self):
|
|
jpayne@69
|
21177 * free(self.buffer.s) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21178 * ks_destroy(self.kstream)
|
|
jpayne@69
|
21179 * bgzf_close(self.fh)
|
|
jpayne@69
|
21180 */
|
|
jpayne@69
|
21181 free(__pyx_v_self->buffer.s);
|
|
jpayne@69
|
21182
|
|
jpayne@69
|
21183 /* "pysam/libctabix.pyx":1171
|
|
jpayne@69
|
21184 * def __dealloc__(self):
|
|
jpayne@69
|
21185 * free(self.buffer.s)
|
|
jpayne@69
|
21186 * ks_destroy(self.kstream) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21187 * bgzf_close(self.fh)
|
|
jpayne@69
|
21188 *
|
|
jpayne@69
|
21189 */
|
|
jpayne@69
|
21190 ks_destroy(__pyx_v_self->kstream);
|
|
jpayne@69
|
21191
|
|
jpayne@69
|
21192 /* "pysam/libctabix.pyx":1172
|
|
jpayne@69
|
21193 * free(self.buffer.s)
|
|
jpayne@69
|
21194 * ks_destroy(self.kstream)
|
|
jpayne@69
|
21195 * bgzf_close(self.fh) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21196 *
|
|
jpayne@69
|
21197 * def __next__(self):
|
|
jpayne@69
|
21198 */
|
|
jpayne@69
|
21199 (void)(bgzf_close(__pyx_v_self->fh));
|
|
jpayne@69
|
21200
|
|
jpayne@69
|
21201 /* "pysam/libctabix.pyx":1169
|
|
jpayne@69
|
21202 * raise StopIteration
|
|
jpayne@69
|
21203 *
|
|
jpayne@69
|
21204 * def __dealloc__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21205 * free(self.buffer.s)
|
|
jpayne@69
|
21206 * ks_destroy(self.kstream)
|
|
jpayne@69
|
21207 */
|
|
jpayne@69
|
21208
|
|
jpayne@69
|
21209 /* function exit code */
|
|
jpayne@69
|
21210 goto __pyx_L0;
|
|
jpayne@69
|
21211 __pyx_L1_error:;
|
|
jpayne@69
|
21212 __Pyx_WriteUnraisable("pysam.libctabix.tabix_file_iterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0);
|
|
jpayne@69
|
21213 __pyx_L0:;
|
|
jpayne@69
|
21214 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
21215 }
|
|
jpayne@69
|
21216
|
|
jpayne@69
|
21217 /* "pysam/libctabix.pyx":1174
|
|
jpayne@69
|
21218 * bgzf_close(self.fh)
|
|
jpayne@69
|
21219 *
|
|
jpayne@69
|
21220 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21221 * return self.__cnext__()
|
|
jpayne@69
|
21222 *
|
|
jpayne@69
|
21223 */
|
|
jpayne@69
|
21224
|
|
jpayne@69
|
21225 /* Python wrapper */
|
|
jpayne@69
|
21226 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(PyObject *__pyx_v_self); /*proto*/
|
|
jpayne@69
|
21227 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(PyObject *__pyx_v_self) {
|
|
jpayne@69
|
21228 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21229 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
21230 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21231 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
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|
jpayne@69
|
21232 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21233 __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_6__next__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self));
|
|
jpayne@69
|
21234
|
|
jpayne@69
|
21235 /* function exit code */
|
|
jpayne@69
|
21236 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21237 return __pyx_r;
|
|
jpayne@69
|
21238 }
|
|
jpayne@69
|
21239
|
|
jpayne@69
|
21240 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) {
|
|
jpayne@69
|
21241 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
21242 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21243 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21244 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
21245 int __pyx_lineno = 0;
|
|
jpayne@69
|
21246 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21247 int __pyx_clineno = 0;
|
|
jpayne@69
|
21248 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
21249 __Pyx_TraceCall("__next__", __pyx_f[0], 1174, 0, __PYX_ERR(0, 1174, __pyx_L1_error));
|
|
jpayne@69
|
21250
|
|
jpayne@69
|
21251 /* "pysam/libctabix.pyx":1175
|
|
jpayne@69
|
21252 *
|
|
jpayne@69
|
21253 * def __next__(self):
|
|
jpayne@69
|
21254 * return self.__cnext__() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21255 *
|
|
jpayne@69
|
21256 *
|
|
jpayne@69
|
21257 */
|
|
jpayne@69
|
21258 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
21259 __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1175, __pyx_L1_error)
|
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jpayne@69
|
21260 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
21261 __pyx_r = __pyx_t_1;
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jpayne@69
|
21262 __pyx_t_1 = 0;
|
|
jpayne@69
|
21263 goto __pyx_L0;
|
|
jpayne@69
|
21264
|
|
jpayne@69
|
21265 /* "pysam/libctabix.pyx":1174
|
|
jpayne@69
|
21266 * bgzf_close(self.fh)
|
|
jpayne@69
|
21267 *
|
|
jpayne@69
|
21268 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21269 * return self.__cnext__()
|
|
jpayne@69
|
21270 *
|
|
jpayne@69
|
21271 */
|
|
jpayne@69
|
21272
|
|
jpayne@69
|
21273 /* function exit code */
|
|
jpayne@69
|
21274 __pyx_L1_error:;
|
|
jpayne@69
|
21275 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
21276 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21277 __pyx_r = NULL;
|
|
jpayne@69
|
21278 __pyx_L0:;
|
|
jpayne@69
|
21279 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
21280 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
21281 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21282 return __pyx_r;
|
|
jpayne@69
|
21283 }
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|
jpayne@69
|
21284
|
|
jpayne@69
|
21285 /* "(tree fragment)":1
|
|
jpayne@69
|
21286 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21287 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21288 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
21289 */
|
|
jpayne@69
|
21290
|
|
jpayne@69
|
21291 /* Python wrapper */
|
|
jpayne@69
|
21292 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
21293 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21294 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21295 #else
|
|
jpayne@69
|
21296 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21297 #endif
|
|
jpayne@69
|
21298 ); /*proto*/
|
|
jpayne@69
|
21299 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__, "tabix_file_iterator.__reduce_cython__(self)");
|
|
jpayne@69
|
21300 static PyMethodDef __pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__};
|
|
jpayne@69
|
21301 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
21302 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21303 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21304 #else
|
|
jpayne@69
|
21305 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21306 #endif
|
|
jpayne@69
|
21307 ) {
|
|
jpayne@69
|
21308 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21309 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
21310 #endif
|
|
jpayne@69
|
21311 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21312 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
21313 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21314 __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0);
|
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jpayne@69
|
21315 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21316 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
21317 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
21318 #else
|
|
jpayne@69
|
21319 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
21320 #endif
|
|
jpayne@69
|
21321 #endif
|
|
jpayne@69
|
21322 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21323 if (unlikely(__pyx_nargs > 0)) {
|
|
jpayne@69
|
21324 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
|
|
jpayne@69
|
21325 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
|
|
jpayne@69
|
21326 __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self));
|
|
jpayne@69
|
21327
|
|
jpayne@69
|
21328 /* function exit code */
|
|
jpayne@69
|
21329 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21330 return __pyx_r;
|
|
jpayne@69
|
21331 }
|
|
jpayne@69
|
21332
|
|
jpayne@69
|
21333 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) {
|
|
jpayne@69
|
21334 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
21335 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21336 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21337 int __pyx_lineno = 0;
|
|
jpayne@69
|
21338 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21339 int __pyx_clineno = 0;
|
|
jpayne@69
|
21340 __Pyx_TraceFrameInit(__pyx_codeobj__46)
|
|
jpayne@69
|
21341 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
|
|
jpayne@69
|
21342 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
21343
|
|
jpayne@69
|
21344 /* "(tree fragment)":2
|
|
jpayne@69
|
21345 * def __reduce_cython__(self):
|
|
jpayne@69
|
21346 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21347 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
21348 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21349 */
|
|
jpayne@69
|
21350 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
|
|
jpayne@69
|
21351 __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
21352
|
|
jpayne@69
|
21353 /* "(tree fragment)":1
|
|
jpayne@69
|
21354 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21355 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21356 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
21357 */
|
|
jpayne@69
|
21358
|
|
jpayne@69
|
21359 /* function exit code */
|
|
jpayne@69
|
21360 __pyx_L1_error:;
|
|
jpayne@69
|
21361 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21362 __pyx_r = NULL;
|
|
jpayne@69
|
21363 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
21364 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
21365 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21366 return __pyx_r;
|
|
jpayne@69
|
21367 }
|
|
jpayne@69
|
21368
|
|
jpayne@69
|
21369 /* "(tree fragment)":3
|
|
jpayne@69
|
21370 * def __reduce_cython__(self):
|
|
jpayne@69
|
21371 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21372 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21373 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21374 */
|
|
jpayne@69
|
21375
|
|
jpayne@69
|
21376 /* Python wrapper */
|
|
jpayne@69
|
21377 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
21378 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21379 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21380 #else
|
|
jpayne@69
|
21381 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21382 #endif
|
|
jpayne@69
|
21383 ); /*proto*/
|
|
jpayne@69
|
21384 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__, "tabix_file_iterator.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
21385 static PyMethodDef __pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__};
|
|
jpayne@69
|
21386 static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
21387 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21388 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21389 #else
|
|
jpayne@69
|
21390 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21391 #endif
|
|
jpayne@69
|
21392 ) {
|
|
jpayne@69
|
21393 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
21394 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21395 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
21396 #endif
|
|
jpayne@69
|
21397 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21398 PyObject* values[1] = {0};
|
|
jpayne@69
|
21399 int __pyx_lineno = 0;
|
|
jpayne@69
|
21400 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21401 int __pyx_clineno = 0;
|
|
jpayne@69
|
21402 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
21403 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21404 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
21405 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21406 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
21407 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
21408 #else
|
|
jpayne@69
|
21409 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
21410 #endif
|
|
jpayne@69
|
21411 #endif
|
|
jpayne@69
|
21412 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21413 {
|
|
jpayne@69
|
21414 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
21415 if (__pyx_kwds) {
|
|
jpayne@69
|
21416 Py_ssize_t kw_args;
|
|
jpayne@69
|
21417 switch (__pyx_nargs) {
|
|
jpayne@69
|
21418 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21419 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21420 case 0: break;
|
|
jpayne@69
|
21421 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21422 }
|
|
jpayne@69
|
21423 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
21424 switch (__pyx_nargs) {
|
|
jpayne@69
|
21425 case 0:
|
|
jpayne@69
|
21426 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
21427 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
21428 kw_args--;
|
|
jpayne@69
|
21429 }
|
|
jpayne@69
|
21430 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
21431 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21432 }
|
|
jpayne@69
|
21433 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
21434 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
21435 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
21436 }
|
|
jpayne@69
|
21437 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
21438 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21439 } else {
|
|
jpayne@69
|
21440 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21441 }
|
|
jpayne@69
|
21442 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
21443 }
|
|
jpayne@69
|
21444 goto __pyx_L6_skip;
|
|
jpayne@69
|
21445 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
21446 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
21447 __pyx_L6_skip:;
|
|
jpayne@69
|
21448 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
21449 __pyx_L3_error:;
|
|
jpayne@69
|
21450 {
|
|
jpayne@69
|
21451 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21452 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21453 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21454 }
|
|
jpayne@69
|
21455 }
|
|
jpayne@69
|
21456 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21457 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21458 return NULL;
|
|
jpayne@69
|
21459 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
21460 __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
21461
|
|
jpayne@69
|
21462 /* function exit code */
|
|
jpayne@69
|
21463 {
|
|
jpayne@69
|
21464 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21465 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21466 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21467 }
|
|
jpayne@69
|
21468 }
|
|
jpayne@69
|
21469 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21470 return __pyx_r;
|
|
jpayne@69
|
21471 }
|
|
jpayne@69
|
21472
|
|
jpayne@69
|
21473 static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
21474 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
21475 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21476 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21477 int __pyx_lineno = 0;
|
|
jpayne@69
|
21478 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21479 int __pyx_clineno = 0;
|
|
jpayne@69
|
21480 __Pyx_TraceFrameInit(__pyx_codeobj__47)
|
|
jpayne@69
|
21481 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
21482 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
21483
|
|
jpayne@69
|
21484 /* "(tree fragment)":4
|
|
jpayne@69
|
21485 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21486 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
21487 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21488 */
|
|
jpayne@69
|
21489 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
|
|
jpayne@69
|
21490 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
21491
|
|
jpayne@69
|
21492 /* "(tree fragment)":3
|
|
jpayne@69
|
21493 * def __reduce_cython__(self):
|
|
jpayne@69
|
21494 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21495 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21496 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
21497 */
|
|
jpayne@69
|
21498
|
|
jpayne@69
|
21499 /* function exit code */
|
|
jpayne@69
|
21500 __pyx_L1_error:;
|
|
jpayne@69
|
21501 __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21502 __pyx_r = NULL;
|
|
jpayne@69
|
21503 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
21504 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
21505 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21506 return __pyx_r;
|
|
jpayne@69
|
21507 }
|
|
jpayne@69
|
21508
|
|
jpayne@69
|
21509 /* "pysam/libctabix.pyx":1183
|
|
jpayne@69
|
21510 * Permits the use of file-like objects for example from the gzip module.
|
|
jpayne@69
|
21511 * '''
|
|
jpayne@69
|
21512 * def __init__(self, infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21513 *
|
|
jpayne@69
|
21514 * self.infile = infile
|
|
jpayne@69
|
21515 */
|
|
jpayne@69
|
21516
|
|
jpayne@69
|
21517 /* Python wrapper */
|
|
jpayne@69
|
21518 static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self,
|
|
jpayne@69
|
21519 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21520 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21521 #else
|
|
jpayne@69
|
21522 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21523 #endif
|
|
jpayne@69
|
21524 ); /*proto*/
|
|
jpayne@69
|
21525 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_22tabix_generic_iterator___init__, "tabix_generic_iterator.__init__(self, infile, parser)");
|
|
jpayne@69
|
21526 static PyMethodDef __pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_1__init__ = {"__init__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_22tabix_generic_iterator___init__};
|
|
jpayne@69
|
21527 static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self,
|
|
jpayne@69
|
21528 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21529 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21530 #else
|
|
jpayne@69
|
21531 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21532 #endif
|
|
jpayne@69
|
21533 ) {
|
|
jpayne@69
|
21534 PyObject *__pyx_v_self = 0;
|
|
jpayne@69
|
21535 PyObject *__pyx_v_infile = 0;
|
|
jpayne@69
|
21536 PyObject *__pyx_v_parser = 0;
|
|
jpayne@69
|
21537 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21538 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
21539 #endif
|
|
jpayne@69
|
21540 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21541 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
21542 int __pyx_lineno = 0;
|
|
jpayne@69
|
21543 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21544 int __pyx_clineno = 0;
|
|
jpayne@69
|
21545 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
21546 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21547 __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
|
|
jpayne@69
|
21548 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21549 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
21550 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
21551 #else
|
|
jpayne@69
|
21552 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
21553 #endif
|
|
jpayne@69
|
21554 #endif
|
|
jpayne@69
|
21555 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21556 {
|
|
jpayne@69
|
21557 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_infile,&__pyx_n_s_parser,0};
|
|
jpayne@69
|
21558 if (__pyx_kwds) {
|
|
jpayne@69
|
21559 Py_ssize_t kw_args;
|
|
jpayne@69
|
21560 switch (__pyx_nargs) {
|
|
jpayne@69
|
21561 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
21562 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21563 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
21564 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21565 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21566 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21567 case 0: break;
|
|
jpayne@69
|
21568 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21569 }
|
|
jpayne@69
|
21570 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
21571 switch (__pyx_nargs) {
|
|
jpayne@69
|
21572 case 0:
|
|
jpayne@69
|
21573 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
|
|
jpayne@69
|
21574 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
21575 kw_args--;
|
|
jpayne@69
|
21576 }
|
|
jpayne@69
|
21577 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21578 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21579 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21580 case 1:
|
|
jpayne@69
|
21581 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_infile)) != 0)) {
|
|
jpayne@69
|
21582 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
21583 kw_args--;
|
|
jpayne@69
|
21584 }
|
|
jpayne@69
|
21585 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21586 else {
|
|
jpayne@69
|
21587 __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21588 }
|
|
jpayne@69
|
21589 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21590 case 2:
|
|
jpayne@69
|
21591 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) {
|
|
jpayne@69
|
21592 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
21593 kw_args--;
|
|
jpayne@69
|
21594 }
|
|
jpayne@69
|
21595 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21596 else {
|
|
jpayne@69
|
21597 __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21598 }
|
|
jpayne@69
|
21599 }
|
|
jpayne@69
|
21600 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
21601 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
21602 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21603 }
|
|
jpayne@69
|
21604 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
21605 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21606 } else {
|
|
jpayne@69
|
21607 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21608 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
21609 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
21610 }
|
|
jpayne@69
|
21611 __pyx_v_self = values[0];
|
|
jpayne@69
|
21612 __pyx_v_infile = values[1];
|
|
jpayne@69
|
21613 __pyx_v_parser = values[2];
|
|
jpayne@69
|
21614 }
|
|
jpayne@69
|
21615 goto __pyx_L6_skip;
|
|
jpayne@69
|
21616 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
21617 __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 1183, __pyx_L3_error)
|
|
jpayne@69
|
21618 __pyx_L6_skip:;
|
|
jpayne@69
|
21619 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
21620 __pyx_L3_error:;
|
|
jpayne@69
|
21621 {
|
|
jpayne@69
|
21622 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21623 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21624 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21625 }
|
|
jpayne@69
|
21626 }
|
|
jpayne@69
|
21627 __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21628 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21629 return NULL;
|
|
jpayne@69
|
21630 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
21631 __pyx_r = __pyx_pf_5pysam_9libctabix_22tabix_generic_iterator___init__(__pyx_self, __pyx_v_self, __pyx_v_infile, __pyx_v_parser);
|
|
jpayne@69
|
21632
|
|
jpayne@69
|
21633 /* function exit code */
|
|
jpayne@69
|
21634 {
|
|
jpayne@69
|
21635 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21636 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21637 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21638 }
|
|
jpayne@69
|
21639 }
|
|
jpayne@69
|
21640 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21641 return __pyx_r;
|
|
jpayne@69
|
21642 }
|
|
jpayne@69
|
21643
|
|
jpayne@69
|
21644 static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) {
|
|
jpayne@69
|
21645 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
21646 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21647 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21648 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
21649 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
21650 int __pyx_t_3;
|
|
jpayne@69
|
21651 int __pyx_lineno = 0;
|
|
jpayne@69
|
21652 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21653 int __pyx_clineno = 0;
|
|
jpayne@69
|
21654 __Pyx_TraceFrameInit(__pyx_codeobj__48)
|
|
jpayne@69
|
21655 __Pyx_RefNannySetupContext("__init__", 1);
|
|
jpayne@69
|
21656 __Pyx_TraceCall("__init__", __pyx_f[0], 1183, 0, __PYX_ERR(0, 1183, __pyx_L1_error));
|
|
jpayne@69
|
21657
|
|
jpayne@69
|
21658 /* "pysam/libctabix.pyx":1185
|
|
jpayne@69
|
21659 * def __init__(self, infile, parser):
|
|
jpayne@69
|
21660 *
|
|
jpayne@69
|
21661 * self.infile = infile # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21662 * if self.infile.closed:
|
|
jpayne@69
|
21663 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
21664 */
|
|
jpayne@69
|
21665 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_infile, __pyx_v_infile) < 0) __PYX_ERR(0, 1185, __pyx_L1_error)
|
|
jpayne@69
|
21666
|
|
jpayne@69
|
21667 /* "pysam/libctabix.pyx":1186
|
|
jpayne@69
|
21668 *
|
|
jpayne@69
|
21669 * self.infile = infile
|
|
jpayne@69
|
21670 * if self.infile.closed: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21671 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
21672 * self.parser = parser
|
|
jpayne@69
|
21673 */
|
|
jpayne@69
|
21674 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_infile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1186, __pyx_L1_error)
|
|
jpayne@69
|
21675 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
21676 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_closed); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1186, __pyx_L1_error)
|
|
jpayne@69
|
21677 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
21678 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
21679 __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 1186, __pyx_L1_error)
|
|
jpayne@69
|
21680 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
21681 if (unlikely(__pyx_t_3)) {
|
|
jpayne@69
|
21682
|
|
jpayne@69
|
21683 /* "pysam/libctabix.pyx":1187
|
|
jpayne@69
|
21684 * self.infile = infile
|
|
jpayne@69
|
21685 * if self.infile.closed:
|
|
jpayne@69
|
21686 * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21687 * self.parser = parser
|
|
jpayne@69
|
21688 *
|
|
jpayne@69
|
21689 */
|
|
jpayne@69
|
21690 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1187, __pyx_L1_error)
|
|
jpayne@69
|
21691 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
21692 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
21693 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
21694 __PYX_ERR(0, 1187, __pyx_L1_error)
|
|
jpayne@69
|
21695
|
|
jpayne@69
|
21696 /* "pysam/libctabix.pyx":1186
|
|
jpayne@69
|
21697 *
|
|
jpayne@69
|
21698 * self.infile = infile
|
|
jpayne@69
|
21699 * if self.infile.closed: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21700 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
21701 * self.parser = parser
|
|
jpayne@69
|
21702 */
|
|
jpayne@69
|
21703 }
|
|
jpayne@69
|
21704
|
|
jpayne@69
|
21705 /* "pysam/libctabix.pyx":1188
|
|
jpayne@69
|
21706 * if self.infile.closed:
|
|
jpayne@69
|
21707 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
21708 * self.parser = parser # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21709 *
|
|
jpayne@69
|
21710 * def __iter__(self):
|
|
jpayne@69
|
21711 */
|
|
jpayne@69
|
21712 if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_parser, __pyx_v_parser) < 0) __PYX_ERR(0, 1188, __pyx_L1_error)
|
|
jpayne@69
|
21713
|
|
jpayne@69
|
21714 /* "pysam/libctabix.pyx":1183
|
|
jpayne@69
|
21715 * Permits the use of file-like objects for example from the gzip module.
|
|
jpayne@69
|
21716 * '''
|
|
jpayne@69
|
21717 * def __init__(self, infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21718 *
|
|
jpayne@69
|
21719 * self.infile = infile
|
|
jpayne@69
|
21720 */
|
|
jpayne@69
|
21721
|
|
jpayne@69
|
21722 /* function exit code */
|
|
jpayne@69
|
21723 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
21724 goto __pyx_L0;
|
|
jpayne@69
|
21725 __pyx_L1_error:;
|
|
jpayne@69
|
21726 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
21727 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
21728 __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21729 __pyx_r = NULL;
|
|
jpayne@69
|
21730 __pyx_L0:;
|
|
jpayne@69
|
21731 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
21732 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
21733 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21734 return __pyx_r;
|
|
jpayne@69
|
21735 }
|
|
jpayne@69
|
21736
|
|
jpayne@69
|
21737 /* "pysam/libctabix.pyx":1190
|
|
jpayne@69
|
21738 * self.parser = parser
|
|
jpayne@69
|
21739 *
|
|
jpayne@69
|
21740 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21741 * return self
|
|
jpayne@69
|
21742 *
|
|
jpayne@69
|
21743 */
|
|
jpayne@69
|
21744
|
|
jpayne@69
|
21745 /* Python wrapper */
|
|
jpayne@69
|
21746 static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self,
|
|
jpayne@69
|
21747 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21748 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21749 #else
|
|
jpayne@69
|
21750 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21751 #endif
|
|
jpayne@69
|
21752 ); /*proto*/
|
|
jpayne@69
|
21753 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_2__iter__, "tabix_generic_iterator.__iter__(self)");
|
|
jpayne@69
|
21754 static PyMethodDef __pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_3__iter__ = {"__iter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_3__iter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_2__iter__};
|
|
jpayne@69
|
21755 static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self,
|
|
jpayne@69
|
21756 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21757 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21758 #else
|
|
jpayne@69
|
21759 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21760 #endif
|
|
jpayne@69
|
21761 ) {
|
|
jpayne@69
|
21762 PyObject *__pyx_v_self = 0;
|
|
jpayne@69
|
21763 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21764 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
21765 #endif
|
|
jpayne@69
|
21766 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21767 PyObject* values[1] = {0};
|
|
jpayne@69
|
21768 int __pyx_lineno = 0;
|
|
jpayne@69
|
21769 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21770 int __pyx_clineno = 0;
|
|
jpayne@69
|
21771 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
21772 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21773 __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
|
|
jpayne@69
|
21774 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21775 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
21776 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
21777 #else
|
|
jpayne@69
|
21778 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
21779 #endif
|
|
jpayne@69
|
21780 #endif
|
|
jpayne@69
|
21781 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21782 {
|
|
jpayne@69
|
21783 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
|
|
jpayne@69
|
21784 if (__pyx_kwds) {
|
|
jpayne@69
|
21785 Py_ssize_t kw_args;
|
|
jpayne@69
|
21786 switch (__pyx_nargs) {
|
|
jpayne@69
|
21787 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21788 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21789 case 0: break;
|
|
jpayne@69
|
21790 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21791 }
|
|
jpayne@69
|
21792 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
21793 switch (__pyx_nargs) {
|
|
jpayne@69
|
21794 case 0:
|
|
jpayne@69
|
21795 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
|
|
jpayne@69
|
21796 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
21797 kw_args--;
|
|
jpayne@69
|
21798 }
|
|
jpayne@69
|
21799 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1190, __pyx_L3_error)
|
|
jpayne@69
|
21800 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21801 }
|
|
jpayne@69
|
21802 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
21803 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
21804 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__iter__") < 0)) __PYX_ERR(0, 1190, __pyx_L3_error)
|
|
jpayne@69
|
21805 }
|
|
jpayne@69
|
21806 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
21807 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21808 } else {
|
|
jpayne@69
|
21809 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21810 }
|
|
jpayne@69
|
21811 __pyx_v_self = values[0];
|
|
jpayne@69
|
21812 }
|
|
jpayne@69
|
21813 goto __pyx_L6_skip;
|
|
jpayne@69
|
21814 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
21815 __Pyx_RaiseArgtupleInvalid("__iter__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 1190, __pyx_L3_error)
|
|
jpayne@69
|
21816 __pyx_L6_skip:;
|
|
jpayne@69
|
21817 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
21818 __pyx_L3_error:;
|
|
jpayne@69
|
21819 {
|
|
jpayne@69
|
21820 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21821 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21822 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21823 }
|
|
jpayne@69
|
21824 }
|
|
jpayne@69
|
21825 __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21826 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21827 return NULL;
|
|
jpayne@69
|
21828 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
21829 __pyx_r = __pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_2__iter__(__pyx_self, __pyx_v_self);
|
|
jpayne@69
|
21830
|
|
jpayne@69
|
21831 /* function exit code */
|
|
jpayne@69
|
21832 {
|
|
jpayne@69
|
21833 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21834 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21835 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21836 }
|
|
jpayne@69
|
21837 }
|
|
jpayne@69
|
21838 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
21839 return __pyx_r;
|
|
jpayne@69
|
21840 }
|
|
jpayne@69
|
21841
|
|
jpayne@69
|
21842 static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
|
|
jpayne@69
|
21843 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
21844 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21845 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21846 int __pyx_lineno = 0;
|
|
jpayne@69
|
21847 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21848 int __pyx_clineno = 0;
|
|
jpayne@69
|
21849 __Pyx_TraceFrameInit(__pyx_codeobj__49)
|
|
jpayne@69
|
21850 __Pyx_RefNannySetupContext("__iter__", 1);
|
|
jpayne@69
|
21851 __Pyx_TraceCall("__iter__", __pyx_f[0], 1190, 0, __PYX_ERR(0, 1190, __pyx_L1_error));
|
|
jpayne@69
|
21852
|
|
jpayne@69
|
21853 /* "pysam/libctabix.pyx":1191
|
|
jpayne@69
|
21854 *
|
|
jpayne@69
|
21855 * def __iter__(self):
|
|
jpayne@69
|
21856 * return self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21857 *
|
|
jpayne@69
|
21858 * # cython version - required for python 3
|
|
jpayne@69
|
21859 */
|
|
jpayne@69
|
21860 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
21861 __Pyx_INCREF(__pyx_v_self);
|
|
jpayne@69
|
21862 __pyx_r = __pyx_v_self;
|
|
jpayne@69
|
21863 goto __pyx_L0;
|
|
jpayne@69
|
21864
|
|
jpayne@69
|
21865 /* "pysam/libctabix.pyx":1190
|
|
jpayne@69
|
21866 * self.parser = parser
|
|
jpayne@69
|
21867 *
|
|
jpayne@69
|
21868 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21869 * return self
|
|
jpayne@69
|
21870 *
|
|
jpayne@69
|
21871 */
|
|
jpayne@69
|
21872
|
|
jpayne@69
|
21873 /* function exit code */
|
|
jpayne@69
|
21874 __pyx_L1_error:;
|
|
jpayne@69
|
21875 __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21876 __pyx_r = NULL;
|
|
jpayne@69
|
21877 __pyx_L0:;
|
|
jpayne@69
|
21878 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
21879 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
21880 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21881 return __pyx_r;
|
|
jpayne@69
|
21882 }
|
|
jpayne@69
|
21883
|
|
jpayne@69
|
21884 /* "pysam/libctabix.pyx":1194
|
|
jpayne@69
|
21885 *
|
|
jpayne@69
|
21886 * # cython version - required for python 3
|
|
jpayne@69
|
21887 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
21888 *
|
|
jpayne@69
|
21889 * cdef char * b
|
|
jpayne@69
|
21890 */
|
|
jpayne@69
|
21891
|
|
jpayne@69
|
21892 /* Python wrapper */
|
|
jpayne@69
|
21893 static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self,
|
|
jpayne@69
|
21894 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21895 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21896 #else
|
|
jpayne@69
|
21897 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21898 #endif
|
|
jpayne@69
|
21899 ); /*proto*/
|
|
jpayne@69
|
21900 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_4__next__, "tabix_generic_iterator.__next__(self)");
|
|
jpayne@69
|
21901 static PyMethodDef __pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_5__next__ = {"__next__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_5__next__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_4__next__};
|
|
jpayne@69
|
21902 static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self,
|
|
jpayne@69
|
21903 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21904 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
21905 #else
|
|
jpayne@69
|
21906 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
21907 #endif
|
|
jpayne@69
|
21908 ) {
|
|
jpayne@69
|
21909 PyObject *__pyx_v_self = 0;
|
|
jpayne@69
|
21910 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21911 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
21912 #endif
|
|
jpayne@69
|
21913 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
21914 PyObject* values[1] = {0};
|
|
jpayne@69
|
21915 int __pyx_lineno = 0;
|
|
jpayne@69
|
21916 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
21917 int __pyx_clineno = 0;
|
|
jpayne@69
|
21918 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
21919 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
21920 __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
|
|
jpayne@69
|
21921 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
21922 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
21923 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
21924 #else
|
|
jpayne@69
|
21925 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
21926 #endif
|
|
jpayne@69
|
21927 #endif
|
|
jpayne@69
|
21928 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
21929 {
|
|
jpayne@69
|
21930 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0};
|
|
jpayne@69
|
21931 if (__pyx_kwds) {
|
|
jpayne@69
|
21932 Py_ssize_t kw_args;
|
|
jpayne@69
|
21933 switch (__pyx_nargs) {
|
|
jpayne@69
|
21934 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21935 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
21936 case 0: break;
|
|
jpayne@69
|
21937 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21938 }
|
|
jpayne@69
|
21939 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
21940 switch (__pyx_nargs) {
|
|
jpayne@69
|
21941 case 0:
|
|
jpayne@69
|
21942 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) {
|
|
jpayne@69
|
21943 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
21944 kw_args--;
|
|
jpayne@69
|
21945 }
|
|
jpayne@69
|
21946 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1194, __pyx_L3_error)
|
|
jpayne@69
|
21947 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21948 }
|
|
jpayne@69
|
21949 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
21950 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
21951 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__next__") < 0)) __PYX_ERR(0, 1194, __pyx_L3_error)
|
|
jpayne@69
|
21952 }
|
|
jpayne@69
|
21953 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
21954 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
21955 } else {
|
|
jpayne@69
|
21956 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
21957 }
|
|
jpayne@69
|
21958 __pyx_v_self = values[0];
|
|
jpayne@69
|
21959 }
|
|
jpayne@69
|
21960 goto __pyx_L6_skip;
|
|
jpayne@69
|
21961 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
21962 __Pyx_RaiseArgtupleInvalid("__next__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 1194, __pyx_L3_error)
|
|
jpayne@69
|
21963 __pyx_L6_skip:;
|
|
jpayne@69
|
21964 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
21965 __pyx_L3_error:;
|
|
jpayne@69
|
21966 {
|
|
jpayne@69
|
21967 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21968 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21969 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21970 }
|
|
jpayne@69
|
21971 }
|
|
jpayne@69
|
21972 __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
21973 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21974 return NULL;
|
|
jpayne@69
|
21975 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
21976 __pyx_r = __pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_4__next__(__pyx_self, __pyx_v_self);
|
|
jpayne@69
|
21977
|
|
jpayne@69
|
21978 /* function exit code */
|
|
jpayne@69
|
21979 {
|
|
jpayne@69
|
21980 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
21981 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
21982 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
21983 }
|
|
jpayne@69
|
21984 }
|
|
jpayne@69
|
21985 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
21986 return __pyx_r;
|
|
jpayne@69
|
21987 }
|
|
jpayne@69
|
21988
|
|
jpayne@69
|
21989 static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
|
|
jpayne@69
|
21990 char *__pyx_v_b;
|
|
jpayne@69
|
21991 char *__pyx_v_cpy;
|
|
jpayne@69
|
21992 size_t __pyx_v_nbytes;
|
|
jpayne@69
|
21993 PyObject *__pyx_v_encoding = NULL;
|
|
jpayne@69
|
21994 PyObject *__pyx_v_line = NULL;
|
|
jpayne@69
|
21995 PyObject *__pyx_v_s = NULL;
|
|
jpayne@69
|
21996 PyObject *__pyx_v_bytes_cpy = NULL;
|
|
jpayne@69
|
21997 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
21998 __Pyx_TraceDeclarations
|
|
jpayne@69
|
21999 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
22000 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
22001 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
22002 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
22003 unsigned int __pyx_t_4;
|
|
jpayne@69
|
22004 int __pyx_t_5;
|
|
jpayne@69
|
22005 int __pyx_t_6;
|
|
jpayne@69
|
22006 struct __pyx_opt_args_5pysam_9libcutils_force_bytes __pyx_t_7;
|
|
jpayne@69
|
22007 char *__pyx_t_8;
|
|
jpayne@69
|
22008 Py_ssize_t __pyx_t_9;
|
|
jpayne@69
|
22009 PyObject *__pyx_t_10 = NULL;
|
|
jpayne@69
|
22010 PyObject *__pyx_t_11 = NULL;
|
|
jpayne@69
|
22011 int __pyx_lineno = 0;
|
|
jpayne@69
|
22012 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
22013 int __pyx_clineno = 0;
|
|
jpayne@69
|
22014 __Pyx_TraceFrameInit(__pyx_codeobj__50)
|
|
jpayne@69
|
22015 __Pyx_RefNannySetupContext("__next__", 1);
|
|
jpayne@69
|
22016 __Pyx_TraceCall("__next__", __pyx_f[0], 1194, 0, __PYX_ERR(0, 1194, __pyx_L1_error));
|
|
jpayne@69
|
22017
|
|
jpayne@69
|
22018 /* "pysam/libctabix.pyx":1200
|
|
jpayne@69
|
22019 * cdef size_t nbytes
|
|
jpayne@69
|
22020 *
|
|
jpayne@69
|
22021 * encoding = self.parser.get_encoding() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22022 *
|
|
jpayne@69
|
22023 * # note that GzipFile.close() does not close the file
|
|
jpayne@69
|
22024 */
|
|
jpayne@69
|
22025 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1200, __pyx_L1_error)
|
|
jpayne@69
|
22026 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
22027 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_get_encoding); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1200, __pyx_L1_error)
|
|
jpayne@69
|
22028 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22029 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
22030 __pyx_t_2 = NULL;
|
|
jpayne@69
|
22031 __pyx_t_4 = 0;
|
|
jpayne@69
|
22032 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
22033 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
22034 __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
22035 if (likely(__pyx_t_2)) {
|
|
jpayne@69
|
22036 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
22037 __Pyx_INCREF(__pyx_t_2);
|
|
jpayne@69
|
22038 __Pyx_INCREF(function);
|
|
jpayne@69
|
22039 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
22040 __pyx_t_4 = 1;
|
|
jpayne@69
|
22041 }
|
|
jpayne@69
|
22042 }
|
|
jpayne@69
|
22043 #endif
|
|
jpayne@69
|
22044 {
|
|
jpayne@69
|
22045 PyObject *__pyx_callargs[2] = {__pyx_t_2, NULL};
|
|
jpayne@69
|
22046 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
|
|
jpayne@69
|
22047 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
22048 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1200, __pyx_L1_error)
|
|
jpayne@69
|
22049 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
22050 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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|
jpayne@69
|
22051 }
|
|
jpayne@69
|
22052 __pyx_v_encoding = __pyx_t_1;
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|
jpayne@69
|
22053 __pyx_t_1 = 0;
|
|
jpayne@69
|
22054
|
|
jpayne@69
|
22055 /* "pysam/libctabix.pyx":1204
|
|
jpayne@69
|
22056 * # note that GzipFile.close() does not close the file
|
|
jpayne@69
|
22057 * # reading is still possible.
|
|
jpayne@69
|
22058 * if self.infile.closed: # <<<<<<<<<<<<<<
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|
jpayne@69
|
22059 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
22060 *
|
|
jpayne@69
|
22061 */
|
|
jpayne@69
|
22062 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_infile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1204, __pyx_L1_error)
|
|
jpayne@69
|
22063 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
22064 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_closed); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1204, __pyx_L1_error)
|
|
jpayne@69
|
22065 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22066 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
22067 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 1204, __pyx_L1_error)
|
|
jpayne@69
|
22068 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
22069 if (unlikely(__pyx_t_5)) {
|
|
jpayne@69
|
22070
|
|
jpayne@69
|
22071 /* "pysam/libctabix.pyx":1205
|
|
jpayne@69
|
22072 * # reading is still possible.
|
|
jpayne@69
|
22073 * if self.infile.closed:
|
|
jpayne@69
|
22074 * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22075 *
|
|
jpayne@69
|
22076 * while 1:
|
|
jpayne@69
|
22077 */
|
|
jpayne@69
|
22078 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1205, __pyx_L1_error)
|
|
jpayne@69
|
22079 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22080 __Pyx_Raise(__pyx_t_3, 0, 0, 0);
|
|
jpayne@69
|
22081 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
22082 __PYX_ERR(0, 1205, __pyx_L1_error)
|
|
jpayne@69
|
22083
|
|
jpayne@69
|
22084 /* "pysam/libctabix.pyx":1204
|
|
jpayne@69
|
22085 * # note that GzipFile.close() does not close the file
|
|
jpayne@69
|
22086 * # reading is still possible.
|
|
jpayne@69
|
22087 * if self.infile.closed: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22088 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
22089 *
|
|
jpayne@69
|
22090 */
|
|
jpayne@69
|
22091 }
|
|
jpayne@69
|
22092
|
|
jpayne@69
|
22093 /* "pysam/libctabix.pyx":1207
|
|
jpayne@69
|
22094 * raise ValueError("I/O operation on closed file.")
|
|
jpayne@69
|
22095 *
|
|
jpayne@69
|
22096 * while 1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22097 *
|
|
jpayne@69
|
22098 * line = self.infile.readline()
|
|
jpayne@69
|
22099 */
|
|
jpayne@69
|
22100 while (1) {
|
|
jpayne@69
|
22101
|
|
jpayne@69
|
22102 /* "pysam/libctabix.pyx":1209
|
|
jpayne@69
|
22103 * while 1:
|
|
jpayne@69
|
22104 *
|
|
jpayne@69
|
22105 * line = self.infile.readline() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22106 * if not line:
|
|
jpayne@69
|
22107 * break
|
|
jpayne@69
|
22108 */
|
|
jpayne@69
|
22109 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_infile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1209, __pyx_L1_error)
|
|
jpayne@69
|
22110 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
22111 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_readline); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1209, __pyx_L1_error)
|
|
jpayne@69
|
22112 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
22113 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
22114 __pyx_t_1 = NULL;
|
|
jpayne@69
|
22115 __pyx_t_4 = 0;
|
|
jpayne@69
|
22116 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
22117 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
22118 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
22119 if (likely(__pyx_t_1)) {
|
|
jpayne@69
|
22120 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
22121 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
22122 __Pyx_INCREF(function);
|
|
jpayne@69
|
22123 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
22124 __pyx_t_4 = 1;
|
|
jpayne@69
|
22125 }
|
|
jpayne@69
|
22126 }
|
|
jpayne@69
|
22127 #endif
|
|
jpayne@69
|
22128 {
|
|
jpayne@69
|
22129 PyObject *__pyx_callargs[2] = {__pyx_t_1, NULL};
|
|
jpayne@69
|
22130 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4);
|
|
jpayne@69
|
22131 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
22132 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1209, __pyx_L1_error)
|
|
jpayne@69
|
22133 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22134 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
22135 }
|
|
jpayne@69
|
22136 __Pyx_XDECREF_SET(__pyx_v_line, __pyx_t_3);
|
|
jpayne@69
|
22137 __pyx_t_3 = 0;
|
|
jpayne@69
|
22138
|
|
jpayne@69
|
22139 /* "pysam/libctabix.pyx":1210
|
|
jpayne@69
|
22140 *
|
|
jpayne@69
|
22141 * line = self.infile.readline()
|
|
jpayne@69
|
22142 * if not line: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22143 * break
|
|
jpayne@69
|
22144 *
|
|
jpayne@69
|
22145 */
|
|
jpayne@69
|
22146 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_line); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 1210, __pyx_L1_error)
|
|
jpayne@69
|
22147 __pyx_t_6 = (!__pyx_t_5);
|
|
jpayne@69
|
22148 if (__pyx_t_6) {
|
|
jpayne@69
|
22149
|
|
jpayne@69
|
22150 /* "pysam/libctabix.pyx":1211
|
|
jpayne@69
|
22151 * line = self.infile.readline()
|
|
jpayne@69
|
22152 * if not line:
|
|
jpayne@69
|
22153 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22154 *
|
|
jpayne@69
|
22155 * s = force_bytes(line, encoding)
|
|
jpayne@69
|
22156 */
|
|
jpayne@69
|
22157 goto __pyx_L5_break;
|
|
jpayne@69
|
22158
|
|
jpayne@69
|
22159 /* "pysam/libctabix.pyx":1210
|
|
jpayne@69
|
22160 *
|
|
jpayne@69
|
22161 * line = self.infile.readline()
|
|
jpayne@69
|
22162 * if not line: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22163 * break
|
|
jpayne@69
|
22164 *
|
|
jpayne@69
|
22165 */
|
|
jpayne@69
|
22166 }
|
|
jpayne@69
|
22167
|
|
jpayne@69
|
22168 /* "pysam/libctabix.pyx":1213
|
|
jpayne@69
|
22169 * break
|
|
jpayne@69
|
22170 *
|
|
jpayne@69
|
22171 * s = force_bytes(line, encoding) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22172 * b = s
|
|
jpayne@69
|
22173 * nbytes = len(line)
|
|
jpayne@69
|
22174 */
|
|
jpayne@69
|
22175 __pyx_t_7.__pyx_n = 1;
|
|
jpayne@69
|
22176 __pyx_t_7.encoding = __pyx_v_encoding;
|
|
jpayne@69
|
22177 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_line, &__pyx_t_7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1213, __pyx_L1_error)
|
|
jpayne@69
|
22178 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22179 __Pyx_XDECREF_SET(__pyx_v_s, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
22180 __pyx_t_3 = 0;
|
|
jpayne@69
|
22181
|
|
jpayne@69
|
22182 /* "pysam/libctabix.pyx":1214
|
|
jpayne@69
|
22183 *
|
|
jpayne@69
|
22184 * s = force_bytes(line, encoding)
|
|
jpayne@69
|
22185 * b = s # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22186 * nbytes = len(line)
|
|
jpayne@69
|
22187 * assert b[nbytes] == b'\0'
|
|
jpayne@69
|
22188 */
|
|
jpayne@69
|
22189 if (unlikely(__pyx_v_s == Py_None)) {
|
|
jpayne@69
|
22190 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
22191 __PYX_ERR(0, 1214, __pyx_L1_error)
|
|
jpayne@69
|
22192 }
|
|
jpayne@69
|
22193 __pyx_t_8 = __Pyx_PyBytes_AsWritableString(__pyx_v_s); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 1214, __pyx_L1_error)
|
|
jpayne@69
|
22194 __pyx_v_b = __pyx_t_8;
|
|
jpayne@69
|
22195
|
|
jpayne@69
|
22196 /* "pysam/libctabix.pyx":1215
|
|
jpayne@69
|
22197 * s = force_bytes(line, encoding)
|
|
jpayne@69
|
22198 * b = s
|
|
jpayne@69
|
22199 * nbytes = len(line) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22200 * assert b[nbytes] == b'\0'
|
|
jpayne@69
|
22201 *
|
|
jpayne@69
|
22202 */
|
|
jpayne@69
|
22203 __pyx_t_9 = PyObject_Length(__pyx_v_line); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 1215, __pyx_L1_error)
|
|
jpayne@69
|
22204 __pyx_v_nbytes = __pyx_t_9;
|
|
jpayne@69
|
22205
|
|
jpayne@69
|
22206 /* "pysam/libctabix.pyx":1216
|
|
jpayne@69
|
22207 * b = s
|
|
jpayne@69
|
22208 * nbytes = len(line)
|
|
jpayne@69
|
22209 * assert b[nbytes] == b'\0' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22210 *
|
|
jpayne@69
|
22211 * # skip comments
|
|
jpayne@69
|
22212 */
|
|
jpayne@69
|
22213 #ifndef CYTHON_WITHOUT_ASSERTIONS
|
|
jpayne@69
|
22214 if (unlikely(__pyx_assertions_enabled())) {
|
|
jpayne@69
|
22215 __pyx_t_6 = ((__pyx_v_b[__pyx_v_nbytes]) == '\x00');
|
|
jpayne@69
|
22216 if (unlikely(!__pyx_t_6)) {
|
|
jpayne@69
|
22217 __Pyx_Raise(__pyx_builtin_AssertionError, 0, 0, 0);
|
|
jpayne@69
|
22218 __PYX_ERR(0, 1216, __pyx_L1_error)
|
|
jpayne@69
|
22219 }
|
|
jpayne@69
|
22220 }
|
|
jpayne@69
|
22221 #else
|
|
jpayne@69
|
22222 if ((1)); else __PYX_ERR(0, 1216, __pyx_L1_error)
|
|
jpayne@69
|
22223 #endif
|
|
jpayne@69
|
22224
|
|
jpayne@69
|
22225 /* "pysam/libctabix.pyx":1219
|
|
jpayne@69
|
22226 *
|
|
jpayne@69
|
22227 * # skip comments
|
|
jpayne@69
|
22228 * if b[0] == b'#': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22229 * continue
|
|
jpayne@69
|
22230 *
|
|
jpayne@69
|
22231 */
|
|
jpayne@69
|
22232 __pyx_t_6 = ((__pyx_v_b[0]) == '#');
|
|
jpayne@69
|
22233 if (__pyx_t_6) {
|
|
jpayne@69
|
22234
|
|
jpayne@69
|
22235 /* "pysam/libctabix.pyx":1220
|
|
jpayne@69
|
22236 * # skip comments
|
|
jpayne@69
|
22237 * if b[0] == b'#':
|
|
jpayne@69
|
22238 * continue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22239 *
|
|
jpayne@69
|
22240 * # skip empty lines
|
|
jpayne@69
|
22241 */
|
|
jpayne@69
|
22242 goto __pyx_L4_continue;
|
|
jpayne@69
|
22243
|
|
jpayne@69
|
22244 /* "pysam/libctabix.pyx":1219
|
|
jpayne@69
|
22245 *
|
|
jpayne@69
|
22246 * # skip comments
|
|
jpayne@69
|
22247 * if b[0] == b'#': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22248 * continue
|
|
jpayne@69
|
22249 *
|
|
jpayne@69
|
22250 */
|
|
jpayne@69
|
22251 }
|
|
jpayne@69
|
22252
|
|
jpayne@69
|
22253 /* "pysam/libctabix.pyx":1223
|
|
jpayne@69
|
22254 *
|
|
jpayne@69
|
22255 * # skip empty lines
|
|
jpayne@69
|
22256 * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22257 * continue
|
|
jpayne@69
|
22258 *
|
|
jpayne@69
|
22259 */
|
|
jpayne@69
|
22260 __pyx_t_5 = ((__pyx_v_b[0]) == '\x00');
|
|
jpayne@69
|
22261 if (!__pyx_t_5) {
|
|
jpayne@69
|
22262 } else {
|
|
jpayne@69
|
22263 __pyx_t_6 = __pyx_t_5;
|
|
jpayne@69
|
22264 goto __pyx_L9_bool_binop_done;
|
|
jpayne@69
|
22265 }
|
|
jpayne@69
|
22266 __pyx_t_5 = ((__pyx_v_b[0]) == '\n');
|
|
jpayne@69
|
22267 if (!__pyx_t_5) {
|
|
jpayne@69
|
22268 } else {
|
|
jpayne@69
|
22269 __pyx_t_6 = __pyx_t_5;
|
|
jpayne@69
|
22270 goto __pyx_L9_bool_binop_done;
|
|
jpayne@69
|
22271 }
|
|
jpayne@69
|
22272 __pyx_t_5 = ((__pyx_v_b[0]) == '\r');
|
|
jpayne@69
|
22273 __pyx_t_6 = __pyx_t_5;
|
|
jpayne@69
|
22274 __pyx_L9_bool_binop_done:;
|
|
jpayne@69
|
22275 if (__pyx_t_6) {
|
|
jpayne@69
|
22276
|
|
jpayne@69
|
22277 /* "pysam/libctabix.pyx":1224
|
|
jpayne@69
|
22278 * # skip empty lines
|
|
jpayne@69
|
22279 * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r':
|
|
jpayne@69
|
22280 * continue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22281 *
|
|
jpayne@69
|
22282 * # make sure that entry is complete
|
|
jpayne@69
|
22283 */
|
|
jpayne@69
|
22284 goto __pyx_L4_continue;
|
|
jpayne@69
|
22285
|
|
jpayne@69
|
22286 /* "pysam/libctabix.pyx":1223
|
|
jpayne@69
|
22287 *
|
|
jpayne@69
|
22288 * # skip empty lines
|
|
jpayne@69
|
22289 * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22290 * continue
|
|
jpayne@69
|
22291 *
|
|
jpayne@69
|
22292 */
|
|
jpayne@69
|
22293 }
|
|
jpayne@69
|
22294
|
|
jpayne@69
|
22295 /* "pysam/libctabix.pyx":1227
|
|
jpayne@69
|
22296 *
|
|
jpayne@69
|
22297 * # make sure that entry is complete
|
|
jpayne@69
|
22298 * if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22299 * raise ValueError("incomplete line at %s" % line)
|
|
jpayne@69
|
22300 *
|
|
jpayne@69
|
22301 */
|
|
jpayne@69
|
22302 __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n');
|
|
jpayne@69
|
22303 if (__pyx_t_5) {
|
|
jpayne@69
|
22304 } else {
|
|
jpayne@69
|
22305 __pyx_t_6 = __pyx_t_5;
|
|
jpayne@69
|
22306 goto __pyx_L13_bool_binop_done;
|
|
jpayne@69
|
22307 }
|
|
jpayne@69
|
22308 __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r');
|
|
jpayne@69
|
22309 __pyx_t_6 = __pyx_t_5;
|
|
jpayne@69
|
22310 __pyx_L13_bool_binop_done:;
|
|
jpayne@69
|
22311 if (unlikely(__pyx_t_6)) {
|
|
jpayne@69
|
22312
|
|
jpayne@69
|
22313 /* "pysam/libctabix.pyx":1228
|
|
jpayne@69
|
22314 * # make sure that entry is complete
|
|
jpayne@69
|
22315 * if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r':
|
|
jpayne@69
|
22316 * raise ValueError("incomplete line at %s" % line) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22317 *
|
|
jpayne@69
|
22318 * bytes_cpy = <bytes> b
|
|
jpayne@69
|
22319 */
|
|
jpayne@69
|
22320 __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_incomplete_line_at_s, __pyx_v_line); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1228, __pyx_L1_error)
|
|
jpayne@69
|
22321 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22322 __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1228, __pyx_L1_error)
|
|
jpayne@69
|
22323 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
22324 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
22325 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
22326 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
22327 __PYX_ERR(0, 1228, __pyx_L1_error)
|
|
jpayne@69
|
22328
|
|
jpayne@69
|
22329 /* "pysam/libctabix.pyx":1227
|
|
jpayne@69
|
22330 *
|
|
jpayne@69
|
22331 * # make sure that entry is complete
|
|
jpayne@69
|
22332 * if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r': # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22333 * raise ValueError("incomplete line at %s" % line)
|
|
jpayne@69
|
22334 *
|
|
jpayne@69
|
22335 */
|
|
jpayne@69
|
22336 }
|
|
jpayne@69
|
22337
|
|
jpayne@69
|
22338 /* "pysam/libctabix.pyx":1230
|
|
jpayne@69
|
22339 * raise ValueError("incomplete line at %s" % line)
|
|
jpayne@69
|
22340 *
|
|
jpayne@69
|
22341 * bytes_cpy = <bytes> b # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22342 * cpy = <char *> bytes_cpy
|
|
jpayne@69
|
22343 *
|
|
jpayne@69
|
22344 */
|
|
jpayne@69
|
22345 __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1230, __pyx_L1_error)
|
|
jpayne@69
|
22346 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
22347 __pyx_t_3 = __pyx_t_2;
|
|
jpayne@69
|
22348 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
22349 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
22350 __pyx_v_bytes_cpy = ((PyObject*)__pyx_t_3);
|
|
jpayne@69
|
22351 __pyx_t_3 = 0;
|
|
jpayne@69
|
22352
|
|
jpayne@69
|
22353 /* "pysam/libctabix.pyx":1231
|
|
jpayne@69
|
22354 *
|
|
jpayne@69
|
22355 * bytes_cpy = <bytes> b
|
|
jpayne@69
|
22356 * cpy = <char *> bytes_cpy # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22357 *
|
|
jpayne@69
|
22358 * return self.parser(cpy, nbytes)
|
|
jpayne@69
|
22359 */
|
|
jpayne@69
|
22360 if (unlikely(__pyx_v_bytes_cpy == Py_None)) {
|
|
jpayne@69
|
22361 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
22362 __PYX_ERR(0, 1231, __pyx_L1_error)
|
|
jpayne@69
|
22363 }
|
|
jpayne@69
|
22364 __pyx_t_8 = __Pyx_PyBytes_AsWritableString(__pyx_v_bytes_cpy); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 1231, __pyx_L1_error)
|
|
jpayne@69
|
22365 __pyx_v_cpy = ((char *)__pyx_t_8);
|
|
jpayne@69
|
22366
|
|
jpayne@69
|
22367 /* "pysam/libctabix.pyx":1233
|
|
jpayne@69
|
22368 * cpy = <char *> bytes_cpy
|
|
jpayne@69
|
22369 *
|
|
jpayne@69
|
22370 * return self.parser(cpy, nbytes) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22371 *
|
|
jpayne@69
|
22372 * raise StopIteration
|
|
jpayne@69
|
22373 */
|
|
jpayne@69
|
22374 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
22375 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1233, __pyx_L1_error)
|
|
jpayne@69
|
22376 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
22377 __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_cpy); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1233, __pyx_L1_error)
|
|
jpayne@69
|
22378 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
22379 __pyx_t_10 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 1233, __pyx_L1_error)
|
|
jpayne@69
|
22380 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
22381 __pyx_t_11 = NULL;
|
|
jpayne@69
|
22382 __pyx_t_4 = 0;
|
|
jpayne@69
|
22383 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
22384 if (likely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
22385 __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_2);
|
|
jpayne@69
|
22386 if (likely(__pyx_t_11)) {
|
|
jpayne@69
|
22387 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
|
|
jpayne@69
|
22388 __Pyx_INCREF(__pyx_t_11);
|
|
jpayne@69
|
22389 __Pyx_INCREF(function);
|
|
jpayne@69
|
22390 __Pyx_DECREF_SET(__pyx_t_2, function);
|
|
jpayne@69
|
22391 __pyx_t_4 = 1;
|
|
jpayne@69
|
22392 }
|
|
jpayne@69
|
22393 }
|
|
jpayne@69
|
22394 #endif
|
|
jpayne@69
|
22395 {
|
|
jpayne@69
|
22396 PyObject *__pyx_callargs[3] = {__pyx_t_11, __pyx_t_1, __pyx_t_10};
|
|
jpayne@69
|
22397 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
|
|
jpayne@69
|
22398 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
22399 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
22400 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
22401 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1233, __pyx_L1_error)
|
|
jpayne@69
|
22402 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
22403 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
22404 }
|
|
jpayne@69
|
22405 __pyx_r = __pyx_t_3;
|
|
jpayne@69
|
22406 __pyx_t_3 = 0;
|
|
jpayne@69
|
22407 goto __pyx_L0;
|
|
jpayne@69
|
22408 __pyx_L4_continue:;
|
|
jpayne@69
|
22409 }
|
|
jpayne@69
|
22410 __pyx_L5_break:;
|
|
jpayne@69
|
22411
|
|
jpayne@69
|
22412 /* "pysam/libctabix.pyx":1235
|
|
jpayne@69
|
22413 * return self.parser(cpy, nbytes)
|
|
jpayne@69
|
22414 *
|
|
jpayne@69
|
22415 * raise StopIteration # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22416 *
|
|
jpayne@69
|
22417 *
|
|
jpayne@69
|
22418 */
|
|
jpayne@69
|
22419 __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
|
|
jpayne@69
|
22420 __PYX_ERR(0, 1235, __pyx_L1_error)
|
|
jpayne@69
|
22421
|
|
jpayne@69
|
22422 /* "pysam/libctabix.pyx":1194
|
|
jpayne@69
|
22423 *
|
|
jpayne@69
|
22424 * # cython version - required for python 3
|
|
jpayne@69
|
22425 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22426 *
|
|
jpayne@69
|
22427 * cdef char * b
|
|
jpayne@69
|
22428 */
|
|
jpayne@69
|
22429
|
|
jpayne@69
|
22430 /* function exit code */
|
|
jpayne@69
|
22431 __pyx_L1_error:;
|
|
jpayne@69
|
22432 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
22433 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
22434 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
22435 __Pyx_XDECREF(__pyx_t_10);
|
|
jpayne@69
|
22436 __Pyx_XDECREF(__pyx_t_11);
|
|
jpayne@69
|
22437 __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
22438 __pyx_r = NULL;
|
|
jpayne@69
|
22439 __pyx_L0:;
|
|
jpayne@69
|
22440 __Pyx_XDECREF(__pyx_v_encoding);
|
|
jpayne@69
|
22441 __Pyx_XDECREF(__pyx_v_line);
|
|
jpayne@69
|
22442 __Pyx_XDECREF(__pyx_v_s);
|
|
jpayne@69
|
22443 __Pyx_XDECREF(__pyx_v_bytes_cpy);
|
|
jpayne@69
|
22444 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
22445 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
22446 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22447 return __pyx_r;
|
|
jpayne@69
|
22448 }
|
|
jpayne@69
|
22449
|
|
jpayne@69
|
22450 /* "pysam/libctabix.pyx":1238
|
|
jpayne@69
|
22451 *
|
|
jpayne@69
|
22452 *
|
|
jpayne@69
|
22453 * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22454 * """return an iterator over all entries in a file.
|
|
jpayne@69
|
22455 *
|
|
jpayne@69
|
22456 */
|
|
jpayne@69
|
22457
|
|
jpayne@69
|
22458 /* Python wrapper */
|
|
jpayne@69
|
22459 static PyObject *__pyx_pw_5pysam_9libctabix_5tabix_iterator(PyObject *__pyx_self,
|
|
jpayne@69
|
22460 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22461 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
22462 #else
|
|
jpayne@69
|
22463 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
22464 #endif
|
|
jpayne@69
|
22465 ); /*proto*/
|
|
jpayne@69
|
22466 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_4tabix_iterator, "tabix_iterator(infile, parser)\nreturn an iterator over all entries in a file.\n \n Results are returned parsed as specified by the *parser*. If\n *parser* is None, the results are returned as an unparsed string.\n Otherwise, *parser* is assumed to be a functor that will return\n parsed data (see for example :class:`~pysam.asTuple` and\n :class:`~pysam.asGTF`).\n\n ");
|
|
jpayne@69
|
22467 static PyMethodDef __pyx_mdef_5pysam_9libctabix_5tabix_iterator = {"tabix_iterator", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5tabix_iterator, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_4tabix_iterator};
|
|
jpayne@69
|
22468 static PyObject *__pyx_pw_5pysam_9libctabix_5tabix_iterator(PyObject *__pyx_self,
|
|
jpayne@69
|
22469 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22470 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
22471 #else
|
|
jpayne@69
|
22472 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
22473 #endif
|
|
jpayne@69
|
22474 ) {
|
|
jpayne@69
|
22475 PyObject *__pyx_v_infile = 0;
|
|
jpayne@69
|
22476 PyObject *__pyx_v_parser = 0;
|
|
jpayne@69
|
22477 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22478 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
22479 #endif
|
|
jpayne@69
|
22480 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
22481 PyObject* values[2] = {0,0};
|
|
jpayne@69
|
22482 int __pyx_lineno = 0;
|
|
jpayne@69
|
22483 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
22484 int __pyx_clineno = 0;
|
|
jpayne@69
|
22485 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
22486 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
22487 __Pyx_RefNannySetupContext("tabix_iterator (wrapper)", 0);
|
|
jpayne@69
|
22488 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22489 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
22490 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
22491 #else
|
|
jpayne@69
|
22492 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
22493 #endif
|
|
jpayne@69
|
22494 #endif
|
|
jpayne@69
|
22495 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
22496 {
|
|
jpayne@69
|
22497 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_infile,&__pyx_n_s_parser,0};
|
|
jpayne@69
|
22498 if (__pyx_kwds) {
|
|
jpayne@69
|
22499 Py_ssize_t kw_args;
|
|
jpayne@69
|
22500 switch (__pyx_nargs) {
|
|
jpayne@69
|
22501 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
22502 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22503 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
22504 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22505 case 0: break;
|
|
jpayne@69
|
22506 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22507 }
|
|
jpayne@69
|
22508 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
22509 switch (__pyx_nargs) {
|
|
jpayne@69
|
22510 case 0:
|
|
jpayne@69
|
22511 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_infile)) != 0)) {
|
|
jpayne@69
|
22512 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
22513 kw_args--;
|
|
jpayne@69
|
22514 }
|
|
jpayne@69
|
22515 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1238, __pyx_L3_error)
|
|
jpayne@69
|
22516 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22517 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22518 case 1:
|
|
jpayne@69
|
22519 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) {
|
|
jpayne@69
|
22520 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
22521 kw_args--;
|
|
jpayne@69
|
22522 }
|
|
jpayne@69
|
22523 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1238, __pyx_L3_error)
|
|
jpayne@69
|
22524 else {
|
|
jpayne@69
|
22525 __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); __PYX_ERR(0, 1238, __pyx_L3_error)
|
|
jpayne@69
|
22526 }
|
|
jpayne@69
|
22527 }
|
|
jpayne@69
|
22528 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
22529 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
22530 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "tabix_iterator") < 0)) __PYX_ERR(0, 1238, __pyx_L3_error)
|
|
jpayne@69
|
22531 }
|
|
jpayne@69
|
22532 } else if (unlikely(__pyx_nargs != 2)) {
|
|
jpayne@69
|
22533 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22534 } else {
|
|
jpayne@69
|
22535 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
22536 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
22537 }
|
|
jpayne@69
|
22538 __pyx_v_infile = values[0];
|
|
jpayne@69
|
22539 __pyx_v_parser = values[1];
|
|
jpayne@69
|
22540 }
|
|
jpayne@69
|
22541 goto __pyx_L6_skip;
|
|
jpayne@69
|
22542 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
22543 __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 1238, __pyx_L3_error)
|
|
jpayne@69
|
22544 __pyx_L6_skip:;
|
|
jpayne@69
|
22545 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
22546 __pyx_L3_error:;
|
|
jpayne@69
|
22547 {
|
|
jpayne@69
|
22548 Py_ssize_t __pyx_temp;
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jpayne@69
|
22549 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
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jpayne@69
|
22550 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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jpayne@69
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22551 }
|
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jpayne@69
|
22552 }
|
|
jpayne@69
|
22553 __Pyx_AddTraceback("pysam.libctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
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jpayne@69
|
22554 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
22555 return NULL;
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jpayne@69
|
22556 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
22557 __pyx_r = __pyx_pf_5pysam_9libctabix_4tabix_iterator(__pyx_self, __pyx_v_infile, __pyx_v_parser);
|
|
jpayne@69
|
22558
|
|
jpayne@69
|
22559 /* function exit code */
|
|
jpayne@69
|
22560 {
|
|
jpayne@69
|
22561 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
22562 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
22563 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
22564 }
|
|
jpayne@69
|
22565 }
|
|
jpayne@69
|
22566 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
22567 return __pyx_r;
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|
jpayne@69
|
22568 }
|
|
jpayne@69
|
22569
|
|
jpayne@69
|
22570 static PyObject *__pyx_pf_5pysam_9libctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) {
|
|
jpayne@69
|
22571 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
22572 __Pyx_TraceDeclarations
|
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jpayne@69
|
22573 __Pyx_RefNannyDeclarations
|
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jpayne@69
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22574 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
22575 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
22576 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
22577 unsigned int __pyx_t_4;
|
|
jpayne@69
|
22578 int __pyx_lineno = 0;
|
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jpayne@69
|
22579 const char *__pyx_filename = NULL;
|
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jpayne@69
|
22580 int __pyx_clineno = 0;
|
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jpayne@69
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22581 __Pyx_TraceFrameInit(__pyx_codeobj__51)
|
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jpayne@69
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22582 __Pyx_RefNannySetupContext("tabix_iterator", 1);
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jpayne@69
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22583 __Pyx_TraceCall("tabix_iterator", __pyx_f[0], 1238, 0, __PYX_ERR(0, 1238, __pyx_L1_error));
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jpayne@69
|
22584
|
|
jpayne@69
|
22585 /* "pysam/libctabix.pyx":1248
|
|
jpayne@69
|
22586 *
|
|
jpayne@69
|
22587 * """
|
|
jpayne@69
|
22588 * return tabix_generic_iterator(infile, parser) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22589 *
|
|
jpayne@69
|
22590 *
|
|
jpayne@69
|
22591 */
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|
jpayne@69
|
22592 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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22593 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_tabix_generic_iterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1248, __pyx_L1_error)
|
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jpayne@69
|
22594 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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22595 __pyx_t_3 = NULL;
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jpayne@69
|
22596 __pyx_t_4 = 0;
|
|
jpayne@69
|
22597 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
22598 if (unlikely(PyMethod_Check(__pyx_t_2))) {
|
|
jpayne@69
|
22599 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
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jpayne@69
|
22600 if (likely(__pyx_t_3)) {
|
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jpayne@69
|
22601 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
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jpayne@69
|
22602 __Pyx_INCREF(__pyx_t_3);
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jpayne@69
|
22603 __Pyx_INCREF(function);
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jpayne@69
|
22604 __Pyx_DECREF_SET(__pyx_t_2, function);
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jpayne@69
|
22605 __pyx_t_4 = 1;
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jpayne@69
|
22606 }
|
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jpayne@69
|
22607 }
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jpayne@69
|
22608 #endif
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jpayne@69
|
22609 {
|
|
jpayne@69
|
22610 PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_infile, __pyx_v_parser};
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jpayne@69
|
22611 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4);
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jpayne@69
|
22612 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
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jpayne@69
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22613 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1248, __pyx_L1_error)
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jpayne@69
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22614 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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22615 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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22616 }
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jpayne@69
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22617 __pyx_r = __pyx_t_1;
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jpayne@69
|
22618 __pyx_t_1 = 0;
|
|
jpayne@69
|
22619 goto __pyx_L0;
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jpayne@69
|
22620
|
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jpayne@69
|
22621 /* "pysam/libctabix.pyx":1238
|
|
jpayne@69
|
22622 *
|
|
jpayne@69
|
22623 *
|
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jpayne@69
|
22624 * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<<
|
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jpayne@69
|
22625 * """return an iterator over all entries in a file.
|
|
jpayne@69
|
22626 *
|
|
jpayne@69
|
22627 */
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|
jpayne@69
|
22628
|
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jpayne@69
|
22629 /* function exit code */
|
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jpayne@69
|
22630 __pyx_L1_error:;
|
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jpayne@69
|
22631 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
|
22632 __Pyx_XDECREF(__pyx_t_2);
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jpayne@69
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22633 __Pyx_XDECREF(__pyx_t_3);
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jpayne@69
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22634 __Pyx_AddTraceback("pysam.libctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
|
22635 __pyx_r = NULL;
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jpayne@69
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22636 __pyx_L0:;
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jpayne@69
|
22637 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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22638 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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22639 __Pyx_RefNannyFinishContext();
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jpayne@69
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22640 return __pyx_r;
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jpayne@69
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22641 }
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jpayne@69
|
22642
|
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jpayne@69
|
22643 /* "(tree fragment)":1
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jpayne@69
|
22644 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
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jpayne@69
|
22645 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
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jpayne@69
|
22646 * def __setstate_cython__(self, __pyx_state):
|
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jpayne@69
|
22647 */
|
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jpayne@69
|
22648
|
|
jpayne@69
|
22649 /* Python wrapper */
|
|
jpayne@69
|
22650 static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__(PyObject *__pyx_v_self,
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jpayne@69
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22651 #if CYTHON_METH_FASTCALL
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jpayne@69
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22652 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
|
22653 #else
|
|
jpayne@69
|
22654 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
|
22655 #endif
|
|
jpayne@69
|
22656 ); /*proto*/
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jpayne@69
|
22657 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9Tabixfile___reduce_cython__, "Tabixfile.__reduce_cython__(self)");
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jpayne@69
|
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|
jpayne@69
|
22659 static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__(PyObject *__pyx_v_self,
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jpayne@69
|
22660 #if CYTHON_METH_FASTCALL
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jpayne@69
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22661 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
|
22662 #else
|
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jpayne@69
|
22663 PyObject *__pyx_args, PyObject *__pyx_kwds
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jpayne@69
|
22664 #endif
|
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jpayne@69
|
22665 ) {
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|
jpayne@69
|
22666 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22667 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
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jpayne@69
|
22668 #endif
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jpayne@69
|
22669 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
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jpayne@69
|
22670 PyObject *__pyx_r = 0;
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jpayne@69
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22671 __Pyx_RefNannyDeclarations
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jpayne@69
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jpayne@69
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22673 #if !CYTHON_METH_FASTCALL
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jpayne@69
|
22674 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
22675 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
22676 #else
|
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jpayne@69
|
22677 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
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jpayne@69
|
22678 #endif
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jpayne@69
|
22679 #endif
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jpayne@69
|
22680 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
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jpayne@69
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22681 if (unlikely(__pyx_nargs > 0)) {
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jpayne@69
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22682 __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;}
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jpayne@69
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22683 if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL;
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jpayne@69
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22684 __pyx_r = __pyx_pf_5pysam_9libctabix_9Tabixfile___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_Tabixfile *)__pyx_v_self));
|
|
jpayne@69
|
22685
|
|
jpayne@69
|
22686 /* function exit code */
|
|
jpayne@69
|
22687 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
22688 return __pyx_r;
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jpayne@69
|
22689 }
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jpayne@69
|
22690
|
|
jpayne@69
|
22691 static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile___reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self) {
|
|
jpayne@69
|
22692 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
22693 __Pyx_TraceDeclarations
|
|
jpayne@69
|
22694 __Pyx_RefNannyDeclarations
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jpayne@69
|
22695 int __pyx_lineno = 0;
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jpayne@69
|
22696 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
22697 int __pyx_clineno = 0;
|
|
jpayne@69
|
22698 __Pyx_TraceFrameInit(__pyx_codeobj__52)
|
|
jpayne@69
|
22699 __Pyx_RefNannySetupContext("__reduce_cython__", 1);
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jpayne@69
|
22700 __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
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jpayne@69
|
22701
|
|
jpayne@69
|
22702 /* "(tree fragment)":2
|
|
jpayne@69
|
22703 * def __reduce_cython__(self):
|
|
jpayne@69
|
22704 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22705 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
22706 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22707 */
|
|
jpayne@69
|
22708 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
|
|
jpayne@69
|
22709 __PYX_ERR(1, 2, __pyx_L1_error)
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jpayne@69
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22710
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jpayne@69
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22711 /* "(tree fragment)":1
|
|
jpayne@69
|
22712 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
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jpayne@69
|
22713 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22714 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
22715 */
|
|
jpayne@69
|
22716
|
|
jpayne@69
|
22717 /* function exit code */
|
|
jpayne@69
|
22718 __pyx_L1_error:;
|
|
jpayne@69
|
22719 __Pyx_AddTraceback("pysam.libctabix.Tabixfile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
22720 __pyx_r = NULL;
|
|
jpayne@69
|
22721 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
22722 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
22723 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22724 return __pyx_r;
|
|
jpayne@69
|
22725 }
|
|
jpayne@69
|
22726
|
|
jpayne@69
|
22727 /* "(tree fragment)":3
|
|
jpayne@69
|
22728 * def __reduce_cython__(self):
|
|
jpayne@69
|
22729 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22730 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22731 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22732 */
|
|
jpayne@69
|
22733
|
|
jpayne@69
|
22734 /* Python wrapper */
|
|
jpayne@69
|
22735 static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
22736 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22737 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
22738 #else
|
|
jpayne@69
|
22739 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
22740 #endif
|
|
jpayne@69
|
22741 ); /*proto*/
|
|
jpayne@69
|
22742 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9Tabixfile_2__setstate_cython__, "Tabixfile.__setstate_cython__(self, __pyx_state)");
|
|
jpayne@69
|
22743 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9Tabixfile_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile_2__setstate_cython__};
|
|
jpayne@69
|
22744 static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__(PyObject *__pyx_v_self,
|
|
jpayne@69
|
22745 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22746 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
22747 #else
|
|
jpayne@69
|
22748 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
22749 #endif
|
|
jpayne@69
|
22750 ) {
|
|
jpayne@69
|
22751 CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
22752 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22753 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
22754 #endif
|
|
jpayne@69
|
22755 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
22756 PyObject* values[1] = {0};
|
|
jpayne@69
|
22757 int __pyx_lineno = 0;
|
|
jpayne@69
|
22758 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
22759 int __pyx_clineno = 0;
|
|
jpayne@69
|
22760 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
22761 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
22762 __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0);
|
|
jpayne@69
|
22763 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22764 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
22765 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
22766 #else
|
|
jpayne@69
|
22767 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
22768 #endif
|
|
jpayne@69
|
22769 #endif
|
|
jpayne@69
|
22770 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
22771 {
|
|
jpayne@69
|
22772 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
22773 if (__pyx_kwds) {
|
|
jpayne@69
|
22774 Py_ssize_t kw_args;
|
|
jpayne@69
|
22775 switch (__pyx_nargs) {
|
|
jpayne@69
|
22776 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
22777 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22778 case 0: break;
|
|
jpayne@69
|
22779 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22780 }
|
|
jpayne@69
|
22781 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
22782 switch (__pyx_nargs) {
|
|
jpayne@69
|
22783 case 0:
|
|
jpayne@69
|
22784 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
22785 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
22786 kw_args--;
|
|
jpayne@69
|
22787 }
|
|
jpayne@69
|
22788 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
22789 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22790 }
|
|
jpayne@69
|
22791 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
22792 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
22793 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
22794 }
|
|
jpayne@69
|
22795 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
22796 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22797 } else {
|
|
jpayne@69
|
22798 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
22799 }
|
|
jpayne@69
|
22800 __pyx_v___pyx_state = values[0];
|
|
jpayne@69
|
22801 }
|
|
jpayne@69
|
22802 goto __pyx_L6_skip;
|
|
jpayne@69
|
22803 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
22804 __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error)
|
|
jpayne@69
|
22805 __pyx_L6_skip:;
|
|
jpayne@69
|
22806 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
22807 __pyx_L3_error:;
|
|
jpayne@69
|
22808 {
|
|
jpayne@69
|
22809 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
22810 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
22811 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
22812 }
|
|
jpayne@69
|
22813 }
|
|
jpayne@69
|
22814 __Pyx_AddTraceback("pysam.libctabix.Tabixfile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
22815 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22816 return NULL;
|
|
jpayne@69
|
22817 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
22818 __pyx_r = __pyx_pf_5pysam_9libctabix_9Tabixfile_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_Tabixfile *)__pyx_v_self), __pyx_v___pyx_state);
|
|
jpayne@69
|
22819
|
|
jpayne@69
|
22820 /* function exit code */
|
|
jpayne@69
|
22821 {
|
|
jpayne@69
|
22822 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
22823 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
22824 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
22825 }
|
|
jpayne@69
|
22826 }
|
|
jpayne@69
|
22827 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22828 return __pyx_r;
|
|
jpayne@69
|
22829 }
|
|
jpayne@69
|
22830
|
|
jpayne@69
|
22831 static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile_2__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
22832 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
22833 __Pyx_TraceDeclarations
|
|
jpayne@69
|
22834 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
22835 int __pyx_lineno = 0;
|
|
jpayne@69
|
22836 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
22837 int __pyx_clineno = 0;
|
|
jpayne@69
|
22838 __Pyx_TraceFrameInit(__pyx_codeobj__53)
|
|
jpayne@69
|
22839 __Pyx_RefNannySetupContext("__setstate_cython__", 1);
|
|
jpayne@69
|
22840 __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error));
|
|
jpayne@69
|
22841
|
|
jpayne@69
|
22842 /* "(tree fragment)":4
|
|
jpayne@69
|
22843 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22844 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
22845 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22846 */
|
|
jpayne@69
|
22847 __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0);
|
|
jpayne@69
|
22848 __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
22849
|
|
jpayne@69
|
22850 /* "(tree fragment)":3
|
|
jpayne@69
|
22851 * def __reduce_cython__(self):
|
|
jpayne@69
|
22852 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22853 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22854 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
22855 */
|
|
jpayne@69
|
22856
|
|
jpayne@69
|
22857 /* function exit code */
|
|
jpayne@69
|
22858 __pyx_L1_error:;
|
|
jpayne@69
|
22859 __Pyx_AddTraceback("pysam.libctabix.Tabixfile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
22860 __pyx_r = NULL;
|
|
jpayne@69
|
22861 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
22862 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
22863 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22864 return __pyx_r;
|
|
jpayne@69
|
22865 }
|
|
jpayne@69
|
22866
|
|
jpayne@69
|
22867 /* "(tree fragment)":1
|
|
jpayne@69
|
22868 * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
22869 * cdef object __pyx_PickleError
|
|
jpayne@69
|
22870 * cdef object __pyx_result
|
|
jpayne@69
|
22871 */
|
|
jpayne@69
|
22872
|
|
jpayne@69
|
22873 /* Python wrapper */
|
|
jpayne@69
|
22874 static PyObject *__pyx_pw_5pysam_9libctabix_7__pyx_unpickle_Parser(PyObject *__pyx_self,
|
|
jpayne@69
|
22875 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22876 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
22877 #else
|
|
jpayne@69
|
22878 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
22879 #endif
|
|
jpayne@69
|
22880 ); /*proto*/
|
|
jpayne@69
|
22881 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6__pyx_unpickle_Parser, "__pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state)");
|
|
jpayne@69
|
22882 static PyMethodDef __pyx_mdef_5pysam_9libctabix_7__pyx_unpickle_Parser = {"__pyx_unpickle_Parser", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7__pyx_unpickle_Parser, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6__pyx_unpickle_Parser};
|
|
jpayne@69
|
22883 static PyObject *__pyx_pw_5pysam_9libctabix_7__pyx_unpickle_Parser(PyObject *__pyx_self,
|
|
jpayne@69
|
22884 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22885 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
22886 #else
|
|
jpayne@69
|
22887 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
22888 #endif
|
|
jpayne@69
|
22889 ) {
|
|
jpayne@69
|
22890 PyObject *__pyx_v___pyx_type = 0;
|
|
jpayne@69
|
22891 long __pyx_v___pyx_checksum;
|
|
jpayne@69
|
22892 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
22893 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22894 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
22895 #endif
|
|
jpayne@69
|
22896 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
22897 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
22898 int __pyx_lineno = 0;
|
|
jpayne@69
|
22899 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
22900 int __pyx_clineno = 0;
|
|
jpayne@69
|
22901 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
22902 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
22903 __Pyx_RefNannySetupContext("__pyx_unpickle_Parser (wrapper)", 0);
|
|
jpayne@69
|
22904 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
22905 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
22906 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
22907 #else
|
|
jpayne@69
|
22908 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
22909 #endif
|
|
jpayne@69
|
22910 #endif
|
|
jpayne@69
|
22911 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
22912 {
|
|
jpayne@69
|
22913 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
22914 if (__pyx_kwds) {
|
|
jpayne@69
|
22915 Py_ssize_t kw_args;
|
|
jpayne@69
|
22916 switch (__pyx_nargs) {
|
|
jpayne@69
|
22917 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
22918 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22919 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
22920 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22921 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
22922 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22923 case 0: break;
|
|
jpayne@69
|
22924 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22925 }
|
|
jpayne@69
|
22926 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
22927 switch (__pyx_nargs) {
|
|
jpayne@69
|
22928 case 0:
|
|
jpayne@69
|
22929 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
|
|
jpayne@69
|
22930 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
22931 kw_args--;
|
|
jpayne@69
|
22932 }
|
|
jpayne@69
|
22933 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22934 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22935 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22936 case 1:
|
|
jpayne@69
|
22937 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
|
|
jpayne@69
|
22938 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
22939 kw_args--;
|
|
jpayne@69
|
22940 }
|
|
jpayne@69
|
22941 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22942 else {
|
|
jpayne@69
|
22943 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Parser", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22944 }
|
|
jpayne@69
|
22945 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
22946 case 2:
|
|
jpayne@69
|
22947 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
22948 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
22949 kw_args--;
|
|
jpayne@69
|
22950 }
|
|
jpayne@69
|
22951 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22952 else {
|
|
jpayne@69
|
22953 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Parser", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22954 }
|
|
jpayne@69
|
22955 }
|
|
jpayne@69
|
22956 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
22957 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
22958 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_Parser") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22959 }
|
|
jpayne@69
|
22960 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
22961 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
22962 } else {
|
|
jpayne@69
|
22963 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
22964 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
22965 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
22966 }
|
|
jpayne@69
|
22967 __pyx_v___pyx_type = values[0];
|
|
jpayne@69
|
22968 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22969 __pyx_v___pyx_state = values[2];
|
|
jpayne@69
|
22970 }
|
|
jpayne@69
|
22971 goto __pyx_L6_skip;
|
|
jpayne@69
|
22972 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
22973 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Parser", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
22974 __pyx_L6_skip:;
|
|
jpayne@69
|
22975 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
22976 __pyx_L3_error:;
|
|
jpayne@69
|
22977 {
|
|
jpayne@69
|
22978 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
22979 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
22980 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
22981 }
|
|
jpayne@69
|
22982 }
|
|
jpayne@69
|
22983 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_Parser", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
22984 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22985 return NULL;
|
|
jpayne@69
|
22986 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
22987 __pyx_r = __pyx_pf_5pysam_9libctabix_6__pyx_unpickle_Parser(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
|
|
jpayne@69
|
22988
|
|
jpayne@69
|
22989 /* function exit code */
|
|
jpayne@69
|
22990 {
|
|
jpayne@69
|
22991 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
22992 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
22993 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
22994 }
|
|
jpayne@69
|
22995 }
|
|
jpayne@69
|
22996 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
22997 return __pyx_r;
|
|
jpayne@69
|
22998 }
|
|
jpayne@69
|
22999
|
|
jpayne@69
|
23000 static PyObject *__pyx_pf_5pysam_9libctabix_6__pyx_unpickle_Parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
23001 PyObject *__pyx_v___pyx_PickleError = 0;
|
|
jpayne@69
|
23002 PyObject *__pyx_v___pyx_result = 0;
|
|
jpayne@69
|
23003 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
23004 __Pyx_TraceDeclarations
|
|
jpayne@69
|
23005 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
23006 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
23007 int __pyx_t_2;
|
|
jpayne@69
|
23008 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
23009 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
23010 unsigned int __pyx_t_5;
|
|
jpayne@69
|
23011 int __pyx_lineno = 0;
|
|
jpayne@69
|
23012 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23013 int __pyx_clineno = 0;
|
|
jpayne@69
|
23014 __Pyx_TraceFrameInit(__pyx_codeobj__54)
|
|
jpayne@69
|
23015 __Pyx_RefNannySetupContext("__pyx_unpickle_Parser", 1);
|
|
jpayne@69
|
23016 __Pyx_TraceCall("__pyx_unpickle_Parser", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
23017
|
|
jpayne@69
|
23018 /* "(tree fragment)":4
|
|
jpayne@69
|
23019 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23020 * cdef object __pyx_result
|
|
jpayne@69
|
23021 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23022 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23023 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23024 */
|
|
jpayne@69
|
23025 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
23026 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23027 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
23028 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23029 if (__pyx_t_2) {
|
|
jpayne@69
|
23030
|
|
jpayne@69
|
23031 /* "(tree fragment)":5
|
|
jpayne@69
|
23032 * cdef object __pyx_result
|
|
jpayne@69
|
23033 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
23034 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23035 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23036 * __pyx_result = Parser.__new__(__pyx_type)
|
|
jpayne@69
|
23037 */
|
|
jpayne@69
|
23038 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23039 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23040 __Pyx_INCREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
23041 __Pyx_GIVEREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
23042 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
23043 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23044 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23045 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23046 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23047 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23048 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
23049 __pyx_v___pyx_PickleError = __pyx_t_1;
|
|
jpayne@69
|
23050 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23051 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23052
|
|
jpayne@69
|
23053 /* "(tree fragment)":6
|
|
jpayne@69
|
23054 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
23055 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23056 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23057 * __pyx_result = Parser.__new__(__pyx_type)
|
|
jpayne@69
|
23058 * if __pyx_state is not None:
|
|
jpayne@69
|
23059 */
|
|
jpayne@69
|
23060 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23061 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
23062 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23063 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23064 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23065 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
|
|
jpayne@69
|
23066 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23067 __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23068
|
|
jpayne@69
|
23069 /* "(tree fragment)":4
|
|
jpayne@69
|
23070 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23071 * cdef object __pyx_result
|
|
jpayne@69
|
23072 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23073 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23074 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23075 */
|
|
jpayne@69
|
23076 }
|
|
jpayne@69
|
23077
|
|
jpayne@69
|
23078 /* "(tree fragment)":7
|
|
jpayne@69
|
23079 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23080 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23081 * __pyx_result = Parser.__new__(__pyx_type) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23082 * if __pyx_state is not None:
|
|
jpayne@69
|
23083 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23084 */
|
|
jpayne@69
|
23085 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
23086 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23087 __pyx_t_4 = NULL;
|
|
jpayne@69
|
23088 __pyx_t_5 = 0;
|
|
jpayne@69
|
23089 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
23090 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
23091 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
23092 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
23093 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
23094 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
23095 __Pyx_INCREF(function);
|
|
jpayne@69
|
23096 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
23097 __pyx_t_5 = 1;
|
|
jpayne@69
|
23098 }
|
|
jpayne@69
|
23099 }
|
|
jpayne@69
|
23100 #endif
|
|
jpayne@69
|
23101 {
|
|
jpayne@69
|
23102 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
|
|
jpayne@69
|
23103 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
23104 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
23105 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
23106 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23107 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23108 }
|
|
jpayne@69
|
23109 __pyx_v___pyx_result = __pyx_t_1;
|
|
jpayne@69
|
23110 __pyx_t_1 = 0;
|
|
jpayne@69
|
23111
|
|
jpayne@69
|
23112 /* "(tree fragment)":8
|
|
jpayne@69
|
23113 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23114 * __pyx_result = Parser.__new__(__pyx_type)
|
|
jpayne@69
|
23115 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23116 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23117 * return __pyx_result
|
|
jpayne@69
|
23118 */
|
|
jpayne@69
|
23119 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
|
|
jpayne@69
|
23120 if (__pyx_t_2) {
|
|
jpayne@69
|
23121
|
|
jpayne@69
|
23122 /* "(tree fragment)":9
|
|
jpayne@69
|
23123 * __pyx_result = Parser.__new__(__pyx_type)
|
|
jpayne@69
|
23124 * if __pyx_state is not None:
|
|
jpayne@69
|
23125 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23126 * return __pyx_result
|
|
jpayne@69
|
23127 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23128 */
|
|
jpayne@69
|
23129 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
23130 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
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jpayne@69
|
23131 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23132 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23133
|
|
jpayne@69
|
23134 /* "(tree fragment)":8
|
|
jpayne@69
|
23135 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23136 * __pyx_result = Parser.__new__(__pyx_type)
|
|
jpayne@69
|
23137 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23138 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23139 * return __pyx_result
|
|
jpayne@69
|
23140 */
|
|
jpayne@69
|
23141 }
|
|
jpayne@69
|
23142
|
|
jpayne@69
|
23143 /* "(tree fragment)":10
|
|
jpayne@69
|
23144 * if __pyx_state is not None:
|
|
jpayne@69
|
23145 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23146 * return __pyx_result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23147 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23148 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23149 */
|
|
jpayne@69
|
23150 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
23151 __Pyx_INCREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
23152 __pyx_r = __pyx_v___pyx_result;
|
|
jpayne@69
|
23153 goto __pyx_L0;
|
|
jpayne@69
|
23154
|
|
jpayne@69
|
23155 /* "(tree fragment)":1
|
|
jpayne@69
|
23156 * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23157 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23158 * cdef object __pyx_result
|
|
jpayne@69
|
23159 */
|
|
jpayne@69
|
23160
|
|
jpayne@69
|
23161 /* function exit code */
|
|
jpayne@69
|
23162 __pyx_L1_error:;
|
|
jpayne@69
|
23163 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
23164 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
23165 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
23166 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_Parser", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
23167 __pyx_r = NULL;
|
|
jpayne@69
|
23168 __pyx_L0:;
|
|
jpayne@69
|
23169 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
|
|
jpayne@69
|
23170 __Pyx_XDECREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
23171 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
|
23172 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
23173 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23174 return __pyx_r;
|
|
jpayne@69
|
23175 }
|
|
jpayne@69
|
23176
|
|
jpayne@69
|
23177 /* "(tree fragment)":11
|
|
jpayne@69
|
23178 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23179 * return __pyx_result
|
|
jpayne@69
|
23180 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23181 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23182 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23183 */
|
|
jpayne@69
|
23184
|
|
jpayne@69
|
23185 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
23186 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
23187 __Pyx_TraceDeclarations
|
|
jpayne@69
|
23188 __Pyx_RefNannyDeclarations
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|
jpayne@69
|
23189 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
23190 int __pyx_t_2;
|
|
jpayne@69
|
23191 Py_ssize_t __pyx_t_3;
|
|
jpayne@69
|
23192 int __pyx_t_4;
|
|
jpayne@69
|
23193 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
23194 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
23195 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
23196 unsigned int __pyx_t_8;
|
|
jpayne@69
|
23197 int __pyx_lineno = 0;
|
|
jpayne@69
|
23198 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23199 int __pyx_clineno = 0;
|
|
jpayne@69
|
23200 __Pyx_RefNannySetupContext("__pyx_unpickle_Parser__set_state", 1);
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jpayne@69
|
23201 __Pyx_TraceCall("__pyx_unpickle_Parser__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error));
|
|
jpayne@69
|
23202
|
|
jpayne@69
|
23203 /* "(tree fragment)":12
|
|
jpayne@69
|
23204 * return __pyx_result
|
|
jpayne@69
|
23205 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23206 * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23207 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23208 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
23209 */
|
|
jpayne@69
|
23210 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
23211 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
23212 __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
23213 }
|
|
jpayne@69
|
23214 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
23215 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23216 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
23217 __Pyx_GOTREF(__pyx_v___pyx_result->encoding);
|
|
jpayne@69
|
23218 __Pyx_DECREF(__pyx_v___pyx_result->encoding);
|
|
jpayne@69
|
23219 __pyx_v___pyx_result->encoding = __pyx_t_1;
|
|
jpayne@69
|
23220 __pyx_t_1 = 0;
|
|
jpayne@69
|
23221
|
|
jpayne@69
|
23222 /* "(tree fragment)":13
|
|
jpayne@69
|
23223 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23224 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23225 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23226 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
23227 */
|
|
jpayne@69
|
23228 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
23229 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
|
|
jpayne@69
|
23230 __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
23231 }
|
|
jpayne@69
|
23232 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
23233 __pyx_t_4 = (__pyx_t_3 > 1);
|
|
jpayne@69
|
23234 if (__pyx_t_4) {
|
|
jpayne@69
|
23235 } else {
|
|
jpayne@69
|
23236 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
23237 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
23238 }
|
|
jpayne@69
|
23239 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
23240 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
23241 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
23242 if (__pyx_t_2) {
|
|
jpayne@69
|
23243
|
|
jpayne@69
|
23244 /* "(tree fragment)":14
|
|
jpayne@69
|
23245 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23246 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23247 * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23248 */
|
|
jpayne@69
|
23249 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23250 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
23251 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23252 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
23253 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
23254 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
23255 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
23256 __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23257 }
|
|
jpayne@69
|
23258 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23259 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
23260 __pyx_t_7 = NULL;
|
|
jpayne@69
|
23261 __pyx_t_8 = 0;
|
|
jpayne@69
|
23262 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
23263 if (likely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
23264 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
23265 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
23266 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
23267 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
23268 __Pyx_INCREF(function);
|
|
jpayne@69
|
23269 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
23270 __pyx_t_8 = 1;
|
|
jpayne@69
|
23271 }
|
|
jpayne@69
|
23272 }
|
|
jpayne@69
|
23273 #endif
|
|
jpayne@69
|
23274 {
|
|
jpayne@69
|
23275 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
|
|
jpayne@69
|
23276 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
|
|
jpayne@69
|
23277 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
23278 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
23279 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23280 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23281 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
23282 }
|
|
jpayne@69
|
23283 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23284
|
|
jpayne@69
|
23285 /* "(tree fragment)":13
|
|
jpayne@69
|
23286 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23287 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23288 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23289 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
23290 */
|
|
jpayne@69
|
23291 }
|
|
jpayne@69
|
23292
|
|
jpayne@69
|
23293 /* "(tree fragment)":11
|
|
jpayne@69
|
23294 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23295 * return __pyx_result
|
|
jpayne@69
|
23296 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23297 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23298 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23299 */
|
|
jpayne@69
|
23300
|
|
jpayne@69
|
23301 /* function exit code */
|
|
jpayne@69
|
23302 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
23303 goto __pyx_L0;
|
|
jpayne@69
|
23304 __pyx_L1_error:;
|
|
jpayne@69
|
23305 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
23306 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
23307 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
23308 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
23309 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_Parser__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
23310 __pyx_r = 0;
|
|
jpayne@69
|
23311 __pyx_L0:;
|
|
jpayne@69
|
23312 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
23313 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
23314 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23315 return __pyx_r;
|
|
jpayne@69
|
23316 }
|
|
jpayne@69
|
23317
|
|
jpayne@69
|
23318 /* "(tree fragment)":1
|
|
jpayne@69
|
23319 * def __pyx_unpickle_asTuple(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23320 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23321 * cdef object __pyx_result
|
|
jpayne@69
|
23322 */
|
|
jpayne@69
|
23323
|
|
jpayne@69
|
23324 /* Python wrapper */
|
|
jpayne@69
|
23325 static PyObject *__pyx_pw_5pysam_9libctabix_9__pyx_unpickle_asTuple(PyObject *__pyx_self,
|
|
jpayne@69
|
23326 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23327 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
23328 #else
|
|
jpayne@69
|
23329 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
23330 #endif
|
|
jpayne@69
|
23331 ); /*proto*/
|
|
jpayne@69
|
23332 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_8__pyx_unpickle_asTuple, "__pyx_unpickle_asTuple(__pyx_type, long __pyx_checksum, __pyx_state)");
|
|
jpayne@69
|
23333 static PyMethodDef __pyx_mdef_5pysam_9libctabix_9__pyx_unpickle_asTuple = {"__pyx_unpickle_asTuple", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9__pyx_unpickle_asTuple, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_8__pyx_unpickle_asTuple};
|
|
jpayne@69
|
23334 static PyObject *__pyx_pw_5pysam_9libctabix_9__pyx_unpickle_asTuple(PyObject *__pyx_self,
|
|
jpayne@69
|
23335 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23336 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
23337 #else
|
|
jpayne@69
|
23338 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
23339 #endif
|
|
jpayne@69
|
23340 ) {
|
|
jpayne@69
|
23341 PyObject *__pyx_v___pyx_type = 0;
|
|
jpayne@69
|
23342 long __pyx_v___pyx_checksum;
|
|
jpayne@69
|
23343 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
23344 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23345 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
23346 #endif
|
|
jpayne@69
|
23347 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
23348 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
23349 int __pyx_lineno = 0;
|
|
jpayne@69
|
23350 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23351 int __pyx_clineno = 0;
|
|
jpayne@69
|
23352 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
23353 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
23354 __Pyx_RefNannySetupContext("__pyx_unpickle_asTuple (wrapper)", 0);
|
|
jpayne@69
|
23355 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23356 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
23357 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
23358 #else
|
|
jpayne@69
|
23359 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
23360 #endif
|
|
jpayne@69
|
23361 #endif
|
|
jpayne@69
|
23362 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
23363 {
|
|
jpayne@69
|
23364 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
23365 if (__pyx_kwds) {
|
|
jpayne@69
|
23366 Py_ssize_t kw_args;
|
|
jpayne@69
|
23367 switch (__pyx_nargs) {
|
|
jpayne@69
|
23368 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
23369 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23370 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
23371 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23372 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
23373 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23374 case 0: break;
|
|
jpayne@69
|
23375 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
23376 }
|
|
jpayne@69
|
23377 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
23378 switch (__pyx_nargs) {
|
|
jpayne@69
|
23379 case 0:
|
|
jpayne@69
|
23380 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
|
|
jpayne@69
|
23381 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
23382 kw_args--;
|
|
jpayne@69
|
23383 }
|
|
jpayne@69
|
23384 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23385 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
23386 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23387 case 1:
|
|
jpayne@69
|
23388 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
|
|
jpayne@69
|
23389 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
23390 kw_args--;
|
|
jpayne@69
|
23391 }
|
|
jpayne@69
|
23392 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23393 else {
|
|
jpayne@69
|
23394 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asTuple", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23395 }
|
|
jpayne@69
|
23396 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23397 case 2:
|
|
jpayne@69
|
23398 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
23399 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
23400 kw_args--;
|
|
jpayne@69
|
23401 }
|
|
jpayne@69
|
23402 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23403 else {
|
|
jpayne@69
|
23404 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asTuple", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23405 }
|
|
jpayne@69
|
23406 }
|
|
jpayne@69
|
23407 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
23408 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
23409 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asTuple") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23410 }
|
|
jpayne@69
|
23411 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
23412 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
23413 } else {
|
|
jpayne@69
|
23414 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
23415 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
23416 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
23417 }
|
|
jpayne@69
|
23418 __pyx_v___pyx_type = values[0];
|
|
jpayne@69
|
23419 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23420 __pyx_v___pyx_state = values[2];
|
|
jpayne@69
|
23421 }
|
|
jpayne@69
|
23422 goto __pyx_L6_skip;
|
|
jpayne@69
|
23423 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
23424 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asTuple", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23425 __pyx_L6_skip:;
|
|
jpayne@69
|
23426 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
23427 __pyx_L3_error:;
|
|
jpayne@69
|
23428 {
|
|
jpayne@69
|
23429 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
23430 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
23431 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
23432 }
|
|
jpayne@69
|
23433 }
|
|
jpayne@69
|
23434 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asTuple", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
23435 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23436 return NULL;
|
|
jpayne@69
|
23437 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
23438 __pyx_r = __pyx_pf_5pysam_9libctabix_8__pyx_unpickle_asTuple(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
|
|
jpayne@69
|
23439
|
|
jpayne@69
|
23440 /* function exit code */
|
|
jpayne@69
|
23441 {
|
|
jpayne@69
|
23442 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
23443 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
23444 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
23445 }
|
|
jpayne@69
|
23446 }
|
|
jpayne@69
|
23447 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23448 return __pyx_r;
|
|
jpayne@69
|
23449 }
|
|
jpayne@69
|
23450
|
|
jpayne@69
|
23451 static PyObject *__pyx_pf_5pysam_9libctabix_8__pyx_unpickle_asTuple(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
23452 PyObject *__pyx_v___pyx_PickleError = 0;
|
|
jpayne@69
|
23453 PyObject *__pyx_v___pyx_result = 0;
|
|
jpayne@69
|
23454 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
23455 __Pyx_TraceDeclarations
|
|
jpayne@69
|
23456 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
23457 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
23458 int __pyx_t_2;
|
|
jpayne@69
|
23459 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
23460 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
23461 unsigned int __pyx_t_5;
|
|
jpayne@69
|
23462 int __pyx_lineno = 0;
|
|
jpayne@69
|
23463 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23464 int __pyx_clineno = 0;
|
|
jpayne@69
|
23465 __Pyx_TraceFrameInit(__pyx_codeobj__57)
|
|
jpayne@69
|
23466 __Pyx_RefNannySetupContext("__pyx_unpickle_asTuple", 1);
|
|
jpayne@69
|
23467 __Pyx_TraceCall("__pyx_unpickle_asTuple", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
23468
|
|
jpayne@69
|
23469 /* "(tree fragment)":4
|
|
jpayne@69
|
23470 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23471 * cdef object __pyx_result
|
|
jpayne@69
|
23472 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23473 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23474 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23475 */
|
|
jpayne@69
|
23476 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
23477 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23478 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
23479 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23480 if (__pyx_t_2) {
|
|
jpayne@69
|
23481
|
|
jpayne@69
|
23482 /* "(tree fragment)":5
|
|
jpayne@69
|
23483 * cdef object __pyx_result
|
|
jpayne@69
|
23484 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
23485 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23486 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23487 * __pyx_result = asTuple.__new__(__pyx_type)
|
|
jpayne@69
|
23488 */
|
|
jpayne@69
|
23489 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23490 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23491 __Pyx_INCREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
23492 __Pyx_GIVEREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
23493 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
23494 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23495 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23496 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23497 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23498 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23499 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
23500 __pyx_v___pyx_PickleError = __pyx_t_1;
|
|
jpayne@69
|
23501 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23502 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23503
|
|
jpayne@69
|
23504 /* "(tree fragment)":6
|
|
jpayne@69
|
23505 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
23506 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23507 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23508 * __pyx_result = asTuple.__new__(__pyx_type)
|
|
jpayne@69
|
23509 * if __pyx_state is not None:
|
|
jpayne@69
|
23510 */
|
|
jpayne@69
|
23511 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23512 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23513 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23514 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23515 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23516 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
|
|
jpayne@69
|
23517 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23518 __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23519
|
|
jpayne@69
|
23520 /* "(tree fragment)":4
|
|
jpayne@69
|
23521 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23522 * cdef object __pyx_result
|
|
jpayne@69
|
23523 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23524 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23525 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23526 */
|
|
jpayne@69
|
23527 }
|
|
jpayne@69
|
23528
|
|
jpayne@69
|
23529 /* "(tree fragment)":7
|
|
jpayne@69
|
23530 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23531 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23532 * __pyx_result = asTuple.__new__(__pyx_type) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23533 * if __pyx_state is not None:
|
|
jpayne@69
|
23534 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23535 */
|
|
jpayne@69
|
23536 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asTuple), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
23537 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23538 __pyx_t_4 = NULL;
|
|
jpayne@69
|
23539 __pyx_t_5 = 0;
|
|
jpayne@69
|
23540 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
23541 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
23542 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
23543 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
23544 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
23545 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
23546 __Pyx_INCREF(function);
|
|
jpayne@69
|
23547 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
23548 __pyx_t_5 = 1;
|
|
jpayne@69
|
23549 }
|
|
jpayne@69
|
23550 }
|
|
jpayne@69
|
23551 #endif
|
|
jpayne@69
|
23552 {
|
|
jpayne@69
|
23553 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
|
|
jpayne@69
|
23554 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
23555 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
23556 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
23557 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23558 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23559 }
|
|
jpayne@69
|
23560 __pyx_v___pyx_result = __pyx_t_1;
|
|
jpayne@69
|
23561 __pyx_t_1 = 0;
|
|
jpayne@69
|
23562
|
|
jpayne@69
|
23563 /* "(tree fragment)":8
|
|
jpayne@69
|
23564 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23565 * __pyx_result = asTuple.__new__(__pyx_type)
|
|
jpayne@69
|
23566 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23567 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23568 * return __pyx_result
|
|
jpayne@69
|
23569 */
|
|
jpayne@69
|
23570 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
|
|
jpayne@69
|
23571 if (__pyx_t_2) {
|
|
jpayne@69
|
23572
|
|
jpayne@69
|
23573 /* "(tree fragment)":9
|
|
jpayne@69
|
23574 * __pyx_result = asTuple.__new__(__pyx_type)
|
|
jpayne@69
|
23575 * if __pyx_state is not None:
|
|
jpayne@69
|
23576 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23577 * return __pyx_result
|
|
jpayne@69
|
23578 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23579 */
|
|
jpayne@69
|
23580 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
23581 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(((struct __pyx_obj_5pysam_9libctabix_asTuple *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
23582 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23583 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23584
|
|
jpayne@69
|
23585 /* "(tree fragment)":8
|
|
jpayne@69
|
23586 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23587 * __pyx_result = asTuple.__new__(__pyx_type)
|
|
jpayne@69
|
23588 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23589 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23590 * return __pyx_result
|
|
jpayne@69
|
23591 */
|
|
jpayne@69
|
23592 }
|
|
jpayne@69
|
23593
|
|
jpayne@69
|
23594 /* "(tree fragment)":10
|
|
jpayne@69
|
23595 * if __pyx_state is not None:
|
|
jpayne@69
|
23596 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23597 * return __pyx_result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23598 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23599 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23600 */
|
|
jpayne@69
|
23601 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
23602 __Pyx_INCREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
23603 __pyx_r = __pyx_v___pyx_result;
|
|
jpayne@69
|
23604 goto __pyx_L0;
|
|
jpayne@69
|
23605
|
|
jpayne@69
|
23606 /* "(tree fragment)":1
|
|
jpayne@69
|
23607 * def __pyx_unpickle_asTuple(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23608 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23609 * cdef object __pyx_result
|
|
jpayne@69
|
23610 */
|
|
jpayne@69
|
23611
|
|
jpayne@69
|
23612 /* function exit code */
|
|
jpayne@69
|
23613 __pyx_L1_error:;
|
|
jpayne@69
|
23614 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
23615 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
23616 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
23617 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asTuple", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
23618 __pyx_r = NULL;
|
|
jpayne@69
|
23619 __pyx_L0:;
|
|
jpayne@69
|
23620 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
|
|
jpayne@69
|
23621 __Pyx_XDECREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
23622 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
23623 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
23624 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23625 return __pyx_r;
|
|
jpayne@69
|
23626 }
|
|
jpayne@69
|
23627
|
|
jpayne@69
|
23628 /* "(tree fragment)":11
|
|
jpayne@69
|
23629 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23630 * return __pyx_result
|
|
jpayne@69
|
23631 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23632 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23633 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23634 */
|
|
jpayne@69
|
23635
|
|
jpayne@69
|
23636 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
23637 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
23638 __Pyx_TraceDeclarations
|
|
jpayne@69
|
23639 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
23640 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
23641 int __pyx_t_2;
|
|
jpayne@69
|
23642 Py_ssize_t __pyx_t_3;
|
|
jpayne@69
|
23643 int __pyx_t_4;
|
|
jpayne@69
|
23644 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
23645 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
23646 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
23647 unsigned int __pyx_t_8;
|
|
jpayne@69
|
23648 int __pyx_lineno = 0;
|
|
jpayne@69
|
23649 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23650 int __pyx_clineno = 0;
|
|
jpayne@69
|
23651 __Pyx_RefNannySetupContext("__pyx_unpickle_asTuple__set_state", 1);
|
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jpayne@69
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23652 __Pyx_TraceCall("__pyx_unpickle_asTuple__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error));
|
|
jpayne@69
|
23653
|
|
jpayne@69
|
23654 /* "(tree fragment)":12
|
|
jpayne@69
|
23655 * return __pyx_result
|
|
jpayne@69
|
23656 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23657 * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23658 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23659 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
23660 */
|
|
jpayne@69
|
23661 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
23662 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
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jpayne@69
|
23663 __PYX_ERR(1, 12, __pyx_L1_error)
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jpayne@69
|
23664 }
|
|
jpayne@69
|
23665 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
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jpayne@69
|
23666 __Pyx_GOTREF(__pyx_t_1);
|
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jpayne@69
|
23667 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
23668 __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
23669 __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
23670 __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1;
|
|
jpayne@69
|
23671 __pyx_t_1 = 0;
|
|
jpayne@69
|
23672
|
|
jpayne@69
|
23673 /* "(tree fragment)":13
|
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jpayne@69
|
23674 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23675 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23676 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23677 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
23678 */
|
|
jpayne@69
|
23679 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
23680 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
|
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jpayne@69
|
23681 __PYX_ERR(1, 13, __pyx_L1_error)
|
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jpayne@69
|
23682 }
|
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jpayne@69
|
23683 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
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jpayne@69
|
23684 __pyx_t_4 = (__pyx_t_3 > 1);
|
|
jpayne@69
|
23685 if (__pyx_t_4) {
|
|
jpayne@69
|
23686 } else {
|
|
jpayne@69
|
23687 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
23688 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
23689 }
|
|
jpayne@69
|
23690 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
23691 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
23692 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
23693 if (__pyx_t_2) {
|
|
jpayne@69
|
23694
|
|
jpayne@69
|
23695 /* "(tree fragment)":14
|
|
jpayne@69
|
23696 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23697 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23698 * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23699 */
|
|
jpayne@69
|
23700 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23701 __Pyx_GOTREF(__pyx_t_5);
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jpayne@69
|
23702 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23703 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
23704 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
23705 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
23706 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
23707 __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23708 }
|
|
jpayne@69
|
23709 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
23710 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
23711 __pyx_t_7 = NULL;
|
|
jpayne@69
|
23712 __pyx_t_8 = 0;
|
|
jpayne@69
|
23713 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
23714 if (likely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
23715 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
23716 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
23717 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
23718 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
23719 __Pyx_INCREF(function);
|
|
jpayne@69
|
23720 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
23721 __pyx_t_8 = 1;
|
|
jpayne@69
|
23722 }
|
|
jpayne@69
|
23723 }
|
|
jpayne@69
|
23724 #endif
|
|
jpayne@69
|
23725 {
|
|
jpayne@69
|
23726 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
|
|
jpayne@69
|
23727 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
|
|
jpayne@69
|
23728 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
23729 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
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jpayne@69
|
23730 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error)
|
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jpayne@69
|
23731 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23732 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
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jpayne@69
|
23733 }
|
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jpayne@69
|
23734 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23735
|
|
jpayne@69
|
23736 /* "(tree fragment)":13
|
|
jpayne@69
|
23737 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
23738 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23739 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23740 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
23741 */
|
|
jpayne@69
|
23742 }
|
|
jpayne@69
|
23743
|
|
jpayne@69
|
23744 /* "(tree fragment)":11
|
|
jpayne@69
|
23745 * __pyx_unpickle_asTuple__set_state(<asTuple> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23746 * return __pyx_result
|
|
jpayne@69
|
23747 * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23748 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
23749 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
23750 */
|
|
jpayne@69
|
23751
|
|
jpayne@69
|
23752 /* function exit code */
|
|
jpayne@69
|
23753 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
23754 goto __pyx_L0;
|
|
jpayne@69
|
23755 __pyx_L1_error:;
|
|
jpayne@69
|
23756 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
23757 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
23758 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
23759 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
23760 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asTuple__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
23761 __pyx_r = 0;
|
|
jpayne@69
|
23762 __pyx_L0:;
|
|
jpayne@69
|
23763 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
23764 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
23765 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23766 return __pyx_r;
|
|
jpayne@69
|
23767 }
|
|
jpayne@69
|
23768
|
|
jpayne@69
|
23769 /* "(tree fragment)":1
|
|
jpayne@69
|
23770 * def __pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23771 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23772 * cdef object __pyx_result
|
|
jpayne@69
|
23773 */
|
|
jpayne@69
|
23774
|
|
jpayne@69
|
23775 /* Python wrapper */
|
|
jpayne@69
|
23776 static PyObject *__pyx_pw_5pysam_9libctabix_11__pyx_unpickle_asGFF3(PyObject *__pyx_self,
|
|
jpayne@69
|
23777 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23778 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
23779 #else
|
|
jpayne@69
|
23780 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
23781 #endif
|
|
jpayne@69
|
23782 ); /*proto*/
|
|
jpayne@69
|
23783 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10__pyx_unpickle_asGFF3, "__pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state)");
|
|
jpayne@69
|
23784 static PyMethodDef __pyx_mdef_5pysam_9libctabix_11__pyx_unpickle_asGFF3 = {"__pyx_unpickle_asGFF3", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_11__pyx_unpickle_asGFF3, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10__pyx_unpickle_asGFF3};
|
|
jpayne@69
|
23785 static PyObject *__pyx_pw_5pysam_9libctabix_11__pyx_unpickle_asGFF3(PyObject *__pyx_self,
|
|
jpayne@69
|
23786 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23787 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
23788 #else
|
|
jpayne@69
|
23789 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
23790 #endif
|
|
jpayne@69
|
23791 ) {
|
|
jpayne@69
|
23792 PyObject *__pyx_v___pyx_type = 0;
|
|
jpayne@69
|
23793 long __pyx_v___pyx_checksum;
|
|
jpayne@69
|
23794 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
23795 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23796 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
23797 #endif
|
|
jpayne@69
|
23798 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
23799 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
23800 int __pyx_lineno = 0;
|
|
jpayne@69
|
23801 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23802 int __pyx_clineno = 0;
|
|
jpayne@69
|
23803 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
23804 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
23805 __Pyx_RefNannySetupContext("__pyx_unpickle_asGFF3 (wrapper)", 0);
|
|
jpayne@69
|
23806 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
23807 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
23808 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
23809 #else
|
|
jpayne@69
|
23810 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
23811 #endif
|
|
jpayne@69
|
23812 #endif
|
|
jpayne@69
|
23813 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
23814 {
|
|
jpayne@69
|
23815 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
23816 if (__pyx_kwds) {
|
|
jpayne@69
|
23817 Py_ssize_t kw_args;
|
|
jpayne@69
|
23818 switch (__pyx_nargs) {
|
|
jpayne@69
|
23819 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
23820 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23821 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
23822 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23823 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
23824 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23825 case 0: break;
|
|
jpayne@69
|
23826 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
23827 }
|
|
jpayne@69
|
23828 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
23829 switch (__pyx_nargs) {
|
|
jpayne@69
|
23830 case 0:
|
|
jpayne@69
|
23831 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
|
|
jpayne@69
|
23832 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
23833 kw_args--;
|
|
jpayne@69
|
23834 }
|
|
jpayne@69
|
23835 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23836 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
23837 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23838 case 1:
|
|
jpayne@69
|
23839 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
|
|
jpayne@69
|
23840 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
23841 kw_args--;
|
|
jpayne@69
|
23842 }
|
|
jpayne@69
|
23843 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23844 else {
|
|
jpayne@69
|
23845 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGFF3", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23846 }
|
|
jpayne@69
|
23847 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
23848 case 2:
|
|
jpayne@69
|
23849 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
23850 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
23851 kw_args--;
|
|
jpayne@69
|
23852 }
|
|
jpayne@69
|
23853 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23854 else {
|
|
jpayne@69
|
23855 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGFF3", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23856 }
|
|
jpayne@69
|
23857 }
|
|
jpayne@69
|
23858 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
23859 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
23860 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asGFF3") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23861 }
|
|
jpayne@69
|
23862 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
23863 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
23864 } else {
|
|
jpayne@69
|
23865 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
23866 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
23867 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
23868 }
|
|
jpayne@69
|
23869 __pyx_v___pyx_type = values[0];
|
|
jpayne@69
|
23870 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23871 __pyx_v___pyx_state = values[2];
|
|
jpayne@69
|
23872 }
|
|
jpayne@69
|
23873 goto __pyx_L6_skip;
|
|
jpayne@69
|
23874 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
23875 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGFF3", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
23876 __pyx_L6_skip:;
|
|
jpayne@69
|
23877 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
23878 __pyx_L3_error:;
|
|
jpayne@69
|
23879 {
|
|
jpayne@69
|
23880 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
23881 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
23882 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
23883 }
|
|
jpayne@69
|
23884 }
|
|
jpayne@69
|
23885 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGFF3", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
23886 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23887 return NULL;
|
|
jpayne@69
|
23888 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
23889 __pyx_r = __pyx_pf_5pysam_9libctabix_10__pyx_unpickle_asGFF3(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
|
|
jpayne@69
|
23890
|
|
jpayne@69
|
23891 /* function exit code */
|
|
jpayne@69
|
23892 {
|
|
jpayne@69
|
23893 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
23894 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
23895 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
23896 }
|
|
jpayne@69
|
23897 }
|
|
jpayne@69
|
23898 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
23899 return __pyx_r;
|
|
jpayne@69
|
23900 }
|
|
jpayne@69
|
23901
|
|
jpayne@69
|
23902 static PyObject *__pyx_pf_5pysam_9libctabix_10__pyx_unpickle_asGFF3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
23903 PyObject *__pyx_v___pyx_PickleError = 0;
|
|
jpayne@69
|
23904 PyObject *__pyx_v___pyx_result = 0;
|
|
jpayne@69
|
23905 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
23906 __Pyx_TraceDeclarations
|
|
jpayne@69
|
23907 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
23908 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
23909 int __pyx_t_2;
|
|
jpayne@69
|
23910 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
23911 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
23912 unsigned int __pyx_t_5;
|
|
jpayne@69
|
23913 int __pyx_lineno = 0;
|
|
jpayne@69
|
23914 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
23915 int __pyx_clineno = 0;
|
|
jpayne@69
|
23916 __Pyx_TraceFrameInit(__pyx_codeobj__58)
|
|
jpayne@69
|
23917 __Pyx_RefNannySetupContext("__pyx_unpickle_asGFF3", 1);
|
|
jpayne@69
|
23918 __Pyx_TraceCall("__pyx_unpickle_asGFF3", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
23919
|
|
jpayne@69
|
23920 /* "(tree fragment)":4
|
|
jpayne@69
|
23921 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23922 * cdef object __pyx_result
|
|
jpayne@69
|
23923 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23924 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23925 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23926 */
|
|
jpayne@69
|
23927 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
23928 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23929 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
23930 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23931 if (__pyx_t_2) {
|
|
jpayne@69
|
23932
|
|
jpayne@69
|
23933 /* "(tree fragment)":5
|
|
jpayne@69
|
23934 * cdef object __pyx_result
|
|
jpayne@69
|
23935 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
23936 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23937 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23938 * __pyx_result = asGFF3.__new__(__pyx_type)
|
|
jpayne@69
|
23939 */
|
|
jpayne@69
|
23940 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23941 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23942 __Pyx_INCREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
23943 __Pyx_GIVEREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
23944 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
23945 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23946 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23947 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23948 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
23949 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23950 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
23951 __pyx_v___pyx_PickleError = __pyx_t_1;
|
|
jpayne@69
|
23952 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23953 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23954
|
|
jpayne@69
|
23955 /* "(tree fragment)":6
|
|
jpayne@69
|
23956 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
23957 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23958 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23959 * __pyx_result = asGFF3.__new__(__pyx_type)
|
|
jpayne@69
|
23960 * if __pyx_state is not None:
|
|
jpayne@69
|
23961 */
|
|
jpayne@69
|
23962 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23963 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23964 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23965 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
23966 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
23967 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
|
|
jpayne@69
|
23968 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
23969 __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
23970
|
|
jpayne@69
|
23971 /* "(tree fragment)":4
|
|
jpayne@69
|
23972 * cdef object __pyx_PickleError
|
|
jpayne@69
|
23973 * cdef object __pyx_result
|
|
jpayne@69
|
23974 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23975 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23976 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23977 */
|
|
jpayne@69
|
23978 }
|
|
jpayne@69
|
23979
|
|
jpayne@69
|
23980 /* "(tree fragment)":7
|
|
jpayne@69
|
23981 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
23982 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
23983 * __pyx_result = asGFF3.__new__(__pyx_type) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
23984 * if __pyx_state is not None:
|
|
jpayne@69
|
23985 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
23986 */
|
|
jpayne@69
|
23987 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asGFF3), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
23988 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
23989 __pyx_t_4 = NULL;
|
|
jpayne@69
|
23990 __pyx_t_5 = 0;
|
|
jpayne@69
|
23991 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
23992 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
23993 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
23994 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
23995 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
23996 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
23997 __Pyx_INCREF(function);
|
|
jpayne@69
|
23998 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
23999 __pyx_t_5 = 1;
|
|
jpayne@69
|
24000 }
|
|
jpayne@69
|
24001 }
|
|
jpayne@69
|
24002 #endif
|
|
jpayne@69
|
24003 {
|
|
jpayne@69
|
24004 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
|
|
jpayne@69
|
24005 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
24006 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
24007 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
24008 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24009 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24010 }
|
|
jpayne@69
|
24011 __pyx_v___pyx_result = __pyx_t_1;
|
|
jpayne@69
|
24012 __pyx_t_1 = 0;
|
|
jpayne@69
|
24013
|
|
jpayne@69
|
24014 /* "(tree fragment)":8
|
|
jpayne@69
|
24015 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24016 * __pyx_result = asGFF3.__new__(__pyx_type)
|
|
jpayne@69
|
24017 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24018 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24019 * return __pyx_result
|
|
jpayne@69
|
24020 */
|
|
jpayne@69
|
24021 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
|
|
jpayne@69
|
24022 if (__pyx_t_2) {
|
|
jpayne@69
|
24023
|
|
jpayne@69
|
24024 /* "(tree fragment)":9
|
|
jpayne@69
|
24025 * __pyx_result = asGFF3.__new__(__pyx_type)
|
|
jpayne@69
|
24026 * if __pyx_state is not None:
|
|
jpayne@69
|
24027 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24028 * return __pyx_result
|
|
jpayne@69
|
24029 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24030 */
|
|
jpayne@69
|
24031 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
24032 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
24033 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24034 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24035
|
|
jpayne@69
|
24036 /* "(tree fragment)":8
|
|
jpayne@69
|
24037 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24038 * __pyx_result = asGFF3.__new__(__pyx_type)
|
|
jpayne@69
|
24039 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24040 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24041 * return __pyx_result
|
|
jpayne@69
|
24042 */
|
|
jpayne@69
|
24043 }
|
|
jpayne@69
|
24044
|
|
jpayne@69
|
24045 /* "(tree fragment)":10
|
|
jpayne@69
|
24046 * if __pyx_state is not None:
|
|
jpayne@69
|
24047 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24048 * return __pyx_result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24049 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24050 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24051 */
|
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jpayne@69
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24052 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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24053 __Pyx_INCREF(__pyx_v___pyx_result);
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jpayne@69
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24054 __pyx_r = __pyx_v___pyx_result;
|
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jpayne@69
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24055 goto __pyx_L0;
|
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jpayne@69
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24056
|
|
jpayne@69
|
24057 /* "(tree fragment)":1
|
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jpayne@69
|
24058 * def __pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24059 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24060 * cdef object __pyx_result
|
|
jpayne@69
|
24061 */
|
|
jpayne@69
|
24062
|
|
jpayne@69
|
24063 /* function exit code */
|
|
jpayne@69
|
24064 __pyx_L1_error:;
|
|
jpayne@69
|
24065 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
24066 __Pyx_XDECREF(__pyx_t_3);
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jpayne@69
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24067 __Pyx_XDECREF(__pyx_t_4);
|
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jpayne@69
|
24068 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGFF3", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24069 __pyx_r = NULL;
|
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jpayne@69
|
24070 __pyx_L0:;
|
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jpayne@69
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24071 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
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jpayne@69
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24072 __Pyx_XDECREF(__pyx_v___pyx_result);
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jpayne@69
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24073 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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24074 __Pyx_TraceReturn(__pyx_r, 0);
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jpayne@69
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24075 __Pyx_RefNannyFinishContext();
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jpayne@69
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24076 return __pyx_r;
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jpayne@69
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24077 }
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jpayne@69
|
24078
|
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jpayne@69
|
24079 /* "(tree fragment)":11
|
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jpayne@69
|
24080 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24081 * return __pyx_result
|
|
jpayne@69
|
24082 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24083 * __pyx_result.encoding = __pyx_state[0]
|
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jpayne@69
|
24084 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
24085 */
|
|
jpayne@69
|
24086
|
|
jpayne@69
|
24087 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
24088 PyObject *__pyx_r = NULL;
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jpayne@69
|
24089 __Pyx_TraceDeclarations
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jpayne@69
|
24090 __Pyx_RefNannyDeclarations
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jpayne@69
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jpayne@69
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24092 int __pyx_t_2;
|
|
jpayne@69
|
24093 Py_ssize_t __pyx_t_3;
|
|
jpayne@69
|
24094 int __pyx_t_4;
|
|
jpayne@69
|
24095 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
24096 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
24097 PyObject *__pyx_t_7 = NULL;
|
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jpayne@69
|
24098 unsigned int __pyx_t_8;
|
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jpayne@69
|
24099 int __pyx_lineno = 0;
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jpayne@69
|
24100 const char *__pyx_filename = NULL;
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jpayne@69
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24101 int __pyx_clineno = 0;
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jpayne@69
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24102 __Pyx_RefNannySetupContext("__pyx_unpickle_asGFF3__set_state", 1);
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jpayne@69
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|
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jpayne@69
|
24104
|
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jpayne@69
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24105 /* "(tree fragment)":12
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jpayne@69
|
24106 * return __pyx_result
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jpayne@69
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24107 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24108 * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<<
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jpayne@69
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24109 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
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|
jpayne@69
|
24110 * __pyx_result.__dict__.update(__pyx_state[1])
|
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jpayne@69
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24111 */
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jpayne@69
|
24112 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
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jpayne@69
|
24113 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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jpayne@69
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24114 __PYX_ERR(1, 12, __pyx_L1_error)
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jpayne@69
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24115 }
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jpayne@69
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24116 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
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jpayne@69
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24117 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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24118 __Pyx_GIVEREF(__pyx_t_1);
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
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24122 __pyx_t_1 = 0;
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jpayne@69
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24123
|
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jpayne@69
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24124 /* "(tree fragment)":13
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jpayne@69
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24125 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24126 * __pyx_result.encoding = __pyx_state[0]
|
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jpayne@69
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24127 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
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jpayne@69
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24128 * __pyx_result.__dict__.update(__pyx_state[1])
|
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jpayne@69
|
24129 */
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jpayne@69
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24130 if (unlikely(__pyx_v___pyx_state == Py_None)) {
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jpayne@69
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24131 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
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jpayne@69
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24132 __PYX_ERR(1, 13, __pyx_L1_error)
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jpayne@69
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24133 }
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jpayne@69
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24134 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
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jpayne@69
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24135 __pyx_t_4 = (__pyx_t_3 > 1);
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jpayne@69
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24136 if (__pyx_t_4) {
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jpayne@69
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24137 } else {
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jpayne@69
|
24138 __pyx_t_2 = __pyx_t_4;
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jpayne@69
|
24139 goto __pyx_L4_bool_binop_done;
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jpayne@69
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24140 }
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jpayne@69
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24141 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
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jpayne@69
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24142 __pyx_t_2 = __pyx_t_4;
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jpayne@69
|
24143 __pyx_L4_bool_binop_done:;
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jpayne@69
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jpayne@69
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24145
|
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jpayne@69
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24146 /* "(tree fragment)":14
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jpayne@69
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24147 * __pyx_result.encoding = __pyx_state[0]
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jpayne@69
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|
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jpayne@69
|
24149 * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<<
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jpayne@69
|
24150 */
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jpayne@69
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24151 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
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jpayne@69
|
24152 __Pyx_GOTREF(__pyx_t_5);
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jpayne@69
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24153 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
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jpayne@69
|
24154 __Pyx_GOTREF(__pyx_t_6);
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jpayne@69
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24155 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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jpayne@69
|
24156 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
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jpayne@69
|
24157 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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jpayne@69
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24158 __PYX_ERR(1, 14, __pyx_L1_error)
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jpayne@69
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24159 }
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jpayne@69
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24160 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
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jpayne@69
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24161 __Pyx_GOTREF(__pyx_t_5);
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jpayne@69
|
24162 __pyx_t_7 = NULL;
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jpayne@69
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24163 __pyx_t_8 = 0;
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jpayne@69
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24164 #if CYTHON_UNPACK_METHODS
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|
jpayne@69
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24165 if (likely(PyMethod_Check(__pyx_t_6))) {
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jpayne@69
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24166 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
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jpayne@69
|
24167 if (likely(__pyx_t_7)) {
|
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jpayne@69
|
24168 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
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jpayne@69
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24169 __Pyx_INCREF(__pyx_t_7);
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
|
24174 }
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jpayne@69
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jpayne@69
|
24176 {
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jpayne@69
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24177 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
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jpayne@69
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24178 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
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jpayne@69
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24179 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
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24183 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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jpayne@69
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24184 }
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jpayne@69
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24185 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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24186
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jpayne@69
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24187 /* "(tree fragment)":13
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jpayne@69
|
24188 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24189 * __pyx_result.encoding = __pyx_state[0]
|
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jpayne@69
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24190 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
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|
jpayne@69
|
24191 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
24192 */
|
|
jpayne@69
|
24193 }
|
|
jpayne@69
|
24194
|
|
jpayne@69
|
24195 /* "(tree fragment)":11
|
|
jpayne@69
|
24196 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24197 * return __pyx_result
|
|
jpayne@69
|
24198 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24199 * __pyx_result.encoding = __pyx_state[0]
|
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jpayne@69
|
24200 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
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jpayne@69
|
24201 */
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jpayne@69
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24202
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jpayne@69
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24203 /* function exit code */
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jpayne@69
|
24204 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
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jpayne@69
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24205 goto __pyx_L0;
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jpayne@69
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jpayne@69
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24207 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
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jpayne@69
|
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jpayne@69
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24210 __Pyx_XDECREF(__pyx_t_7);
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jpayne@69
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24211 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGFF3__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24212 __pyx_r = 0;
|
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jpayne@69
|
24213 __pyx_L0:;
|
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jpayne@69
|
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jpayne@69
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jpayne@69
|
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|
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jpayne@69
|
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jpayne@69
|
24218 }
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|
jpayne@69
|
24219
|
|
jpayne@69
|
24220 /* "(tree fragment)":1
|
|
jpayne@69
|
24221 * def __pyx_unpickle_asGTF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24222 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24223 * cdef object __pyx_result
|
|
jpayne@69
|
24224 */
|
|
jpayne@69
|
24225
|
|
jpayne@69
|
24226 /* Python wrapper */
|
|
jpayne@69
|
24227 static PyObject *__pyx_pw_5pysam_9libctabix_13__pyx_unpickle_asGTF(PyObject *__pyx_self,
|
|
jpayne@69
|
24228 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24229 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
24230 #else
|
|
jpayne@69
|
24231 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
24232 #endif
|
|
jpayne@69
|
24233 ); /*proto*/
|
|
jpayne@69
|
24234 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_12__pyx_unpickle_asGTF, "__pyx_unpickle_asGTF(__pyx_type, long __pyx_checksum, __pyx_state)");
|
|
jpayne@69
|
24235 static PyMethodDef __pyx_mdef_5pysam_9libctabix_13__pyx_unpickle_asGTF = {"__pyx_unpickle_asGTF", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13__pyx_unpickle_asGTF, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_12__pyx_unpickle_asGTF};
|
|
jpayne@69
|
24236 static PyObject *__pyx_pw_5pysam_9libctabix_13__pyx_unpickle_asGTF(PyObject *__pyx_self,
|
|
jpayne@69
|
24237 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24238 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
24239 #else
|
|
jpayne@69
|
24240 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
24241 #endif
|
|
jpayne@69
|
24242 ) {
|
|
jpayne@69
|
24243 PyObject *__pyx_v___pyx_type = 0;
|
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jpayne@69
|
24244 long __pyx_v___pyx_checksum;
|
|
jpayne@69
|
24245 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
24246 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24247 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
24248 #endif
|
|
jpayne@69
|
24249 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
24250 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
24251 int __pyx_lineno = 0;
|
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jpayne@69
|
24252 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
24253 int __pyx_clineno = 0;
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jpayne@69
|
24254 PyObject *__pyx_r = 0;
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jpayne@69
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24255 __Pyx_RefNannyDeclarations
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jpayne@69
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24256 __Pyx_RefNannySetupContext("__pyx_unpickle_asGTF (wrapper)", 0);
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jpayne@69
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24257 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24258 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
24259 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
24260 #else
|
|
jpayne@69
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24261 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
24262 #endif
|
|
jpayne@69
|
24263 #endif
|
|
jpayne@69
|
24264 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
24265 {
|
|
jpayne@69
|
24266 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
24267 if (__pyx_kwds) {
|
|
jpayne@69
|
24268 Py_ssize_t kw_args;
|
|
jpayne@69
|
24269 switch (__pyx_nargs) {
|
|
jpayne@69
|
24270 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
24271 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24272 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
24273 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24274 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
24275 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24276 case 0: break;
|
|
jpayne@69
|
24277 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
24278 }
|
|
jpayne@69
|
24279 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
24280 switch (__pyx_nargs) {
|
|
jpayne@69
|
24281 case 0:
|
|
jpayne@69
|
24282 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
|
|
jpayne@69
|
24283 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
24284 kw_args--;
|
|
jpayne@69
|
24285 }
|
|
jpayne@69
|
24286 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24287 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
24288 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24289 case 1:
|
|
jpayne@69
|
24290 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
|
|
jpayne@69
|
24291 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
24292 kw_args--;
|
|
jpayne@69
|
24293 }
|
|
jpayne@69
|
24294 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24295 else {
|
|
jpayne@69
|
24296 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGTF", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24297 }
|
|
jpayne@69
|
24298 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24299 case 2:
|
|
jpayne@69
|
24300 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
24301 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
24302 kw_args--;
|
|
jpayne@69
|
24303 }
|
|
jpayne@69
|
24304 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24305 else {
|
|
jpayne@69
|
24306 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGTF", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24307 }
|
|
jpayne@69
|
24308 }
|
|
jpayne@69
|
24309 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
24310 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
24311 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asGTF") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24312 }
|
|
jpayne@69
|
24313 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
24314 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
24315 } else {
|
|
jpayne@69
|
24316 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
24317 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
24318 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
24319 }
|
|
jpayne@69
|
24320 __pyx_v___pyx_type = values[0];
|
|
jpayne@69
|
24321 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24322 __pyx_v___pyx_state = values[2];
|
|
jpayne@69
|
24323 }
|
|
jpayne@69
|
24324 goto __pyx_L6_skip;
|
|
jpayne@69
|
24325 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
24326 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGTF", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24327 __pyx_L6_skip:;
|
|
jpayne@69
|
24328 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
24329 __pyx_L3_error:;
|
|
jpayne@69
|
24330 {
|
|
jpayne@69
|
24331 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
24332 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
24333 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
24334 }
|
|
jpayne@69
|
24335 }
|
|
jpayne@69
|
24336 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGTF", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24337 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24338 return NULL;
|
|
jpayne@69
|
24339 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
24340 __pyx_r = __pyx_pf_5pysam_9libctabix_12__pyx_unpickle_asGTF(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
|
|
jpayne@69
|
24341
|
|
jpayne@69
|
24342 /* function exit code */
|
|
jpayne@69
|
24343 {
|
|
jpayne@69
|
24344 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
24345 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
24346 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
24347 }
|
|
jpayne@69
|
24348 }
|
|
jpayne@69
|
24349 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24350 return __pyx_r;
|
|
jpayne@69
|
24351 }
|
|
jpayne@69
|
24352
|
|
jpayne@69
|
24353 static PyObject *__pyx_pf_5pysam_9libctabix_12__pyx_unpickle_asGTF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
24354 PyObject *__pyx_v___pyx_PickleError = 0;
|
|
jpayne@69
|
24355 PyObject *__pyx_v___pyx_result = 0;
|
|
jpayne@69
|
24356 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
24357 __Pyx_TraceDeclarations
|
|
jpayne@69
|
24358 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
24359 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
24360 int __pyx_t_2;
|
|
jpayne@69
|
24361 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
24362 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
24363 unsigned int __pyx_t_5;
|
|
jpayne@69
|
24364 int __pyx_lineno = 0;
|
|
jpayne@69
|
24365 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
24366 int __pyx_clineno = 0;
|
|
jpayne@69
|
24367 __Pyx_TraceFrameInit(__pyx_codeobj__59)
|
|
jpayne@69
|
24368 __Pyx_RefNannySetupContext("__pyx_unpickle_asGTF", 1);
|
|
jpayne@69
|
24369 __Pyx_TraceCall("__pyx_unpickle_asGTF", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
24370
|
|
jpayne@69
|
24371 /* "(tree fragment)":4
|
|
jpayne@69
|
24372 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24373 * cdef object __pyx_result
|
|
jpayne@69
|
24374 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24375 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24376 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24377 */
|
|
jpayne@69
|
24378 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
24379 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24380 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
24381 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24382 if (__pyx_t_2) {
|
|
jpayne@69
|
24383
|
|
jpayne@69
|
24384 /* "(tree fragment)":5
|
|
jpayne@69
|
24385 * cdef object __pyx_result
|
|
jpayne@69
|
24386 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
24387 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24388 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24389 * __pyx_result = asGTF.__new__(__pyx_type)
|
|
jpayne@69
|
24390 */
|
|
jpayne@69
|
24391 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
24392 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24393 __Pyx_INCREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
24394 __Pyx_GIVEREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
24395 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
24396 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
24397 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
24398 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24399 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
24400 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24401 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
24402 __pyx_v___pyx_PickleError = __pyx_t_1;
|
|
jpayne@69
|
24403 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24404 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24405
|
|
jpayne@69
|
24406 /* "(tree fragment)":6
|
|
jpayne@69
|
24407 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
24408 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24409 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24410 * __pyx_result = asGTF.__new__(__pyx_type)
|
|
jpayne@69
|
24411 * if __pyx_state is not None:
|
|
jpayne@69
|
24412 */
|
|
jpayne@69
|
24413 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
24414 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
24415 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
24416 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24417 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24418 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
|
|
jpayne@69
|
24419 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24420 __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
24421
|
|
jpayne@69
|
24422 /* "(tree fragment)":4
|
|
jpayne@69
|
24423 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24424 * cdef object __pyx_result
|
|
jpayne@69
|
24425 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24426 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24427 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24428 */
|
|
jpayne@69
|
24429 }
|
|
jpayne@69
|
24430
|
|
jpayne@69
|
24431 /* "(tree fragment)":7
|
|
jpayne@69
|
24432 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24433 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24434 * __pyx_result = asGTF.__new__(__pyx_type) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24435 * if __pyx_state is not None:
|
|
jpayne@69
|
24436 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24437 */
|
|
jpayne@69
|
24438 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asGTF), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
24439 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
24440 __pyx_t_4 = NULL;
|
|
jpayne@69
|
24441 __pyx_t_5 = 0;
|
|
jpayne@69
|
24442 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
24443 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
24444 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
24445 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
24446 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
24447 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
24448 __Pyx_INCREF(function);
|
|
jpayne@69
|
24449 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
24450 __pyx_t_5 = 1;
|
|
jpayne@69
|
24451 }
|
|
jpayne@69
|
24452 }
|
|
jpayne@69
|
24453 #endif
|
|
jpayne@69
|
24454 {
|
|
jpayne@69
|
24455 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
|
|
jpayne@69
|
24456 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
24457 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
24458 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
24459 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24460 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24461 }
|
|
jpayne@69
|
24462 __pyx_v___pyx_result = __pyx_t_1;
|
|
jpayne@69
|
24463 __pyx_t_1 = 0;
|
|
jpayne@69
|
24464
|
|
jpayne@69
|
24465 /* "(tree fragment)":8
|
|
jpayne@69
|
24466 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24467 * __pyx_result = asGTF.__new__(__pyx_type)
|
|
jpayne@69
|
24468 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24469 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24470 * return __pyx_result
|
|
jpayne@69
|
24471 */
|
|
jpayne@69
|
24472 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
|
|
jpayne@69
|
24473 if (__pyx_t_2) {
|
|
jpayne@69
|
24474
|
|
jpayne@69
|
24475 /* "(tree fragment)":9
|
|
jpayne@69
|
24476 * __pyx_result = asGTF.__new__(__pyx_type)
|
|
jpayne@69
|
24477 * if __pyx_state is not None:
|
|
jpayne@69
|
24478 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24479 * return __pyx_result
|
|
jpayne@69
|
24480 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24481 */
|
|
jpayne@69
|
24482 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
24483 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(((struct __pyx_obj_5pysam_9libctabix_asGTF *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
24484 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24485 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24486
|
|
jpayne@69
|
24487 /* "(tree fragment)":8
|
|
jpayne@69
|
24488 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24489 * __pyx_result = asGTF.__new__(__pyx_type)
|
|
jpayne@69
|
24490 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24491 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24492 * return __pyx_result
|
|
jpayne@69
|
24493 */
|
|
jpayne@69
|
24494 }
|
|
jpayne@69
|
24495
|
|
jpayne@69
|
24496 /* "(tree fragment)":10
|
|
jpayne@69
|
24497 * if __pyx_state is not None:
|
|
jpayne@69
|
24498 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24499 * return __pyx_result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24500 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24501 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24502 */
|
|
jpayne@69
|
24503 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
24504 __Pyx_INCREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
24505 __pyx_r = __pyx_v___pyx_result;
|
|
jpayne@69
|
24506 goto __pyx_L0;
|
|
jpayne@69
|
24507
|
|
jpayne@69
|
24508 /* "(tree fragment)":1
|
|
jpayne@69
|
24509 * def __pyx_unpickle_asGTF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24510 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24511 * cdef object __pyx_result
|
|
jpayne@69
|
24512 */
|
|
jpayne@69
|
24513
|
|
jpayne@69
|
24514 /* function exit code */
|
|
jpayne@69
|
24515 __pyx_L1_error:;
|
|
jpayne@69
|
24516 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
24517 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
24518 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
24519 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGTF", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24520 __pyx_r = NULL;
|
|
jpayne@69
|
24521 __pyx_L0:;
|
|
jpayne@69
|
24522 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
|
|
jpayne@69
|
24523 __Pyx_XDECREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
24524 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
24525 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
24526 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24527 return __pyx_r;
|
|
jpayne@69
|
24528 }
|
|
jpayne@69
|
24529
|
|
jpayne@69
|
24530 /* "(tree fragment)":11
|
|
jpayne@69
|
24531 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24532 * return __pyx_result
|
|
jpayne@69
|
24533 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24534 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24535 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
24536 */
|
|
jpayne@69
|
24537
|
|
jpayne@69
|
24538 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
24539 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
24540 __Pyx_TraceDeclarations
|
|
jpayne@69
|
24541 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
24542 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
24543 int __pyx_t_2;
|
|
jpayne@69
|
24544 Py_ssize_t __pyx_t_3;
|
|
jpayne@69
|
24545 int __pyx_t_4;
|
|
jpayne@69
|
24546 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
24547 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
24548 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
24549 unsigned int __pyx_t_8;
|
|
jpayne@69
|
24550 int __pyx_lineno = 0;
|
|
jpayne@69
|
24551 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
24552 int __pyx_clineno = 0;
|
|
jpayne@69
|
24553 __Pyx_RefNannySetupContext("__pyx_unpickle_asGTF__set_state", 1);
|
|
jpayne@69
|
24554 __Pyx_TraceCall("__pyx_unpickle_asGTF__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error));
|
|
jpayne@69
|
24555
|
|
jpayne@69
|
24556 /* "(tree fragment)":12
|
|
jpayne@69
|
24557 * return __pyx_result
|
|
jpayne@69
|
24558 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24559 * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24560 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
24561 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
24562 */
|
|
jpayne@69
|
24563 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
24564 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
24565 __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
24566 }
|
|
jpayne@69
|
24567 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
24568 __Pyx_GOTREF(__pyx_t_1);
|
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jpayne@69
|
24569 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
24570 __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
24571 __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
24572 __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1;
|
|
jpayne@69
|
24573 __pyx_t_1 = 0;
|
|
jpayne@69
|
24574
|
|
jpayne@69
|
24575 /* "(tree fragment)":13
|
|
jpayne@69
|
24576 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24577 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24578 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24579 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
24580 */
|
|
jpayne@69
|
24581 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
24582 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
|
|
jpayne@69
|
24583 __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
24584 }
|
|
jpayne@69
|
24585 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
24586 __pyx_t_4 = (__pyx_t_3 > 1);
|
|
jpayne@69
|
24587 if (__pyx_t_4) {
|
|
jpayne@69
|
24588 } else {
|
|
jpayne@69
|
24589 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
24590 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
24591 }
|
|
jpayne@69
|
24592 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
24593 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
24594 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
24595 if (__pyx_t_2) {
|
|
jpayne@69
|
24596
|
|
jpayne@69
|
24597 /* "(tree fragment)":14
|
|
jpayne@69
|
24598 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24599 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
24600 * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24601 */
|
|
jpayne@69
|
24602 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
24603 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
24604 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
24605 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
24606 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
24607 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
24608 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
24609 __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
24610 }
|
|
jpayne@69
|
24611 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
24612 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
24613 __pyx_t_7 = NULL;
|
|
jpayne@69
|
24614 __pyx_t_8 = 0;
|
|
jpayne@69
|
24615 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
24616 if (likely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
24617 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
24618 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
24619 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
24620 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
24621 __Pyx_INCREF(function);
|
|
jpayne@69
|
24622 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
24623 __pyx_t_8 = 1;
|
|
jpayne@69
|
24624 }
|
|
jpayne@69
|
24625 }
|
|
jpayne@69
|
24626 #endif
|
|
jpayne@69
|
24627 {
|
|
jpayne@69
|
24628 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
|
|
jpayne@69
|
24629 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
|
|
jpayne@69
|
24630 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
24631 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
24632 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
24633 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24634 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
24635 }
|
|
jpayne@69
|
24636 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24637
|
|
jpayne@69
|
24638 /* "(tree fragment)":13
|
|
jpayne@69
|
24639 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24640 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24641 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24642 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
24643 */
|
|
jpayne@69
|
24644 }
|
|
jpayne@69
|
24645
|
|
jpayne@69
|
24646 /* "(tree fragment)":11
|
|
jpayne@69
|
24647 * __pyx_unpickle_asGTF__set_state(<asGTF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24648 * return __pyx_result
|
|
jpayne@69
|
24649 * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24650 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24651 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
24652 */
|
|
jpayne@69
|
24653
|
|
jpayne@69
|
24654 /* function exit code */
|
|
jpayne@69
|
24655 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
24656 goto __pyx_L0;
|
|
jpayne@69
|
24657 __pyx_L1_error:;
|
|
jpayne@69
|
24658 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
24659 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
24660 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
24661 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
24662 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGTF__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24663 __pyx_r = 0;
|
|
jpayne@69
|
24664 __pyx_L0:;
|
|
jpayne@69
|
24665 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
24666 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
24667 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24668 return __pyx_r;
|
|
jpayne@69
|
24669 }
|
|
jpayne@69
|
24670
|
|
jpayne@69
|
24671 /* "(tree fragment)":1
|
|
jpayne@69
|
24672 * def __pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24673 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24674 * cdef object __pyx_result
|
|
jpayne@69
|
24675 */
|
|
jpayne@69
|
24676
|
|
jpayne@69
|
24677 /* Python wrapper */
|
|
jpayne@69
|
24678 static PyObject *__pyx_pw_5pysam_9libctabix_15__pyx_unpickle_asBed(PyObject *__pyx_self,
|
|
jpayne@69
|
24679 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24680 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
24681 #else
|
|
jpayne@69
|
24682 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
24683 #endif
|
|
jpayne@69
|
24684 ); /*proto*/
|
|
jpayne@69
|
24685 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14__pyx_unpickle_asBed, "__pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state)");
|
|
jpayne@69
|
24686 static PyMethodDef __pyx_mdef_5pysam_9libctabix_15__pyx_unpickle_asBed = {"__pyx_unpickle_asBed", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_15__pyx_unpickle_asBed, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14__pyx_unpickle_asBed};
|
|
jpayne@69
|
24687 static PyObject *__pyx_pw_5pysam_9libctabix_15__pyx_unpickle_asBed(PyObject *__pyx_self,
|
|
jpayne@69
|
24688 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24689 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
24690 #else
|
|
jpayne@69
|
24691 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
24692 #endif
|
|
jpayne@69
|
24693 ) {
|
|
jpayne@69
|
24694 PyObject *__pyx_v___pyx_type = 0;
|
|
jpayne@69
|
24695 long __pyx_v___pyx_checksum;
|
|
jpayne@69
|
24696 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
24697 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24698 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
24699 #endif
|
|
jpayne@69
|
24700 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
24701 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
24702 int __pyx_lineno = 0;
|
|
jpayne@69
|
24703 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
24704 int __pyx_clineno = 0;
|
|
jpayne@69
|
24705 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
24706 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
24707 __Pyx_RefNannySetupContext("__pyx_unpickle_asBed (wrapper)", 0);
|
|
jpayne@69
|
24708 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
24709 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
24710 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
24711 #else
|
|
jpayne@69
|
24712 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
24713 #endif
|
|
jpayne@69
|
24714 #endif
|
|
jpayne@69
|
24715 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
24716 {
|
|
jpayne@69
|
24717 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
24718 if (__pyx_kwds) {
|
|
jpayne@69
|
24719 Py_ssize_t kw_args;
|
|
jpayne@69
|
24720 switch (__pyx_nargs) {
|
|
jpayne@69
|
24721 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
24722 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24723 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
24724 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24725 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
24726 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24727 case 0: break;
|
|
jpayne@69
|
24728 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
24729 }
|
|
jpayne@69
|
24730 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
24731 switch (__pyx_nargs) {
|
|
jpayne@69
|
24732 case 0:
|
|
jpayne@69
|
24733 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
|
|
jpayne@69
|
24734 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
24735 kw_args--;
|
|
jpayne@69
|
24736 }
|
|
jpayne@69
|
24737 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24738 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
24739 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24740 case 1:
|
|
jpayne@69
|
24741 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
|
|
jpayne@69
|
24742 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
24743 kw_args--;
|
|
jpayne@69
|
24744 }
|
|
jpayne@69
|
24745 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24746 else {
|
|
jpayne@69
|
24747 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asBed", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24748 }
|
|
jpayne@69
|
24749 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
24750 case 2:
|
|
jpayne@69
|
24751 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
24752 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
24753 kw_args--;
|
|
jpayne@69
|
24754 }
|
|
jpayne@69
|
24755 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24756 else {
|
|
jpayne@69
|
24757 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asBed", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24758 }
|
|
jpayne@69
|
24759 }
|
|
jpayne@69
|
24760 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
24761 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
24762 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asBed") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24763 }
|
|
jpayne@69
|
24764 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
24765 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
24766 } else {
|
|
jpayne@69
|
24767 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
24768 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
24769 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
24770 }
|
|
jpayne@69
|
24771 __pyx_v___pyx_type = values[0];
|
|
jpayne@69
|
24772 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24773 __pyx_v___pyx_state = values[2];
|
|
jpayne@69
|
24774 }
|
|
jpayne@69
|
24775 goto __pyx_L6_skip;
|
|
jpayne@69
|
24776 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
24777 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asBed", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
24778 __pyx_L6_skip:;
|
|
jpayne@69
|
24779 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
24780 __pyx_L3_error:;
|
|
jpayne@69
|
24781 {
|
|
jpayne@69
|
24782 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
24783 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
24784 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
24785 }
|
|
jpayne@69
|
24786 }
|
|
jpayne@69
|
24787 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asBed", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24788 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24789 return NULL;
|
|
jpayne@69
|
24790 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
24791 __pyx_r = __pyx_pf_5pysam_9libctabix_14__pyx_unpickle_asBed(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
|
|
jpayne@69
|
24792
|
|
jpayne@69
|
24793 /* function exit code */
|
|
jpayne@69
|
24794 {
|
|
jpayne@69
|
24795 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
24796 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
24797 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
24798 }
|
|
jpayne@69
|
24799 }
|
|
jpayne@69
|
24800 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24801 return __pyx_r;
|
|
jpayne@69
|
24802 }
|
|
jpayne@69
|
24803
|
|
jpayne@69
|
24804 static PyObject *__pyx_pf_5pysam_9libctabix_14__pyx_unpickle_asBed(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
24805 PyObject *__pyx_v___pyx_PickleError = 0;
|
|
jpayne@69
|
24806 PyObject *__pyx_v___pyx_result = 0;
|
|
jpayne@69
|
24807 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
24808 __Pyx_TraceDeclarations
|
|
jpayne@69
|
24809 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
24810 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
24811 int __pyx_t_2;
|
|
jpayne@69
|
24812 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
24813 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
24814 unsigned int __pyx_t_5;
|
|
jpayne@69
|
24815 int __pyx_lineno = 0;
|
|
jpayne@69
|
24816 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
24817 int __pyx_clineno = 0;
|
|
jpayne@69
|
24818 __Pyx_TraceFrameInit(__pyx_codeobj__60)
|
|
jpayne@69
|
24819 __Pyx_RefNannySetupContext("__pyx_unpickle_asBed", 1);
|
|
jpayne@69
|
24820 __Pyx_TraceCall("__pyx_unpickle_asBed", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
24821
|
|
jpayne@69
|
24822 /* "(tree fragment)":4
|
|
jpayne@69
|
24823 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24824 * cdef object __pyx_result
|
|
jpayne@69
|
24825 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24826 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24827 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24828 */
|
|
jpayne@69
|
24829 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
24830 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24831 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
24832 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24833 if (__pyx_t_2) {
|
|
jpayne@69
|
24834
|
|
jpayne@69
|
24835 /* "(tree fragment)":5
|
|
jpayne@69
|
24836 * cdef object __pyx_result
|
|
jpayne@69
|
24837 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
24838 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24839 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24840 * __pyx_result = asBed.__new__(__pyx_type)
|
|
jpayne@69
|
24841 */
|
|
jpayne@69
|
24842 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
24843 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24844 __Pyx_INCREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
24845 __Pyx_GIVEREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
24846 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
24847 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
24848 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
24849 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24850 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
24851 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24852 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
24853 __pyx_v___pyx_PickleError = __pyx_t_1;
|
|
jpayne@69
|
24854 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24855 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24856
|
|
jpayne@69
|
24857 /* "(tree fragment)":6
|
|
jpayne@69
|
24858 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
24859 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24860 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24861 * __pyx_result = asBed.__new__(__pyx_type)
|
|
jpayne@69
|
24862 * if __pyx_state is not None:
|
|
jpayne@69
|
24863 */
|
|
jpayne@69
|
24864 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
24865 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
24866 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
24867 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24868 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24869 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
|
|
jpayne@69
|
24870 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24871 __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
24872
|
|
jpayne@69
|
24873 /* "(tree fragment)":4
|
|
jpayne@69
|
24874 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24875 * cdef object __pyx_result
|
|
jpayne@69
|
24876 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24877 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24878 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24879 */
|
|
jpayne@69
|
24880 }
|
|
jpayne@69
|
24881
|
|
jpayne@69
|
24882 /* "(tree fragment)":7
|
|
jpayne@69
|
24883 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
24884 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24885 * __pyx_result = asBed.__new__(__pyx_type) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24886 * if __pyx_state is not None:
|
|
jpayne@69
|
24887 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24888 */
|
|
jpayne@69
|
24889 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asBed), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
24890 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
24891 __pyx_t_4 = NULL;
|
|
jpayne@69
|
24892 __pyx_t_5 = 0;
|
|
jpayne@69
|
24893 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
24894 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
24895 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
24896 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
24897 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
24898 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
24899 __Pyx_INCREF(function);
|
|
jpayne@69
|
24900 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
24901 __pyx_t_5 = 1;
|
|
jpayne@69
|
24902 }
|
|
jpayne@69
|
24903 }
|
|
jpayne@69
|
24904 #endif
|
|
jpayne@69
|
24905 {
|
|
jpayne@69
|
24906 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
|
|
jpayne@69
|
24907 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
24908 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
24909 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
24910 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24911 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
24912 }
|
|
jpayne@69
|
24913 __pyx_v___pyx_result = __pyx_t_1;
|
|
jpayne@69
|
24914 __pyx_t_1 = 0;
|
|
jpayne@69
|
24915
|
|
jpayne@69
|
24916 /* "(tree fragment)":8
|
|
jpayne@69
|
24917 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24918 * __pyx_result = asBed.__new__(__pyx_type)
|
|
jpayne@69
|
24919 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24920 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24921 * return __pyx_result
|
|
jpayne@69
|
24922 */
|
|
jpayne@69
|
24923 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
|
|
jpayne@69
|
24924 if (__pyx_t_2) {
|
|
jpayne@69
|
24925
|
|
jpayne@69
|
24926 /* "(tree fragment)":9
|
|
jpayne@69
|
24927 * __pyx_result = asBed.__new__(__pyx_type)
|
|
jpayne@69
|
24928 * if __pyx_state is not None:
|
|
jpayne@69
|
24929 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24930 * return __pyx_result
|
|
jpayne@69
|
24931 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24932 */
|
|
jpayne@69
|
24933 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
24934 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(((struct __pyx_obj_5pysam_9libctabix_asBed *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
24935 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
24936 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
24937
|
|
jpayne@69
|
24938 /* "(tree fragment)":8
|
|
jpayne@69
|
24939 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
24940 * __pyx_result = asBed.__new__(__pyx_type)
|
|
jpayne@69
|
24941 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24942 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24943 * return __pyx_result
|
|
jpayne@69
|
24944 */
|
|
jpayne@69
|
24945 }
|
|
jpayne@69
|
24946
|
|
jpayne@69
|
24947 /* "(tree fragment)":10
|
|
jpayne@69
|
24948 * if __pyx_state is not None:
|
|
jpayne@69
|
24949 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24950 * return __pyx_result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24951 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
24952 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24953 */
|
|
jpayne@69
|
24954 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
24955 __Pyx_INCREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
24956 __pyx_r = __pyx_v___pyx_result;
|
|
jpayne@69
|
24957 goto __pyx_L0;
|
|
jpayne@69
|
24958
|
|
jpayne@69
|
24959 /* "(tree fragment)":1
|
|
jpayne@69
|
24960 * def __pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24961 * cdef object __pyx_PickleError
|
|
jpayne@69
|
24962 * cdef object __pyx_result
|
|
jpayne@69
|
24963 */
|
|
jpayne@69
|
24964
|
|
jpayne@69
|
24965 /* function exit code */
|
|
jpayne@69
|
24966 __pyx_L1_error:;
|
|
jpayne@69
|
24967 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
24968 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
24969 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
24970 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asBed", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
24971 __pyx_r = NULL;
|
|
jpayne@69
|
24972 __pyx_L0:;
|
|
jpayne@69
|
24973 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
|
|
jpayne@69
|
24974 __Pyx_XDECREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
24975 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
24976 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
24977 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
24978 return __pyx_r;
|
|
jpayne@69
|
24979 }
|
|
jpayne@69
|
24980
|
|
jpayne@69
|
24981 /* "(tree fragment)":11
|
|
jpayne@69
|
24982 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
24983 * return __pyx_result
|
|
jpayne@69
|
24984 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
24985 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
24986 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
24987 */
|
|
jpayne@69
|
24988
|
|
jpayne@69
|
24989 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
24990 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
24991 __Pyx_TraceDeclarations
|
|
jpayne@69
|
24992 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
24993 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
24994 int __pyx_t_2;
|
|
jpayne@69
|
24995 Py_ssize_t __pyx_t_3;
|
|
jpayne@69
|
24996 int __pyx_t_4;
|
|
jpayne@69
|
24997 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
24998 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
24999 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
25000 unsigned int __pyx_t_8;
|
|
jpayne@69
|
25001 int __pyx_lineno = 0;
|
|
jpayne@69
|
25002 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
25003 int __pyx_clineno = 0;
|
|
jpayne@69
|
25004 __Pyx_RefNannySetupContext("__pyx_unpickle_asBed__set_state", 1);
|
|
jpayne@69
|
25005 __Pyx_TraceCall("__pyx_unpickle_asBed__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error));
|
|
jpayne@69
|
25006
|
|
jpayne@69
|
25007 /* "(tree fragment)":12
|
|
jpayne@69
|
25008 * return __pyx_result
|
|
jpayne@69
|
25009 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25010 * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25011 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25012 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
25013 */
|
|
jpayne@69
|
25014 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
25015 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
25016 __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
25017 }
|
|
jpayne@69
|
25018 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
25019 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25020 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
25021 __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
25022 __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
25023 __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1;
|
|
jpayne@69
|
25024 __pyx_t_1 = 0;
|
|
jpayne@69
|
25025
|
|
jpayne@69
|
25026 /* "(tree fragment)":13
|
|
jpayne@69
|
25027 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25028 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25029 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25030 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
25031 */
|
|
jpayne@69
|
25032 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
25033 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
|
|
jpayne@69
|
25034 __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
25035 }
|
|
jpayne@69
|
25036 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
25037 __pyx_t_4 = (__pyx_t_3 > 1);
|
|
jpayne@69
|
25038 if (__pyx_t_4) {
|
|
jpayne@69
|
25039 } else {
|
|
jpayne@69
|
25040 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
25041 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
25042 }
|
|
jpayne@69
|
25043 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
25044 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
25045 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
25046 if (__pyx_t_2) {
|
|
jpayne@69
|
25047
|
|
jpayne@69
|
25048 /* "(tree fragment)":14
|
|
jpayne@69
|
25049 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25050 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25051 * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25052 */
|
|
jpayne@69
|
25053 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25054 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
25055 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25056 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
25057 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
25058 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
25059 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
25060 __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25061 }
|
|
jpayne@69
|
25062 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25063 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
25064 __pyx_t_7 = NULL;
|
|
jpayne@69
|
25065 __pyx_t_8 = 0;
|
|
jpayne@69
|
25066 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
25067 if (likely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
25068 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
25069 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
25070 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
25071 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
25072 __Pyx_INCREF(function);
|
|
jpayne@69
|
25073 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
25074 __pyx_t_8 = 1;
|
|
jpayne@69
|
25075 }
|
|
jpayne@69
|
25076 }
|
|
jpayne@69
|
25077 #endif
|
|
jpayne@69
|
25078 {
|
|
jpayne@69
|
25079 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
|
|
jpayne@69
|
25080 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
|
|
jpayne@69
|
25081 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
25082 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
25083 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25084 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25085 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
25086 }
|
|
jpayne@69
|
25087 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25088
|
|
jpayne@69
|
25089 /* "(tree fragment)":13
|
|
jpayne@69
|
25090 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25091 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25092 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25093 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
25094 */
|
|
jpayne@69
|
25095 }
|
|
jpayne@69
|
25096
|
|
jpayne@69
|
25097 /* "(tree fragment)":11
|
|
jpayne@69
|
25098 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25099 * return __pyx_result
|
|
jpayne@69
|
25100 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25101 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25102 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25103 */
|
|
jpayne@69
|
25104
|
|
jpayne@69
|
25105 /* function exit code */
|
|
jpayne@69
|
25106 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
25107 goto __pyx_L0;
|
|
jpayne@69
|
25108 __pyx_L1_error:;
|
|
jpayne@69
|
25109 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
25110 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
25111 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
25112 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
25113 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asBed__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
25114 __pyx_r = 0;
|
|
jpayne@69
|
25115 __pyx_L0:;
|
|
jpayne@69
|
25116 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
25117 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
25118 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
25119 return __pyx_r;
|
|
jpayne@69
|
25120 }
|
|
jpayne@69
|
25121
|
|
jpayne@69
|
25122 /* "(tree fragment)":1
|
|
jpayne@69
|
25123 * def __pyx_unpickle_asVCF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25124 * cdef object __pyx_PickleError
|
|
jpayne@69
|
25125 * cdef object __pyx_result
|
|
jpayne@69
|
25126 */
|
|
jpayne@69
|
25127
|
|
jpayne@69
|
25128 /* Python wrapper */
|
|
jpayne@69
|
25129 static PyObject *__pyx_pw_5pysam_9libctabix_17__pyx_unpickle_asVCF(PyObject *__pyx_self,
|
|
jpayne@69
|
25130 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
25131 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
25132 #else
|
|
jpayne@69
|
25133 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
25134 #endif
|
|
jpayne@69
|
25135 ); /*proto*/
|
|
jpayne@69
|
25136 PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16__pyx_unpickle_asVCF, "__pyx_unpickle_asVCF(__pyx_type, long __pyx_checksum, __pyx_state)");
|
|
jpayne@69
|
25137 static PyMethodDef __pyx_mdef_5pysam_9libctabix_17__pyx_unpickle_asVCF = {"__pyx_unpickle_asVCF", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_17__pyx_unpickle_asVCF, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16__pyx_unpickle_asVCF};
|
|
jpayne@69
|
25138 static PyObject *__pyx_pw_5pysam_9libctabix_17__pyx_unpickle_asVCF(PyObject *__pyx_self,
|
|
jpayne@69
|
25139 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
25140 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
25141 #else
|
|
jpayne@69
|
25142 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
25143 #endif
|
|
jpayne@69
|
25144 ) {
|
|
jpayne@69
|
25145 PyObject *__pyx_v___pyx_type = 0;
|
|
jpayne@69
|
25146 long __pyx_v___pyx_checksum;
|
|
jpayne@69
|
25147 PyObject *__pyx_v___pyx_state = 0;
|
|
jpayne@69
|
25148 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
25149 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
25150 #endif
|
|
jpayne@69
|
25151 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
25152 PyObject* values[3] = {0,0,0};
|
|
jpayne@69
|
25153 int __pyx_lineno = 0;
|
|
jpayne@69
|
25154 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
25155 int __pyx_clineno = 0;
|
|
jpayne@69
|
25156 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
25157 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
25158 __Pyx_RefNannySetupContext("__pyx_unpickle_asVCF (wrapper)", 0);
|
|
jpayne@69
|
25159 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
25160 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
25161 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
25162 #else
|
|
jpayne@69
|
25163 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
25164 #endif
|
|
jpayne@69
|
25165 #endif
|
|
jpayne@69
|
25166 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
25167 {
|
|
jpayne@69
|
25168 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0};
|
|
jpayne@69
|
25169 if (__pyx_kwds) {
|
|
jpayne@69
|
25170 Py_ssize_t kw_args;
|
|
jpayne@69
|
25171 switch (__pyx_nargs) {
|
|
jpayne@69
|
25172 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
25173 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
25174 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
25175 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
25176 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
25177 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
25178 case 0: break;
|
|
jpayne@69
|
25179 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
25180 }
|
|
jpayne@69
|
25181 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
25182 switch (__pyx_nargs) {
|
|
jpayne@69
|
25183 case 0:
|
|
jpayne@69
|
25184 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) {
|
|
jpayne@69
|
25185 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
25186 kw_args--;
|
|
jpayne@69
|
25187 }
|
|
jpayne@69
|
25188 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25189 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
25190 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
25191 case 1:
|
|
jpayne@69
|
25192 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) {
|
|
jpayne@69
|
25193 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
25194 kw_args--;
|
|
jpayne@69
|
25195 }
|
|
jpayne@69
|
25196 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25197 else {
|
|
jpayne@69
|
25198 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCF", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25199 }
|
|
jpayne@69
|
25200 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
25201 case 2:
|
|
jpayne@69
|
25202 if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) {
|
|
jpayne@69
|
25203 (void)__Pyx_Arg_NewRef_FASTCALL(values[2]);
|
|
jpayne@69
|
25204 kw_args--;
|
|
jpayne@69
|
25205 }
|
|
jpayne@69
|
25206 else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25207 else {
|
|
jpayne@69
|
25208 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCF", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25209 }
|
|
jpayne@69
|
25210 }
|
|
jpayne@69
|
25211 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
25212 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
25213 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asVCF") < 0)) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25214 }
|
|
jpayne@69
|
25215 } else if (unlikely(__pyx_nargs != 3)) {
|
|
jpayne@69
|
25216 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
25217 } else {
|
|
jpayne@69
|
25218 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
25219 values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
25220 values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
25221 }
|
|
jpayne@69
|
25222 __pyx_v___pyx_type = values[0];
|
|
jpayne@69
|
25223 __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25224 __pyx_v___pyx_state = values[2];
|
|
jpayne@69
|
25225 }
|
|
jpayne@69
|
25226 goto __pyx_L6_skip;
|
|
jpayne@69
|
25227 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
25228 __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCF", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error)
|
|
jpayne@69
|
25229 __pyx_L6_skip:;
|
|
jpayne@69
|
25230 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
25231 __pyx_L3_error:;
|
|
jpayne@69
|
25232 {
|
|
jpayne@69
|
25233 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
25234 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
25235 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
25236 }
|
|
jpayne@69
|
25237 }
|
|
jpayne@69
|
25238 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asVCF", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
25239 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
25240 return NULL;
|
|
jpayne@69
|
25241 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
25242 __pyx_r = __pyx_pf_5pysam_9libctabix_16__pyx_unpickle_asVCF(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state);
|
|
jpayne@69
|
25243
|
|
jpayne@69
|
25244 /* function exit code */
|
|
jpayne@69
|
25245 {
|
|
jpayne@69
|
25246 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
25247 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
25248 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
25249 }
|
|
jpayne@69
|
25250 }
|
|
jpayne@69
|
25251 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
25252 return __pyx_r;
|
|
jpayne@69
|
25253 }
|
|
jpayne@69
|
25254
|
|
jpayne@69
|
25255 static PyObject *__pyx_pf_5pysam_9libctabix_16__pyx_unpickle_asVCF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
25256 PyObject *__pyx_v___pyx_PickleError = 0;
|
|
jpayne@69
|
25257 PyObject *__pyx_v___pyx_result = 0;
|
|
jpayne@69
|
25258 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
25259 __Pyx_TraceDeclarations
|
|
jpayne@69
|
25260 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
25261 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
25262 int __pyx_t_2;
|
|
jpayne@69
|
25263 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
25264 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
25265 unsigned int __pyx_t_5;
|
|
jpayne@69
|
25266 int __pyx_lineno = 0;
|
|
jpayne@69
|
25267 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
25268 int __pyx_clineno = 0;
|
|
jpayne@69
|
25269 __Pyx_TraceFrameInit(__pyx_codeobj__61)
|
|
jpayne@69
|
25270 __Pyx_RefNannySetupContext("__pyx_unpickle_asVCF", 1);
|
|
jpayne@69
|
25271 __Pyx_TraceCall("__pyx_unpickle_asVCF", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error));
|
|
jpayne@69
|
25272
|
|
jpayne@69
|
25273 /* "(tree fragment)":4
|
|
jpayne@69
|
25274 * cdef object __pyx_PickleError
|
|
jpayne@69
|
25275 * cdef object __pyx_result
|
|
jpayne@69
|
25276 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25277 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
25278 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
25279 */
|
|
jpayne@69
|
25280 __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
25281 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25282 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
25283 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25284 if (__pyx_t_2) {
|
|
jpayne@69
|
25285
|
|
jpayne@69
|
25286 /* "(tree fragment)":5
|
|
jpayne@69
|
25287 * cdef object __pyx_result
|
|
jpayne@69
|
25288 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
25289 * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25290 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
25291 * __pyx_result = asVCF.__new__(__pyx_type)
|
|
jpayne@69
|
25292 */
|
|
jpayne@69
|
25293 __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
25294 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25295 __Pyx_INCREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
25296 __Pyx_GIVEREF(__pyx_n_s_PickleError);
|
|
jpayne@69
|
25297 if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error);
|
|
jpayne@69
|
25298 __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
25299 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
25300 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25301 __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error)
|
|
jpayne@69
|
25302 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25303 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
25304 __pyx_v___pyx_PickleError = __pyx_t_1;
|
|
jpayne@69
|
25305 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25306 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
25307
|
|
jpayne@69
|
25308 /* "(tree fragment)":6
|
|
jpayne@69
|
25309 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f):
|
|
jpayne@69
|
25310 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
25311 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25312 * __pyx_result = asVCF.__new__(__pyx_type)
|
|
jpayne@69
|
25313 * if __pyx_state is not None:
|
|
jpayne@69
|
25314 */
|
|
jpayne@69
|
25315 __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
25316 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
25317 __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
25318 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25319 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
25320 __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0);
|
|
jpayne@69
|
25321 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25322 __PYX_ERR(1, 6, __pyx_L1_error)
|
|
jpayne@69
|
25323
|
|
jpayne@69
|
25324 /* "(tree fragment)":4
|
|
jpayne@69
|
25325 * cdef object __pyx_PickleError
|
|
jpayne@69
|
25326 * cdef object __pyx_result
|
|
jpayne@69
|
25327 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25328 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
25329 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
25330 */
|
|
jpayne@69
|
25331 }
|
|
jpayne@69
|
25332
|
|
jpayne@69
|
25333 /* "(tree fragment)":7
|
|
jpayne@69
|
25334 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
25335 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
25336 * __pyx_result = asVCF.__new__(__pyx_type) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25337 * if __pyx_state is not None:
|
|
jpayne@69
|
25338 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25339 */
|
|
jpayne@69
|
25340 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asVCF), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
25341 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
25342 __pyx_t_4 = NULL;
|
|
jpayne@69
|
25343 __pyx_t_5 = 0;
|
|
jpayne@69
|
25344 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
25345 if (likely(PyMethod_Check(__pyx_t_3))) {
|
|
jpayne@69
|
25346 __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3);
|
|
jpayne@69
|
25347 if (likely(__pyx_t_4)) {
|
|
jpayne@69
|
25348 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
|
|
jpayne@69
|
25349 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
25350 __Pyx_INCREF(function);
|
|
jpayne@69
|
25351 __Pyx_DECREF_SET(__pyx_t_3, function);
|
|
jpayne@69
|
25352 __pyx_t_5 = 1;
|
|
jpayne@69
|
25353 }
|
|
jpayne@69
|
25354 }
|
|
jpayne@69
|
25355 #endif
|
|
jpayne@69
|
25356 {
|
|
jpayne@69
|
25357 PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type};
|
|
jpayne@69
|
25358 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5);
|
|
jpayne@69
|
25359 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
25360 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error)
|
|
jpayne@69
|
25361 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25362 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
25363 }
|
|
jpayne@69
|
25364 __pyx_v___pyx_result = __pyx_t_1;
|
|
jpayne@69
|
25365 __pyx_t_1 = 0;
|
|
jpayne@69
|
25366
|
|
jpayne@69
|
25367 /* "(tree fragment)":8
|
|
jpayne@69
|
25368 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
25369 * __pyx_result = asVCF.__new__(__pyx_type)
|
|
jpayne@69
|
25370 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25371 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25372 * return __pyx_result
|
|
jpayne@69
|
25373 */
|
|
jpayne@69
|
25374 __pyx_t_2 = (__pyx_v___pyx_state != Py_None);
|
|
jpayne@69
|
25375 if (__pyx_t_2) {
|
|
jpayne@69
|
25376
|
|
jpayne@69
|
25377 /* "(tree fragment)":9
|
|
jpayne@69
|
25378 * __pyx_result = asVCF.__new__(__pyx_type)
|
|
jpayne@69
|
25379 * if __pyx_state is not None:
|
|
jpayne@69
|
25380 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25381 * return __pyx_result
|
|
jpayne@69
|
25382 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25383 */
|
|
jpayne@69
|
25384 if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
25385 __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(((struct __pyx_obj_5pysam_9libctabix_asVCF *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error)
|
|
jpayne@69
|
25386 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25387 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25388
|
|
jpayne@69
|
25389 /* "(tree fragment)":8
|
|
jpayne@69
|
25390 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
25391 * __pyx_result = asVCF.__new__(__pyx_type)
|
|
jpayne@69
|
25392 * if __pyx_state is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25393 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25394 * return __pyx_result
|
|
jpayne@69
|
25395 */
|
|
jpayne@69
|
25396 }
|
|
jpayne@69
|
25397
|
|
jpayne@69
|
25398 /* "(tree fragment)":10
|
|
jpayne@69
|
25399 * if __pyx_state is not None:
|
|
jpayne@69
|
25400 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25401 * return __pyx_result # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25402 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25403 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25404 */
|
|
jpayne@69
|
25405 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
25406 __Pyx_INCREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
25407 __pyx_r = __pyx_v___pyx_result;
|
|
jpayne@69
|
25408 goto __pyx_L0;
|
|
jpayne@69
|
25409
|
|
jpayne@69
|
25410 /* "(tree fragment)":1
|
|
jpayne@69
|
25411 * def __pyx_unpickle_asVCF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25412 * cdef object __pyx_PickleError
|
|
jpayne@69
|
25413 * cdef object __pyx_result
|
|
jpayne@69
|
25414 */
|
|
jpayne@69
|
25415
|
|
jpayne@69
|
25416 /* function exit code */
|
|
jpayne@69
|
25417 __pyx_L1_error:;
|
|
jpayne@69
|
25418 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
25419 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
25420 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
25421 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asVCF", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
25422 __pyx_r = NULL;
|
|
jpayne@69
|
25423 __pyx_L0:;
|
|
jpayne@69
|
25424 __Pyx_XDECREF(__pyx_v___pyx_PickleError);
|
|
jpayne@69
|
25425 __Pyx_XDECREF(__pyx_v___pyx_result);
|
|
jpayne@69
|
25426 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
25427 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
25428 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
25429 return __pyx_r;
|
|
jpayne@69
|
25430 }
|
|
jpayne@69
|
25431
|
|
jpayne@69
|
25432 /* "(tree fragment)":11
|
|
jpayne@69
|
25433 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25434 * return __pyx_result
|
|
jpayne@69
|
25435 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25436 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25437 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25438 */
|
|
jpayne@69
|
25439
|
|
jpayne@69
|
25440 static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) {
|
|
jpayne@69
|
25441 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
25442 __Pyx_TraceDeclarations
|
|
jpayne@69
|
25443 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
25444 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
25445 int __pyx_t_2;
|
|
jpayne@69
|
25446 Py_ssize_t __pyx_t_3;
|
|
jpayne@69
|
25447 int __pyx_t_4;
|
|
jpayne@69
|
25448 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
25449 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
25450 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
25451 unsigned int __pyx_t_8;
|
|
jpayne@69
|
25452 int __pyx_lineno = 0;
|
|
jpayne@69
|
25453 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
25454 int __pyx_clineno = 0;
|
|
jpayne@69
|
25455 __Pyx_RefNannySetupContext("__pyx_unpickle_asVCF__set_state", 1);
|
|
jpayne@69
|
25456 __Pyx_TraceCall("__pyx_unpickle_asVCF__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error));
|
|
jpayne@69
|
25457
|
|
jpayne@69
|
25458 /* "(tree fragment)":12
|
|
jpayne@69
|
25459 * return __pyx_result
|
|
jpayne@69
|
25460 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25461 * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25462 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25463 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
25464 */
|
|
jpayne@69
|
25465 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
25466 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
25467 __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
25468 }
|
|
jpayne@69
|
25469 __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error)
|
|
jpayne@69
|
25470 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25471 __Pyx_GIVEREF(__pyx_t_1);
|
|
jpayne@69
|
25472 __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
25473 __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding);
|
|
jpayne@69
|
25474 __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1;
|
|
jpayne@69
|
25475 __pyx_t_1 = 0;
|
|
jpayne@69
|
25476
|
|
jpayne@69
|
25477 /* "(tree fragment)":13
|
|
jpayne@69
|
25478 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25479 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25480 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25481 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
25482 */
|
|
jpayne@69
|
25483 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
25484 PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
|
|
jpayne@69
|
25485 __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
25486 }
|
|
jpayne@69
|
25487 __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
25488 __pyx_t_4 = (__pyx_t_3 > 1);
|
|
jpayne@69
|
25489 if (__pyx_t_4) {
|
|
jpayne@69
|
25490 } else {
|
|
jpayne@69
|
25491 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
25492 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
25493 }
|
|
jpayne@69
|
25494 __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error)
|
|
jpayne@69
|
25495 __pyx_t_2 = __pyx_t_4;
|
|
jpayne@69
|
25496 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
25497 if (__pyx_t_2) {
|
|
jpayne@69
|
25498
|
|
jpayne@69
|
25499 /* "(tree fragment)":14
|
|
jpayne@69
|
25500 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25501 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25502 * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25503 */
|
|
jpayne@69
|
25504 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25505 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
25506 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25507 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
25508 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
25509 if (unlikely(__pyx_v___pyx_state == Py_None)) {
|
|
jpayne@69
|
25510 PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
|
|
jpayne@69
|
25511 __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25512 }
|
|
jpayne@69
|
25513 __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25514 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
25515 __pyx_t_7 = NULL;
|
|
jpayne@69
|
25516 __pyx_t_8 = 0;
|
|
jpayne@69
|
25517 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
25518 if (likely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
25519 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
25520 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
25521 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
25522 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
25523 __Pyx_INCREF(function);
|
|
jpayne@69
|
25524 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
25525 __pyx_t_8 = 1;
|
|
jpayne@69
|
25526 }
|
|
jpayne@69
|
25527 }
|
|
jpayne@69
|
25528 #endif
|
|
jpayne@69
|
25529 {
|
|
jpayne@69
|
25530 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5};
|
|
jpayne@69
|
25531 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8);
|
|
jpayne@69
|
25532 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
25533 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
25534 if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error)
|
|
jpayne@69
|
25535 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
25536 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
25537 }
|
|
jpayne@69
|
25538 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
25539
|
|
jpayne@69
|
25540 /* "(tree fragment)":13
|
|
jpayne@69
|
25541 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state):
|
|
jpayne@69
|
25542 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25543 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25544 * __pyx_result.__dict__.update(__pyx_state[1])
|
|
jpayne@69
|
25545 */
|
|
jpayne@69
|
25546 }
|
|
jpayne@69
|
25547
|
|
jpayne@69
|
25548 /* "(tree fragment)":11
|
|
jpayne@69
|
25549 * __pyx_unpickle_asVCF__set_state(<asVCF> __pyx_result, __pyx_state)
|
|
jpayne@69
|
25550 * return __pyx_result
|
|
jpayne@69
|
25551 * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
25552 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
25553 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
25554 */
|
|
jpayne@69
|
25555
|
|
jpayne@69
|
25556 /* function exit code */
|
|
jpayne@69
|
25557 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
25558 goto __pyx_L0;
|
|
jpayne@69
|
25559 __pyx_L1_error:;
|
|
jpayne@69
|
25560 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
25561 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
25562 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
25563 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
25564 __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asVCF__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
25565 __pyx_r = 0;
|
|
jpayne@69
|
25566 __pyx_L0:;
|
|
jpayne@69
|
25567 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
25568 __Pyx_TraceReturn(__pyx_r, 0);
|
|
jpayne@69
|
25569 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
25570 return __pyx_r;
|
|
jpayne@69
|
25571 }
|
|
jpayne@69
|
25572 static struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator __pyx_vtable_5pysam_9libctabix_tabix_file_iterator;
|
|
jpayne@69
|
25573
|
|
jpayne@69
|
25574 static PyObject *__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
25575 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p;
|
|
jpayne@69
|
25576 PyObject *o;
|
|
jpayne@69
|
25577 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
25578 allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc);
|
|
jpayne@69
|
25579 o = alloc_func(t, 0);
|
|
jpayne@69
|
25580 #else
|
|
jpayne@69
|
25581 if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) {
|
|
jpayne@69
|
25582 o = (*t->tp_alloc)(t, 0);
|
|
jpayne@69
|
25583 } else {
|
|
jpayne@69
|
25584 o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
|
|
jpayne@69
|
25585 }
|
|
jpayne@69
|
25586 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
25587 #endif
|
|
jpayne@69
|
25588 p = ((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o);
|
|
jpayne@69
|
25589 p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator;
|
|
jpayne@69
|
25590 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
25591 p->infile = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
25592 if (unlikely(__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_1__cinit__(o, a, k) < 0)) goto bad;
|
|
jpayne@69
|
25593 return o;
|
|
jpayne@69
|
25594 bad:
|
|
jpayne@69
|
25595 Py_DECREF(o); o = 0;
|
|
jpayne@69
|
25596 return NULL;
|
|
jpayne@69
|
25597 }
|
|
jpayne@69
|
25598
|
|
jpayne@69
|
25599 static void __pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator(PyObject *o) {
|
|
jpayne@69
|
25600 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o;
|
|
jpayne@69
|
25601 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
25602 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
25603 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator) {
|
|
jpayne@69
|
25604 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
25605 }
|
|
jpayne@69
|
25606 }
|
|
jpayne@69
|
25607 #endif
|
|
jpayne@69
|
25608 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
25609 {
|
|
jpayne@69
|
25610 PyObject *etype, *eval, *etb;
|
|
jpayne@69
|
25611 PyErr_Fetch(&etype, &eval, &etb);
|
|
jpayne@69
|
25612 __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
|
|
jpayne@69
|
25613 __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_5__dealloc__(o);
|
|
jpayne@69
|
25614 __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
|
|
jpayne@69
|
25615 PyErr_Restore(etype, eval, etb);
|
|
jpayne@69
|
25616 }
|
|
jpayne@69
|
25617 Py_CLEAR(p->parser);
|
|
jpayne@69
|
25618 Py_CLEAR(p->infile);
|
|
jpayne@69
|
25619 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
25620 (*Py_TYPE(o)->tp_free)(o);
|
|
jpayne@69
|
25621 #else
|
|
jpayne@69
|
25622 {
|
|
jpayne@69
|
25623 freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free);
|
|
jpayne@69
|
25624 if (tp_free) tp_free(o);
|
|
jpayne@69
|
25625 }
|
|
jpayne@69
|
25626 #endif
|
|
jpayne@69
|
25627 }
|
|
jpayne@69
|
25628
|
|
jpayne@69
|
25629 static int __pyx_tp_traverse_5pysam_9libctabix_tabix_file_iterator(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
25630 int e;
|
|
jpayne@69
|
25631 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o;
|
|
jpayne@69
|
25632 if (p->parser) {
|
|
jpayne@69
|
25633 e = (*v)(((PyObject *)p->parser), a); if (e) return e;
|
|
jpayne@69
|
25634 }
|
|
jpayne@69
|
25635 if (p->infile) {
|
|
jpayne@69
|
25636 e = (*v)(p->infile, a); if (e) return e;
|
|
jpayne@69
|
25637 }
|
|
jpayne@69
|
25638 return 0;
|
|
jpayne@69
|
25639 }
|
|
jpayne@69
|
25640
|
|
jpayne@69
|
25641 static int __pyx_tp_clear_5pysam_9libctabix_tabix_file_iterator(PyObject *o) {
|
|
jpayne@69
|
25642 PyObject* tmp;
|
|
jpayne@69
|
25643 struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o;
|
|
jpayne@69
|
25644 tmp = ((PyObject*)p->parser);
|
|
jpayne@69
|
25645 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
25646 Py_XDECREF(tmp);
|
|
jpayne@69
|
25647 tmp = ((PyObject*)p->infile);
|
|
jpayne@69
|
25648 p->infile = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
25649 Py_XDECREF(tmp);
|
|
jpayne@69
|
25650 return 0;
|
|
jpayne@69
|
25651 }
|
|
jpayne@69
|
25652
|
|
jpayne@69
|
25653 static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {
|
|
jpayne@69
|
25654 PyObject *res = __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(self);
|
|
jpayne@69
|
25655 if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); }
|
|
jpayne@69
|
25656 return res;
|
|
jpayne@69
|
25657 }
|
|
jpayne@69
|
25658
|
|
jpayne@69
|
25659 static PyMethodDef __pyx_methods_5pysam_9libctabix_tabix_file_iterator[] = {
|
|
jpayne@69
|
25660 {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__, METH_NOARGS|METH_COEXIST, 0},
|
|
jpayne@69
|
25661 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__},
|
|
jpayne@69
|
25662 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__},
|
|
jpayne@69
|
25663 {0, 0, 0, 0}
|
|
jpayne@69
|
25664 };
|
|
jpayne@69
|
25665 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
25666 static PyType_Slot __pyx_type_5pysam_9libctabix_tabix_file_iterator_slots[] = {
|
|
jpayne@69
|
25667 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator},
|
|
jpayne@69
|
25668 {Py_tp_doc, (void *)PyDoc_STR("iterate over a compressed or uncompressed ``infile``.\n ")},
|
|
jpayne@69
|
25669 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_tabix_file_iterator},
|
|
jpayne@69
|
25670 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_tabix_file_iterator},
|
|
jpayne@69
|
25671 {Py_tp_iter, (void *)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__},
|
|
jpayne@69
|
25672 {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__},
|
|
jpayne@69
|
25673 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_tabix_file_iterator},
|
|
jpayne@69
|
25674 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator},
|
|
jpayne@69
|
25675 {0, 0},
|
|
jpayne@69
|
25676 };
|
|
jpayne@69
|
25677 static PyType_Spec __pyx_type_5pysam_9libctabix_tabix_file_iterator_spec = {
|
|
jpayne@69
|
25678 "pysam.libctabix.tabix_file_iterator",
|
|
jpayne@69
|
25679 sizeof(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator),
|
|
jpayne@69
|
25680 0,
|
|
jpayne@69
|
25681 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
25682 __pyx_type_5pysam_9libctabix_tabix_file_iterator_slots,
|
|
jpayne@69
|
25683 };
|
|
jpayne@69
|
25684 #else
|
|
jpayne@69
|
25685
|
|
jpayne@69
|
25686 static PyTypeObject __pyx_type_5pysam_9libctabix_tabix_file_iterator = {
|
|
jpayne@69
|
25687 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
25688 "pysam.libctabix.""tabix_file_iterator", /*tp_name*/
|
|
jpayne@69
|
25689 sizeof(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator), /*tp_basicsize*/
|
|
jpayne@69
|
25690 0, /*tp_itemsize*/
|
|
jpayne@69
|
25691 __pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator, /*tp_dealloc*/
|
|
jpayne@69
|
25692 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
25693 0, /*tp_print*/
|
|
jpayne@69
|
25694 #endif
|
|
jpayne@69
|
25695 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
25696 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
25697 #endif
|
|
jpayne@69
|
25698 0, /*tp_getattr*/
|
|
jpayne@69
|
25699 0, /*tp_setattr*/
|
|
jpayne@69
|
25700 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
25701 0, /*tp_compare*/
|
|
jpayne@69
|
25702 #endif
|
|
jpayne@69
|
25703 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
25704 0, /*tp_as_async*/
|
|
jpayne@69
|
25705 #endif
|
|
jpayne@69
|
25706 0, /*tp_repr*/
|
|
jpayne@69
|
25707 0, /*tp_as_number*/
|
|
jpayne@69
|
25708 0, /*tp_as_sequence*/
|
|
jpayne@69
|
25709 0, /*tp_as_mapping*/
|
|
jpayne@69
|
25710 0, /*tp_hash*/
|
|
jpayne@69
|
25711 0, /*tp_call*/
|
|
jpayne@69
|
25712 0, /*tp_str*/
|
|
jpayne@69
|
25713 0, /*tp_getattro*/
|
|
jpayne@69
|
25714 0, /*tp_setattro*/
|
|
jpayne@69
|
25715 0, /*tp_as_buffer*/
|
|
jpayne@69
|
25716 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
25717 PyDoc_STR("iterate over a compressed or uncompressed ``infile``.\n "), /*tp_doc*/
|
|
jpayne@69
|
25718 __pyx_tp_traverse_5pysam_9libctabix_tabix_file_iterator, /*tp_traverse*/
|
|
jpayne@69
|
25719 __pyx_tp_clear_5pysam_9libctabix_tabix_file_iterator, /*tp_clear*/
|
|
jpayne@69
|
25720 0, /*tp_richcompare*/
|
|
jpayne@69
|
25721 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
25722 __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__, /*tp_iter*/
|
|
jpayne@69
|
25723 __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__, /*tp_iternext*/
|
|
jpayne@69
|
25724 __pyx_methods_5pysam_9libctabix_tabix_file_iterator, /*tp_methods*/
|
|
jpayne@69
|
25725 0, /*tp_members*/
|
|
jpayne@69
|
25726 0, /*tp_getset*/
|
|
jpayne@69
|
25727 0, /*tp_base*/
|
|
jpayne@69
|
25728 0, /*tp_dict*/
|
|
jpayne@69
|
25729 0, /*tp_descr_get*/
|
|
jpayne@69
|
25730 0, /*tp_descr_set*/
|
|
jpayne@69
|
25731 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
25732 0, /*tp_dictoffset*/
|
|
jpayne@69
|
25733 #endif
|
|
jpayne@69
|
25734 0, /*tp_init*/
|
|
jpayne@69
|
25735 0, /*tp_alloc*/
|
|
jpayne@69
|
25736 __pyx_tp_new_5pysam_9libctabix_tabix_file_iterator, /*tp_new*/
|
|
jpayne@69
|
25737 0, /*tp_free*/
|
|
jpayne@69
|
25738 0, /*tp_is_gc*/
|
|
jpayne@69
|
25739 0, /*tp_bases*/
|
|
jpayne@69
|
25740 0, /*tp_mro*/
|
|
jpayne@69
|
25741 0, /*tp_cache*/
|
|
jpayne@69
|
25742 0, /*tp_subclasses*/
|
|
jpayne@69
|
25743 0, /*tp_weaklist*/
|
|
jpayne@69
|
25744 0, /*tp_del*/
|
|
jpayne@69
|
25745 0, /*tp_version_tag*/
|
|
jpayne@69
|
25746 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
25747 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
25748 0, /*tp_finalize*/
|
|
jpayne@69
|
25749 #else
|
|
jpayne@69
|
25750 NULL, /*tp_finalize*/
|
|
jpayne@69
|
25751 #endif
|
|
jpayne@69
|
25752 #endif
|
|
jpayne@69
|
25753 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
25754 0, /*tp_vectorcall*/
|
|
jpayne@69
|
25755 #endif
|
|
jpayne@69
|
25756 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
25757 0, /*tp_print*/
|
|
jpayne@69
|
25758 #endif
|
|
jpayne@69
|
25759 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
25760 0, /*tp_watched*/
|
|
jpayne@69
|
25761 #endif
|
|
jpayne@69
|
25762 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
25763 0, /*tp_versions_used*/
|
|
jpayne@69
|
25764 #endif
|
|
jpayne@69
|
25765 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
25766 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
25767 #endif
|
|
jpayne@69
|
25768 };
|
|
jpayne@69
|
25769 #endif
|
|
jpayne@69
|
25770 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile __pyx_vtable_5pysam_9libctabix_TabixFile;
|
|
jpayne@69
|
25771
|
|
jpayne@69
|
25772 static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixFile(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
25773 struct __pyx_obj_5pysam_9libctabix_TabixFile *p;
|
|
jpayne@69
|
25774 PyObject *o = __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_10libchtslib_HTSFile, tp_new, newfunc)(t, a, k);
|
|
jpayne@69
|
25775 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
25776 p = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)o);
|
|
jpayne@69
|
25777 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__pyx_vtabptr_5pysam_9libctabix_TabixFile;
|
|
jpayne@69
|
25778 p->filename_index = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
25779 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
25780 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
25781 if (unlikely(__pyx_pw_5pysam_9libctabix_9TabixFile_1__cinit__(o, a, k) < 0)) goto bad;
|
|
jpayne@69
|
25782 return o;
|
|
jpayne@69
|
25783 bad:
|
|
jpayne@69
|
25784 Py_DECREF(o); o = 0;
|
|
jpayne@69
|
25785 return NULL;
|
|
jpayne@69
|
25786 }
|
|
jpayne@69
|
25787
|
|
jpayne@69
|
25788 static void __pyx_tp_dealloc_5pysam_9libctabix_TabixFile(PyObject *o) {
|
|
jpayne@69
|
25789 struct __pyx_obj_5pysam_9libctabix_TabixFile *p = (struct __pyx_obj_5pysam_9libctabix_TabixFile *)o;
|
|
jpayne@69
|
25790 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
25791 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
25792 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_TabixFile) {
|
|
jpayne@69
|
25793 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
25794 }
|
|
jpayne@69
|
25795 }
|
|
jpayne@69
|
25796 #endif
|
|
jpayne@69
|
25797 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
25798 {
|
|
jpayne@69
|
25799 PyObject *etype, *eval, *etb;
|
|
jpayne@69
|
25800 PyErr_Fetch(&etype, &eval, &etb);
|
|
jpayne@69
|
25801 __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
|
|
jpayne@69
|
25802 __pyx_pw_5pysam_9libctabix_9TabixFile_11__dealloc__(o);
|
|
jpayne@69
|
25803 __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
|
|
jpayne@69
|
25804 PyErr_Restore(etype, eval, etb);
|
|
jpayne@69
|
25805 }
|
|
jpayne@69
|
25806 Py_CLEAR(p->filename_index);
|
|
jpayne@69
|
25807 Py_CLEAR(p->parser);
|
|
jpayne@69
|
25808 Py_CLEAR(p->encoding);
|
|
jpayne@69
|
25809 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
25810 if (!(__pyx_ptype_5pysam_10libchtslib_HTSFile) || PyType_IS_GC(__pyx_ptype_5pysam_10libchtslib_HTSFile)) PyObject_GC_Track(o);
|
|
jpayne@69
|
25811 #else
|
|
jpayne@69
|
25812 if (PyType_IS_GC(__pyx_ptype_5pysam_10libchtslib_HTSFile)) PyObject_GC_Track(o);
|
|
jpayne@69
|
25813 #endif
|
|
jpayne@69
|
25814 if (likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_10libchtslib_HTSFile, tp_dealloc, destructor)(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
25815 }
|
|
jpayne@69
|
25816
|
|
jpayne@69
|
25817 static int __pyx_tp_traverse_5pysam_9libctabix_TabixFile(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
25818 int e;
|
|
jpayne@69
|
25819 struct __pyx_obj_5pysam_9libctabix_TabixFile *p = (struct __pyx_obj_5pysam_9libctabix_TabixFile *)o;
|
|
jpayne@69
|
25820 e = ((likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) ? ((__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_traverse) ? __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9libctabix_TabixFile)); if (e) return e;
|
|
jpayne@69
|
25821 if (p->filename_index) {
|
|
jpayne@69
|
25822 e = (*v)(p->filename_index, a); if (e) return e;
|
|
jpayne@69
|
25823 }
|
|
jpayne@69
|
25824 if (p->parser) {
|
|
jpayne@69
|
25825 e = (*v)(((PyObject *)p->parser), a); if (e) return e;
|
|
jpayne@69
|
25826 }
|
|
jpayne@69
|
25827 if (p->encoding) {
|
|
jpayne@69
|
25828 e = (*v)(p->encoding, a); if (e) return e;
|
|
jpayne@69
|
25829 }
|
|
jpayne@69
|
25830 return 0;
|
|
jpayne@69
|
25831 }
|
|
jpayne@69
|
25832
|
|
jpayne@69
|
25833 static int __pyx_tp_clear_5pysam_9libctabix_TabixFile(PyObject *o) {
|
|
jpayne@69
|
25834 PyObject* tmp;
|
|
jpayne@69
|
25835 struct __pyx_obj_5pysam_9libctabix_TabixFile *p = (struct __pyx_obj_5pysam_9libctabix_TabixFile *)o;
|
|
jpayne@69
|
25836 if (likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) { if (__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_clear) __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
25837 tmp = ((PyObject*)p->filename_index);
|
|
jpayne@69
|
25838 p->filename_index = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
25839 Py_XDECREF(tmp);
|
|
jpayne@69
|
25840 tmp = ((PyObject*)p->parser);
|
|
jpayne@69
|
25841 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
25842 Py_XDECREF(tmp);
|
|
jpayne@69
|
25843 tmp = ((PyObject*)p->encoding);
|
|
jpayne@69
|
25844 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
25845 Py_XDECREF(tmp);
|
|
jpayne@69
|
25846 return 0;
|
|
jpayne@69
|
25847 }
|
|
jpayne@69
|
25848
|
|
jpayne@69
|
25849 static PyObject *__pyx_getprop_5pysam_9libctabix_9TabixFile_header(PyObject *o, CYTHON_UNUSED void *x) {
|
|
jpayne@69
|
25850 return __pyx_pw_5pysam_9libctabix_9TabixFile_6header_1__get__(o);
|
|
jpayne@69
|
25851 }
|
|
jpayne@69
|
25852
|
|
jpayne@69
|
25853 static PyObject *__pyx_getprop_5pysam_9libctabix_9TabixFile_contigs(PyObject *o, CYTHON_UNUSED void *x) {
|
|
jpayne@69
|
25854 return __pyx_pw_5pysam_9libctabix_9TabixFile_7contigs_1__get__(o);
|
|
jpayne@69
|
25855 }
|
|
jpayne@69
|
25856
|
|
jpayne@69
|
25857 static PyObject *__pyx_getprop_5pysam_9libctabix_9TabixFile_filename_index(PyObject *o, CYTHON_UNUSED void *x) {
|
|
jpayne@69
|
25858 return __pyx_pw_5pysam_9libctabix_9TabixFile_14filename_index_1__get__(o);
|
|
jpayne@69
|
25859 }
|
|
jpayne@69
|
25860
|
|
jpayne@69
|
25861 static PyMethodDef __pyx_methods_5pysam_9libctabix_TabixFile[] = {
|
|
jpayne@69
|
25862 {"_open", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_3_open, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_2_open},
|
|
jpayne@69
|
25863 {"_dup", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_4_dup},
|
|
jpayne@69
|
25864 {"fetch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_6fetch},
|
|
jpayne@69
|
25865 {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_9close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_8close},
|
|
jpayne@69
|
25866 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_12__reduce_cython__},
|
|
jpayne@69
|
25867 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_14__setstate_cython__},
|
|
jpayne@69
|
25868 {0, 0, 0, 0}
|
|
jpayne@69
|
25869 };
|
|
jpayne@69
|
25870
|
|
jpayne@69
|
25871 static struct PyGetSetDef __pyx_getsets_5pysam_9libctabix_TabixFile[] = {
|
|
jpayne@69
|
25872 {(char *)"header", __pyx_getprop_5pysam_9libctabix_9TabixFile_header, 0, (char *)PyDoc_STR("the file header.\n\n The file header consists of the lines at the beginning of a\n file that are prefixed by the comment character ``#``.\n \n .. note::\n The header is returned as an iterator presenting lines\n without the newline character.\n "), 0},
|
|
jpayne@69
|
25873 {(char *)"contigs", __pyx_getprop_5pysam_9libctabix_9TabixFile_contigs, 0, (char *)PyDoc_STR("list of chromosome names"), 0},
|
|
jpayne@69
|
25874 {(char *)"filename_index", __pyx_getprop_5pysam_9libctabix_9TabixFile_filename_index, 0, (char *)0, 0},
|
|
jpayne@69
|
25875 {0, 0, 0, 0, 0}
|
|
jpayne@69
|
25876 };
|
|
jpayne@69
|
25877 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
25878 static PyType_Slot __pyx_type_5pysam_9libctabix_TabixFile_slots[] = {
|
|
jpayne@69
|
25879 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
25880 {Py_tp_doc, (void *)PyDoc_STR("Random access to bgzf formatted files that\n have been indexed by :term:`tabix`.\n\n The file is automatically opened. The index file of file\n ``<filename>`` is expected to be called ``<filename>.tbi``\n by default (see parameter `index`).\n \n Parameters\n ----------\n \n filename : string\n Filename of bgzf file to be opened.\n\n index : string\n The filename of the index. If not set, the default is to\n assume that the index is called ``filename.tbi``\n\n mode : char\n The file opening mode. Currently, only ``r`` is permitted.\n \n parser : :class:`pysam.Parser`\n \n sets the default parser for this tabix file. If `parser`\n is None, the results are returned as an unparsed string.\n Otherwise, `parser` is assumed to be a functor that will return\n parsed data (see for example :class:`~pysam.asTuple` and\n :class:`~pysam.asGTF`).\n\n encoding : string\n\n The encoding passed to the parser\n\n threads: integer\n Number of threads to use for decompressing Tabix files.\n (Default=1)\n\n\n Raises\n ------\n \n ValueError\n if index file is missing.\n\n IOError\n if file could not be opened\n ")},
|
|
jpayne@69
|
25881 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
25882 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
25883 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
25884 {Py_tp_getset, (void *)__pyx_getsets_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
25885 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
25886 {0, 0},
|
|
jpayne@69
|
25887 };
|
|
jpayne@69
|
25888 static PyType_Spec __pyx_type_5pysam_9libctabix_TabixFile_spec = {
|
|
jpayne@69
|
25889 "pysam.libctabix.TabixFile",
|
|
jpayne@69
|
25890 sizeof(struct __pyx_obj_5pysam_9libctabix_TabixFile),
|
|
jpayne@69
|
25891 0,
|
|
jpayne@69
|
25892 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE,
|
|
jpayne@69
|
25893 __pyx_type_5pysam_9libctabix_TabixFile_slots,
|
|
jpayne@69
|
25894 };
|
|
jpayne@69
|
25895 #else
|
|
jpayne@69
|
25896
|
|
jpayne@69
|
25897 static PyTypeObject __pyx_type_5pysam_9libctabix_TabixFile = {
|
|
jpayne@69
|
25898 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
25899 "pysam.libctabix.""TabixFile", /*tp_name*/
|
|
jpayne@69
|
25900 sizeof(struct __pyx_obj_5pysam_9libctabix_TabixFile), /*tp_basicsize*/
|
|
jpayne@69
|
25901 0, /*tp_itemsize*/
|
|
jpayne@69
|
25902 __pyx_tp_dealloc_5pysam_9libctabix_TabixFile, /*tp_dealloc*/
|
|
jpayne@69
|
25903 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
25904 0, /*tp_print*/
|
|
jpayne@69
|
25905 #endif
|
|
jpayne@69
|
25906 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
25907 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
25908 #endif
|
|
jpayne@69
|
25909 0, /*tp_getattr*/
|
|
jpayne@69
|
25910 0, /*tp_setattr*/
|
|
jpayne@69
|
25911 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
25912 0, /*tp_compare*/
|
|
jpayne@69
|
25913 #endif
|
|
jpayne@69
|
25914 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
25915 0, /*tp_as_async*/
|
|
jpayne@69
|
25916 #endif
|
|
jpayne@69
|
25917 0, /*tp_repr*/
|
|
jpayne@69
|
25918 0, /*tp_as_number*/
|
|
jpayne@69
|
25919 0, /*tp_as_sequence*/
|
|
jpayne@69
|
25920 0, /*tp_as_mapping*/
|
|
jpayne@69
|
25921 0, /*tp_hash*/
|
|
jpayne@69
|
25922 0, /*tp_call*/
|
|
jpayne@69
|
25923 0, /*tp_str*/
|
|
jpayne@69
|
25924 0, /*tp_getattro*/
|
|
jpayne@69
|
25925 0, /*tp_setattro*/
|
|
jpayne@69
|
25926 0, /*tp_as_buffer*/
|
|
jpayne@69
|
25927 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/
|
|
jpayne@69
|
25928 PyDoc_STR("Random access to bgzf formatted files that\n have been indexed by :term:`tabix`.\n\n The file is automatically opened. The index file of file\n ``<filename>`` is expected to be called ``<filename>.tbi``\n by default (see parameter `index`).\n \n Parameters\n ----------\n \n filename : string\n Filename of bgzf file to be opened.\n\n index : string\n The filename of the index. If not set, the default is to\n assume that the index is called ``filename.tbi``\n\n mode : char\n The file opening mode. Currently, only ``r`` is permitted.\n \n parser : :class:`pysam.Parser`\n \n sets the default parser for this tabix file. If `parser`\n is None, the results are returned as an unparsed string.\n Otherwise, `parser` is assumed to be a functor that will return\n parsed data (see for example :class:`~pysam.asTuple` and\n :class:`~pysam.asGTF`).\n\n encoding : string\n\n The encoding passed to the parser\n\n threads: integer\n Number of threads to use for decompressing Tabix files.\n (Default=1)\n\n\n Raises\n ------\n \n ValueError\n if index file is missing.\n\n IOError\n if file could not be opened\n "), /*tp_doc*/
|
|
jpayne@69
|
25929 __pyx_tp_traverse_5pysam_9libctabix_TabixFile, /*tp_traverse*/
|
|
jpayne@69
|
25930 __pyx_tp_clear_5pysam_9libctabix_TabixFile, /*tp_clear*/
|
|
jpayne@69
|
25931 0, /*tp_richcompare*/
|
|
jpayne@69
|
25932 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
25933 0, /*tp_iter*/
|
|
jpayne@69
|
25934 0, /*tp_iternext*/
|
|
jpayne@69
|
25935 __pyx_methods_5pysam_9libctabix_TabixFile, /*tp_methods*/
|
|
jpayne@69
|
25936 0, /*tp_members*/
|
|
jpayne@69
|
25937 __pyx_getsets_5pysam_9libctabix_TabixFile, /*tp_getset*/
|
|
jpayne@69
|
25938 0, /*tp_base*/
|
|
jpayne@69
|
25939 0, /*tp_dict*/
|
|
jpayne@69
|
25940 0, /*tp_descr_get*/
|
|
jpayne@69
|
25941 0, /*tp_descr_set*/
|
|
jpayne@69
|
25942 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
25943 0, /*tp_dictoffset*/
|
|
jpayne@69
|
25944 #endif
|
|
jpayne@69
|
25945 0, /*tp_init*/
|
|
jpayne@69
|
25946 0, /*tp_alloc*/
|
|
jpayne@69
|
25947 __pyx_tp_new_5pysam_9libctabix_TabixFile, /*tp_new*/
|
|
jpayne@69
|
25948 0, /*tp_free*/
|
|
jpayne@69
|
25949 0, /*tp_is_gc*/
|
|
jpayne@69
|
25950 0, /*tp_bases*/
|
|
jpayne@69
|
25951 0, /*tp_mro*/
|
|
jpayne@69
|
25952 0, /*tp_cache*/
|
|
jpayne@69
|
25953 0, /*tp_subclasses*/
|
|
jpayne@69
|
25954 0, /*tp_weaklist*/
|
|
jpayne@69
|
25955 0, /*tp_del*/
|
|
jpayne@69
|
25956 0, /*tp_version_tag*/
|
|
jpayne@69
|
25957 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
25958 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
25959 0, /*tp_finalize*/
|
|
jpayne@69
|
25960 #else
|
|
jpayne@69
|
25961 NULL, /*tp_finalize*/
|
|
jpayne@69
|
25962 #endif
|
|
jpayne@69
|
25963 #endif
|
|
jpayne@69
|
25964 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
25965 0, /*tp_vectorcall*/
|
|
jpayne@69
|
25966 #endif
|
|
jpayne@69
|
25967 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
25968 0, /*tp_print*/
|
|
jpayne@69
|
25969 #endif
|
|
jpayne@69
|
25970 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
25971 0, /*tp_watched*/
|
|
jpayne@69
|
25972 #endif
|
|
jpayne@69
|
25973 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
25974 0, /*tp_versions_used*/
|
|
jpayne@69
|
25975 #endif
|
|
jpayne@69
|
25976 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
25977 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
25978 #endif
|
|
jpayne@69
|
25979 };
|
|
jpayne@69
|
25980 #endif
|
|
jpayne@69
|
25981 static struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_vtable_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
25982
|
|
jpayne@69
|
25983 static PyObject *__pyx_tp_new_5pysam_9libctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
|
|
jpayne@69
|
25984 struct __pyx_obj_5pysam_9libctabix_Parser *p;
|
|
jpayne@69
|
25985 PyObject *o;
|
|
jpayne@69
|
25986 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
25987 allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc);
|
|
jpayne@69
|
25988 o = alloc_func(t, 0);
|
|
jpayne@69
|
25989 #else
|
|
jpayne@69
|
25990 if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) {
|
|
jpayne@69
|
25991 o = (*t->tp_alloc)(t, 0);
|
|
jpayne@69
|
25992 } else {
|
|
jpayne@69
|
25993 o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
|
|
jpayne@69
|
25994 }
|
|
jpayne@69
|
25995 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
25996 #endif
|
|
jpayne@69
|
25997 p = ((struct __pyx_obj_5pysam_9libctabix_Parser *)o);
|
|
jpayne@69
|
25998 p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
25999 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
26000 return o;
|
|
jpayne@69
|
26001 }
|
|
jpayne@69
|
26002
|
|
jpayne@69
|
26003 static void __pyx_tp_dealloc_5pysam_9libctabix_Parser(PyObject *o) {
|
|
jpayne@69
|
26004 struct __pyx_obj_5pysam_9libctabix_Parser *p = (struct __pyx_obj_5pysam_9libctabix_Parser *)o;
|
|
jpayne@69
|
26005 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26006 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
26007 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_Parser) {
|
|
jpayne@69
|
26008 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
26009 }
|
|
jpayne@69
|
26010 }
|
|
jpayne@69
|
26011 #endif
|
|
jpayne@69
|
26012 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
26013 Py_CLEAR(p->encoding);
|
|
jpayne@69
|
26014 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
26015 (*Py_TYPE(o)->tp_free)(o);
|
|
jpayne@69
|
26016 #else
|
|
jpayne@69
|
26017 {
|
|
jpayne@69
|
26018 freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free);
|
|
jpayne@69
|
26019 if (tp_free) tp_free(o);
|
|
jpayne@69
|
26020 }
|
|
jpayne@69
|
26021 #endif
|
|
jpayne@69
|
26022 }
|
|
jpayne@69
|
26023
|
|
jpayne@69
|
26024 static int __pyx_tp_traverse_5pysam_9libctabix_Parser(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
26025 int e;
|
|
jpayne@69
|
26026 struct __pyx_obj_5pysam_9libctabix_Parser *p = (struct __pyx_obj_5pysam_9libctabix_Parser *)o;
|
|
jpayne@69
|
26027 if (p->encoding) {
|
|
jpayne@69
|
26028 e = (*v)(p->encoding, a); if (e) return e;
|
|
jpayne@69
|
26029 }
|
|
jpayne@69
|
26030 return 0;
|
|
jpayne@69
|
26031 }
|
|
jpayne@69
|
26032
|
|
jpayne@69
|
26033 static int __pyx_tp_clear_5pysam_9libctabix_Parser(PyObject *o) {
|
|
jpayne@69
|
26034 PyObject* tmp;
|
|
jpayne@69
|
26035 struct __pyx_obj_5pysam_9libctabix_Parser *p = (struct __pyx_obj_5pysam_9libctabix_Parser *)o;
|
|
jpayne@69
|
26036 tmp = ((PyObject*)p->encoding);
|
|
jpayne@69
|
26037 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
26038 Py_XDECREF(tmp);
|
|
jpayne@69
|
26039 return 0;
|
|
jpayne@69
|
26040 }
|
|
jpayne@69
|
26041
|
|
jpayne@69
|
26042 static PyMethodDef __pyx_methods_5pysam_9libctabix_Parser[] = {
|
|
jpayne@69
|
26043 {"set_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_2set_encoding},
|
|
jpayne@69
|
26044 {"get_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_4get_encoding},
|
|
jpayne@69
|
26045 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_8__reduce_cython__},
|
|
jpayne@69
|
26046 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_10__setstate_cython__},
|
|
jpayne@69
|
26047 {0, 0, 0, 0}
|
|
jpayne@69
|
26048 };
|
|
jpayne@69
|
26049 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26050 static PyType_Slot __pyx_type_5pysam_9libctabix_Parser_slots[] = {
|
|
jpayne@69
|
26051 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26052 {Py_tp_call, (void *)__pyx_pw_5pysam_9libctabix_6Parser_7__call__},
|
|
jpayne@69
|
26053 {Py_tp_doc, (void *)PyDoc_STR("Parser(encoding=u'ascii')")},
|
|
jpayne@69
|
26054 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26055 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26056 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26057 {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_6Parser_1__init__},
|
|
jpayne@69
|
26058 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26059 {0, 0},
|
|
jpayne@69
|
26060 };
|
|
jpayne@69
|
26061 static PyType_Spec __pyx_type_5pysam_9libctabix_Parser_spec = {
|
|
jpayne@69
|
26062 "pysam.libctabix.Parser",
|
|
jpayne@69
|
26063 sizeof(struct __pyx_obj_5pysam_9libctabix_Parser),
|
|
jpayne@69
|
26064 0,
|
|
jpayne@69
|
26065 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26066 __pyx_type_5pysam_9libctabix_Parser_slots,
|
|
jpayne@69
|
26067 };
|
|
jpayne@69
|
26068 #else
|
|
jpayne@69
|
26069
|
|
jpayne@69
|
26070 static PyTypeObject __pyx_type_5pysam_9libctabix_Parser = {
|
|
jpayne@69
|
26071 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26072 "pysam.libctabix.""Parser", /*tp_name*/
|
|
jpayne@69
|
26073 sizeof(struct __pyx_obj_5pysam_9libctabix_Parser), /*tp_basicsize*/
|
|
jpayne@69
|
26074 0, /*tp_itemsize*/
|
|
jpayne@69
|
26075 __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/
|
|
jpayne@69
|
26076 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26077 0, /*tp_print*/
|
|
jpayne@69
|
26078 #endif
|
|
jpayne@69
|
26079 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26080 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26081 #endif
|
|
jpayne@69
|
26082 0, /*tp_getattr*/
|
|
jpayne@69
|
26083 0, /*tp_setattr*/
|
|
jpayne@69
|
26084 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26085 0, /*tp_compare*/
|
|
jpayne@69
|
26086 #endif
|
|
jpayne@69
|
26087 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26088 0, /*tp_as_async*/
|
|
jpayne@69
|
26089 #endif
|
|
jpayne@69
|
26090 0, /*tp_repr*/
|
|
jpayne@69
|
26091 0, /*tp_as_number*/
|
|
jpayne@69
|
26092 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26093 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26094 0, /*tp_hash*/
|
|
jpayne@69
|
26095 __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/
|
|
jpayne@69
|
26096 0, /*tp_str*/
|
|
jpayne@69
|
26097 0, /*tp_getattro*/
|
|
jpayne@69
|
26098 0, /*tp_setattro*/
|
|
jpayne@69
|
26099 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26100 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26101 PyDoc_STR("Parser(encoding=u'ascii')"), /*tp_doc*/
|
|
jpayne@69
|
26102 __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/
|
|
jpayne@69
|
26103 __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/
|
|
jpayne@69
|
26104 0, /*tp_richcompare*/
|
|
jpayne@69
|
26105 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26106 0, /*tp_iter*/
|
|
jpayne@69
|
26107 0, /*tp_iternext*/
|
|
jpayne@69
|
26108 __pyx_methods_5pysam_9libctabix_Parser, /*tp_methods*/
|
|
jpayne@69
|
26109 0, /*tp_members*/
|
|
jpayne@69
|
26110 0, /*tp_getset*/
|
|
jpayne@69
|
26111 0, /*tp_base*/
|
|
jpayne@69
|
26112 0, /*tp_dict*/
|
|
jpayne@69
|
26113 0, /*tp_descr_get*/
|
|
jpayne@69
|
26114 0, /*tp_descr_set*/
|
|
jpayne@69
|
26115 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26116 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26117 #endif
|
|
jpayne@69
|
26118 __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/
|
|
jpayne@69
|
26119 0, /*tp_alloc*/
|
|
jpayne@69
|
26120 __pyx_tp_new_5pysam_9libctabix_Parser, /*tp_new*/
|
|
jpayne@69
|
26121 0, /*tp_free*/
|
|
jpayne@69
|
26122 0, /*tp_is_gc*/
|
|
jpayne@69
|
26123 0, /*tp_bases*/
|
|
jpayne@69
|
26124 0, /*tp_mro*/
|
|
jpayne@69
|
26125 0, /*tp_cache*/
|
|
jpayne@69
|
26126 0, /*tp_subclasses*/
|
|
jpayne@69
|
26127 0, /*tp_weaklist*/
|
|
jpayne@69
|
26128 0, /*tp_del*/
|
|
jpayne@69
|
26129 0, /*tp_version_tag*/
|
|
jpayne@69
|
26130 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26131 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26132 0, /*tp_finalize*/
|
|
jpayne@69
|
26133 #else
|
|
jpayne@69
|
26134 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26135 #endif
|
|
jpayne@69
|
26136 #endif
|
|
jpayne@69
|
26137 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26138 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26139 #endif
|
|
jpayne@69
|
26140 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26141 0, /*tp_print*/
|
|
jpayne@69
|
26142 #endif
|
|
jpayne@69
|
26143 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26144 0, /*tp_watched*/
|
|
jpayne@69
|
26145 #endif
|
|
jpayne@69
|
26146 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26147 0, /*tp_versions_used*/
|
|
jpayne@69
|
26148 #endif
|
|
jpayne@69
|
26149 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26150 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26151 #endif
|
|
jpayne@69
|
26152 };
|
|
jpayne@69
|
26153 #endif
|
|
jpayne@69
|
26154 static struct __pyx_vtabstruct_5pysam_9libctabix_asTuple __pyx_vtable_5pysam_9libctabix_asTuple;
|
|
jpayne@69
|
26155
|
|
jpayne@69
|
26156 static PyObject *__pyx_tp_new_5pysam_9libctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
26157 struct __pyx_obj_5pysam_9libctabix_asTuple *p;
|
|
jpayne@69
|
26158 PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k);
|
|
jpayne@69
|
26159 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26160 p = ((struct __pyx_obj_5pysam_9libctabix_asTuple *)o);
|
|
jpayne@69
|
26161 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asTuple;
|
|
jpayne@69
|
26162 return o;
|
|
jpayne@69
|
26163 }
|
|
jpayne@69
|
26164
|
|
jpayne@69
|
26165 static PyMethodDef __pyx_methods_5pysam_9libctabix_asTuple[] = {
|
|
jpayne@69
|
26166 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple___reduce_cython__},
|
|
jpayne@69
|
26167 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple_2__setstate_cython__},
|
|
jpayne@69
|
26168 {0, 0, 0, 0}
|
|
jpayne@69
|
26169 };
|
|
jpayne@69
|
26170 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26171 static PyType_Slot __pyx_type_5pysam_9libctabix_asTuple_slots[] = {
|
|
jpayne@69
|
26172 {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a python tuple.\n\n A field in a row is accessed by numeric index.\n ")},
|
|
jpayne@69
|
26173 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26174 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26175 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asTuple},
|
|
jpayne@69
|
26176 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asTuple},
|
|
jpayne@69
|
26177 {0, 0},
|
|
jpayne@69
|
26178 };
|
|
jpayne@69
|
26179 static PyType_Spec __pyx_type_5pysam_9libctabix_asTuple_spec = {
|
|
jpayne@69
|
26180 "pysam.libctabix.asTuple",
|
|
jpayne@69
|
26181 sizeof(struct __pyx_obj_5pysam_9libctabix_asTuple),
|
|
jpayne@69
|
26182 0,
|
|
jpayne@69
|
26183 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26184 __pyx_type_5pysam_9libctabix_asTuple_slots,
|
|
jpayne@69
|
26185 };
|
|
jpayne@69
|
26186 #else
|
|
jpayne@69
|
26187
|
|
jpayne@69
|
26188 static PyTypeObject __pyx_type_5pysam_9libctabix_asTuple = {
|
|
jpayne@69
|
26189 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26190 "pysam.libctabix.""asTuple", /*tp_name*/
|
|
jpayne@69
|
26191 sizeof(struct __pyx_obj_5pysam_9libctabix_asTuple), /*tp_basicsize*/
|
|
jpayne@69
|
26192 0, /*tp_itemsize*/
|
|
jpayne@69
|
26193 __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/
|
|
jpayne@69
|
26194 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26195 0, /*tp_print*/
|
|
jpayne@69
|
26196 #endif
|
|
jpayne@69
|
26197 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26198 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26199 #endif
|
|
jpayne@69
|
26200 0, /*tp_getattr*/
|
|
jpayne@69
|
26201 0, /*tp_setattr*/
|
|
jpayne@69
|
26202 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26203 0, /*tp_compare*/
|
|
jpayne@69
|
26204 #endif
|
|
jpayne@69
|
26205 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26206 0, /*tp_as_async*/
|
|
jpayne@69
|
26207 #endif
|
|
jpayne@69
|
26208 0, /*tp_repr*/
|
|
jpayne@69
|
26209 0, /*tp_as_number*/
|
|
jpayne@69
|
26210 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26211 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26212 0, /*tp_hash*/
|
|
jpayne@69
|
26213 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26214 __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/
|
|
jpayne@69
|
26215 #else
|
|
jpayne@69
|
26216 0, /*tp_call*/
|
|
jpayne@69
|
26217 #endif
|
|
jpayne@69
|
26218 0, /*tp_str*/
|
|
jpayne@69
|
26219 0, /*tp_getattro*/
|
|
jpayne@69
|
26220 0, /*tp_setattro*/
|
|
jpayne@69
|
26221 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26222 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26223 PyDoc_STR("converts a :term:`tabix row` into a python tuple.\n\n A field in a row is accessed by numeric index.\n "), /*tp_doc*/
|
|
jpayne@69
|
26224 __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/
|
|
jpayne@69
|
26225 __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/
|
|
jpayne@69
|
26226 0, /*tp_richcompare*/
|
|
jpayne@69
|
26227 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26228 0, /*tp_iter*/
|
|
jpayne@69
|
26229 0, /*tp_iternext*/
|
|
jpayne@69
|
26230 __pyx_methods_5pysam_9libctabix_asTuple, /*tp_methods*/
|
|
jpayne@69
|
26231 0, /*tp_members*/
|
|
jpayne@69
|
26232 0, /*tp_getset*/
|
|
jpayne@69
|
26233 0, /*tp_base*/
|
|
jpayne@69
|
26234 0, /*tp_dict*/
|
|
jpayne@69
|
26235 0, /*tp_descr_get*/
|
|
jpayne@69
|
26236 0, /*tp_descr_set*/
|
|
jpayne@69
|
26237 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26238 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26239 #endif
|
|
jpayne@69
|
26240 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26241 __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/
|
|
jpayne@69
|
26242 #else
|
|
jpayne@69
|
26243 0, /*tp_init*/
|
|
jpayne@69
|
26244 #endif
|
|
jpayne@69
|
26245 0, /*tp_alloc*/
|
|
jpayne@69
|
26246 __pyx_tp_new_5pysam_9libctabix_asTuple, /*tp_new*/
|
|
jpayne@69
|
26247 0, /*tp_free*/
|
|
jpayne@69
|
26248 0, /*tp_is_gc*/
|
|
jpayne@69
|
26249 0, /*tp_bases*/
|
|
jpayne@69
|
26250 0, /*tp_mro*/
|
|
jpayne@69
|
26251 0, /*tp_cache*/
|
|
jpayne@69
|
26252 0, /*tp_subclasses*/
|
|
jpayne@69
|
26253 0, /*tp_weaklist*/
|
|
jpayne@69
|
26254 0, /*tp_del*/
|
|
jpayne@69
|
26255 0, /*tp_version_tag*/
|
|
jpayne@69
|
26256 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26257 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26258 0, /*tp_finalize*/
|
|
jpayne@69
|
26259 #else
|
|
jpayne@69
|
26260 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26261 #endif
|
|
jpayne@69
|
26262 #endif
|
|
jpayne@69
|
26263 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26264 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26265 #endif
|
|
jpayne@69
|
26266 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26267 0, /*tp_print*/
|
|
jpayne@69
|
26268 #endif
|
|
jpayne@69
|
26269 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26270 0, /*tp_watched*/
|
|
jpayne@69
|
26271 #endif
|
|
jpayne@69
|
26272 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26273 0, /*tp_versions_used*/
|
|
jpayne@69
|
26274 #endif
|
|
jpayne@69
|
26275 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26276 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26277 #endif
|
|
jpayne@69
|
26278 };
|
|
jpayne@69
|
26279 #endif
|
|
jpayne@69
|
26280 static struct __pyx_vtabstruct_5pysam_9libctabix_asGTF __pyx_vtable_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
26281
|
|
jpayne@69
|
26282 static PyObject *__pyx_tp_new_5pysam_9libctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
26283 struct __pyx_obj_5pysam_9libctabix_asGTF *p;
|
|
jpayne@69
|
26284 PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k);
|
|
jpayne@69
|
26285 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26286 p = ((struct __pyx_obj_5pysam_9libctabix_asGTF *)o);
|
|
jpayne@69
|
26287 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
26288 return o;
|
|
jpayne@69
|
26289 }
|
|
jpayne@69
|
26290
|
|
jpayne@69
|
26291 static PyMethodDef __pyx_methods_5pysam_9libctabix_asGTF[] = {
|
|
jpayne@69
|
26292 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF___reduce_cython__},
|
|
jpayne@69
|
26293 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF_2__setstate_cython__},
|
|
jpayne@69
|
26294 {0, 0, 0, 0}
|
|
jpayne@69
|
26295 };
|
|
jpayne@69
|
26296 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26297 static PyType_Slot __pyx_type_5pysam_9libctabix_asGTF_slots[] = {
|
|
jpayne@69
|
26298 {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a GTF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n GTF formatted entries also define the following fields that\n are derived from the attributes field:\n\n +--------------------+------------------------------+\n |*Name* |*Content* |\n +--------------------+------------------------------+\n |gene_id |the gene identifier |\n +--------------------+------------------------------+\n |transcript_id |the transcript identifier |\n +--------------------+-------------------""-----------+\n\n ")},
|
|
jpayne@69
|
26299 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26300 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26301 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asGTF},
|
|
jpayne@69
|
26302 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asGTF},
|
|
jpayne@69
|
26303 {0, 0},
|
|
jpayne@69
|
26304 };
|
|
jpayne@69
|
26305 static PyType_Spec __pyx_type_5pysam_9libctabix_asGTF_spec = {
|
|
jpayne@69
|
26306 "pysam.libctabix.asGTF",
|
|
jpayne@69
|
26307 sizeof(struct __pyx_obj_5pysam_9libctabix_asGTF),
|
|
jpayne@69
|
26308 0,
|
|
jpayne@69
|
26309 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26310 __pyx_type_5pysam_9libctabix_asGTF_slots,
|
|
jpayne@69
|
26311 };
|
|
jpayne@69
|
26312 #else
|
|
jpayne@69
|
26313
|
|
jpayne@69
|
26314 static PyTypeObject __pyx_type_5pysam_9libctabix_asGTF = {
|
|
jpayne@69
|
26315 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26316 "pysam.libctabix.""asGTF", /*tp_name*/
|
|
jpayne@69
|
26317 sizeof(struct __pyx_obj_5pysam_9libctabix_asGTF), /*tp_basicsize*/
|
|
jpayne@69
|
26318 0, /*tp_itemsize*/
|
|
jpayne@69
|
26319 __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/
|
|
jpayne@69
|
26320 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26321 0, /*tp_print*/
|
|
jpayne@69
|
26322 #endif
|
|
jpayne@69
|
26323 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26324 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26325 #endif
|
|
jpayne@69
|
26326 0, /*tp_getattr*/
|
|
jpayne@69
|
26327 0, /*tp_setattr*/
|
|
jpayne@69
|
26328 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26329 0, /*tp_compare*/
|
|
jpayne@69
|
26330 #endif
|
|
jpayne@69
|
26331 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26332 0, /*tp_as_async*/
|
|
jpayne@69
|
26333 #endif
|
|
jpayne@69
|
26334 0, /*tp_repr*/
|
|
jpayne@69
|
26335 0, /*tp_as_number*/
|
|
jpayne@69
|
26336 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26337 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26338 0, /*tp_hash*/
|
|
jpayne@69
|
26339 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26340 __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/
|
|
jpayne@69
|
26341 #else
|
|
jpayne@69
|
26342 0, /*tp_call*/
|
|
jpayne@69
|
26343 #endif
|
|
jpayne@69
|
26344 0, /*tp_str*/
|
|
jpayne@69
|
26345 0, /*tp_getattro*/
|
|
jpayne@69
|
26346 0, /*tp_setattro*/
|
|
jpayne@69
|
26347 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26348 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26349 PyDoc_STR("converts a :term:`tabix row` into a GTF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n GTF formatted entries also define the following fields that\n are derived from the attributes field:\n\n +--------------------+------------------------------+\n |*Name* |*Content* |\n +--------------------+------------------------------+\n |gene_id |the gene identifier |\n +--------------------+------------------------------+\n |transcript_id |the transcript identifier |\n +--------------------+-------------------""-----------+\n\n "), /*tp_doc*/
|
|
jpayne@69
|
26350 __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/
|
|
jpayne@69
|
26351 __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/
|
|
jpayne@69
|
26352 0, /*tp_richcompare*/
|
|
jpayne@69
|
26353 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26354 0, /*tp_iter*/
|
|
jpayne@69
|
26355 0, /*tp_iternext*/
|
|
jpayne@69
|
26356 __pyx_methods_5pysam_9libctabix_asGTF, /*tp_methods*/
|
|
jpayne@69
|
26357 0, /*tp_members*/
|
|
jpayne@69
|
26358 0, /*tp_getset*/
|
|
jpayne@69
|
26359 0, /*tp_base*/
|
|
jpayne@69
|
26360 0, /*tp_dict*/
|
|
jpayne@69
|
26361 0, /*tp_descr_get*/
|
|
jpayne@69
|
26362 0, /*tp_descr_set*/
|
|
jpayne@69
|
26363 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26364 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26365 #endif
|
|
jpayne@69
|
26366 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26367 __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/
|
|
jpayne@69
|
26368 #else
|
|
jpayne@69
|
26369 0, /*tp_init*/
|
|
jpayne@69
|
26370 #endif
|
|
jpayne@69
|
26371 0, /*tp_alloc*/
|
|
jpayne@69
|
26372 __pyx_tp_new_5pysam_9libctabix_asGTF, /*tp_new*/
|
|
jpayne@69
|
26373 0, /*tp_free*/
|
|
jpayne@69
|
26374 0, /*tp_is_gc*/
|
|
jpayne@69
|
26375 0, /*tp_bases*/
|
|
jpayne@69
|
26376 0, /*tp_mro*/
|
|
jpayne@69
|
26377 0, /*tp_cache*/
|
|
jpayne@69
|
26378 0, /*tp_subclasses*/
|
|
jpayne@69
|
26379 0, /*tp_weaklist*/
|
|
jpayne@69
|
26380 0, /*tp_del*/
|
|
jpayne@69
|
26381 0, /*tp_version_tag*/
|
|
jpayne@69
|
26382 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26383 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26384 0, /*tp_finalize*/
|
|
jpayne@69
|
26385 #else
|
|
jpayne@69
|
26386 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26387 #endif
|
|
jpayne@69
|
26388 #endif
|
|
jpayne@69
|
26389 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26390 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26391 #endif
|
|
jpayne@69
|
26392 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26393 0, /*tp_print*/
|
|
jpayne@69
|
26394 #endif
|
|
jpayne@69
|
26395 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26396 0, /*tp_watched*/
|
|
jpayne@69
|
26397 #endif
|
|
jpayne@69
|
26398 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26399 0, /*tp_versions_used*/
|
|
jpayne@69
|
26400 #endif
|
|
jpayne@69
|
26401 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26402 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26403 #endif
|
|
jpayne@69
|
26404 };
|
|
jpayne@69
|
26405 #endif
|
|
jpayne@69
|
26406 static struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 __pyx_vtable_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
26407
|
|
jpayne@69
|
26408 static PyObject *__pyx_tp_new_5pysam_9libctabix_asGFF3(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
26409 struct __pyx_obj_5pysam_9libctabix_asGFF3 *p;
|
|
jpayne@69
|
26410 PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k);
|
|
jpayne@69
|
26411 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26412 p = ((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)o);
|
|
jpayne@69
|
26413 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
26414 return o;
|
|
jpayne@69
|
26415 }
|
|
jpayne@69
|
26416
|
|
jpayne@69
|
26417 static PyMethodDef __pyx_methods_5pysam_9libctabix_asGFF3[] = {
|
|
jpayne@69
|
26418 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3___reduce_cython__},
|
|
jpayne@69
|
26419 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3_2__setstate_cython__},
|
|
jpayne@69
|
26420 {0, 0, 0, 0}
|
|
jpayne@69
|
26421 };
|
|
jpayne@69
|
26422 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26423 static PyType_Slot __pyx_type_5pysam_9libctabix_asGFF3_slots[] = {
|
|
jpayne@69
|
26424 {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a GFF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n ")},
|
|
jpayne@69
|
26425 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26426 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26427 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asGFF3},
|
|
jpayne@69
|
26428 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asGFF3},
|
|
jpayne@69
|
26429 {0, 0},
|
|
jpayne@69
|
26430 };
|
|
jpayne@69
|
26431 static PyType_Spec __pyx_type_5pysam_9libctabix_asGFF3_spec = {
|
|
jpayne@69
|
26432 "pysam.libctabix.asGFF3",
|
|
jpayne@69
|
26433 sizeof(struct __pyx_obj_5pysam_9libctabix_asGFF3),
|
|
jpayne@69
|
26434 0,
|
|
jpayne@69
|
26435 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26436 __pyx_type_5pysam_9libctabix_asGFF3_slots,
|
|
jpayne@69
|
26437 };
|
|
jpayne@69
|
26438 #else
|
|
jpayne@69
|
26439
|
|
jpayne@69
|
26440 static PyTypeObject __pyx_type_5pysam_9libctabix_asGFF3 = {
|
|
jpayne@69
|
26441 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26442 "pysam.libctabix.""asGFF3", /*tp_name*/
|
|
jpayne@69
|
26443 sizeof(struct __pyx_obj_5pysam_9libctabix_asGFF3), /*tp_basicsize*/
|
|
jpayne@69
|
26444 0, /*tp_itemsize*/
|
|
jpayne@69
|
26445 __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/
|
|
jpayne@69
|
26446 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26447 0, /*tp_print*/
|
|
jpayne@69
|
26448 #endif
|
|
jpayne@69
|
26449 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26450 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26451 #endif
|
|
jpayne@69
|
26452 0, /*tp_getattr*/
|
|
jpayne@69
|
26453 0, /*tp_setattr*/
|
|
jpayne@69
|
26454 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26455 0, /*tp_compare*/
|
|
jpayne@69
|
26456 #endif
|
|
jpayne@69
|
26457 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26458 0, /*tp_as_async*/
|
|
jpayne@69
|
26459 #endif
|
|
jpayne@69
|
26460 0, /*tp_repr*/
|
|
jpayne@69
|
26461 0, /*tp_as_number*/
|
|
jpayne@69
|
26462 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26463 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26464 0, /*tp_hash*/
|
|
jpayne@69
|
26465 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26466 __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/
|
|
jpayne@69
|
26467 #else
|
|
jpayne@69
|
26468 0, /*tp_call*/
|
|
jpayne@69
|
26469 #endif
|
|
jpayne@69
|
26470 0, /*tp_str*/
|
|
jpayne@69
|
26471 0, /*tp_getattro*/
|
|
jpayne@69
|
26472 0, /*tp_setattro*/
|
|
jpayne@69
|
26473 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26474 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26475 PyDoc_STR("converts a :term:`tabix row` into a GFF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n "), /*tp_doc*/
|
|
jpayne@69
|
26476 __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/
|
|
jpayne@69
|
26477 __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/
|
|
jpayne@69
|
26478 0, /*tp_richcompare*/
|
|
jpayne@69
|
26479 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26480 0, /*tp_iter*/
|
|
jpayne@69
|
26481 0, /*tp_iternext*/
|
|
jpayne@69
|
26482 __pyx_methods_5pysam_9libctabix_asGFF3, /*tp_methods*/
|
|
jpayne@69
|
26483 0, /*tp_members*/
|
|
jpayne@69
|
26484 0, /*tp_getset*/
|
|
jpayne@69
|
26485 0, /*tp_base*/
|
|
jpayne@69
|
26486 0, /*tp_dict*/
|
|
jpayne@69
|
26487 0, /*tp_descr_get*/
|
|
jpayne@69
|
26488 0, /*tp_descr_set*/
|
|
jpayne@69
|
26489 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26490 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26491 #endif
|
|
jpayne@69
|
26492 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26493 __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/
|
|
jpayne@69
|
26494 #else
|
|
jpayne@69
|
26495 0, /*tp_init*/
|
|
jpayne@69
|
26496 #endif
|
|
jpayne@69
|
26497 0, /*tp_alloc*/
|
|
jpayne@69
|
26498 __pyx_tp_new_5pysam_9libctabix_asGFF3, /*tp_new*/
|
|
jpayne@69
|
26499 0, /*tp_free*/
|
|
jpayne@69
|
26500 0, /*tp_is_gc*/
|
|
jpayne@69
|
26501 0, /*tp_bases*/
|
|
jpayne@69
|
26502 0, /*tp_mro*/
|
|
jpayne@69
|
26503 0, /*tp_cache*/
|
|
jpayne@69
|
26504 0, /*tp_subclasses*/
|
|
jpayne@69
|
26505 0, /*tp_weaklist*/
|
|
jpayne@69
|
26506 0, /*tp_del*/
|
|
jpayne@69
|
26507 0, /*tp_version_tag*/
|
|
jpayne@69
|
26508 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26509 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26510 0, /*tp_finalize*/
|
|
jpayne@69
|
26511 #else
|
|
jpayne@69
|
26512 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26513 #endif
|
|
jpayne@69
|
26514 #endif
|
|
jpayne@69
|
26515 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26516 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26517 #endif
|
|
jpayne@69
|
26518 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26519 0, /*tp_print*/
|
|
jpayne@69
|
26520 #endif
|
|
jpayne@69
|
26521 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26522 0, /*tp_watched*/
|
|
jpayne@69
|
26523 #endif
|
|
jpayne@69
|
26524 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26525 0, /*tp_versions_used*/
|
|
jpayne@69
|
26526 #endif
|
|
jpayne@69
|
26527 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26528 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26529 #endif
|
|
jpayne@69
|
26530 };
|
|
jpayne@69
|
26531 #endif
|
|
jpayne@69
|
26532 static struct __pyx_vtabstruct_5pysam_9libctabix_asBed __pyx_vtable_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
26533
|
|
jpayne@69
|
26534 static PyObject *__pyx_tp_new_5pysam_9libctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
26535 struct __pyx_obj_5pysam_9libctabix_asBed *p;
|
|
jpayne@69
|
26536 PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k);
|
|
jpayne@69
|
26537 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26538 p = ((struct __pyx_obj_5pysam_9libctabix_asBed *)o);
|
|
jpayne@69
|
26539 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
26540 return o;
|
|
jpayne@69
|
26541 }
|
|
jpayne@69
|
26542
|
|
jpayne@69
|
26543 static PyMethodDef __pyx_methods_5pysam_9libctabix_asBed[] = {
|
|
jpayne@69
|
26544 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed___reduce_cython__},
|
|
jpayne@69
|
26545 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed_2__setstate_cython__},
|
|
jpayne@69
|
26546 {0, 0, 0, 0}
|
|
jpayne@69
|
26547 };
|
|
jpayne@69
|
26548 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26549 static PyType_Slot __pyx_type_5pysam_9libctabix_asBed_slots[] = {
|
|
jpayne@69
|
26550 {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n +-----------+-----------+------------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +-----------+-----------+------------------------------------------+\n |1 |contig |contig |\n | | | |\n +-----------+-----------+------------------------------------------+\n |2 |start |genomic start coordinate (zero-based) |\n +-----------+-----------+------------------------------------------+\n |3 |end |genomic end coordinate plus one |\n | | |(zero-based) |\n +-----------+-----------+------------------------------------------+\n |4 |name |name of feature. |\n +-----------+-----------+------------------------------------------+\n |5 |score |score of feature |\n +-----------+-----------+------------------------------------------+\n |6 |strand |strand of feature |\n +-----------+-----------+------------------------------------------+\n |7 |thickStart |thickStart |\n +-----------+-----------+------------------------------------------+\n |8 |thickEnd |thickEnd |\n +-----------+-----------+------------------------------------------+\n |9 |itemRGB |itemRGB |\n +-----------+-----------+------------------------------------------+\n |10 |blockCount |number of bocks |\n +-----------+-----------+---------------------------------------""---+\n |11 |blockSizes |',' separated string of block sizes |\n +-----------+-----------+------------------------------------------+\n |12 |blockStarts|',' separated string of block genomic |\n | | |start positions |\n +-----------+-----------+------------------------------------------+\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceding\n need to be defined as well.\n\n ")},
|
|
jpayne@69
|
26551 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26552 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26553 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asBed},
|
|
jpayne@69
|
26554 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asBed},
|
|
jpayne@69
|
26555 {0, 0},
|
|
jpayne@69
|
26556 };
|
|
jpayne@69
|
26557 static PyType_Spec __pyx_type_5pysam_9libctabix_asBed_spec = {
|
|
jpayne@69
|
26558 "pysam.libctabix.asBed",
|
|
jpayne@69
|
26559 sizeof(struct __pyx_obj_5pysam_9libctabix_asBed),
|
|
jpayne@69
|
26560 0,
|
|
jpayne@69
|
26561 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26562 __pyx_type_5pysam_9libctabix_asBed_slots,
|
|
jpayne@69
|
26563 };
|
|
jpayne@69
|
26564 #else
|
|
jpayne@69
|
26565
|
|
jpayne@69
|
26566 static PyTypeObject __pyx_type_5pysam_9libctabix_asBed = {
|
|
jpayne@69
|
26567 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26568 "pysam.libctabix.""asBed", /*tp_name*/
|
|
jpayne@69
|
26569 sizeof(struct __pyx_obj_5pysam_9libctabix_asBed), /*tp_basicsize*/
|
|
jpayne@69
|
26570 0, /*tp_itemsize*/
|
|
jpayne@69
|
26571 __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/
|
|
jpayne@69
|
26572 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26573 0, /*tp_print*/
|
|
jpayne@69
|
26574 #endif
|
|
jpayne@69
|
26575 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26576 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26577 #endif
|
|
jpayne@69
|
26578 0, /*tp_getattr*/
|
|
jpayne@69
|
26579 0, /*tp_setattr*/
|
|
jpayne@69
|
26580 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26581 0, /*tp_compare*/
|
|
jpayne@69
|
26582 #endif
|
|
jpayne@69
|
26583 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26584 0, /*tp_as_async*/
|
|
jpayne@69
|
26585 #endif
|
|
jpayne@69
|
26586 0, /*tp_repr*/
|
|
jpayne@69
|
26587 0, /*tp_as_number*/
|
|
jpayne@69
|
26588 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26589 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26590 0, /*tp_hash*/
|
|
jpayne@69
|
26591 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26592 __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/
|
|
jpayne@69
|
26593 #else
|
|
jpayne@69
|
26594 0, /*tp_call*/
|
|
jpayne@69
|
26595 #endif
|
|
jpayne@69
|
26596 0, /*tp_str*/
|
|
jpayne@69
|
26597 0, /*tp_getattro*/
|
|
jpayne@69
|
26598 0, /*tp_setattro*/
|
|
jpayne@69
|
26599 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26600 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26601 PyDoc_STR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n +-----------+-----------+------------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +-----------+-----------+------------------------------------------+\n |1 |contig |contig |\n | | | |\n +-----------+-----------+------------------------------------------+\n |2 |start |genomic start coordinate (zero-based) |\n +-----------+-----------+------------------------------------------+\n |3 |end |genomic end coordinate plus one |\n | | |(zero-based) |\n +-----------+-----------+------------------------------------------+\n |4 |name |name of feature. |\n +-----------+-----------+------------------------------------------+\n |5 |score |score of feature |\n +-----------+-----------+------------------------------------------+\n |6 |strand |strand of feature |\n +-----------+-----------+------------------------------------------+\n |7 |thickStart |thickStart |\n +-----------+-----------+------------------------------------------+\n |8 |thickEnd |thickEnd |\n +-----------+-----------+------------------------------------------+\n |9 |itemRGB |itemRGB |\n +-----------+-----------+------------------------------------------+\n |10 |blockCount |number of bocks |\n +-----------+-----------+---------------------------------------""---+\n |11 |blockSizes |',' separated string of block sizes |\n +-----------+-----------+------------------------------------------+\n |12 |blockStarts|',' separated string of block genomic |\n | | |start positions |\n +-----------+-----------+------------------------------------------+\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceding\n need to be defined as well.\n\n "), /*tp_doc*/
|
|
jpayne@69
|
26602 __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/
|
|
jpayne@69
|
26603 __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/
|
|
jpayne@69
|
26604 0, /*tp_richcompare*/
|
|
jpayne@69
|
26605 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26606 0, /*tp_iter*/
|
|
jpayne@69
|
26607 0, /*tp_iternext*/
|
|
jpayne@69
|
26608 __pyx_methods_5pysam_9libctabix_asBed, /*tp_methods*/
|
|
jpayne@69
|
26609 0, /*tp_members*/
|
|
jpayne@69
|
26610 0, /*tp_getset*/
|
|
jpayne@69
|
26611 0, /*tp_base*/
|
|
jpayne@69
|
26612 0, /*tp_dict*/
|
|
jpayne@69
|
26613 0, /*tp_descr_get*/
|
|
jpayne@69
|
26614 0, /*tp_descr_set*/
|
|
jpayne@69
|
26615 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26616 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26617 #endif
|
|
jpayne@69
|
26618 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26619 __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/
|
|
jpayne@69
|
26620 #else
|
|
jpayne@69
|
26621 0, /*tp_init*/
|
|
jpayne@69
|
26622 #endif
|
|
jpayne@69
|
26623 0, /*tp_alloc*/
|
|
jpayne@69
|
26624 __pyx_tp_new_5pysam_9libctabix_asBed, /*tp_new*/
|
|
jpayne@69
|
26625 0, /*tp_free*/
|
|
jpayne@69
|
26626 0, /*tp_is_gc*/
|
|
jpayne@69
|
26627 0, /*tp_bases*/
|
|
jpayne@69
|
26628 0, /*tp_mro*/
|
|
jpayne@69
|
26629 0, /*tp_cache*/
|
|
jpayne@69
|
26630 0, /*tp_subclasses*/
|
|
jpayne@69
|
26631 0, /*tp_weaklist*/
|
|
jpayne@69
|
26632 0, /*tp_del*/
|
|
jpayne@69
|
26633 0, /*tp_version_tag*/
|
|
jpayne@69
|
26634 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26635 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26636 0, /*tp_finalize*/
|
|
jpayne@69
|
26637 #else
|
|
jpayne@69
|
26638 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26639 #endif
|
|
jpayne@69
|
26640 #endif
|
|
jpayne@69
|
26641 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26642 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26643 #endif
|
|
jpayne@69
|
26644 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26645 0, /*tp_print*/
|
|
jpayne@69
|
26646 #endif
|
|
jpayne@69
|
26647 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26648 0, /*tp_watched*/
|
|
jpayne@69
|
26649 #endif
|
|
jpayne@69
|
26650 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26651 0, /*tp_versions_used*/
|
|
jpayne@69
|
26652 #endif
|
|
jpayne@69
|
26653 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26654 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26655 #endif
|
|
jpayne@69
|
26656 };
|
|
jpayne@69
|
26657 #endif
|
|
jpayne@69
|
26658 static struct __pyx_vtabstruct_5pysam_9libctabix_asVCF __pyx_vtable_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
26659
|
|
jpayne@69
|
26660 static PyObject *__pyx_tp_new_5pysam_9libctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
26661 struct __pyx_obj_5pysam_9libctabix_asVCF *p;
|
|
jpayne@69
|
26662 PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k);
|
|
jpayne@69
|
26663 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26664 p = ((struct __pyx_obj_5pysam_9libctabix_asVCF *)o);
|
|
jpayne@69
|
26665 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
26666 return o;
|
|
jpayne@69
|
26667 }
|
|
jpayne@69
|
26668
|
|
jpayne@69
|
26669 static PyMethodDef __pyx_methods_5pysam_9libctabix_asVCF[] = {
|
|
jpayne@69
|
26670 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF___reduce_cython__},
|
|
jpayne@69
|
26671 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF_2__setstate_cython__},
|
|
jpayne@69
|
26672 {0, 0, 0, 0}
|
|
jpayne@69
|
26673 };
|
|
jpayne@69
|
26674 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26675 static PyType_Slot __pyx_type_5pysam_9libctabix_asVCF_slots[] = {
|
|
jpayne@69
|
26676 {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n +----------+---------+------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +----------+---------+------------------------------------+\n |1 |contig |chromosome |\n +----------+---------+------------------------------------+\n |2 |pos |chromosomal position, zero-based |\n +----------+---------+------------------------------------+\n |3 |id |id |\n +----------+---------+------------------------------------+\n |4 |ref |reference allele |\n +----------+---------+------------------------------------+\n |5 |alt |alternate alleles |\n +----------+---------+------------------------------------+\n |6 |qual |quality |\n +----------+---------+------------------------------------+\n |7 |filter |filter |\n +----------+---------+------------------------------------+\n |8 |info |info |\n +----------+---------+------------------------------------+\n |9 |format |format specifier. |\n +----------+---------+------------------------------------+\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n ")},
|
|
jpayne@69
|
26677 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26678 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser},
|
|
jpayne@69
|
26679 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asVCF},
|
|
jpayne@69
|
26680 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asVCF},
|
|
jpayne@69
|
26681 {0, 0},
|
|
jpayne@69
|
26682 };
|
|
jpayne@69
|
26683 static PyType_Spec __pyx_type_5pysam_9libctabix_asVCF_spec = {
|
|
jpayne@69
|
26684 "pysam.libctabix.asVCF",
|
|
jpayne@69
|
26685 sizeof(struct __pyx_obj_5pysam_9libctabix_asVCF),
|
|
jpayne@69
|
26686 0,
|
|
jpayne@69
|
26687 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26688 __pyx_type_5pysam_9libctabix_asVCF_slots,
|
|
jpayne@69
|
26689 };
|
|
jpayne@69
|
26690 #else
|
|
jpayne@69
|
26691
|
|
jpayne@69
|
26692 static PyTypeObject __pyx_type_5pysam_9libctabix_asVCF = {
|
|
jpayne@69
|
26693 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26694 "pysam.libctabix.""asVCF", /*tp_name*/
|
|
jpayne@69
|
26695 sizeof(struct __pyx_obj_5pysam_9libctabix_asVCF), /*tp_basicsize*/
|
|
jpayne@69
|
26696 0, /*tp_itemsize*/
|
|
jpayne@69
|
26697 __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/
|
|
jpayne@69
|
26698 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26699 0, /*tp_print*/
|
|
jpayne@69
|
26700 #endif
|
|
jpayne@69
|
26701 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26702 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26703 #endif
|
|
jpayne@69
|
26704 0, /*tp_getattr*/
|
|
jpayne@69
|
26705 0, /*tp_setattr*/
|
|
jpayne@69
|
26706 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26707 0, /*tp_compare*/
|
|
jpayne@69
|
26708 #endif
|
|
jpayne@69
|
26709 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26710 0, /*tp_as_async*/
|
|
jpayne@69
|
26711 #endif
|
|
jpayne@69
|
26712 0, /*tp_repr*/
|
|
jpayne@69
|
26713 0, /*tp_as_number*/
|
|
jpayne@69
|
26714 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26715 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26716 0, /*tp_hash*/
|
|
jpayne@69
|
26717 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26718 __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/
|
|
jpayne@69
|
26719 #else
|
|
jpayne@69
|
26720 0, /*tp_call*/
|
|
jpayne@69
|
26721 #endif
|
|
jpayne@69
|
26722 0, /*tp_str*/
|
|
jpayne@69
|
26723 0, /*tp_getattro*/
|
|
jpayne@69
|
26724 0, /*tp_setattro*/
|
|
jpayne@69
|
26725 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26726 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26727 PyDoc_STR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n +----------+---------+------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +----------+---------+------------------------------------+\n |1 |contig |chromosome |\n +----------+---------+------------------------------------+\n |2 |pos |chromosomal position, zero-based |\n +----------+---------+------------------------------------+\n |3 |id |id |\n +----------+---------+------------------------------------+\n |4 |ref |reference allele |\n +----------+---------+------------------------------------+\n |5 |alt |alternate alleles |\n +----------+---------+------------------------------------+\n |6 |qual |quality |\n +----------+---------+------------------------------------+\n |7 |filter |filter |\n +----------+---------+------------------------------------+\n |8 |info |info |\n +----------+---------+------------------------------------+\n |9 |format |format specifier. |\n +----------+---------+------------------------------------+\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n "), /*tp_doc*/
|
|
jpayne@69
|
26728 __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/
|
|
jpayne@69
|
26729 __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/
|
|
jpayne@69
|
26730 0, /*tp_richcompare*/
|
|
jpayne@69
|
26731 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26732 0, /*tp_iter*/
|
|
jpayne@69
|
26733 0, /*tp_iternext*/
|
|
jpayne@69
|
26734 __pyx_methods_5pysam_9libctabix_asVCF, /*tp_methods*/
|
|
jpayne@69
|
26735 0, /*tp_members*/
|
|
jpayne@69
|
26736 0, /*tp_getset*/
|
|
jpayne@69
|
26737 0, /*tp_base*/
|
|
jpayne@69
|
26738 0, /*tp_dict*/
|
|
jpayne@69
|
26739 0, /*tp_descr_get*/
|
|
jpayne@69
|
26740 0, /*tp_descr_set*/
|
|
jpayne@69
|
26741 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26742 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26743 #endif
|
|
jpayne@69
|
26744 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
26745 __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/
|
|
jpayne@69
|
26746 #else
|
|
jpayne@69
|
26747 0, /*tp_init*/
|
|
jpayne@69
|
26748 #endif
|
|
jpayne@69
|
26749 0, /*tp_alloc*/
|
|
jpayne@69
|
26750 __pyx_tp_new_5pysam_9libctabix_asVCF, /*tp_new*/
|
|
jpayne@69
|
26751 0, /*tp_free*/
|
|
jpayne@69
|
26752 0, /*tp_is_gc*/
|
|
jpayne@69
|
26753 0, /*tp_bases*/
|
|
jpayne@69
|
26754 0, /*tp_mro*/
|
|
jpayne@69
|
26755 0, /*tp_cache*/
|
|
jpayne@69
|
26756 0, /*tp_subclasses*/
|
|
jpayne@69
|
26757 0, /*tp_weaklist*/
|
|
jpayne@69
|
26758 0, /*tp_del*/
|
|
jpayne@69
|
26759 0, /*tp_version_tag*/
|
|
jpayne@69
|
26760 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26761 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26762 0, /*tp_finalize*/
|
|
jpayne@69
|
26763 #else
|
|
jpayne@69
|
26764 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26765 #endif
|
|
jpayne@69
|
26766 #endif
|
|
jpayne@69
|
26767 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26768 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26769 #endif
|
|
jpayne@69
|
26770 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26771 0, /*tp_print*/
|
|
jpayne@69
|
26772 #endif
|
|
jpayne@69
|
26773 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26774 0, /*tp_watched*/
|
|
jpayne@69
|
26775 #endif
|
|
jpayne@69
|
26776 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26777 0, /*tp_versions_used*/
|
|
jpayne@69
|
26778 #endif
|
|
jpayne@69
|
26779 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26780 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26781 #endif
|
|
jpayne@69
|
26782 };
|
|
jpayne@69
|
26783 #endif
|
|
jpayne@69
|
26784 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator __pyx_vtable_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
26785
|
|
jpayne@69
|
26786 static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
|
|
jpayne@69
|
26787 struct __pyx_obj_5pysam_9libctabix_TabixIterator *p;
|
|
jpayne@69
|
26788 PyObject *o;
|
|
jpayne@69
|
26789 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
26790 allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc);
|
|
jpayne@69
|
26791 o = alloc_func(t, 0);
|
|
jpayne@69
|
26792 #else
|
|
jpayne@69
|
26793 if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) {
|
|
jpayne@69
|
26794 o = (*t->tp_alloc)(t, 0);
|
|
jpayne@69
|
26795 } else {
|
|
jpayne@69
|
26796 o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
|
|
jpayne@69
|
26797 }
|
|
jpayne@69
|
26798 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26799 #endif
|
|
jpayne@69
|
26800 p = ((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o);
|
|
jpayne@69
|
26801 p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
26802 p->tabixfile = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
26803 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
26804 return o;
|
|
jpayne@69
|
26805 }
|
|
jpayne@69
|
26806
|
|
jpayne@69
|
26807 static void __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator(PyObject *o) {
|
|
jpayne@69
|
26808 struct __pyx_obj_5pysam_9libctabix_TabixIterator *p = (struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o;
|
|
jpayne@69
|
26809 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26810 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
26811 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator) {
|
|
jpayne@69
|
26812 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
26813 }
|
|
jpayne@69
|
26814 }
|
|
jpayne@69
|
26815 #endif
|
|
jpayne@69
|
26816 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
26817 {
|
|
jpayne@69
|
26818 PyObject *etype, *eval, *etb;
|
|
jpayne@69
|
26819 PyErr_Fetch(&etype, &eval, &etb);
|
|
jpayne@69
|
26820 __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
|
|
jpayne@69
|
26821 __pyx_pw_5pysam_9libctabix_13TabixIterator_7__dealloc__(o);
|
|
jpayne@69
|
26822 __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
|
|
jpayne@69
|
26823 PyErr_Restore(etype, eval, etb);
|
|
jpayne@69
|
26824 }
|
|
jpayne@69
|
26825 Py_CLEAR(p->tabixfile);
|
|
jpayne@69
|
26826 Py_CLEAR(p->encoding);
|
|
jpayne@69
|
26827 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
26828 (*Py_TYPE(o)->tp_free)(o);
|
|
jpayne@69
|
26829 #else
|
|
jpayne@69
|
26830 {
|
|
jpayne@69
|
26831 freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free);
|
|
jpayne@69
|
26832 if (tp_free) tp_free(o);
|
|
jpayne@69
|
26833 }
|
|
jpayne@69
|
26834 #endif
|
|
jpayne@69
|
26835 }
|
|
jpayne@69
|
26836
|
|
jpayne@69
|
26837 static int __pyx_tp_traverse_5pysam_9libctabix_TabixIterator(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
26838 int e;
|
|
jpayne@69
|
26839 struct __pyx_obj_5pysam_9libctabix_TabixIterator *p = (struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o;
|
|
jpayne@69
|
26840 if (p->tabixfile) {
|
|
jpayne@69
|
26841 e = (*v)(((PyObject *)p->tabixfile), a); if (e) return e;
|
|
jpayne@69
|
26842 }
|
|
jpayne@69
|
26843 if (p->encoding) {
|
|
jpayne@69
|
26844 e = (*v)(p->encoding, a); if (e) return e;
|
|
jpayne@69
|
26845 }
|
|
jpayne@69
|
26846 return 0;
|
|
jpayne@69
|
26847 }
|
|
jpayne@69
|
26848
|
|
jpayne@69
|
26849 static int __pyx_tp_clear_5pysam_9libctabix_TabixIterator(PyObject *o) {
|
|
jpayne@69
|
26850 PyObject* tmp;
|
|
jpayne@69
|
26851 struct __pyx_obj_5pysam_9libctabix_TabixIterator *p = (struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o;
|
|
jpayne@69
|
26852 tmp = ((PyObject*)p->tabixfile);
|
|
jpayne@69
|
26853 p->tabixfile = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
26854 Py_XDECREF(tmp);
|
|
jpayne@69
|
26855 tmp = ((PyObject*)p->encoding);
|
|
jpayne@69
|
26856 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
26857 Py_XDECREF(tmp);
|
|
jpayne@69
|
26858 return 0;
|
|
jpayne@69
|
26859 }
|
|
jpayne@69
|
26860
|
|
jpayne@69
|
26861 static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {
|
|
jpayne@69
|
26862 PyObject *res = __pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(self);
|
|
jpayne@69
|
26863 if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); }
|
|
jpayne@69
|
26864 return res;
|
|
jpayne@69
|
26865 }
|
|
jpayne@69
|
26866
|
|
jpayne@69
|
26867 static PyMethodDef __pyx_methods_5pysam_9libctabix_TabixIterator[] = {
|
|
jpayne@69
|
26868 {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_13TabixIterator_4__next__},
|
|
jpayne@69
|
26869 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_8__reduce_cython__},
|
|
jpayne@69
|
26870 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_10__setstate_cython__},
|
|
jpayne@69
|
26871 {0, 0, 0, 0}
|
|
jpayne@69
|
26872 };
|
|
jpayne@69
|
26873 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26874 static PyType_Slot __pyx_type_5pysam_9libctabix_TabixIterator_slots[] = {
|
|
jpayne@69
|
26875 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_TabixIterator},
|
|
jpayne@69
|
26876 {Py_tp_doc, (void *)PyDoc_STR("TabixIterator(encoding=u'ascii')\niterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n ")},
|
|
jpayne@69
|
26877 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixIterator},
|
|
jpayne@69
|
26878 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixIterator},
|
|
jpayne@69
|
26879 {Py_tp_iter, (void *)__pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__},
|
|
jpayne@69
|
26880 {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__},
|
|
jpayne@69
|
26881 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_TabixIterator},
|
|
jpayne@69
|
26882 {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__},
|
|
jpayne@69
|
26883 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_TabixIterator},
|
|
jpayne@69
|
26884 {0, 0},
|
|
jpayne@69
|
26885 };
|
|
jpayne@69
|
26886 static PyType_Spec __pyx_type_5pysam_9libctabix_TabixIterator_spec = {
|
|
jpayne@69
|
26887 "pysam.libctabix.TabixIterator",
|
|
jpayne@69
|
26888 sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIterator),
|
|
jpayne@69
|
26889 0,
|
|
jpayne@69
|
26890 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
26891 __pyx_type_5pysam_9libctabix_TabixIterator_slots,
|
|
jpayne@69
|
26892 };
|
|
jpayne@69
|
26893 #else
|
|
jpayne@69
|
26894
|
|
jpayne@69
|
26895 static PyTypeObject __pyx_type_5pysam_9libctabix_TabixIterator = {
|
|
jpayne@69
|
26896 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
26897 "pysam.libctabix.""TabixIterator", /*tp_name*/
|
|
jpayne@69
|
26898 sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIterator), /*tp_basicsize*/
|
|
jpayne@69
|
26899 0, /*tp_itemsize*/
|
|
jpayne@69
|
26900 __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator, /*tp_dealloc*/
|
|
jpayne@69
|
26901 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
26902 0, /*tp_print*/
|
|
jpayne@69
|
26903 #endif
|
|
jpayne@69
|
26904 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
26905 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
26906 #endif
|
|
jpayne@69
|
26907 0, /*tp_getattr*/
|
|
jpayne@69
|
26908 0, /*tp_setattr*/
|
|
jpayne@69
|
26909 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
26910 0, /*tp_compare*/
|
|
jpayne@69
|
26911 #endif
|
|
jpayne@69
|
26912 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
26913 0, /*tp_as_async*/
|
|
jpayne@69
|
26914 #endif
|
|
jpayne@69
|
26915 0, /*tp_repr*/
|
|
jpayne@69
|
26916 0, /*tp_as_number*/
|
|
jpayne@69
|
26917 0, /*tp_as_sequence*/
|
|
jpayne@69
|
26918 0, /*tp_as_mapping*/
|
|
jpayne@69
|
26919 0, /*tp_hash*/
|
|
jpayne@69
|
26920 0, /*tp_call*/
|
|
jpayne@69
|
26921 0, /*tp_str*/
|
|
jpayne@69
|
26922 0, /*tp_getattro*/
|
|
jpayne@69
|
26923 0, /*tp_setattro*/
|
|
jpayne@69
|
26924 0, /*tp_as_buffer*/
|
|
jpayne@69
|
26925 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
26926 PyDoc_STR("TabixIterator(encoding=u'ascii')\niterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/
|
|
jpayne@69
|
26927 __pyx_tp_traverse_5pysam_9libctabix_TabixIterator, /*tp_traverse*/
|
|
jpayne@69
|
26928 __pyx_tp_clear_5pysam_9libctabix_TabixIterator, /*tp_clear*/
|
|
jpayne@69
|
26929 0, /*tp_richcompare*/
|
|
jpayne@69
|
26930 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
26931 __pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__, /*tp_iter*/
|
|
jpayne@69
|
26932 __pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__, /*tp_iternext*/
|
|
jpayne@69
|
26933 __pyx_methods_5pysam_9libctabix_TabixIterator, /*tp_methods*/
|
|
jpayne@69
|
26934 0, /*tp_members*/
|
|
jpayne@69
|
26935 0, /*tp_getset*/
|
|
jpayne@69
|
26936 0, /*tp_base*/
|
|
jpayne@69
|
26937 0, /*tp_dict*/
|
|
jpayne@69
|
26938 0, /*tp_descr_get*/
|
|
jpayne@69
|
26939 0, /*tp_descr_set*/
|
|
jpayne@69
|
26940 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
26941 0, /*tp_dictoffset*/
|
|
jpayne@69
|
26942 #endif
|
|
jpayne@69
|
26943 __pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__, /*tp_init*/
|
|
jpayne@69
|
26944 0, /*tp_alloc*/
|
|
jpayne@69
|
26945 __pyx_tp_new_5pysam_9libctabix_TabixIterator, /*tp_new*/
|
|
jpayne@69
|
26946 0, /*tp_free*/
|
|
jpayne@69
|
26947 0, /*tp_is_gc*/
|
|
jpayne@69
|
26948 0, /*tp_bases*/
|
|
jpayne@69
|
26949 0, /*tp_mro*/
|
|
jpayne@69
|
26950 0, /*tp_cache*/
|
|
jpayne@69
|
26951 0, /*tp_subclasses*/
|
|
jpayne@69
|
26952 0, /*tp_weaklist*/
|
|
jpayne@69
|
26953 0, /*tp_del*/
|
|
jpayne@69
|
26954 0, /*tp_version_tag*/
|
|
jpayne@69
|
26955 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
26956 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26957 0, /*tp_finalize*/
|
|
jpayne@69
|
26958 #else
|
|
jpayne@69
|
26959 NULL, /*tp_finalize*/
|
|
jpayne@69
|
26960 #endif
|
|
jpayne@69
|
26961 #endif
|
|
jpayne@69
|
26962 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
26963 0, /*tp_vectorcall*/
|
|
jpayne@69
|
26964 #endif
|
|
jpayne@69
|
26965 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
26966 0, /*tp_print*/
|
|
jpayne@69
|
26967 #endif
|
|
jpayne@69
|
26968 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
26969 0, /*tp_watched*/
|
|
jpayne@69
|
26970 #endif
|
|
jpayne@69
|
26971 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
26972 0, /*tp_versions_used*/
|
|
jpayne@69
|
26973 #endif
|
|
jpayne@69
|
26974 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
26975 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
26976 #endif
|
|
jpayne@69
|
26977 };
|
|
jpayne@69
|
26978 #endif
|
|
jpayne@69
|
26979 static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed __pyx_vtable_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
26980
|
|
jpayne@69
|
26981 static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
26982 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p;
|
|
jpayne@69
|
26983 PyObject *o = __pyx_tp_new_5pysam_9libctabix_TabixIterator(t, a, k);
|
|
jpayne@69
|
26984 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
26985 p = ((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o);
|
|
jpayne@69
|
26986 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator*)__pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
26987 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
26988 return o;
|
|
jpayne@69
|
26989 }
|
|
jpayne@69
|
26990
|
|
jpayne@69
|
26991 static void __pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed(PyObject *o) {
|
|
jpayne@69
|
26992 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o;
|
|
jpayne@69
|
26993 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
26994 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
26995 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed) {
|
|
jpayne@69
|
26996 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
26997 }
|
|
jpayne@69
|
26998 }
|
|
jpayne@69
|
26999 #endif
|
|
jpayne@69
|
27000 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
27001 Py_CLEAR(p->parser);
|
|
jpayne@69
|
27002 PyObject_GC_Track(o);
|
|
jpayne@69
|
27003 __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator(o);
|
|
jpayne@69
|
27004 }
|
|
jpayne@69
|
27005
|
|
jpayne@69
|
27006 static int __pyx_tp_traverse_5pysam_9libctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
27007 int e;
|
|
jpayne@69
|
27008 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o;
|
|
jpayne@69
|
27009 e = __pyx_tp_traverse_5pysam_9libctabix_TabixIterator(o, v, a); if (e) return e;
|
|
jpayne@69
|
27010 if (p->parser) {
|
|
jpayne@69
|
27011 e = (*v)(((PyObject *)p->parser), a); if (e) return e;
|
|
jpayne@69
|
27012 }
|
|
jpayne@69
|
27013 return 0;
|
|
jpayne@69
|
27014 }
|
|
jpayne@69
|
27015
|
|
jpayne@69
|
27016 static int __pyx_tp_clear_5pysam_9libctabix_TabixIteratorParsed(PyObject *o) {
|
|
jpayne@69
|
27017 PyObject* tmp;
|
|
jpayne@69
|
27018 struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o;
|
|
jpayne@69
|
27019 __pyx_tp_clear_5pysam_9libctabix_TabixIterator(o);
|
|
jpayne@69
|
27020 tmp = ((PyObject*)p->parser);
|
|
jpayne@69
|
27021 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
27022 Py_XDECREF(tmp);
|
|
jpayne@69
|
27023 return 0;
|
|
jpayne@69
|
27024 }
|
|
jpayne@69
|
27025
|
|
jpayne@69
|
27026 static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {
|
|
jpayne@69
|
27027 PyObject *res = __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(self);
|
|
jpayne@69
|
27028 if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); }
|
|
jpayne@69
|
27029 return res;
|
|
jpayne@69
|
27030 }
|
|
jpayne@69
|
27031
|
|
jpayne@69
|
27032 static PyMethodDef __pyx_methods_5pysam_9libctabix_TabixIteratorParsed[] = {
|
|
jpayne@69
|
27033 {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_2__next__},
|
|
jpayne@69
|
27034 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__},
|
|
jpayne@69
|
27035 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__},
|
|
jpayne@69
|
27036 {0, 0, 0, 0}
|
|
jpayne@69
|
27037 };
|
|
jpayne@69
|
27038 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27039 static PyType_Slot __pyx_type_5pysam_9libctabix_TabixIteratorParsed_slots[] = {
|
|
jpayne@69
|
27040 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed},
|
|
jpayne@69
|
27041 {Py_tp_doc, (void *)PyDoc_STR("TabixIteratorParsed(Parser parser)\niterates over mapped reads in a region.\n\n The *parser* determines the encoding.\n\n Returns parsed data.\n ")},
|
|
jpayne@69
|
27042 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixIteratorParsed},
|
|
jpayne@69
|
27043 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixIteratorParsed},
|
|
jpayne@69
|
27044 {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__},
|
|
jpayne@69
|
27045 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_TabixIteratorParsed},
|
|
jpayne@69
|
27046 {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__},
|
|
jpayne@69
|
27047 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed},
|
|
jpayne@69
|
27048 {0, 0},
|
|
jpayne@69
|
27049 };
|
|
jpayne@69
|
27050 static PyType_Spec __pyx_type_5pysam_9libctabix_TabixIteratorParsed_spec = {
|
|
jpayne@69
|
27051 "pysam.libctabix.TabixIteratorParsed",
|
|
jpayne@69
|
27052 sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed),
|
|
jpayne@69
|
27053 0,
|
|
jpayne@69
|
27054 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
27055 __pyx_type_5pysam_9libctabix_TabixIteratorParsed_slots,
|
|
jpayne@69
|
27056 };
|
|
jpayne@69
|
27057 #else
|
|
jpayne@69
|
27058
|
|
jpayne@69
|
27059 static PyTypeObject __pyx_type_5pysam_9libctabix_TabixIteratorParsed = {
|
|
jpayne@69
|
27060 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
27061 "pysam.libctabix.""TabixIteratorParsed", /*tp_name*/
|
|
jpayne@69
|
27062 sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed), /*tp_basicsize*/
|
|
jpayne@69
|
27063 0, /*tp_itemsize*/
|
|
jpayne@69
|
27064 __pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed, /*tp_dealloc*/
|
|
jpayne@69
|
27065 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
27066 0, /*tp_print*/
|
|
jpayne@69
|
27067 #endif
|
|
jpayne@69
|
27068 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
27069 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
27070 #endif
|
|
jpayne@69
|
27071 0, /*tp_getattr*/
|
|
jpayne@69
|
27072 0, /*tp_setattr*/
|
|
jpayne@69
|
27073 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
27074 0, /*tp_compare*/
|
|
jpayne@69
|
27075 #endif
|
|
jpayne@69
|
27076 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
27077 0, /*tp_as_async*/
|
|
jpayne@69
|
27078 #endif
|
|
jpayne@69
|
27079 0, /*tp_repr*/
|
|
jpayne@69
|
27080 0, /*tp_as_number*/
|
|
jpayne@69
|
27081 0, /*tp_as_sequence*/
|
|
jpayne@69
|
27082 0, /*tp_as_mapping*/
|
|
jpayne@69
|
27083 0, /*tp_hash*/
|
|
jpayne@69
|
27084 0, /*tp_call*/
|
|
jpayne@69
|
27085 0, /*tp_str*/
|
|
jpayne@69
|
27086 0, /*tp_getattro*/
|
|
jpayne@69
|
27087 0, /*tp_setattro*/
|
|
jpayne@69
|
27088 0, /*tp_as_buffer*/
|
|
jpayne@69
|
27089 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
27090 PyDoc_STR("TabixIteratorParsed(Parser parser)\niterates over mapped reads in a region.\n\n The *parser* determines the encoding.\n\n Returns parsed data.\n "), /*tp_doc*/
|
|
jpayne@69
|
27091 __pyx_tp_traverse_5pysam_9libctabix_TabixIteratorParsed, /*tp_traverse*/
|
|
jpayne@69
|
27092 __pyx_tp_clear_5pysam_9libctabix_TabixIteratorParsed, /*tp_clear*/
|
|
jpayne@69
|
27093 0, /*tp_richcompare*/
|
|
jpayne@69
|
27094 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
27095 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
27096 __pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__, /*tp_iter*/
|
|
jpayne@69
|
27097 #else
|
|
jpayne@69
|
27098 0, /*tp_iter*/
|
|
jpayne@69
|
27099 #endif
|
|
jpayne@69
|
27100 __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__, /*tp_iternext*/
|
|
jpayne@69
|
27101 __pyx_methods_5pysam_9libctabix_TabixIteratorParsed, /*tp_methods*/
|
|
jpayne@69
|
27102 0, /*tp_members*/
|
|
jpayne@69
|
27103 0, /*tp_getset*/
|
|
jpayne@69
|
27104 0, /*tp_base*/
|
|
jpayne@69
|
27105 0, /*tp_dict*/
|
|
jpayne@69
|
27106 0, /*tp_descr_get*/
|
|
jpayne@69
|
27107 0, /*tp_descr_set*/
|
|
jpayne@69
|
27108 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27109 0, /*tp_dictoffset*/
|
|
jpayne@69
|
27110 #endif
|
|
jpayne@69
|
27111 __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__, /*tp_init*/
|
|
jpayne@69
|
27112 0, /*tp_alloc*/
|
|
jpayne@69
|
27113 __pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed, /*tp_new*/
|
|
jpayne@69
|
27114 0, /*tp_free*/
|
|
jpayne@69
|
27115 0, /*tp_is_gc*/
|
|
jpayne@69
|
27116 0, /*tp_bases*/
|
|
jpayne@69
|
27117 0, /*tp_mro*/
|
|
jpayne@69
|
27118 0, /*tp_cache*/
|
|
jpayne@69
|
27119 0, /*tp_subclasses*/
|
|
jpayne@69
|
27120 0, /*tp_weaklist*/
|
|
jpayne@69
|
27121 0, /*tp_del*/
|
|
jpayne@69
|
27122 0, /*tp_version_tag*/
|
|
jpayne@69
|
27123 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
27124 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27125 0, /*tp_finalize*/
|
|
jpayne@69
|
27126 #else
|
|
jpayne@69
|
27127 NULL, /*tp_finalize*/
|
|
jpayne@69
|
27128 #endif
|
|
jpayne@69
|
27129 #endif
|
|
jpayne@69
|
27130 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
27131 0, /*tp_vectorcall*/
|
|
jpayne@69
|
27132 #endif
|
|
jpayne@69
|
27133 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
27134 0, /*tp_print*/
|
|
jpayne@69
|
27135 #endif
|
|
jpayne@69
|
27136 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
27137 0, /*tp_watched*/
|
|
jpayne@69
|
27138 #endif
|
|
jpayne@69
|
27139 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
27140 0, /*tp_versions_used*/
|
|
jpayne@69
|
27141 #endif
|
|
jpayne@69
|
27142 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
27143 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
27144 #endif
|
|
jpayne@69
|
27145 };
|
|
jpayne@69
|
27146 #endif
|
|
jpayne@69
|
27147 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_vtable_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
27148
|
|
jpayne@69
|
27149 static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
|
|
jpayne@69
|
27150 struct __pyx_obj_5pysam_9libctabix_GZIterator *p;
|
|
jpayne@69
|
27151 PyObject *o;
|
|
jpayne@69
|
27152 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
27153 allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc);
|
|
jpayne@69
|
27154 o = alloc_func(t, 0);
|
|
jpayne@69
|
27155 #else
|
|
jpayne@69
|
27156 if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) {
|
|
jpayne@69
|
27157 o = (*t->tp_alloc)(t, 0);
|
|
jpayne@69
|
27158 } else {
|
|
jpayne@69
|
27159 o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
|
|
jpayne@69
|
27160 }
|
|
jpayne@69
|
27161 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
27162 #endif
|
|
jpayne@69
|
27163 p = ((struct __pyx_obj_5pysam_9libctabix_GZIterator *)o);
|
|
jpayne@69
|
27164 p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
27165 p->_filename = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
27166 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
27167 return o;
|
|
jpayne@69
|
27168 }
|
|
jpayne@69
|
27169
|
|
jpayne@69
|
27170 static void __pyx_tp_dealloc_5pysam_9libctabix_GZIterator(PyObject *o) {
|
|
jpayne@69
|
27171 struct __pyx_obj_5pysam_9libctabix_GZIterator *p = (struct __pyx_obj_5pysam_9libctabix_GZIterator *)o;
|
|
jpayne@69
|
27172 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27173 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
27174 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_GZIterator) {
|
|
jpayne@69
|
27175 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
27176 }
|
|
jpayne@69
|
27177 }
|
|
jpayne@69
|
27178 #endif
|
|
jpayne@69
|
27179 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
27180 {
|
|
jpayne@69
|
27181 PyObject *etype, *eval, *etb;
|
|
jpayne@69
|
27182 PyErr_Fetch(&etype, &eval, &etb);
|
|
jpayne@69
|
27183 __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
|
|
jpayne@69
|
27184 __pyx_pw_5pysam_9libctabix_10GZIterator_3__dealloc__(o);
|
|
jpayne@69
|
27185 __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
|
|
jpayne@69
|
27186 PyErr_Restore(etype, eval, etb);
|
|
jpayne@69
|
27187 }
|
|
jpayne@69
|
27188 Py_CLEAR(p->_filename);
|
|
jpayne@69
|
27189 Py_CLEAR(p->encoding);
|
|
jpayne@69
|
27190 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
27191 (*Py_TYPE(o)->tp_free)(o);
|
|
jpayne@69
|
27192 #else
|
|
jpayne@69
|
27193 {
|
|
jpayne@69
|
27194 freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free);
|
|
jpayne@69
|
27195 if (tp_free) tp_free(o);
|
|
jpayne@69
|
27196 }
|
|
jpayne@69
|
27197 #endif
|
|
jpayne@69
|
27198 }
|
|
jpayne@69
|
27199
|
|
jpayne@69
|
27200 static int __pyx_tp_traverse_5pysam_9libctabix_GZIterator(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
27201 int e;
|
|
jpayne@69
|
27202 struct __pyx_obj_5pysam_9libctabix_GZIterator *p = (struct __pyx_obj_5pysam_9libctabix_GZIterator *)o;
|
|
jpayne@69
|
27203 if (p->_filename) {
|
|
jpayne@69
|
27204 e = (*v)(p->_filename, a); if (e) return e;
|
|
jpayne@69
|
27205 }
|
|
jpayne@69
|
27206 if (p->encoding) {
|
|
jpayne@69
|
27207 e = (*v)(p->encoding, a); if (e) return e;
|
|
jpayne@69
|
27208 }
|
|
jpayne@69
|
27209 return 0;
|
|
jpayne@69
|
27210 }
|
|
jpayne@69
|
27211
|
|
jpayne@69
|
27212 static int __pyx_tp_clear_5pysam_9libctabix_GZIterator(PyObject *o) {
|
|
jpayne@69
|
27213 PyObject* tmp;
|
|
jpayne@69
|
27214 struct __pyx_obj_5pysam_9libctabix_GZIterator *p = (struct __pyx_obj_5pysam_9libctabix_GZIterator *)o;
|
|
jpayne@69
|
27215 tmp = ((PyObject*)p->_filename);
|
|
jpayne@69
|
27216 p->_filename = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
27217 Py_XDECREF(tmp);
|
|
jpayne@69
|
27218 tmp = ((PyObject*)p->encoding);
|
|
jpayne@69
|
27219 p->encoding = Py_None; Py_INCREF(Py_None);
|
|
jpayne@69
|
27220 Py_XDECREF(tmp);
|
|
jpayne@69
|
27221 return 0;
|
|
jpayne@69
|
27222 }
|
|
jpayne@69
|
27223
|
|
jpayne@69
|
27224 static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {
|
|
jpayne@69
|
27225 PyObject *res = __pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(self);
|
|
jpayne@69
|
27226 if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); }
|
|
jpayne@69
|
27227 return res;
|
|
jpayne@69
|
27228 }
|
|
jpayne@69
|
27229
|
|
jpayne@69
|
27230 static PyMethodDef __pyx_methods_5pysam_9libctabix_GZIterator[] = {
|
|
jpayne@69
|
27231 {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_10GZIterator_7__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_10GZIterator_6__next__},
|
|
jpayne@69
|
27232 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_8__reduce_cython__},
|
|
jpayne@69
|
27233 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_10__setstate_cython__},
|
|
jpayne@69
|
27234 {0, 0, 0, 0}
|
|
jpayne@69
|
27235 };
|
|
jpayne@69
|
27236 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27237 static PyType_Slot __pyx_type_5pysam_9libctabix_GZIterator_slots[] = {
|
|
jpayne@69
|
27238 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27239 {Py_tp_doc, (void *)PyDoc_STR("GZIterator(filename, int buffer_size=65536, encoding=u'ascii')")},
|
|
jpayne@69
|
27240 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27241 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27242 {Py_tp_iter, (void *)__pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__},
|
|
jpayne@69
|
27243 {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_10GZIterator_7__next__},
|
|
jpayne@69
|
27244 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27245 {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_10GZIterator_1__init__},
|
|
jpayne@69
|
27246 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27247 {0, 0},
|
|
jpayne@69
|
27248 };
|
|
jpayne@69
|
27249 static PyType_Spec __pyx_type_5pysam_9libctabix_GZIterator_spec = {
|
|
jpayne@69
|
27250 "pysam.libctabix.GZIterator",
|
|
jpayne@69
|
27251 sizeof(struct __pyx_obj_5pysam_9libctabix_GZIterator),
|
|
jpayne@69
|
27252 0,
|
|
jpayne@69
|
27253 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
27254 __pyx_type_5pysam_9libctabix_GZIterator_slots,
|
|
jpayne@69
|
27255 };
|
|
jpayne@69
|
27256 #else
|
|
jpayne@69
|
27257
|
|
jpayne@69
|
27258 static PyTypeObject __pyx_type_5pysam_9libctabix_GZIterator = {
|
|
jpayne@69
|
27259 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
27260 "pysam.libctabix.""GZIterator", /*tp_name*/
|
|
jpayne@69
|
27261 sizeof(struct __pyx_obj_5pysam_9libctabix_GZIterator), /*tp_basicsize*/
|
|
jpayne@69
|
27262 0, /*tp_itemsize*/
|
|
jpayne@69
|
27263 __pyx_tp_dealloc_5pysam_9libctabix_GZIterator, /*tp_dealloc*/
|
|
jpayne@69
|
27264 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
27265 0, /*tp_print*/
|
|
jpayne@69
|
27266 #endif
|
|
jpayne@69
|
27267 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
27268 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
27269 #endif
|
|
jpayne@69
|
27270 0, /*tp_getattr*/
|
|
jpayne@69
|
27271 0, /*tp_setattr*/
|
|
jpayne@69
|
27272 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
27273 0, /*tp_compare*/
|
|
jpayne@69
|
27274 #endif
|
|
jpayne@69
|
27275 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
27276 0, /*tp_as_async*/
|
|
jpayne@69
|
27277 #endif
|
|
jpayne@69
|
27278 0, /*tp_repr*/
|
|
jpayne@69
|
27279 0, /*tp_as_number*/
|
|
jpayne@69
|
27280 0, /*tp_as_sequence*/
|
|
jpayne@69
|
27281 0, /*tp_as_mapping*/
|
|
jpayne@69
|
27282 0, /*tp_hash*/
|
|
jpayne@69
|
27283 0, /*tp_call*/
|
|
jpayne@69
|
27284 0, /*tp_str*/
|
|
jpayne@69
|
27285 0, /*tp_getattro*/
|
|
jpayne@69
|
27286 0, /*tp_setattro*/
|
|
jpayne@69
|
27287 0, /*tp_as_buffer*/
|
|
jpayne@69
|
27288 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
27289 PyDoc_STR("GZIterator(filename, int buffer_size=65536, encoding=u'ascii')"), /*tp_doc*/
|
|
jpayne@69
|
27290 __pyx_tp_traverse_5pysam_9libctabix_GZIterator, /*tp_traverse*/
|
|
jpayne@69
|
27291 __pyx_tp_clear_5pysam_9libctabix_GZIterator, /*tp_clear*/
|
|
jpayne@69
|
27292 0, /*tp_richcompare*/
|
|
jpayne@69
|
27293 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
27294 __pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__, /*tp_iter*/
|
|
jpayne@69
|
27295 __pyx_pw_5pysam_9libctabix_10GZIterator_7__next__, /*tp_iternext*/
|
|
jpayne@69
|
27296 __pyx_methods_5pysam_9libctabix_GZIterator, /*tp_methods*/
|
|
jpayne@69
|
27297 0, /*tp_members*/
|
|
jpayne@69
|
27298 0, /*tp_getset*/
|
|
jpayne@69
|
27299 0, /*tp_base*/
|
|
jpayne@69
|
27300 0, /*tp_dict*/
|
|
jpayne@69
|
27301 0, /*tp_descr_get*/
|
|
jpayne@69
|
27302 0, /*tp_descr_set*/
|
|
jpayne@69
|
27303 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27304 0, /*tp_dictoffset*/
|
|
jpayne@69
|
27305 #endif
|
|
jpayne@69
|
27306 __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__, /*tp_init*/
|
|
jpayne@69
|
27307 0, /*tp_alloc*/
|
|
jpayne@69
|
27308 __pyx_tp_new_5pysam_9libctabix_GZIterator, /*tp_new*/
|
|
jpayne@69
|
27309 0, /*tp_free*/
|
|
jpayne@69
|
27310 0, /*tp_is_gc*/
|
|
jpayne@69
|
27311 0, /*tp_bases*/
|
|
jpayne@69
|
27312 0, /*tp_mro*/
|
|
jpayne@69
|
27313 0, /*tp_cache*/
|
|
jpayne@69
|
27314 0, /*tp_subclasses*/
|
|
jpayne@69
|
27315 0, /*tp_weaklist*/
|
|
jpayne@69
|
27316 0, /*tp_del*/
|
|
jpayne@69
|
27317 0, /*tp_version_tag*/
|
|
jpayne@69
|
27318 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
27319 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27320 0, /*tp_finalize*/
|
|
jpayne@69
|
27321 #else
|
|
jpayne@69
|
27322 NULL, /*tp_finalize*/
|
|
jpayne@69
|
27323 #endif
|
|
jpayne@69
|
27324 #endif
|
|
jpayne@69
|
27325 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
27326 0, /*tp_vectorcall*/
|
|
jpayne@69
|
27327 #endif
|
|
jpayne@69
|
27328 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
27329 0, /*tp_print*/
|
|
jpayne@69
|
27330 #endif
|
|
jpayne@69
|
27331 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
27332 0, /*tp_watched*/
|
|
jpayne@69
|
27333 #endif
|
|
jpayne@69
|
27334 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
27335 0, /*tp_versions_used*/
|
|
jpayne@69
|
27336 #endif
|
|
jpayne@69
|
27337 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
27338 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
27339 #endif
|
|
jpayne@69
|
27340 };
|
|
jpayne@69
|
27341 #endif
|
|
jpayne@69
|
27342 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead __pyx_vtable_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
27343
|
|
jpayne@69
|
27344 static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorHead(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
27345 struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *p;
|
|
jpayne@69
|
27346 PyObject *o = __pyx_tp_new_5pysam_9libctabix_GZIterator(t, a, k);
|
|
jpayne@69
|
27347 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
27348 p = ((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)o);
|
|
jpayne@69
|
27349 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator*)__pyx_vtabptr_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
27350 return o;
|
|
jpayne@69
|
27351 }
|
|
jpayne@69
|
27352
|
|
jpayne@69
|
27353 static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {
|
|
jpayne@69
|
27354 PyObject *res = __pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(self);
|
|
jpayne@69
|
27355 if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); }
|
|
jpayne@69
|
27356 return res;
|
|
jpayne@69
|
27357 }
|
|
jpayne@69
|
27358
|
|
jpayne@69
|
27359 static PyMethodDef __pyx_methods_5pysam_9libctabix_GZIteratorHead[] = {
|
|
jpayne@69
|
27360 {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_14GZIteratorHead___next__},
|
|
jpayne@69
|
27361 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__},
|
|
jpayne@69
|
27362 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__},
|
|
jpayne@69
|
27363 {0, 0, 0, 0}
|
|
jpayne@69
|
27364 };
|
|
jpayne@69
|
27365 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27366 static PyType_Slot __pyx_type_5pysam_9libctabix_GZIteratorHead_slots[] = {
|
|
jpayne@69
|
27367 {Py_tp_doc, (void *)PyDoc_STR("iterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n ")},
|
|
jpayne@69
|
27368 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27369 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_GZIterator},
|
|
jpayne@69
|
27370 {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__},
|
|
jpayne@69
|
27371 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_GZIteratorHead},
|
|
jpayne@69
|
27372 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_GZIteratorHead},
|
|
jpayne@69
|
27373 {0, 0},
|
|
jpayne@69
|
27374 };
|
|
jpayne@69
|
27375 static PyType_Spec __pyx_type_5pysam_9libctabix_GZIteratorHead_spec = {
|
|
jpayne@69
|
27376 "pysam.libctabix.GZIteratorHead",
|
|
jpayne@69
|
27377 sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead),
|
|
jpayne@69
|
27378 0,
|
|
jpayne@69
|
27379 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
27380 __pyx_type_5pysam_9libctabix_GZIteratorHead_slots,
|
|
jpayne@69
|
27381 };
|
|
jpayne@69
|
27382 #else
|
|
jpayne@69
|
27383
|
|
jpayne@69
|
27384 static PyTypeObject __pyx_type_5pysam_9libctabix_GZIteratorHead = {
|
|
jpayne@69
|
27385 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
27386 "pysam.libctabix.""GZIteratorHead", /*tp_name*/
|
|
jpayne@69
|
27387 sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead), /*tp_basicsize*/
|
|
jpayne@69
|
27388 0, /*tp_itemsize*/
|
|
jpayne@69
|
27389 __pyx_tp_dealloc_5pysam_9libctabix_GZIterator, /*tp_dealloc*/
|
|
jpayne@69
|
27390 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
27391 0, /*tp_print*/
|
|
jpayne@69
|
27392 #endif
|
|
jpayne@69
|
27393 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
27394 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
27395 #endif
|
|
jpayne@69
|
27396 0, /*tp_getattr*/
|
|
jpayne@69
|
27397 0, /*tp_setattr*/
|
|
jpayne@69
|
27398 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
27399 0, /*tp_compare*/
|
|
jpayne@69
|
27400 #endif
|
|
jpayne@69
|
27401 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
27402 0, /*tp_as_async*/
|
|
jpayne@69
|
27403 #endif
|
|
jpayne@69
|
27404 0, /*tp_repr*/
|
|
jpayne@69
|
27405 0, /*tp_as_number*/
|
|
jpayne@69
|
27406 0, /*tp_as_sequence*/
|
|
jpayne@69
|
27407 0, /*tp_as_mapping*/
|
|
jpayne@69
|
27408 0, /*tp_hash*/
|
|
jpayne@69
|
27409 0, /*tp_call*/
|
|
jpayne@69
|
27410 0, /*tp_str*/
|
|
jpayne@69
|
27411 0, /*tp_getattro*/
|
|
jpayne@69
|
27412 0, /*tp_setattro*/
|
|
jpayne@69
|
27413 0, /*tp_as_buffer*/
|
|
jpayne@69
|
27414 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
27415 PyDoc_STR("iterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n "), /*tp_doc*/
|
|
jpayne@69
|
27416 __pyx_tp_traverse_5pysam_9libctabix_GZIterator, /*tp_traverse*/
|
|
jpayne@69
|
27417 __pyx_tp_clear_5pysam_9libctabix_GZIterator, /*tp_clear*/
|
|
jpayne@69
|
27418 0, /*tp_richcompare*/
|
|
jpayne@69
|
27419 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
27420 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
27421 __pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__, /*tp_iter*/
|
|
jpayne@69
|
27422 #else
|
|
jpayne@69
|
27423 0, /*tp_iter*/
|
|
jpayne@69
|
27424 #endif
|
|
jpayne@69
|
27425 __pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__, /*tp_iternext*/
|
|
jpayne@69
|
27426 __pyx_methods_5pysam_9libctabix_GZIteratorHead, /*tp_methods*/
|
|
jpayne@69
|
27427 0, /*tp_members*/
|
|
jpayne@69
|
27428 0, /*tp_getset*/
|
|
jpayne@69
|
27429 0, /*tp_base*/
|
|
jpayne@69
|
27430 0, /*tp_dict*/
|
|
jpayne@69
|
27431 0, /*tp_descr_get*/
|
|
jpayne@69
|
27432 0, /*tp_descr_set*/
|
|
jpayne@69
|
27433 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27434 0, /*tp_dictoffset*/
|
|
jpayne@69
|
27435 #endif
|
|
jpayne@69
|
27436 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
27437 __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__, /*tp_init*/
|
|
jpayne@69
|
27438 #else
|
|
jpayne@69
|
27439 0, /*tp_init*/
|
|
jpayne@69
|
27440 #endif
|
|
jpayne@69
|
27441 0, /*tp_alloc*/
|
|
jpayne@69
|
27442 __pyx_tp_new_5pysam_9libctabix_GZIteratorHead, /*tp_new*/
|
|
jpayne@69
|
27443 0, /*tp_free*/
|
|
jpayne@69
|
27444 0, /*tp_is_gc*/
|
|
jpayne@69
|
27445 0, /*tp_bases*/
|
|
jpayne@69
|
27446 0, /*tp_mro*/
|
|
jpayne@69
|
27447 0, /*tp_cache*/
|
|
jpayne@69
|
27448 0, /*tp_subclasses*/
|
|
jpayne@69
|
27449 0, /*tp_weaklist*/
|
|
jpayne@69
|
27450 0, /*tp_del*/
|
|
jpayne@69
|
27451 0, /*tp_version_tag*/
|
|
jpayne@69
|
27452 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
27453 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27454 0, /*tp_finalize*/
|
|
jpayne@69
|
27455 #else
|
|
jpayne@69
|
27456 NULL, /*tp_finalize*/
|
|
jpayne@69
|
27457 #endif
|
|
jpayne@69
|
27458 #endif
|
|
jpayne@69
|
27459 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
27460 0, /*tp_vectorcall*/
|
|
jpayne@69
|
27461 #endif
|
|
jpayne@69
|
27462 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
27463 0, /*tp_print*/
|
|
jpayne@69
|
27464 #endif
|
|
jpayne@69
|
27465 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
27466 0, /*tp_watched*/
|
|
jpayne@69
|
27467 #endif
|
|
jpayne@69
|
27468 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
27469 0, /*tp_versions_used*/
|
|
jpayne@69
|
27470 #endif
|
|
jpayne@69
|
27471 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
27472 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
27473 #endif
|
|
jpayne@69
|
27474 };
|
|
jpayne@69
|
27475 #endif
|
|
jpayne@69
|
27476 static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed __pyx_vtable_5pysam_9libctabix_GZIteratorParsed;
|
|
jpayne@69
|
27477
|
|
jpayne@69
|
27478 static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
27479 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p;
|
|
jpayne@69
|
27480 PyObject *o = __pyx_tp_new_5pysam_9libctabix_GZIterator(t, a, k);
|
|
jpayne@69
|
27481 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
27482 p = ((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o);
|
|
jpayne@69
|
27483 p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator*)__pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed;
|
|
jpayne@69
|
27484 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
27485 return o;
|
|
jpayne@69
|
27486 }
|
|
jpayne@69
|
27487
|
|
jpayne@69
|
27488 static void __pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed(PyObject *o) {
|
|
jpayne@69
|
27489 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o;
|
|
jpayne@69
|
27490 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27491 if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) {
|
|
jpayne@69
|
27492 if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed) {
|
|
jpayne@69
|
27493 if (PyObject_CallFinalizerFromDealloc(o)) return;
|
|
jpayne@69
|
27494 }
|
|
jpayne@69
|
27495 }
|
|
jpayne@69
|
27496 #endif
|
|
jpayne@69
|
27497 PyObject_GC_UnTrack(o);
|
|
jpayne@69
|
27498 Py_CLEAR(p->parser);
|
|
jpayne@69
|
27499 PyObject_GC_Track(o);
|
|
jpayne@69
|
27500 __pyx_tp_dealloc_5pysam_9libctabix_GZIterator(o);
|
|
jpayne@69
|
27501 }
|
|
jpayne@69
|
27502
|
|
jpayne@69
|
27503 static int __pyx_tp_traverse_5pysam_9libctabix_GZIteratorParsed(PyObject *o, visitproc v, void *a) {
|
|
jpayne@69
|
27504 int e;
|
|
jpayne@69
|
27505 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o;
|
|
jpayne@69
|
27506 e = __pyx_tp_traverse_5pysam_9libctabix_GZIterator(o, v, a); if (e) return e;
|
|
jpayne@69
|
27507 if (p->parser) {
|
|
jpayne@69
|
27508 e = (*v)(((PyObject *)p->parser), a); if (e) return e;
|
|
jpayne@69
|
27509 }
|
|
jpayne@69
|
27510 return 0;
|
|
jpayne@69
|
27511 }
|
|
jpayne@69
|
27512
|
|
jpayne@69
|
27513 static int __pyx_tp_clear_5pysam_9libctabix_GZIteratorParsed(PyObject *o) {
|
|
jpayne@69
|
27514 PyObject* tmp;
|
|
jpayne@69
|
27515 struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o;
|
|
jpayne@69
|
27516 __pyx_tp_clear_5pysam_9libctabix_GZIterator(o);
|
|
jpayne@69
|
27517 tmp = ((PyObject*)p->parser);
|
|
jpayne@69
|
27518 p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None);
|
|
jpayne@69
|
27519 Py_XDECREF(tmp);
|
|
jpayne@69
|
27520 return 0;
|
|
jpayne@69
|
27521 }
|
|
jpayne@69
|
27522
|
|
jpayne@69
|
27523 static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {
|
|
jpayne@69
|
27524 PyObject *res = __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(self);
|
|
jpayne@69
|
27525 if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); }
|
|
jpayne@69
|
27526 return res;
|
|
jpayne@69
|
27527 }
|
|
jpayne@69
|
27528
|
|
jpayne@69
|
27529 static PyMethodDef __pyx_methods_5pysam_9libctabix_GZIteratorParsed[] = {
|
|
jpayne@69
|
27530 {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_2__next__},
|
|
jpayne@69
|
27531 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__},
|
|
jpayne@69
|
27532 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__},
|
|
jpayne@69
|
27533 {0, 0, 0, 0}
|
|
jpayne@69
|
27534 };
|
|
jpayne@69
|
27535 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27536 static PyType_Slot __pyx_type_5pysam_9libctabix_GZIteratorParsed_slots[] = {
|
|
jpayne@69
|
27537 {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed},
|
|
jpayne@69
|
27538 {Py_tp_doc, (void *)PyDoc_STR("GZIteratorParsed(parser)\niterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n ")},
|
|
jpayne@69
|
27539 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_GZIteratorParsed},
|
|
jpayne@69
|
27540 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_GZIteratorParsed},
|
|
jpayne@69
|
27541 {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__},
|
|
jpayne@69
|
27542 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_GZIteratorParsed},
|
|
jpayne@69
|
27543 {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__},
|
|
jpayne@69
|
27544 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_GZIteratorParsed},
|
|
jpayne@69
|
27545 {0, 0},
|
|
jpayne@69
|
27546 };
|
|
jpayne@69
|
27547 static PyType_Spec __pyx_type_5pysam_9libctabix_GZIteratorParsed_spec = {
|
|
jpayne@69
|
27548 "pysam.libctabix.GZIteratorParsed",
|
|
jpayne@69
|
27549 sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed),
|
|
jpayne@69
|
27550 0,
|
|
jpayne@69
|
27551 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC,
|
|
jpayne@69
|
27552 __pyx_type_5pysam_9libctabix_GZIteratorParsed_slots,
|
|
jpayne@69
|
27553 };
|
|
jpayne@69
|
27554 #else
|
|
jpayne@69
|
27555
|
|
jpayne@69
|
27556 static PyTypeObject __pyx_type_5pysam_9libctabix_GZIteratorParsed = {
|
|
jpayne@69
|
27557 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
27558 "pysam.libctabix.""GZIteratorParsed", /*tp_name*/
|
|
jpayne@69
|
27559 sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed), /*tp_basicsize*/
|
|
jpayne@69
|
27560 0, /*tp_itemsize*/
|
|
jpayne@69
|
27561 __pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed, /*tp_dealloc*/
|
|
jpayne@69
|
27562 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
27563 0, /*tp_print*/
|
|
jpayne@69
|
27564 #endif
|
|
jpayne@69
|
27565 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
27566 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
27567 #endif
|
|
jpayne@69
|
27568 0, /*tp_getattr*/
|
|
jpayne@69
|
27569 0, /*tp_setattr*/
|
|
jpayne@69
|
27570 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
27571 0, /*tp_compare*/
|
|
jpayne@69
|
27572 #endif
|
|
jpayne@69
|
27573 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
27574 0, /*tp_as_async*/
|
|
jpayne@69
|
27575 #endif
|
|
jpayne@69
|
27576 0, /*tp_repr*/
|
|
jpayne@69
|
27577 0, /*tp_as_number*/
|
|
jpayne@69
|
27578 0, /*tp_as_sequence*/
|
|
jpayne@69
|
27579 0, /*tp_as_mapping*/
|
|
jpayne@69
|
27580 0, /*tp_hash*/
|
|
jpayne@69
|
27581 0, /*tp_call*/
|
|
jpayne@69
|
27582 0, /*tp_str*/
|
|
jpayne@69
|
27583 0, /*tp_getattro*/
|
|
jpayne@69
|
27584 0, /*tp_setattro*/
|
|
jpayne@69
|
27585 0, /*tp_as_buffer*/
|
|
jpayne@69
|
27586 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
|
|
jpayne@69
|
27587 PyDoc_STR("GZIteratorParsed(parser)\niterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n "), /*tp_doc*/
|
|
jpayne@69
|
27588 __pyx_tp_traverse_5pysam_9libctabix_GZIteratorParsed, /*tp_traverse*/
|
|
jpayne@69
|
27589 __pyx_tp_clear_5pysam_9libctabix_GZIteratorParsed, /*tp_clear*/
|
|
jpayne@69
|
27590 0, /*tp_richcompare*/
|
|
jpayne@69
|
27591 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
27592 #if CYTHON_COMPILING_IN_PYPY || 0
|
|
jpayne@69
|
27593 __pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__, /*tp_iter*/
|
|
jpayne@69
|
27594 #else
|
|
jpayne@69
|
27595 0, /*tp_iter*/
|
|
jpayne@69
|
27596 #endif
|
|
jpayne@69
|
27597 __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__, /*tp_iternext*/
|
|
jpayne@69
|
27598 __pyx_methods_5pysam_9libctabix_GZIteratorParsed, /*tp_methods*/
|
|
jpayne@69
|
27599 0, /*tp_members*/
|
|
jpayne@69
|
27600 0, /*tp_getset*/
|
|
jpayne@69
|
27601 0, /*tp_base*/
|
|
jpayne@69
|
27602 0, /*tp_dict*/
|
|
jpayne@69
|
27603 0, /*tp_descr_get*/
|
|
jpayne@69
|
27604 0, /*tp_descr_set*/
|
|
jpayne@69
|
27605 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27606 0, /*tp_dictoffset*/
|
|
jpayne@69
|
27607 #endif
|
|
jpayne@69
|
27608 __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__, /*tp_init*/
|
|
jpayne@69
|
27609 0, /*tp_alloc*/
|
|
jpayne@69
|
27610 __pyx_tp_new_5pysam_9libctabix_GZIteratorParsed, /*tp_new*/
|
|
jpayne@69
|
27611 0, /*tp_free*/
|
|
jpayne@69
|
27612 0, /*tp_is_gc*/
|
|
jpayne@69
|
27613 0, /*tp_bases*/
|
|
jpayne@69
|
27614 0, /*tp_mro*/
|
|
jpayne@69
|
27615 0, /*tp_cache*/
|
|
jpayne@69
|
27616 0, /*tp_subclasses*/
|
|
jpayne@69
|
27617 0, /*tp_weaklist*/
|
|
jpayne@69
|
27618 0, /*tp_del*/
|
|
jpayne@69
|
27619 0, /*tp_version_tag*/
|
|
jpayne@69
|
27620 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
27621 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27622 0, /*tp_finalize*/
|
|
jpayne@69
|
27623 #else
|
|
jpayne@69
|
27624 NULL, /*tp_finalize*/
|
|
jpayne@69
|
27625 #endif
|
|
jpayne@69
|
27626 #endif
|
|
jpayne@69
|
27627 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
27628 0, /*tp_vectorcall*/
|
|
jpayne@69
|
27629 #endif
|
|
jpayne@69
|
27630 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
27631 0, /*tp_print*/
|
|
jpayne@69
|
27632 #endif
|
|
jpayne@69
|
27633 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
27634 0, /*tp_watched*/
|
|
jpayne@69
|
27635 #endif
|
|
jpayne@69
|
27636 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
27637 0, /*tp_versions_used*/
|
|
jpayne@69
|
27638 #endif
|
|
jpayne@69
|
27639 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
27640 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
27641 #endif
|
|
jpayne@69
|
27642 };
|
|
jpayne@69
|
27643 #endif
|
|
jpayne@69
|
27644 static struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile __pyx_vtable_5pysam_9libctabix_Tabixfile;
|
|
jpayne@69
|
27645
|
|
jpayne@69
|
27646 static PyObject *__pyx_tp_new_5pysam_9libctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) {
|
|
jpayne@69
|
27647 struct __pyx_obj_5pysam_9libctabix_Tabixfile *p;
|
|
jpayne@69
|
27648 PyObject *o = __pyx_tp_new_5pysam_9libctabix_TabixFile(t, a, k);
|
|
jpayne@69
|
27649 if (unlikely(!o)) return 0;
|
|
jpayne@69
|
27650 p = ((struct __pyx_obj_5pysam_9libctabix_Tabixfile *)o);
|
|
jpayne@69
|
27651 p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__pyx_vtabptr_5pysam_9libctabix_Tabixfile;
|
|
jpayne@69
|
27652 return o;
|
|
jpayne@69
|
27653 }
|
|
jpayne@69
|
27654
|
|
jpayne@69
|
27655 static PyMethodDef __pyx_methods_5pysam_9libctabix_Tabixfile[] = {
|
|
jpayne@69
|
27656 {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile___reduce_cython__},
|
|
jpayne@69
|
27657 {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile_2__setstate_cython__},
|
|
jpayne@69
|
27658 {0, 0, 0, 0}
|
|
jpayne@69
|
27659 };
|
|
jpayne@69
|
27660 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27661 static PyType_Slot __pyx_type_5pysam_9libctabix_Tabixfile_slots[] = {
|
|
jpayne@69
|
27662 {Py_tp_doc, (void *)PyDoc_STR("Tabixfile is deprecated: use TabixFile instead")},
|
|
jpayne@69
|
27663 {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
27664 {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixFile},
|
|
jpayne@69
|
27665 {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_Tabixfile},
|
|
jpayne@69
|
27666 {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_Tabixfile},
|
|
jpayne@69
|
27667 {0, 0},
|
|
jpayne@69
|
27668 };
|
|
jpayne@69
|
27669 static PyType_Spec __pyx_type_5pysam_9libctabix_Tabixfile_spec = {
|
|
jpayne@69
|
27670 "pysam.libctabix.Tabixfile",
|
|
jpayne@69
|
27671 sizeof(struct __pyx_obj_5pysam_9libctabix_Tabixfile),
|
|
jpayne@69
|
27672 0,
|
|
jpayne@69
|
27673 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE,
|
|
jpayne@69
|
27674 __pyx_type_5pysam_9libctabix_Tabixfile_slots,
|
|
jpayne@69
|
27675 };
|
|
jpayne@69
|
27676 #else
|
|
jpayne@69
|
27677
|
|
jpayne@69
|
27678 static PyTypeObject __pyx_type_5pysam_9libctabix_Tabixfile = {
|
|
jpayne@69
|
27679 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
27680 "pysam.libctabix.""Tabixfile", /*tp_name*/
|
|
jpayne@69
|
27681 sizeof(struct __pyx_obj_5pysam_9libctabix_Tabixfile), /*tp_basicsize*/
|
|
jpayne@69
|
27682 0, /*tp_itemsize*/
|
|
jpayne@69
|
27683 __pyx_tp_dealloc_5pysam_9libctabix_TabixFile, /*tp_dealloc*/
|
|
jpayne@69
|
27684 #if PY_VERSION_HEX < 0x030800b4
|
|
jpayne@69
|
27685 0, /*tp_print*/
|
|
jpayne@69
|
27686 #endif
|
|
jpayne@69
|
27687 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
27688 0, /*tp_vectorcall_offset*/
|
|
jpayne@69
|
27689 #endif
|
|
jpayne@69
|
27690 0, /*tp_getattr*/
|
|
jpayne@69
|
27691 0, /*tp_setattr*/
|
|
jpayne@69
|
27692 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
27693 0, /*tp_compare*/
|
|
jpayne@69
|
27694 #endif
|
|
jpayne@69
|
27695 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
27696 0, /*tp_as_async*/
|
|
jpayne@69
|
27697 #endif
|
|
jpayne@69
|
27698 0, /*tp_repr*/
|
|
jpayne@69
|
27699 0, /*tp_as_number*/
|
|
jpayne@69
|
27700 0, /*tp_as_sequence*/
|
|
jpayne@69
|
27701 0, /*tp_as_mapping*/
|
|
jpayne@69
|
27702 0, /*tp_hash*/
|
|
jpayne@69
|
27703 0, /*tp_call*/
|
|
jpayne@69
|
27704 0, /*tp_str*/
|
|
jpayne@69
|
27705 0, /*tp_getattro*/
|
|
jpayne@69
|
27706 0, /*tp_setattro*/
|
|
jpayne@69
|
27707 0, /*tp_as_buffer*/
|
|
jpayne@69
|
27708 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/
|
|
jpayne@69
|
27709 PyDoc_STR("Tabixfile is deprecated: use TabixFile instead"), /*tp_doc*/
|
|
jpayne@69
|
27710 __pyx_tp_traverse_5pysam_9libctabix_TabixFile, /*tp_traverse*/
|
|
jpayne@69
|
27711 __pyx_tp_clear_5pysam_9libctabix_TabixFile, /*tp_clear*/
|
|
jpayne@69
|
27712 0, /*tp_richcompare*/
|
|
jpayne@69
|
27713 0, /*tp_weaklistoffset*/
|
|
jpayne@69
|
27714 0, /*tp_iter*/
|
|
jpayne@69
|
27715 0, /*tp_iternext*/
|
|
jpayne@69
|
27716 __pyx_methods_5pysam_9libctabix_Tabixfile, /*tp_methods*/
|
|
jpayne@69
|
27717 0, /*tp_members*/
|
|
jpayne@69
|
27718 0, /*tp_getset*/
|
|
jpayne@69
|
27719 0, /*tp_base*/
|
|
jpayne@69
|
27720 0, /*tp_dict*/
|
|
jpayne@69
|
27721 0, /*tp_descr_get*/
|
|
jpayne@69
|
27722 0, /*tp_descr_set*/
|
|
jpayne@69
|
27723 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
27724 0, /*tp_dictoffset*/
|
|
jpayne@69
|
27725 #endif
|
|
jpayne@69
|
27726 0, /*tp_init*/
|
|
jpayne@69
|
27727 0, /*tp_alloc*/
|
|
jpayne@69
|
27728 __pyx_tp_new_5pysam_9libctabix_Tabixfile, /*tp_new*/
|
|
jpayne@69
|
27729 0, /*tp_free*/
|
|
jpayne@69
|
27730 0, /*tp_is_gc*/
|
|
jpayne@69
|
27731 0, /*tp_bases*/
|
|
jpayne@69
|
27732 0, /*tp_mro*/
|
|
jpayne@69
|
27733 0, /*tp_cache*/
|
|
jpayne@69
|
27734 0, /*tp_subclasses*/
|
|
jpayne@69
|
27735 0, /*tp_weaklist*/
|
|
jpayne@69
|
27736 0, /*tp_del*/
|
|
jpayne@69
|
27737 0, /*tp_version_tag*/
|
|
jpayne@69
|
27738 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
27739 #if CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
27740 0, /*tp_finalize*/
|
|
jpayne@69
|
27741 #else
|
|
jpayne@69
|
27742 NULL, /*tp_finalize*/
|
|
jpayne@69
|
27743 #endif
|
|
jpayne@69
|
27744 #endif
|
|
jpayne@69
|
27745 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
27746 0, /*tp_vectorcall*/
|
|
jpayne@69
|
27747 #endif
|
|
jpayne@69
|
27748 #if __PYX_NEED_TP_PRINT_SLOT == 1
|
|
jpayne@69
|
27749 0, /*tp_print*/
|
|
jpayne@69
|
27750 #endif
|
|
jpayne@69
|
27751 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
27752 0, /*tp_watched*/
|
|
jpayne@69
|
27753 #endif
|
|
jpayne@69
|
27754 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
27755 0, /*tp_versions_used*/
|
|
jpayne@69
|
27756 #endif
|
|
jpayne@69
|
27757 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
27758 0, /*tp_pypy_flags*/
|
|
jpayne@69
|
27759 #endif
|
|
jpayne@69
|
27760 };
|
|
jpayne@69
|
27761 #endif
|
|
jpayne@69
|
27762
|
|
jpayne@69
|
27763 static PyMethodDef __pyx_methods[] = {
|
|
jpayne@69
|
27764 {0, 0, 0, 0}
|
|
jpayne@69
|
27765 };
|
|
jpayne@69
|
27766 #ifndef CYTHON_SMALL_CODE
|
|
jpayne@69
|
27767 #if defined(__clang__)
|
|
jpayne@69
|
27768 #define CYTHON_SMALL_CODE
|
|
jpayne@69
|
27769 #elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))
|
|
jpayne@69
|
27770 #define CYTHON_SMALL_CODE __attribute__((cold))
|
|
jpayne@69
|
27771 #else
|
|
jpayne@69
|
27772 #define CYTHON_SMALL_CODE
|
|
jpayne@69
|
27773 #endif
|
|
jpayne@69
|
27774 #endif
|
|
jpayne@69
|
27775 /* #### Code section: pystring_table ### */
|
|
jpayne@69
|
27776
|
|
jpayne@69
|
27777 static int __Pyx_CreateStringTabAndInitStrings(void) {
|
|
jpayne@69
|
27778 __Pyx_StringTabEntry __pyx_string_tab[] = {
|
|
jpayne@69
|
27779 {&__pyx_n_s_AssertionError, __pyx_k_AssertionError, sizeof(__pyx_k_AssertionError), 0, 0, 1, 1},
|
|
jpayne@69
|
27780 {&__pyx_kp_u_Could_not_open_file, __pyx_k_Could_not_open_file, sizeof(__pyx_k_Could_not_open_file), 0, 1, 0, 0},
|
|
jpayne@69
|
27781 {&__pyx_n_s_EmptyIterator, __pyx_k_EmptyIterator, sizeof(__pyx_k_EmptyIterator), 0, 0, 1, 1},
|
|
jpayne@69
|
27782 {&__pyx_n_s_EmptyIterator___iter, __pyx_k_EmptyIterator___iter, sizeof(__pyx_k_EmptyIterator___iter), 0, 0, 1, 1},
|
|
jpayne@69
|
27783 {&__pyx_n_s_EmptyIterator___next, __pyx_k_EmptyIterator___next, sizeof(__pyx_k_EmptyIterator___next), 0, 0, 1, 1},
|
|
jpayne@69
|
27784 {&__pyx_kp_u_Filename_s_already_exists_use_fo, __pyx_k_Filename_s_already_exists_use_fo, sizeof(__pyx_k_Filename_s_already_exists_use_fo), 0, 1, 0, 0},
|
|
jpayne@69
|
27785 {&__pyx_n_s_GZIterator, __pyx_k_GZIterator, sizeof(__pyx_k_GZIterator), 0, 0, 1, 1},
|
|
jpayne@69
|
27786 {&__pyx_n_u_GZIterator, __pyx_k_GZIterator, sizeof(__pyx_k_GZIterator), 0, 1, 0, 1},
|
|
jpayne@69
|
27787 {&__pyx_n_s_GZIteratorHead, __pyx_k_GZIteratorHead, sizeof(__pyx_k_GZIteratorHead), 0, 0, 1, 1},
|
|
jpayne@69
|
27788 {&__pyx_n_u_GZIteratorHead, __pyx_k_GZIteratorHead, sizeof(__pyx_k_GZIteratorHead), 0, 1, 0, 1},
|
|
jpayne@69
|
27789 {&__pyx_n_s_GZIteratorHead___reduce_cython, __pyx_k_GZIteratorHead___reduce_cython, sizeof(__pyx_k_GZIteratorHead___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27790 {&__pyx_n_s_GZIteratorHead___setstate_cython, __pyx_k_GZIteratorHead___setstate_cython, sizeof(__pyx_k_GZIteratorHead___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27791 {&__pyx_n_s_GZIteratorParsed, __pyx_k_GZIteratorParsed, sizeof(__pyx_k_GZIteratorParsed), 0, 0, 1, 1},
|
|
jpayne@69
|
27792 {&__pyx_n_s_GZIteratorParsed___reduce_cython, __pyx_k_GZIteratorParsed___reduce_cython, sizeof(__pyx_k_GZIteratorParsed___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27793 {&__pyx_n_s_GZIteratorParsed___setstate_cyth, __pyx_k_GZIteratorParsed___setstate_cyth, sizeof(__pyx_k_GZIteratorParsed___setstate_cyth), 0, 0, 1, 1},
|
|
jpayne@69
|
27794 {&__pyx_n_s_GZIterator___reduce_cython, __pyx_k_GZIterator___reduce_cython, sizeof(__pyx_k_GZIterator___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27795 {&__pyx_n_s_GZIterator___setstate_cython, __pyx_k_GZIterator___setstate_cython, sizeof(__pyx_k_GZIterator___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27796 {&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1},
|
|
jpayne@69
|
27797 {&__pyx_kp_u_I_O_operation_on_closed_file, __pyx_k_I_O_operation_on_closed_file, sizeof(__pyx_k_I_O_operation_on_closed_file), 0, 1, 0, 0},
|
|
jpayne@69
|
27798 {&__pyx_kp_u_I_O_operation_on_closed_file_2, __pyx_k_I_O_operation_on_closed_file_2, sizeof(__pyx_k_I_O_operation_on_closed_file_2), 0, 1, 0, 0},
|
|
jpayne@69
|
27799 {&__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_k_Incompatible_checksums_0x_x_vs_0, sizeof(__pyx_k_Incompatible_checksums_0x_x_vs_0), 0, 0, 1, 0},
|
|
jpayne@69
|
27800 {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1},
|
|
jpayne@69
|
27801 {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1},
|
|
jpayne@69
|
27802 {&__pyx_kp_u_No_such_file_or_directory_s, __pyx_k_No_such_file_or_directory_s, sizeof(__pyx_k_No_such_file_or_directory_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27803 {&__pyx_n_s_NotImplementedError, __pyx_k_NotImplementedError, sizeof(__pyx_k_NotImplementedError), 0, 0, 1, 1},
|
|
jpayne@69
|
27804 {&__pyx_n_s_OSError, __pyx_k_OSError, sizeof(__pyx_k_OSError), 0, 0, 1, 1},
|
|
jpayne@69
|
27805 {&__pyx_n_s_O_RDONLY, __pyx_k_O_RDONLY, sizeof(__pyx_k_O_RDONLY), 0, 0, 1, 1},
|
|
jpayne@69
|
27806 {&__pyx_n_s_Parser, __pyx_k_Parser, sizeof(__pyx_k_Parser), 0, 0, 1, 1},
|
|
jpayne@69
|
27807 {&__pyx_n_s_Parser___reduce_cython, __pyx_k_Parser___reduce_cython, sizeof(__pyx_k_Parser___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27808 {&__pyx_n_s_Parser___setstate_cython, __pyx_k_Parser___setstate_cython, sizeof(__pyx_k_Parser___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27809 {&__pyx_n_s_Parser_get_encoding, __pyx_k_Parser_get_encoding, sizeof(__pyx_k_Parser_get_encoding), 0, 0, 1, 1},
|
|
jpayne@69
|
27810 {&__pyx_n_s_Parser_set_encoding, __pyx_k_Parser_set_encoding, sizeof(__pyx_k_Parser_set_encoding), 0, 0, 1, 1},
|
|
jpayne@69
|
27811 {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1},
|
|
jpayne@69
|
27812 {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1},
|
|
jpayne@69
|
27813 {&__pyx_n_s_TabixFile, __pyx_k_TabixFile, sizeof(__pyx_k_TabixFile), 0, 0, 1, 1},
|
|
jpayne@69
|
27814 {&__pyx_n_u_TabixFile, __pyx_k_TabixFile, sizeof(__pyx_k_TabixFile), 0, 1, 0, 1},
|
|
jpayne@69
|
27815 {&__pyx_n_s_TabixFile___reduce_cython, __pyx_k_TabixFile___reduce_cython, sizeof(__pyx_k_TabixFile___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27816 {&__pyx_n_s_TabixFile___setstate_cython, __pyx_k_TabixFile___setstate_cython, sizeof(__pyx_k_TabixFile___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27817 {&__pyx_n_s_TabixFile__dup, __pyx_k_TabixFile__dup, sizeof(__pyx_k_TabixFile__dup), 0, 0, 1, 1},
|
|
jpayne@69
|
27818 {&__pyx_n_s_TabixFile__open, __pyx_k_TabixFile__open, sizeof(__pyx_k_TabixFile__open), 0, 0, 1, 1},
|
|
jpayne@69
|
27819 {&__pyx_n_s_TabixFile_close, __pyx_k_TabixFile_close, sizeof(__pyx_k_TabixFile_close), 0, 0, 1, 1},
|
|
jpayne@69
|
27820 {&__pyx_n_s_TabixFile_fetch, __pyx_k_TabixFile_fetch, sizeof(__pyx_k_TabixFile_fetch), 0, 0, 1, 1},
|
|
jpayne@69
|
27821 {&__pyx_n_s_TabixIterator, __pyx_k_TabixIterator, sizeof(__pyx_k_TabixIterator), 0, 0, 1, 1},
|
|
jpayne@69
|
27822 {&__pyx_n_s_TabixIteratorParsed, __pyx_k_TabixIteratorParsed, sizeof(__pyx_k_TabixIteratorParsed), 0, 0, 1, 1},
|
|
jpayne@69
|
27823 {&__pyx_n_s_TabixIteratorParsed___reduce_cyt, __pyx_k_TabixIteratorParsed___reduce_cyt, sizeof(__pyx_k_TabixIteratorParsed___reduce_cyt), 0, 0, 1, 1},
|
|
jpayne@69
|
27824 {&__pyx_n_s_TabixIteratorParsed___setstate_c, __pyx_k_TabixIteratorParsed___setstate_c, sizeof(__pyx_k_TabixIteratorParsed___setstate_c), 0, 0, 1, 1},
|
|
jpayne@69
|
27825 {&__pyx_n_s_TabixIterator___reduce_cython, __pyx_k_TabixIterator___reduce_cython, sizeof(__pyx_k_TabixIterator___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27826 {&__pyx_n_s_TabixIterator___setstate_cython, __pyx_k_TabixIterator___setstate_cython, sizeof(__pyx_k_TabixIterator___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27827 {&__pyx_n_s_Tabixfile, __pyx_k_Tabixfile, sizeof(__pyx_k_Tabixfile), 0, 0, 1, 1},
|
|
jpayne@69
|
27828 {&__pyx_n_u_Tabixfile, __pyx_k_Tabixfile, sizeof(__pyx_k_Tabixfile), 0, 1, 0, 1},
|
|
jpayne@69
|
27829 {&__pyx_n_s_Tabixfile___reduce_cython, __pyx_k_Tabixfile___reduce_cython, sizeof(__pyx_k_Tabixfile___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27830 {&__pyx_n_s_Tabixfile___setstate_cython, __pyx_k_Tabixfile___setstate_cython, sizeof(__pyx_k_Tabixfile___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27831 {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1},
|
|
jpayne@69
|
27832 {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
|
|
jpayne@69
|
27833 {&__pyx_n_s_WINDOW_SIZE, __pyx_k_WINDOW_SIZE, sizeof(__pyx_k_WINDOW_SIZE), 0, 0, 1, 1},
|
|
jpayne@69
|
27834 {&__pyx_kp_b__16, __pyx_k__16, sizeof(__pyx_k__16), 0, 0, 0, 0},
|
|
jpayne@69
|
27835 {&__pyx_kp_u__39, __pyx_k__39, sizeof(__pyx_k__39), 0, 1, 0, 0},
|
|
jpayne@69
|
27836 {&__pyx_kp_u__42, __pyx_k__42, sizeof(__pyx_k__42), 0, 1, 0, 0},
|
|
jpayne@69
|
27837 {&__pyx_kp_u__43, __pyx_k__43, sizeof(__pyx_k__43), 0, 1, 0, 0},
|
|
jpayne@69
|
27838 {&__pyx_kp_u__44, __pyx_k__44, sizeof(__pyx_k__44), 0, 1, 0, 0},
|
|
jpayne@69
|
27839 {&__pyx_kp_u__56, __pyx_k__56, sizeof(__pyx_k__56), 0, 1, 0, 0},
|
|
jpayne@69
|
27840 {&__pyx_n_s__62, __pyx_k__62, sizeof(__pyx_k__62), 0, 0, 1, 1},
|
|
jpayne@69
|
27841 {&__pyx_n_s__78, __pyx_k__78, sizeof(__pyx_k__78), 0, 0, 1, 1},
|
|
jpayne@69
|
27842 {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1},
|
|
jpayne@69
|
27843 {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1},
|
|
jpayne@69
|
27844 {&__pyx_n_s_asBed, __pyx_k_asBed, sizeof(__pyx_k_asBed), 0, 0, 1, 1},
|
|
jpayne@69
|
27845 {&__pyx_n_u_asBed, __pyx_k_asBed, sizeof(__pyx_k_asBed), 0, 1, 0, 1},
|
|
jpayne@69
|
27846 {&__pyx_n_s_asBed___reduce_cython, __pyx_k_asBed___reduce_cython, sizeof(__pyx_k_asBed___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27847 {&__pyx_n_s_asBed___setstate_cython, __pyx_k_asBed___setstate_cython, sizeof(__pyx_k_asBed___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27848 {&__pyx_n_s_asGFF3, __pyx_k_asGFF3, sizeof(__pyx_k_asGFF3), 0, 0, 1, 1},
|
|
jpayne@69
|
27849 {&__pyx_n_u_asGFF3, __pyx_k_asGFF3, sizeof(__pyx_k_asGFF3), 0, 1, 0, 1},
|
|
jpayne@69
|
27850 {&__pyx_n_s_asGFF3___reduce_cython, __pyx_k_asGFF3___reduce_cython, sizeof(__pyx_k_asGFF3___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27851 {&__pyx_n_s_asGFF3___setstate_cython, __pyx_k_asGFF3___setstate_cython, sizeof(__pyx_k_asGFF3___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27852 {&__pyx_n_s_asGTF, __pyx_k_asGTF, sizeof(__pyx_k_asGTF), 0, 0, 1, 1},
|
|
jpayne@69
|
27853 {&__pyx_n_u_asGTF, __pyx_k_asGTF, sizeof(__pyx_k_asGTF), 0, 1, 0, 1},
|
|
jpayne@69
|
27854 {&__pyx_n_s_asGTF___reduce_cython, __pyx_k_asGTF___reduce_cython, sizeof(__pyx_k_asGTF___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27855 {&__pyx_n_s_asGTF___setstate_cython, __pyx_k_asGTF___setstate_cython, sizeof(__pyx_k_asGTF___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27856 {&__pyx_n_s_asTuple, __pyx_k_asTuple, sizeof(__pyx_k_asTuple), 0, 0, 1, 1},
|
|
jpayne@69
|
27857 {&__pyx_n_u_asTuple, __pyx_k_asTuple, sizeof(__pyx_k_asTuple), 0, 1, 0, 1},
|
|
jpayne@69
|
27858 {&__pyx_n_s_asTuple___reduce_cython, __pyx_k_asTuple___reduce_cython, sizeof(__pyx_k_asTuple___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27859 {&__pyx_n_s_asTuple___setstate_cython, __pyx_k_asTuple___setstate_cython, sizeof(__pyx_k_asTuple___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27860 {&__pyx_n_s_asVCF, __pyx_k_asVCF, sizeof(__pyx_k_asVCF), 0, 0, 1, 1},
|
|
jpayne@69
|
27861 {&__pyx_n_u_asVCF, __pyx_k_asVCF, sizeof(__pyx_k_asVCF), 0, 1, 0, 1},
|
|
jpayne@69
|
27862 {&__pyx_n_s_asVCF___reduce_cython, __pyx_k_asVCF___reduce_cython, sizeof(__pyx_k_asVCF___reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27863 {&__pyx_n_s_asVCF___setstate_cython, __pyx_k_asVCF___setstate_cython, sizeof(__pyx_k_asVCF___setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27864 {&__pyx_n_u_ascii, __pyx_k_ascii, sizeof(__pyx_k_ascii), 0, 1, 0, 1},
|
|
jpayne@69
|
27865 {&__pyx_n_s_asyncio_coroutines, __pyx_k_asyncio_coroutines, sizeof(__pyx_k_asyncio_coroutines), 0, 0, 1, 1},
|
|
jpayne@69
|
27866 {&__pyx_n_s_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 1, 1},
|
|
jpayne@69
|
27867 {&__pyx_n_u_bcf, __pyx_k_bcf, sizeof(__pyx_k_bcf), 0, 1, 0, 1},
|
|
jpayne@69
|
27868 {&__pyx_n_u_bed, __pyx_k_bed, sizeof(__pyx_k_bed), 0, 1, 0, 1},
|
|
jpayne@69
|
27869 {&__pyx_n_s_buffer, __pyx_k_buffer, sizeof(__pyx_k_buffer), 0, 0, 1, 1},
|
|
jpayne@69
|
27870 {&__pyx_n_s_buffer_size, __pyx_k_buffer_size, sizeof(__pyx_k_buffer_size), 0, 0, 1, 1},
|
|
jpayne@69
|
27871 {&__pyx_kp_u_building_of_index_for_failed, __pyx_k_building_of_index_for_failed, sizeof(__pyx_k_building_of_index_for_failed), 0, 1, 0, 0},
|
|
jpayne@69
|
27872 {&__pyx_n_s_bytes_cpy, __pyx_k_bytes_cpy, sizeof(__pyx_k_bytes_cpy), 0, 0, 1, 1},
|
|
jpayne@69
|
27873 {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1},
|
|
jpayne@69
|
27874 {&__pyx_n_s_cfilename, __pyx_k_cfilename, sizeof(__pyx_k_cfilename), 0, 0, 1, 1},
|
|
jpayne@69
|
27875 {&__pyx_n_s_cfilename_index, __pyx_k_cfilename_index, sizeof(__pyx_k_cfilename_index), 0, 0, 1, 1},
|
|
jpayne@69
|
27876 {&__pyx_n_s_cfn, __pyx_k_cfn, sizeof(__pyx_k_cfn), 0, 0, 1, 1},
|
|
jpayne@69
|
27877 {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1},
|
|
jpayne@69
|
27878 {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
|
|
jpayne@69
|
27879 {&__pyx_n_s_closed, __pyx_k_closed, sizeof(__pyx_k_closed), 0, 0, 1, 1},
|
|
jpayne@69
|
27880 {&__pyx_n_s_conf, __pyx_k_conf, sizeof(__pyx_k_conf), 0, 0, 1, 1},
|
|
jpayne@69
|
27881 {&__pyx_n_s_conf_data, __pyx_k_conf_data, sizeof(__pyx_k_conf_data), 0, 0, 1, 1},
|
|
jpayne@69
|
27882 {&__pyx_n_s_contigs, __pyx_k_contigs, sizeof(__pyx_k_contigs), 0, 0, 1, 1},
|
|
jpayne@69
|
27883 {&__pyx_kp_u_could_not_create_iterator_for_re, __pyx_k_could_not_create_iterator_for_re, sizeof(__pyx_k_could_not_create_iterator_for_re), 0, 1, 0, 0},
|
|
jpayne@69
|
27884 {&__pyx_kp_u_could_not_create_iterator_possib, __pyx_k_could_not_create_iterator_possib, sizeof(__pyx_k_could_not_create_iterator_possib), 0, 1, 0, 0},
|
|
jpayne@69
|
27885 {&__pyx_kp_u_could_not_load_tbi_csi_index_of, __pyx_k_could_not_load_tbi_csi_index_of, sizeof(__pyx_k_could_not_load_tbi_csi_index_of), 0, 1, 0, 0},
|
|
jpayne@69
|
27886 {&__pyx_kp_u_could_not_open_file_s, __pyx_k_could_not_open_file_s, sizeof(__pyx_k_could_not_open_file_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27887 {&__pyx_kp_u_could_not_open_for_reading_heade, __pyx_k_could_not_open_for_reading_heade, sizeof(__pyx_k_could_not_open_for_reading_heade), 0, 1, 0, 0},
|
|
jpayne@69
|
27888 {&__pyx_kp_u_could_not_open_index_for_s, __pyx_k_could_not_open_index_for_s, sizeof(__pyx_k_could_not_open_index_for_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27889 {&__pyx_kp_u_could_not_open_s_for_reading, __pyx_k_could_not_open_s_for_reading, sizeof(__pyx_k_could_not_open_s_for_reading), 0, 1, 0, 0},
|
|
jpayne@69
|
27890 {&__pyx_kp_u_could_not_open_s_for_writing, __pyx_k_could_not_open_s_for_writing, sizeof(__pyx_k_could_not_open_s_for_writing), 0, 1, 0, 0},
|
|
jpayne@69
|
27891 {&__pyx_n_s_cpy, __pyx_k_cpy, sizeof(__pyx_k_cpy), 0, 0, 1, 1},
|
|
jpayne@69
|
27892 {&__pyx_n_s_csi, __pyx_k_csi, sizeof(__pyx_k_csi), 0, 0, 1, 1},
|
|
jpayne@69
|
27893 {&__pyx_kp_u_csi_2, __pyx_k_csi_2, sizeof(__pyx_k_csi_2), 0, 1, 0, 0},
|
|
jpayne@69
|
27894 {&__pyx_n_s_cstr, __pyx_k_cstr, sizeof(__pyx_k_cstr), 0, 0, 1, 1},
|
|
jpayne@69
|
27895 {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1},
|
|
jpayne@69
|
27896 {&__pyx_n_s_dict_2, __pyx_k_dict_2, sizeof(__pyx_k_dict_2), 0, 0, 1, 1},
|
|
jpayne@69
|
27897 {&__pyx_kp_u_disable, __pyx_k_disable, sizeof(__pyx_k_disable), 0, 1, 0, 0},
|
|
jpayne@69
|
27898 {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1},
|
|
jpayne@69
|
27899 {&__pyx_n_s_dup, __pyx_k_dup, sizeof(__pyx_k_dup), 0, 0, 1, 1},
|
|
jpayne@69
|
27900 {&__pyx_kp_s_empty_iterator, __pyx_k_empty_iterator, sizeof(__pyx_k_empty_iterator), 0, 0, 1, 0},
|
|
jpayne@69
|
27901 {&__pyx_kp_u_enable, __pyx_k_enable, sizeof(__pyx_k_enable), 0, 1, 0, 0},
|
|
jpayne@69
|
27902 {&__pyx_n_s_encoding, __pyx_k_encoding, sizeof(__pyx_k_encoding), 0, 0, 1, 1},
|
|
jpayne@69
|
27903 {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1},
|
|
jpayne@69
|
27904 {&__pyx_n_s_end_col, __pyx_k_end_col, sizeof(__pyx_k_end_col), 0, 0, 1, 1},
|
|
jpayne@69
|
27905 {&__pyx_kp_u_end_out_of_range_i, __pyx_k_end_out_of_range_i, sizeof(__pyx_k_end_out_of_range_i), 0, 1, 0, 0},
|
|
jpayne@69
|
27906 {&__pyx_kp_u_error_i_when_closing_file_s, __pyx_k_error_i_when_closing_file_s, sizeof(__pyx_k_error_i_when_closing_file_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27907 {&__pyx_kp_u_error_i_when_writing_to_file_s, __pyx_k_error_i_when_writing_to_file_s, sizeof(__pyx_k_error_i_when_writing_to_file_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27908 {&__pyx_n_s_exists, __pyx_k_exists, sizeof(__pyx_k_exists), 0, 0, 1, 1},
|
|
jpayne@69
|
27909 {&__pyx_n_s_fd_src, __pyx_k_fd_src, sizeof(__pyx_k_fd_src), 0, 0, 1, 1},
|
|
jpayne@69
|
27910 {&__pyx_n_s_fetch, __pyx_k_fetch, sizeof(__pyx_k_fetch), 0, 0, 1, 1},
|
|
jpayne@69
|
27911 {&__pyx_kp_u_file_s_not_found, __pyx_k_file_s_not_found, sizeof(__pyx_k_file_s_not_found), 0, 1, 0, 0},
|
|
jpayne@69
|
27912 {&__pyx_n_s_filename, __pyx_k_filename, sizeof(__pyx_k_filename), 0, 0, 1, 1},
|
|
jpayne@69
|
27913 {&__pyx_n_s_filename_in, __pyx_k_filename_in, sizeof(__pyx_k_filename_in), 0, 0, 1, 1},
|
|
jpayne@69
|
27914 {&__pyx_n_s_filename_index, __pyx_k_filename_index, sizeof(__pyx_k_filename_index), 0, 0, 1, 1},
|
|
jpayne@69
|
27915 {&__pyx_n_s_filename_out, __pyx_k_filename_out, sizeof(__pyx_k_filename_out), 0, 0, 1, 1},
|
|
jpayne@69
|
27916 {&__pyx_kp_u_filename_s_already_exists_use_fo, __pyx_k_filename_s_already_exists_use_fo, sizeof(__pyx_k_filename_s_already_exists_use_fo), 0, 1, 0, 0},
|
|
jpayne@69
|
27917 {&__pyx_n_s_fileobj, __pyx_k_fileobj, sizeof(__pyx_k_fileobj), 0, 0, 1, 1},
|
|
jpayne@69
|
27918 {&__pyx_n_s_fmt, __pyx_k_fmt, sizeof(__pyx_k_fmt), 0, 0, 1, 1},
|
|
jpayne@69
|
27919 {&__pyx_n_s_fn, __pyx_k_fn, sizeof(__pyx_k_fn), 0, 0, 1, 1},
|
|
jpayne@69
|
27920 {&__pyx_n_s_fn_index, __pyx_k_fn_index, sizeof(__pyx_k_fn_index), 0, 0, 1, 1},
|
|
jpayne@69
|
27921 {&__pyx_n_s_fnidx, __pyx_k_fnidx, sizeof(__pyx_k_fnidx), 0, 0, 1, 1},
|
|
jpayne@69
|
27922 {&__pyx_n_s_force, __pyx_k_force, sizeof(__pyx_k_force), 0, 0, 1, 1},
|
|
jpayne@69
|
27923 {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1},
|
|
jpayne@69
|
27924 {&__pyx_n_s_fp, __pyx_k_fp, sizeof(__pyx_k_fp), 0, 0, 1, 1},
|
|
jpayne@69
|
27925 {&__pyx_kp_u_gc, __pyx_k_gc, sizeof(__pyx_k_gc), 0, 1, 0, 0},
|
|
jpayne@69
|
27926 {&__pyx_n_s_get_encoding, __pyx_k_get_encoding, sizeof(__pyx_k_get_encoding), 0, 0, 1, 1},
|
|
jpayne@69
|
27927 {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1},
|
|
jpayne@69
|
27928 {&__pyx_n_u_gff, __pyx_k_gff, sizeof(__pyx_k_gff), 0, 1, 0, 1},
|
|
jpayne@69
|
27929 {&__pyx_kp_u_gz, __pyx_k_gz, sizeof(__pyx_k_gz), 0, 1, 0, 0},
|
|
jpayne@69
|
27930 {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
|
|
jpayne@69
|
27931 {&__pyx_kp_u_incomplete_line_at_s, __pyx_k_incomplete_line_at_s, sizeof(__pyx_k_incomplete_line_at_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27932 {&__pyx_n_s_index, __pyx_k_index, sizeof(__pyx_k_index), 0, 0, 1, 1},
|
|
jpayne@69
|
27933 {&__pyx_kp_u_index_s_not_found, __pyx_k_index_s_not_found, sizeof(__pyx_k_index_s_not_found), 0, 1, 0, 0},
|
|
jpayne@69
|
27934 {&__pyx_n_s_infile, __pyx_k_infile, sizeof(__pyx_k_infile), 0, 0, 1, 1},
|
|
jpayne@69
|
27935 {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1},
|
|
jpayne@69
|
27936 {&__pyx_n_s_init_subclass, __pyx_k_init_subclass, sizeof(__pyx_k_init_subclass), 0, 0, 1, 1},
|
|
jpayne@69
|
27937 {&__pyx_n_s_initializing, __pyx_k_initializing, sizeof(__pyx_k_initializing), 0, 0, 1, 1},
|
|
jpayne@69
|
27938 {&__pyx_kp_u_invalid_file_opening_mode_s, __pyx_k_invalid_file_opening_mode_s, sizeof(__pyx_k_invalid_file_opening_mode_s), 0, 1, 0, 0},
|
|
jpayne@69
|
27939 {&__pyx_n_s_is_coroutine, __pyx_k_is_coroutine, sizeof(__pyx_k_is_coroutine), 0, 0, 1, 1},
|
|
jpayne@69
|
27940 {&__pyx_n_s_is_empty, __pyx_k_is_empty, sizeof(__pyx_k_is_empty), 0, 0, 1, 1},
|
|
jpayne@69
|
27941 {&__pyx_n_s_is_open, __pyx_k_is_open, sizeof(__pyx_k_is_open), 0, 0, 1, 1},
|
|
jpayne@69
|
27942 {&__pyx_kp_u_isenabled, __pyx_k_isenabled, sizeof(__pyx_k_isenabled), 0, 1, 0, 0},
|
|
jpayne@69
|
27943 {&__pyx_n_s_iter, __pyx_k_iter, sizeof(__pyx_k_iter), 0, 0, 1, 1},
|
|
jpayne@69
|
27944 {&__pyx_kp_s_iterate_over_infile_Permits_the, __pyx_k_iterate_over_infile_Permits_the, sizeof(__pyx_k_iterate_over_infile_Permits_the), 0, 0, 1, 0},
|
|
jpayne@69
|
27945 {&__pyx_kp_u_iteration_on_closed_file, __pyx_k_iteration_on_closed_file, sizeof(__pyx_k_iteration_on_closed_file), 0, 1, 0, 0},
|
|
jpayne@69
|
27946 {&__pyx_n_s_itr, __pyx_k_itr, sizeof(__pyx_k_itr), 0, 0, 1, 1},
|
|
jpayne@69
|
27947 {&__pyx_n_s_keep_original, __pyx_k_keep_original, sizeof(__pyx_k_keep_original), 0, 0, 1, 1},
|
|
jpayne@69
|
27948 {&__pyx_n_s_keys, __pyx_k_keys, sizeof(__pyx_k_keys), 0, 0, 1, 1},
|
|
jpayne@69
|
27949 {&__pyx_n_s_length, __pyx_k_length, sizeof(__pyx_k_length), 0, 0, 1, 1},
|
|
jpayne@69
|
27950 {&__pyx_n_s_line, __pyx_k_line, sizeof(__pyx_k_line), 0, 0, 1, 1},
|
|
jpayne@69
|
27951 {&__pyx_n_s_line_skip, __pyx_k_line_skip, sizeof(__pyx_k_line_skip), 0, 0, 1, 1},
|
|
jpayne@69
|
27952 {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
|
|
jpayne@69
|
27953 {&__pyx_n_s_meta_char, __pyx_k_meta_char, sizeof(__pyx_k_meta_char), 0, 0, 1, 1},
|
|
jpayne@69
|
27954 {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1},
|
|
jpayne@69
|
27955 {&__pyx_n_s_min_shift, __pyx_k_min_shift, sizeof(__pyx_k_min_shift), 0, 0, 1, 1},
|
|
jpayne@69
|
27956 {&__pyx_n_s_mode, __pyx_k_mode, sizeof(__pyx_k_mode), 0, 0, 1, 1},
|
|
jpayne@69
|
27957 {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1},
|
|
jpayne@69
|
27958 {&__pyx_n_s_multiple_iterators, __pyx_k_multiple_iterators, sizeof(__pyx_k_multiple_iterators), 0, 0, 1, 1},
|
|
jpayne@69
|
27959 {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1},
|
|
jpayne@69
|
27960 {&__pyx_n_s_nbytes, __pyx_k_nbytes, sizeof(__pyx_k_nbytes), 0, 0, 1, 1},
|
|
jpayne@69
|
27961 {&__pyx_kp_u_neither_preset_nor_seq_col_start, __pyx_k_neither_preset_nor_seq_col_start, sizeof(__pyx_k_neither_preset_nor_seq_col_start), 0, 1, 0, 0},
|
|
jpayne@69
|
27962 {&__pyx_n_s_new, __pyx_k_new, sizeof(__pyx_k_new), 0, 0, 1, 1},
|
|
jpayne@69
|
27963 {&__pyx_n_s_next, __pyx_k_next, sizeof(__pyx_k_next), 0, 0, 1, 1},
|
|
jpayne@69
|
27964 {&__pyx_kp_s_no_default___reduce___due_to_non, __pyx_k_no_default___reduce___due_to_non, sizeof(__pyx_k_no_default___reduce___due_to_non), 0, 0, 1, 0},
|
|
jpayne@69
|
27965 {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1},
|
|
jpayne@69
|
27966 {&__pyx_n_s_os, __pyx_k_os, sizeof(__pyx_k_os), 0, 0, 1, 1},
|
|
jpayne@69
|
27967 {&__pyx_kp_u_parse_method_of_s_not_implemente, __pyx_k_parse_method_of_s_not_implemente, sizeof(__pyx_k_parse_method_of_s_not_implemente), 0, 1, 0, 0},
|
|
jpayne@69
|
27968 {&__pyx_n_s_parser, __pyx_k_parser, sizeof(__pyx_k_parser), 0, 0, 1, 1},
|
|
jpayne@69
|
27969 {&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1},
|
|
jpayne@69
|
27970 {&__pyx_n_s_pickle, __pyx_k_pickle, sizeof(__pyx_k_pickle), 0, 0, 1, 1},
|
|
jpayne@69
|
27971 {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1},
|
|
jpayne@69
|
27972 {&__pyx_n_s_preset, __pyx_k_preset, sizeof(__pyx_k_preset), 0, 0, 1, 1},
|
|
jpayne@69
|
27973 {&__pyx_n_s_preset2conf, __pyx_k_preset2conf, sizeof(__pyx_k_preset2conf), 0, 0, 1, 1},
|
|
jpayne@69
|
27974 {&__pyx_n_u_psltbl, __pyx_k_psltbl, sizeof(__pyx_k_psltbl), 0, 1, 0, 1},
|
|
jpayne@69
|
27975 {&__pyx_n_s_pysam_libctabix, __pyx_k_pysam_libctabix, sizeof(__pyx_k_pysam_libctabix), 0, 0, 1, 1},
|
|
jpayne@69
|
27976 {&__pyx_kp_s_pysam_libctabix_pyx, __pyx_k_pysam_libctabix_pyx, sizeof(__pyx_k_pysam_libctabix_pyx), 0, 0, 1, 0},
|
|
jpayne@69
|
27977 {&__pyx_n_s_pyx_PickleError, __pyx_k_pyx_PickleError, sizeof(__pyx_k_pyx_PickleError), 0, 0, 1, 1},
|
|
jpayne@69
|
27978 {&__pyx_n_s_pyx_checksum, __pyx_k_pyx_checksum, sizeof(__pyx_k_pyx_checksum), 0, 0, 1, 1},
|
|
jpayne@69
|
27979 {&__pyx_n_s_pyx_result, __pyx_k_pyx_result, sizeof(__pyx_k_pyx_result), 0, 0, 1, 1},
|
|
jpayne@69
|
27980 {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1},
|
|
jpayne@69
|
27981 {&__pyx_n_s_pyx_type, __pyx_k_pyx_type, sizeof(__pyx_k_pyx_type), 0, 0, 1, 1},
|
|
jpayne@69
|
27982 {&__pyx_n_s_pyx_unpickle_Parser, __pyx_k_pyx_unpickle_Parser, sizeof(__pyx_k_pyx_unpickle_Parser), 0, 0, 1, 1},
|
|
jpayne@69
|
27983 {&__pyx_n_s_pyx_unpickle_asBed, __pyx_k_pyx_unpickle_asBed, sizeof(__pyx_k_pyx_unpickle_asBed), 0, 0, 1, 1},
|
|
jpayne@69
|
27984 {&__pyx_n_s_pyx_unpickle_asGFF3, __pyx_k_pyx_unpickle_asGFF3, sizeof(__pyx_k_pyx_unpickle_asGFF3), 0, 0, 1, 1},
|
|
jpayne@69
|
27985 {&__pyx_n_s_pyx_unpickle_asGTF, __pyx_k_pyx_unpickle_asGTF, sizeof(__pyx_k_pyx_unpickle_asGTF), 0, 0, 1, 1},
|
|
jpayne@69
|
27986 {&__pyx_n_s_pyx_unpickle_asTuple, __pyx_k_pyx_unpickle_asTuple, sizeof(__pyx_k_pyx_unpickle_asTuple), 0, 0, 1, 1},
|
|
jpayne@69
|
27987 {&__pyx_n_s_pyx_unpickle_asVCF, __pyx_k_pyx_unpickle_asVCF, sizeof(__pyx_k_pyx_unpickle_asVCF), 0, 0, 1, 1},
|
|
jpayne@69
|
27988 {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1},
|
|
jpayne@69
|
27989 {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1},
|
|
jpayne@69
|
27990 {&__pyx_n_s_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 0, 1, 1},
|
|
jpayne@69
|
27991 {&__pyx_n_u_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 1, 0, 1},
|
|
jpayne@69
|
27992 {&__pyx_n_s_readline, __pyx_k_readline, sizeof(__pyx_k_readline), 0, 0, 1, 1},
|
|
jpayne@69
|
27993 {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1},
|
|
jpayne@69
|
27994 {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
27995 {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 0, 0, 1, 1},
|
|
jpayne@69
|
27996 {&__pyx_n_s_reference, __pyx_k_reference, sizeof(__pyx_k_reference), 0, 0, 1, 1},
|
|
jpayne@69
|
27997 {&__pyx_n_s_region, __pyx_k_region, sizeof(__pyx_k_region), 0, 0, 1, 1},
|
|
jpayne@69
|
27998 {&__pyx_n_s_retval, __pyx_k_retval, sizeof(__pyx_k_retval), 0, 0, 1, 1},
|
|
jpayne@69
|
27999 {&__pyx_kp_u_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 1, 0, 0},
|
|
jpayne@69
|
28000 {&__pyx_n_s_s_2, __pyx_k_s_2, sizeof(__pyx_k_s_2), 0, 0, 1, 1},
|
|
jpayne@69
|
28001 {&__pyx_kp_u_s_i, __pyx_k_s_i, sizeof(__pyx_k_s_i), 0, 1, 0, 0},
|
|
jpayne@69
|
28002 {&__pyx_kp_u_s_i_i, __pyx_k_s_i_i, sizeof(__pyx_k_s_i_i), 0, 1, 0, 0},
|
|
jpayne@69
|
28003 {&__pyx_n_u_sam, __pyx_k_sam, sizeof(__pyx_k_sam), 0, 1, 0, 1},
|
|
jpayne@69
|
28004 {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1},
|
|
jpayne@69
|
28005 {&__pyx_kp_s_self_gzipfile_self_kstream_canno, __pyx_k_self_gzipfile_self_kstream_canno, sizeof(__pyx_k_self_gzipfile_self_kstream_canno), 0, 0, 1, 0},
|
|
jpayne@69
|
28006 {&__pyx_kp_s_self_iterator_cannot_be_converte, __pyx_k_self_iterator_cannot_be_converte, sizeof(__pyx_k_self_iterator_cannot_be_converte), 0, 0, 1, 0},
|
|
jpayne@69
|
28007 {&__pyx_n_s_seq_col, __pyx_k_seq_col, sizeof(__pyx_k_seq_col), 0, 0, 1, 1},
|
|
jpayne@69
|
28008 {&__pyx_n_s_set_encoding, __pyx_k_set_encoding, sizeof(__pyx_k_set_encoding), 0, 0, 1, 1},
|
|
jpayne@69
|
28009 {&__pyx_n_s_set_name, __pyx_k_set_name, sizeof(__pyx_k_set_name), 0, 0, 1, 1},
|
|
jpayne@69
|
28010 {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1},
|
|
jpayne@69
|
28011 {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1},
|
|
jpayne@69
|
28012 {&__pyx_n_s_spec, __pyx_k_spec, sizeof(__pyx_k_spec), 0, 0, 1, 1},
|
|
jpayne@69
|
28013 {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
|
|
jpayne@69
|
28014 {&__pyx_n_s_start_col, __pyx_k_start_col, sizeof(__pyx_k_start_col), 0, 0, 1, 1},
|
|
jpayne@69
|
28015 {&__pyx_kp_u_start_i_end_i, __pyx_k_start_i_end_i, sizeof(__pyx_k_start_i_end_i), 0, 1, 0, 0},
|
|
jpayne@69
|
28016 {&__pyx_kp_u_start_out_of_range_i, __pyx_k_start_out_of_range_i, sizeof(__pyx_k_start_out_of_range_i), 0, 1, 0, 0},
|
|
jpayne@69
|
28017 {&__pyx_n_s_state, __pyx_k_state, sizeof(__pyx_k_state), 0, 0, 1, 1},
|
|
jpayne@69
|
28018 {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0},
|
|
jpayne@69
|
28019 {&__pyx_n_s_suffix, __pyx_k_suffix, sizeof(__pyx_k_suffix), 0, 0, 1, 1},
|
|
jpayne@69
|
28020 {&__pyx_n_s_super, __pyx_k_super, sizeof(__pyx_k_super), 0, 0, 1, 1},
|
|
jpayne@69
|
28021 {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1},
|
|
jpayne@69
|
28022 {&__pyx_n_s_tabix_compress, __pyx_k_tabix_compress, sizeof(__pyx_k_tabix_compress), 0, 0, 1, 1},
|
|
jpayne@69
|
28023 {&__pyx_n_u_tabix_compress, __pyx_k_tabix_compress, sizeof(__pyx_k_tabix_compress), 0, 1, 0, 1},
|
|
jpayne@69
|
28024 {&__pyx_n_s_tabix_file_iterator, __pyx_k_tabix_file_iterator, sizeof(__pyx_k_tabix_file_iterator), 0, 0, 1, 1},
|
|
jpayne@69
|
28025 {&__pyx_n_u_tabix_file_iterator, __pyx_k_tabix_file_iterator, sizeof(__pyx_k_tabix_file_iterator), 0, 1, 0, 1},
|
|
jpayne@69
|
28026 {&__pyx_n_s_tabix_file_iterator___reduce_cyt, __pyx_k_tabix_file_iterator___reduce_cyt, sizeof(__pyx_k_tabix_file_iterator___reduce_cyt), 0, 0, 1, 1},
|
|
jpayne@69
|
28027 {&__pyx_n_s_tabix_file_iterator___setstate_c, __pyx_k_tabix_file_iterator___setstate_c, sizeof(__pyx_k_tabix_file_iterator___setstate_c), 0, 0, 1, 1},
|
|
jpayne@69
|
28028 {&__pyx_n_s_tabix_generic_iterator, __pyx_k_tabix_generic_iterator, sizeof(__pyx_k_tabix_generic_iterator), 0, 0, 1, 1},
|
|
jpayne@69
|
28029 {&__pyx_n_u_tabix_generic_iterator, __pyx_k_tabix_generic_iterator, sizeof(__pyx_k_tabix_generic_iterator), 0, 1, 0, 1},
|
|
jpayne@69
|
28030 {&__pyx_n_s_tabix_generic_iterator___init, __pyx_k_tabix_generic_iterator___init, sizeof(__pyx_k_tabix_generic_iterator___init), 0, 0, 1, 1},
|
|
jpayne@69
|
28031 {&__pyx_n_s_tabix_generic_iterator___iter, __pyx_k_tabix_generic_iterator___iter, sizeof(__pyx_k_tabix_generic_iterator___iter), 0, 0, 1, 1},
|
|
jpayne@69
|
28032 {&__pyx_n_s_tabix_generic_iterator___next, __pyx_k_tabix_generic_iterator___next, sizeof(__pyx_k_tabix_generic_iterator___next), 0, 0, 1, 1},
|
|
jpayne@69
|
28033 {&__pyx_n_s_tabix_index, __pyx_k_tabix_index, sizeof(__pyx_k_tabix_index), 0, 0, 1, 1},
|
|
jpayne@69
|
28034 {&__pyx_n_u_tabix_index, __pyx_k_tabix_index, sizeof(__pyx_k_tabix_index), 0, 1, 0, 1},
|
|
jpayne@69
|
28035 {&__pyx_n_s_tabix_iterator, __pyx_k_tabix_iterator, sizeof(__pyx_k_tabix_iterator), 0, 0, 1, 1},
|
|
jpayne@69
|
28036 {&__pyx_n_u_tabix_iterator, __pyx_k_tabix_iterator, sizeof(__pyx_k_tabix_iterator), 0, 1, 0, 1},
|
|
jpayne@69
|
28037 {&__pyx_kp_u_tbi, __pyx_k_tbi, sizeof(__pyx_k_tbi), 0, 1, 0, 0},
|
|
jpayne@69
|
28038 {&__pyx_n_s_tell, __pyx_k_tell, sizeof(__pyx_k_tell), 0, 0, 1, 1},
|
|
jpayne@69
|
28039 {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
|
|
jpayne@69
|
28040 {&__pyx_n_s_threads, __pyx_k_threads, sizeof(__pyx_k_threads), 0, 0, 1, 1},
|
|
jpayne@69
|
28041 {&__pyx_kp_u_unknown_preset, __pyx_k_unknown_preset, sizeof(__pyx_k_unknown_preset), 0, 1, 0, 0},
|
|
jpayne@69
|
28042 {&__pyx_n_s_unlink, __pyx_k_unlink, sizeof(__pyx_k_unlink), 0, 0, 1, 1},
|
|
jpayne@69
|
28043 {&__pyx_n_s_update, __pyx_k_update, sizeof(__pyx_k_update), 0, 0, 1, 1},
|
|
jpayne@69
|
28044 {&__pyx_n_s_use_setstate, __pyx_k_use_setstate, sizeof(__pyx_k_use_setstate), 0, 0, 1, 1},
|
|
jpayne@69
|
28045 {&__pyx_kp_u_valid_presets_are, __pyx_k_valid_presets_are, sizeof(__pyx_k_valid_presets_are), 0, 1, 0, 0},
|
|
jpayne@69
|
28046 {&__pyx_n_u_vcf, __pyx_k_vcf, sizeof(__pyx_k_vcf), 0, 1, 0, 1},
|
|
jpayne@69
|
28047 {&__pyx_kp_u_writing_failed, __pyx_k_writing_failed, sizeof(__pyx_k_writing_failed), 0, 1, 0, 0},
|
|
jpayne@69
|
28048 {&__pyx_n_s_zerobased, __pyx_k_zerobased, sizeof(__pyx_k_zerobased), 0, 0, 1, 1},
|
|
jpayne@69
|
28049 {0, 0, 0, 0, 0, 0, 0}
|
|
jpayne@69
|
28050 };
|
|
jpayne@69
|
28051 return __Pyx_InitStrings(__pyx_string_tab);
|
|
jpayne@69
|
28052 }
|
|
jpayne@69
|
28053 /* #### Code section: cached_builtins ### */
|
|
jpayne@69
|
28054 static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
|
|
jpayne@69
|
28055 __pyx_builtin_NotImplementedError = __Pyx_GetBuiltinName(__pyx_n_s_NotImplementedError); if (!__pyx_builtin_NotImplementedError) __PYX_ERR(0, 94, __pyx_L1_error)
|
|
jpayne@69
|
28056 __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 361, __pyx_L1_error)
|
|
jpayne@69
|
28057 __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) __PYX_ERR(0, 378, __pyx_L1_error)
|
|
jpayne@69
|
28058 __pyx_builtin_OSError = __Pyx_GetBuiltinName(__pyx_n_s_OSError); if (!__pyx_builtin_OSError) __PYX_ERR(0, 560, __pyx_L1_error)
|
|
jpayne@69
|
28059 __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
|
|
jpayne@69
|
28060 __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) __PYX_ERR(0, 671, __pyx_L1_error)
|
|
jpayne@69
|
28061 __pyx_builtin_super = __Pyx_GetBuiltinName(__pyx_n_s_super); if (!__pyx_builtin_super) __PYX_ERR(0, 701, __pyx_L1_error)
|
|
jpayne@69
|
28062 __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) __PYX_ERR(0, 969, __pyx_L1_error)
|
|
jpayne@69
|
28063 __pyx_builtin_AssertionError = __Pyx_GetBuiltinName(__pyx_n_s_AssertionError); if (!__pyx_builtin_AssertionError) __PYX_ERR(0, 1216, __pyx_L1_error)
|
|
jpayne@69
|
28064 __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) __PYX_ERR(3, 120, __pyx_L1_error)
|
|
jpayne@69
|
28065 return 0;
|
|
jpayne@69
|
28066 __pyx_L1_error:;
|
|
jpayne@69
|
28067 return -1;
|
|
jpayne@69
|
28068 }
|
|
jpayne@69
|
28069 /* #### Code section: cached_constants ### */
|
|
jpayne@69
|
28070
|
|
jpayne@69
|
28071 static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) {
|
|
jpayne@69
|
28072 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
28073 __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
|
|
jpayne@69
|
28074
|
|
jpayne@69
|
28075 /* "pysam/libctabix.pyx":444
|
|
jpayne@69
|
28076 * '''
|
|
jpayne@69
|
28077 * if not self.is_open():
|
|
jpayne@69
|
28078 * raise ValueError("I/O operation on closed file") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28079 *
|
|
jpayne@69
|
28080 * # convert coordinates to region string, which is one-based
|
|
jpayne@69
|
28081 */
|
|
jpayne@69
|
28082 __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_u_I_O_operation_on_closed_file); if (unlikely(!__pyx_tuple__19)) __PYX_ERR(0, 444, __pyx_L1_error)
|
|
jpayne@69
|
28083 __Pyx_GOTREF(__pyx_tuple__19);
|
|
jpayne@69
|
28084 __Pyx_GIVEREF(__pyx_tuple__19);
|
|
jpayne@69
|
28085
|
|
jpayne@69
|
28086 /* "pysam/libctabix.pyx":499
|
|
jpayne@69
|
28087 * # when accessing a tabix file created prior tabix 1.0
|
|
jpayne@69
|
28088 * # the full-file iterator is empty.
|
|
jpayne@69
|
28089 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28090 * "could not create iterator, possible "
|
|
jpayne@69
|
28091 * "tabix version mismatch")
|
|
jpayne@69
|
28092 */
|
|
jpayne@69
|
28093 __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_u_could_not_create_iterator_possib); if (unlikely(!__pyx_tuple__20)) __PYX_ERR(0, 499, __pyx_L1_error)
|
|
jpayne@69
|
28094 __Pyx_GOTREF(__pyx_tuple__20);
|
|
jpayne@69
|
28095 __Pyx_GIVEREF(__pyx_tuple__20);
|
|
jpayne@69
|
28096
|
|
jpayne@69
|
28097 /* "pysam/libctabix.pyx":669
|
|
jpayne@69
|
28098 * cdef int retval = self.__cnext__()
|
|
jpayne@69
|
28099 * if retval == -5:
|
|
jpayne@69
|
28100 * raise IOError("iteration on closed file") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28101 * elif retval < 0:
|
|
jpayne@69
|
28102 * raise StopIteration
|
|
jpayne@69
|
28103 */
|
|
jpayne@69
|
28104 __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_u_iteration_on_closed_file); if (unlikely(!__pyx_tuple__24)) __PYX_ERR(0, 669, __pyx_L1_error)
|
|
jpayne@69
|
28105 __Pyx_GOTREF(__pyx_tuple__24);
|
|
jpayne@69
|
28106 __Pyx_GIVEREF(__pyx_tuple__24);
|
|
jpayne@69
|
28107
|
|
jpayne@69
|
28108 /* "pysam/libctabix.pyx":859
|
|
jpayne@69
|
28109 * if r < 0:
|
|
jpayne@69
|
28110 * free(buffer)
|
|
jpayne@69
|
28111 * raise IOError("writing failed") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28112 *
|
|
jpayne@69
|
28113 * free(buffer)
|
|
jpayne@69
|
28114 */
|
|
jpayne@69
|
28115 __pyx_tuple__38 = PyTuple_Pack(1, __pyx_kp_u_writing_failed); if (unlikely(!__pyx_tuple__38)) __PYX_ERR(0, 859, __pyx_L1_error)
|
|
jpayne@69
|
28116 __Pyx_GOTREF(__pyx_tuple__38);
|
|
jpayne@69
|
28117 __Pyx_GIVEREF(__pyx_tuple__38);
|
|
jpayne@69
|
28118
|
|
jpayne@69
|
28119 /* "pysam/libctabix.pyx":930
|
|
jpayne@69
|
28120 * if preset is None and \
|
|
jpayne@69
|
28121 * (seq_col is None or start_col is None or end_col is None):
|
|
jpayne@69
|
28122 * raise ValueError( # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28123 * "neither preset nor seq_col,start_col and end_col given")
|
|
jpayne@69
|
28124 *
|
|
jpayne@69
|
28125 */
|
|
jpayne@69
|
28126 __pyx_tuple__41 = PyTuple_Pack(1, __pyx_kp_u_neither_preset_nor_seq_col_start); if (unlikely(!__pyx_tuple__41)) __PYX_ERR(0, 930, __pyx_L1_error)
|
|
jpayne@69
|
28127 __Pyx_GOTREF(__pyx_tuple__41);
|
|
jpayne@69
|
28128 __Pyx_GIVEREF(__pyx_tuple__41);
|
|
jpayne@69
|
28129
|
|
jpayne@69
|
28130 /* "pysam/libctabix.pyx":1108
|
|
jpayne@69
|
28131 *
|
|
jpayne@69
|
28132 * if infile.closed:
|
|
jpayne@69
|
28133 * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28134 *
|
|
jpayne@69
|
28135 * self.infile = infile
|
|
jpayne@69
|
28136 */
|
|
jpayne@69
|
28137 __pyx_tuple__45 = PyTuple_Pack(1, __pyx_kp_u_I_O_operation_on_closed_file_2); if (unlikely(!__pyx_tuple__45)) __PYX_ERR(0, 1108, __pyx_L1_error)
|
|
jpayne@69
|
28138 __Pyx_GOTREF(__pyx_tuple__45);
|
|
jpayne@69
|
28139 __Pyx_GIVEREF(__pyx_tuple__45);
|
|
jpayne@69
|
28140
|
|
jpayne@69
|
28141 /* "(tree fragment)":4
|
|
jpayne@69
|
28142 * cdef object __pyx_PickleError
|
|
jpayne@69
|
28143 * cdef object __pyx_result
|
|
jpayne@69
|
28144 * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28145 * from pickle import PickleError as __pyx_PickleError
|
|
jpayne@69
|
28146 * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum
|
|
jpayne@69
|
28147 */
|
|
jpayne@69
|
28148 __pyx_tuple__55 = PyTuple_Pack(3, __pyx_int_243541226, __pyx_int_21667264, __pyx_int_139192863); if (unlikely(!__pyx_tuple__55)) __PYX_ERR(1, 4, __pyx_L1_error)
|
|
jpayne@69
|
28149 __Pyx_GOTREF(__pyx_tuple__55);
|
|
jpayne@69
|
28150 __Pyx_GIVEREF(__pyx_tuple__55);
|
|
jpayne@69
|
28151
|
|
jpayne@69
|
28152 /* "pysam/libctabix.pyx":87
|
|
jpayne@69
|
28153 * self.encoding = encoding
|
|
jpayne@69
|
28154 *
|
|
jpayne@69
|
28155 * def set_encoding(self, encoding): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28156 * self.encoding = encoding
|
|
jpayne@69
|
28157 *
|
|
jpayne@69
|
28158 */
|
|
jpayne@69
|
28159 __pyx_tuple__63 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_encoding); if (unlikely(!__pyx_tuple__63)) __PYX_ERR(0, 87, __pyx_L1_error)
|
|
jpayne@69
|
28160 __Pyx_GOTREF(__pyx_tuple__63);
|
|
jpayne@69
|
28161 __Pyx_GIVEREF(__pyx_tuple__63);
|
|
jpayne@69
|
28162 __pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_set_encoding, 87, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 87, __pyx_L1_error)
|
|
jpayne@69
|
28163
|
|
jpayne@69
|
28164 /* "pysam/libctabix.pyx":90
|
|
jpayne@69
|
28165 * self.encoding = encoding
|
|
jpayne@69
|
28166 *
|
|
jpayne@69
|
28167 * def get_encoding(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28168 * return self.encoding
|
|
jpayne@69
|
28169 *
|
|
jpayne@69
|
28170 */
|
|
jpayne@69
|
28171 __pyx_tuple__64 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__64)) __PYX_ERR(0, 90, __pyx_L1_error)
|
|
jpayne@69
|
28172 __Pyx_GOTREF(__pyx_tuple__64);
|
|
jpayne@69
|
28173 __Pyx_GIVEREF(__pyx_tuple__64);
|
|
jpayne@69
|
28174 __pyx_codeobj__2 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_get_encoding, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__2)) __PYX_ERR(0, 90, __pyx_L1_error)
|
|
jpayne@69
|
28175
|
|
jpayne@69
|
28176 /* "(tree fragment)":1
|
|
jpayne@69
|
28177 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28178 * cdef tuple state
|
|
jpayne@69
|
28179 * cdef object _dict
|
|
jpayne@69
|
28180 */
|
|
jpayne@69
|
28181 __pyx_tuple__65 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_state, __pyx_n_s_dict_2, __pyx_n_s_use_setstate); if (unlikely(!__pyx_tuple__65)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28182 __Pyx_GOTREF(__pyx_tuple__65);
|
|
jpayne@69
|
28183 __Pyx_GIVEREF(__pyx_tuple__65);
|
|
jpayne@69
|
28184 __pyx_codeobj__3 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28185
|
|
jpayne@69
|
28186 /* "(tree fragment)":16
|
|
jpayne@69
|
28187 * else:
|
|
jpayne@69
|
28188 * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
28189 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28190 * __pyx_unpickle_Parser__set_state(self, __pyx_state)
|
|
jpayne@69
|
28191 */
|
|
jpayne@69
|
28192 __pyx_tuple__66 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_pyx_state); if (unlikely(!__pyx_tuple__66)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28193 __Pyx_GOTREF(__pyx_tuple__66);
|
|
jpayne@69
|
28194 __Pyx_GIVEREF(__pyx_tuple__66);
|
|
jpayne@69
|
28195 __pyx_codeobj__4 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__4)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28196
|
|
jpayne@69
|
28197 /* "(tree fragment)":1
|
|
jpayne@69
|
28198 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28199 * cdef tuple state
|
|
jpayne@69
|
28200 * cdef object _dict
|
|
jpayne@69
|
28201 */
|
|
jpayne@69
|
28202 __pyx_codeobj__5 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__5)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28203
|
|
jpayne@69
|
28204 /* "(tree fragment)":16
|
|
jpayne@69
|
28205 * else:
|
|
jpayne@69
|
28206 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
28207 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28208 * __pyx_unpickle_asTuple__set_state(self, __pyx_state)
|
|
jpayne@69
|
28209 */
|
|
jpayne@69
|
28210 __pyx_codeobj__6 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__6)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28211
|
|
jpayne@69
|
28212 /* "(tree fragment)":1
|
|
jpayne@69
|
28213 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28214 * cdef tuple state
|
|
jpayne@69
|
28215 * cdef object _dict
|
|
jpayne@69
|
28216 */
|
|
jpayne@69
|
28217 __pyx_codeobj__7 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__7)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28218
|
|
jpayne@69
|
28219 /* "(tree fragment)":16
|
|
jpayne@69
|
28220 * else:
|
|
jpayne@69
|
28221 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
28222 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28223 * __pyx_unpickle_asGFF3__set_state(self, __pyx_state)
|
|
jpayne@69
|
28224 */
|
|
jpayne@69
|
28225 __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28226
|
|
jpayne@69
|
28227 /* "(tree fragment)":1
|
|
jpayne@69
|
28228 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28229 * cdef tuple state
|
|
jpayne@69
|
28230 * cdef object _dict
|
|
jpayne@69
|
28231 */
|
|
jpayne@69
|
28232 __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28233
|
|
jpayne@69
|
28234 /* "(tree fragment)":16
|
|
jpayne@69
|
28235 * else:
|
|
jpayne@69
|
28236 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
28237 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28238 * __pyx_unpickle_asGTF__set_state(self, __pyx_state)
|
|
jpayne@69
|
28239 */
|
|
jpayne@69
|
28240 __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28241
|
|
jpayne@69
|
28242 /* "(tree fragment)":1
|
|
jpayne@69
|
28243 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28244 * cdef tuple state
|
|
jpayne@69
|
28245 * cdef object _dict
|
|
jpayne@69
|
28246 */
|
|
jpayne@69
|
28247 __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28248
|
|
jpayne@69
|
28249 /* "(tree fragment)":16
|
|
jpayne@69
|
28250 * else:
|
|
jpayne@69
|
28251 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
28252 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28253 * __pyx_unpickle_asBed__set_state(self, __pyx_state)
|
|
jpayne@69
|
28254 */
|
|
jpayne@69
|
28255 __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28256
|
|
jpayne@69
|
28257 /* "(tree fragment)":1
|
|
jpayne@69
|
28258 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28259 * cdef tuple state
|
|
jpayne@69
|
28260 * cdef object _dict
|
|
jpayne@69
|
28261 */
|
|
jpayne@69
|
28262 __pyx_codeobj__13 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__13)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28263
|
|
jpayne@69
|
28264 /* "(tree fragment)":16
|
|
jpayne@69
|
28265 * else:
|
|
jpayne@69
|
28266 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
28267 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28268 * __pyx_unpickle_asVCF__set_state(self, __pyx_state)
|
|
jpayne@69
|
28269 */
|
|
jpayne@69
|
28270 __pyx_codeobj__14 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__14)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
28271
|
|
jpayne@69
|
28272 /* "pysam/libctabix.pyx":352
|
|
jpayne@69
|
28273 * self.encoding = encoding
|
|
jpayne@69
|
28274 *
|
|
jpayne@69
|
28275 * def _open( self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28276 * filename,
|
|
jpayne@69
|
28277 * mode='r',
|
|
jpayne@69
|
28278 */
|
|
jpayne@69
|
28279 __pyx_tuple__67 = PyTuple_Pack(8, __pyx_n_s_self, __pyx_n_s_filename, __pyx_n_s_mode, __pyx_n_s_index, __pyx_n_s_threads, __pyx_n_s_filename_index, __pyx_n_s_cfilename, __pyx_n_s_cfilename_index); if (unlikely(!__pyx_tuple__67)) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
28280 __Pyx_GOTREF(__pyx_tuple__67);
|
|
jpayne@69
|
28281 __Pyx_GIVEREF(__pyx_tuple__67);
|
|
jpayne@69
|
28282 __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(5, 0, 0, 8, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_open, 352, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
28283 __pyx_tuple__68 = PyTuple_Pack(3, __pyx_n_u_r, Py_None, __pyx_int_1); if (unlikely(!__pyx_tuple__68)) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
28284 __Pyx_GOTREF(__pyx_tuple__68);
|
|
jpayne@69
|
28285 __Pyx_GIVEREF(__pyx_tuple__68);
|
|
jpayne@69
|
28286
|
|
jpayne@69
|
28287 /* "pysam/libctabix.pyx":404
|
|
jpayne@69
|
28288 * self.start_offset = self.tell()
|
|
jpayne@69
|
28289 *
|
|
jpayne@69
|
28290 * def _dup(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28291 * '''return a copy of this tabix file.
|
|
jpayne@69
|
28292 *
|
|
jpayne@69
|
28293 */
|
|
jpayne@69
|
28294 __pyx_codeobj__17 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_dup, 404, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) __PYX_ERR(0, 404, __pyx_L1_error)
|
|
jpayne@69
|
28295
|
|
jpayne@69
|
28296 /* "pysam/libctabix.pyx":416
|
|
jpayne@69
|
28297 * encoding=self.encoding)
|
|
jpayne@69
|
28298 *
|
|
jpayne@69
|
28299 * def fetch(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28300 * reference=None,
|
|
jpayne@69
|
28301 * start=None,
|
|
jpayne@69
|
28302 */
|
|
jpayne@69
|
28303 __pyx_tuple__69 = PyTuple_Pack(12, __pyx_n_s_self, __pyx_n_s_reference, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_region, __pyx_n_s_parser, __pyx_n_s_multiple_iterators, __pyx_n_s_itr, __pyx_n_s_cstr, __pyx_n_s_fileobj, __pyx_n_s_s_2, __pyx_n_s_a); if (unlikely(!__pyx_tuple__69)) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
28304 __Pyx_GOTREF(__pyx_tuple__69);
|
|
jpayne@69
|
28305 __Pyx_GIVEREF(__pyx_tuple__69);
|
|
jpayne@69
|
28306 __pyx_codeobj__18 = (PyObject*)__Pyx_PyCode_New(7, 0, 0, 12, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_fetch, 416, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__18)) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
28307 __pyx_tuple__70 = PyTuple_Pack(6, Py_None, Py_None, Py_None, Py_None, Py_None, Py_False); if (unlikely(!__pyx_tuple__70)) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
28308 __Pyx_GOTREF(__pyx_tuple__70);
|
|
jpayne@69
|
28309 __Pyx_GIVEREF(__pyx_tuple__70);
|
|
jpayne@69
|
28310
|
|
jpayne@69
|
28311 /* "pysam/libctabix.pyx":598
|
|
jpayne@69
|
28312 * return result
|
|
jpayne@69
|
28313 *
|
|
jpayne@69
|
28314 * def close(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28315 * '''
|
|
jpayne@69
|
28316 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
28317 */
|
|
jpayne@69
|
28318 __pyx_codeobj__21 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_close, 598, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__21)) __PYX_ERR(0, 598, __pyx_L1_error)
|
|
jpayne@69
|
28319
|
|
jpayne@69
|
28320 /* "(tree fragment)":1
|
|
jpayne@69
|
28321 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28322 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28323 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28324 */
|
|
jpayne@69
|
28325 __pyx_codeobj__22 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__22)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28326
|
|
jpayne@69
|
28327 /* "(tree fragment)":3
|
|
jpayne@69
|
28328 * def __reduce_cython__(self):
|
|
jpayne@69
|
28329 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28330 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28331 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28332 */
|
|
jpayne@69
|
28333 __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28334
|
|
jpayne@69
|
28335 /* "(tree fragment)":1
|
|
jpayne@69
|
28336 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28337 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28338 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28339 */
|
|
jpayne@69
|
28340 __pyx_codeobj__25 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__25)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28341
|
|
jpayne@69
|
28342 /* "(tree fragment)":3
|
|
jpayne@69
|
28343 * def __reduce_cython__(self):
|
|
jpayne@69
|
28344 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28345 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28346 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28347 */
|
|
jpayne@69
|
28348 __pyx_codeobj__26 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__26)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28349
|
|
jpayne@69
|
28350 /* "pysam/libctabix.pyx":685
|
|
jpayne@69
|
28351 * '''empty iterator'''
|
|
jpayne@69
|
28352 *
|
|
jpayne@69
|
28353 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28354 * return self
|
|
jpayne@69
|
28355 *
|
|
jpayne@69
|
28356 */
|
|
jpayne@69
|
28357 __pyx_codeobj__27 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_iter, 685, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__27)) __PYX_ERR(0, 685, __pyx_L1_error)
|
|
jpayne@69
|
28358
|
|
jpayne@69
|
28359 /* "pysam/libctabix.pyx":688
|
|
jpayne@69
|
28360 * return self
|
|
jpayne@69
|
28361 *
|
|
jpayne@69
|
28362 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28363 * raise StopIteration()
|
|
jpayne@69
|
28364 *
|
|
jpayne@69
|
28365 */
|
|
jpayne@69
|
28366 __pyx_codeobj__28 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_next, 688, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__28)) __PYX_ERR(0, 688, __pyx_L1_error)
|
|
jpayne@69
|
28367
|
|
jpayne@69
|
28368 /* "(tree fragment)":1
|
|
jpayne@69
|
28369 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28370 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28371 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28372 */
|
|
jpayne@69
|
28373 __pyx_codeobj__29 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__29)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28374
|
|
jpayne@69
|
28375 /* "(tree fragment)":3
|
|
jpayne@69
|
28376 * def __reduce_cython__(self):
|
|
jpayne@69
|
28377 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28378 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28379 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28380 */
|
|
jpayne@69
|
28381 __pyx_codeobj__30 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__30)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28382
|
|
jpayne@69
|
28383 /* "(tree fragment)":1
|
|
jpayne@69
|
28384 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28385 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28386 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28387 */
|
|
jpayne@69
|
28388 __pyx_codeobj__31 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__31)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28389
|
|
jpayne@69
|
28390 /* "(tree fragment)":3
|
|
jpayne@69
|
28391 * def __reduce_cython__(self):
|
|
jpayne@69
|
28392 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28393 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28394 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28395 */
|
|
jpayne@69
|
28396 __pyx_codeobj__32 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__32)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28397
|
|
jpayne@69
|
28398 /* "(tree fragment)":1
|
|
jpayne@69
|
28399 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28400 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28401 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28402 */
|
|
jpayne@69
|
28403 __pyx_codeobj__33 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__33)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28404
|
|
jpayne@69
|
28405 /* "(tree fragment)":3
|
|
jpayne@69
|
28406 * def __reduce_cython__(self):
|
|
jpayne@69
|
28407 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28408 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28409 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28410 */
|
|
jpayne@69
|
28411 __pyx_codeobj__34 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__34)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28412
|
|
jpayne@69
|
28413 /* "(tree fragment)":1
|
|
jpayne@69
|
28414 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28415 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28416 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28417 */
|
|
jpayne@69
|
28418 __pyx_codeobj__35 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__35)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28419
|
|
jpayne@69
|
28420 /* "(tree fragment)":3
|
|
jpayne@69
|
28421 * def __reduce_cython__(self):
|
|
jpayne@69
|
28422 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28423 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28424 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
28425 */
|
|
jpayne@69
|
28426 __pyx_codeobj__36 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__36)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28427
|
|
jpayne@69
|
28428 /* "pysam/libctabix.pyx":811
|
|
jpayne@69
|
28429 *
|
|
jpayne@69
|
28430 *
|
|
jpayne@69
|
28431 * def tabix_compress(filename_in, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28432 * filename_out,
|
|
jpayne@69
|
28433 * force=False):
|
|
jpayne@69
|
28434 */
|
|
jpayne@69
|
28435 __pyx_tuple__71 = PyTuple_Pack(13, __pyx_n_s_filename_in, __pyx_n_s_filename_out, __pyx_n_s_force, __pyx_n_s_WINDOW_SIZE, __pyx_n_s_c, __pyx_n_s_r, __pyx_n_s_buffer, __pyx_n_s_fp, __pyx_n_s_fd_src, __pyx_n_s_is_empty, __pyx_n_s_O_RDONLY, __pyx_n_s_fn, __pyx_n_s_cfn); if (unlikely(!__pyx_tuple__71)) __PYX_ERR(0, 811, __pyx_L1_error)
|
|
jpayne@69
|
28436 __Pyx_GOTREF(__pyx_tuple__71);
|
|
jpayne@69
|
28437 __Pyx_GIVEREF(__pyx_tuple__71);
|
|
jpayne@69
|
28438 __pyx_codeobj__37 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 13, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_tabix_compress, 811, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__37)) __PYX_ERR(0, 811, __pyx_L1_error)
|
|
jpayne@69
|
28439 __pyx_tuple__72 = PyTuple_Pack(1, ((PyObject *)Py_False)); if (unlikely(!__pyx_tuple__72)) __PYX_ERR(0, 811, __pyx_L1_error)
|
|
jpayne@69
|
28440 __Pyx_GOTREF(__pyx_tuple__72);
|
|
jpayne@69
|
28441 __Pyx_GIVEREF(__pyx_tuple__72);
|
|
jpayne@69
|
28442
|
|
jpayne@69
|
28443 /* "pysam/libctabix.pyx":873
|
|
jpayne@69
|
28444 *
|
|
jpayne@69
|
28445 *
|
|
jpayne@69
|
28446 * def tabix_index(filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28447 * force=False,
|
|
jpayne@69
|
28448 * seq_col=None,
|
|
jpayne@69
|
28449 */
|
|
jpayne@69
|
28450 __pyx_tuple__73 = PyTuple_Pack(24, __pyx_n_s_filename, __pyx_n_s_force, __pyx_n_s_seq_col, __pyx_n_s_start_col, __pyx_n_s_end_col, __pyx_n_s_preset, __pyx_n_s_meta_char, __pyx_n_s_line_skip, __pyx_n_s_zerobased, __pyx_n_s_min_shift, __pyx_n_s_index, __pyx_n_s_keep_original, __pyx_n_s_csi, __pyx_n_s_fn, __pyx_n_s_cfn, __pyx_n_s_fp, __pyx_n_s_fmt, __pyx_n_s_preset2conf, __pyx_n_s_conf_data, __pyx_n_s_conf, __pyx_n_s_suffix, __pyx_n_s_fn_index, __pyx_n_s_fnidx, __pyx_n_s_retval); if (unlikely(!__pyx_tuple__73)) __PYX_ERR(0, 873, __pyx_L1_error)
|
|
jpayne@69
|
28451 __Pyx_GOTREF(__pyx_tuple__73);
|
|
jpayne@69
|
28452 __Pyx_GIVEREF(__pyx_tuple__73);
|
|
jpayne@69
|
28453 __pyx_codeobj__40 = (PyObject*)__Pyx_PyCode_New(13, 0, 0, 24, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__73, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_tabix_index, 873, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__40)) __PYX_ERR(0, 873, __pyx_L1_error)
|
|
jpayne@69
|
28454
|
|
jpayne@69
|
28455 /* "(tree fragment)":1
|
|
jpayne@69
|
28456 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28457 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28458 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28459 */
|
|
jpayne@69
|
28460 __pyx_codeobj__46 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__46)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28461
|
|
jpayne@69
|
28462 /* "(tree fragment)":3
|
|
jpayne@69
|
28463 * def __reduce_cython__(self):
|
|
jpayne@69
|
28464 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28465 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28466 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28467 */
|
|
jpayne@69
|
28468 __pyx_codeobj__47 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__47)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28469
|
|
jpayne@69
|
28470 /* "pysam/libctabix.pyx":1183
|
|
jpayne@69
|
28471 * Permits the use of file-like objects for example from the gzip module.
|
|
jpayne@69
|
28472 * '''
|
|
jpayne@69
|
28473 * def __init__(self, infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28474 *
|
|
jpayne@69
|
28475 * self.infile = infile
|
|
jpayne@69
|
28476 */
|
|
jpayne@69
|
28477 __pyx_tuple__74 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_infile, __pyx_n_s_parser); if (unlikely(!__pyx_tuple__74)) __PYX_ERR(0, 1183, __pyx_L1_error)
|
|
jpayne@69
|
28478 __Pyx_GOTREF(__pyx_tuple__74);
|
|
jpayne@69
|
28479 __Pyx_GIVEREF(__pyx_tuple__74);
|
|
jpayne@69
|
28480 __pyx_codeobj__48 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_init, 1183, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__48)) __PYX_ERR(0, 1183, __pyx_L1_error)
|
|
jpayne@69
|
28481
|
|
jpayne@69
|
28482 /* "pysam/libctabix.pyx":1190
|
|
jpayne@69
|
28483 * self.parser = parser
|
|
jpayne@69
|
28484 *
|
|
jpayne@69
|
28485 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28486 * return self
|
|
jpayne@69
|
28487 *
|
|
jpayne@69
|
28488 */
|
|
jpayne@69
|
28489 __pyx_codeobj__49 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_iter, 1190, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__49)) __PYX_ERR(0, 1190, __pyx_L1_error)
|
|
jpayne@69
|
28490
|
|
jpayne@69
|
28491 /* "pysam/libctabix.pyx":1194
|
|
jpayne@69
|
28492 *
|
|
jpayne@69
|
28493 * # cython version - required for python 3
|
|
jpayne@69
|
28494 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28495 *
|
|
jpayne@69
|
28496 * cdef char * b
|
|
jpayne@69
|
28497 */
|
|
jpayne@69
|
28498 __pyx_tuple__75 = PyTuple_Pack(8, __pyx_n_s_self, __pyx_n_s_b, __pyx_n_s_cpy, __pyx_n_s_nbytes, __pyx_n_s_encoding, __pyx_n_s_line, __pyx_n_s_s_2, __pyx_n_s_bytes_cpy); if (unlikely(!__pyx_tuple__75)) __PYX_ERR(0, 1194, __pyx_L1_error)
|
|
jpayne@69
|
28499 __Pyx_GOTREF(__pyx_tuple__75);
|
|
jpayne@69
|
28500 __Pyx_GIVEREF(__pyx_tuple__75);
|
|
jpayne@69
|
28501 __pyx_codeobj__50 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 8, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_next, 1194, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__50)) __PYX_ERR(0, 1194, __pyx_L1_error)
|
|
jpayne@69
|
28502
|
|
jpayne@69
|
28503 /* "pysam/libctabix.pyx":1238
|
|
jpayne@69
|
28504 *
|
|
jpayne@69
|
28505 *
|
|
jpayne@69
|
28506 * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28507 * """return an iterator over all entries in a file.
|
|
jpayne@69
|
28508 *
|
|
jpayne@69
|
28509 */
|
|
jpayne@69
|
28510 __pyx_tuple__76 = PyTuple_Pack(2, __pyx_n_s_infile, __pyx_n_s_parser); if (unlikely(!__pyx_tuple__76)) __PYX_ERR(0, 1238, __pyx_L1_error)
|
|
jpayne@69
|
28511 __Pyx_GOTREF(__pyx_tuple__76);
|
|
jpayne@69
|
28512 __Pyx_GIVEREF(__pyx_tuple__76);
|
|
jpayne@69
|
28513 __pyx_codeobj__51 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_tabix_iterator, 1238, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__51)) __PYX_ERR(0, 1238, __pyx_L1_error)
|
|
jpayne@69
|
28514
|
|
jpayne@69
|
28515 /* "(tree fragment)":1
|
|
jpayne@69
|
28516 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28517 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28518 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
28519 */
|
|
jpayne@69
|
28520 __pyx_codeobj__52 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__52)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28521
|
|
jpayne@69
|
28522 /* "(tree fragment)":3
|
|
jpayne@69
|
28523 * def __reduce_cython__(self):
|
|
jpayne@69
|
28524 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28525 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28526 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
28527 */
|
|
jpayne@69
|
28528 __pyx_codeobj__53 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__53)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
28529
|
|
jpayne@69
|
28530 /* "(tree fragment)":1
|
|
jpayne@69
|
28531 * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
28532 * cdef object __pyx_PickleError
|
|
jpayne@69
|
28533 * cdef object __pyx_result
|
|
jpayne@69
|
28534 */
|
|
jpayne@69
|
28535 __pyx_tuple__77 = PyTuple_Pack(5, __pyx_n_s_pyx_type, __pyx_n_s_pyx_checksum, __pyx_n_s_pyx_state, __pyx_n_s_pyx_PickleError, __pyx_n_s_pyx_result); if (unlikely(!__pyx_tuple__77)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28536 __Pyx_GOTREF(__pyx_tuple__77);
|
|
jpayne@69
|
28537 __Pyx_GIVEREF(__pyx_tuple__77);
|
|
jpayne@69
|
28538 __pyx_codeobj__54 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_Parser, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__54)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28539 __pyx_codeobj__57 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asTuple, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__57)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28540 __pyx_codeobj__58 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asGFF3, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__58)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28541 __pyx_codeobj__59 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asGTF, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__59)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28542 __pyx_codeobj__60 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asBed, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__60)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28543 __pyx_codeobj__61 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asVCF, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__61)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
28544 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
28545 return 0;
|
|
jpayne@69
|
28546 __pyx_L1_error:;
|
|
jpayne@69
|
28547 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
28548 return -1;
|
|
jpayne@69
|
28549 }
|
|
jpayne@69
|
28550 /* #### Code section: init_constants ### */
|
|
jpayne@69
|
28551
|
|
jpayne@69
|
28552 static CYTHON_SMALL_CODE int __Pyx_InitConstants(void) {
|
|
jpayne@69
|
28553 __pyx_umethod_PyDict_Type_keys.type = (PyObject*)&PyDict_Type;
|
|
jpayne@69
|
28554 __pyx_umethod_PyDict_Type_keys.method_name = &__pyx_n_s_keys;
|
|
jpayne@69
|
28555 if (__Pyx_CreateStringTabAndInitStrings() < 0) __PYX_ERR(0, 1, __pyx_L1_error);
|
|
jpayne@69
|
28556 __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28557 __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28558 __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28559 __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28560 __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28561 __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28562 __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28563 __pyx_int_17 = PyInt_FromLong(17); if (unlikely(!__pyx_int_17)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28564 __pyx_int_18 = PyInt_FromLong(18); if (unlikely(!__pyx_int_18)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28565 __pyx_int_35 = PyInt_FromLong(35); if (unlikely(!__pyx_int_35)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28566 __pyx_int_64 = PyInt_FromLong(64); if (unlikely(!__pyx_int_64)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28567 __pyx_int_21667264 = PyInt_FromLong(21667264L); if (unlikely(!__pyx_int_21667264)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28568 __pyx_int_139192863 = PyInt_FromLong(139192863L); if (unlikely(!__pyx_int_139192863)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28569 __pyx_int_243541226 = PyInt_FromLong(243541226L); if (unlikely(!__pyx_int_243541226)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28570 __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28571 return 0;
|
|
jpayne@69
|
28572 __pyx_L1_error:;
|
|
jpayne@69
|
28573 return -1;
|
|
jpayne@69
|
28574 }
|
|
jpayne@69
|
28575 /* #### Code section: init_globals ### */
|
|
jpayne@69
|
28576
|
|
jpayne@69
|
28577 static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) {
|
|
jpayne@69
|
28578 /* AssertionsEnabled.init */
|
|
jpayne@69
|
28579 if (likely(__Pyx_init_assertions_enabled() == 0)); else
|
|
jpayne@69
|
28580
|
|
jpayne@69
|
28581 if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
28582
|
|
jpayne@69
|
28583 return 0;
|
|
jpayne@69
|
28584 __pyx_L1_error:;
|
|
jpayne@69
|
28585 return -1;
|
|
jpayne@69
|
28586 }
|
|
jpayne@69
|
28587 /* #### Code section: init_module ### */
|
|
jpayne@69
|
28588
|
|
jpayne@69
|
28589 static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/
|
|
jpayne@69
|
28590 static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/
|
|
jpayne@69
|
28591 static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/
|
|
jpayne@69
|
28592 static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/
|
|
jpayne@69
|
28593 static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/
|
|
jpayne@69
|
28594 static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/
|
|
jpayne@69
|
28595 static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/
|
|
jpayne@69
|
28596
|
|
jpayne@69
|
28597 static int __Pyx_modinit_global_init_code(void) {
|
|
jpayne@69
|
28598 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
28599 __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0);
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28600 /*--- Global init code ---*/
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28601 __Pyx_RefNannyFinishContext();
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28602 return 0;
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28603 }
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28604
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jpayne@69
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28605 static int __Pyx_modinit_variable_export_code(void) {
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28606 __Pyx_RefNannyDeclarations
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28607 __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0);
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28608 /*--- Variable export code ---*/
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28609 __Pyx_RefNannyFinishContext();
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28610 return 0;
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28611 }
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28612
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28613 static int __Pyx_modinit_function_export_code(void) {
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28614 __Pyx_RefNannyDeclarations
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28618 return 0;
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28619 }
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28620
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28621 static int __Pyx_modinit_type_init_code(void) {
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28622 __Pyx_RefNannyDeclarations
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28623 PyObject *__pyx_t_1 = NULL;
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28625 int __pyx_lineno = 0;
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28626 const char *__pyx_filename = NULL;
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28627 int __pyx_clineno = 0;
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28628 __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
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28630 __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator = &__pyx_vtable_5pysam_9libctabix_tabix_file_iterator;
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jpayne@69
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28631 __pyx_vtable_5pysam_9libctabix_tabix_file_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *))__pyx_f_5pysam_9libctabix_19tabix_file_iterator___cnext__;
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jpayne@69
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28632 #if CYTHON_USE_TYPE_SPECS
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jpayne@69
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28633 __pyx_ptype_5pysam_9libctabix_tabix_file_iterator = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_tabix_file_iterator_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_tabix_file_iterator)) __PYX_ERR(0, 1098, __pyx_L1_error)
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jpayne@69
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28634 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_tabix_file_iterator_spec, __pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error)
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28635 #else
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28637 #endif
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28638 #if !CYTHON_COMPILING_IN_LIMITED_API
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28639 #endif
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28640 #if !CYTHON_USE_TYPE_SPECS
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28641 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error)
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28642 #endif
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jpayne@69
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28644 __pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_print = 0;
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28645 #endif
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28646 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28647 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_getattro == PyObject_GenericGetAttr)) {
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jpayne@69
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28648 __pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_getattro = __Pyx_PyObject_GenericGetAttr;
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jpayne@69
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28649 }
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28650 #endif
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28651 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator, __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error)
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28652 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28653 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error)
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28654 #endif
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28655 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_tabix_file_iterator, (PyObject *) __pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error)
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jpayne@69
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28656 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28657 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error)
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28658 #endif
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jpayne@69
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28659 __pyx_t_1 = PyImport_ImportModule("pysam.libchtslib"); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
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28660 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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28662 __pyx_vtabptr_5pysam_10libchtslib_HTSFile = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__Pyx_GetVtable(__pyx_ptype_5pysam_10libchtslib_HTSFile); if (unlikely(!__pyx_vtabptr_5pysam_10libchtslib_HTSFile)) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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28663 __pyx_vtabptr_5pysam_9libctabix_TabixFile = &__pyx_vtable_5pysam_9libctabix_TabixFile;
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jpayne@69
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28664 __pyx_vtable_5pysam_9libctabix_TabixFile.__pyx_base = *__pyx_vtabptr_5pysam_10libchtslib_HTSFile;
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jpayne@69
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28665 #if CYTHON_USE_TYPE_SPECS
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jpayne@69
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28667 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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28668 __pyx_ptype_5pysam_9libctabix_TabixFile = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_TabixFile_spec, __pyx_t_2);
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jpayne@69
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28669 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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28670 if (unlikely(!__pyx_ptype_5pysam_9libctabix_TabixFile)) __PYX_ERR(0, 287, __pyx_L1_error)
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jpayne@69
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28671 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_TabixFile_spec, __pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error)
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jpayne@69
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28672 #else
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jpayne@69
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28673 __pyx_ptype_5pysam_9libctabix_TabixFile = &__pyx_type_5pysam_9libctabix_TabixFile;
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jpayne@69
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28674 #endif
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jpayne@69
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28675 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28676 __pyx_ptype_5pysam_9libctabix_TabixFile->tp_base = __pyx_ptype_5pysam_10libchtslib_HTSFile;
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jpayne@69
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28677 #endif
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28678 #if !CYTHON_USE_TYPE_SPECS
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jpayne@69
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28679 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error)
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28680 #endif
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jpayne@69
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28682 __pyx_ptype_5pysam_9libctabix_TabixFile->tp_print = 0;
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jpayne@69
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28683 #endif
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jpayne@69
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28684 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28685 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_TabixFile->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_TabixFile->tp_getattro == PyObject_GenericGetAttr)) {
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jpayne@69
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28686 __pyx_ptype_5pysam_9libctabix_TabixFile->tp_getattro = __Pyx_PyObject_GenericGetAttr;
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28687 }
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28688 #endif
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28689 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_vtabptr_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error)
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jpayne@69
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28690 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28691 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error)
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jpayne@69
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28692 #endif
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jpayne@69
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jpayne@69
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28694 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28695 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error)
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28696 #endif
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jpayne@69
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28697 __pyx_vtabptr_5pysam_9libctabix_Parser = &__pyx_vtable_5pysam_9libctabix_Parser;
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jpayne@69
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28698 __pyx_vtable_5pysam_9libctabix_Parser.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_6Parser_parse;
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jpayne@69
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28699 #if CYTHON_USE_TYPE_SPECS
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jpayne@69
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jpayne@69
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28701 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_Parser_spec, __pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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28702 #else
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jpayne@69
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28703 __pyx_ptype_5pysam_9libctabix_Parser = &__pyx_type_5pysam_9libctabix_Parser;
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jpayne@69
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28704 #endif
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jpayne@69
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28705 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28706 #endif
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jpayne@69
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28707 #if !CYTHON_USE_TYPE_SPECS
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jpayne@69
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28709 #endif
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28710 #if PY_MAJOR_VERSION < 3
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jpayne@69
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28711 __pyx_ptype_5pysam_9libctabix_Parser->tp_print = 0;
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jpayne@69
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28712 #endif
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jpayne@69
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28713 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
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28714 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_Parser->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_Parser->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
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28715 __pyx_ptype_5pysam_9libctabix_Parser->tp_getattro = __Pyx_PyObject_GenericGetAttr;
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jpayne@69
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28716 }
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jpayne@69
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28717 #endif
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jpayne@69
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28718 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_Parser, __pyx_vtabptr_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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28719 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28720 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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28721 #endif
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jpayne@69
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28722 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Parser, (PyObject *) __pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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28723 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28724 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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28725 #endif
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jpayne@69
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28726 __pyx_vtabptr_5pysam_9libctabix_asTuple = &__pyx_vtable_5pysam_9libctabix_asTuple;
|
|
jpayne@69
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28727 __pyx_vtable_5pysam_9libctabix_asTuple.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
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28728 __pyx_vtable_5pysam_9libctabix_asTuple.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_7asTuple_parse;
|
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jpayne@69
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28729 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
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28730 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28731 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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28732 __pyx_ptype_5pysam_9libctabix_asTuple = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asTuple_spec, __pyx_t_2);
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jpayne@69
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28733 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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28734 if (unlikely(!__pyx_ptype_5pysam_9libctabix_asTuple)) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28735 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asTuple_spec, __pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28736 #else
|
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jpayne@69
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28737 __pyx_ptype_5pysam_9libctabix_asTuple = &__pyx_type_5pysam_9libctabix_asTuple;
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jpayne@69
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28738 #endif
|
|
jpayne@69
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28739 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
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28740 __pyx_ptype_5pysam_9libctabix_asTuple->tp_base = __pyx_ptype_5pysam_9libctabix_Parser;
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jpayne@69
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28741 #endif
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jpayne@69
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28742 #if !CYTHON_USE_TYPE_SPECS
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jpayne@69
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28743 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28744 #endif
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jpayne@69
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28745 #if PY_MAJOR_VERSION < 3
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jpayne@69
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28746 __pyx_ptype_5pysam_9libctabix_asTuple->tp_print = 0;
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jpayne@69
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28747 #endif
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jpayne@69
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28748 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28749 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asTuple->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asTuple->tp_getattro == PyObject_GenericGetAttr)) {
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jpayne@69
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28750 __pyx_ptype_5pysam_9libctabix_asTuple->tp_getattro = __Pyx_PyObject_GenericGetAttr;
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jpayne@69
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28751 }
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jpayne@69
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28752 #endif
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jpayne@69
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28753 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asTuple, __pyx_vtabptr_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28754 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28755 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
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28756 #endif
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jpayne@69
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28757 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asTuple, (PyObject *) __pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28758 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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28759 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
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jpayne@69
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28760 #endif
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jpayne@69
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28761 __pyx_vtabptr_5pysam_9libctabix_asGTF = &__pyx_vtable_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
28762 __pyx_vtable_5pysam_9libctabix_asGTF.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28763 __pyx_vtable_5pysam_9libctabix_asGTF.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_5asGTF_parse;
|
|
jpayne@69
|
28764 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28765 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28766 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
28767 __pyx_ptype_5pysam_9libctabix_asGTF = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asGTF_spec, __pyx_t_2);
|
|
jpayne@69
|
28768 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
28769 if (unlikely(!__pyx_ptype_5pysam_9libctabix_asGTF)) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28770 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asGTF_spec, __pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28771 #else
|
|
jpayne@69
|
28772 __pyx_ptype_5pysam_9libctabix_asGTF = &__pyx_type_5pysam_9libctabix_asGTF;
|
|
jpayne@69
|
28773 #endif
|
|
jpayne@69
|
28774 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28775 __pyx_ptype_5pysam_9libctabix_asGTF->tp_base = __pyx_ptype_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28776 #endif
|
|
jpayne@69
|
28777 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28778 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28779 #endif
|
|
jpayne@69
|
28780 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28781 __pyx_ptype_5pysam_9libctabix_asGTF->tp_print = 0;
|
|
jpayne@69
|
28782 #endif
|
|
jpayne@69
|
28783 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28784 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asGTF->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asGTF->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
28785 __pyx_ptype_5pysam_9libctabix_asGTF->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
28786 }
|
|
jpayne@69
|
28787 #endif
|
|
jpayne@69
|
28788 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asGTF, __pyx_vtabptr_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28789 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28790 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28791 #endif
|
|
jpayne@69
|
28792 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asGTF, (PyObject *) __pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28793 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28794 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error)
|
|
jpayne@69
|
28795 #endif
|
|
jpayne@69
|
28796 __pyx_vtabptr_5pysam_9libctabix_asGFF3 = &__pyx_vtable_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
28797 __pyx_vtable_5pysam_9libctabix_asGFF3.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28798 __pyx_vtable_5pysam_9libctabix_asGFF3.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_6asGFF3_parse;
|
|
jpayne@69
|
28799 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28800 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28801 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
28802 __pyx_ptype_5pysam_9libctabix_asGFF3 = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asGFF3_spec, __pyx_t_2);
|
|
jpayne@69
|
28803 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
28804 if (unlikely(!__pyx_ptype_5pysam_9libctabix_asGFF3)) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28805 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asGFF3_spec, __pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28806 #else
|
|
jpayne@69
|
28807 __pyx_ptype_5pysam_9libctabix_asGFF3 = &__pyx_type_5pysam_9libctabix_asGFF3;
|
|
jpayne@69
|
28808 #endif
|
|
jpayne@69
|
28809 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28810 __pyx_ptype_5pysam_9libctabix_asGFF3->tp_base = __pyx_ptype_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28811 #endif
|
|
jpayne@69
|
28812 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28813 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28814 #endif
|
|
jpayne@69
|
28815 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28816 __pyx_ptype_5pysam_9libctabix_asGFF3->tp_print = 0;
|
|
jpayne@69
|
28817 #endif
|
|
jpayne@69
|
28818 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28819 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asGFF3->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asGFF3->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
28820 __pyx_ptype_5pysam_9libctabix_asGFF3->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
28821 }
|
|
jpayne@69
|
28822 #endif
|
|
jpayne@69
|
28823 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asGFF3, __pyx_vtabptr_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28824 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28825 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28826 #endif
|
|
jpayne@69
|
28827 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asGFF3, (PyObject *) __pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28828 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28829 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
28830 #endif
|
|
jpayne@69
|
28831 __pyx_vtabptr_5pysam_9libctabix_asBed = &__pyx_vtable_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
28832 __pyx_vtable_5pysam_9libctabix_asBed.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28833 __pyx_vtable_5pysam_9libctabix_asBed.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_5asBed_parse;
|
|
jpayne@69
|
28834 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28835 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28836 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
28837 __pyx_ptype_5pysam_9libctabix_asBed = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asBed_spec, __pyx_t_2);
|
|
jpayne@69
|
28838 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
28839 if (unlikely(!__pyx_ptype_5pysam_9libctabix_asBed)) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28840 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asBed_spec, __pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28841 #else
|
|
jpayne@69
|
28842 __pyx_ptype_5pysam_9libctabix_asBed = &__pyx_type_5pysam_9libctabix_asBed;
|
|
jpayne@69
|
28843 #endif
|
|
jpayne@69
|
28844 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28845 __pyx_ptype_5pysam_9libctabix_asBed->tp_base = __pyx_ptype_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28846 #endif
|
|
jpayne@69
|
28847 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28848 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28849 #endif
|
|
jpayne@69
|
28850 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28851 __pyx_ptype_5pysam_9libctabix_asBed->tp_print = 0;
|
|
jpayne@69
|
28852 #endif
|
|
jpayne@69
|
28853 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28854 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asBed->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asBed->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
28855 __pyx_ptype_5pysam_9libctabix_asBed->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
28856 }
|
|
jpayne@69
|
28857 #endif
|
|
jpayne@69
|
28858 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asBed, __pyx_vtabptr_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28859 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28860 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28861 #endif
|
|
jpayne@69
|
28862 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asBed, (PyObject *) __pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28863 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28864 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error)
|
|
jpayne@69
|
28865 #endif
|
|
jpayne@69
|
28866 __pyx_vtabptr_5pysam_9libctabix_asVCF = &__pyx_vtable_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
28867 __pyx_vtable_5pysam_9libctabix_asVCF.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28868 __pyx_vtable_5pysam_9libctabix_asVCF.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_5asVCF_parse;
|
|
jpayne@69
|
28869 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28870 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28871 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
28872 __pyx_ptype_5pysam_9libctabix_asVCF = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asVCF_spec, __pyx_t_2);
|
|
jpayne@69
|
28873 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
28874 if (unlikely(!__pyx_ptype_5pysam_9libctabix_asVCF)) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28875 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asVCF_spec, __pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28876 #else
|
|
jpayne@69
|
28877 __pyx_ptype_5pysam_9libctabix_asVCF = &__pyx_type_5pysam_9libctabix_asVCF;
|
|
jpayne@69
|
28878 #endif
|
|
jpayne@69
|
28879 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28880 __pyx_ptype_5pysam_9libctabix_asVCF->tp_base = __pyx_ptype_5pysam_9libctabix_Parser;
|
|
jpayne@69
|
28881 #endif
|
|
jpayne@69
|
28882 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28883 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28884 #endif
|
|
jpayne@69
|
28885 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28886 __pyx_ptype_5pysam_9libctabix_asVCF->tp_print = 0;
|
|
jpayne@69
|
28887 #endif
|
|
jpayne@69
|
28888 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28889 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asVCF->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asVCF->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
28890 __pyx_ptype_5pysam_9libctabix_asVCF->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
28891 }
|
|
jpayne@69
|
28892 #endif
|
|
jpayne@69
|
28893 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asVCF, __pyx_vtabptr_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28894 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28895 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28896 #endif
|
|
jpayne@69
|
28897 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asVCF, (PyObject *) __pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28898 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28899 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
28900 #endif
|
|
jpayne@69
|
28901 __pyx_vtabptr_5pysam_9libctabix_TabixIterator = &__pyx_vtable_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
28902 __pyx_vtable_5pysam_9libctabix_TabixIterator.__pyx___cnext__ = (int (*)(struct __pyx_obj_5pysam_9libctabix_TabixIterator *))__pyx_f_5pysam_9libctabix_13TabixIterator___cnext__;
|
|
jpayne@69
|
28903 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28904 __pyx_ptype_5pysam_9libctabix_TabixIterator = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_TabixIterator_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_TabixIterator)) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28905 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_TabixIterator_spec, __pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28906 #else
|
|
jpayne@69
|
28907 __pyx_ptype_5pysam_9libctabix_TabixIterator = &__pyx_type_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
28908 #endif
|
|
jpayne@69
|
28909 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28910 #endif
|
|
jpayne@69
|
28911 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28912 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28913 #endif
|
|
jpayne@69
|
28914 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28915 __pyx_ptype_5pysam_9libctabix_TabixIterator->tp_print = 0;
|
|
jpayne@69
|
28916 #endif
|
|
jpayne@69
|
28917 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28918 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_TabixIterator->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_TabixIterator->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
28919 __pyx_ptype_5pysam_9libctabix_TabixIterator->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
28920 }
|
|
jpayne@69
|
28921 #endif
|
|
jpayne@69
|
28922 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
28923 {
|
|
jpayne@69
|
28924 PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28925 if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) {
|
|
jpayne@69
|
28926 __pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
|
|
jpayne@69
|
28927 __pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__.doc = __pyx_doc_5pysam_9libctabix_13TabixIterator_4__next__;
|
|
jpayne@69
|
28928 ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__;
|
|
jpayne@69
|
28929 }
|
|
jpayne@69
|
28930 }
|
|
jpayne@69
|
28931 #endif
|
|
jpayne@69
|
28932 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_TabixIterator, __pyx_vtabptr_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28933 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28934 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28935 #endif
|
|
jpayne@69
|
28936 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_TabixIterator, (PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28937 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28938 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error)
|
|
jpayne@69
|
28939 #endif
|
|
jpayne@69
|
28940 __pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed = &__pyx_vtable_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
28941 __pyx_vtable_5pysam_9libctabix_TabixIteratorParsed.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
28942 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28943 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28944 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
28945 __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_TabixIteratorParsed_spec, __pyx_t_2);
|
|
jpayne@69
|
28946 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
28947 if (unlikely(!__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed)) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28948 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_TabixIteratorParsed_spec, __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28949 #else
|
|
jpayne@69
|
28950 __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed = &__pyx_type_5pysam_9libctabix_TabixIteratorParsed;
|
|
jpayne@69
|
28951 #endif
|
|
jpayne@69
|
28952 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28953 __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_base = __pyx_ptype_5pysam_9libctabix_TabixIterator;
|
|
jpayne@69
|
28954 #endif
|
|
jpayne@69
|
28955 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28956 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28957 #endif
|
|
jpayne@69
|
28958 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28959 __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_print = 0;
|
|
jpayne@69
|
28960 #endif
|
|
jpayne@69
|
28961 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28962 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
28963 __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
28964 }
|
|
jpayne@69
|
28965 #endif
|
|
jpayne@69
|
28966 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
28967 {
|
|
jpayne@69
|
28968 PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28969 if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) {
|
|
jpayne@69
|
28970 __pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
|
|
jpayne@69
|
28971 __pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__.doc = __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_2__next__;
|
|
jpayne@69
|
28972 ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__;
|
|
jpayne@69
|
28973 }
|
|
jpayne@69
|
28974 }
|
|
jpayne@69
|
28975 #endif
|
|
jpayne@69
|
28976 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed, __pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28977 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28978 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28979 #endif
|
|
jpayne@69
|
28980 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_TabixIteratorParsed, (PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28981 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28982 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error)
|
|
jpayne@69
|
28983 #endif
|
|
jpayne@69
|
28984 __pyx_vtabptr_5pysam_9libctabix_GZIterator = &__pyx_vtable_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
28985 __pyx_vtable_5pysam_9libctabix_GZIterator.__pyx___cnext__ = (int (*)(struct __pyx_obj_5pysam_9libctabix_GZIterator *))__pyx_f_5pysam_9libctabix_10GZIterator___cnext__;
|
|
jpayne@69
|
28986 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28987 __pyx_ptype_5pysam_9libctabix_GZIterator = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_GZIterator_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_GZIterator)) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
28988 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_GZIterator_spec, __pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
28989 #else
|
|
jpayne@69
|
28990 __pyx_ptype_5pysam_9libctabix_GZIterator = &__pyx_type_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
28991 #endif
|
|
jpayne@69
|
28992 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
28993 #endif
|
|
jpayne@69
|
28994 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
28995 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
28996 #endif
|
|
jpayne@69
|
28997 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
28998 __pyx_ptype_5pysam_9libctabix_GZIterator->tp_print = 0;
|
|
jpayne@69
|
28999 #endif
|
|
jpayne@69
|
29000 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29001 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_GZIterator->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_GZIterator->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
29002 __pyx_ptype_5pysam_9libctabix_GZIterator->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
29003 }
|
|
jpayne@69
|
29004 #endif
|
|
jpayne@69
|
29005 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
29006 {
|
|
jpayne@69
|
29007 PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator, "__init__"); if (unlikely(!wrapper)) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
29008 if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) {
|
|
jpayne@69
|
29009 __pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
|
|
jpayne@69
|
29010 __pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__.doc = __pyx_doc_5pysam_9libctabix_10GZIterator___init__;
|
|
jpayne@69
|
29011 ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__;
|
|
jpayne@69
|
29012 }
|
|
jpayne@69
|
29013 }
|
|
jpayne@69
|
29014 #endif
|
|
jpayne@69
|
29015 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
29016 {
|
|
jpayne@69
|
29017 PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
29018 if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) {
|
|
jpayne@69
|
29019 __pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
|
|
jpayne@69
|
29020 __pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__.doc = __pyx_doc_5pysam_9libctabix_10GZIterator_6__next__;
|
|
jpayne@69
|
29021 ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__;
|
|
jpayne@69
|
29022 }
|
|
jpayne@69
|
29023 }
|
|
jpayne@69
|
29024 #endif
|
|
jpayne@69
|
29025 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_GZIterator, __pyx_vtabptr_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
29026 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29027 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
29028 #endif
|
|
jpayne@69
|
29029 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GZIterator, (PyObject *) __pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
29030 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29031 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error)
|
|
jpayne@69
|
29032 #endif
|
|
jpayne@69
|
29033 __pyx_vtabptr_5pysam_9libctabix_GZIteratorHead = &__pyx_vtable_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
29034 __pyx_vtable_5pysam_9libctabix_GZIteratorHead.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
29035 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
29036 __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29037 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29038 __pyx_ptype_5pysam_9libctabix_GZIteratorHead = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_GZIteratorHead_spec, __pyx_t_2);
|
|
jpayne@69
|
29039 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29040 if (unlikely(!__pyx_ptype_5pysam_9libctabix_GZIteratorHead)) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29041 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_GZIteratorHead_spec, __pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29042 #else
|
|
jpayne@69
|
29043 __pyx_ptype_5pysam_9libctabix_GZIteratorHead = &__pyx_type_5pysam_9libctabix_GZIteratorHead;
|
|
jpayne@69
|
29044 #endif
|
|
jpayne@69
|
29045 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29046 __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_base = __pyx_ptype_5pysam_9libctabix_GZIterator;
|
|
jpayne@69
|
29047 #endif
|
|
jpayne@69
|
29048 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
29049 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29050 #endif
|
|
jpayne@69
|
29051 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
29052 __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_print = 0;
|
|
jpayne@69
|
29053 #endif
|
|
jpayne@69
|
29054 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29055 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
29056 __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_getattro = __Pyx_PyObject_GenericGetAttr;
|
|
jpayne@69
|
29057 }
|
|
jpayne@69
|
29058 #endif
|
|
jpayne@69
|
29059 #if CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
29060 {
|
|
jpayne@69
|
29061 PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIteratorHead, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29062 if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) {
|
|
jpayne@69
|
29063 __pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
|
|
jpayne@69
|
29064 __pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__.doc = __pyx_doc_5pysam_9libctabix_14GZIteratorHead___next__;
|
|
jpayne@69
|
29065 ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__;
|
|
jpayne@69
|
29066 }
|
|
jpayne@69
|
29067 }
|
|
jpayne@69
|
29068 #endif
|
|
jpayne@69
|
29069 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_GZIteratorHead, __pyx_vtabptr_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29070 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29071 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
|
29072 #endif
|
|
jpayne@69
|
29073 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GZIteratorHead, (PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error)
|
|
jpayne@69
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29074 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29075 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error)
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jpayne@69
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29076 #endif
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jpayne@69
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29077 __pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed = &__pyx_vtable_5pysam_9libctabix_GZIteratorParsed;
|
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jpayne@69
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29078 __pyx_vtable_5pysam_9libctabix_GZIteratorParsed.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_GZIterator;
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jpayne@69
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29079 #if CYTHON_USE_TYPE_SPECS
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jpayne@69
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jpayne@69
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29081 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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jpayne@69
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29083 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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29084 if (unlikely(!__pyx_ptype_5pysam_9libctabix_GZIteratorParsed)) __PYX_ERR(0, 792, __pyx_L1_error)
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jpayne@69
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29085 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_GZIteratorParsed_spec, __pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error)
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jpayne@69
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29086 #else
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jpayne@69
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29087 __pyx_ptype_5pysam_9libctabix_GZIteratorParsed = &__pyx_type_5pysam_9libctabix_GZIteratorParsed;
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jpayne@69
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29088 #endif
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jpayne@69
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29089 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29090 __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_base = __pyx_ptype_5pysam_9libctabix_GZIterator;
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jpayne@69
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29091 #endif
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jpayne@69
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29092 #if !CYTHON_USE_TYPE_SPECS
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jpayne@69
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29093 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error)
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jpayne@69
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29094 #endif
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jpayne@69
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29095 #if PY_MAJOR_VERSION < 3
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jpayne@69
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29096 __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_print = 0;
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jpayne@69
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29097 #endif
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jpayne@69
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29098 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29099 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_getattro == PyObject_GenericGetAttr)) {
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jpayne@69
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29100 __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_getattro = __Pyx_PyObject_GenericGetAttr;
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jpayne@69
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29101 }
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jpayne@69
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jpayne@69
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29103 #if CYTHON_UPDATE_DESCRIPTOR_DOC
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jpayne@69
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29104 {
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jpayne@69
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29105 PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIteratorParsed, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 792, __pyx_L1_error)
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jpayne@69
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29106 if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) {
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jpayne@69
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29107 __pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
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jpayne@69
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29108 __pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__.doc = __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_2__next__;
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jpayne@69
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29109 ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__;
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jpayne@69
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29110 }
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jpayne@69
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29111 }
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29112 #endif
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jpayne@69
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29113 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed, __pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error)
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jpayne@69
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29114 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29115 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error)
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29116 #endif
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jpayne@69
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29118 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29119 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error)
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29120 #endif
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jpayne@69
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jpayne@69
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29122 __pyx_vtable_5pysam_9libctabix_Tabixfile.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_TabixFile;
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jpayne@69
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29123 #if CYTHON_USE_TYPE_SPECS
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jpayne@69
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jpayne@69
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29125 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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29126 __pyx_ptype_5pysam_9libctabix_Tabixfile = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_Tabixfile_spec, __pyx_t_2);
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jpayne@69
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29127 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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29128 if (unlikely(!__pyx_ptype_5pysam_9libctabix_Tabixfile)) __PYX_ERR(0, 1251, __pyx_L1_error)
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jpayne@69
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29129 if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_Tabixfile_spec, __pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error)
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jpayne@69
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29130 #else
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jpayne@69
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29131 __pyx_ptype_5pysam_9libctabix_Tabixfile = &__pyx_type_5pysam_9libctabix_Tabixfile;
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jpayne@69
|
29132 #endif
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jpayne@69
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29133 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29134 __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_base = __pyx_ptype_5pysam_9libctabix_TabixFile;
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jpayne@69
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29135 #endif
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jpayne@69
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29136 #if !CYTHON_USE_TYPE_SPECS
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jpayne@69
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29137 if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error)
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jpayne@69
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29138 #endif
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jpayne@69
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29139 #if PY_MAJOR_VERSION < 3
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jpayne@69
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29140 __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_print = 0;
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jpayne@69
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29141 #endif
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jpayne@69
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29142 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29143 if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_Tabixfile->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_getattro == PyObject_GenericGetAttr)) {
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jpayne@69
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29144 __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_getattro = __Pyx_PyObject_GenericGetAttr;
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jpayne@69
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29145 }
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jpayne@69
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29146 #endif
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jpayne@69
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29147 if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_Tabixfile, __pyx_vtabptr_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error)
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jpayne@69
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29148 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29149 if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error)
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29150 #endif
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29151 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Tabixfile, (PyObject *) __pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error)
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jpayne@69
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29152 #if !CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29153 if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error)
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29154 #endif
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29156 __Pyx_RefNannyFinishContext();
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jpayne@69
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29157 return 0;
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29159 __Pyx_XDECREF(__pyx_t_1);
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29160 __Pyx_XDECREF(__pyx_t_2);
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29161 __Pyx_RefNannyFinishContext();
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jpayne@69
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29162 return -1;
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jpayne@69
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29163 }
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jpayne@69
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29164
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jpayne@69
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29165 static int __Pyx_modinit_type_import_code(void) {
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jpayne@69
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29166 __Pyx_RefNannyDeclarations
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29167 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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29169 const char *__pyx_filename = NULL;
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29170 int __pyx_clineno = 0;
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29171 __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0);
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29174 __Pyx_GOTREF(__pyx_t_1);
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29175 __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type",
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jpayne@69
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29176 #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000
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jpayne@69
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29177 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject),
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jpayne@69
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29178 #elif CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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29179 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject),
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jpayne@69
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29180 #else
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jpayne@69
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29181 sizeof(PyHeapTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyHeapTypeObject),
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29182 #endif
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29183 __Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(5, 9, __pyx_L1_error)
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29186 __Pyx_GOTREF(__pyx_t_1);
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29187 __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyBoolObject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4bool_bool) __PYX_ERR(6, 8, __pyx_L1_error)
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29188 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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29190 __Pyx_GOTREF(__pyx_t_1);
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29191 __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyComplexObject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_7complex_complex) __PYX_ERR(7, 15, __pyx_L1_error)
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29192 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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29196 __pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy)) __PYX_ERR(8, 5, __pyx_L1_error)
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29205 __pyx_vtabptr_5pysam_16libctabixproxies_BedProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_BedProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_BedProxy)) __PYX_ERR(8, 46, __pyx_L1_error)
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|
jpayne@69
|
29206 __pyx_ptype_5pysam_16libctabixproxies_VCFProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_VCFProxy) __PYX_ERR(8, 58, __pyx_L1_error)
|
|
jpayne@69
|
29207 __pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_VCFProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy)) __PYX_ERR(8, 58, __pyx_L1_error)
|
|
jpayne@69
|
29208 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
29209 __pyx_t_1 = PyImport_ImportModule("array"); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 69, __pyx_L1_error)
|
|
jpayne@69
|
29210 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
29211 __pyx_ptype_7cpython_5array_array = __Pyx_ImportType_3_0_11(__pyx_t_1, "array", "array", sizeof(arrayobject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(arrayobject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_5array_array) __PYX_ERR(3, 69, __pyx_L1_error)
|
|
jpayne@69
|
29212 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
29213 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
29214 return 0;
|
|
jpayne@69
|
29215 __pyx_L1_error:;
|
|
jpayne@69
|
29216 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
29217 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
29218 return -1;
|
|
jpayne@69
|
29219 }
|
|
jpayne@69
|
29220
|
|
jpayne@69
|
29221 static int __Pyx_modinit_variable_import_code(void) {
|
|
jpayne@69
|
29222 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
29223 __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0);
|
|
jpayne@69
|
29224 /*--- Variable import code ---*/
|
|
jpayne@69
|
29225 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
29226 return 0;
|
|
jpayne@69
|
29227 }
|
|
jpayne@69
|
29228
|
|
jpayne@69
|
29229 static int __Pyx_modinit_function_import_code(void) {
|
|
jpayne@69
|
29230 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
29231 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
29232 int __pyx_lineno = 0;
|
|
jpayne@69
|
29233 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
29234 int __pyx_clineno = 0;
|
|
jpayne@69
|
29235 __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0);
|
|
jpayne@69
|
29236 /*--- Function import code ---*/
|
|
jpayne@69
|
29237 __pyx_t_1 = PyImport_ImportModule("pysam.libcutils"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
29238 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
29239 if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "charptr_to_str", (void (**)(void))&__pyx_f_5pysam_9libcutils_charptr_to_str, "PyObject *(char const *, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
29240 if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "force_str", (void (**)(void))&__pyx_f_5pysam_9libcutils_force_str, "PyObject *(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
29241 if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "force_bytes", (void (**)(void))&__pyx_f_5pysam_9libcutils_force_bytes, "PyObject *(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_bytes *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
29242 if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "encode_filename", (void (**)(void))&__pyx_f_5pysam_9libcutils_encode_filename, "PyObject *(PyObject *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
29243 if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "from_string_and_size", (void (**)(void))&__pyx_f_5pysam_9libcutils_from_string_and_size, "PyObject *(char const *, size_t)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
29244 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
29245 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
29246 return 0;
|
|
jpayne@69
|
29247 __pyx_L1_error:;
|
|
jpayne@69
|
29248 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
29249 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
29250 return -1;
|
|
jpayne@69
|
29251 }
|
|
jpayne@69
|
29252
|
|
jpayne@69
|
29253
|
|
jpayne@69
|
29254 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
29255 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
29256 static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
|
|
jpayne@69
|
29257 static int __pyx_pymod_exec_libctabix(PyObject* module); /*proto*/
|
|
jpayne@69
|
29258 static PyModuleDef_Slot __pyx_moduledef_slots[] = {
|
|
jpayne@69
|
29259 {Py_mod_create, (void*)__pyx_pymod_create},
|
|
jpayne@69
|
29260 {Py_mod_exec, (void*)__pyx_pymod_exec_libctabix},
|
|
jpayne@69
|
29261 {0, NULL}
|
|
jpayne@69
|
29262 };
|
|
jpayne@69
|
29263 #endif
|
|
jpayne@69
|
29264
|
|
jpayne@69
|
29265 #ifdef __cplusplus
|
|
jpayne@69
|
29266 namespace {
|
|
jpayne@69
|
29267 struct PyModuleDef __pyx_moduledef =
|
|
jpayne@69
|
29268 #else
|
|
jpayne@69
|
29269 static struct PyModuleDef __pyx_moduledef =
|
|
jpayne@69
|
29270 #endif
|
|
jpayne@69
|
29271 {
|
|
jpayne@69
|
29272 PyModuleDef_HEAD_INIT,
|
|
jpayne@69
|
29273 "libctabix",
|
|
jpayne@69
|
29274 0, /* m_doc */
|
|
jpayne@69
|
29275 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
29276 0, /* m_size */
|
|
jpayne@69
|
29277 #elif CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
29278 sizeof(__pyx_mstate), /* m_size */
|
|
jpayne@69
|
29279 #else
|
|
jpayne@69
|
29280 -1, /* m_size */
|
|
jpayne@69
|
29281 #endif
|
|
jpayne@69
|
29282 __pyx_methods /* m_methods */,
|
|
jpayne@69
|
29283 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
29284 __pyx_moduledef_slots, /* m_slots */
|
|
jpayne@69
|
29285 #else
|
|
jpayne@69
|
29286 NULL, /* m_reload */
|
|
jpayne@69
|
29287 #endif
|
|
jpayne@69
|
29288 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
29289 __pyx_m_traverse, /* m_traverse */
|
|
jpayne@69
|
29290 __pyx_m_clear, /* m_clear */
|
|
jpayne@69
|
29291 NULL /* m_free */
|
|
jpayne@69
|
29292 #else
|
|
jpayne@69
|
29293 NULL, /* m_traverse */
|
|
jpayne@69
|
29294 NULL, /* m_clear */
|
|
jpayne@69
|
29295 NULL /* m_free */
|
|
jpayne@69
|
29296 #endif
|
|
jpayne@69
|
29297 };
|
|
jpayne@69
|
29298 #ifdef __cplusplus
|
|
jpayne@69
|
29299 } /* anonymous namespace */
|
|
jpayne@69
|
29300 #endif
|
|
jpayne@69
|
29301 #endif
|
|
jpayne@69
|
29302
|
|
jpayne@69
|
29303 #ifndef CYTHON_NO_PYINIT_EXPORT
|
|
jpayne@69
|
29304 #define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
|
|
jpayne@69
|
29305 #elif PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
29306 #ifdef __cplusplus
|
|
jpayne@69
|
29307 #define __Pyx_PyMODINIT_FUNC extern "C" void
|
|
jpayne@69
|
29308 #else
|
|
jpayne@69
|
29309 #define __Pyx_PyMODINIT_FUNC void
|
|
jpayne@69
|
29310 #endif
|
|
jpayne@69
|
29311 #else
|
|
jpayne@69
|
29312 #ifdef __cplusplus
|
|
jpayne@69
|
29313 #define __Pyx_PyMODINIT_FUNC extern "C" PyObject *
|
|
jpayne@69
|
29314 #else
|
|
jpayne@69
|
29315 #define __Pyx_PyMODINIT_FUNC PyObject *
|
|
jpayne@69
|
29316 #endif
|
|
jpayne@69
|
29317 #endif
|
|
jpayne@69
|
29318
|
|
jpayne@69
|
29319
|
|
jpayne@69
|
29320 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
29321 __Pyx_PyMODINIT_FUNC initlibctabix(void) CYTHON_SMALL_CODE; /*proto*/
|
|
jpayne@69
|
29322 __Pyx_PyMODINIT_FUNC initlibctabix(void)
|
|
jpayne@69
|
29323 #else
|
|
jpayne@69
|
29324 __Pyx_PyMODINIT_FUNC PyInit_libctabix(void) CYTHON_SMALL_CODE; /*proto*/
|
|
jpayne@69
|
29325 __Pyx_PyMODINIT_FUNC PyInit_libctabix(void)
|
|
jpayne@69
|
29326 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
29327 {
|
|
jpayne@69
|
29328 return PyModuleDef_Init(&__pyx_moduledef);
|
|
jpayne@69
|
29329 }
|
|
jpayne@69
|
29330 static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) {
|
|
jpayne@69
|
29331 #if PY_VERSION_HEX >= 0x030700A1
|
|
jpayne@69
|
29332 static PY_INT64_T main_interpreter_id = -1;
|
|
jpayne@69
|
29333 PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp);
|
|
jpayne@69
|
29334 if (main_interpreter_id == -1) {
|
|
jpayne@69
|
29335 main_interpreter_id = current_id;
|
|
jpayne@69
|
29336 return (unlikely(current_id == -1)) ? -1 : 0;
|
|
jpayne@69
|
29337 } else if (unlikely(main_interpreter_id != current_id))
|
|
jpayne@69
|
29338 #else
|
|
jpayne@69
|
29339 static PyInterpreterState *main_interpreter = NULL;
|
|
jpayne@69
|
29340 PyInterpreterState *current_interpreter = PyThreadState_Get()->interp;
|
|
jpayne@69
|
29341 if (!main_interpreter) {
|
|
jpayne@69
|
29342 main_interpreter = current_interpreter;
|
|
jpayne@69
|
29343 } else if (unlikely(main_interpreter != current_interpreter))
|
|
jpayne@69
|
29344 #endif
|
|
jpayne@69
|
29345 {
|
|
jpayne@69
|
29346 PyErr_SetString(
|
|
jpayne@69
|
29347 PyExc_ImportError,
|
|
jpayne@69
|
29348 "Interpreter change detected - this module can only be loaded into one interpreter per process.");
|
|
jpayne@69
|
29349 return -1;
|
|
jpayne@69
|
29350 }
|
|
jpayne@69
|
29351 return 0;
|
|
jpayne@69
|
29352 }
|
|
jpayne@69
|
29353 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29354 static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *module, const char* from_name, const char* to_name, int allow_none)
|
|
jpayne@69
|
29355 #else
|
|
jpayne@69
|
29356 static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *moddict, const char* from_name, const char* to_name, int allow_none)
|
|
jpayne@69
|
29357 #endif
|
|
jpayne@69
|
29358 {
|
|
jpayne@69
|
29359 PyObject *value = PyObject_GetAttrString(spec, from_name);
|
|
jpayne@69
|
29360 int result = 0;
|
|
jpayne@69
|
29361 if (likely(value)) {
|
|
jpayne@69
|
29362 if (allow_none || value != Py_None) {
|
|
jpayne@69
|
29363 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29364 result = PyModule_AddObject(module, to_name, value);
|
|
jpayne@69
|
29365 #else
|
|
jpayne@69
|
29366 result = PyDict_SetItemString(moddict, to_name, value);
|
|
jpayne@69
|
29367 #endif
|
|
jpayne@69
|
29368 }
|
|
jpayne@69
|
29369 Py_DECREF(value);
|
|
jpayne@69
|
29370 } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) {
|
|
jpayne@69
|
29371 PyErr_Clear();
|
|
jpayne@69
|
29372 } else {
|
|
jpayne@69
|
29373 result = -1;
|
|
jpayne@69
|
29374 }
|
|
jpayne@69
|
29375 return result;
|
|
jpayne@69
|
29376 }
|
|
jpayne@69
|
29377 static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def) {
|
|
jpayne@69
|
29378 PyObject *module = NULL, *moddict, *modname;
|
|
jpayne@69
|
29379 CYTHON_UNUSED_VAR(def);
|
|
jpayne@69
|
29380 if (__Pyx_check_single_interpreter())
|
|
jpayne@69
|
29381 return NULL;
|
|
jpayne@69
|
29382 if (__pyx_m)
|
|
jpayne@69
|
29383 return __Pyx_NewRef(__pyx_m);
|
|
jpayne@69
|
29384 modname = PyObject_GetAttrString(spec, "name");
|
|
jpayne@69
|
29385 if (unlikely(!modname)) goto bad;
|
|
jpayne@69
|
29386 module = PyModule_NewObject(modname);
|
|
jpayne@69
|
29387 Py_DECREF(modname);
|
|
jpayne@69
|
29388 if (unlikely(!module)) goto bad;
|
|
jpayne@69
|
29389 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
29390 moddict = module;
|
|
jpayne@69
|
29391 #else
|
|
jpayne@69
|
29392 moddict = PyModule_GetDict(module);
|
|
jpayne@69
|
29393 if (unlikely(!moddict)) goto bad;
|
|
jpayne@69
|
29394 #endif
|
|
jpayne@69
|
29395 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad;
|
|
jpayne@69
|
29396 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad;
|
|
jpayne@69
|
29397 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad;
|
|
jpayne@69
|
29398 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad;
|
|
jpayne@69
|
29399 return module;
|
|
jpayne@69
|
29400 bad:
|
|
jpayne@69
|
29401 Py_XDECREF(module);
|
|
jpayne@69
|
29402 return NULL;
|
|
jpayne@69
|
29403 }
|
|
jpayne@69
|
29404
|
|
jpayne@69
|
29405
|
|
jpayne@69
|
29406 static CYTHON_SMALL_CODE int __pyx_pymod_exec_libctabix(PyObject *__pyx_pyinit_module)
|
|
jpayne@69
|
29407 #endif
|
|
jpayne@69
|
29408 #endif
|
|
jpayne@69
|
29409 {
|
|
jpayne@69
|
29410 int stringtab_initialized = 0;
|
|
jpayne@69
|
29411 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
29412 int pystate_addmodule_run = 0;
|
|
jpayne@69
|
29413 #endif
|
|
jpayne@69
|
29414 __Pyx_TraceDeclarations
|
|
jpayne@69
|
29415 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
29416 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
29417 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
29418 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
29419 int __pyx_lineno = 0;
|
|
jpayne@69
|
29420 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
29421 int __pyx_clineno = 0;
|
|
jpayne@69
|
29422 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
29423 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
29424 if (__pyx_m) {
|
|
jpayne@69
|
29425 if (__pyx_m == __pyx_pyinit_module) return 0;
|
|
jpayne@69
|
29426 PyErr_SetString(PyExc_RuntimeError, "Module 'libctabix' has already been imported. Re-initialisation is not supported.");
|
|
jpayne@69
|
29427 return -1;
|
|
jpayne@69
|
29428 }
|
|
jpayne@69
|
29429 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
29430 if (__pyx_m) return __Pyx_NewRef(__pyx_m);
|
|
jpayne@69
|
29431 #endif
|
|
jpayne@69
|
29432 /*--- Module creation code ---*/
|
|
jpayne@69
|
29433 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
29434 __pyx_m = __pyx_pyinit_module;
|
|
jpayne@69
|
29435 Py_INCREF(__pyx_m);
|
|
jpayne@69
|
29436 #else
|
|
jpayne@69
|
29437 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
29438 __pyx_m = Py_InitModule4("libctabix", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
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29439 if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
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29440 #elif CYTHON_USE_MODULE_STATE
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29441 __pyx_t_1 = PyModule_Create(&__pyx_moduledef); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29442 {
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jpayne@69
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29443 int add_module_result = PyState_AddModule(__pyx_t_1, &__pyx_moduledef);
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jpayne@69
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29444 __pyx_t_1 = 0; /* transfer ownership from __pyx_t_1 to "libctabix" pseudovariable */
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29445 if (unlikely((add_module_result < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29446 pystate_addmodule_run = 1;
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29447 }
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jpayne@69
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29448 #else
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29449 __pyx_m = PyModule_Create(&__pyx_moduledef);
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29453 CYTHON_UNUSED_VAR(__pyx_t_1);
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29457 __pyx_cython_runtime = __Pyx_PyImport_AddModuleRef((const char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error)
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29465 Py_FatalError("failed to import 'refnanny' module");
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29468 __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_libctabix(void)", 0);
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29483 if (__pyx_Coroutine_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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29484 #endif
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29486 if (__pyx_Generator_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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29487 #endif
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29490 #endif
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29492 if (__pyx_StopAsyncIteration_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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29493 #endif
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jpayne@69
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29495 /*--- Threads initialization code ---*/
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29496 #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
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jpayne@69
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29497 PyEval_InitThreads();
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29498 #endif
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29499 /*--- Initialize various global constants etc. ---*/
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29500 if (__Pyx_InitConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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29501 stringtab_initialized = 1;
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29502 if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29503 #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
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jpayne@69
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29504 if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29505 #endif
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29506 if (__pyx_module_is_main_pysam__libctabix) {
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29507 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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29508 }
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29509 #if PY_MAJOR_VERSION >= 3
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jpayne@69
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29510 {
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jpayne@69
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29511 PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
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29512 if (!PyDict_GetItemString(modules, "pysam.libctabix")) {
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29513 if (unlikely((PyDict_SetItemString(modules, "pysam.libctabix", __pyx_m) < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29514 }
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29515 }
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29516 #endif
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29519 /*--- Constants init code ---*/
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29521 /*--- Global type/function init code ---*/
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jpayne@69
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29522 (void)__Pyx_modinit_global_init_code();
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29523 (void)__Pyx_modinit_variable_export_code();
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jpayne@69
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29524 (void)__Pyx_modinit_function_export_code();
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jpayne@69
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29525 if (unlikely((__Pyx_modinit_type_init_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
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29526 if (unlikely((__Pyx_modinit_type_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29527 (void)__Pyx_modinit_variable_import_code();
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jpayne@69
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29528 if (unlikely((__Pyx_modinit_function_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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29529 /*--- Execution code ---*/
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29530 #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
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29531 if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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29532 #endif
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29533 __Pyx_TraceCall("__Pyx_PyMODINIT_FUNC PyInit_libctabix(void)", __pyx_f[0], 1, 0, __PYX_ERR(0, 1, __pyx_L1_error));
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29534
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jpayne@69
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29535 /* "pysam/libctabix.pyx":57
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jpayne@69
|
29536 * #
|
|
jpayne@69
|
29537 * ###############################################################################
|
|
jpayne@69
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29538 * import os # <<<<<<<<<<<<<<
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|
jpayne@69
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29539 * import sys
|
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jpayne@69
|
29540 *
|
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jpayne@69
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29541 */
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jpayne@69
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29542 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_os, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 57, __pyx_L1_error)
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29543 __Pyx_GOTREF(__pyx_t_2);
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29544 if (PyDict_SetItem(__pyx_d, __pyx_n_s_os, __pyx_t_2) < 0) __PYX_ERR(0, 57, __pyx_L1_error)
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29545 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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29546
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jpayne@69
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29547 /* "pysam/libctabix.pyx":58
|
|
jpayne@69
|
29548 * ###############################################################################
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|
jpayne@69
|
29549 * import os
|
|
jpayne@69
|
29550 * import sys # <<<<<<<<<<<<<<
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jpayne@69
|
29551 *
|
|
jpayne@69
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29552 * from libc.stdio cimport printf, fprintf, stderr
|
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jpayne@69
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29553 */
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jpayne@69
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29554 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_sys, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 58, __pyx_L1_error)
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29555 __Pyx_GOTREF(__pyx_t_2);
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29556 if (PyDict_SetItem(__pyx_d, __pyx_n_s_sys, __pyx_t_2) < 0) __PYX_ERR(0, 58, __pyx_L1_error)
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29557 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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29558
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jpayne@69
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29559 /* "pysam/libctabix.pyx":87
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jpayne@69
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29560 * self.encoding = encoding
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jpayne@69
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29561 *
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jpayne@69
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29562 * def set_encoding(self, encoding): # <<<<<<<<<<<<<<
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jpayne@69
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29563 * self.encoding = encoding
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jpayne@69
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29564 *
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jpayne@69
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29565 */
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29566 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6Parser_3set_encoding, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Parser_set_encoding, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj_)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 87, __pyx_L1_error)
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29567 __Pyx_GOTREF(__pyx_t_2);
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29568 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser, __pyx_n_s_set_encoding, __pyx_t_2) < 0) __PYX_ERR(0, 87, __pyx_L1_error)
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29569 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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29570 PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser);
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29571
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29572 /* "pysam/libctabix.pyx":90
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jpayne@69
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29573 * self.encoding = encoding
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29574 *
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29582 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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29583 PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser);
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29584
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29589 */
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29594 PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser);
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29595
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29597 * else:
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jpayne@69
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29599 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
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29601 */
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29609 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
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29615 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asTuple, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
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29616 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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29617 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asTuple);
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29618
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jpayne@69
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29619 /* "(tree fragment)":16
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jpayne@69
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29620 * else:
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29621 * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state)
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29622 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
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29623 * __pyx_unpickle_asTuple__set_state(self, __pyx_state)
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jpayne@69
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29624 */
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jpayne@69
|
29627 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asTuple, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29628 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29629 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asTuple);
|
|
jpayne@69
|
29630
|
|
jpayne@69
|
29631 /* "(tree fragment)":1
|
|
jpayne@69
|
29632 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29633 * cdef tuple state
|
|
jpayne@69
|
29634 * cdef object _dict
|
|
jpayne@69
|
29635 */
|
|
jpayne@69
|
29636 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6asGFF3_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGFF3___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__7)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29637 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29638 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGFF3, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29639 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29640 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGFF3);
|
|
jpayne@69
|
29641
|
|
jpayne@69
|
29642 /* "(tree fragment)":16
|
|
jpayne@69
|
29643 * else:
|
|
jpayne@69
|
29644 * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
29645 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29646 * __pyx_unpickle_asGFF3__set_state(self, __pyx_state)
|
|
jpayne@69
|
29647 */
|
|
jpayne@69
|
29648 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6asGFF3_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGFF3___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__8)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29649 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29650 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGFF3, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29651 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29652 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGFF3);
|
|
jpayne@69
|
29653
|
|
jpayne@69
|
29654 /* "(tree fragment)":1
|
|
jpayne@69
|
29655 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29656 * cdef tuple state
|
|
jpayne@69
|
29657 * cdef object _dict
|
|
jpayne@69
|
29658 */
|
|
jpayne@69
|
29659 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asGTF_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGTF___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__9)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29660 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29661 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGTF, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29662 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29663 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGTF);
|
|
jpayne@69
|
29664
|
|
jpayne@69
|
29665 /* "(tree fragment)":16
|
|
jpayne@69
|
29666 * else:
|
|
jpayne@69
|
29667 * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
29668 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29669 * __pyx_unpickle_asGTF__set_state(self, __pyx_state)
|
|
jpayne@69
|
29670 */
|
|
jpayne@69
|
29671 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asGTF_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGTF___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29672 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29673 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGTF, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29674 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29675 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGTF);
|
|
jpayne@69
|
29676
|
|
jpayne@69
|
29677 /* "(tree fragment)":1
|
|
jpayne@69
|
29678 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29679 * cdef tuple state
|
|
jpayne@69
|
29680 * cdef object _dict
|
|
jpayne@69
|
29681 */
|
|
jpayne@69
|
29682 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asBed_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asBed___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__11)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29683 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29684 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asBed, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29685 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29686 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asBed);
|
|
jpayne@69
|
29687
|
|
jpayne@69
|
29688 /* "(tree fragment)":16
|
|
jpayne@69
|
29689 * else:
|
|
jpayne@69
|
29690 * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
29691 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29692 * __pyx_unpickle_asBed__set_state(self, __pyx_state)
|
|
jpayne@69
|
29693 */
|
|
jpayne@69
|
29694 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asBed_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asBed___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__12)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29695 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29696 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asBed, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29697 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29698 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asBed);
|
|
jpayne@69
|
29699
|
|
jpayne@69
|
29700 /* "(tree fragment)":1
|
|
jpayne@69
|
29701 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29702 * cdef tuple state
|
|
jpayne@69
|
29703 * cdef object _dict
|
|
jpayne@69
|
29704 */
|
|
jpayne@69
|
29705 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asVCF_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asVCF___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__13)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29706 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29707 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asVCF, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29708 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29709 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asVCF);
|
|
jpayne@69
|
29710
|
|
jpayne@69
|
29711 /* "(tree fragment)":16
|
|
jpayne@69
|
29712 * else:
|
|
jpayne@69
|
29713 * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state)
|
|
jpayne@69
|
29714 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29715 * __pyx_unpickle_asVCF__set_state(self, __pyx_state)
|
|
jpayne@69
|
29716 */
|
|
jpayne@69
|
29717 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asVCF_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asVCF___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__14)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29718 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29719 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asVCF, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error)
|
|
jpayne@69
|
29720 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29721 PyType_Modified(__pyx_ptype_5pysam_9libctabix_asVCF);
|
|
jpayne@69
|
29722
|
|
jpayne@69
|
29723 /* "pysam/libctabix.pyx":352
|
|
jpayne@69
|
29724 * self.encoding = encoding
|
|
jpayne@69
|
29725 *
|
|
jpayne@69
|
29726 * def _open( self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29727 * filename,
|
|
jpayne@69
|
29728 * mode='r',
|
|
jpayne@69
|
29729 */
|
|
jpayne@69
|
29730 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_3_open, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile__open, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__15)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
29731 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29732 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__68);
|
|
jpayne@69
|
29733 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_open, __pyx_t_2) < 0) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
29734 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29735 PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
29736
|
|
jpayne@69
|
29737 /* "pysam/libctabix.pyx":404
|
|
jpayne@69
|
29738 * self.start_offset = self.tell()
|
|
jpayne@69
|
29739 *
|
|
jpayne@69
|
29740 * def _dup(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29741 * '''return a copy of this tabix file.
|
|
jpayne@69
|
29742 *
|
|
jpayne@69
|
29743 */
|
|
jpayne@69
|
29744 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_5_dup, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile__dup, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__17)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 404, __pyx_L1_error)
|
|
jpayne@69
|
29745 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29746 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_dup, __pyx_t_2) < 0) __PYX_ERR(0, 404, __pyx_L1_error)
|
|
jpayne@69
|
29747 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29748 PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
29749
|
|
jpayne@69
|
29750 /* "pysam/libctabix.pyx":416
|
|
jpayne@69
|
29751 * encoding=self.encoding)
|
|
jpayne@69
|
29752 *
|
|
jpayne@69
|
29753 * def fetch(self, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29754 * reference=None,
|
|
jpayne@69
|
29755 * start=None,
|
|
jpayne@69
|
29756 */
|
|
jpayne@69
|
29757 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_7fetch, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile_fetch, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__18)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
29758 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29759 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__70);
|
|
jpayne@69
|
29760 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_fetch, __pyx_t_2) < 0) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
29761 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29762 PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
29763
|
|
jpayne@69
|
29764 /* "pysam/libctabix.pyx":598
|
|
jpayne@69
|
29765 * return result
|
|
jpayne@69
|
29766 *
|
|
jpayne@69
|
29767 * def close(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29768 * '''
|
|
jpayne@69
|
29769 * closes the :class:`pysam.TabixFile`.'''
|
|
jpayne@69
|
29770 */
|
|
jpayne@69
|
29771 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_9close, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile_close, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__21)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 598, __pyx_L1_error)
|
|
jpayne@69
|
29772 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29773 if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_close, __pyx_t_2) < 0) __PYX_ERR(0, 598, __pyx_L1_error)
|
|
jpayne@69
|
29774 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29775 PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile);
|
|
jpayne@69
|
29776
|
|
jpayne@69
|
29777 /* "(tree fragment)":1
|
|
jpayne@69
|
29778 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29779 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
29780 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
29781 */
|
|
jpayne@69
|
29782 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_13__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__22)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29783 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29784 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29785 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29786
|
|
jpayne@69
|
29787 /* "(tree fragment)":3
|
|
jpayne@69
|
29788 * def __reduce_cython__(self):
|
|
jpayne@69
|
29789 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
29790 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29791 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
29792 */
|
|
jpayne@69
|
29793 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_15__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__23)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29794 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29795 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29796 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29797
|
|
jpayne@69
|
29798 /* "(tree fragment)":1
|
|
jpayne@69
|
29799 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29800 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29801 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
29802 */
|
|
jpayne@69
|
29803 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13TabixIterator_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIterator___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__25)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29804 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29805 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29806 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29807
|
|
jpayne@69
|
29808 /* "(tree fragment)":3
|
|
jpayne@69
|
29809 * def __reduce_cython__(self):
|
|
jpayne@69
|
29810 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29811 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29812 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29813 */
|
|
jpayne@69
|
29814 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13TabixIterator_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIterator___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__26)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29815 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29816 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29817 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29818
|
|
jpayne@69
|
29819 /* "pysam/libctabix.pyx":682
|
|
jpayne@69
|
29820 *
|
|
jpayne@69
|
29821 *
|
|
jpayne@69
|
29822 * class EmptyIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29823 * '''empty iterator'''
|
|
jpayne@69
|
29824 *
|
|
jpayne@69
|
29825 */
|
|
jpayne@69
|
29826 __pyx_t_2 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_EmptyIterator, __pyx_n_s_EmptyIterator, (PyObject *) NULL, __pyx_n_s_pysam_libctabix, __pyx_kp_s_empty_iterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 682, __pyx_L1_error)
|
|
jpayne@69
|
29827 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29828
|
|
jpayne@69
|
29829 /* "pysam/libctabix.pyx":685
|
|
jpayne@69
|
29830 * '''empty iterator'''
|
|
jpayne@69
|
29831 *
|
|
jpayne@69
|
29832 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29833 * return self
|
|
jpayne@69
|
29834 *
|
|
jpayne@69
|
29835 */
|
|
jpayne@69
|
29836 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13EmptyIterator_1__iter__, 0, __pyx_n_s_EmptyIterator___iter, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__27)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 685, __pyx_L1_error)
|
|
jpayne@69
|
29837 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
29838 if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_iter, __pyx_t_3) < 0) __PYX_ERR(0, 685, __pyx_L1_error)
|
|
jpayne@69
|
29839 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
29840
|
|
jpayne@69
|
29841 /* "pysam/libctabix.pyx":688
|
|
jpayne@69
|
29842 * return self
|
|
jpayne@69
|
29843 *
|
|
jpayne@69
|
29844 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29845 * raise StopIteration()
|
|
jpayne@69
|
29846 *
|
|
jpayne@69
|
29847 */
|
|
jpayne@69
|
29848 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13EmptyIterator_3__next__, 0, __pyx_n_s_EmptyIterator___next, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__28)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 688, __pyx_L1_error)
|
|
jpayne@69
|
29849 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
29850 if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_next, __pyx_t_3) < 0) __PYX_ERR(0, 688, __pyx_L1_error)
|
|
jpayne@69
|
29851 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
29852
|
|
jpayne@69
|
29853 /* "pysam/libctabix.pyx":682
|
|
jpayne@69
|
29854 *
|
|
jpayne@69
|
29855 *
|
|
jpayne@69
|
29856 * class EmptyIterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29857 * '''empty iterator'''
|
|
jpayne@69
|
29858 *
|
|
jpayne@69
|
29859 */
|
|
jpayne@69
|
29860 __pyx_t_3 = __Pyx_Py3ClassCreate(((PyObject*)&PyType_Type), __pyx_n_s_EmptyIterator, __pyx_empty_tuple, __pyx_t_2, NULL, 0, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 682, __pyx_L1_error)
|
|
jpayne@69
|
29861 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
29862 if (PyDict_SetItem(__pyx_d, __pyx_n_s_EmptyIterator, __pyx_t_3) < 0) __PYX_ERR(0, 682, __pyx_L1_error)
|
|
jpayne@69
|
29863 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
29864 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29865
|
|
jpayne@69
|
29866 /* "(tree fragment)":1
|
|
jpayne@69
|
29867 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29868 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29869 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
29870 */
|
|
jpayne@69
|
29871 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIteratorParsed___reduce_cyt, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__29)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29872 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29873 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29874 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29875
|
|
jpayne@69
|
29876 /* "(tree fragment)":3
|
|
jpayne@69
|
29877 * def __reduce_cython__(self):
|
|
jpayne@69
|
29878 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29879 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29880 * raise TypeError, "self.iterator cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29881 */
|
|
jpayne@69
|
29882 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIteratorParsed___setstate_c, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__30)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29883 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29884 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29885 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29886
|
|
jpayne@69
|
29887 /* "(tree fragment)":1
|
|
jpayne@69
|
29888 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29889 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29890 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
29891 */
|
|
jpayne@69
|
29892 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_10GZIterator_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIterator___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__31)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29893 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29894 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29895 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29896
|
|
jpayne@69
|
29897 /* "(tree fragment)":3
|
|
jpayne@69
|
29898 * def __reduce_cython__(self):
|
|
jpayne@69
|
29899 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29900 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29901 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29902 */
|
|
jpayne@69
|
29903 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_10GZIterator_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIterator___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__32)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29904 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29905 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29906 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29907
|
|
jpayne@69
|
29908 /* "(tree fragment)":1
|
|
jpayne@69
|
29909 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29910 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29911 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
29912 */
|
|
jpayne@69
|
29913 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorHead___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__33)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29914 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29915 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29916 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29917
|
|
jpayne@69
|
29918 /* "(tree fragment)":3
|
|
jpayne@69
|
29919 * def __reduce_cython__(self):
|
|
jpayne@69
|
29920 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29921 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29922 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29923 */
|
|
jpayne@69
|
29924 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorHead___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__34)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29925 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29926 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29927 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29928
|
|
jpayne@69
|
29929 /* "(tree fragment)":1
|
|
jpayne@69
|
29930 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29931 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29932 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
29933 */
|
|
jpayne@69
|
29934 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorParsed___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__35)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29935 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29936 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
29937 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29938
|
|
jpayne@69
|
29939 /* "(tree fragment)":3
|
|
jpayne@69
|
29940 * def __reduce_cython__(self):
|
|
jpayne@69
|
29941 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29942 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29943 * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"
|
|
jpayne@69
|
29944 */
|
|
jpayne@69
|
29945 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorParsed___setstate_cyth, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__36)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29946 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29947 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
29948 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29949
|
|
jpayne@69
|
29950 /* "pysam/libctabix.pyx":811
|
|
jpayne@69
|
29951 *
|
|
jpayne@69
|
29952 *
|
|
jpayne@69
|
29953 * def tabix_compress(filename_in, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29954 * filename_out,
|
|
jpayne@69
|
29955 * force=False):
|
|
jpayne@69
|
29956 */
|
|
jpayne@69
|
29957 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_1tabix_compress, 0, __pyx_n_s_tabix_compress, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__37)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 811, __pyx_L1_error)
|
|
jpayne@69
|
29958 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29959 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__72);
|
|
jpayne@69
|
29960 if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_compress, __pyx_t_2) < 0) __PYX_ERR(0, 811, __pyx_L1_error)
|
|
jpayne@69
|
29961 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
29962
|
|
jpayne@69
|
29963 /* "pysam/libctabix.pyx":880
|
|
jpayne@69
|
29964 * preset=None,
|
|
jpayne@69
|
29965 * meta_char="#",
|
|
jpayne@69
|
29966 * int line_skip=0, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29967 * zerobased=False,
|
|
jpayne@69
|
29968 * int min_shift=-1,
|
|
jpayne@69
|
29969 */
|
|
jpayne@69
|
29970 __pyx_t_2 = __Pyx_PyInt_From_int(((int)0)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 880, __pyx_L1_error)
|
|
jpayne@69
|
29971 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
29972
|
|
jpayne@69
|
29973 /* "pysam/libctabix.pyx":882
|
|
jpayne@69
|
29974 * int line_skip=0,
|
|
jpayne@69
|
29975 * zerobased=False,
|
|
jpayne@69
|
29976 * int min_shift=-1, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29977 * index=None,
|
|
jpayne@69
|
29978 * keep_original=False,
|
|
jpayne@69
|
29979 */
|
|
jpayne@69
|
29980 __pyx_t_3 = __Pyx_PyInt_From_int(((int)-1)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 882, __pyx_L1_error)
|
|
jpayne@69
|
29981 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
29982
|
|
jpayne@69
|
29983 /* "pysam/libctabix.pyx":873
|
|
jpayne@69
|
29984 *
|
|
jpayne@69
|
29985 *
|
|
jpayne@69
|
29986 * def tabix_index(filename, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
29987 * force=False,
|
|
jpayne@69
|
29988 * seq_col=None,
|
|
jpayne@69
|
29989 */
|
|
jpayne@69
|
29990 __pyx_t_4 = PyTuple_New(12); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 873, __pyx_L1_error)
|
|
jpayne@69
|
29991 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
29992 __Pyx_INCREF(((PyObject *)Py_False));
|
|
jpayne@69
|
29993 __Pyx_GIVEREF(((PyObject *)Py_False));
|
|
jpayne@69
|
29994 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
29995 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
29996 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
29997 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
29998 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
29999 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
30000 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30001 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
30002 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
30003 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 3, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30004 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
30005 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
30006 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 4, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30007 __Pyx_INCREF(((PyObject*)__pyx_kp_u__39));
|
|
jpayne@69
|
30008 __Pyx_GIVEREF(((PyObject*)__pyx_kp_u__39));
|
|
jpayne@69
|
30009 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 5, ((PyObject*)__pyx_kp_u__39))) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30010 __Pyx_GIVEREF(__pyx_t_2);
|
|
jpayne@69
|
30011 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 6, __pyx_t_2)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30012 __Pyx_INCREF(((PyObject *)Py_False));
|
|
jpayne@69
|
30013 __Pyx_GIVEREF(((PyObject *)Py_False));
|
|
jpayne@69
|
30014 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 7, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30015 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
30016 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 8, __pyx_t_3)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30017 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
30018 __Pyx_GIVEREF(Py_None);
|
|
jpayne@69
|
30019 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 9, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30020 __Pyx_INCREF(((PyObject *)Py_False));
|
|
jpayne@69
|
30021 __Pyx_GIVEREF(((PyObject *)Py_False));
|
|
jpayne@69
|
30022 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 10, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30023 __Pyx_INCREF(((PyObject *)Py_False));
|
|
jpayne@69
|
30024 __Pyx_GIVEREF(((PyObject *)Py_False));
|
|
jpayne@69
|
30025 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 11, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error);
|
|
jpayne@69
|
30026 __pyx_t_2 = 0;
|
|
jpayne@69
|
30027 __pyx_t_3 = 0;
|
|
jpayne@69
|
30028 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_3tabix_index, 0, __pyx_n_s_tabix_index, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__40)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 873, __pyx_L1_error)
|
|
jpayne@69
|
30029 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30030 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_t_4);
|
|
jpayne@69
|
30031 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
30032 if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_index, __pyx_t_3) < 0) __PYX_ERR(0, 873, __pyx_L1_error)
|
|
jpayne@69
|
30033 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30034
|
|
jpayne@69
|
30035 /* "(tree fragment)":1
|
|
jpayne@69
|
30036 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30037 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
30038 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
30039 */
|
|
jpayne@69
|
30040 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_tabix_file_iterator___reduce_cyt, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__46)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30041 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30042 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30043 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30044
|
|
jpayne@69
|
30045 /* "(tree fragment)":3
|
|
jpayne@69
|
30046 * def __reduce_cython__(self):
|
|
jpayne@69
|
30047 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
30048 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30049 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
30050 */
|
|
jpayne@69
|
30051 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_tabix_file_iterator___setstate_c, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__47)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
30052 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30053 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
30054 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30055
|
|
jpayne@69
|
30056 /* "pysam/libctabix.pyx":1178
|
|
jpayne@69
|
30057 *
|
|
jpayne@69
|
30058 *
|
|
jpayne@69
|
30059 * class tabix_generic_iterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30060 * '''iterate over ``infile``.
|
|
jpayne@69
|
30061 *
|
|
jpayne@69
|
30062 */
|
|
jpayne@69
|
30063 __pyx_t_3 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_tabix_generic_iterator, __pyx_n_s_tabix_generic_iterator, (PyObject *) NULL, __pyx_n_s_pysam_libctabix, __pyx_kp_s_iterate_over_infile_Permits_the); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1178, __pyx_L1_error)
|
|
jpayne@69
|
30064 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30065
|
|
jpayne@69
|
30066 /* "pysam/libctabix.pyx":1183
|
|
jpayne@69
|
30067 * Permits the use of file-like objects for example from the gzip module.
|
|
jpayne@69
|
30068 * '''
|
|
jpayne@69
|
30069 * def __init__(self, infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30070 *
|
|
jpayne@69
|
30071 * self.infile = infile
|
|
jpayne@69
|
30072 */
|
|
jpayne@69
|
30073 __pyx_t_4 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_1__init__, 0, __pyx_n_s_tabix_generic_iterator___init, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__48)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1183, __pyx_L1_error)
|
|
jpayne@69
|
30074 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
30075 if (__Pyx_SetNameInClass(__pyx_t_3, __pyx_n_s_init, __pyx_t_4) < 0) __PYX_ERR(0, 1183, __pyx_L1_error)
|
|
jpayne@69
|
30076 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
30077
|
|
jpayne@69
|
30078 /* "pysam/libctabix.pyx":1190
|
|
jpayne@69
|
30079 * self.parser = parser
|
|
jpayne@69
|
30080 *
|
|
jpayne@69
|
30081 * def __iter__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30082 * return self
|
|
jpayne@69
|
30083 *
|
|
jpayne@69
|
30084 */
|
|
jpayne@69
|
30085 __pyx_t_4 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_3__iter__, 0, __pyx_n_s_tabix_generic_iterator___iter, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__49)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1190, __pyx_L1_error)
|
|
jpayne@69
|
30086 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
30087 if (__Pyx_SetNameInClass(__pyx_t_3, __pyx_n_s_iter, __pyx_t_4) < 0) __PYX_ERR(0, 1190, __pyx_L1_error)
|
|
jpayne@69
|
30088 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
30089
|
|
jpayne@69
|
30090 /* "pysam/libctabix.pyx":1194
|
|
jpayne@69
|
30091 *
|
|
jpayne@69
|
30092 * # cython version - required for python 3
|
|
jpayne@69
|
30093 * def __next__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30094 *
|
|
jpayne@69
|
30095 * cdef char * b
|
|
jpayne@69
|
30096 */
|
|
jpayne@69
|
30097 __pyx_t_4 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_5__next__, 0, __pyx_n_s_tabix_generic_iterator___next, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__50)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1194, __pyx_L1_error)
|
|
jpayne@69
|
30098 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
30099 if (__Pyx_SetNameInClass(__pyx_t_3, __pyx_n_s_next, __pyx_t_4) < 0) __PYX_ERR(0, 1194, __pyx_L1_error)
|
|
jpayne@69
|
30100 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
30101
|
|
jpayne@69
|
30102 /* "pysam/libctabix.pyx":1178
|
|
jpayne@69
|
30103 *
|
|
jpayne@69
|
30104 *
|
|
jpayne@69
|
30105 * class tabix_generic_iterator: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30106 * '''iterate over ``infile``.
|
|
jpayne@69
|
30107 *
|
|
jpayne@69
|
30108 */
|
|
jpayne@69
|
30109 __pyx_t_4 = __Pyx_Py3ClassCreate(((PyObject*)&PyType_Type), __pyx_n_s_tabix_generic_iterator, __pyx_empty_tuple, __pyx_t_3, NULL, 0, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1178, __pyx_L1_error)
|
|
jpayne@69
|
30110 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
30111 if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_generic_iterator, __pyx_t_4) < 0) __PYX_ERR(0, 1178, __pyx_L1_error)
|
|
jpayne@69
|
30112 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
30113 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30114
|
|
jpayne@69
|
30115 /* "pysam/libctabix.pyx":1238
|
|
jpayne@69
|
30116 *
|
|
jpayne@69
|
30117 *
|
|
jpayne@69
|
30118 * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30119 * """return an iterator over all entries in a file.
|
|
jpayne@69
|
30120 *
|
|
jpayne@69
|
30121 */
|
|
jpayne@69
|
30122 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5tabix_iterator, 0, __pyx_n_s_tabix_iterator, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__51)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1238, __pyx_L1_error)
|
|
jpayne@69
|
30123 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30124 if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_iterator, __pyx_t_3) < 0) __PYX_ERR(0, 1238, __pyx_L1_error)
|
|
jpayne@69
|
30125 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30126
|
|
jpayne@69
|
30127 /* "(tree fragment)":1
|
|
jpayne@69
|
30128 * def __reduce_cython__(self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30129 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
30130 * def __setstate_cython__(self, __pyx_state):
|
|
jpayne@69
|
30131 */
|
|
jpayne@69
|
30132 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9Tabixfile_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Tabixfile___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__52)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30133 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30134 if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30135 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30136
|
|
jpayne@69
|
30137 /* "(tree fragment)":3
|
|
jpayne@69
|
30138 * def __reduce_cython__(self):
|
|
jpayne@69
|
30139 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
30140 * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30141 * raise TypeError, "no default __reduce__ due to non-trivial __cinit__"
|
|
jpayne@69
|
30142 */
|
|
jpayne@69
|
30143 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9Tabixfile_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Tabixfile___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__53)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
30144 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30145 if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error)
|
|
jpayne@69
|
30146 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30147
|
|
jpayne@69
|
30148 /* "pysam/libctabix.pyx":1256
|
|
jpayne@69
|
30149 *
|
|
jpayne@69
|
30150 *
|
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jpayne@69
|
30151 * __all__ = [ # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30152 * "tabix_index",
|
|
jpayne@69
|
30153 * "tabix_compress",
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jpayne@69
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30154 */
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jpayne@69
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30155 __pyx_t_3 = PyList_New(14); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1256, __pyx_L1_error)
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30156 __Pyx_GOTREF(__pyx_t_3);
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30157 __Pyx_INCREF(__pyx_n_u_tabix_index);
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30158 __Pyx_GIVEREF(__pyx_n_u_tabix_index);
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30159 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_u_tabix_index)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
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30160 __Pyx_INCREF(__pyx_n_u_tabix_compress);
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jpayne@69
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30161 __Pyx_GIVEREF(__pyx_n_u_tabix_compress);
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jpayne@69
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30162 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 1, __pyx_n_u_tabix_compress)) __PYX_ERR(0, 1256, __pyx_L1_error);
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30163 __Pyx_INCREF(__pyx_n_u_TabixFile);
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30164 __Pyx_GIVEREF(__pyx_n_u_TabixFile);
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jpayne@69
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30165 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 2, __pyx_n_u_TabixFile)) __PYX_ERR(0, 1256, __pyx_L1_error);
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30166 __Pyx_INCREF(__pyx_n_u_Tabixfile);
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30167 __Pyx_GIVEREF(__pyx_n_u_Tabixfile);
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jpayne@69
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30168 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 3, __pyx_n_u_Tabixfile)) __PYX_ERR(0, 1256, __pyx_L1_error);
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30169 __Pyx_INCREF(__pyx_n_u_asTuple);
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30170 __Pyx_GIVEREF(__pyx_n_u_asTuple);
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jpayne@69
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30171 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 4, __pyx_n_u_asTuple)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
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30172 __Pyx_INCREF(__pyx_n_u_asGTF);
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jpayne@69
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30173 __Pyx_GIVEREF(__pyx_n_u_asGTF);
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jpayne@69
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30174 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 5, __pyx_n_u_asGTF)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
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30175 __Pyx_INCREF(__pyx_n_u_asGFF3);
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jpayne@69
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30176 __Pyx_GIVEREF(__pyx_n_u_asGFF3);
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jpayne@69
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30177 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 6, __pyx_n_u_asGFF3)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
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30178 __Pyx_INCREF(__pyx_n_u_asVCF);
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jpayne@69
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30179 __Pyx_GIVEREF(__pyx_n_u_asVCF);
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jpayne@69
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30180 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 7, __pyx_n_u_asVCF)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
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30181 __Pyx_INCREF(__pyx_n_u_asBed);
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jpayne@69
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30182 __Pyx_GIVEREF(__pyx_n_u_asBed);
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jpayne@69
|
30183 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 8, __pyx_n_u_asBed)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
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30184 __Pyx_INCREF(__pyx_n_u_GZIterator);
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jpayne@69
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30185 __Pyx_GIVEREF(__pyx_n_u_GZIterator);
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jpayne@69
|
30186 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 9, __pyx_n_u_GZIterator)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
|
30187 __Pyx_INCREF(__pyx_n_u_GZIteratorHead);
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jpayne@69
|
30188 __Pyx_GIVEREF(__pyx_n_u_GZIteratorHead);
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jpayne@69
|
30189 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 10, __pyx_n_u_GZIteratorHead)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
|
30190 __Pyx_INCREF(__pyx_n_u_tabix_iterator);
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jpayne@69
|
30191 __Pyx_GIVEREF(__pyx_n_u_tabix_iterator);
|
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jpayne@69
|
30192 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 11, __pyx_n_u_tabix_iterator)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
|
30193 __Pyx_INCREF(__pyx_n_u_tabix_generic_iterator);
|
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jpayne@69
|
30194 __Pyx_GIVEREF(__pyx_n_u_tabix_generic_iterator);
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jpayne@69
|
30195 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 12, __pyx_n_u_tabix_generic_iterator)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
|
30196 __Pyx_INCREF(__pyx_n_u_tabix_file_iterator);
|
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jpayne@69
|
30197 __Pyx_GIVEREF(__pyx_n_u_tabix_file_iterator);
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jpayne@69
|
30198 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 13, __pyx_n_u_tabix_file_iterator)) __PYX_ERR(0, 1256, __pyx_L1_error);
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jpayne@69
|
30199 if (PyDict_SetItem(__pyx_d, __pyx_n_s_all, __pyx_t_3) < 0) __PYX_ERR(0, 1256, __pyx_L1_error)
|
|
jpayne@69
|
30200 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30201
|
|
jpayne@69
|
30202 /* "(tree fragment)":1
|
|
jpayne@69
|
30203 * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30204 * cdef object __pyx_PickleError
|
|
jpayne@69
|
30205 * cdef object __pyx_result
|
|
jpayne@69
|
30206 */
|
|
jpayne@69
|
30207 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_7__pyx_unpickle_Parser, 0, __pyx_n_s_pyx_unpickle_Parser, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__54)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30208 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30209 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_Parser, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30210 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30211
|
|
jpayne@69
|
30212 /* "(tree fragment)":11
|
|
jpayne@69
|
30213 * __pyx_unpickle_Parser__set_state(<Parser> __pyx_result, __pyx_state)
|
|
jpayne@69
|
30214 * return __pyx_result
|
|
jpayne@69
|
30215 * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30216 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
30217 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
30218 */
|
|
jpayne@69
|
30219 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9__pyx_unpickle_asTuple, 0, __pyx_n_s_pyx_unpickle_asTuple, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__57)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30220 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30221 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asTuple, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30222 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30223
|
|
jpayne@69
|
30224 /* "(tree fragment)":1
|
|
jpayne@69
|
30225 * def __pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30226 * cdef object __pyx_PickleError
|
|
jpayne@69
|
30227 * cdef object __pyx_result
|
|
jpayne@69
|
30228 */
|
|
jpayne@69
|
30229 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_11__pyx_unpickle_asGFF3, 0, __pyx_n_s_pyx_unpickle_asGFF3, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__58)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30230 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30231 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asGFF3, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30232 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30233
|
|
jpayne@69
|
30234 /* "(tree fragment)":11
|
|
jpayne@69
|
30235 * __pyx_unpickle_asGFF3__set_state(<asGFF3> __pyx_result, __pyx_state)
|
|
jpayne@69
|
30236 * return __pyx_result
|
|
jpayne@69
|
30237 * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30238 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
30239 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
30240 */
|
|
jpayne@69
|
30241 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13__pyx_unpickle_asGTF, 0, __pyx_n_s_pyx_unpickle_asGTF, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__59)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30242 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30243 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asGTF, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30244 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30245
|
|
jpayne@69
|
30246 /* "(tree fragment)":1
|
|
jpayne@69
|
30247 * def __pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30248 * cdef object __pyx_PickleError
|
|
jpayne@69
|
30249 * cdef object __pyx_result
|
|
jpayne@69
|
30250 */
|
|
jpayne@69
|
30251 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_15__pyx_unpickle_asBed, 0, __pyx_n_s_pyx_unpickle_asBed, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__60)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30252 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30253 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asBed, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30254 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30255
|
|
jpayne@69
|
30256 /* "(tree fragment)":11
|
|
jpayne@69
|
30257 * __pyx_unpickle_asBed__set_state(<asBed> __pyx_result, __pyx_state)
|
|
jpayne@69
|
30258 * return __pyx_result
|
|
jpayne@69
|
30259 * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30260 * __pyx_result.encoding = __pyx_state[0]
|
|
jpayne@69
|
30261 * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'):
|
|
jpayne@69
|
30262 */
|
|
jpayne@69
|
30263 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_17__pyx_unpickle_asVCF, 0, __pyx_n_s_pyx_unpickle_asVCF, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__61)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30264 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30265 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asVCF, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error)
|
|
jpayne@69
|
30266 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30267
|
|
jpayne@69
|
30268 /* "pysam/libctabix.pyx":1
|
|
jpayne@69
|
30269 * # cython: language_level=3 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
30270 * # cython: embedsignature=True
|
|
jpayne@69
|
30271 * # cython: profile=True
|
|
jpayne@69
|
30272 */
|
|
jpayne@69
|
30273 __pyx_t_3 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
30274 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
30275 if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
30276 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
30277 __Pyx_TraceReturn(Py_None, 0);
|
|
jpayne@69
|
30278
|
|
jpayne@69
|
30279 /*--- Wrapped vars code ---*/
|
|
jpayne@69
|
30280
|
|
jpayne@69
|
30281 goto __pyx_L0;
|
|
jpayne@69
|
30282 __pyx_L1_error:;
|
|
jpayne@69
|
30283 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
30284 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
30285 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
30286 if (__pyx_m) {
|
|
jpayne@69
|
30287 if (__pyx_d && stringtab_initialized) {
|
|
jpayne@69
|
30288 __Pyx_AddTraceback("init pysam.libctabix", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
30289 }
|
|
jpayne@69
|
30290 #if !CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
30291 Py_CLEAR(__pyx_m);
|
|
jpayne@69
|
30292 #else
|
|
jpayne@69
|
30293 Py_DECREF(__pyx_m);
|
|
jpayne@69
|
30294 if (pystate_addmodule_run) {
|
|
jpayne@69
|
30295 PyObject *tp, *value, *tb;
|
|
jpayne@69
|
30296 PyErr_Fetch(&tp, &value, &tb);
|
|
jpayne@69
|
30297 PyState_RemoveModule(&__pyx_moduledef);
|
|
jpayne@69
|
30298 PyErr_Restore(tp, value, tb);
|
|
jpayne@69
|
30299 }
|
|
jpayne@69
|
30300 #endif
|
|
jpayne@69
|
30301 } else if (!PyErr_Occurred()) {
|
|
jpayne@69
|
30302 PyErr_SetString(PyExc_ImportError, "init pysam.libctabix");
|
|
jpayne@69
|
30303 }
|
|
jpayne@69
|
30304 __pyx_L0:;
|
|
jpayne@69
|
30305 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
30306 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
30307 return (__pyx_m != NULL) ? 0 : -1;
|
|
jpayne@69
|
30308 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30309 return __pyx_m;
|
|
jpayne@69
|
30310 #else
|
|
jpayne@69
|
30311 return;
|
|
jpayne@69
|
30312 #endif
|
|
jpayne@69
|
30313 }
|
|
jpayne@69
|
30314 /* #### Code section: cleanup_globals ### */
|
|
jpayne@69
|
30315 /* #### Code section: cleanup_module ### */
|
|
jpayne@69
|
30316 /* #### Code section: main_method ### */
|
|
jpayne@69
|
30317 /* #### Code section: utility_code_pragmas ### */
|
|
jpayne@69
|
30318 #ifdef _MSC_VER
|
|
jpayne@69
|
30319 #pragma warning( push )
|
|
jpayne@69
|
30320 /* Warning 4127: conditional expression is constant
|
|
jpayne@69
|
30321 * Cython uses constant conditional expressions to allow in inline functions to be optimized at
|
|
jpayne@69
|
30322 * compile-time, so this warning is not useful
|
|
jpayne@69
|
30323 */
|
|
jpayne@69
|
30324 #pragma warning( disable : 4127 )
|
|
jpayne@69
|
30325 #endif
|
|
jpayne@69
|
30326
|
|
jpayne@69
|
30327
|
|
jpayne@69
|
30328
|
|
jpayne@69
|
30329 /* #### Code section: utility_code_def ### */
|
|
jpayne@69
|
30330
|
|
jpayne@69
|
30331 /* --- Runtime support code --- */
|
|
jpayne@69
|
30332 /* Refnanny */
|
|
jpayne@69
|
30333 #if CYTHON_REFNANNY
|
|
jpayne@69
|
30334 static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
|
|
jpayne@69
|
30335 PyObject *m = NULL, *p = NULL;
|
|
jpayne@69
|
30336 void *r = NULL;
|
|
jpayne@69
|
30337 m = PyImport_ImportModule(modname);
|
|
jpayne@69
|
30338 if (!m) goto end;
|
|
jpayne@69
|
30339 p = PyObject_GetAttrString(m, "RefNannyAPI");
|
|
jpayne@69
|
30340 if (!p) goto end;
|
|
jpayne@69
|
30341 r = PyLong_AsVoidPtr(p);
|
|
jpayne@69
|
30342 end:
|
|
jpayne@69
|
30343 Py_XDECREF(p);
|
|
jpayne@69
|
30344 Py_XDECREF(m);
|
|
jpayne@69
|
30345 return (__Pyx_RefNannyAPIStruct *)r;
|
|
jpayne@69
|
30346 }
|
|
jpayne@69
|
30347 #endif
|
|
jpayne@69
|
30348
|
|
jpayne@69
|
30349 /* PyErrExceptionMatches */
|
|
jpayne@69
|
30350 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
30351 static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
|
|
jpayne@69
|
30352 Py_ssize_t i, n;
|
|
jpayne@69
|
30353 n = PyTuple_GET_SIZE(tuple);
|
|
jpayne@69
|
30354 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30355 for (i=0; i<n; i++) {
|
|
jpayne@69
|
30356 if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
|
|
jpayne@69
|
30357 }
|
|
jpayne@69
|
30358 #endif
|
|
jpayne@69
|
30359 for (i=0; i<n; i++) {
|
|
jpayne@69
|
30360 if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1;
|
|
jpayne@69
|
30361 }
|
|
jpayne@69
|
30362 return 0;
|
|
jpayne@69
|
30363 }
|
|
jpayne@69
|
30364 static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
|
|
jpayne@69
|
30365 int result;
|
|
jpayne@69
|
30366 PyObject *exc_type;
|
|
jpayne@69
|
30367 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
30368 PyObject *current_exception = tstate->current_exception;
|
|
jpayne@69
|
30369 if (unlikely(!current_exception)) return 0;
|
|
jpayne@69
|
30370 exc_type = (PyObject*) Py_TYPE(current_exception);
|
|
jpayne@69
|
30371 if (exc_type == err) return 1;
|
|
jpayne@69
|
30372 #else
|
|
jpayne@69
|
30373 exc_type = tstate->curexc_type;
|
|
jpayne@69
|
30374 if (exc_type == err) return 1;
|
|
jpayne@69
|
30375 if (unlikely(!exc_type)) return 0;
|
|
jpayne@69
|
30376 #endif
|
|
jpayne@69
|
30377 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30378 Py_INCREF(exc_type);
|
|
jpayne@69
|
30379 #endif
|
|
jpayne@69
|
30380 if (unlikely(PyTuple_Check(err))) {
|
|
jpayne@69
|
30381 result = __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err);
|
|
jpayne@69
|
30382 } else {
|
|
jpayne@69
|
30383 result = __Pyx_PyErr_GivenExceptionMatches(exc_type, err);
|
|
jpayne@69
|
30384 }
|
|
jpayne@69
|
30385 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30386 Py_DECREF(exc_type);
|
|
jpayne@69
|
30387 #endif
|
|
jpayne@69
|
30388 return result;
|
|
jpayne@69
|
30389 }
|
|
jpayne@69
|
30390 #endif
|
|
jpayne@69
|
30391
|
|
jpayne@69
|
30392 /* PyErrFetchRestore */
|
|
jpayne@69
|
30393 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
30394 static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
|
|
jpayne@69
|
30395 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
30396 PyObject *tmp_value;
|
|
jpayne@69
|
30397 assert(type == NULL || (value != NULL && type == (PyObject*) Py_TYPE(value)));
|
|
jpayne@69
|
30398 if (value) {
|
|
jpayne@69
|
30399 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
30400 if (unlikely(((PyBaseExceptionObject*) value)->traceback != tb))
|
|
jpayne@69
|
30401 #endif
|
|
jpayne@69
|
30402 PyException_SetTraceback(value, tb);
|
|
jpayne@69
|
30403 }
|
|
jpayne@69
|
30404 tmp_value = tstate->current_exception;
|
|
jpayne@69
|
30405 tstate->current_exception = value;
|
|
jpayne@69
|
30406 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
30407 Py_XDECREF(type);
|
|
jpayne@69
|
30408 Py_XDECREF(tb);
|
|
jpayne@69
|
30409 #else
|
|
jpayne@69
|
30410 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
30411 tmp_type = tstate->curexc_type;
|
|
jpayne@69
|
30412 tmp_value = tstate->curexc_value;
|
|
jpayne@69
|
30413 tmp_tb = tstate->curexc_traceback;
|
|
jpayne@69
|
30414 tstate->curexc_type = type;
|
|
jpayne@69
|
30415 tstate->curexc_value = value;
|
|
jpayne@69
|
30416 tstate->curexc_traceback = tb;
|
|
jpayne@69
|
30417 Py_XDECREF(tmp_type);
|
|
jpayne@69
|
30418 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
30419 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
30420 #endif
|
|
jpayne@69
|
30421 }
|
|
jpayne@69
|
30422 static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
|
|
jpayne@69
|
30423 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
30424 PyObject* exc_value;
|
|
jpayne@69
|
30425 exc_value = tstate->current_exception;
|
|
jpayne@69
|
30426 tstate->current_exception = 0;
|
|
jpayne@69
|
30427 *value = exc_value;
|
|
jpayne@69
|
30428 *type = NULL;
|
|
jpayne@69
|
30429 *tb = NULL;
|
|
jpayne@69
|
30430 if (exc_value) {
|
|
jpayne@69
|
30431 *type = (PyObject*) Py_TYPE(exc_value);
|
|
jpayne@69
|
30432 Py_INCREF(*type);
|
|
jpayne@69
|
30433 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
30434 *tb = ((PyBaseExceptionObject*) exc_value)->traceback;
|
|
jpayne@69
|
30435 Py_XINCREF(*tb);
|
|
jpayne@69
|
30436 #else
|
|
jpayne@69
|
30437 *tb = PyException_GetTraceback(exc_value);
|
|
jpayne@69
|
30438 #endif
|
|
jpayne@69
|
30439 }
|
|
jpayne@69
|
30440 #else
|
|
jpayne@69
|
30441 *type = tstate->curexc_type;
|
|
jpayne@69
|
30442 *value = tstate->curexc_value;
|
|
jpayne@69
|
30443 *tb = tstate->curexc_traceback;
|
|
jpayne@69
|
30444 tstate->curexc_type = 0;
|
|
jpayne@69
|
30445 tstate->curexc_value = 0;
|
|
jpayne@69
|
30446 tstate->curexc_traceback = 0;
|
|
jpayne@69
|
30447 #endif
|
|
jpayne@69
|
30448 }
|
|
jpayne@69
|
30449 #endif
|
|
jpayne@69
|
30450
|
|
jpayne@69
|
30451 /* PyObjectGetAttrStr */
|
|
jpayne@69
|
30452 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
30453 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
|
|
jpayne@69
|
30454 PyTypeObject* tp = Py_TYPE(obj);
|
|
jpayne@69
|
30455 if (likely(tp->tp_getattro))
|
|
jpayne@69
|
30456 return tp->tp_getattro(obj, attr_name);
|
|
jpayne@69
|
30457 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30458 if (likely(tp->tp_getattr))
|
|
jpayne@69
|
30459 return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
|
|
jpayne@69
|
30460 #endif
|
|
jpayne@69
|
30461 return PyObject_GetAttr(obj, attr_name);
|
|
jpayne@69
|
30462 }
|
|
jpayne@69
|
30463 #endif
|
|
jpayne@69
|
30464
|
|
jpayne@69
|
30465 /* PyObjectGetAttrStrNoError */
|
|
jpayne@69
|
30466 #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1
|
|
jpayne@69
|
30467 static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) {
|
|
jpayne@69
|
30468 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
30469 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
30470 if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
|
|
jpayne@69
|
30471 __Pyx_PyErr_Clear();
|
|
jpayne@69
|
30472 }
|
|
jpayne@69
|
30473 #endif
|
|
jpayne@69
|
30474 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) {
|
|
jpayne@69
|
30475 PyObject *result;
|
|
jpayne@69
|
30476 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
30477 (void) PyObject_GetOptionalAttr(obj, attr_name, &result);
|
|
jpayne@69
|
30478 return result;
|
|
jpayne@69
|
30479 #else
|
|
jpayne@69
|
30480 #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1
|
|
jpayne@69
|
30481 PyTypeObject* tp = Py_TYPE(obj);
|
|
jpayne@69
|
30482 if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
30483 return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1);
|
|
jpayne@69
|
30484 }
|
|
jpayne@69
|
30485 #endif
|
|
jpayne@69
|
30486 result = __Pyx_PyObject_GetAttrStr(obj, attr_name);
|
|
jpayne@69
|
30487 if (unlikely(!result)) {
|
|
jpayne@69
|
30488 __Pyx_PyObject_GetAttrStr_ClearAttributeError();
|
|
jpayne@69
|
30489 }
|
|
jpayne@69
|
30490 return result;
|
|
jpayne@69
|
30491 #endif
|
|
jpayne@69
|
30492 }
|
|
jpayne@69
|
30493
|
|
jpayne@69
|
30494 /* GetBuiltinName */
|
|
jpayne@69
|
30495 static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
|
|
jpayne@69
|
30496 PyObject* result = __Pyx_PyObject_GetAttrStrNoError(__pyx_b, name);
|
|
jpayne@69
|
30497 if (unlikely(!result) && !PyErr_Occurred()) {
|
|
jpayne@69
|
30498 PyErr_Format(PyExc_NameError,
|
|
jpayne@69
|
30499 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30500 "name '%U' is not defined", name);
|
|
jpayne@69
|
30501 #else
|
|
jpayne@69
|
30502 "name '%.200s' is not defined", PyString_AS_STRING(name));
|
|
jpayne@69
|
30503 #endif
|
|
jpayne@69
|
30504 }
|
|
jpayne@69
|
30505 return result;
|
|
jpayne@69
|
30506 }
|
|
jpayne@69
|
30507
|
|
jpayne@69
|
30508 /* TupleAndListFromArray */
|
|
jpayne@69
|
30509 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
30510 static CYTHON_INLINE void __Pyx_copy_object_array(PyObject *const *CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) {
|
|
jpayne@69
|
30511 PyObject *v;
|
|
jpayne@69
|
30512 Py_ssize_t i;
|
|
jpayne@69
|
30513 for (i = 0; i < length; i++) {
|
|
jpayne@69
|
30514 v = dest[i] = src[i];
|
|
jpayne@69
|
30515 Py_INCREF(v);
|
|
jpayne@69
|
30516 }
|
|
jpayne@69
|
30517 }
|
|
jpayne@69
|
30518 static CYTHON_INLINE PyObject *
|
|
jpayne@69
|
30519 __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n)
|
|
jpayne@69
|
30520 {
|
|
jpayne@69
|
30521 PyObject *res;
|
|
jpayne@69
|
30522 if (n <= 0) {
|
|
jpayne@69
|
30523 Py_INCREF(__pyx_empty_tuple);
|
|
jpayne@69
|
30524 return __pyx_empty_tuple;
|
|
jpayne@69
|
30525 }
|
|
jpayne@69
|
30526 res = PyTuple_New(n);
|
|
jpayne@69
|
30527 if (unlikely(res == NULL)) return NULL;
|
|
jpayne@69
|
30528 __Pyx_copy_object_array(src, ((PyTupleObject*)res)->ob_item, n);
|
|
jpayne@69
|
30529 return res;
|
|
jpayne@69
|
30530 }
|
|
jpayne@69
|
30531 static CYTHON_INLINE PyObject *
|
|
jpayne@69
|
30532 __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n)
|
|
jpayne@69
|
30533 {
|
|
jpayne@69
|
30534 PyObject *res;
|
|
jpayne@69
|
30535 if (n <= 0) {
|
|
jpayne@69
|
30536 return PyList_New(0);
|
|
jpayne@69
|
30537 }
|
|
jpayne@69
|
30538 res = PyList_New(n);
|
|
jpayne@69
|
30539 if (unlikely(res == NULL)) return NULL;
|
|
jpayne@69
|
30540 __Pyx_copy_object_array(src, ((PyListObject*)res)->ob_item, n);
|
|
jpayne@69
|
30541 return res;
|
|
jpayne@69
|
30542 }
|
|
jpayne@69
|
30543 #endif
|
|
jpayne@69
|
30544
|
|
jpayne@69
|
30545 /* BytesEquals */
|
|
jpayne@69
|
30546 static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
|
|
jpayne@69
|
30547 #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
30548 return PyObject_RichCompareBool(s1, s2, equals);
|
|
jpayne@69
|
30549 #else
|
|
jpayne@69
|
30550 if (s1 == s2) {
|
|
jpayne@69
|
30551 return (equals == Py_EQ);
|
|
jpayne@69
|
30552 } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
|
|
jpayne@69
|
30553 const char *ps1, *ps2;
|
|
jpayne@69
|
30554 Py_ssize_t length = PyBytes_GET_SIZE(s1);
|
|
jpayne@69
|
30555 if (length != PyBytes_GET_SIZE(s2))
|
|
jpayne@69
|
30556 return (equals == Py_NE);
|
|
jpayne@69
|
30557 ps1 = PyBytes_AS_STRING(s1);
|
|
jpayne@69
|
30558 ps2 = PyBytes_AS_STRING(s2);
|
|
jpayne@69
|
30559 if (ps1[0] != ps2[0]) {
|
|
jpayne@69
|
30560 return (equals == Py_NE);
|
|
jpayne@69
|
30561 } else if (length == 1) {
|
|
jpayne@69
|
30562 return (equals == Py_EQ);
|
|
jpayne@69
|
30563 } else {
|
|
jpayne@69
|
30564 int result;
|
|
jpayne@69
|
30565 #if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000)
|
|
jpayne@69
|
30566 Py_hash_t hash1, hash2;
|
|
jpayne@69
|
30567 hash1 = ((PyBytesObject*)s1)->ob_shash;
|
|
jpayne@69
|
30568 hash2 = ((PyBytesObject*)s2)->ob_shash;
|
|
jpayne@69
|
30569 if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
|
|
jpayne@69
|
30570 return (equals == Py_NE);
|
|
jpayne@69
|
30571 }
|
|
jpayne@69
|
30572 #endif
|
|
jpayne@69
|
30573 result = memcmp(ps1, ps2, (size_t)length);
|
|
jpayne@69
|
30574 return (equals == Py_EQ) ? (result == 0) : (result != 0);
|
|
jpayne@69
|
30575 }
|
|
jpayne@69
|
30576 } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
|
|
jpayne@69
|
30577 return (equals == Py_NE);
|
|
jpayne@69
|
30578 } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
|
|
jpayne@69
|
30579 return (equals == Py_NE);
|
|
jpayne@69
|
30580 } else {
|
|
jpayne@69
|
30581 int result;
|
|
jpayne@69
|
30582 PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
|
|
jpayne@69
|
30583 if (!py_result)
|
|
jpayne@69
|
30584 return -1;
|
|
jpayne@69
|
30585 result = __Pyx_PyObject_IsTrue(py_result);
|
|
jpayne@69
|
30586 Py_DECREF(py_result);
|
|
jpayne@69
|
30587 return result;
|
|
jpayne@69
|
30588 }
|
|
jpayne@69
|
30589 #endif
|
|
jpayne@69
|
30590 }
|
|
jpayne@69
|
30591
|
|
jpayne@69
|
30592 /* UnicodeEquals */
|
|
jpayne@69
|
30593 static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
|
|
jpayne@69
|
30594 #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
30595 return PyObject_RichCompareBool(s1, s2, equals);
|
|
jpayne@69
|
30596 #else
|
|
jpayne@69
|
30597 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30598 PyObject* owned_ref = NULL;
|
|
jpayne@69
|
30599 #endif
|
|
jpayne@69
|
30600 int s1_is_unicode, s2_is_unicode;
|
|
jpayne@69
|
30601 if (s1 == s2) {
|
|
jpayne@69
|
30602 goto return_eq;
|
|
jpayne@69
|
30603 }
|
|
jpayne@69
|
30604 s1_is_unicode = PyUnicode_CheckExact(s1);
|
|
jpayne@69
|
30605 s2_is_unicode = PyUnicode_CheckExact(s2);
|
|
jpayne@69
|
30606 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30607 if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
|
|
jpayne@69
|
30608 owned_ref = PyUnicode_FromObject(s2);
|
|
jpayne@69
|
30609 if (unlikely(!owned_ref))
|
|
jpayne@69
|
30610 return -1;
|
|
jpayne@69
|
30611 s2 = owned_ref;
|
|
jpayne@69
|
30612 s2_is_unicode = 1;
|
|
jpayne@69
|
30613 } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
|
|
jpayne@69
|
30614 owned_ref = PyUnicode_FromObject(s1);
|
|
jpayne@69
|
30615 if (unlikely(!owned_ref))
|
|
jpayne@69
|
30616 return -1;
|
|
jpayne@69
|
30617 s1 = owned_ref;
|
|
jpayne@69
|
30618 s1_is_unicode = 1;
|
|
jpayne@69
|
30619 } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
|
|
jpayne@69
|
30620 return __Pyx_PyBytes_Equals(s1, s2, equals);
|
|
jpayne@69
|
30621 }
|
|
jpayne@69
|
30622 #endif
|
|
jpayne@69
|
30623 if (s1_is_unicode & s2_is_unicode) {
|
|
jpayne@69
|
30624 Py_ssize_t length;
|
|
jpayne@69
|
30625 int kind;
|
|
jpayne@69
|
30626 void *data1, *data2;
|
|
jpayne@69
|
30627 if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
|
|
jpayne@69
|
30628 return -1;
|
|
jpayne@69
|
30629 length = __Pyx_PyUnicode_GET_LENGTH(s1);
|
|
jpayne@69
|
30630 if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
|
|
jpayne@69
|
30631 goto return_ne;
|
|
jpayne@69
|
30632 }
|
|
jpayne@69
|
30633 #if CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
30634 {
|
|
jpayne@69
|
30635 Py_hash_t hash1, hash2;
|
|
jpayne@69
|
30636 #if CYTHON_PEP393_ENABLED
|
|
jpayne@69
|
30637 hash1 = ((PyASCIIObject*)s1)->hash;
|
|
jpayne@69
|
30638 hash2 = ((PyASCIIObject*)s2)->hash;
|
|
jpayne@69
|
30639 #else
|
|
jpayne@69
|
30640 hash1 = ((PyUnicodeObject*)s1)->hash;
|
|
jpayne@69
|
30641 hash2 = ((PyUnicodeObject*)s2)->hash;
|
|
jpayne@69
|
30642 #endif
|
|
jpayne@69
|
30643 if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
|
|
jpayne@69
|
30644 goto return_ne;
|
|
jpayne@69
|
30645 }
|
|
jpayne@69
|
30646 }
|
|
jpayne@69
|
30647 #endif
|
|
jpayne@69
|
30648 kind = __Pyx_PyUnicode_KIND(s1);
|
|
jpayne@69
|
30649 if (kind != __Pyx_PyUnicode_KIND(s2)) {
|
|
jpayne@69
|
30650 goto return_ne;
|
|
jpayne@69
|
30651 }
|
|
jpayne@69
|
30652 data1 = __Pyx_PyUnicode_DATA(s1);
|
|
jpayne@69
|
30653 data2 = __Pyx_PyUnicode_DATA(s2);
|
|
jpayne@69
|
30654 if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
|
|
jpayne@69
|
30655 goto return_ne;
|
|
jpayne@69
|
30656 } else if (length == 1) {
|
|
jpayne@69
|
30657 goto return_eq;
|
|
jpayne@69
|
30658 } else {
|
|
jpayne@69
|
30659 int result = memcmp(data1, data2, (size_t)(length * kind));
|
|
jpayne@69
|
30660 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30661 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
30662 #endif
|
|
jpayne@69
|
30663 return (equals == Py_EQ) ? (result == 0) : (result != 0);
|
|
jpayne@69
|
30664 }
|
|
jpayne@69
|
30665 } else if ((s1 == Py_None) & s2_is_unicode) {
|
|
jpayne@69
|
30666 goto return_ne;
|
|
jpayne@69
|
30667 } else if ((s2 == Py_None) & s1_is_unicode) {
|
|
jpayne@69
|
30668 goto return_ne;
|
|
jpayne@69
|
30669 } else {
|
|
jpayne@69
|
30670 int result;
|
|
jpayne@69
|
30671 PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
|
|
jpayne@69
|
30672 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30673 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
30674 #endif
|
|
jpayne@69
|
30675 if (!py_result)
|
|
jpayne@69
|
30676 return -1;
|
|
jpayne@69
|
30677 result = __Pyx_PyObject_IsTrue(py_result);
|
|
jpayne@69
|
30678 Py_DECREF(py_result);
|
|
jpayne@69
|
30679 return result;
|
|
jpayne@69
|
30680 }
|
|
jpayne@69
|
30681 return_eq:
|
|
jpayne@69
|
30682 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30683 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
30684 #endif
|
|
jpayne@69
|
30685 return (equals == Py_EQ);
|
|
jpayne@69
|
30686 return_ne:
|
|
jpayne@69
|
30687 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30688 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
30689 #endif
|
|
jpayne@69
|
30690 return (equals == Py_NE);
|
|
jpayne@69
|
30691 #endif
|
|
jpayne@69
|
30692 }
|
|
jpayne@69
|
30693
|
|
jpayne@69
|
30694 /* fastcall */
|
|
jpayne@69
|
30695 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
30696 static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s)
|
|
jpayne@69
|
30697 {
|
|
jpayne@69
|
30698 Py_ssize_t i, n = PyTuple_GET_SIZE(kwnames);
|
|
jpayne@69
|
30699 for (i = 0; i < n; i++)
|
|
jpayne@69
|
30700 {
|
|
jpayne@69
|
30701 if (s == PyTuple_GET_ITEM(kwnames, i)) return kwvalues[i];
|
|
jpayne@69
|
30702 }
|
|
jpayne@69
|
30703 for (i = 0; i < n; i++)
|
|
jpayne@69
|
30704 {
|
|
jpayne@69
|
30705 int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ);
|
|
jpayne@69
|
30706 if (unlikely(eq != 0)) {
|
|
jpayne@69
|
30707 if (unlikely(eq < 0)) return NULL;
|
|
jpayne@69
|
30708 return kwvalues[i];
|
|
jpayne@69
|
30709 }
|
|
jpayne@69
|
30710 }
|
|
jpayne@69
|
30711 return NULL;
|
|
jpayne@69
|
30712 }
|
|
jpayne@69
|
30713 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
30714 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) {
|
|
jpayne@69
|
30715 Py_ssize_t i, nkwargs = PyTuple_GET_SIZE(kwnames);
|
|
jpayne@69
|
30716 PyObject *dict;
|
|
jpayne@69
|
30717 dict = PyDict_New();
|
|
jpayne@69
|
30718 if (unlikely(!dict))
|
|
jpayne@69
|
30719 return NULL;
|
|
jpayne@69
|
30720 for (i=0; i<nkwargs; i++) {
|
|
jpayne@69
|
30721 PyObject *key = PyTuple_GET_ITEM(kwnames, i);
|
|
jpayne@69
|
30722 if (unlikely(PyDict_SetItem(dict, key, kwvalues[i]) < 0))
|
|
jpayne@69
|
30723 goto bad;
|
|
jpayne@69
|
30724 }
|
|
jpayne@69
|
30725 return dict;
|
|
jpayne@69
|
30726 bad:
|
|
jpayne@69
|
30727 Py_DECREF(dict);
|
|
jpayne@69
|
30728 return NULL;
|
|
jpayne@69
|
30729 }
|
|
jpayne@69
|
30730 #endif
|
|
jpayne@69
|
30731 #endif
|
|
jpayne@69
|
30732
|
|
jpayne@69
|
30733 /* RaiseDoubleKeywords */
|
|
jpayne@69
|
30734 static void __Pyx_RaiseDoubleKeywordsError(
|
|
jpayne@69
|
30735 const char* func_name,
|
|
jpayne@69
|
30736 PyObject* kw_name)
|
|
jpayne@69
|
30737 {
|
|
jpayne@69
|
30738 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
30739 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30740 "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
|
|
jpayne@69
|
30741 #else
|
|
jpayne@69
|
30742 "%s() got multiple values for keyword argument '%s'", func_name,
|
|
jpayne@69
|
30743 PyString_AsString(kw_name));
|
|
jpayne@69
|
30744 #endif
|
|
jpayne@69
|
30745 }
|
|
jpayne@69
|
30746
|
|
jpayne@69
|
30747 /* ParseKeywords */
|
|
jpayne@69
|
30748 static int __Pyx_ParseOptionalKeywords(
|
|
jpayne@69
|
30749 PyObject *kwds,
|
|
jpayne@69
|
30750 PyObject *const *kwvalues,
|
|
jpayne@69
|
30751 PyObject **argnames[],
|
|
jpayne@69
|
30752 PyObject *kwds2,
|
|
jpayne@69
|
30753 PyObject *values[],
|
|
jpayne@69
|
30754 Py_ssize_t num_pos_args,
|
|
jpayne@69
|
30755 const char* function_name)
|
|
jpayne@69
|
30756 {
|
|
jpayne@69
|
30757 PyObject *key = 0, *value = 0;
|
|
jpayne@69
|
30758 Py_ssize_t pos = 0;
|
|
jpayne@69
|
30759 PyObject*** name;
|
|
jpayne@69
|
30760 PyObject*** first_kw_arg = argnames + num_pos_args;
|
|
jpayne@69
|
30761 int kwds_is_tuple = CYTHON_METH_FASTCALL && likely(PyTuple_Check(kwds));
|
|
jpayne@69
|
30762 while (1) {
|
|
jpayne@69
|
30763 Py_XDECREF(key); key = NULL;
|
|
jpayne@69
|
30764 Py_XDECREF(value); value = NULL;
|
|
jpayne@69
|
30765 if (kwds_is_tuple) {
|
|
jpayne@69
|
30766 Py_ssize_t size;
|
|
jpayne@69
|
30767 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
30768 size = PyTuple_GET_SIZE(kwds);
|
|
jpayne@69
|
30769 #else
|
|
jpayne@69
|
30770 size = PyTuple_Size(kwds);
|
|
jpayne@69
|
30771 if (size < 0) goto bad;
|
|
jpayne@69
|
30772 #endif
|
|
jpayne@69
|
30773 if (pos >= size) break;
|
|
jpayne@69
|
30774 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30775 key = __Pyx_PySequence_ITEM(kwds, pos);
|
|
jpayne@69
|
30776 if (!key) goto bad;
|
|
jpayne@69
|
30777 #elif CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
30778 key = PyTuple_GET_ITEM(kwds, pos);
|
|
jpayne@69
|
30779 #else
|
|
jpayne@69
|
30780 key = PyTuple_GetItem(kwds, pos);
|
|
jpayne@69
|
30781 if (!key) goto bad;
|
|
jpayne@69
|
30782 #endif
|
|
jpayne@69
|
30783 value = kwvalues[pos];
|
|
jpayne@69
|
30784 pos++;
|
|
jpayne@69
|
30785 }
|
|
jpayne@69
|
30786 else
|
|
jpayne@69
|
30787 {
|
|
jpayne@69
|
30788 if (!PyDict_Next(kwds, &pos, &key, &value)) break;
|
|
jpayne@69
|
30789 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30790 Py_INCREF(key);
|
|
jpayne@69
|
30791 #endif
|
|
jpayne@69
|
30792 }
|
|
jpayne@69
|
30793 name = first_kw_arg;
|
|
jpayne@69
|
30794 while (*name && (**name != key)) name++;
|
|
jpayne@69
|
30795 if (*name) {
|
|
jpayne@69
|
30796 values[name-argnames] = value;
|
|
jpayne@69
|
30797 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30798 Py_INCREF(value);
|
|
jpayne@69
|
30799 Py_DECREF(key);
|
|
jpayne@69
|
30800 #endif
|
|
jpayne@69
|
30801 key = NULL;
|
|
jpayne@69
|
30802 value = NULL;
|
|
jpayne@69
|
30803 continue;
|
|
jpayne@69
|
30804 }
|
|
jpayne@69
|
30805 #if !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30806 Py_INCREF(key);
|
|
jpayne@69
|
30807 #endif
|
|
jpayne@69
|
30808 Py_INCREF(value);
|
|
jpayne@69
|
30809 name = first_kw_arg;
|
|
jpayne@69
|
30810 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30811 if (likely(PyString_Check(key))) {
|
|
jpayne@69
|
30812 while (*name) {
|
|
jpayne@69
|
30813 if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
|
|
jpayne@69
|
30814 && _PyString_Eq(**name, key)) {
|
|
jpayne@69
|
30815 values[name-argnames] = value;
|
|
jpayne@69
|
30816 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30817 value = NULL;
|
|
jpayne@69
|
30818 #endif
|
|
jpayne@69
|
30819 break;
|
|
jpayne@69
|
30820 }
|
|
jpayne@69
|
30821 name++;
|
|
jpayne@69
|
30822 }
|
|
jpayne@69
|
30823 if (*name) continue;
|
|
jpayne@69
|
30824 else {
|
|
jpayne@69
|
30825 PyObject*** argname = argnames;
|
|
jpayne@69
|
30826 while (argname != first_kw_arg) {
|
|
jpayne@69
|
30827 if ((**argname == key) || (
|
|
jpayne@69
|
30828 (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
|
|
jpayne@69
|
30829 && _PyString_Eq(**argname, key))) {
|
|
jpayne@69
|
30830 goto arg_passed_twice;
|
|
jpayne@69
|
30831 }
|
|
jpayne@69
|
30832 argname++;
|
|
jpayne@69
|
30833 }
|
|
jpayne@69
|
30834 }
|
|
jpayne@69
|
30835 } else
|
|
jpayne@69
|
30836 #endif
|
|
jpayne@69
|
30837 if (likely(PyUnicode_Check(key))) {
|
|
jpayne@69
|
30838 while (*name) {
|
|
jpayne@69
|
30839 int cmp = (
|
|
jpayne@69
|
30840 #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30841 (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
|
|
jpayne@69
|
30842 #endif
|
|
jpayne@69
|
30843 PyUnicode_Compare(**name, key)
|
|
jpayne@69
|
30844 );
|
|
jpayne@69
|
30845 if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
|
|
jpayne@69
|
30846 if (cmp == 0) {
|
|
jpayne@69
|
30847 values[name-argnames] = value;
|
|
jpayne@69
|
30848 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
30849 value = NULL;
|
|
jpayne@69
|
30850 #endif
|
|
jpayne@69
|
30851 break;
|
|
jpayne@69
|
30852 }
|
|
jpayne@69
|
30853 name++;
|
|
jpayne@69
|
30854 }
|
|
jpayne@69
|
30855 if (*name) continue;
|
|
jpayne@69
|
30856 else {
|
|
jpayne@69
|
30857 PyObject*** argname = argnames;
|
|
jpayne@69
|
30858 while (argname != first_kw_arg) {
|
|
jpayne@69
|
30859 int cmp = (**argname == key) ? 0 :
|
|
jpayne@69
|
30860 #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30861 (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
|
|
jpayne@69
|
30862 #endif
|
|
jpayne@69
|
30863 PyUnicode_Compare(**argname, key);
|
|
jpayne@69
|
30864 if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
|
|
jpayne@69
|
30865 if (cmp == 0) goto arg_passed_twice;
|
|
jpayne@69
|
30866 argname++;
|
|
jpayne@69
|
30867 }
|
|
jpayne@69
|
30868 }
|
|
jpayne@69
|
30869 } else
|
|
jpayne@69
|
30870 goto invalid_keyword_type;
|
|
jpayne@69
|
30871 if (kwds2) {
|
|
jpayne@69
|
30872 if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
|
|
jpayne@69
|
30873 } else {
|
|
jpayne@69
|
30874 goto invalid_keyword;
|
|
jpayne@69
|
30875 }
|
|
jpayne@69
|
30876 }
|
|
jpayne@69
|
30877 Py_XDECREF(key);
|
|
jpayne@69
|
30878 Py_XDECREF(value);
|
|
jpayne@69
|
30879 return 0;
|
|
jpayne@69
|
30880 arg_passed_twice:
|
|
jpayne@69
|
30881 __Pyx_RaiseDoubleKeywordsError(function_name, key);
|
|
jpayne@69
|
30882 goto bad;
|
|
jpayne@69
|
30883 invalid_keyword_type:
|
|
jpayne@69
|
30884 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
30885 "%.200s() keywords must be strings", function_name);
|
|
jpayne@69
|
30886 goto bad;
|
|
jpayne@69
|
30887 invalid_keyword:
|
|
jpayne@69
|
30888 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
30889 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
30890 "%.200s() got an unexpected keyword argument '%.200s'",
|
|
jpayne@69
|
30891 function_name, PyString_AsString(key));
|
|
jpayne@69
|
30892 #else
|
|
jpayne@69
|
30893 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
30894 "%s() got an unexpected keyword argument '%U'",
|
|
jpayne@69
|
30895 function_name, key);
|
|
jpayne@69
|
30896 #endif
|
|
jpayne@69
|
30897 bad:
|
|
jpayne@69
|
30898 Py_XDECREF(key);
|
|
jpayne@69
|
30899 Py_XDECREF(value);
|
|
jpayne@69
|
30900 return -1;
|
|
jpayne@69
|
30901 }
|
|
jpayne@69
|
30902
|
|
jpayne@69
|
30903 /* RaiseArgTupleInvalid */
|
|
jpayne@69
|
30904 static void __Pyx_RaiseArgtupleInvalid(
|
|
jpayne@69
|
30905 const char* func_name,
|
|
jpayne@69
|
30906 int exact,
|
|
jpayne@69
|
30907 Py_ssize_t num_min,
|
|
jpayne@69
|
30908 Py_ssize_t num_max,
|
|
jpayne@69
|
30909 Py_ssize_t num_found)
|
|
jpayne@69
|
30910 {
|
|
jpayne@69
|
30911 Py_ssize_t num_expected;
|
|
jpayne@69
|
30912 const char *more_or_less;
|
|
jpayne@69
|
30913 if (num_found < num_min) {
|
|
jpayne@69
|
30914 num_expected = num_min;
|
|
jpayne@69
|
30915 more_or_less = "at least";
|
|
jpayne@69
|
30916 } else {
|
|
jpayne@69
|
30917 num_expected = num_max;
|
|
jpayne@69
|
30918 more_or_less = "at most";
|
|
jpayne@69
|
30919 }
|
|
jpayne@69
|
30920 if (exact) {
|
|
jpayne@69
|
30921 more_or_less = "exactly";
|
|
jpayne@69
|
30922 }
|
|
jpayne@69
|
30923 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
30924 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
30925 func_name, more_or_less, num_expected,
|
|
jpayne@69
|
30926 (num_expected == 1) ? "" : "s", num_found);
|
|
jpayne@69
|
30927 }
|
|
jpayne@69
|
30928
|
|
jpayne@69
|
30929 /* Profile */
|
|
jpayne@69
|
30930 #if CYTHON_PROFILE
|
|
jpayne@69
|
30931 static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
|
|
jpayne@69
|
30932 PyFrameObject** frame,
|
|
jpayne@69
|
30933 PyThreadState* tstate,
|
|
jpayne@69
|
30934 const char *funcname,
|
|
jpayne@69
|
30935 const char *srcfile,
|
|
jpayne@69
|
30936 int firstlineno) {
|
|
jpayne@69
|
30937 PyObject *type, *value, *traceback;
|
|
jpayne@69
|
30938 int retval;
|
|
jpayne@69
|
30939 if (*frame == NULL || !CYTHON_PROFILE_REUSE_FRAME) {
|
|
jpayne@69
|
30940 if (*code == NULL) {
|
|
jpayne@69
|
30941 *code = __Pyx_createFrameCodeObject(funcname, srcfile, firstlineno);
|
|
jpayne@69
|
30942 if (*code == NULL) return 0;
|
|
jpayne@69
|
30943 }
|
|
jpayne@69
|
30944 *frame = PyFrame_New(
|
|
jpayne@69
|
30945 tstate, /*PyThreadState *tstate*/
|
|
jpayne@69
|
30946 *code, /*PyCodeObject *code*/
|
|
jpayne@69
|
30947 __pyx_d, /*PyObject *globals*/
|
|
jpayne@69
|
30948 0 /*PyObject *locals*/
|
|
jpayne@69
|
30949 );
|
|
jpayne@69
|
30950 if (*frame == NULL) return 0;
|
|
jpayne@69
|
30951 if (CYTHON_TRACE && (*frame)->f_trace == NULL) {
|
|
jpayne@69
|
30952 Py_INCREF(Py_None);
|
|
jpayne@69
|
30953 (*frame)->f_trace = Py_None;
|
|
jpayne@69
|
30954 }
|
|
jpayne@69
|
30955 #if PY_VERSION_HEX < 0x030400B1
|
|
jpayne@69
|
30956 } else {
|
|
jpayne@69
|
30957 (*frame)->f_tstate = tstate;
|
|
jpayne@69
|
30958 #endif
|
|
jpayne@69
|
30959 }
|
|
jpayne@69
|
30960 __Pyx_PyFrame_SetLineNumber(*frame, firstlineno);
|
|
jpayne@69
|
30961 retval = 1;
|
|
jpayne@69
|
30962 __Pyx_EnterTracing(tstate);
|
|
jpayne@69
|
30963 __Pyx_ErrFetchInState(tstate, &type, &value, &traceback);
|
|
jpayne@69
|
30964 #if CYTHON_TRACE
|
|
jpayne@69
|
30965 if (tstate->c_tracefunc)
|
|
jpayne@69
|
30966 retval = tstate->c_tracefunc(tstate->c_traceobj, *frame, PyTrace_CALL, NULL) == 0;
|
|
jpayne@69
|
30967 if (retval && tstate->c_profilefunc)
|
|
jpayne@69
|
30968 #endif
|
|
jpayne@69
|
30969 retval = tstate->c_profilefunc(tstate->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
|
|
jpayne@69
|
30970 __Pyx_LeaveTracing(tstate);
|
|
jpayne@69
|
30971 if (retval) {
|
|
jpayne@69
|
30972 __Pyx_ErrRestoreInState(tstate, type, value, traceback);
|
|
jpayne@69
|
30973 return __Pyx_IsTracing(tstate, 0, 0) && retval;
|
|
jpayne@69
|
30974 } else {
|
|
jpayne@69
|
30975 Py_XDECREF(type);
|
|
jpayne@69
|
30976 Py_XDECREF(value);
|
|
jpayne@69
|
30977 Py_XDECREF(traceback);
|
|
jpayne@69
|
30978 return -1;
|
|
jpayne@69
|
30979 }
|
|
jpayne@69
|
30980 }
|
|
jpayne@69
|
30981 static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
|
|
jpayne@69
|
30982 PyCodeObject *py_code = 0;
|
|
jpayne@69
|
30983 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
30984 py_code = PyCode_NewEmpty(srcfile, funcname, firstlineno);
|
|
jpayne@69
|
30985 if (likely(py_code)) {
|
|
jpayne@69
|
30986 py_code->co_flags |= CO_OPTIMIZED | CO_NEWLOCALS;
|
|
jpayne@69
|
30987 }
|
|
jpayne@69
|
30988 #else
|
|
jpayne@69
|
30989 PyObject *py_srcfile = 0;
|
|
jpayne@69
|
30990 PyObject *py_funcname = 0;
|
|
jpayne@69
|
30991 py_funcname = PyString_FromString(funcname);
|
|
jpayne@69
|
30992 if (unlikely(!py_funcname)) goto bad;
|
|
jpayne@69
|
30993 py_srcfile = PyString_FromString(srcfile);
|
|
jpayne@69
|
30994 if (unlikely(!py_srcfile)) goto bad;
|
|
jpayne@69
|
30995 py_code = PyCode_New(
|
|
jpayne@69
|
30996 0,
|
|
jpayne@69
|
30997 0,
|
|
jpayne@69
|
30998 0,
|
|
jpayne@69
|
30999 CO_OPTIMIZED | CO_NEWLOCALS,
|
|
jpayne@69
|
31000 __pyx_empty_bytes, /*PyObject *code,*/
|
|
jpayne@69
|
31001 __pyx_empty_tuple, /*PyObject *consts,*/
|
|
jpayne@69
|
31002 __pyx_empty_tuple, /*PyObject *names,*/
|
|
jpayne@69
|
31003 __pyx_empty_tuple, /*PyObject *varnames,*/
|
|
jpayne@69
|
31004 __pyx_empty_tuple, /*PyObject *freevars,*/
|
|
jpayne@69
|
31005 __pyx_empty_tuple, /*PyObject *cellvars,*/
|
|
jpayne@69
|
31006 py_srcfile, /*PyObject *filename,*/
|
|
jpayne@69
|
31007 py_funcname, /*PyObject *name,*/
|
|
jpayne@69
|
31008 firstlineno,
|
|
jpayne@69
|
31009 __pyx_empty_bytes /*PyObject *lnotab*/
|
|
jpayne@69
|
31010 );
|
|
jpayne@69
|
31011 bad:
|
|
jpayne@69
|
31012 Py_XDECREF(py_srcfile);
|
|
jpayne@69
|
31013 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
31014 #endif
|
|
jpayne@69
|
31015 return py_code;
|
|
jpayne@69
|
31016 }
|
|
jpayne@69
|
31017 #endif
|
|
jpayne@69
|
31018
|
|
jpayne@69
|
31019 /* KeywordStringCheck */
|
|
jpayne@69
|
31020 static int __Pyx_CheckKeywordStrings(
|
|
jpayne@69
|
31021 PyObject *kw,
|
|
jpayne@69
|
31022 const char* function_name,
|
|
jpayne@69
|
31023 int kw_allowed)
|
|
jpayne@69
|
31024 {
|
|
jpayne@69
|
31025 PyObject* key = 0;
|
|
jpayne@69
|
31026 Py_ssize_t pos = 0;
|
|
jpayne@69
|
31027 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
31028 if (!kw_allowed && PyDict_Next(kw, &pos, &key, 0))
|
|
jpayne@69
|
31029 goto invalid_keyword;
|
|
jpayne@69
|
31030 return 1;
|
|
jpayne@69
|
31031 #else
|
|
jpayne@69
|
31032 if (CYTHON_METH_FASTCALL && likely(PyTuple_Check(kw))) {
|
|
jpayne@69
|
31033 Py_ssize_t kwsize;
|
|
jpayne@69
|
31034 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
31035 kwsize = PyTuple_GET_SIZE(kw);
|
|
jpayne@69
|
31036 #else
|
|
jpayne@69
|
31037 kwsize = PyTuple_Size(kw);
|
|
jpayne@69
|
31038 if (kwsize < 0) return 0;
|
|
jpayne@69
|
31039 #endif
|
|
jpayne@69
|
31040 if (unlikely(kwsize == 0))
|
|
jpayne@69
|
31041 return 1;
|
|
jpayne@69
|
31042 if (!kw_allowed) {
|
|
jpayne@69
|
31043 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
31044 key = PyTuple_GET_ITEM(kw, 0);
|
|
jpayne@69
|
31045 #else
|
|
jpayne@69
|
31046 key = PyTuple_GetItem(kw, pos);
|
|
jpayne@69
|
31047 if (!key) return 0;
|
|
jpayne@69
|
31048 #endif
|
|
jpayne@69
|
31049 goto invalid_keyword;
|
|
jpayne@69
|
31050 }
|
|
jpayne@69
|
31051 #if PY_VERSION_HEX < 0x03090000
|
|
jpayne@69
|
31052 for (pos = 0; pos < kwsize; pos++) {
|
|
jpayne@69
|
31053 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
31054 key = PyTuple_GET_ITEM(kw, pos);
|
|
jpayne@69
|
31055 #else
|
|
jpayne@69
|
31056 key = PyTuple_GetItem(kw, pos);
|
|
jpayne@69
|
31057 if (!key) return 0;
|
|
jpayne@69
|
31058 #endif
|
|
jpayne@69
|
31059 if (unlikely(!PyUnicode_Check(key)))
|
|
jpayne@69
|
31060 goto invalid_keyword_type;
|
|
jpayne@69
|
31061 }
|
|
jpayne@69
|
31062 #endif
|
|
jpayne@69
|
31063 return 1;
|
|
jpayne@69
|
31064 }
|
|
jpayne@69
|
31065 while (PyDict_Next(kw, &pos, &key, 0)) {
|
|
jpayne@69
|
31066 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31067 if (unlikely(!PyString_Check(key)))
|
|
jpayne@69
|
31068 #endif
|
|
jpayne@69
|
31069 if (unlikely(!PyUnicode_Check(key)))
|
|
jpayne@69
|
31070 goto invalid_keyword_type;
|
|
jpayne@69
|
31071 }
|
|
jpayne@69
|
31072 if (!kw_allowed && unlikely(key))
|
|
jpayne@69
|
31073 goto invalid_keyword;
|
|
jpayne@69
|
31074 return 1;
|
|
jpayne@69
|
31075 invalid_keyword_type:
|
|
jpayne@69
|
31076 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
31077 "%.200s() keywords must be strings", function_name);
|
|
jpayne@69
|
31078 return 0;
|
|
jpayne@69
|
31079 #endif
|
|
jpayne@69
|
31080 invalid_keyword:
|
|
jpayne@69
|
31081 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31082 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
31083 "%.200s() got an unexpected keyword argument '%.200s'",
|
|
jpayne@69
|
31084 function_name, PyString_AsString(key));
|
|
jpayne@69
|
31085 #else
|
|
jpayne@69
|
31086 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
31087 "%s() got an unexpected keyword argument '%U'",
|
|
jpayne@69
|
31088 function_name, key);
|
|
jpayne@69
|
31089 #endif
|
|
jpayne@69
|
31090 return 0;
|
|
jpayne@69
|
31091 }
|
|
jpayne@69
|
31092
|
|
jpayne@69
|
31093 /* PyFunctionFastCall */
|
|
jpayne@69
|
31094 #if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL
|
|
jpayne@69
|
31095 static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
|
|
jpayne@69
|
31096 PyObject *globals) {
|
|
jpayne@69
|
31097 PyFrameObject *f;
|
|
jpayne@69
|
31098 PyThreadState *tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
31099 PyObject **fastlocals;
|
|
jpayne@69
|
31100 Py_ssize_t i;
|
|
jpayne@69
|
31101 PyObject *result;
|
|
jpayne@69
|
31102 assert(globals != NULL);
|
|
jpayne@69
|
31103 /* XXX Perhaps we should create a specialized
|
|
jpayne@69
|
31104 PyFrame_New() that doesn't take locals, but does
|
|
jpayne@69
|
31105 take builtins without sanity checking them.
|
|
jpayne@69
|
31106 */
|
|
jpayne@69
|
31107 assert(tstate != NULL);
|
|
jpayne@69
|
31108 f = PyFrame_New(tstate, co, globals, NULL);
|
|
jpayne@69
|
31109 if (f == NULL) {
|
|
jpayne@69
|
31110 return NULL;
|
|
jpayne@69
|
31111 }
|
|
jpayne@69
|
31112 fastlocals = __Pyx_PyFrame_GetLocalsplus(f);
|
|
jpayne@69
|
31113 for (i = 0; i < na; i++) {
|
|
jpayne@69
|
31114 Py_INCREF(*args);
|
|
jpayne@69
|
31115 fastlocals[i] = *args++;
|
|
jpayne@69
|
31116 }
|
|
jpayne@69
|
31117 result = PyEval_EvalFrameEx(f,0);
|
|
jpayne@69
|
31118 ++tstate->recursion_depth;
|
|
jpayne@69
|
31119 Py_DECREF(f);
|
|
jpayne@69
|
31120 --tstate->recursion_depth;
|
|
jpayne@69
|
31121 return result;
|
|
jpayne@69
|
31122 }
|
|
jpayne@69
|
31123 static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) {
|
|
jpayne@69
|
31124 PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
|
|
jpayne@69
|
31125 PyObject *globals = PyFunction_GET_GLOBALS(func);
|
|
jpayne@69
|
31126 PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
|
|
jpayne@69
|
31127 PyObject *closure;
|
|
jpayne@69
|
31128 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
31129 PyObject *kwdefs;
|
|
jpayne@69
|
31130 #endif
|
|
jpayne@69
|
31131 PyObject *kwtuple, **k;
|
|
jpayne@69
|
31132 PyObject **d;
|
|
jpayne@69
|
31133 Py_ssize_t nd;
|
|
jpayne@69
|
31134 Py_ssize_t nk;
|
|
jpayne@69
|
31135 PyObject *result;
|
|
jpayne@69
|
31136 assert(kwargs == NULL || PyDict_Check(kwargs));
|
|
jpayne@69
|
31137 nk = kwargs ? PyDict_Size(kwargs) : 0;
|
|
jpayne@69
|
31138 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31139 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) {
|
|
jpayne@69
|
31140 return NULL;
|
|
jpayne@69
|
31141 }
|
|
jpayne@69
|
31142 #else
|
|
jpayne@69
|
31143 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) {
|
|
jpayne@69
|
31144 return NULL;
|
|
jpayne@69
|
31145 }
|
|
jpayne@69
|
31146 #endif
|
|
jpayne@69
|
31147 if (
|
|
jpayne@69
|
31148 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
31149 co->co_kwonlyargcount == 0 &&
|
|
jpayne@69
|
31150 #endif
|
|
jpayne@69
|
31151 likely(kwargs == NULL || nk == 0) &&
|
|
jpayne@69
|
31152 co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
|
|
jpayne@69
|
31153 if (argdefs == NULL && co->co_argcount == nargs) {
|
|
jpayne@69
|
31154 result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
|
|
jpayne@69
|
31155 goto done;
|
|
jpayne@69
|
31156 }
|
|
jpayne@69
|
31157 else if (nargs == 0 && argdefs != NULL
|
|
jpayne@69
|
31158 && co->co_argcount == Py_SIZE(argdefs)) {
|
|
jpayne@69
|
31159 /* function called with no arguments, but all parameters have
|
|
jpayne@69
|
31160 a default value: use default values as arguments .*/
|
|
jpayne@69
|
31161 args = &PyTuple_GET_ITEM(argdefs, 0);
|
|
jpayne@69
|
31162 result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
|
|
jpayne@69
|
31163 goto done;
|
|
jpayne@69
|
31164 }
|
|
jpayne@69
|
31165 }
|
|
jpayne@69
|
31166 if (kwargs != NULL) {
|
|
jpayne@69
|
31167 Py_ssize_t pos, i;
|
|
jpayne@69
|
31168 kwtuple = PyTuple_New(2 * nk);
|
|
jpayne@69
|
31169 if (kwtuple == NULL) {
|
|
jpayne@69
|
31170 result = NULL;
|
|
jpayne@69
|
31171 goto done;
|
|
jpayne@69
|
31172 }
|
|
jpayne@69
|
31173 k = &PyTuple_GET_ITEM(kwtuple, 0);
|
|
jpayne@69
|
31174 pos = i = 0;
|
|
jpayne@69
|
31175 while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
|
|
jpayne@69
|
31176 Py_INCREF(k[i]);
|
|
jpayne@69
|
31177 Py_INCREF(k[i+1]);
|
|
jpayne@69
|
31178 i += 2;
|
|
jpayne@69
|
31179 }
|
|
jpayne@69
|
31180 nk = i / 2;
|
|
jpayne@69
|
31181 }
|
|
jpayne@69
|
31182 else {
|
|
jpayne@69
|
31183 kwtuple = NULL;
|
|
jpayne@69
|
31184 k = NULL;
|
|
jpayne@69
|
31185 }
|
|
jpayne@69
|
31186 closure = PyFunction_GET_CLOSURE(func);
|
|
jpayne@69
|
31187 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
31188 kwdefs = PyFunction_GET_KW_DEFAULTS(func);
|
|
jpayne@69
|
31189 #endif
|
|
jpayne@69
|
31190 if (argdefs != NULL) {
|
|
jpayne@69
|
31191 d = &PyTuple_GET_ITEM(argdefs, 0);
|
|
jpayne@69
|
31192 nd = Py_SIZE(argdefs);
|
|
jpayne@69
|
31193 }
|
|
jpayne@69
|
31194 else {
|
|
jpayne@69
|
31195 d = NULL;
|
|
jpayne@69
|
31196 nd = 0;
|
|
jpayne@69
|
31197 }
|
|
jpayne@69
|
31198 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
31199 result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
|
|
jpayne@69
|
31200 args, (int)nargs,
|
|
jpayne@69
|
31201 k, (int)nk,
|
|
jpayne@69
|
31202 d, (int)nd, kwdefs, closure);
|
|
jpayne@69
|
31203 #else
|
|
jpayne@69
|
31204 result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
|
|
jpayne@69
|
31205 args, (int)nargs,
|
|
jpayne@69
|
31206 k, (int)nk,
|
|
jpayne@69
|
31207 d, (int)nd, closure);
|
|
jpayne@69
|
31208 #endif
|
|
jpayne@69
|
31209 Py_XDECREF(kwtuple);
|
|
jpayne@69
|
31210 done:
|
|
jpayne@69
|
31211 Py_LeaveRecursiveCall();
|
|
jpayne@69
|
31212 return result;
|
|
jpayne@69
|
31213 }
|
|
jpayne@69
|
31214 #endif
|
|
jpayne@69
|
31215
|
|
jpayne@69
|
31216 /* PyObjectCall */
|
|
jpayne@69
|
31217 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
31218 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
|
|
jpayne@69
|
31219 PyObject *result;
|
|
jpayne@69
|
31220 ternaryfunc call = Py_TYPE(func)->tp_call;
|
|
jpayne@69
|
31221 if (unlikely(!call))
|
|
jpayne@69
|
31222 return PyObject_Call(func, arg, kw);
|
|
jpayne@69
|
31223 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31224 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
|
|
jpayne@69
|
31225 return NULL;
|
|
jpayne@69
|
31226 #else
|
|
jpayne@69
|
31227 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object")))
|
|
jpayne@69
|
31228 return NULL;
|
|
jpayne@69
|
31229 #endif
|
|
jpayne@69
|
31230 result = (*call)(func, arg, kw);
|
|
jpayne@69
|
31231 Py_LeaveRecursiveCall();
|
|
jpayne@69
|
31232 if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
|
|
jpayne@69
|
31233 PyErr_SetString(
|
|
jpayne@69
|
31234 PyExc_SystemError,
|
|
jpayne@69
|
31235 "NULL result without error in PyObject_Call");
|
|
jpayne@69
|
31236 }
|
|
jpayne@69
|
31237 return result;
|
|
jpayne@69
|
31238 }
|
|
jpayne@69
|
31239 #endif
|
|
jpayne@69
|
31240
|
|
jpayne@69
|
31241 /* PyObjectCallMethO */
|
|
jpayne@69
|
31242 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
31243 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
|
|
jpayne@69
|
31244 PyObject *self, *result;
|
|
jpayne@69
|
31245 PyCFunction cfunc;
|
|
jpayne@69
|
31246 cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func);
|
|
jpayne@69
|
31247 self = __Pyx_CyOrPyCFunction_GET_SELF(func);
|
|
jpayne@69
|
31248 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31249 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
|
|
jpayne@69
|
31250 return NULL;
|
|
jpayne@69
|
31251 #else
|
|
jpayne@69
|
31252 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object")))
|
|
jpayne@69
|
31253 return NULL;
|
|
jpayne@69
|
31254 #endif
|
|
jpayne@69
|
31255 result = cfunc(self, arg);
|
|
jpayne@69
|
31256 Py_LeaveRecursiveCall();
|
|
jpayne@69
|
31257 if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
|
|
jpayne@69
|
31258 PyErr_SetString(
|
|
jpayne@69
|
31259 PyExc_SystemError,
|
|
jpayne@69
|
31260 "NULL result without error in PyObject_Call");
|
|
jpayne@69
|
31261 }
|
|
jpayne@69
|
31262 return result;
|
|
jpayne@69
|
31263 }
|
|
jpayne@69
|
31264 #endif
|
|
jpayne@69
|
31265
|
|
jpayne@69
|
31266 /* PyObjectFastCall */
|
|
jpayne@69
|
31267 #if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
31268 static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) {
|
|
jpayne@69
|
31269 PyObject *argstuple;
|
|
jpayne@69
|
31270 PyObject *result = 0;
|
|
jpayne@69
|
31271 size_t i;
|
|
jpayne@69
|
31272 argstuple = PyTuple_New((Py_ssize_t)nargs);
|
|
jpayne@69
|
31273 if (unlikely(!argstuple)) return NULL;
|
|
jpayne@69
|
31274 for (i = 0; i < nargs; i++) {
|
|
jpayne@69
|
31275 Py_INCREF(args[i]);
|
|
jpayne@69
|
31276 if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
|
|
jpayne@69
|
31277 }
|
|
jpayne@69
|
31278 result = __Pyx_PyObject_Call(func, argstuple, kwargs);
|
|
jpayne@69
|
31279 bad:
|
|
jpayne@69
|
31280 Py_DECREF(argstuple);
|
|
jpayne@69
|
31281 return result;
|
|
jpayne@69
|
31282 }
|
|
jpayne@69
|
31283 #endif
|
|
jpayne@69
|
31284 static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) {
|
|
jpayne@69
|
31285 Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs);
|
|
jpayne@69
|
31286 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
31287 if (nargs == 0 && kwargs == NULL) {
|
|
jpayne@69
|
31288 if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS))
|
|
jpayne@69
|
31289 return __Pyx_PyObject_CallMethO(func, NULL);
|
|
jpayne@69
|
31290 }
|
|
jpayne@69
|
31291 else if (nargs == 1 && kwargs == NULL) {
|
|
jpayne@69
|
31292 if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O))
|
|
jpayne@69
|
31293 return __Pyx_PyObject_CallMethO(func, args[0]);
|
|
jpayne@69
|
31294 }
|
|
jpayne@69
|
31295 #endif
|
|
jpayne@69
|
31296 #if PY_VERSION_HEX < 0x030800B1
|
|
jpayne@69
|
31297 #if CYTHON_FAST_PYCCALL
|
|
jpayne@69
|
31298 if (PyCFunction_Check(func)) {
|
|
jpayne@69
|
31299 if (kwargs) {
|
|
jpayne@69
|
31300 return _PyCFunction_FastCallDict(func, args, nargs, kwargs);
|
|
jpayne@69
|
31301 } else {
|
|
jpayne@69
|
31302 return _PyCFunction_FastCallKeywords(func, args, nargs, NULL);
|
|
jpayne@69
|
31303 }
|
|
jpayne@69
|
31304 }
|
|
jpayne@69
|
31305 #if PY_VERSION_HEX >= 0x030700A1
|
|
jpayne@69
|
31306 if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) {
|
|
jpayne@69
|
31307 return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL);
|
|
jpayne@69
|
31308 }
|
|
jpayne@69
|
31309 #endif
|
|
jpayne@69
|
31310 #endif
|
|
jpayne@69
|
31311 #if CYTHON_FAST_PYCALL
|
|
jpayne@69
|
31312 if (PyFunction_Check(func)) {
|
|
jpayne@69
|
31313 return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs);
|
|
jpayne@69
|
31314 }
|
|
jpayne@69
|
31315 #endif
|
|
jpayne@69
|
31316 #endif
|
|
jpayne@69
|
31317 if (kwargs == NULL) {
|
|
jpayne@69
|
31318 #if CYTHON_VECTORCALL
|
|
jpayne@69
|
31319 #if PY_VERSION_HEX < 0x03090000
|
|
jpayne@69
|
31320 vectorcallfunc f = _PyVectorcall_Function(func);
|
|
jpayne@69
|
31321 #else
|
|
jpayne@69
|
31322 vectorcallfunc f = PyVectorcall_Function(func);
|
|
jpayne@69
|
31323 #endif
|
|
jpayne@69
|
31324 if (f) {
|
|
jpayne@69
|
31325 return f(func, args, (size_t)nargs, NULL);
|
|
jpayne@69
|
31326 }
|
|
jpayne@69
|
31327 #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
31328 if (__Pyx_CyFunction_CheckExact(func)) {
|
|
jpayne@69
|
31329 __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func);
|
|
jpayne@69
|
31330 if (f) return f(func, args, (size_t)nargs, NULL);
|
|
jpayne@69
|
31331 }
|
|
jpayne@69
|
31332 #endif
|
|
jpayne@69
|
31333 }
|
|
jpayne@69
|
31334 if (nargs == 0) {
|
|
jpayne@69
|
31335 return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs);
|
|
jpayne@69
|
31336 }
|
|
jpayne@69
|
31337 #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
31338 return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs);
|
|
jpayne@69
|
31339 #else
|
|
jpayne@69
|
31340 return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs);
|
|
jpayne@69
|
31341 #endif
|
|
jpayne@69
|
31342 }
|
|
jpayne@69
|
31343
|
|
jpayne@69
|
31344 /* PyObjectCallOneArg */
|
|
jpayne@69
|
31345 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
|
|
jpayne@69
|
31346 PyObject *args[2] = {NULL, arg};
|
|
jpayne@69
|
31347 return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
|
|
jpayne@69
|
31348 }
|
|
jpayne@69
|
31349
|
|
jpayne@69
|
31350 /* RaiseException */
|
|
jpayne@69
|
31351 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31352 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
|
|
jpayne@69
|
31353 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
31354 CYTHON_UNUSED_VAR(cause);
|
|
jpayne@69
|
31355 Py_XINCREF(type);
|
|
jpayne@69
|
31356 if (!value || value == Py_None)
|
|
jpayne@69
|
31357 value = NULL;
|
|
jpayne@69
|
31358 else
|
|
jpayne@69
|
31359 Py_INCREF(value);
|
|
jpayne@69
|
31360 if (!tb || tb == Py_None)
|
|
jpayne@69
|
31361 tb = NULL;
|
|
jpayne@69
|
31362 else {
|
|
jpayne@69
|
31363 Py_INCREF(tb);
|
|
jpayne@69
|
31364 if (!PyTraceBack_Check(tb)) {
|
|
jpayne@69
|
31365 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31366 "raise: arg 3 must be a traceback or None");
|
|
jpayne@69
|
31367 goto raise_error;
|
|
jpayne@69
|
31368 }
|
|
jpayne@69
|
31369 }
|
|
jpayne@69
|
31370 if (PyType_Check(type)) {
|
|
jpayne@69
|
31371 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
31372 if (!value) {
|
|
jpayne@69
|
31373 Py_INCREF(Py_None);
|
|
jpayne@69
|
31374 value = Py_None;
|
|
jpayne@69
|
31375 }
|
|
jpayne@69
|
31376 #endif
|
|
jpayne@69
|
31377 PyErr_NormalizeException(&type, &value, &tb);
|
|
jpayne@69
|
31378 } else {
|
|
jpayne@69
|
31379 if (value) {
|
|
jpayne@69
|
31380 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31381 "instance exception may not have a separate value");
|
|
jpayne@69
|
31382 goto raise_error;
|
|
jpayne@69
|
31383 }
|
|
jpayne@69
|
31384 value = type;
|
|
jpayne@69
|
31385 type = (PyObject*) Py_TYPE(type);
|
|
jpayne@69
|
31386 Py_INCREF(type);
|
|
jpayne@69
|
31387 if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
|
|
jpayne@69
|
31388 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31389 "raise: exception class must be a subclass of BaseException");
|
|
jpayne@69
|
31390 goto raise_error;
|
|
jpayne@69
|
31391 }
|
|
jpayne@69
|
31392 }
|
|
jpayne@69
|
31393 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
31394 __Pyx_ErrRestore(type, value, tb);
|
|
jpayne@69
|
31395 return;
|
|
jpayne@69
|
31396 raise_error:
|
|
jpayne@69
|
31397 Py_XDECREF(value);
|
|
jpayne@69
|
31398 Py_XDECREF(type);
|
|
jpayne@69
|
31399 Py_XDECREF(tb);
|
|
jpayne@69
|
31400 return;
|
|
jpayne@69
|
31401 }
|
|
jpayne@69
|
31402 #else
|
|
jpayne@69
|
31403 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
|
|
jpayne@69
|
31404 PyObject* owned_instance = NULL;
|
|
jpayne@69
|
31405 if (tb == Py_None) {
|
|
jpayne@69
|
31406 tb = 0;
|
|
jpayne@69
|
31407 } else if (tb && !PyTraceBack_Check(tb)) {
|
|
jpayne@69
|
31408 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31409 "raise: arg 3 must be a traceback or None");
|
|
jpayne@69
|
31410 goto bad;
|
|
jpayne@69
|
31411 }
|
|
jpayne@69
|
31412 if (value == Py_None)
|
|
jpayne@69
|
31413 value = 0;
|
|
jpayne@69
|
31414 if (PyExceptionInstance_Check(type)) {
|
|
jpayne@69
|
31415 if (value) {
|
|
jpayne@69
|
31416 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31417 "instance exception may not have a separate value");
|
|
jpayne@69
|
31418 goto bad;
|
|
jpayne@69
|
31419 }
|
|
jpayne@69
|
31420 value = type;
|
|
jpayne@69
|
31421 type = (PyObject*) Py_TYPE(value);
|
|
jpayne@69
|
31422 } else if (PyExceptionClass_Check(type)) {
|
|
jpayne@69
|
31423 PyObject *instance_class = NULL;
|
|
jpayne@69
|
31424 if (value && PyExceptionInstance_Check(value)) {
|
|
jpayne@69
|
31425 instance_class = (PyObject*) Py_TYPE(value);
|
|
jpayne@69
|
31426 if (instance_class != type) {
|
|
jpayne@69
|
31427 int is_subclass = PyObject_IsSubclass(instance_class, type);
|
|
jpayne@69
|
31428 if (!is_subclass) {
|
|
jpayne@69
|
31429 instance_class = NULL;
|
|
jpayne@69
|
31430 } else if (unlikely(is_subclass == -1)) {
|
|
jpayne@69
|
31431 goto bad;
|
|
jpayne@69
|
31432 } else {
|
|
jpayne@69
|
31433 type = instance_class;
|
|
jpayne@69
|
31434 }
|
|
jpayne@69
|
31435 }
|
|
jpayne@69
|
31436 }
|
|
jpayne@69
|
31437 if (!instance_class) {
|
|
jpayne@69
|
31438 PyObject *args;
|
|
jpayne@69
|
31439 if (!value)
|
|
jpayne@69
|
31440 args = PyTuple_New(0);
|
|
jpayne@69
|
31441 else if (PyTuple_Check(value)) {
|
|
jpayne@69
|
31442 Py_INCREF(value);
|
|
jpayne@69
|
31443 args = value;
|
|
jpayne@69
|
31444 } else
|
|
jpayne@69
|
31445 args = PyTuple_Pack(1, value);
|
|
jpayne@69
|
31446 if (!args)
|
|
jpayne@69
|
31447 goto bad;
|
|
jpayne@69
|
31448 owned_instance = PyObject_Call(type, args, NULL);
|
|
jpayne@69
|
31449 Py_DECREF(args);
|
|
jpayne@69
|
31450 if (!owned_instance)
|
|
jpayne@69
|
31451 goto bad;
|
|
jpayne@69
|
31452 value = owned_instance;
|
|
jpayne@69
|
31453 if (!PyExceptionInstance_Check(value)) {
|
|
jpayne@69
|
31454 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
31455 "calling %R should have returned an instance of "
|
|
jpayne@69
|
31456 "BaseException, not %R",
|
|
jpayne@69
|
31457 type, Py_TYPE(value));
|
|
jpayne@69
|
31458 goto bad;
|
|
jpayne@69
|
31459 }
|
|
jpayne@69
|
31460 }
|
|
jpayne@69
|
31461 } else {
|
|
jpayne@69
|
31462 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31463 "raise: exception class must be a subclass of BaseException");
|
|
jpayne@69
|
31464 goto bad;
|
|
jpayne@69
|
31465 }
|
|
jpayne@69
|
31466 if (cause) {
|
|
jpayne@69
|
31467 PyObject *fixed_cause;
|
|
jpayne@69
|
31468 if (cause == Py_None) {
|
|
jpayne@69
|
31469 fixed_cause = NULL;
|
|
jpayne@69
|
31470 } else if (PyExceptionClass_Check(cause)) {
|
|
jpayne@69
|
31471 fixed_cause = PyObject_CallObject(cause, NULL);
|
|
jpayne@69
|
31472 if (fixed_cause == NULL)
|
|
jpayne@69
|
31473 goto bad;
|
|
jpayne@69
|
31474 } else if (PyExceptionInstance_Check(cause)) {
|
|
jpayne@69
|
31475 fixed_cause = cause;
|
|
jpayne@69
|
31476 Py_INCREF(fixed_cause);
|
|
jpayne@69
|
31477 } else {
|
|
jpayne@69
|
31478 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
31479 "exception causes must derive from "
|
|
jpayne@69
|
31480 "BaseException");
|
|
jpayne@69
|
31481 goto bad;
|
|
jpayne@69
|
31482 }
|
|
jpayne@69
|
31483 PyException_SetCause(value, fixed_cause);
|
|
jpayne@69
|
31484 }
|
|
jpayne@69
|
31485 PyErr_SetObject(type, value);
|
|
jpayne@69
|
31486 if (tb) {
|
|
jpayne@69
|
31487 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
31488 PyException_SetTraceback(value, tb);
|
|
jpayne@69
|
31489 #elif CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
31490 PyThreadState *tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
31491 PyObject* tmp_tb = tstate->curexc_traceback;
|
|
jpayne@69
|
31492 if (tb != tmp_tb) {
|
|
jpayne@69
|
31493 Py_INCREF(tb);
|
|
jpayne@69
|
31494 tstate->curexc_traceback = tb;
|
|
jpayne@69
|
31495 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
31496 }
|
|
jpayne@69
|
31497 #else
|
|
jpayne@69
|
31498 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
31499 PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
|
|
jpayne@69
|
31500 Py_INCREF(tb);
|
|
jpayne@69
|
31501 PyErr_Restore(tmp_type, tmp_value, tb);
|
|
jpayne@69
|
31502 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
31503 #endif
|
|
jpayne@69
|
31504 }
|
|
jpayne@69
|
31505 bad:
|
|
jpayne@69
|
31506 Py_XDECREF(owned_instance);
|
|
jpayne@69
|
31507 return;
|
|
jpayne@69
|
31508 }
|
|
jpayne@69
|
31509 #endif
|
|
jpayne@69
|
31510
|
|
jpayne@69
|
31511 /* GetAttr3 */
|
|
jpayne@69
|
31512 #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1
|
|
jpayne@69
|
31513 static PyObject *__Pyx_GetAttr3Default(PyObject *d) {
|
|
jpayne@69
|
31514 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
31515 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
31516 if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
|
|
jpayne@69
|
31517 return NULL;
|
|
jpayne@69
|
31518 __Pyx_PyErr_Clear();
|
|
jpayne@69
|
31519 Py_INCREF(d);
|
|
jpayne@69
|
31520 return d;
|
|
jpayne@69
|
31521 }
|
|
jpayne@69
|
31522 #endif
|
|
jpayne@69
|
31523 static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) {
|
|
jpayne@69
|
31524 PyObject *r;
|
|
jpayne@69
|
31525 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
31526 int res = PyObject_GetOptionalAttr(o, n, &r);
|
|
jpayne@69
|
31527 return (res != 0) ? r : __Pyx_NewRef(d);
|
|
jpayne@69
|
31528 #else
|
|
jpayne@69
|
31529 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
31530 if (likely(PyString_Check(n))) {
|
|
jpayne@69
|
31531 r = __Pyx_PyObject_GetAttrStrNoError(o, n);
|
|
jpayne@69
|
31532 if (unlikely(!r) && likely(!PyErr_Occurred())) {
|
|
jpayne@69
|
31533 r = __Pyx_NewRef(d);
|
|
jpayne@69
|
31534 }
|
|
jpayne@69
|
31535 return r;
|
|
jpayne@69
|
31536 }
|
|
jpayne@69
|
31537 #endif
|
|
jpayne@69
|
31538 r = PyObject_GetAttr(o, n);
|
|
jpayne@69
|
31539 return (likely(r)) ? r : __Pyx_GetAttr3Default(d);
|
|
jpayne@69
|
31540 #endif
|
|
jpayne@69
|
31541 }
|
|
jpayne@69
|
31542
|
|
jpayne@69
|
31543 /* PyDictVersioning */
|
|
jpayne@69
|
31544 #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
31545 static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) {
|
|
jpayne@69
|
31546 PyObject *dict = Py_TYPE(obj)->tp_dict;
|
|
jpayne@69
|
31547 return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
|
|
jpayne@69
|
31548 }
|
|
jpayne@69
|
31549 static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) {
|
|
jpayne@69
|
31550 PyObject **dictptr = NULL;
|
|
jpayne@69
|
31551 Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset;
|
|
jpayne@69
|
31552 if (offset) {
|
|
jpayne@69
|
31553 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
31554 dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj);
|
|
jpayne@69
|
31555 #else
|
|
jpayne@69
|
31556 dictptr = _PyObject_GetDictPtr(obj);
|
|
jpayne@69
|
31557 #endif
|
|
jpayne@69
|
31558 }
|
|
jpayne@69
|
31559 return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
|
|
jpayne@69
|
31560 }
|
|
jpayne@69
|
31561 static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) {
|
|
jpayne@69
|
31562 PyObject *dict = Py_TYPE(obj)->tp_dict;
|
|
jpayne@69
|
31563 if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
|
|
jpayne@69
|
31564 return 0;
|
|
jpayne@69
|
31565 return obj_dict_version == __Pyx_get_object_dict_version(obj);
|
|
jpayne@69
|
31566 }
|
|
jpayne@69
|
31567 #endif
|
|
jpayne@69
|
31568
|
|
jpayne@69
|
31569 /* GetModuleGlobalName */
|
|
jpayne@69
|
31570 #if CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
31571 static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value)
|
|
jpayne@69
|
31572 #else
|
|
jpayne@69
|
31573 static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name)
|
|
jpayne@69
|
31574 #endif
|
|
jpayne@69
|
31575 {
|
|
jpayne@69
|
31576 PyObject *result;
|
|
jpayne@69
|
31577 #if !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
31578 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
31579 result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash);
|
|
jpayne@69
|
31580 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
|
|
jpayne@69
|
31581 if (likely(result)) {
|
|
jpayne@69
|
31582 return __Pyx_NewRef(result);
|
|
jpayne@69
|
31583 } else if (unlikely(PyErr_Occurred())) {
|
|
jpayne@69
|
31584 return NULL;
|
|
jpayne@69
|
31585 }
|
|
jpayne@69
|
31586 #elif CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
31587 if (unlikely(!__pyx_m)) {
|
|
jpayne@69
|
31588 return NULL;
|
|
jpayne@69
|
31589 }
|
|
jpayne@69
|
31590 result = PyObject_GetAttr(__pyx_m, name);
|
|
jpayne@69
|
31591 if (likely(result)) {
|
|
jpayne@69
|
31592 return result;
|
|
jpayne@69
|
31593 }
|
|
jpayne@69
|
31594 #else
|
|
jpayne@69
|
31595 result = PyDict_GetItem(__pyx_d, name);
|
|
jpayne@69
|
31596 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
|
|
jpayne@69
|
31597 if (likely(result)) {
|
|
jpayne@69
|
31598 return __Pyx_NewRef(result);
|
|
jpayne@69
|
31599 }
|
|
jpayne@69
|
31600 #endif
|
|
jpayne@69
|
31601 #else
|
|
jpayne@69
|
31602 result = PyObject_GetItem(__pyx_d, name);
|
|
jpayne@69
|
31603 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
|
|
jpayne@69
|
31604 if (likely(result)) {
|
|
jpayne@69
|
31605 return __Pyx_NewRef(result);
|
|
jpayne@69
|
31606 }
|
|
jpayne@69
|
31607 PyErr_Clear();
|
|
jpayne@69
|
31608 #endif
|
|
jpayne@69
|
31609 return __Pyx_GetBuiltinName(name);
|
|
jpayne@69
|
31610 }
|
|
jpayne@69
|
31611
|
|
jpayne@69
|
31612 /* RaiseUnexpectedTypeError */
|
|
jpayne@69
|
31613 static int
|
|
jpayne@69
|
31614 __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj)
|
|
jpayne@69
|
31615 {
|
|
jpayne@69
|
31616 __Pyx_TypeName obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
31617 PyErr_Format(PyExc_TypeError, "Expected %s, got " __Pyx_FMT_TYPENAME,
|
|
jpayne@69
|
31618 expected, obj_type_name);
|
|
jpayne@69
|
31619 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
31620 return 0;
|
|
jpayne@69
|
31621 }
|
|
jpayne@69
|
31622
|
|
jpayne@69
|
31623 /* ExtTypeTest */
|
|
jpayne@69
|
31624 static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
|
|
jpayne@69
|
31625 __Pyx_TypeName obj_type_name;
|
|
jpayne@69
|
31626 __Pyx_TypeName type_name;
|
|
jpayne@69
|
31627 if (unlikely(!type)) {
|
|
jpayne@69
|
31628 PyErr_SetString(PyExc_SystemError, "Missing type object");
|
|
jpayne@69
|
31629 return 0;
|
|
jpayne@69
|
31630 }
|
|
jpayne@69
|
31631 if (likely(__Pyx_TypeCheck(obj, type)))
|
|
jpayne@69
|
31632 return 1;
|
|
jpayne@69
|
31633 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
31634 type_name = __Pyx_PyType_GetName(type);
|
|
jpayne@69
|
31635 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
31636 "Cannot convert " __Pyx_FMT_TYPENAME " to " __Pyx_FMT_TYPENAME,
|
|
jpayne@69
|
31637 obj_type_name, type_name);
|
|
jpayne@69
|
31638 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
31639 __Pyx_DECREF_TypeName(type_name);
|
|
jpayne@69
|
31640 return 0;
|
|
jpayne@69
|
31641 }
|
|
jpayne@69
|
31642
|
|
jpayne@69
|
31643 /* PyIntBinop */
|
|
jpayne@69
|
31644 #if !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
31645 static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) {
|
|
jpayne@69
|
31646 CYTHON_MAYBE_UNUSED_VAR(intval);
|
|
jpayne@69
|
31647 CYTHON_MAYBE_UNUSED_VAR(inplace);
|
|
jpayne@69
|
31648 CYTHON_UNUSED_VAR(zerodivision_check);
|
|
jpayne@69
|
31649 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31650 if (likely(PyInt_CheckExact(op1))) {
|
|
jpayne@69
|
31651 const long b = intval;
|
|
jpayne@69
|
31652 long x;
|
|
jpayne@69
|
31653 long a = PyInt_AS_LONG(op1);
|
|
jpayne@69
|
31654
|
|
jpayne@69
|
31655 x = (long)((unsigned long)a + (unsigned long)b);
|
|
jpayne@69
|
31656 if (likely((x^a) >= 0 || (x^b) >= 0))
|
|
jpayne@69
|
31657 return PyInt_FromLong(x);
|
|
jpayne@69
|
31658 return PyLong_Type.tp_as_number->nb_add(op1, op2);
|
|
jpayne@69
|
31659 }
|
|
jpayne@69
|
31660 #endif
|
|
jpayne@69
|
31661 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
31662 if (likely(PyLong_CheckExact(op1))) {
|
|
jpayne@69
|
31663 const long b = intval;
|
|
jpayne@69
|
31664 long a, x;
|
|
jpayne@69
|
31665 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31666 const PY_LONG_LONG llb = intval;
|
|
jpayne@69
|
31667 PY_LONG_LONG lla, llx;
|
|
jpayne@69
|
31668 #endif
|
|
jpayne@69
|
31669 if (unlikely(__Pyx_PyLong_IsZero(op1))) {
|
|
jpayne@69
|
31670 return __Pyx_NewRef(op2);
|
|
jpayne@69
|
31671 }
|
|
jpayne@69
|
31672 if (likely(__Pyx_PyLong_IsCompact(op1))) {
|
|
jpayne@69
|
31673 a = __Pyx_PyLong_CompactValue(op1);
|
|
jpayne@69
|
31674 } else {
|
|
jpayne@69
|
31675 const digit* digits = __Pyx_PyLong_Digits(op1);
|
|
jpayne@69
|
31676 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1);
|
|
jpayne@69
|
31677 switch (size) {
|
|
jpayne@69
|
31678 case -2:
|
|
jpayne@69
|
31679 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
31680 a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
31681 break;
|
|
jpayne@69
|
31682 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31683 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
31684 lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
31685 goto long_long;
|
|
jpayne@69
|
31686 #endif
|
|
jpayne@69
|
31687 }
|
|
jpayne@69
|
31688 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
31689 case 2:
|
|
jpayne@69
|
31690 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
31691 a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
31692 break;
|
|
jpayne@69
|
31693 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31694 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
31695 lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
31696 goto long_long;
|
|
jpayne@69
|
31697 #endif
|
|
jpayne@69
|
31698 }
|
|
jpayne@69
|
31699 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
31700 case -3:
|
|
jpayne@69
|
31701 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
31702 a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
31703 break;
|
|
jpayne@69
|
31704 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31705 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
31706 lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
31707 goto long_long;
|
|
jpayne@69
|
31708 #endif
|
|
jpayne@69
|
31709 }
|
|
jpayne@69
|
31710 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
31711 case 3:
|
|
jpayne@69
|
31712 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
31713 a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
31714 break;
|
|
jpayne@69
|
31715 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31716 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
31717 lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
31718 goto long_long;
|
|
jpayne@69
|
31719 #endif
|
|
jpayne@69
|
31720 }
|
|
jpayne@69
|
31721 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
31722 case -4:
|
|
jpayne@69
|
31723 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
31724 a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
31725 break;
|
|
jpayne@69
|
31726 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31727 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
31728 lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
31729 goto long_long;
|
|
jpayne@69
|
31730 #endif
|
|
jpayne@69
|
31731 }
|
|
jpayne@69
|
31732 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
31733 case 4:
|
|
jpayne@69
|
31734 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
31735 a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
31736 break;
|
|
jpayne@69
|
31737 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31738 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
31739 lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
31740 goto long_long;
|
|
jpayne@69
|
31741 #endif
|
|
jpayne@69
|
31742 }
|
|
jpayne@69
|
31743 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
31744 default: return PyLong_Type.tp_as_number->nb_add(op1, op2);
|
|
jpayne@69
|
31745 }
|
|
jpayne@69
|
31746 }
|
|
jpayne@69
|
31747 x = a + b;
|
|
jpayne@69
|
31748 return PyLong_FromLong(x);
|
|
jpayne@69
|
31749 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
31750 long_long:
|
|
jpayne@69
|
31751 llx = lla + llb;
|
|
jpayne@69
|
31752 return PyLong_FromLongLong(llx);
|
|
jpayne@69
|
31753 #endif
|
|
jpayne@69
|
31754
|
|
jpayne@69
|
31755
|
|
jpayne@69
|
31756 }
|
|
jpayne@69
|
31757 #endif
|
|
jpayne@69
|
31758 if (PyFloat_CheckExact(op1)) {
|
|
jpayne@69
|
31759 const long b = intval;
|
|
jpayne@69
|
31760 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
31761 double a = __pyx_PyFloat_AsDouble(op1);
|
|
jpayne@69
|
31762 #else
|
|
jpayne@69
|
31763 double a = PyFloat_AS_DOUBLE(op1);
|
|
jpayne@69
|
31764 #endif
|
|
jpayne@69
|
31765 double result;
|
|
jpayne@69
|
31766
|
|
jpayne@69
|
31767 PyFPE_START_PROTECT("add", return NULL)
|
|
jpayne@69
|
31768 result = ((double)a) + (double)b;
|
|
jpayne@69
|
31769 PyFPE_END_PROTECT(result)
|
|
jpayne@69
|
31770 return PyFloat_FromDouble(result);
|
|
jpayne@69
|
31771 }
|
|
jpayne@69
|
31772 return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2);
|
|
jpayne@69
|
31773 }
|
|
jpayne@69
|
31774 #endif
|
|
jpayne@69
|
31775
|
|
jpayne@69
|
31776 /* WriteUnraisableException */
|
|
jpayne@69
|
31777 static void __Pyx_WriteUnraisable(const char *name, int clineno,
|
|
jpayne@69
|
31778 int lineno, const char *filename,
|
|
jpayne@69
|
31779 int full_traceback, int nogil) {
|
|
jpayne@69
|
31780 PyObject *old_exc, *old_val, *old_tb;
|
|
jpayne@69
|
31781 PyObject *ctx;
|
|
jpayne@69
|
31782 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
31783 #ifdef WITH_THREAD
|
|
jpayne@69
|
31784 PyGILState_STATE state;
|
|
jpayne@69
|
31785 if (nogil)
|
|
jpayne@69
|
31786 state = PyGILState_Ensure();
|
|
jpayne@69
|
31787 else state = (PyGILState_STATE)0;
|
|
jpayne@69
|
31788 #endif
|
|
jpayne@69
|
31789 CYTHON_UNUSED_VAR(clineno);
|
|
jpayne@69
|
31790 CYTHON_UNUSED_VAR(lineno);
|
|
jpayne@69
|
31791 CYTHON_UNUSED_VAR(filename);
|
|
jpayne@69
|
31792 CYTHON_MAYBE_UNUSED_VAR(nogil);
|
|
jpayne@69
|
31793 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
31794 __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
|
|
jpayne@69
|
31795 if (full_traceback) {
|
|
jpayne@69
|
31796 Py_XINCREF(old_exc);
|
|
jpayne@69
|
31797 Py_XINCREF(old_val);
|
|
jpayne@69
|
31798 Py_XINCREF(old_tb);
|
|
jpayne@69
|
31799 __Pyx_ErrRestore(old_exc, old_val, old_tb);
|
|
jpayne@69
|
31800 PyErr_PrintEx(0);
|
|
jpayne@69
|
31801 }
|
|
jpayne@69
|
31802 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31803 ctx = PyString_FromString(name);
|
|
jpayne@69
|
31804 #else
|
|
jpayne@69
|
31805 ctx = PyUnicode_FromString(name);
|
|
jpayne@69
|
31806 #endif
|
|
jpayne@69
|
31807 __Pyx_ErrRestore(old_exc, old_val, old_tb);
|
|
jpayne@69
|
31808 if (!ctx) {
|
|
jpayne@69
|
31809 PyErr_WriteUnraisable(Py_None);
|
|
jpayne@69
|
31810 } else {
|
|
jpayne@69
|
31811 PyErr_WriteUnraisable(ctx);
|
|
jpayne@69
|
31812 Py_DECREF(ctx);
|
|
jpayne@69
|
31813 }
|
|
jpayne@69
|
31814 #ifdef WITH_THREAD
|
|
jpayne@69
|
31815 if (nogil)
|
|
jpayne@69
|
31816 PyGILState_Release(state);
|
|
jpayne@69
|
31817 #endif
|
|
jpayne@69
|
31818 }
|
|
jpayne@69
|
31819
|
|
jpayne@69
|
31820 /* PyObjectCallNoArg */
|
|
jpayne@69
|
31821 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
|
|
jpayne@69
|
31822 PyObject *arg[2] = {NULL, NULL};
|
|
jpayne@69
|
31823 return __Pyx_PyObject_FastCall(func, arg + 1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
|
|
jpayne@69
|
31824 }
|
|
jpayne@69
|
31825
|
|
jpayne@69
|
31826 /* ArgTypeTest */
|
|
jpayne@69
|
31827 static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact)
|
|
jpayne@69
|
31828 {
|
|
jpayne@69
|
31829 __Pyx_TypeName type_name;
|
|
jpayne@69
|
31830 __Pyx_TypeName obj_type_name;
|
|
jpayne@69
|
31831 if (unlikely(!type)) {
|
|
jpayne@69
|
31832 PyErr_SetString(PyExc_SystemError, "Missing type object");
|
|
jpayne@69
|
31833 return 0;
|
|
jpayne@69
|
31834 }
|
|
jpayne@69
|
31835 else if (exact) {
|
|
jpayne@69
|
31836 #if PY_MAJOR_VERSION == 2
|
|
jpayne@69
|
31837 if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1;
|
|
jpayne@69
|
31838 #endif
|
|
jpayne@69
|
31839 }
|
|
jpayne@69
|
31840 else {
|
|
jpayne@69
|
31841 if (likely(__Pyx_TypeCheck(obj, type))) return 1;
|
|
jpayne@69
|
31842 }
|
|
jpayne@69
|
31843 type_name = __Pyx_PyType_GetName(type);
|
|
jpayne@69
|
31844 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
31845 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
31846 "Argument '%.200s' has incorrect type (expected " __Pyx_FMT_TYPENAME
|
|
jpayne@69
|
31847 ", got " __Pyx_FMT_TYPENAME ")", name, type_name, obj_type_name);
|
|
jpayne@69
|
31848 __Pyx_DECREF_TypeName(type_name);
|
|
jpayne@69
|
31849 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
31850 return 0;
|
|
jpayne@69
|
31851 }
|
|
jpayne@69
|
31852
|
|
jpayne@69
|
31853 /* PyObjectFormatAndDecref */
|
|
jpayne@69
|
31854 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f) {
|
|
jpayne@69
|
31855 if (unlikely(!s)) return NULL;
|
|
jpayne@69
|
31856 if (likely(PyUnicode_CheckExact(s))) return s;
|
|
jpayne@69
|
31857 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
31858 if (likely(PyString_CheckExact(s))) {
|
|
jpayne@69
|
31859 PyObject *result = PyUnicode_FromEncodedObject(s, NULL, "strict");
|
|
jpayne@69
|
31860 Py_DECREF(s);
|
|
jpayne@69
|
31861 return result;
|
|
jpayne@69
|
31862 }
|
|
jpayne@69
|
31863 #endif
|
|
jpayne@69
|
31864 return __Pyx_PyObject_FormatAndDecref(s, f);
|
|
jpayne@69
|
31865 }
|
|
jpayne@69
|
31866 static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f) {
|
|
jpayne@69
|
31867 PyObject *result;
|
|
jpayne@69
|
31868 if (unlikely(!s)) return NULL;
|
|
jpayne@69
|
31869 result = PyObject_Format(s, f);
|
|
jpayne@69
|
31870 Py_DECREF(s);
|
|
jpayne@69
|
31871 return result;
|
|
jpayne@69
|
31872 }
|
|
jpayne@69
|
31873
|
|
jpayne@69
|
31874 /* JoinPyUnicode */
|
|
jpayne@69
|
31875 static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength,
|
|
jpayne@69
|
31876 Py_UCS4 max_char) {
|
|
jpayne@69
|
31877 #if CYTHON_USE_UNICODE_INTERNALS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
31878 PyObject *result_uval;
|
|
jpayne@69
|
31879 int result_ukind, kind_shift;
|
|
jpayne@69
|
31880 Py_ssize_t i, char_pos;
|
|
jpayne@69
|
31881 void *result_udata;
|
|
jpayne@69
|
31882 CYTHON_MAYBE_UNUSED_VAR(max_char);
|
|
jpayne@69
|
31883 #if CYTHON_PEP393_ENABLED
|
|
jpayne@69
|
31884 result_uval = PyUnicode_New(result_ulength, max_char);
|
|
jpayne@69
|
31885 if (unlikely(!result_uval)) return NULL;
|
|
jpayne@69
|
31886 result_ukind = (max_char <= 255) ? PyUnicode_1BYTE_KIND : (max_char <= 65535) ? PyUnicode_2BYTE_KIND : PyUnicode_4BYTE_KIND;
|
|
jpayne@69
|
31887 kind_shift = (result_ukind == PyUnicode_4BYTE_KIND) ? 2 : result_ukind - 1;
|
|
jpayne@69
|
31888 result_udata = PyUnicode_DATA(result_uval);
|
|
jpayne@69
|
31889 #else
|
|
jpayne@69
|
31890 result_uval = PyUnicode_FromUnicode(NULL, result_ulength);
|
|
jpayne@69
|
31891 if (unlikely(!result_uval)) return NULL;
|
|
jpayne@69
|
31892 result_ukind = sizeof(Py_UNICODE);
|
|
jpayne@69
|
31893 kind_shift = (result_ukind == 4) ? 2 : result_ukind - 1;
|
|
jpayne@69
|
31894 result_udata = PyUnicode_AS_UNICODE(result_uval);
|
|
jpayne@69
|
31895 #endif
|
|
jpayne@69
|
31896 assert(kind_shift == 2 || kind_shift == 1 || kind_shift == 0);
|
|
jpayne@69
|
31897 char_pos = 0;
|
|
jpayne@69
|
31898 for (i=0; i < value_count; i++) {
|
|
jpayne@69
|
31899 int ukind;
|
|
jpayne@69
|
31900 Py_ssize_t ulength;
|
|
jpayne@69
|
31901 void *udata;
|
|
jpayne@69
|
31902 PyObject *uval = PyTuple_GET_ITEM(value_tuple, i);
|
|
jpayne@69
|
31903 if (unlikely(__Pyx_PyUnicode_READY(uval)))
|
|
jpayne@69
|
31904 goto bad;
|
|
jpayne@69
|
31905 ulength = __Pyx_PyUnicode_GET_LENGTH(uval);
|
|
jpayne@69
|
31906 if (unlikely(!ulength))
|
|
jpayne@69
|
31907 continue;
|
|
jpayne@69
|
31908 if (unlikely((PY_SSIZE_T_MAX >> kind_shift) - ulength < char_pos))
|
|
jpayne@69
|
31909 goto overflow;
|
|
jpayne@69
|
31910 ukind = __Pyx_PyUnicode_KIND(uval);
|
|
jpayne@69
|
31911 udata = __Pyx_PyUnicode_DATA(uval);
|
|
jpayne@69
|
31912 if (!CYTHON_PEP393_ENABLED || ukind == result_ukind) {
|
|
jpayne@69
|
31913 memcpy((char *)result_udata + (char_pos << kind_shift), udata, (size_t) (ulength << kind_shift));
|
|
jpayne@69
|
31914 } else {
|
|
jpayne@69
|
31915 #if PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
31916 if (unlikely(PyUnicode_CopyCharacters(result_uval, char_pos, uval, 0, ulength) < 0)) goto bad;
|
|
jpayne@69
|
31917 #elif CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030300F0 || defined(_PyUnicode_FastCopyCharacters)
|
|
jpayne@69
|
31918 _PyUnicode_FastCopyCharacters(result_uval, char_pos, uval, 0, ulength);
|
|
jpayne@69
|
31919 #else
|
|
jpayne@69
|
31920 Py_ssize_t j;
|
|
jpayne@69
|
31921 for (j=0; j < ulength; j++) {
|
|
jpayne@69
|
31922 Py_UCS4 uchar = __Pyx_PyUnicode_READ(ukind, udata, j);
|
|
jpayne@69
|
31923 __Pyx_PyUnicode_WRITE(result_ukind, result_udata, char_pos+j, uchar);
|
|
jpayne@69
|
31924 }
|
|
jpayne@69
|
31925 #endif
|
|
jpayne@69
|
31926 }
|
|
jpayne@69
|
31927 char_pos += ulength;
|
|
jpayne@69
|
31928 }
|
|
jpayne@69
|
31929 return result_uval;
|
|
jpayne@69
|
31930 overflow:
|
|
jpayne@69
|
31931 PyErr_SetString(PyExc_OverflowError, "join() result is too long for a Python string");
|
|
jpayne@69
|
31932 bad:
|
|
jpayne@69
|
31933 Py_DECREF(result_uval);
|
|
jpayne@69
|
31934 return NULL;
|
|
jpayne@69
|
31935 #else
|
|
jpayne@69
|
31936 CYTHON_UNUSED_VAR(max_char);
|
|
jpayne@69
|
31937 CYTHON_UNUSED_VAR(result_ulength);
|
|
jpayne@69
|
31938 CYTHON_UNUSED_VAR(value_count);
|
|
jpayne@69
|
31939 return PyUnicode_Join(__pyx_empty_unicode, value_tuple);
|
|
jpayne@69
|
31940 #endif
|
|
jpayne@69
|
31941 }
|
|
jpayne@69
|
31942
|
|
jpayne@69
|
31943 /* DictGetItem */
|
|
jpayne@69
|
31944 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
31945 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
|
|
jpayne@69
|
31946 PyObject *value;
|
|
jpayne@69
|
31947 value = PyDict_GetItemWithError(d, key);
|
|
jpayne@69
|
31948 if (unlikely(!value)) {
|
|
jpayne@69
|
31949 if (!PyErr_Occurred()) {
|
|
jpayne@69
|
31950 if (unlikely(PyTuple_Check(key))) {
|
|
jpayne@69
|
31951 PyObject* args = PyTuple_Pack(1, key);
|
|
jpayne@69
|
31952 if (likely(args)) {
|
|
jpayne@69
|
31953 PyErr_SetObject(PyExc_KeyError, args);
|
|
jpayne@69
|
31954 Py_DECREF(args);
|
|
jpayne@69
|
31955 }
|
|
jpayne@69
|
31956 } else {
|
|
jpayne@69
|
31957 PyErr_SetObject(PyExc_KeyError, key);
|
|
jpayne@69
|
31958 }
|
|
jpayne@69
|
31959 }
|
|
jpayne@69
|
31960 return NULL;
|
|
jpayne@69
|
31961 }
|
|
jpayne@69
|
31962 Py_INCREF(value);
|
|
jpayne@69
|
31963 return value;
|
|
jpayne@69
|
31964 }
|
|
jpayne@69
|
31965 #endif
|
|
jpayne@69
|
31966
|
|
jpayne@69
|
31967 /* GetTopmostException */
|
|
jpayne@69
|
31968 #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
31969 static _PyErr_StackItem *
|
|
jpayne@69
|
31970 __Pyx_PyErr_GetTopmostException(PyThreadState *tstate)
|
|
jpayne@69
|
31971 {
|
|
jpayne@69
|
31972 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
31973 while ((exc_info->exc_value == NULL || exc_info->exc_value == Py_None) &&
|
|
jpayne@69
|
31974 exc_info->previous_item != NULL)
|
|
jpayne@69
|
31975 {
|
|
jpayne@69
|
31976 exc_info = exc_info->previous_item;
|
|
jpayne@69
|
31977 }
|
|
jpayne@69
|
31978 return exc_info;
|
|
jpayne@69
|
31979 }
|
|
jpayne@69
|
31980 #endif
|
|
jpayne@69
|
31981
|
|
jpayne@69
|
31982 /* SaveResetException */
|
|
jpayne@69
|
31983 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
31984 static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
|
|
jpayne@69
|
31985 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
31986 _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
|
|
jpayne@69
|
31987 PyObject *exc_value = exc_info->exc_value;
|
|
jpayne@69
|
31988 if (exc_value == NULL || exc_value == Py_None) {
|
|
jpayne@69
|
31989 *value = NULL;
|
|
jpayne@69
|
31990 *type = NULL;
|
|
jpayne@69
|
31991 *tb = NULL;
|
|
jpayne@69
|
31992 } else {
|
|
jpayne@69
|
31993 *value = exc_value;
|
|
jpayne@69
|
31994 Py_INCREF(*value);
|
|
jpayne@69
|
31995 *type = (PyObject*) Py_TYPE(exc_value);
|
|
jpayne@69
|
31996 Py_INCREF(*type);
|
|
jpayne@69
|
31997 *tb = PyException_GetTraceback(exc_value);
|
|
jpayne@69
|
31998 }
|
|
jpayne@69
|
31999 #elif CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
32000 _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
|
|
jpayne@69
|
32001 *type = exc_info->exc_type;
|
|
jpayne@69
|
32002 *value = exc_info->exc_value;
|
|
jpayne@69
|
32003 *tb = exc_info->exc_traceback;
|
|
jpayne@69
|
32004 Py_XINCREF(*type);
|
|
jpayne@69
|
32005 Py_XINCREF(*value);
|
|
jpayne@69
|
32006 Py_XINCREF(*tb);
|
|
jpayne@69
|
32007 #else
|
|
jpayne@69
|
32008 *type = tstate->exc_type;
|
|
jpayne@69
|
32009 *value = tstate->exc_value;
|
|
jpayne@69
|
32010 *tb = tstate->exc_traceback;
|
|
jpayne@69
|
32011 Py_XINCREF(*type);
|
|
jpayne@69
|
32012 Py_XINCREF(*value);
|
|
jpayne@69
|
32013 Py_XINCREF(*tb);
|
|
jpayne@69
|
32014 #endif
|
|
jpayne@69
|
32015 }
|
|
jpayne@69
|
32016 static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
|
|
jpayne@69
|
32017 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
32018 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
32019 PyObject *tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
32020 exc_info->exc_value = value;
|
|
jpayne@69
|
32021 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
32022 Py_XDECREF(type);
|
|
jpayne@69
|
32023 Py_XDECREF(tb);
|
|
jpayne@69
|
32024 #else
|
|
jpayne@69
|
32025 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
32026 #if CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
32027 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
32028 tmp_type = exc_info->exc_type;
|
|
jpayne@69
|
32029 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
32030 tmp_tb = exc_info->exc_traceback;
|
|
jpayne@69
|
32031 exc_info->exc_type = type;
|
|
jpayne@69
|
32032 exc_info->exc_value = value;
|
|
jpayne@69
|
32033 exc_info->exc_traceback = tb;
|
|
jpayne@69
|
32034 #else
|
|
jpayne@69
|
32035 tmp_type = tstate->exc_type;
|
|
jpayne@69
|
32036 tmp_value = tstate->exc_value;
|
|
jpayne@69
|
32037 tmp_tb = tstate->exc_traceback;
|
|
jpayne@69
|
32038 tstate->exc_type = type;
|
|
jpayne@69
|
32039 tstate->exc_value = value;
|
|
jpayne@69
|
32040 tstate->exc_traceback = tb;
|
|
jpayne@69
|
32041 #endif
|
|
jpayne@69
|
32042 Py_XDECREF(tmp_type);
|
|
jpayne@69
|
32043 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
32044 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
32045 #endif
|
|
jpayne@69
|
32046 }
|
|
jpayne@69
|
32047 #endif
|
|
jpayne@69
|
32048
|
|
jpayne@69
|
32049 /* GetException */
|
|
jpayne@69
|
32050 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
32051 static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb)
|
|
jpayne@69
|
32052 #else
|
|
jpayne@69
|
32053 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
|
|
jpayne@69
|
32054 #endif
|
|
jpayne@69
|
32055 {
|
|
jpayne@69
|
32056 PyObject *local_type = NULL, *local_value, *local_tb = NULL;
|
|
jpayne@69
|
32057 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
32058 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
32059 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
32060 local_value = tstate->current_exception;
|
|
jpayne@69
|
32061 tstate->current_exception = 0;
|
|
jpayne@69
|
32062 if (likely(local_value)) {
|
|
jpayne@69
|
32063 local_type = (PyObject*) Py_TYPE(local_value);
|
|
jpayne@69
|
32064 Py_INCREF(local_type);
|
|
jpayne@69
|
32065 local_tb = PyException_GetTraceback(local_value);
|
|
jpayne@69
|
32066 }
|
|
jpayne@69
|
32067 #else
|
|
jpayne@69
|
32068 local_type = tstate->curexc_type;
|
|
jpayne@69
|
32069 local_value = tstate->curexc_value;
|
|
jpayne@69
|
32070 local_tb = tstate->curexc_traceback;
|
|
jpayne@69
|
32071 tstate->curexc_type = 0;
|
|
jpayne@69
|
32072 tstate->curexc_value = 0;
|
|
jpayne@69
|
32073 tstate->curexc_traceback = 0;
|
|
jpayne@69
|
32074 #endif
|
|
jpayne@69
|
32075 #else
|
|
jpayne@69
|
32076 PyErr_Fetch(&local_type, &local_value, &local_tb);
|
|
jpayne@69
|
32077 #endif
|
|
jpayne@69
|
32078 PyErr_NormalizeException(&local_type, &local_value, &local_tb);
|
|
jpayne@69
|
32079 #if CYTHON_FAST_THREAD_STATE && PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
32080 if (unlikely(tstate->current_exception))
|
|
jpayne@69
|
32081 #elif CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
32082 if (unlikely(tstate->curexc_type))
|
|
jpayne@69
|
32083 #else
|
|
jpayne@69
|
32084 if (unlikely(PyErr_Occurred()))
|
|
jpayne@69
|
32085 #endif
|
|
jpayne@69
|
32086 goto bad;
|
|
jpayne@69
|
32087 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32088 if (local_tb) {
|
|
jpayne@69
|
32089 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
|
|
jpayne@69
|
32090 goto bad;
|
|
jpayne@69
|
32091 }
|
|
jpayne@69
|
32092 #endif
|
|
jpayne@69
|
32093 Py_XINCREF(local_tb);
|
|
jpayne@69
|
32094 Py_XINCREF(local_type);
|
|
jpayne@69
|
32095 Py_XINCREF(local_value);
|
|
jpayne@69
|
32096 *type = local_type;
|
|
jpayne@69
|
32097 *value = local_value;
|
|
jpayne@69
|
32098 *tb = local_tb;
|
|
jpayne@69
|
32099 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
32100 #if CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
32101 {
|
|
jpayne@69
|
32102 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
32103 #if PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
32104 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
32105 exc_info->exc_value = local_value;
|
|
jpayne@69
|
32106 tmp_type = NULL;
|
|
jpayne@69
|
32107 tmp_tb = NULL;
|
|
jpayne@69
|
32108 Py_XDECREF(local_type);
|
|
jpayne@69
|
32109 Py_XDECREF(local_tb);
|
|
jpayne@69
|
32110 #else
|
|
jpayne@69
|
32111 tmp_type = exc_info->exc_type;
|
|
jpayne@69
|
32112 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
32113 tmp_tb = exc_info->exc_traceback;
|
|
jpayne@69
|
32114 exc_info->exc_type = local_type;
|
|
jpayne@69
|
32115 exc_info->exc_value = local_value;
|
|
jpayne@69
|
32116 exc_info->exc_traceback = local_tb;
|
|
jpayne@69
|
32117 #endif
|
|
jpayne@69
|
32118 }
|
|
jpayne@69
|
32119 #else
|
|
jpayne@69
|
32120 tmp_type = tstate->exc_type;
|
|
jpayne@69
|
32121 tmp_value = tstate->exc_value;
|
|
jpayne@69
|
32122 tmp_tb = tstate->exc_traceback;
|
|
jpayne@69
|
32123 tstate->exc_type = local_type;
|
|
jpayne@69
|
32124 tstate->exc_value = local_value;
|
|
jpayne@69
|
32125 tstate->exc_traceback = local_tb;
|
|
jpayne@69
|
32126 #endif
|
|
jpayne@69
|
32127 Py_XDECREF(tmp_type);
|
|
jpayne@69
|
32128 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
32129 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
32130 #else
|
|
jpayne@69
|
32131 PyErr_SetExcInfo(local_type, local_value, local_tb);
|
|
jpayne@69
|
32132 #endif
|
|
jpayne@69
|
32133 return 0;
|
|
jpayne@69
|
32134 bad:
|
|
jpayne@69
|
32135 *type = 0;
|
|
jpayne@69
|
32136 *value = 0;
|
|
jpayne@69
|
32137 *tb = 0;
|
|
jpayne@69
|
32138 Py_XDECREF(local_type);
|
|
jpayne@69
|
32139 Py_XDECREF(local_value);
|
|
jpayne@69
|
32140 Py_XDECREF(local_tb);
|
|
jpayne@69
|
32141 return -1;
|
|
jpayne@69
|
32142 }
|
|
jpayne@69
|
32143
|
|
jpayne@69
|
32144 /* UnpackUnboundCMethod */
|
|
jpayne@69
|
32145 static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) {
|
|
jpayne@69
|
32146 PyObject *result;
|
|
jpayne@69
|
32147 PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args));
|
|
jpayne@69
|
32148 if (unlikely(!selfless_args)) return NULL;
|
|
jpayne@69
|
32149 result = PyObject_Call(method, selfless_args, kwargs);
|
|
jpayne@69
|
32150 Py_DECREF(selfless_args);
|
|
jpayne@69
|
32151 return result;
|
|
jpayne@69
|
32152 }
|
|
jpayne@69
|
32153 static PyMethodDef __Pyx_UnboundCMethod_Def = {
|
|
jpayne@69
|
32154 "CythonUnboundCMethod",
|
|
jpayne@69
|
32155 __PYX_REINTERPRET_FUNCION(PyCFunction, __Pyx_SelflessCall),
|
|
jpayne@69
|
32156 METH_VARARGS | METH_KEYWORDS,
|
|
jpayne@69
|
32157 NULL
|
|
jpayne@69
|
32158 };
|
|
jpayne@69
|
32159 static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) {
|
|
jpayne@69
|
32160 PyObject *method;
|
|
jpayne@69
|
32161 method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name);
|
|
jpayne@69
|
32162 if (unlikely(!method))
|
|
jpayne@69
|
32163 return -1;
|
|
jpayne@69
|
32164 target->method = method;
|
|
jpayne@69
|
32165 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
32166 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32167 if (likely(__Pyx_TypeCheck(method, &PyMethodDescr_Type)))
|
|
jpayne@69
|
32168 #else
|
|
jpayne@69
|
32169 if (likely(!__Pyx_CyOrPyCFunction_Check(method)))
|
|
jpayne@69
|
32170 #endif
|
|
jpayne@69
|
32171 {
|
|
jpayne@69
|
32172 PyMethodDescrObject *descr = (PyMethodDescrObject*) method;
|
|
jpayne@69
|
32173 target->func = descr->d_method->ml_meth;
|
|
jpayne@69
|
32174 target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_STACKLESS);
|
|
jpayne@69
|
32175 } else
|
|
jpayne@69
|
32176 #endif
|
|
jpayne@69
|
32177 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
32178 #else
|
|
jpayne@69
|
32179 if (PyCFunction_Check(method))
|
|
jpayne@69
|
32180 #endif
|
|
jpayne@69
|
32181 {
|
|
jpayne@69
|
32182 PyObject *self;
|
|
jpayne@69
|
32183 int self_found;
|
|
jpayne@69
|
32184 #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
32185 self = PyObject_GetAttrString(method, "__self__");
|
|
jpayne@69
|
32186 if (!self) {
|
|
jpayne@69
|
32187 PyErr_Clear();
|
|
jpayne@69
|
32188 }
|
|
jpayne@69
|
32189 #else
|
|
jpayne@69
|
32190 self = PyCFunction_GET_SELF(method);
|
|
jpayne@69
|
32191 #endif
|
|
jpayne@69
|
32192 self_found = (self && self != Py_None);
|
|
jpayne@69
|
32193 #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
32194 Py_XDECREF(self);
|
|
jpayne@69
|
32195 #endif
|
|
jpayne@69
|
32196 if (self_found) {
|
|
jpayne@69
|
32197 PyObject *unbound_method = PyCFunction_New(&__Pyx_UnboundCMethod_Def, method);
|
|
jpayne@69
|
32198 if (unlikely(!unbound_method)) return -1;
|
|
jpayne@69
|
32199 Py_DECREF(method);
|
|
jpayne@69
|
32200 target->method = unbound_method;
|
|
jpayne@69
|
32201 }
|
|
jpayne@69
|
32202 }
|
|
jpayne@69
|
32203 return 0;
|
|
jpayne@69
|
32204 }
|
|
jpayne@69
|
32205
|
|
jpayne@69
|
32206 /* CallUnboundCMethod0 */
|
|
jpayne@69
|
32207 static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) {
|
|
jpayne@69
|
32208 PyObject *args, *result = NULL;
|
|
jpayne@69
|
32209 if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL;
|
|
jpayne@69
|
32210 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
32211 args = PyTuple_New(1);
|
|
jpayne@69
|
32212 if (unlikely(!args)) goto bad;
|
|
jpayne@69
|
32213 Py_INCREF(self);
|
|
jpayne@69
|
32214 PyTuple_SET_ITEM(args, 0, self);
|
|
jpayne@69
|
32215 #else
|
|
jpayne@69
|
32216 args = PyTuple_Pack(1, self);
|
|
jpayne@69
|
32217 if (unlikely(!args)) goto bad;
|
|
jpayne@69
|
32218 #endif
|
|
jpayne@69
|
32219 result = __Pyx_PyObject_Call(cfunc->method, args, NULL);
|
|
jpayne@69
|
32220 Py_DECREF(args);
|
|
jpayne@69
|
32221 bad:
|
|
jpayne@69
|
32222 return result;
|
|
jpayne@69
|
32223 }
|
|
jpayne@69
|
32224
|
|
jpayne@69
|
32225 /* py_dict_keys */
|
|
jpayne@69
|
32226 static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) {
|
|
jpayne@69
|
32227 if (PY_MAJOR_VERSION >= 3)
|
|
jpayne@69
|
32228 return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_keys, d);
|
|
jpayne@69
|
32229 else
|
|
jpayne@69
|
32230 return PyDict_Keys(d);
|
|
jpayne@69
|
32231 }
|
|
jpayne@69
|
32232
|
|
jpayne@69
|
32233 /* UnicodeAsUCS4 */
|
|
jpayne@69
|
32234 static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject* x) {
|
|
jpayne@69
|
32235 Py_ssize_t length;
|
|
jpayne@69
|
32236 #if CYTHON_PEP393_ENABLED
|
|
jpayne@69
|
32237 length = PyUnicode_GET_LENGTH(x);
|
|
jpayne@69
|
32238 if (likely(length == 1)) {
|
|
jpayne@69
|
32239 return PyUnicode_READ_CHAR(x, 0);
|
|
jpayne@69
|
32240 }
|
|
jpayne@69
|
32241 #else
|
|
jpayne@69
|
32242 length = PyUnicode_GET_SIZE(x);
|
|
jpayne@69
|
32243 if (likely(length == 1)) {
|
|
jpayne@69
|
32244 return PyUnicode_AS_UNICODE(x)[0];
|
|
jpayne@69
|
32245 }
|
|
jpayne@69
|
32246 #if Py_UNICODE_SIZE == 2
|
|
jpayne@69
|
32247 else if (PyUnicode_GET_SIZE(x) == 2) {
|
|
jpayne@69
|
32248 Py_UCS4 high_val = PyUnicode_AS_UNICODE(x)[0];
|
|
jpayne@69
|
32249 if (high_val >= 0xD800 && high_val <= 0xDBFF) {
|
|
jpayne@69
|
32250 Py_UCS4 low_val = PyUnicode_AS_UNICODE(x)[1];
|
|
jpayne@69
|
32251 if (low_val >= 0xDC00 && low_val <= 0xDFFF) {
|
|
jpayne@69
|
32252 return 0x10000 + (((high_val & ((1<<10)-1)) << 10) | (low_val & ((1<<10)-1)));
|
|
jpayne@69
|
32253 }
|
|
jpayne@69
|
32254 }
|
|
jpayne@69
|
32255 }
|
|
jpayne@69
|
32256 #endif
|
|
jpayne@69
|
32257 #endif
|
|
jpayne@69
|
32258 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
32259 "only single character unicode strings can be converted to Py_UCS4, "
|
|
jpayne@69
|
32260 "got length %" CYTHON_FORMAT_SSIZE_T "d", length);
|
|
jpayne@69
|
32261 return (Py_UCS4)-1;
|
|
jpayne@69
|
32262 }
|
|
jpayne@69
|
32263
|
|
jpayne@69
|
32264 /* object_ord */
|
|
jpayne@69
|
32265 static long __Pyx__PyObject_Ord(PyObject* c) {
|
|
jpayne@69
|
32266 Py_ssize_t size;
|
|
jpayne@69
|
32267 if (PyBytes_Check(c)) {
|
|
jpayne@69
|
32268 size = PyBytes_GET_SIZE(c);
|
|
jpayne@69
|
32269 if (likely(size == 1)) {
|
|
jpayne@69
|
32270 return (unsigned char) PyBytes_AS_STRING(c)[0];
|
|
jpayne@69
|
32271 }
|
|
jpayne@69
|
32272 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32273 } else if (PyUnicode_Check(c)) {
|
|
jpayne@69
|
32274 return (long)__Pyx_PyUnicode_AsPy_UCS4(c);
|
|
jpayne@69
|
32275 #endif
|
|
jpayne@69
|
32276 #if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
|
|
jpayne@69
|
32277 } else if (PyByteArray_Check(c)) {
|
|
jpayne@69
|
32278 size = PyByteArray_GET_SIZE(c);
|
|
jpayne@69
|
32279 if (likely(size == 1)) {
|
|
jpayne@69
|
32280 return (unsigned char) PyByteArray_AS_STRING(c)[0];
|
|
jpayne@69
|
32281 }
|
|
jpayne@69
|
32282 #endif
|
|
jpayne@69
|
32283 } else {
|
|
jpayne@69
|
32284 __Pyx_TypeName c_type_name = __Pyx_PyType_GetName(Py_TYPE(c));
|
|
jpayne@69
|
32285 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
32286 "ord() expected string of length 1, but " __Pyx_FMT_TYPENAME " found",
|
|
jpayne@69
|
32287 c_type_name);
|
|
jpayne@69
|
32288 __Pyx_DECREF_TypeName(c_type_name);
|
|
jpayne@69
|
32289 return (long)(Py_UCS4)-1;
|
|
jpayne@69
|
32290 }
|
|
jpayne@69
|
32291 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
32292 "ord() expected a character, but string of length %zd found", size);
|
|
jpayne@69
|
32293 return (long)(Py_UCS4)-1;
|
|
jpayne@69
|
32294 }
|
|
jpayne@69
|
32295
|
|
jpayne@69
|
32296 /* RaiseTooManyValuesToUnpack */
|
|
jpayne@69
|
32297 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
|
|
jpayne@69
|
32298 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
32299 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
|
|
jpayne@69
|
32300 }
|
|
jpayne@69
|
32301
|
|
jpayne@69
|
32302 /* RaiseNeedMoreValuesToUnpack */
|
|
jpayne@69
|
32303 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
|
|
jpayne@69
|
32304 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
32305 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
|
|
jpayne@69
|
32306 index, (index == 1) ? "" : "s");
|
|
jpayne@69
|
32307 }
|
|
jpayne@69
|
32308
|
|
jpayne@69
|
32309 /* IterFinish */
|
|
jpayne@69
|
32310 static CYTHON_INLINE int __Pyx_IterFinish(void) {
|
|
jpayne@69
|
32311 PyObject* exc_type;
|
|
jpayne@69
|
32312 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
32313 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
32314 exc_type = __Pyx_PyErr_CurrentExceptionType();
|
|
jpayne@69
|
32315 if (unlikely(exc_type)) {
|
|
jpayne@69
|
32316 if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)))
|
|
jpayne@69
|
32317 return -1;
|
|
jpayne@69
|
32318 __Pyx_PyErr_Clear();
|
|
jpayne@69
|
32319 return 0;
|
|
jpayne@69
|
32320 }
|
|
jpayne@69
|
32321 return 0;
|
|
jpayne@69
|
32322 }
|
|
jpayne@69
|
32323
|
|
jpayne@69
|
32324 /* UnpackItemEndCheck */
|
|
jpayne@69
|
32325 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
|
|
jpayne@69
|
32326 if (unlikely(retval)) {
|
|
jpayne@69
|
32327 Py_DECREF(retval);
|
|
jpayne@69
|
32328 __Pyx_RaiseTooManyValuesError(expected);
|
|
jpayne@69
|
32329 return -1;
|
|
jpayne@69
|
32330 }
|
|
jpayne@69
|
32331 return __Pyx_IterFinish();
|
|
jpayne@69
|
32332 }
|
|
jpayne@69
|
32333
|
|
jpayne@69
|
32334 /* PyObjectSetAttrStr */
|
|
jpayne@69
|
32335 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
32336 static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
|
|
jpayne@69
|
32337 PyTypeObject* tp = Py_TYPE(obj);
|
|
jpayne@69
|
32338 if (likely(tp->tp_setattro))
|
|
jpayne@69
|
32339 return tp->tp_setattro(obj, attr_name, value);
|
|
jpayne@69
|
32340 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32341 if (likely(tp->tp_setattr))
|
|
jpayne@69
|
32342 return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
|
|
jpayne@69
|
32343 #endif
|
|
jpayne@69
|
32344 return PyObject_SetAttr(obj, attr_name, value);
|
|
jpayne@69
|
32345 }
|
|
jpayne@69
|
32346 #endif
|
|
jpayne@69
|
32347
|
|
jpayne@69
|
32348 /* Import */
|
|
jpayne@69
|
32349 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
|
|
jpayne@69
|
32350 PyObject *module = 0;
|
|
jpayne@69
|
32351 PyObject *empty_dict = 0;
|
|
jpayne@69
|
32352 PyObject *empty_list = 0;
|
|
jpayne@69
|
32353 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32354 PyObject *py_import;
|
|
jpayne@69
|
32355 py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
|
|
jpayne@69
|
32356 if (unlikely(!py_import))
|
|
jpayne@69
|
32357 goto bad;
|
|
jpayne@69
|
32358 if (!from_list) {
|
|
jpayne@69
|
32359 empty_list = PyList_New(0);
|
|
jpayne@69
|
32360 if (unlikely(!empty_list))
|
|
jpayne@69
|
32361 goto bad;
|
|
jpayne@69
|
32362 from_list = empty_list;
|
|
jpayne@69
|
32363 }
|
|
jpayne@69
|
32364 #endif
|
|
jpayne@69
|
32365 empty_dict = PyDict_New();
|
|
jpayne@69
|
32366 if (unlikely(!empty_dict))
|
|
jpayne@69
|
32367 goto bad;
|
|
jpayne@69
|
32368 {
|
|
jpayne@69
|
32369 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32370 if (level == -1) {
|
|
jpayne@69
|
32371 if (strchr(__Pyx_MODULE_NAME, '.') != NULL) {
|
|
jpayne@69
|
32372 module = PyImport_ImportModuleLevelObject(
|
|
jpayne@69
|
32373 name, __pyx_d, empty_dict, from_list, 1);
|
|
jpayne@69
|
32374 if (unlikely(!module)) {
|
|
jpayne@69
|
32375 if (unlikely(!PyErr_ExceptionMatches(PyExc_ImportError)))
|
|
jpayne@69
|
32376 goto bad;
|
|
jpayne@69
|
32377 PyErr_Clear();
|
|
jpayne@69
|
32378 }
|
|
jpayne@69
|
32379 }
|
|
jpayne@69
|
32380 level = 0;
|
|
jpayne@69
|
32381 }
|
|
jpayne@69
|
32382 #endif
|
|
jpayne@69
|
32383 if (!module) {
|
|
jpayne@69
|
32384 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32385 PyObject *py_level = PyInt_FromLong(level);
|
|
jpayne@69
|
32386 if (unlikely(!py_level))
|
|
jpayne@69
|
32387 goto bad;
|
|
jpayne@69
|
32388 module = PyObject_CallFunctionObjArgs(py_import,
|
|
jpayne@69
|
32389 name, __pyx_d, empty_dict, from_list, py_level, (PyObject *)NULL);
|
|
jpayne@69
|
32390 Py_DECREF(py_level);
|
|
jpayne@69
|
32391 #else
|
|
jpayne@69
|
32392 module = PyImport_ImportModuleLevelObject(
|
|
jpayne@69
|
32393 name, __pyx_d, empty_dict, from_list, level);
|
|
jpayne@69
|
32394 #endif
|
|
jpayne@69
|
32395 }
|
|
jpayne@69
|
32396 }
|
|
jpayne@69
|
32397 bad:
|
|
jpayne@69
|
32398 Py_XDECREF(empty_dict);
|
|
jpayne@69
|
32399 Py_XDECREF(empty_list);
|
|
jpayne@69
|
32400 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32401 Py_XDECREF(py_import);
|
|
jpayne@69
|
32402 #endif
|
|
jpayne@69
|
32403 return module;
|
|
jpayne@69
|
32404 }
|
|
jpayne@69
|
32405
|
|
jpayne@69
|
32406 /* ImportFrom */
|
|
jpayne@69
|
32407 static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
|
|
jpayne@69
|
32408 PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
|
|
jpayne@69
|
32409 if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
|
|
jpayne@69
|
32410 const char* module_name_str = 0;
|
|
jpayne@69
|
32411 PyObject* module_name = 0;
|
|
jpayne@69
|
32412 PyObject* module_dot = 0;
|
|
jpayne@69
|
32413 PyObject* full_name = 0;
|
|
jpayne@69
|
32414 PyErr_Clear();
|
|
jpayne@69
|
32415 module_name_str = PyModule_GetName(module);
|
|
jpayne@69
|
32416 if (unlikely(!module_name_str)) { goto modbad; }
|
|
jpayne@69
|
32417 module_name = PyUnicode_FromString(module_name_str);
|
|
jpayne@69
|
32418 if (unlikely(!module_name)) { goto modbad; }
|
|
jpayne@69
|
32419 module_dot = PyUnicode_Concat(module_name, __pyx_kp_u__56);
|
|
jpayne@69
|
32420 if (unlikely(!module_dot)) { goto modbad; }
|
|
jpayne@69
|
32421 full_name = PyUnicode_Concat(module_dot, name);
|
|
jpayne@69
|
32422 if (unlikely(!full_name)) { goto modbad; }
|
|
jpayne@69
|
32423 #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400)
|
|
jpayne@69
|
32424 {
|
|
jpayne@69
|
32425 PyObject *modules = PyImport_GetModuleDict();
|
|
jpayne@69
|
32426 if (unlikely(!modules))
|
|
jpayne@69
|
32427 goto modbad;
|
|
jpayne@69
|
32428 value = PyObject_GetItem(modules, full_name);
|
|
jpayne@69
|
32429 }
|
|
jpayne@69
|
32430 #else
|
|
jpayne@69
|
32431 value = PyImport_GetModule(full_name);
|
|
jpayne@69
|
32432 #endif
|
|
jpayne@69
|
32433 modbad:
|
|
jpayne@69
|
32434 Py_XDECREF(full_name);
|
|
jpayne@69
|
32435 Py_XDECREF(module_dot);
|
|
jpayne@69
|
32436 Py_XDECREF(module_name);
|
|
jpayne@69
|
32437 }
|
|
jpayne@69
|
32438 if (unlikely(!value)) {
|
|
jpayne@69
|
32439 PyErr_Format(PyExc_ImportError,
|
|
jpayne@69
|
32440 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32441 "cannot import name %.230s", PyString_AS_STRING(name));
|
|
jpayne@69
|
32442 #else
|
|
jpayne@69
|
32443 "cannot import name %S", name);
|
|
jpayne@69
|
32444 #endif
|
|
jpayne@69
|
32445 }
|
|
jpayne@69
|
32446 return value;
|
|
jpayne@69
|
32447 }
|
|
jpayne@69
|
32448
|
|
jpayne@69
|
32449 /* GetItemInt */
|
|
jpayne@69
|
32450 static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
|
|
jpayne@69
|
32451 PyObject *r;
|
|
jpayne@69
|
32452 if (unlikely(!j)) return NULL;
|
|
jpayne@69
|
32453 r = PyObject_GetItem(o, j);
|
|
jpayne@69
|
32454 Py_DECREF(j);
|
|
jpayne@69
|
32455 return r;
|
|
jpayne@69
|
32456 }
|
|
jpayne@69
|
32457 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
32458 CYTHON_NCP_UNUSED int wraparound,
|
|
jpayne@69
|
32459 CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
32460 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32461 Py_ssize_t wrapped_i = i;
|
|
jpayne@69
|
32462 if (wraparound & unlikely(i < 0)) {
|
|
jpayne@69
|
32463 wrapped_i += PyList_GET_SIZE(o);
|
|
jpayne@69
|
32464 }
|
|
jpayne@69
|
32465 if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) {
|
|
jpayne@69
|
32466 PyObject *r = PyList_GET_ITEM(o, wrapped_i);
|
|
jpayne@69
|
32467 Py_INCREF(r);
|
|
jpayne@69
|
32468 return r;
|
|
jpayne@69
|
32469 }
|
|
jpayne@69
|
32470 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
|
|
jpayne@69
|
32471 #else
|
|
jpayne@69
|
32472 return PySequence_GetItem(o, i);
|
|
jpayne@69
|
32473 #endif
|
|
jpayne@69
|
32474 }
|
|
jpayne@69
|
32475 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
32476 CYTHON_NCP_UNUSED int wraparound,
|
|
jpayne@69
|
32477 CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
32478 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32479 Py_ssize_t wrapped_i = i;
|
|
jpayne@69
|
32480 if (wraparound & unlikely(i < 0)) {
|
|
jpayne@69
|
32481 wrapped_i += PyTuple_GET_SIZE(o);
|
|
jpayne@69
|
32482 }
|
|
jpayne@69
|
32483 if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) {
|
|
jpayne@69
|
32484 PyObject *r = PyTuple_GET_ITEM(o, wrapped_i);
|
|
jpayne@69
|
32485 Py_INCREF(r);
|
|
jpayne@69
|
32486 return r;
|
|
jpayne@69
|
32487 }
|
|
jpayne@69
|
32488 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
|
|
jpayne@69
|
32489 #else
|
|
jpayne@69
|
32490 return PySequence_GetItem(o, i);
|
|
jpayne@69
|
32491 #endif
|
|
jpayne@69
|
32492 }
|
|
jpayne@69
|
32493 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
|
|
jpayne@69
|
32494 CYTHON_NCP_UNUSED int wraparound,
|
|
jpayne@69
|
32495 CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
32496 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
32497 if (is_list || PyList_CheckExact(o)) {
|
|
jpayne@69
|
32498 Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
|
|
jpayne@69
|
32499 if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) {
|
|
jpayne@69
|
32500 PyObject *r = PyList_GET_ITEM(o, n);
|
|
jpayne@69
|
32501 Py_INCREF(r);
|
|
jpayne@69
|
32502 return r;
|
|
jpayne@69
|
32503 }
|
|
jpayne@69
|
32504 }
|
|
jpayne@69
|
32505 else if (PyTuple_CheckExact(o)) {
|
|
jpayne@69
|
32506 Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
|
|
jpayne@69
|
32507 if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) {
|
|
jpayne@69
|
32508 PyObject *r = PyTuple_GET_ITEM(o, n);
|
|
jpayne@69
|
32509 Py_INCREF(r);
|
|
jpayne@69
|
32510 return r;
|
|
jpayne@69
|
32511 }
|
|
jpayne@69
|
32512 } else {
|
|
jpayne@69
|
32513 PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping;
|
|
jpayne@69
|
32514 PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence;
|
|
jpayne@69
|
32515 if (mm && mm->mp_subscript) {
|
|
jpayne@69
|
32516 PyObject *r, *key = PyInt_FromSsize_t(i);
|
|
jpayne@69
|
32517 if (unlikely(!key)) return NULL;
|
|
jpayne@69
|
32518 r = mm->mp_subscript(o, key);
|
|
jpayne@69
|
32519 Py_DECREF(key);
|
|
jpayne@69
|
32520 return r;
|
|
jpayne@69
|
32521 }
|
|
jpayne@69
|
32522 if (likely(sm && sm->sq_item)) {
|
|
jpayne@69
|
32523 if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) {
|
|
jpayne@69
|
32524 Py_ssize_t l = sm->sq_length(o);
|
|
jpayne@69
|
32525 if (likely(l >= 0)) {
|
|
jpayne@69
|
32526 i += l;
|
|
jpayne@69
|
32527 } else {
|
|
jpayne@69
|
32528 if (!PyErr_ExceptionMatches(PyExc_OverflowError))
|
|
jpayne@69
|
32529 return NULL;
|
|
jpayne@69
|
32530 PyErr_Clear();
|
|
jpayne@69
|
32531 }
|
|
jpayne@69
|
32532 }
|
|
jpayne@69
|
32533 return sm->sq_item(o, i);
|
|
jpayne@69
|
32534 }
|
|
jpayne@69
|
32535 }
|
|
jpayne@69
|
32536 #else
|
|
jpayne@69
|
32537 if (is_list || !PyMapping_Check(o)) {
|
|
jpayne@69
|
32538 return PySequence_GetItem(o, i);
|
|
jpayne@69
|
32539 }
|
|
jpayne@69
|
32540 #endif
|
|
jpayne@69
|
32541 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
|
|
jpayne@69
|
32542 }
|
|
jpayne@69
|
32543
|
|
jpayne@69
|
32544 /* GetAttr */
|
|
jpayne@69
|
32545 static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) {
|
|
jpayne@69
|
32546 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
32547 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32548 if (likely(PyUnicode_Check(n)))
|
|
jpayne@69
|
32549 #else
|
|
jpayne@69
|
32550 if (likely(PyString_Check(n)))
|
|
jpayne@69
|
32551 #endif
|
|
jpayne@69
|
32552 return __Pyx_PyObject_GetAttrStr(o, n);
|
|
jpayne@69
|
32553 #endif
|
|
jpayne@69
|
32554 return PyObject_GetAttr(o, n);
|
|
jpayne@69
|
32555 }
|
|
jpayne@69
|
32556
|
|
jpayne@69
|
32557 /* HasAttr */
|
|
jpayne@69
|
32558 static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) {
|
|
jpayne@69
|
32559 PyObject *r;
|
|
jpayne@69
|
32560 if (unlikely(!__Pyx_PyBaseString_Check(n))) {
|
|
jpayne@69
|
32561 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
32562 "hasattr(): attribute name must be string");
|
|
jpayne@69
|
32563 return -1;
|
|
jpayne@69
|
32564 }
|
|
jpayne@69
|
32565 r = __Pyx_GetAttr(o, n);
|
|
jpayne@69
|
32566 if (!r) {
|
|
jpayne@69
|
32567 PyErr_Clear();
|
|
jpayne@69
|
32568 return 0;
|
|
jpayne@69
|
32569 } else {
|
|
jpayne@69
|
32570 Py_DECREF(r);
|
|
jpayne@69
|
32571 return 1;
|
|
jpayne@69
|
32572 }
|
|
jpayne@69
|
32573 }
|
|
jpayne@69
|
32574
|
|
jpayne@69
|
32575 /* CallNextTpDealloc */
|
|
jpayne@69
|
32576 static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
|
|
jpayne@69
|
32577 PyTypeObject* type = Py_TYPE(obj);
|
|
jpayne@69
|
32578 destructor tp_dealloc = NULL;
|
|
jpayne@69
|
32579 while (type && __Pyx_PyType_GetSlot(type, tp_dealloc, destructor) != current_tp_dealloc)
|
|
jpayne@69
|
32580 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
|
|
jpayne@69
|
32581 while (type && (tp_dealloc = __Pyx_PyType_GetSlot(type, tp_dealloc, destructor)) == current_tp_dealloc)
|
|
jpayne@69
|
32582 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
|
|
jpayne@69
|
32583 if (type)
|
|
jpayne@69
|
32584 tp_dealloc(obj);
|
|
jpayne@69
|
32585 }
|
|
jpayne@69
|
32586
|
|
jpayne@69
|
32587 /* CallNextTpTraverse */
|
|
jpayne@69
|
32588 static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
|
|
jpayne@69
|
32589 PyTypeObject* type = Py_TYPE(obj);
|
|
jpayne@69
|
32590 traverseproc tp_traverse = NULL;
|
|
jpayne@69
|
32591 while (type && __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc) != current_tp_traverse)
|
|
jpayne@69
|
32592 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
|
|
jpayne@69
|
32593 while (type && (tp_traverse = __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc)) == current_tp_traverse)
|
|
jpayne@69
|
32594 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
|
|
jpayne@69
|
32595 if (type && tp_traverse)
|
|
jpayne@69
|
32596 return tp_traverse(obj, v, a);
|
|
jpayne@69
|
32597 return 0;
|
|
jpayne@69
|
32598 }
|
|
jpayne@69
|
32599
|
|
jpayne@69
|
32600 /* CallNextTpClear */
|
|
jpayne@69
|
32601 static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
|
|
jpayne@69
|
32602 PyTypeObject* type = Py_TYPE(obj);
|
|
jpayne@69
|
32603 inquiry tp_clear = NULL;
|
|
jpayne@69
|
32604 while (type && __Pyx_PyType_GetSlot(type, tp_clear, inquiry) != current_tp_clear)
|
|
jpayne@69
|
32605 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
|
|
jpayne@69
|
32606 while (type && (tp_clear = __Pyx_PyType_GetSlot(type, tp_clear, inquiry)) == current_tp_clear)
|
|
jpayne@69
|
32607 type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*);
|
|
jpayne@69
|
32608 if (type && tp_clear)
|
|
jpayne@69
|
32609 tp_clear(obj);
|
|
jpayne@69
|
32610 }
|
|
jpayne@69
|
32611
|
|
jpayne@69
|
32612 /* FixUpExtensionType */
|
|
jpayne@69
|
32613 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
32614 static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type) {
|
|
jpayne@69
|
32615 #if PY_VERSION_HEX > 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
32616 CYTHON_UNUSED_VAR(spec);
|
|
jpayne@69
|
32617 CYTHON_UNUSED_VAR(type);
|
|
jpayne@69
|
32618 #else
|
|
jpayne@69
|
32619 const PyType_Slot *slot = spec->slots;
|
|
jpayne@69
|
32620 while (slot && slot->slot && slot->slot != Py_tp_members)
|
|
jpayne@69
|
32621 slot++;
|
|
jpayne@69
|
32622 if (slot && slot->slot == Py_tp_members) {
|
|
jpayne@69
|
32623 int changed = 0;
|
|
jpayne@69
|
32624 #if !(PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON)
|
|
jpayne@69
|
32625 const
|
|
jpayne@69
|
32626 #endif
|
|
jpayne@69
|
32627 PyMemberDef *memb = (PyMemberDef*) slot->pfunc;
|
|
jpayne@69
|
32628 while (memb && memb->name) {
|
|
jpayne@69
|
32629 if (memb->name[0] == '_' && memb->name[1] == '_') {
|
|
jpayne@69
|
32630 #if PY_VERSION_HEX < 0x030900b1
|
|
jpayne@69
|
32631 if (strcmp(memb->name, "__weaklistoffset__") == 0) {
|
|
jpayne@69
|
32632 assert(memb->type == T_PYSSIZET);
|
|
jpayne@69
|
32633 assert(memb->flags == READONLY);
|
|
jpayne@69
|
32634 type->tp_weaklistoffset = memb->offset;
|
|
jpayne@69
|
32635 changed = 1;
|
|
jpayne@69
|
32636 }
|
|
jpayne@69
|
32637 else if (strcmp(memb->name, "__dictoffset__") == 0) {
|
|
jpayne@69
|
32638 assert(memb->type == T_PYSSIZET);
|
|
jpayne@69
|
32639 assert(memb->flags == READONLY);
|
|
jpayne@69
|
32640 type->tp_dictoffset = memb->offset;
|
|
jpayne@69
|
32641 changed = 1;
|
|
jpayne@69
|
32642 }
|
|
jpayne@69
|
32643 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
32644 else if (strcmp(memb->name, "__vectorcalloffset__") == 0) {
|
|
jpayne@69
|
32645 assert(memb->type == T_PYSSIZET);
|
|
jpayne@69
|
32646 assert(memb->flags == READONLY);
|
|
jpayne@69
|
32647 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
32648 type->tp_vectorcall_offset = memb->offset;
|
|
jpayne@69
|
32649 #else
|
|
jpayne@69
|
32650 type->tp_print = (printfunc) memb->offset;
|
|
jpayne@69
|
32651 #endif
|
|
jpayne@69
|
32652 changed = 1;
|
|
jpayne@69
|
32653 }
|
|
jpayne@69
|
32654 #endif
|
|
jpayne@69
|
32655 #else
|
|
jpayne@69
|
32656 if ((0));
|
|
jpayne@69
|
32657 #endif
|
|
jpayne@69
|
32658 #if PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
32659 else if (strcmp(memb->name, "__module__") == 0) {
|
|
jpayne@69
|
32660 PyObject *descr;
|
|
jpayne@69
|
32661 assert(memb->type == T_OBJECT);
|
|
jpayne@69
|
32662 assert(memb->flags == 0 || memb->flags == READONLY);
|
|
jpayne@69
|
32663 descr = PyDescr_NewMember(type, memb);
|
|
jpayne@69
|
32664 if (unlikely(!descr))
|
|
jpayne@69
|
32665 return -1;
|
|
jpayne@69
|
32666 if (unlikely(PyDict_SetItem(type->tp_dict, PyDescr_NAME(descr), descr) < 0)) {
|
|
jpayne@69
|
32667 Py_DECREF(descr);
|
|
jpayne@69
|
32668 return -1;
|
|
jpayne@69
|
32669 }
|
|
jpayne@69
|
32670 Py_DECREF(descr);
|
|
jpayne@69
|
32671 changed = 1;
|
|
jpayne@69
|
32672 }
|
|
jpayne@69
|
32673 #endif
|
|
jpayne@69
|
32674 }
|
|
jpayne@69
|
32675 memb++;
|
|
jpayne@69
|
32676 }
|
|
jpayne@69
|
32677 if (changed)
|
|
jpayne@69
|
32678 PyType_Modified(type);
|
|
jpayne@69
|
32679 }
|
|
jpayne@69
|
32680 #endif
|
|
jpayne@69
|
32681 return 0;
|
|
jpayne@69
|
32682 }
|
|
jpayne@69
|
32683 #endif
|
|
jpayne@69
|
32684
|
|
jpayne@69
|
32685 /* PyObjectGetMethod */
|
|
jpayne@69
|
32686 static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) {
|
|
jpayne@69
|
32687 PyObject *attr;
|
|
jpayne@69
|
32688 #if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
32689 __Pyx_TypeName type_name;
|
|
jpayne@69
|
32690 PyTypeObject *tp = Py_TYPE(obj);
|
|
jpayne@69
|
32691 PyObject *descr;
|
|
jpayne@69
|
32692 descrgetfunc f = NULL;
|
|
jpayne@69
|
32693 PyObject **dictptr, *dict;
|
|
jpayne@69
|
32694 int meth_found = 0;
|
|
jpayne@69
|
32695 assert (*method == NULL);
|
|
jpayne@69
|
32696 if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
32697 attr = __Pyx_PyObject_GetAttrStr(obj, name);
|
|
jpayne@69
|
32698 goto try_unpack;
|
|
jpayne@69
|
32699 }
|
|
jpayne@69
|
32700 if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) {
|
|
jpayne@69
|
32701 return 0;
|
|
jpayne@69
|
32702 }
|
|
jpayne@69
|
32703 descr = _PyType_Lookup(tp, name);
|
|
jpayne@69
|
32704 if (likely(descr != NULL)) {
|
|
jpayne@69
|
32705 Py_INCREF(descr);
|
|
jpayne@69
|
32706 #if defined(Py_TPFLAGS_METHOD_DESCRIPTOR) && Py_TPFLAGS_METHOD_DESCRIPTOR
|
|
jpayne@69
|
32707 if (__Pyx_PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_METHOD_DESCRIPTOR))
|
|
jpayne@69
|
32708 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32709 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
32710 if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr)))
|
|
jpayne@69
|
32711 #else
|
|
jpayne@69
|
32712 if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type)))
|
|
jpayne@69
|
32713 #endif
|
|
jpayne@69
|
32714 #else
|
|
jpayne@69
|
32715 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
32716 if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr)))
|
|
jpayne@69
|
32717 #else
|
|
jpayne@69
|
32718 if (likely(PyFunction_Check(descr)))
|
|
jpayne@69
|
32719 #endif
|
|
jpayne@69
|
32720 #endif
|
|
jpayne@69
|
32721 {
|
|
jpayne@69
|
32722 meth_found = 1;
|
|
jpayne@69
|
32723 } else {
|
|
jpayne@69
|
32724 f = Py_TYPE(descr)->tp_descr_get;
|
|
jpayne@69
|
32725 if (f != NULL && PyDescr_IsData(descr)) {
|
|
jpayne@69
|
32726 attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
|
|
jpayne@69
|
32727 Py_DECREF(descr);
|
|
jpayne@69
|
32728 goto try_unpack;
|
|
jpayne@69
|
32729 }
|
|
jpayne@69
|
32730 }
|
|
jpayne@69
|
32731 }
|
|
jpayne@69
|
32732 dictptr = _PyObject_GetDictPtr(obj);
|
|
jpayne@69
|
32733 if (dictptr != NULL && (dict = *dictptr) != NULL) {
|
|
jpayne@69
|
32734 Py_INCREF(dict);
|
|
jpayne@69
|
32735 attr = __Pyx_PyDict_GetItemStr(dict, name);
|
|
jpayne@69
|
32736 if (attr != NULL) {
|
|
jpayne@69
|
32737 Py_INCREF(attr);
|
|
jpayne@69
|
32738 Py_DECREF(dict);
|
|
jpayne@69
|
32739 Py_XDECREF(descr);
|
|
jpayne@69
|
32740 goto try_unpack;
|
|
jpayne@69
|
32741 }
|
|
jpayne@69
|
32742 Py_DECREF(dict);
|
|
jpayne@69
|
32743 }
|
|
jpayne@69
|
32744 if (meth_found) {
|
|
jpayne@69
|
32745 *method = descr;
|
|
jpayne@69
|
32746 return 1;
|
|
jpayne@69
|
32747 }
|
|
jpayne@69
|
32748 if (f != NULL) {
|
|
jpayne@69
|
32749 attr = f(descr, obj, (PyObject *)Py_TYPE(obj));
|
|
jpayne@69
|
32750 Py_DECREF(descr);
|
|
jpayne@69
|
32751 goto try_unpack;
|
|
jpayne@69
|
32752 }
|
|
jpayne@69
|
32753 if (likely(descr != NULL)) {
|
|
jpayne@69
|
32754 *method = descr;
|
|
jpayne@69
|
32755 return 0;
|
|
jpayne@69
|
32756 }
|
|
jpayne@69
|
32757 type_name = __Pyx_PyType_GetName(tp);
|
|
jpayne@69
|
32758 PyErr_Format(PyExc_AttributeError,
|
|
jpayne@69
|
32759 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32760 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'",
|
|
jpayne@69
|
32761 type_name, name);
|
|
jpayne@69
|
32762 #else
|
|
jpayne@69
|
32763 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'",
|
|
jpayne@69
|
32764 type_name, PyString_AS_STRING(name));
|
|
jpayne@69
|
32765 #endif
|
|
jpayne@69
|
32766 __Pyx_DECREF_TypeName(type_name);
|
|
jpayne@69
|
32767 return 0;
|
|
jpayne@69
|
32768 #else
|
|
jpayne@69
|
32769 attr = __Pyx_PyObject_GetAttrStr(obj, name);
|
|
jpayne@69
|
32770 goto try_unpack;
|
|
jpayne@69
|
32771 #endif
|
|
jpayne@69
|
32772 try_unpack:
|
|
jpayne@69
|
32773 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
32774 if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) {
|
|
jpayne@69
|
32775 PyObject *function = PyMethod_GET_FUNCTION(attr);
|
|
jpayne@69
|
32776 Py_INCREF(function);
|
|
jpayne@69
|
32777 Py_DECREF(attr);
|
|
jpayne@69
|
32778 *method = function;
|
|
jpayne@69
|
32779 return 1;
|
|
jpayne@69
|
32780 }
|
|
jpayne@69
|
32781 #endif
|
|
jpayne@69
|
32782 *method = attr;
|
|
jpayne@69
|
32783 return 0;
|
|
jpayne@69
|
32784 }
|
|
jpayne@69
|
32785
|
|
jpayne@69
|
32786 /* PyObjectCallMethod0 */
|
|
jpayne@69
|
32787 static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) {
|
|
jpayne@69
|
32788 PyObject *method = NULL, *result = NULL;
|
|
jpayne@69
|
32789 int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method);
|
|
jpayne@69
|
32790 if (likely(is_method)) {
|
|
jpayne@69
|
32791 result = __Pyx_PyObject_CallOneArg(method, obj);
|
|
jpayne@69
|
32792 Py_DECREF(method);
|
|
jpayne@69
|
32793 return result;
|
|
jpayne@69
|
32794 }
|
|
jpayne@69
|
32795 if (unlikely(!method)) goto bad;
|
|
jpayne@69
|
32796 result = __Pyx_PyObject_CallNoArg(method);
|
|
jpayne@69
|
32797 Py_DECREF(method);
|
|
jpayne@69
|
32798 bad:
|
|
jpayne@69
|
32799 return result;
|
|
jpayne@69
|
32800 }
|
|
jpayne@69
|
32801
|
|
jpayne@69
|
32802 /* ValidateBasesTuple */
|
|
jpayne@69
|
32803 #if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
32804 static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases) {
|
|
jpayne@69
|
32805 Py_ssize_t i, n;
|
|
jpayne@69
|
32806 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
32807 n = PyTuple_GET_SIZE(bases);
|
|
jpayne@69
|
32808 #else
|
|
jpayne@69
|
32809 n = PyTuple_Size(bases);
|
|
jpayne@69
|
32810 if (n < 0) return -1;
|
|
jpayne@69
|
32811 #endif
|
|
jpayne@69
|
32812 for (i = 1; i < n; i++)
|
|
jpayne@69
|
32813 {
|
|
jpayne@69
|
32814 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32815 PyObject *b0 = PySequence_GetItem(bases, i);
|
|
jpayne@69
|
32816 if (!b0) return -1;
|
|
jpayne@69
|
32817 #elif CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
32818 PyObject *b0 = PyTuple_GET_ITEM(bases, i);
|
|
jpayne@69
|
32819 #else
|
|
jpayne@69
|
32820 PyObject *b0 = PyTuple_GetItem(bases, i);
|
|
jpayne@69
|
32821 if (!b0) return -1;
|
|
jpayne@69
|
32822 #endif
|
|
jpayne@69
|
32823 PyTypeObject *b;
|
|
jpayne@69
|
32824 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32825 if (PyClass_Check(b0))
|
|
jpayne@69
|
32826 {
|
|
jpayne@69
|
32827 PyErr_Format(PyExc_TypeError, "base class '%.200s' is an old-style class",
|
|
jpayne@69
|
32828 PyString_AS_STRING(((PyClassObject*)b0)->cl_name));
|
|
jpayne@69
|
32829 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32830 Py_DECREF(b0);
|
|
jpayne@69
|
32831 #endif
|
|
jpayne@69
|
32832 return -1;
|
|
jpayne@69
|
32833 }
|
|
jpayne@69
|
32834 #endif
|
|
jpayne@69
|
32835 b = (PyTypeObject*) b0;
|
|
jpayne@69
|
32836 if (!__Pyx_PyType_HasFeature(b, Py_TPFLAGS_HEAPTYPE))
|
|
jpayne@69
|
32837 {
|
|
jpayne@69
|
32838 __Pyx_TypeName b_name = __Pyx_PyType_GetName(b);
|
|
jpayne@69
|
32839 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
32840 "base class '" __Pyx_FMT_TYPENAME "' is not a heap type", b_name);
|
|
jpayne@69
|
32841 __Pyx_DECREF_TypeName(b_name);
|
|
jpayne@69
|
32842 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32843 Py_DECREF(b0);
|
|
jpayne@69
|
32844 #endif
|
|
jpayne@69
|
32845 return -1;
|
|
jpayne@69
|
32846 }
|
|
jpayne@69
|
32847 if (dictoffset == 0)
|
|
jpayne@69
|
32848 {
|
|
jpayne@69
|
32849 Py_ssize_t b_dictoffset = 0;
|
|
jpayne@69
|
32850 #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
32851 b_dictoffset = b->tp_dictoffset;
|
|
jpayne@69
|
32852 #else
|
|
jpayne@69
|
32853 PyObject *py_b_dictoffset = PyObject_GetAttrString((PyObject*)b, "__dictoffset__");
|
|
jpayne@69
|
32854 if (!py_b_dictoffset) goto dictoffset_return;
|
|
jpayne@69
|
32855 b_dictoffset = PyLong_AsSsize_t(py_b_dictoffset);
|
|
jpayne@69
|
32856 Py_DECREF(py_b_dictoffset);
|
|
jpayne@69
|
32857 if (b_dictoffset == -1 && PyErr_Occurred()) goto dictoffset_return;
|
|
jpayne@69
|
32858 #endif
|
|
jpayne@69
|
32859 if (b_dictoffset) {
|
|
jpayne@69
|
32860 {
|
|
jpayne@69
|
32861 __Pyx_TypeName b_name = __Pyx_PyType_GetName(b);
|
|
jpayne@69
|
32862 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
32863 "extension type '%.200s' has no __dict__ slot, "
|
|
jpayne@69
|
32864 "but base type '" __Pyx_FMT_TYPENAME "' has: "
|
|
jpayne@69
|
32865 "either add 'cdef dict __dict__' to the extension type "
|
|
jpayne@69
|
32866 "or add '__slots__ = [...]' to the base type",
|
|
jpayne@69
|
32867 type_name, b_name);
|
|
jpayne@69
|
32868 __Pyx_DECREF_TypeName(b_name);
|
|
jpayne@69
|
32869 }
|
|
jpayne@69
|
32870 #if !(CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY)
|
|
jpayne@69
|
32871 dictoffset_return:
|
|
jpayne@69
|
32872 #endif
|
|
jpayne@69
|
32873 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32874 Py_DECREF(b0);
|
|
jpayne@69
|
32875 #endif
|
|
jpayne@69
|
32876 return -1;
|
|
jpayne@69
|
32877 }
|
|
jpayne@69
|
32878 }
|
|
jpayne@69
|
32879 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
32880 Py_DECREF(b0);
|
|
jpayne@69
|
32881 #endif
|
|
jpayne@69
|
32882 }
|
|
jpayne@69
|
32883 return 0;
|
|
jpayne@69
|
32884 }
|
|
jpayne@69
|
32885 #endif
|
|
jpayne@69
|
32886
|
|
jpayne@69
|
32887 /* PyType_Ready */
|
|
jpayne@69
|
32888 static int __Pyx_PyType_Ready(PyTypeObject *t) {
|
|
jpayne@69
|
32889 #if CYTHON_USE_TYPE_SPECS || !(CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API) || defined(PYSTON_MAJOR_VERSION)
|
|
jpayne@69
|
32890 (void)__Pyx_PyObject_CallMethod0;
|
|
jpayne@69
|
32891 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
32892 (void)__Pyx_validate_bases_tuple;
|
|
jpayne@69
|
32893 #endif
|
|
jpayne@69
|
32894 return PyType_Ready(t);
|
|
jpayne@69
|
32895 #else
|
|
jpayne@69
|
32896 int r;
|
|
jpayne@69
|
32897 PyObject *bases = __Pyx_PyType_GetSlot(t, tp_bases, PyObject*);
|
|
jpayne@69
|
32898 if (bases && unlikely(__Pyx_validate_bases_tuple(t->tp_name, t->tp_dictoffset, bases) == -1))
|
|
jpayne@69
|
32899 return -1;
|
|
jpayne@69
|
32900 #if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION)
|
|
jpayne@69
|
32901 {
|
|
jpayne@69
|
32902 int gc_was_enabled;
|
|
jpayne@69
|
32903 #if PY_VERSION_HEX >= 0x030A00b1
|
|
jpayne@69
|
32904 gc_was_enabled = PyGC_Disable();
|
|
jpayne@69
|
32905 (void)__Pyx_PyObject_CallMethod0;
|
|
jpayne@69
|
32906 #else
|
|
jpayne@69
|
32907 PyObject *ret, *py_status;
|
|
jpayne@69
|
32908 PyObject *gc = NULL;
|
|
jpayne@69
|
32909 #if PY_VERSION_HEX >= 0x030700a1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM+0 >= 0x07030400)
|
|
jpayne@69
|
32910 gc = PyImport_GetModule(__pyx_kp_u_gc);
|
|
jpayne@69
|
32911 #endif
|
|
jpayne@69
|
32912 if (unlikely(!gc)) gc = PyImport_Import(__pyx_kp_u_gc);
|
|
jpayne@69
|
32913 if (unlikely(!gc)) return -1;
|
|
jpayne@69
|
32914 py_status = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_isenabled);
|
|
jpayne@69
|
32915 if (unlikely(!py_status)) {
|
|
jpayne@69
|
32916 Py_DECREF(gc);
|
|
jpayne@69
|
32917 return -1;
|
|
jpayne@69
|
32918 }
|
|
jpayne@69
|
32919 gc_was_enabled = __Pyx_PyObject_IsTrue(py_status);
|
|
jpayne@69
|
32920 Py_DECREF(py_status);
|
|
jpayne@69
|
32921 if (gc_was_enabled > 0) {
|
|
jpayne@69
|
32922 ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_disable);
|
|
jpayne@69
|
32923 if (unlikely(!ret)) {
|
|
jpayne@69
|
32924 Py_DECREF(gc);
|
|
jpayne@69
|
32925 return -1;
|
|
jpayne@69
|
32926 }
|
|
jpayne@69
|
32927 Py_DECREF(ret);
|
|
jpayne@69
|
32928 } else if (unlikely(gc_was_enabled == -1)) {
|
|
jpayne@69
|
32929 Py_DECREF(gc);
|
|
jpayne@69
|
32930 return -1;
|
|
jpayne@69
|
32931 }
|
|
jpayne@69
|
32932 #endif
|
|
jpayne@69
|
32933 t->tp_flags |= Py_TPFLAGS_HEAPTYPE;
|
|
jpayne@69
|
32934 #if PY_VERSION_HEX >= 0x030A0000
|
|
jpayne@69
|
32935 t->tp_flags |= Py_TPFLAGS_IMMUTABLETYPE;
|
|
jpayne@69
|
32936 #endif
|
|
jpayne@69
|
32937 #else
|
|
jpayne@69
|
32938 (void)__Pyx_PyObject_CallMethod0;
|
|
jpayne@69
|
32939 #endif
|
|
jpayne@69
|
32940 r = PyType_Ready(t);
|
|
jpayne@69
|
32941 #if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION)
|
|
jpayne@69
|
32942 t->tp_flags &= ~Py_TPFLAGS_HEAPTYPE;
|
|
jpayne@69
|
32943 #if PY_VERSION_HEX >= 0x030A00b1
|
|
jpayne@69
|
32944 if (gc_was_enabled)
|
|
jpayne@69
|
32945 PyGC_Enable();
|
|
jpayne@69
|
32946 #else
|
|
jpayne@69
|
32947 if (gc_was_enabled) {
|
|
jpayne@69
|
32948 PyObject *tp, *v, *tb;
|
|
jpayne@69
|
32949 PyErr_Fetch(&tp, &v, &tb);
|
|
jpayne@69
|
32950 ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_enable);
|
|
jpayne@69
|
32951 if (likely(ret || r == -1)) {
|
|
jpayne@69
|
32952 Py_XDECREF(ret);
|
|
jpayne@69
|
32953 PyErr_Restore(tp, v, tb);
|
|
jpayne@69
|
32954 } else {
|
|
jpayne@69
|
32955 Py_XDECREF(tp);
|
|
jpayne@69
|
32956 Py_XDECREF(v);
|
|
jpayne@69
|
32957 Py_XDECREF(tb);
|
|
jpayne@69
|
32958 r = -1;
|
|
jpayne@69
|
32959 }
|
|
jpayne@69
|
32960 }
|
|
jpayne@69
|
32961 Py_DECREF(gc);
|
|
jpayne@69
|
32962 #endif
|
|
jpayne@69
|
32963 }
|
|
jpayne@69
|
32964 #endif
|
|
jpayne@69
|
32965 return r;
|
|
jpayne@69
|
32966 #endif
|
|
jpayne@69
|
32967 }
|
|
jpayne@69
|
32968
|
|
jpayne@69
|
32969 /* PyObject_GenericGetAttrNoDict */
|
|
jpayne@69
|
32970 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
|
|
jpayne@69
|
32971 static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) {
|
|
jpayne@69
|
32972 __Pyx_TypeName type_name = __Pyx_PyType_GetName(tp);
|
|
jpayne@69
|
32973 PyErr_Format(PyExc_AttributeError,
|
|
jpayne@69
|
32974 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
32975 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'",
|
|
jpayne@69
|
32976 type_name, attr_name);
|
|
jpayne@69
|
32977 #else
|
|
jpayne@69
|
32978 "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'",
|
|
jpayne@69
|
32979 type_name, PyString_AS_STRING(attr_name));
|
|
jpayne@69
|
32980 #endif
|
|
jpayne@69
|
32981 __Pyx_DECREF_TypeName(type_name);
|
|
jpayne@69
|
32982 return NULL;
|
|
jpayne@69
|
32983 }
|
|
jpayne@69
|
32984 static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) {
|
|
jpayne@69
|
32985 PyObject *descr;
|
|
jpayne@69
|
32986 PyTypeObject *tp = Py_TYPE(obj);
|
|
jpayne@69
|
32987 if (unlikely(!PyString_Check(attr_name))) {
|
|
jpayne@69
|
32988 return PyObject_GenericGetAttr(obj, attr_name);
|
|
jpayne@69
|
32989 }
|
|
jpayne@69
|
32990 assert(!tp->tp_dictoffset);
|
|
jpayne@69
|
32991 descr = _PyType_Lookup(tp, attr_name);
|
|
jpayne@69
|
32992 if (unlikely(!descr)) {
|
|
jpayne@69
|
32993 return __Pyx_RaiseGenericGetAttributeError(tp, attr_name);
|
|
jpayne@69
|
32994 }
|
|
jpayne@69
|
32995 Py_INCREF(descr);
|
|
jpayne@69
|
32996 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
32997 if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS)))
|
|
jpayne@69
|
32998 #endif
|
|
jpayne@69
|
32999 {
|
|
jpayne@69
|
33000 descrgetfunc f = Py_TYPE(descr)->tp_descr_get;
|
|
jpayne@69
|
33001 if (unlikely(f)) {
|
|
jpayne@69
|
33002 PyObject *res = f(descr, obj, (PyObject *)tp);
|
|
jpayne@69
|
33003 Py_DECREF(descr);
|
|
jpayne@69
|
33004 return res;
|
|
jpayne@69
|
33005 }
|
|
jpayne@69
|
33006 }
|
|
jpayne@69
|
33007 return descr;
|
|
jpayne@69
|
33008 }
|
|
jpayne@69
|
33009 #endif
|
|
jpayne@69
|
33010
|
|
jpayne@69
|
33011 /* PyObject_GenericGetAttr */
|
|
jpayne@69
|
33012 #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000
|
|
jpayne@69
|
33013 static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) {
|
|
jpayne@69
|
33014 if (unlikely(Py_TYPE(obj)->tp_dictoffset)) {
|
|
jpayne@69
|
33015 return PyObject_GenericGetAttr(obj, attr_name);
|
|
jpayne@69
|
33016 }
|
|
jpayne@69
|
33017 return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name);
|
|
jpayne@69
|
33018 }
|
|
jpayne@69
|
33019 #endif
|
|
jpayne@69
|
33020
|
|
jpayne@69
|
33021 /* SetVTable */
|
|
jpayne@69
|
33022 static int __Pyx_SetVtable(PyTypeObject *type, void *vtable) {
|
|
jpayne@69
|
33023 PyObject *ob = PyCapsule_New(vtable, 0, 0);
|
|
jpayne@69
|
33024 if (unlikely(!ob))
|
|
jpayne@69
|
33025 goto bad;
|
|
jpayne@69
|
33026 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33027 if (unlikely(PyObject_SetAttr((PyObject *) type, __pyx_n_s_pyx_vtable, ob) < 0))
|
|
jpayne@69
|
33028 #else
|
|
jpayne@69
|
33029 if (unlikely(PyDict_SetItem(type->tp_dict, __pyx_n_s_pyx_vtable, ob) < 0))
|
|
jpayne@69
|
33030 #endif
|
|
jpayne@69
|
33031 goto bad;
|
|
jpayne@69
|
33032 Py_DECREF(ob);
|
|
jpayne@69
|
33033 return 0;
|
|
jpayne@69
|
33034 bad:
|
|
jpayne@69
|
33035 Py_XDECREF(ob);
|
|
jpayne@69
|
33036 return -1;
|
|
jpayne@69
|
33037 }
|
|
jpayne@69
|
33038
|
|
jpayne@69
|
33039 /* GetVTable */
|
|
jpayne@69
|
33040 static void* __Pyx_GetVtable(PyTypeObject *type) {
|
|
jpayne@69
|
33041 void* ptr;
|
|
jpayne@69
|
33042 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33043 PyObject *ob = PyObject_GetAttr((PyObject *)type, __pyx_n_s_pyx_vtable);
|
|
jpayne@69
|
33044 #else
|
|
jpayne@69
|
33045 PyObject *ob = PyObject_GetItem(type->tp_dict, __pyx_n_s_pyx_vtable);
|
|
jpayne@69
|
33046 #endif
|
|
jpayne@69
|
33047 if (!ob)
|
|
jpayne@69
|
33048 goto bad;
|
|
jpayne@69
|
33049 ptr = PyCapsule_GetPointer(ob, 0);
|
|
jpayne@69
|
33050 if (!ptr && !PyErr_Occurred())
|
|
jpayne@69
|
33051 PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
|
|
jpayne@69
|
33052 Py_DECREF(ob);
|
|
jpayne@69
|
33053 return ptr;
|
|
jpayne@69
|
33054 bad:
|
|
jpayne@69
|
33055 Py_XDECREF(ob);
|
|
jpayne@69
|
33056 return NULL;
|
|
jpayne@69
|
33057 }
|
|
jpayne@69
|
33058
|
|
jpayne@69
|
33059 /* MergeVTables */
|
|
jpayne@69
|
33060 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33061 static int __Pyx_MergeVtables(PyTypeObject *type) {
|
|
jpayne@69
|
33062 int i;
|
|
jpayne@69
|
33063 void** base_vtables;
|
|
jpayne@69
|
33064 __Pyx_TypeName tp_base_name;
|
|
jpayne@69
|
33065 __Pyx_TypeName base_name;
|
|
jpayne@69
|
33066 void* unknown = (void*)-1;
|
|
jpayne@69
|
33067 PyObject* bases = type->tp_bases;
|
|
jpayne@69
|
33068 int base_depth = 0;
|
|
jpayne@69
|
33069 {
|
|
jpayne@69
|
33070 PyTypeObject* base = type->tp_base;
|
|
jpayne@69
|
33071 while (base) {
|
|
jpayne@69
|
33072 base_depth += 1;
|
|
jpayne@69
|
33073 base = base->tp_base;
|
|
jpayne@69
|
33074 }
|
|
jpayne@69
|
33075 }
|
|
jpayne@69
|
33076 base_vtables = (void**) malloc(sizeof(void*) * (size_t)(base_depth + 1));
|
|
jpayne@69
|
33077 base_vtables[0] = unknown;
|
|
jpayne@69
|
33078 for (i = 1; i < PyTuple_GET_SIZE(bases); i++) {
|
|
jpayne@69
|
33079 void* base_vtable = __Pyx_GetVtable(((PyTypeObject*)PyTuple_GET_ITEM(bases, i)));
|
|
jpayne@69
|
33080 if (base_vtable != NULL) {
|
|
jpayne@69
|
33081 int j;
|
|
jpayne@69
|
33082 PyTypeObject* base = type->tp_base;
|
|
jpayne@69
|
33083 for (j = 0; j < base_depth; j++) {
|
|
jpayne@69
|
33084 if (base_vtables[j] == unknown) {
|
|
jpayne@69
|
33085 base_vtables[j] = __Pyx_GetVtable(base);
|
|
jpayne@69
|
33086 base_vtables[j + 1] = unknown;
|
|
jpayne@69
|
33087 }
|
|
jpayne@69
|
33088 if (base_vtables[j] == base_vtable) {
|
|
jpayne@69
|
33089 break;
|
|
jpayne@69
|
33090 } else if (base_vtables[j] == NULL) {
|
|
jpayne@69
|
33091 goto bad;
|
|
jpayne@69
|
33092 }
|
|
jpayne@69
|
33093 base = base->tp_base;
|
|
jpayne@69
|
33094 }
|
|
jpayne@69
|
33095 }
|
|
jpayne@69
|
33096 }
|
|
jpayne@69
|
33097 PyErr_Clear();
|
|
jpayne@69
|
33098 free(base_vtables);
|
|
jpayne@69
|
33099 return 0;
|
|
jpayne@69
|
33100 bad:
|
|
jpayne@69
|
33101 tp_base_name = __Pyx_PyType_GetName(type->tp_base);
|
|
jpayne@69
|
33102 base_name = __Pyx_PyType_GetName((PyTypeObject*)PyTuple_GET_ITEM(bases, i));
|
|
jpayne@69
|
33103 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
33104 "multiple bases have vtable conflict: '" __Pyx_FMT_TYPENAME "' and '" __Pyx_FMT_TYPENAME "'", tp_base_name, base_name);
|
|
jpayne@69
|
33105 __Pyx_DECREF_TypeName(tp_base_name);
|
|
jpayne@69
|
33106 __Pyx_DECREF_TypeName(base_name);
|
|
jpayne@69
|
33107 free(base_vtables);
|
|
jpayne@69
|
33108 return -1;
|
|
jpayne@69
|
33109 }
|
|
jpayne@69
|
33110 #endif
|
|
jpayne@69
|
33111
|
|
jpayne@69
|
33112 /* SetupReduce */
|
|
jpayne@69
|
33113 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33114 static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) {
|
|
jpayne@69
|
33115 int ret;
|
|
jpayne@69
|
33116 PyObject *name_attr;
|
|
jpayne@69
|
33117 name_attr = __Pyx_PyObject_GetAttrStrNoError(meth, __pyx_n_s_name);
|
|
jpayne@69
|
33118 if (likely(name_attr)) {
|
|
jpayne@69
|
33119 ret = PyObject_RichCompareBool(name_attr, name, Py_EQ);
|
|
jpayne@69
|
33120 } else {
|
|
jpayne@69
|
33121 ret = -1;
|
|
jpayne@69
|
33122 }
|
|
jpayne@69
|
33123 if (unlikely(ret < 0)) {
|
|
jpayne@69
|
33124 PyErr_Clear();
|
|
jpayne@69
|
33125 ret = 0;
|
|
jpayne@69
|
33126 }
|
|
jpayne@69
|
33127 Py_XDECREF(name_attr);
|
|
jpayne@69
|
33128 return ret;
|
|
jpayne@69
|
33129 }
|
|
jpayne@69
|
33130 static int __Pyx_setup_reduce(PyObject* type_obj) {
|
|
jpayne@69
|
33131 int ret = 0;
|
|
jpayne@69
|
33132 PyObject *object_reduce = NULL;
|
|
jpayne@69
|
33133 PyObject *object_getstate = NULL;
|
|
jpayne@69
|
33134 PyObject *object_reduce_ex = NULL;
|
|
jpayne@69
|
33135 PyObject *reduce = NULL;
|
|
jpayne@69
|
33136 PyObject *reduce_ex = NULL;
|
|
jpayne@69
|
33137 PyObject *reduce_cython = NULL;
|
|
jpayne@69
|
33138 PyObject *setstate = NULL;
|
|
jpayne@69
|
33139 PyObject *setstate_cython = NULL;
|
|
jpayne@69
|
33140 PyObject *getstate = NULL;
|
|
jpayne@69
|
33141 #if CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
33142 getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate);
|
|
jpayne@69
|
33143 #else
|
|
jpayne@69
|
33144 getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate);
|
|
jpayne@69
|
33145 if (!getstate && PyErr_Occurred()) {
|
|
jpayne@69
|
33146 goto __PYX_BAD;
|
|
jpayne@69
|
33147 }
|
|
jpayne@69
|
33148 #endif
|
|
jpayne@69
|
33149 if (getstate) {
|
|
jpayne@69
|
33150 #if CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
33151 object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate);
|
|
jpayne@69
|
33152 #else
|
|
jpayne@69
|
33153 object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate);
|
|
jpayne@69
|
33154 if (!object_getstate && PyErr_Occurred()) {
|
|
jpayne@69
|
33155 goto __PYX_BAD;
|
|
jpayne@69
|
33156 }
|
|
jpayne@69
|
33157 #endif
|
|
jpayne@69
|
33158 if (object_getstate != getstate) {
|
|
jpayne@69
|
33159 goto __PYX_GOOD;
|
|
jpayne@69
|
33160 }
|
|
jpayne@69
|
33161 }
|
|
jpayne@69
|
33162 #if CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
33163 object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
|
|
jpayne@69
|
33164 #else
|
|
jpayne@69
|
33165 object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
|
|
jpayne@69
|
33166 #endif
|
|
jpayne@69
|
33167 reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD;
|
|
jpayne@69
|
33168 if (reduce_ex == object_reduce_ex) {
|
|
jpayne@69
|
33169 #if CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
33170 object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
|
|
jpayne@69
|
33171 #else
|
|
jpayne@69
|
33172 object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD;
|
|
jpayne@69
|
33173 #endif
|
|
jpayne@69
|
33174 reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD;
|
|
jpayne@69
|
33175 if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) {
|
|
jpayne@69
|
33176 reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython);
|
|
jpayne@69
|
33177 if (likely(reduce_cython)) {
|
|
jpayne@69
|
33178 ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
|
|
jpayne@69
|
33179 ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
|
|
jpayne@69
|
33180 } else if (reduce == object_reduce || PyErr_Occurred()) {
|
|
jpayne@69
|
33181 goto __PYX_BAD;
|
|
jpayne@69
|
33182 }
|
|
jpayne@69
|
33183 setstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate);
|
|
jpayne@69
|
33184 if (!setstate) PyErr_Clear();
|
|
jpayne@69
|
33185 if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
|
|
jpayne@69
|
33186 setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython);
|
|
jpayne@69
|
33187 if (likely(setstate_cython)) {
|
|
jpayne@69
|
33188 ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
|
|
jpayne@69
|
33189 ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD;
|
|
jpayne@69
|
33190 } else if (!setstate || PyErr_Occurred()) {
|
|
jpayne@69
|
33191 goto __PYX_BAD;
|
|
jpayne@69
|
33192 }
|
|
jpayne@69
|
33193 }
|
|
jpayne@69
|
33194 PyType_Modified((PyTypeObject*)type_obj);
|
|
jpayne@69
|
33195 }
|
|
jpayne@69
|
33196 }
|
|
jpayne@69
|
33197 goto __PYX_GOOD;
|
|
jpayne@69
|
33198 __PYX_BAD:
|
|
jpayne@69
|
33199 if (!PyErr_Occurred()) {
|
|
jpayne@69
|
33200 __Pyx_TypeName type_obj_name =
|
|
jpayne@69
|
33201 __Pyx_PyType_GetName((PyTypeObject*)type_obj);
|
|
jpayne@69
|
33202 PyErr_Format(PyExc_RuntimeError,
|
|
jpayne@69
|
33203 "Unable to initialize pickling for " __Pyx_FMT_TYPENAME, type_obj_name);
|
|
jpayne@69
|
33204 __Pyx_DECREF_TypeName(type_obj_name);
|
|
jpayne@69
|
33205 }
|
|
jpayne@69
|
33206 ret = -1;
|
|
jpayne@69
|
33207 __PYX_GOOD:
|
|
jpayne@69
|
33208 #if !CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
33209 Py_XDECREF(object_reduce);
|
|
jpayne@69
|
33210 Py_XDECREF(object_reduce_ex);
|
|
jpayne@69
|
33211 Py_XDECREF(object_getstate);
|
|
jpayne@69
|
33212 Py_XDECREF(getstate);
|
|
jpayne@69
|
33213 #endif
|
|
jpayne@69
|
33214 Py_XDECREF(reduce);
|
|
jpayne@69
|
33215 Py_XDECREF(reduce_ex);
|
|
jpayne@69
|
33216 Py_XDECREF(reduce_cython);
|
|
jpayne@69
|
33217 Py_XDECREF(setstate);
|
|
jpayne@69
|
33218 Py_XDECREF(setstate_cython);
|
|
jpayne@69
|
33219 return ret;
|
|
jpayne@69
|
33220 }
|
|
jpayne@69
|
33221 #endif
|
|
jpayne@69
|
33222
|
|
jpayne@69
|
33223 /* TypeImport */
|
|
jpayne@69
|
33224 #ifndef __PYX_HAVE_RT_ImportType_3_0_11
|
|
jpayne@69
|
33225 #define __PYX_HAVE_RT_ImportType_3_0_11
|
|
jpayne@69
|
33226 static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject *module, const char *module_name, const char *class_name,
|
|
jpayne@69
|
33227 size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size)
|
|
jpayne@69
|
33228 {
|
|
jpayne@69
|
33229 PyObject *result = 0;
|
|
jpayne@69
|
33230 char warning[200];
|
|
jpayne@69
|
33231 Py_ssize_t basicsize;
|
|
jpayne@69
|
33232 Py_ssize_t itemsize;
|
|
jpayne@69
|
33233 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33234 PyObject *py_basicsize;
|
|
jpayne@69
|
33235 PyObject *py_itemsize;
|
|
jpayne@69
|
33236 #endif
|
|
jpayne@69
|
33237 result = PyObject_GetAttrString(module, class_name);
|
|
jpayne@69
|
33238 if (!result)
|
|
jpayne@69
|
33239 goto bad;
|
|
jpayne@69
|
33240 if (!PyType_Check(result)) {
|
|
jpayne@69
|
33241 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
33242 "%.200s.%.200s is not a type object",
|
|
jpayne@69
|
33243 module_name, class_name);
|
|
jpayne@69
|
33244 goto bad;
|
|
jpayne@69
|
33245 }
|
|
jpayne@69
|
33246 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33247 basicsize = ((PyTypeObject *)result)->tp_basicsize;
|
|
jpayne@69
|
33248 itemsize = ((PyTypeObject *)result)->tp_itemsize;
|
|
jpayne@69
|
33249 #else
|
|
jpayne@69
|
33250 py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
|
|
jpayne@69
|
33251 if (!py_basicsize)
|
|
jpayne@69
|
33252 goto bad;
|
|
jpayne@69
|
33253 basicsize = PyLong_AsSsize_t(py_basicsize);
|
|
jpayne@69
|
33254 Py_DECREF(py_basicsize);
|
|
jpayne@69
|
33255 py_basicsize = 0;
|
|
jpayne@69
|
33256 if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
|
|
jpayne@69
|
33257 goto bad;
|
|
jpayne@69
|
33258 py_itemsize = PyObject_GetAttrString(result, "__itemsize__");
|
|
jpayne@69
|
33259 if (!py_itemsize)
|
|
jpayne@69
|
33260 goto bad;
|
|
jpayne@69
|
33261 itemsize = PyLong_AsSsize_t(py_itemsize);
|
|
jpayne@69
|
33262 Py_DECREF(py_itemsize);
|
|
jpayne@69
|
33263 py_itemsize = 0;
|
|
jpayne@69
|
33264 if (itemsize == (Py_ssize_t)-1 && PyErr_Occurred())
|
|
jpayne@69
|
33265 goto bad;
|
|
jpayne@69
|
33266 #endif
|
|
jpayne@69
|
33267 if (itemsize) {
|
|
jpayne@69
|
33268 if (size % alignment) {
|
|
jpayne@69
|
33269 alignment = size % alignment;
|
|
jpayne@69
|
33270 }
|
|
jpayne@69
|
33271 if (itemsize < (Py_ssize_t)alignment)
|
|
jpayne@69
|
33272 itemsize = (Py_ssize_t)alignment;
|
|
jpayne@69
|
33273 }
|
|
jpayne@69
|
33274 if ((size_t)(basicsize + itemsize) < size) {
|
|
jpayne@69
|
33275 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
33276 "%.200s.%.200s size changed, may indicate binary incompatibility. "
|
|
jpayne@69
|
33277 "Expected %zd from C header, got %zd from PyObject",
|
|
jpayne@69
|
33278 module_name, class_name, size, basicsize+itemsize);
|
|
jpayne@69
|
33279 goto bad;
|
|
jpayne@69
|
33280 }
|
|
jpayne@69
|
33281 if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 &&
|
|
jpayne@69
|
33282 ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) {
|
|
jpayne@69
|
33283 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
33284 "%.200s.%.200s size changed, may indicate binary incompatibility. "
|
|
jpayne@69
|
33285 "Expected %zd from C header, got %zd-%zd from PyObject",
|
|
jpayne@69
|
33286 module_name, class_name, size, basicsize, basicsize+itemsize);
|
|
jpayne@69
|
33287 goto bad;
|
|
jpayne@69
|
33288 }
|
|
jpayne@69
|
33289 else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_11 && (size_t)basicsize > size) {
|
|
jpayne@69
|
33290 PyOS_snprintf(warning, sizeof(warning),
|
|
jpayne@69
|
33291 "%s.%s size changed, may indicate binary incompatibility. "
|
|
jpayne@69
|
33292 "Expected %zd from C header, got %zd from PyObject",
|
|
jpayne@69
|
33293 module_name, class_name, size, basicsize);
|
|
jpayne@69
|
33294 if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
|
|
jpayne@69
|
33295 }
|
|
jpayne@69
|
33296 return (PyTypeObject *)result;
|
|
jpayne@69
|
33297 bad:
|
|
jpayne@69
|
33298 Py_XDECREF(result);
|
|
jpayne@69
|
33299 return NULL;
|
|
jpayne@69
|
33300 }
|
|
jpayne@69
|
33301 #endif
|
|
jpayne@69
|
33302
|
|
jpayne@69
|
33303 /* ImportDottedModule */
|
|
jpayne@69
|
33304 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33305 static PyObject *__Pyx__ImportDottedModule_Error(PyObject *name, PyObject *parts_tuple, Py_ssize_t count) {
|
|
jpayne@69
|
33306 PyObject *partial_name = NULL, *slice = NULL, *sep = NULL;
|
|
jpayne@69
|
33307 if (unlikely(PyErr_Occurred())) {
|
|
jpayne@69
|
33308 PyErr_Clear();
|
|
jpayne@69
|
33309 }
|
|
jpayne@69
|
33310 if (likely(PyTuple_GET_SIZE(parts_tuple) == count)) {
|
|
jpayne@69
|
33311 partial_name = name;
|
|
jpayne@69
|
33312 } else {
|
|
jpayne@69
|
33313 slice = PySequence_GetSlice(parts_tuple, 0, count);
|
|
jpayne@69
|
33314 if (unlikely(!slice))
|
|
jpayne@69
|
33315 goto bad;
|
|
jpayne@69
|
33316 sep = PyUnicode_FromStringAndSize(".", 1);
|
|
jpayne@69
|
33317 if (unlikely(!sep))
|
|
jpayne@69
|
33318 goto bad;
|
|
jpayne@69
|
33319 partial_name = PyUnicode_Join(sep, slice);
|
|
jpayne@69
|
33320 }
|
|
jpayne@69
|
33321 PyErr_Format(
|
|
jpayne@69
|
33322 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
33323 PyExc_ImportError,
|
|
jpayne@69
|
33324 "No module named '%s'", PyString_AS_STRING(partial_name));
|
|
jpayne@69
|
33325 #else
|
|
jpayne@69
|
33326 #if PY_VERSION_HEX >= 0x030600B1
|
|
jpayne@69
|
33327 PyExc_ModuleNotFoundError,
|
|
jpayne@69
|
33328 #else
|
|
jpayne@69
|
33329 PyExc_ImportError,
|
|
jpayne@69
|
33330 #endif
|
|
jpayne@69
|
33331 "No module named '%U'", partial_name);
|
|
jpayne@69
|
33332 #endif
|
|
jpayne@69
|
33333 bad:
|
|
jpayne@69
|
33334 Py_XDECREF(sep);
|
|
jpayne@69
|
33335 Py_XDECREF(slice);
|
|
jpayne@69
|
33336 Py_XDECREF(partial_name);
|
|
jpayne@69
|
33337 return NULL;
|
|
jpayne@69
|
33338 }
|
|
jpayne@69
|
33339 #endif
|
|
jpayne@69
|
33340 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33341 static PyObject *__Pyx__ImportDottedModule_Lookup(PyObject *name) {
|
|
jpayne@69
|
33342 PyObject *imported_module;
|
|
jpayne@69
|
33343 #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400)
|
|
jpayne@69
|
33344 PyObject *modules = PyImport_GetModuleDict();
|
|
jpayne@69
|
33345 if (unlikely(!modules))
|
|
jpayne@69
|
33346 return NULL;
|
|
jpayne@69
|
33347 imported_module = __Pyx_PyDict_GetItemStr(modules, name);
|
|
jpayne@69
|
33348 Py_XINCREF(imported_module);
|
|
jpayne@69
|
33349 #else
|
|
jpayne@69
|
33350 imported_module = PyImport_GetModule(name);
|
|
jpayne@69
|
33351 #endif
|
|
jpayne@69
|
33352 return imported_module;
|
|
jpayne@69
|
33353 }
|
|
jpayne@69
|
33354 #endif
|
|
jpayne@69
|
33355 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33356 static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple) {
|
|
jpayne@69
|
33357 Py_ssize_t i, nparts;
|
|
jpayne@69
|
33358 nparts = PyTuple_GET_SIZE(parts_tuple);
|
|
jpayne@69
|
33359 for (i=1; i < nparts && module; i++) {
|
|
jpayne@69
|
33360 PyObject *part, *submodule;
|
|
jpayne@69
|
33361 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
33362 part = PyTuple_GET_ITEM(parts_tuple, i);
|
|
jpayne@69
|
33363 #else
|
|
jpayne@69
|
33364 part = PySequence_ITEM(parts_tuple, i);
|
|
jpayne@69
|
33365 #endif
|
|
jpayne@69
|
33366 submodule = __Pyx_PyObject_GetAttrStrNoError(module, part);
|
|
jpayne@69
|
33367 #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS)
|
|
jpayne@69
|
33368 Py_DECREF(part);
|
|
jpayne@69
|
33369 #endif
|
|
jpayne@69
|
33370 Py_DECREF(module);
|
|
jpayne@69
|
33371 module = submodule;
|
|
jpayne@69
|
33372 }
|
|
jpayne@69
|
33373 if (unlikely(!module)) {
|
|
jpayne@69
|
33374 return __Pyx__ImportDottedModule_Error(name, parts_tuple, i);
|
|
jpayne@69
|
33375 }
|
|
jpayne@69
|
33376 return module;
|
|
jpayne@69
|
33377 }
|
|
jpayne@69
|
33378 #endif
|
|
jpayne@69
|
33379 static PyObject *__Pyx__ImportDottedModule(PyObject *name, PyObject *parts_tuple) {
|
|
jpayne@69
|
33380 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
33381 PyObject *module, *from_list, *star = __pyx_n_s__62;
|
|
jpayne@69
|
33382 CYTHON_UNUSED_VAR(parts_tuple);
|
|
jpayne@69
|
33383 from_list = PyList_New(1);
|
|
jpayne@69
|
33384 if (unlikely(!from_list))
|
|
jpayne@69
|
33385 return NULL;
|
|
jpayne@69
|
33386 Py_INCREF(star);
|
|
jpayne@69
|
33387 PyList_SET_ITEM(from_list, 0, star);
|
|
jpayne@69
|
33388 module = __Pyx_Import(name, from_list, 0);
|
|
jpayne@69
|
33389 Py_DECREF(from_list);
|
|
jpayne@69
|
33390 return module;
|
|
jpayne@69
|
33391 #else
|
|
jpayne@69
|
33392 PyObject *imported_module;
|
|
jpayne@69
|
33393 PyObject *module = __Pyx_Import(name, NULL, 0);
|
|
jpayne@69
|
33394 if (!parts_tuple || unlikely(!module))
|
|
jpayne@69
|
33395 return module;
|
|
jpayne@69
|
33396 imported_module = __Pyx__ImportDottedModule_Lookup(name);
|
|
jpayne@69
|
33397 if (likely(imported_module)) {
|
|
jpayne@69
|
33398 Py_DECREF(module);
|
|
jpayne@69
|
33399 return imported_module;
|
|
jpayne@69
|
33400 }
|
|
jpayne@69
|
33401 PyErr_Clear();
|
|
jpayne@69
|
33402 return __Pyx_ImportDottedModule_WalkParts(module, name, parts_tuple);
|
|
jpayne@69
|
33403 #endif
|
|
jpayne@69
|
33404 }
|
|
jpayne@69
|
33405 static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple) {
|
|
jpayne@69
|
33406 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030400B1
|
|
jpayne@69
|
33407 PyObject *module = __Pyx__ImportDottedModule_Lookup(name);
|
|
jpayne@69
|
33408 if (likely(module)) {
|
|
jpayne@69
|
33409 PyObject *spec = __Pyx_PyObject_GetAttrStrNoError(module, __pyx_n_s_spec);
|
|
jpayne@69
|
33410 if (likely(spec)) {
|
|
jpayne@69
|
33411 PyObject *unsafe = __Pyx_PyObject_GetAttrStrNoError(spec, __pyx_n_s_initializing);
|
|
jpayne@69
|
33412 if (likely(!unsafe || !__Pyx_PyObject_IsTrue(unsafe))) {
|
|
jpayne@69
|
33413 Py_DECREF(spec);
|
|
jpayne@69
|
33414 spec = NULL;
|
|
jpayne@69
|
33415 }
|
|
jpayne@69
|
33416 Py_XDECREF(unsafe);
|
|
jpayne@69
|
33417 }
|
|
jpayne@69
|
33418 if (likely(!spec)) {
|
|
jpayne@69
|
33419 PyErr_Clear();
|
|
jpayne@69
|
33420 return module;
|
|
jpayne@69
|
33421 }
|
|
jpayne@69
|
33422 Py_DECREF(spec);
|
|
jpayne@69
|
33423 Py_DECREF(module);
|
|
jpayne@69
|
33424 } else if (PyErr_Occurred()) {
|
|
jpayne@69
|
33425 PyErr_Clear();
|
|
jpayne@69
|
33426 }
|
|
jpayne@69
|
33427 #endif
|
|
jpayne@69
|
33428 return __Pyx__ImportDottedModule(name, parts_tuple);
|
|
jpayne@69
|
33429 }
|
|
jpayne@69
|
33430
|
|
jpayne@69
|
33431 /* FetchSharedCythonModule */
|
|
jpayne@69
|
33432 static PyObject *__Pyx_FetchSharedCythonABIModule(void) {
|
|
jpayne@69
|
33433 return __Pyx_PyImport_AddModuleRef((char*) __PYX_ABI_MODULE_NAME);
|
|
jpayne@69
|
33434 }
|
|
jpayne@69
|
33435
|
|
jpayne@69
|
33436 /* FetchCommonType */
|
|
jpayne@69
|
33437 static int __Pyx_VerifyCachedType(PyObject *cached_type,
|
|
jpayne@69
|
33438 const char *name,
|
|
jpayne@69
|
33439 Py_ssize_t basicsize,
|
|
jpayne@69
|
33440 Py_ssize_t expected_basicsize) {
|
|
jpayne@69
|
33441 if (!PyType_Check(cached_type)) {
|
|
jpayne@69
|
33442 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
33443 "Shared Cython type %.200s is not a type object", name);
|
|
jpayne@69
|
33444 return -1;
|
|
jpayne@69
|
33445 }
|
|
jpayne@69
|
33446 if (basicsize != expected_basicsize) {
|
|
jpayne@69
|
33447 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
33448 "Shared Cython type %.200s has the wrong size, try recompiling",
|
|
jpayne@69
|
33449 name);
|
|
jpayne@69
|
33450 return -1;
|
|
jpayne@69
|
33451 }
|
|
jpayne@69
|
33452 return 0;
|
|
jpayne@69
|
33453 }
|
|
jpayne@69
|
33454 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
33455 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
|
|
jpayne@69
|
33456 PyObject* abi_module;
|
|
jpayne@69
|
33457 const char* object_name;
|
|
jpayne@69
|
33458 PyTypeObject *cached_type = NULL;
|
|
jpayne@69
|
33459 abi_module = __Pyx_FetchSharedCythonABIModule();
|
|
jpayne@69
|
33460 if (!abi_module) return NULL;
|
|
jpayne@69
|
33461 object_name = strrchr(type->tp_name, '.');
|
|
jpayne@69
|
33462 object_name = object_name ? object_name+1 : type->tp_name;
|
|
jpayne@69
|
33463 cached_type = (PyTypeObject*) PyObject_GetAttrString(abi_module, object_name);
|
|
jpayne@69
|
33464 if (cached_type) {
|
|
jpayne@69
|
33465 if (__Pyx_VerifyCachedType(
|
|
jpayne@69
|
33466 (PyObject *)cached_type,
|
|
jpayne@69
|
33467 object_name,
|
|
jpayne@69
|
33468 cached_type->tp_basicsize,
|
|
jpayne@69
|
33469 type->tp_basicsize) < 0) {
|
|
jpayne@69
|
33470 goto bad;
|
|
jpayne@69
|
33471 }
|
|
jpayne@69
|
33472 goto done;
|
|
jpayne@69
|
33473 }
|
|
jpayne@69
|
33474 if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
|
|
jpayne@69
|
33475 PyErr_Clear();
|
|
jpayne@69
|
33476 if (PyType_Ready(type) < 0) goto bad;
|
|
jpayne@69
|
33477 if (PyObject_SetAttrString(abi_module, object_name, (PyObject *)type) < 0)
|
|
jpayne@69
|
33478 goto bad;
|
|
jpayne@69
|
33479 Py_INCREF(type);
|
|
jpayne@69
|
33480 cached_type = type;
|
|
jpayne@69
|
33481 done:
|
|
jpayne@69
|
33482 Py_DECREF(abi_module);
|
|
jpayne@69
|
33483 return cached_type;
|
|
jpayne@69
|
33484 bad:
|
|
jpayne@69
|
33485 Py_XDECREF(cached_type);
|
|
jpayne@69
|
33486 cached_type = NULL;
|
|
jpayne@69
|
33487 goto done;
|
|
jpayne@69
|
33488 }
|
|
jpayne@69
|
33489 #else
|
|
jpayne@69
|
33490 static PyTypeObject *__Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases) {
|
|
jpayne@69
|
33491 PyObject *abi_module, *cached_type = NULL;
|
|
jpayne@69
|
33492 const char* object_name = strrchr(spec->name, '.');
|
|
jpayne@69
|
33493 object_name = object_name ? object_name+1 : spec->name;
|
|
jpayne@69
|
33494 abi_module = __Pyx_FetchSharedCythonABIModule();
|
|
jpayne@69
|
33495 if (!abi_module) return NULL;
|
|
jpayne@69
|
33496 cached_type = PyObject_GetAttrString(abi_module, object_name);
|
|
jpayne@69
|
33497 if (cached_type) {
|
|
jpayne@69
|
33498 Py_ssize_t basicsize;
|
|
jpayne@69
|
33499 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33500 PyObject *py_basicsize;
|
|
jpayne@69
|
33501 py_basicsize = PyObject_GetAttrString(cached_type, "__basicsize__");
|
|
jpayne@69
|
33502 if (unlikely(!py_basicsize)) goto bad;
|
|
jpayne@69
|
33503 basicsize = PyLong_AsSsize_t(py_basicsize);
|
|
jpayne@69
|
33504 Py_DECREF(py_basicsize);
|
|
jpayne@69
|
33505 py_basicsize = 0;
|
|
jpayne@69
|
33506 if (unlikely(basicsize == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
|
|
jpayne@69
|
33507 #else
|
|
jpayne@69
|
33508 basicsize = likely(PyType_Check(cached_type)) ? ((PyTypeObject*) cached_type)->tp_basicsize : -1;
|
|
jpayne@69
|
33509 #endif
|
|
jpayne@69
|
33510 if (__Pyx_VerifyCachedType(
|
|
jpayne@69
|
33511 cached_type,
|
|
jpayne@69
|
33512 object_name,
|
|
jpayne@69
|
33513 basicsize,
|
|
jpayne@69
|
33514 spec->basicsize) < 0) {
|
|
jpayne@69
|
33515 goto bad;
|
|
jpayne@69
|
33516 }
|
|
jpayne@69
|
33517 goto done;
|
|
jpayne@69
|
33518 }
|
|
jpayne@69
|
33519 if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
|
|
jpayne@69
|
33520 PyErr_Clear();
|
|
jpayne@69
|
33521 CYTHON_UNUSED_VAR(module);
|
|
jpayne@69
|
33522 cached_type = __Pyx_PyType_FromModuleAndSpec(abi_module, spec, bases);
|
|
jpayne@69
|
33523 if (unlikely(!cached_type)) goto bad;
|
|
jpayne@69
|
33524 if (unlikely(__Pyx_fix_up_extension_type_from_spec(spec, (PyTypeObject *) cached_type) < 0)) goto bad;
|
|
jpayne@69
|
33525 if (PyObject_SetAttrString(abi_module, object_name, cached_type) < 0) goto bad;
|
|
jpayne@69
|
33526 done:
|
|
jpayne@69
|
33527 Py_DECREF(abi_module);
|
|
jpayne@69
|
33528 assert(cached_type == NULL || PyType_Check(cached_type));
|
|
jpayne@69
|
33529 return (PyTypeObject *) cached_type;
|
|
jpayne@69
|
33530 bad:
|
|
jpayne@69
|
33531 Py_XDECREF(cached_type);
|
|
jpayne@69
|
33532 cached_type = NULL;
|
|
jpayne@69
|
33533 goto done;
|
|
jpayne@69
|
33534 }
|
|
jpayne@69
|
33535 #endif
|
|
jpayne@69
|
33536
|
|
jpayne@69
|
33537 /* PyVectorcallFastCallDict */
|
|
jpayne@69
|
33538 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
33539 static PyObject *__Pyx_PyVectorcall_FastCallDict_kw(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw)
|
|
jpayne@69
|
33540 {
|
|
jpayne@69
|
33541 PyObject *res = NULL;
|
|
jpayne@69
|
33542 PyObject *kwnames;
|
|
jpayne@69
|
33543 PyObject **newargs;
|
|
jpayne@69
|
33544 PyObject **kwvalues;
|
|
jpayne@69
|
33545 Py_ssize_t i, pos;
|
|
jpayne@69
|
33546 size_t j;
|
|
jpayne@69
|
33547 PyObject *key, *value;
|
|
jpayne@69
|
33548 unsigned long keys_are_strings;
|
|
jpayne@69
|
33549 Py_ssize_t nkw = PyDict_GET_SIZE(kw);
|
|
jpayne@69
|
33550 newargs = (PyObject **)PyMem_Malloc((nargs + (size_t)nkw) * sizeof(args[0]));
|
|
jpayne@69
|
33551 if (unlikely(newargs == NULL)) {
|
|
jpayne@69
|
33552 PyErr_NoMemory();
|
|
jpayne@69
|
33553 return NULL;
|
|
jpayne@69
|
33554 }
|
|
jpayne@69
|
33555 for (j = 0; j < nargs; j++) newargs[j] = args[j];
|
|
jpayne@69
|
33556 kwnames = PyTuple_New(nkw);
|
|
jpayne@69
|
33557 if (unlikely(kwnames == NULL)) {
|
|
jpayne@69
|
33558 PyMem_Free(newargs);
|
|
jpayne@69
|
33559 return NULL;
|
|
jpayne@69
|
33560 }
|
|
jpayne@69
|
33561 kwvalues = newargs + nargs;
|
|
jpayne@69
|
33562 pos = i = 0;
|
|
jpayne@69
|
33563 keys_are_strings = Py_TPFLAGS_UNICODE_SUBCLASS;
|
|
jpayne@69
|
33564 while (PyDict_Next(kw, &pos, &key, &value)) {
|
|
jpayne@69
|
33565 keys_are_strings &= Py_TYPE(key)->tp_flags;
|
|
jpayne@69
|
33566 Py_INCREF(key);
|
|
jpayne@69
|
33567 Py_INCREF(value);
|
|
jpayne@69
|
33568 PyTuple_SET_ITEM(kwnames, i, key);
|
|
jpayne@69
|
33569 kwvalues[i] = value;
|
|
jpayne@69
|
33570 i++;
|
|
jpayne@69
|
33571 }
|
|
jpayne@69
|
33572 if (unlikely(!keys_are_strings)) {
|
|
jpayne@69
|
33573 PyErr_SetString(PyExc_TypeError, "keywords must be strings");
|
|
jpayne@69
|
33574 goto cleanup;
|
|
jpayne@69
|
33575 }
|
|
jpayne@69
|
33576 res = vc(func, newargs, nargs, kwnames);
|
|
jpayne@69
|
33577 cleanup:
|
|
jpayne@69
|
33578 Py_DECREF(kwnames);
|
|
jpayne@69
|
33579 for (i = 0; i < nkw; i++)
|
|
jpayne@69
|
33580 Py_DECREF(kwvalues[i]);
|
|
jpayne@69
|
33581 PyMem_Free(newargs);
|
|
jpayne@69
|
33582 return res;
|
|
jpayne@69
|
33583 }
|
|
jpayne@69
|
33584 static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw)
|
|
jpayne@69
|
33585 {
|
|
jpayne@69
|
33586 if (likely(kw == NULL) || PyDict_GET_SIZE(kw) == 0) {
|
|
jpayne@69
|
33587 return vc(func, args, nargs, NULL);
|
|
jpayne@69
|
33588 }
|
|
jpayne@69
|
33589 return __Pyx_PyVectorcall_FastCallDict_kw(func, vc, args, nargs, kw);
|
|
jpayne@69
|
33590 }
|
|
jpayne@69
|
33591 #endif
|
|
jpayne@69
|
33592
|
|
jpayne@69
|
33593 /* CythonFunctionShared */
|
|
jpayne@69
|
33594 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33595 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) {
|
|
jpayne@69
|
33596 if (__Pyx_CyFunction_Check(func)) {
|
|
jpayne@69
|
33597 return PyCFunction_GetFunction(((__pyx_CyFunctionObject*)func)->func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
33598 } else if (PyCFunction_Check(func)) {
|
|
jpayne@69
|
33599 return PyCFunction_GetFunction(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
33600 }
|
|
jpayne@69
|
33601 return 0;
|
|
jpayne@69
|
33602 }
|
|
jpayne@69
|
33603 #else
|
|
jpayne@69
|
33604 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) {
|
|
jpayne@69
|
33605 return __Pyx_CyOrPyCFunction_Check(func) && __Pyx_CyOrPyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
33606 }
|
|
jpayne@69
|
33607 #endif
|
|
jpayne@69
|
33608 static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj) {
|
|
jpayne@69
|
33609 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33610 __Pyx_Py_XDECREF_SET(
|
|
jpayne@69
|
33611 __Pyx_CyFunction_GetClassObj(f),
|
|
jpayne@69
|
33612 ((classobj) ? __Pyx_NewRef(classobj) : NULL));
|
|
jpayne@69
|
33613 #else
|
|
jpayne@69
|
33614 __Pyx_Py_XDECREF_SET(
|
|
jpayne@69
|
33615 ((PyCMethodObject *) (f))->mm_class,
|
|
jpayne@69
|
33616 (PyTypeObject*)((classobj) ? __Pyx_NewRef(classobj) : NULL));
|
|
jpayne@69
|
33617 #endif
|
|
jpayne@69
|
33618 }
|
|
jpayne@69
|
33619 static PyObject *
|
|
jpayne@69
|
33620 __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, void *closure)
|
|
jpayne@69
|
33621 {
|
|
jpayne@69
|
33622 CYTHON_UNUSED_VAR(closure);
|
|
jpayne@69
|
33623 if (unlikely(op->func_doc == NULL)) {
|
|
jpayne@69
|
33624 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33625 op->func_doc = PyObject_GetAttrString(op->func, "__doc__");
|
|
jpayne@69
|
33626 if (unlikely(!op->func_doc)) return NULL;
|
|
jpayne@69
|
33627 #else
|
|
jpayne@69
|
33628 if (((PyCFunctionObject*)op)->m_ml->ml_doc) {
|
|
jpayne@69
|
33629 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33630 op->func_doc = PyUnicode_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc);
|
|
jpayne@69
|
33631 #else
|
|
jpayne@69
|
33632 op->func_doc = PyString_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc);
|
|
jpayne@69
|
33633 #endif
|
|
jpayne@69
|
33634 if (unlikely(op->func_doc == NULL))
|
|
jpayne@69
|
33635 return NULL;
|
|
jpayne@69
|
33636 } else {
|
|
jpayne@69
|
33637 Py_INCREF(Py_None);
|
|
jpayne@69
|
33638 return Py_None;
|
|
jpayne@69
|
33639 }
|
|
jpayne@69
|
33640 #endif
|
|
jpayne@69
|
33641 }
|
|
jpayne@69
|
33642 Py_INCREF(op->func_doc);
|
|
jpayne@69
|
33643 return op->func_doc;
|
|
jpayne@69
|
33644 }
|
|
jpayne@69
|
33645 static int
|
|
jpayne@69
|
33646 __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
33647 {
|
|
jpayne@69
|
33648 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33649 if (value == NULL) {
|
|
jpayne@69
|
33650 value = Py_None;
|
|
jpayne@69
|
33651 }
|
|
jpayne@69
|
33652 Py_INCREF(value);
|
|
jpayne@69
|
33653 __Pyx_Py_XDECREF_SET(op->func_doc, value);
|
|
jpayne@69
|
33654 return 0;
|
|
jpayne@69
|
33655 }
|
|
jpayne@69
|
33656 static PyObject *
|
|
jpayne@69
|
33657 __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
33658 {
|
|
jpayne@69
|
33659 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33660 if (unlikely(op->func_name == NULL)) {
|
|
jpayne@69
|
33661 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33662 op->func_name = PyObject_GetAttrString(op->func, "__name__");
|
|
jpayne@69
|
33663 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33664 op->func_name = PyUnicode_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name);
|
|
jpayne@69
|
33665 #else
|
|
jpayne@69
|
33666 op->func_name = PyString_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name);
|
|
jpayne@69
|
33667 #endif
|
|
jpayne@69
|
33668 if (unlikely(op->func_name == NULL))
|
|
jpayne@69
|
33669 return NULL;
|
|
jpayne@69
|
33670 }
|
|
jpayne@69
|
33671 Py_INCREF(op->func_name);
|
|
jpayne@69
|
33672 return op->func_name;
|
|
jpayne@69
|
33673 }
|
|
jpayne@69
|
33674 static int
|
|
jpayne@69
|
33675 __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
33676 {
|
|
jpayne@69
|
33677 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33678 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33679 if (unlikely(value == NULL || !PyUnicode_Check(value)))
|
|
jpayne@69
|
33680 #else
|
|
jpayne@69
|
33681 if (unlikely(value == NULL || !PyString_Check(value)))
|
|
jpayne@69
|
33682 #endif
|
|
jpayne@69
|
33683 {
|
|
jpayne@69
|
33684 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33685 "__name__ must be set to a string object");
|
|
jpayne@69
|
33686 return -1;
|
|
jpayne@69
|
33687 }
|
|
jpayne@69
|
33688 Py_INCREF(value);
|
|
jpayne@69
|
33689 __Pyx_Py_XDECREF_SET(op->func_name, value);
|
|
jpayne@69
|
33690 return 0;
|
|
jpayne@69
|
33691 }
|
|
jpayne@69
|
33692 static PyObject *
|
|
jpayne@69
|
33693 __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
33694 {
|
|
jpayne@69
|
33695 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33696 Py_INCREF(op->func_qualname);
|
|
jpayne@69
|
33697 return op->func_qualname;
|
|
jpayne@69
|
33698 }
|
|
jpayne@69
|
33699 static int
|
|
jpayne@69
|
33700 __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
33701 {
|
|
jpayne@69
|
33702 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33703 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33704 if (unlikely(value == NULL || !PyUnicode_Check(value)))
|
|
jpayne@69
|
33705 #else
|
|
jpayne@69
|
33706 if (unlikely(value == NULL || !PyString_Check(value)))
|
|
jpayne@69
|
33707 #endif
|
|
jpayne@69
|
33708 {
|
|
jpayne@69
|
33709 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33710 "__qualname__ must be set to a string object");
|
|
jpayne@69
|
33711 return -1;
|
|
jpayne@69
|
33712 }
|
|
jpayne@69
|
33713 Py_INCREF(value);
|
|
jpayne@69
|
33714 __Pyx_Py_XDECREF_SET(op->func_qualname, value);
|
|
jpayne@69
|
33715 return 0;
|
|
jpayne@69
|
33716 }
|
|
jpayne@69
|
33717 static PyObject *
|
|
jpayne@69
|
33718 __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
33719 {
|
|
jpayne@69
|
33720 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33721 if (unlikely(op->func_dict == NULL)) {
|
|
jpayne@69
|
33722 op->func_dict = PyDict_New();
|
|
jpayne@69
|
33723 if (unlikely(op->func_dict == NULL))
|
|
jpayne@69
|
33724 return NULL;
|
|
jpayne@69
|
33725 }
|
|
jpayne@69
|
33726 Py_INCREF(op->func_dict);
|
|
jpayne@69
|
33727 return op->func_dict;
|
|
jpayne@69
|
33728 }
|
|
jpayne@69
|
33729 static int
|
|
jpayne@69
|
33730 __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
33731 {
|
|
jpayne@69
|
33732 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33733 if (unlikely(value == NULL)) {
|
|
jpayne@69
|
33734 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33735 "function's dictionary may not be deleted");
|
|
jpayne@69
|
33736 return -1;
|
|
jpayne@69
|
33737 }
|
|
jpayne@69
|
33738 if (unlikely(!PyDict_Check(value))) {
|
|
jpayne@69
|
33739 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33740 "setting function's dictionary to a non-dict");
|
|
jpayne@69
|
33741 return -1;
|
|
jpayne@69
|
33742 }
|
|
jpayne@69
|
33743 Py_INCREF(value);
|
|
jpayne@69
|
33744 __Pyx_Py_XDECREF_SET(op->func_dict, value);
|
|
jpayne@69
|
33745 return 0;
|
|
jpayne@69
|
33746 }
|
|
jpayne@69
|
33747 static PyObject *
|
|
jpayne@69
|
33748 __Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
33749 {
|
|
jpayne@69
|
33750 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33751 Py_INCREF(op->func_globals);
|
|
jpayne@69
|
33752 return op->func_globals;
|
|
jpayne@69
|
33753 }
|
|
jpayne@69
|
33754 static PyObject *
|
|
jpayne@69
|
33755 __Pyx_CyFunction_get_closure(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
33756 {
|
|
jpayne@69
|
33757 CYTHON_UNUSED_VAR(op);
|
|
jpayne@69
|
33758 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33759 Py_INCREF(Py_None);
|
|
jpayne@69
|
33760 return Py_None;
|
|
jpayne@69
|
33761 }
|
|
jpayne@69
|
33762 static PyObject *
|
|
jpayne@69
|
33763 __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
33764 {
|
|
jpayne@69
|
33765 PyObject* result = (op->func_code) ? op->func_code : Py_None;
|
|
jpayne@69
|
33766 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33767 Py_INCREF(result);
|
|
jpayne@69
|
33768 return result;
|
|
jpayne@69
|
33769 }
|
|
jpayne@69
|
33770 static int
|
|
jpayne@69
|
33771 __Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
|
|
jpayne@69
|
33772 int result = 0;
|
|
jpayne@69
|
33773 PyObject *res = op->defaults_getter((PyObject *) op);
|
|
jpayne@69
|
33774 if (unlikely(!res))
|
|
jpayne@69
|
33775 return -1;
|
|
jpayne@69
|
33776 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
33777 op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
|
|
jpayne@69
|
33778 Py_INCREF(op->defaults_tuple);
|
|
jpayne@69
|
33779 op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
|
|
jpayne@69
|
33780 Py_INCREF(op->defaults_kwdict);
|
|
jpayne@69
|
33781 #else
|
|
jpayne@69
|
33782 op->defaults_tuple = __Pyx_PySequence_ITEM(res, 0);
|
|
jpayne@69
|
33783 if (unlikely(!op->defaults_tuple)) result = -1;
|
|
jpayne@69
|
33784 else {
|
|
jpayne@69
|
33785 op->defaults_kwdict = __Pyx_PySequence_ITEM(res, 1);
|
|
jpayne@69
|
33786 if (unlikely(!op->defaults_kwdict)) result = -1;
|
|
jpayne@69
|
33787 }
|
|
jpayne@69
|
33788 #endif
|
|
jpayne@69
|
33789 Py_DECREF(res);
|
|
jpayne@69
|
33790 return result;
|
|
jpayne@69
|
33791 }
|
|
jpayne@69
|
33792 static int
|
|
jpayne@69
|
33793 __Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
33794 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33795 if (!value) {
|
|
jpayne@69
|
33796 value = Py_None;
|
|
jpayne@69
|
33797 } else if (unlikely(value != Py_None && !PyTuple_Check(value))) {
|
|
jpayne@69
|
33798 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33799 "__defaults__ must be set to a tuple object");
|
|
jpayne@69
|
33800 return -1;
|
|
jpayne@69
|
33801 }
|
|
jpayne@69
|
33802 PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__defaults__ will not "
|
|
jpayne@69
|
33803 "currently affect the values used in function calls", 1);
|
|
jpayne@69
|
33804 Py_INCREF(value);
|
|
jpayne@69
|
33805 __Pyx_Py_XDECREF_SET(op->defaults_tuple, value);
|
|
jpayne@69
|
33806 return 0;
|
|
jpayne@69
|
33807 }
|
|
jpayne@69
|
33808 static PyObject *
|
|
jpayne@69
|
33809 __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
33810 PyObject* result = op->defaults_tuple;
|
|
jpayne@69
|
33811 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33812 if (unlikely(!result)) {
|
|
jpayne@69
|
33813 if (op->defaults_getter) {
|
|
jpayne@69
|
33814 if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL;
|
|
jpayne@69
|
33815 result = op->defaults_tuple;
|
|
jpayne@69
|
33816 } else {
|
|
jpayne@69
|
33817 result = Py_None;
|
|
jpayne@69
|
33818 }
|
|
jpayne@69
|
33819 }
|
|
jpayne@69
|
33820 Py_INCREF(result);
|
|
jpayne@69
|
33821 return result;
|
|
jpayne@69
|
33822 }
|
|
jpayne@69
|
33823 static int
|
|
jpayne@69
|
33824 __Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
33825 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33826 if (!value) {
|
|
jpayne@69
|
33827 value = Py_None;
|
|
jpayne@69
|
33828 } else if (unlikely(value != Py_None && !PyDict_Check(value))) {
|
|
jpayne@69
|
33829 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33830 "__kwdefaults__ must be set to a dict object");
|
|
jpayne@69
|
33831 return -1;
|
|
jpayne@69
|
33832 }
|
|
jpayne@69
|
33833 PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__kwdefaults__ will not "
|
|
jpayne@69
|
33834 "currently affect the values used in function calls", 1);
|
|
jpayne@69
|
33835 Py_INCREF(value);
|
|
jpayne@69
|
33836 __Pyx_Py_XDECREF_SET(op->defaults_kwdict, value);
|
|
jpayne@69
|
33837 return 0;
|
|
jpayne@69
|
33838 }
|
|
jpayne@69
|
33839 static PyObject *
|
|
jpayne@69
|
33840 __Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
33841 PyObject* result = op->defaults_kwdict;
|
|
jpayne@69
|
33842 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33843 if (unlikely(!result)) {
|
|
jpayne@69
|
33844 if (op->defaults_getter) {
|
|
jpayne@69
|
33845 if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL;
|
|
jpayne@69
|
33846 result = op->defaults_kwdict;
|
|
jpayne@69
|
33847 } else {
|
|
jpayne@69
|
33848 result = Py_None;
|
|
jpayne@69
|
33849 }
|
|
jpayne@69
|
33850 }
|
|
jpayne@69
|
33851 Py_INCREF(result);
|
|
jpayne@69
|
33852 return result;
|
|
jpayne@69
|
33853 }
|
|
jpayne@69
|
33854 static int
|
|
jpayne@69
|
33855 __Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
33856 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33857 if (!value || value == Py_None) {
|
|
jpayne@69
|
33858 value = NULL;
|
|
jpayne@69
|
33859 } else if (unlikely(!PyDict_Check(value))) {
|
|
jpayne@69
|
33860 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
33861 "__annotations__ must be set to a dict object");
|
|
jpayne@69
|
33862 return -1;
|
|
jpayne@69
|
33863 }
|
|
jpayne@69
|
33864 Py_XINCREF(value);
|
|
jpayne@69
|
33865 __Pyx_Py_XDECREF_SET(op->func_annotations, value);
|
|
jpayne@69
|
33866 return 0;
|
|
jpayne@69
|
33867 }
|
|
jpayne@69
|
33868 static PyObject *
|
|
jpayne@69
|
33869 __Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
33870 PyObject* result = op->func_annotations;
|
|
jpayne@69
|
33871 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33872 if (unlikely(!result)) {
|
|
jpayne@69
|
33873 result = PyDict_New();
|
|
jpayne@69
|
33874 if (unlikely(!result)) return NULL;
|
|
jpayne@69
|
33875 op->func_annotations = result;
|
|
jpayne@69
|
33876 }
|
|
jpayne@69
|
33877 Py_INCREF(result);
|
|
jpayne@69
|
33878 return result;
|
|
jpayne@69
|
33879 }
|
|
jpayne@69
|
33880 static PyObject *
|
|
jpayne@69
|
33881 __Pyx_CyFunction_get_is_coroutine(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
33882 int is_coroutine;
|
|
jpayne@69
|
33883 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33884 if (op->func_is_coroutine) {
|
|
jpayne@69
|
33885 return __Pyx_NewRef(op->func_is_coroutine);
|
|
jpayne@69
|
33886 }
|
|
jpayne@69
|
33887 is_coroutine = op->flags & __Pyx_CYFUNCTION_COROUTINE;
|
|
jpayne@69
|
33888 #if PY_VERSION_HEX >= 0x03050000
|
|
jpayne@69
|
33889 if (is_coroutine) {
|
|
jpayne@69
|
33890 PyObject *module, *fromlist, *marker = __pyx_n_s_is_coroutine;
|
|
jpayne@69
|
33891 fromlist = PyList_New(1);
|
|
jpayne@69
|
33892 if (unlikely(!fromlist)) return NULL;
|
|
jpayne@69
|
33893 Py_INCREF(marker);
|
|
jpayne@69
|
33894 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
33895 PyList_SET_ITEM(fromlist, 0, marker);
|
|
jpayne@69
|
33896 #else
|
|
jpayne@69
|
33897 if (unlikely(PyList_SetItem(fromlist, 0, marker) < 0)) {
|
|
jpayne@69
|
33898 Py_DECREF(marker);
|
|
jpayne@69
|
33899 Py_DECREF(fromlist);
|
|
jpayne@69
|
33900 return NULL;
|
|
jpayne@69
|
33901 }
|
|
jpayne@69
|
33902 #endif
|
|
jpayne@69
|
33903 module = PyImport_ImportModuleLevelObject(__pyx_n_s_asyncio_coroutines, NULL, NULL, fromlist, 0);
|
|
jpayne@69
|
33904 Py_DECREF(fromlist);
|
|
jpayne@69
|
33905 if (unlikely(!module)) goto ignore;
|
|
jpayne@69
|
33906 op->func_is_coroutine = __Pyx_PyObject_GetAttrStr(module, marker);
|
|
jpayne@69
|
33907 Py_DECREF(module);
|
|
jpayne@69
|
33908 if (likely(op->func_is_coroutine)) {
|
|
jpayne@69
|
33909 return __Pyx_NewRef(op->func_is_coroutine);
|
|
jpayne@69
|
33910 }
|
|
jpayne@69
|
33911 ignore:
|
|
jpayne@69
|
33912 PyErr_Clear();
|
|
jpayne@69
|
33913 }
|
|
jpayne@69
|
33914 #endif
|
|
jpayne@69
|
33915 op->func_is_coroutine = __Pyx_PyBool_FromLong(is_coroutine);
|
|
jpayne@69
|
33916 return __Pyx_NewRef(op->func_is_coroutine);
|
|
jpayne@69
|
33917 }
|
|
jpayne@69
|
33918 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33919 static PyObject *
|
|
jpayne@69
|
33920 __Pyx_CyFunction_get_module(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
33921 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33922 return PyObject_GetAttrString(op->func, "__module__");
|
|
jpayne@69
|
33923 }
|
|
jpayne@69
|
33924 static int
|
|
jpayne@69
|
33925 __Pyx_CyFunction_set_module(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
33926 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
33927 return PyObject_SetAttrString(op->func, "__module__", value);
|
|
jpayne@69
|
33928 }
|
|
jpayne@69
|
33929 #endif
|
|
jpayne@69
|
33930 static PyGetSetDef __pyx_CyFunction_getsets[] = {
|
|
jpayne@69
|
33931 {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
|
|
jpayne@69
|
33932 {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
|
|
jpayne@69
|
33933 {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
|
|
jpayne@69
|
33934 {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
|
|
jpayne@69
|
33935 {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
|
|
jpayne@69
|
33936 {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
|
|
jpayne@69
|
33937 {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
|
|
jpayne@69
|
33938 {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
|
|
jpayne@69
|
33939 {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
|
|
jpayne@69
|
33940 {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
|
|
jpayne@69
|
33941 {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
|
|
jpayne@69
|
33942 {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
|
|
jpayne@69
|
33943 {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
|
|
jpayne@69
|
33944 {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
|
|
jpayne@69
|
33945 {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
|
|
jpayne@69
|
33946 {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0},
|
|
jpayne@69
|
33947 {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0},
|
|
jpayne@69
|
33948 {(char *) "_is_coroutine", (getter)__Pyx_CyFunction_get_is_coroutine, 0, 0, 0},
|
|
jpayne@69
|
33949 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33950 {"__module__", (getter)__Pyx_CyFunction_get_module, (setter)__Pyx_CyFunction_set_module, 0, 0},
|
|
jpayne@69
|
33951 #endif
|
|
jpayne@69
|
33952 {0, 0, 0, 0, 0}
|
|
jpayne@69
|
33953 };
|
|
jpayne@69
|
33954 static PyMemberDef __pyx_CyFunction_members[] = {
|
|
jpayne@69
|
33955 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33956 {(char *) "__module__", T_OBJECT, offsetof(PyCFunctionObject, m_module), 0, 0},
|
|
jpayne@69
|
33957 #endif
|
|
jpayne@69
|
33958 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
33959 {(char *) "__dictoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_dict), READONLY, 0},
|
|
jpayne@69
|
33960 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
33961 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
33962 {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_vectorcall), READONLY, 0},
|
|
jpayne@69
|
33963 #else
|
|
jpayne@69
|
33964 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33965 {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(PyCFunctionObject, vectorcall), READONLY, 0},
|
|
jpayne@69
|
33966 #endif
|
|
jpayne@69
|
33967 #endif
|
|
jpayne@69
|
33968 #endif
|
|
jpayne@69
|
33969 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33970 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_weakreflist), READONLY, 0},
|
|
jpayne@69
|
33971 #else
|
|
jpayne@69
|
33972 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(PyCFunctionObject, m_weakreflist), READONLY, 0},
|
|
jpayne@69
|
33973 #endif
|
|
jpayne@69
|
33974 #endif
|
|
jpayne@69
|
33975 {0, 0, 0, 0, 0}
|
|
jpayne@69
|
33976 };
|
|
jpayne@69
|
33977 static PyObject *
|
|
jpayne@69
|
33978 __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, PyObject *args)
|
|
jpayne@69
|
33979 {
|
|
jpayne@69
|
33980 CYTHON_UNUSED_VAR(args);
|
|
jpayne@69
|
33981 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
33982 Py_INCREF(m->func_qualname);
|
|
jpayne@69
|
33983 return m->func_qualname;
|
|
jpayne@69
|
33984 #else
|
|
jpayne@69
|
33985 return PyString_FromString(((PyCFunctionObject*)m)->m_ml->ml_name);
|
|
jpayne@69
|
33986 #endif
|
|
jpayne@69
|
33987 }
|
|
jpayne@69
|
33988 static PyMethodDef __pyx_CyFunction_methods[] = {
|
|
jpayne@69
|
33989 {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
|
|
jpayne@69
|
33990 {0, 0, 0, 0}
|
|
jpayne@69
|
33991 };
|
|
jpayne@69
|
33992 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
33993 #define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist)
|
|
jpayne@69
|
33994 #else
|
|
jpayne@69
|
33995 #define __Pyx_CyFunction_weakreflist(cyfunc) (((PyCFunctionObject*)cyfunc)->m_weakreflist)
|
|
jpayne@69
|
33996 #endif
|
|
jpayne@69
|
33997 static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname,
|
|
jpayne@69
|
33998 PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
|
|
jpayne@69
|
33999 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34000 PyCFunctionObject *cf = (PyCFunctionObject*) op;
|
|
jpayne@69
|
34001 #endif
|
|
jpayne@69
|
34002 if (unlikely(op == NULL))
|
|
jpayne@69
|
34003 return NULL;
|
|
jpayne@69
|
34004 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34005 op->func = PyCFunction_NewEx(ml, (PyObject*)op, module);
|
|
jpayne@69
|
34006 if (unlikely(!op->func)) return NULL;
|
|
jpayne@69
|
34007 #endif
|
|
jpayne@69
|
34008 op->flags = flags;
|
|
jpayne@69
|
34009 __Pyx_CyFunction_weakreflist(op) = NULL;
|
|
jpayne@69
|
34010 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34011 cf->m_ml = ml;
|
|
jpayne@69
|
34012 cf->m_self = (PyObject *) op;
|
|
jpayne@69
|
34013 #endif
|
|
jpayne@69
|
34014 Py_XINCREF(closure);
|
|
jpayne@69
|
34015 op->func_closure = closure;
|
|
jpayne@69
|
34016 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34017 Py_XINCREF(module);
|
|
jpayne@69
|
34018 cf->m_module = module;
|
|
jpayne@69
|
34019 #endif
|
|
jpayne@69
|
34020 op->func_dict = NULL;
|
|
jpayne@69
|
34021 op->func_name = NULL;
|
|
jpayne@69
|
34022 Py_INCREF(qualname);
|
|
jpayne@69
|
34023 op->func_qualname = qualname;
|
|
jpayne@69
|
34024 op->func_doc = NULL;
|
|
jpayne@69
|
34025 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34026 op->func_classobj = NULL;
|
|
jpayne@69
|
34027 #else
|
|
jpayne@69
|
34028 ((PyCMethodObject*)op)->mm_class = NULL;
|
|
jpayne@69
|
34029 #endif
|
|
jpayne@69
|
34030 op->func_globals = globals;
|
|
jpayne@69
|
34031 Py_INCREF(op->func_globals);
|
|
jpayne@69
|
34032 Py_XINCREF(code);
|
|
jpayne@69
|
34033 op->func_code = code;
|
|
jpayne@69
|
34034 op->defaults_pyobjects = 0;
|
|
jpayne@69
|
34035 op->defaults_size = 0;
|
|
jpayne@69
|
34036 op->defaults = NULL;
|
|
jpayne@69
|
34037 op->defaults_tuple = NULL;
|
|
jpayne@69
|
34038 op->defaults_kwdict = NULL;
|
|
jpayne@69
|
34039 op->defaults_getter = NULL;
|
|
jpayne@69
|
34040 op->func_annotations = NULL;
|
|
jpayne@69
|
34041 op->func_is_coroutine = NULL;
|
|
jpayne@69
|
34042 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
34043 switch (ml->ml_flags & (METH_VARARGS | METH_FASTCALL | METH_NOARGS | METH_O | METH_KEYWORDS | METH_METHOD)) {
|
|
jpayne@69
|
34044 case METH_NOARGS:
|
|
jpayne@69
|
34045 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_NOARGS;
|
|
jpayne@69
|
34046 break;
|
|
jpayne@69
|
34047 case METH_O:
|
|
jpayne@69
|
34048 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_O;
|
|
jpayne@69
|
34049 break;
|
|
jpayne@69
|
34050 case METH_METHOD | METH_FASTCALL | METH_KEYWORDS:
|
|
jpayne@69
|
34051 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD;
|
|
jpayne@69
|
34052 break;
|
|
jpayne@69
|
34053 case METH_FASTCALL | METH_KEYWORDS:
|
|
jpayne@69
|
34054 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS;
|
|
jpayne@69
|
34055 break;
|
|
jpayne@69
|
34056 case METH_VARARGS | METH_KEYWORDS:
|
|
jpayne@69
|
34057 __Pyx_CyFunction_func_vectorcall(op) = NULL;
|
|
jpayne@69
|
34058 break;
|
|
jpayne@69
|
34059 default:
|
|
jpayne@69
|
34060 PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction");
|
|
jpayne@69
|
34061 Py_DECREF(op);
|
|
jpayne@69
|
34062 return NULL;
|
|
jpayne@69
|
34063 }
|
|
jpayne@69
|
34064 #endif
|
|
jpayne@69
|
34065 return (PyObject *) op;
|
|
jpayne@69
|
34066 }
|
|
jpayne@69
|
34067 static int
|
|
jpayne@69
|
34068 __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
|
|
jpayne@69
|
34069 {
|
|
jpayne@69
|
34070 Py_CLEAR(m->func_closure);
|
|
jpayne@69
|
34071 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34072 Py_CLEAR(m->func);
|
|
jpayne@69
|
34073 #else
|
|
jpayne@69
|
34074 Py_CLEAR(((PyCFunctionObject*)m)->m_module);
|
|
jpayne@69
|
34075 #endif
|
|
jpayne@69
|
34076 Py_CLEAR(m->func_dict);
|
|
jpayne@69
|
34077 Py_CLEAR(m->func_name);
|
|
jpayne@69
|
34078 Py_CLEAR(m->func_qualname);
|
|
jpayne@69
|
34079 Py_CLEAR(m->func_doc);
|
|
jpayne@69
|
34080 Py_CLEAR(m->func_globals);
|
|
jpayne@69
|
34081 Py_CLEAR(m->func_code);
|
|
jpayne@69
|
34082 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34083 #if PY_VERSION_HEX < 0x030900B1
|
|
jpayne@69
|
34084 Py_CLEAR(__Pyx_CyFunction_GetClassObj(m));
|
|
jpayne@69
|
34085 #else
|
|
jpayne@69
|
34086 {
|
|
jpayne@69
|
34087 PyObject *cls = (PyObject*) ((PyCMethodObject *) (m))->mm_class;
|
|
jpayne@69
|
34088 ((PyCMethodObject *) (m))->mm_class = NULL;
|
|
jpayne@69
|
34089 Py_XDECREF(cls);
|
|
jpayne@69
|
34090 }
|
|
jpayne@69
|
34091 #endif
|
|
jpayne@69
|
34092 #endif
|
|
jpayne@69
|
34093 Py_CLEAR(m->defaults_tuple);
|
|
jpayne@69
|
34094 Py_CLEAR(m->defaults_kwdict);
|
|
jpayne@69
|
34095 Py_CLEAR(m->func_annotations);
|
|
jpayne@69
|
34096 Py_CLEAR(m->func_is_coroutine);
|
|
jpayne@69
|
34097 if (m->defaults) {
|
|
jpayne@69
|
34098 PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
|
|
jpayne@69
|
34099 int i;
|
|
jpayne@69
|
34100 for (i = 0; i < m->defaults_pyobjects; i++)
|
|
jpayne@69
|
34101 Py_XDECREF(pydefaults[i]);
|
|
jpayne@69
|
34102 PyObject_Free(m->defaults);
|
|
jpayne@69
|
34103 m->defaults = NULL;
|
|
jpayne@69
|
34104 }
|
|
jpayne@69
|
34105 return 0;
|
|
jpayne@69
|
34106 }
|
|
jpayne@69
|
34107 static void __Pyx__CyFunction_dealloc(__pyx_CyFunctionObject *m)
|
|
jpayne@69
|
34108 {
|
|
jpayne@69
|
34109 if (__Pyx_CyFunction_weakreflist(m) != NULL)
|
|
jpayne@69
|
34110 PyObject_ClearWeakRefs((PyObject *) m);
|
|
jpayne@69
|
34111 __Pyx_CyFunction_clear(m);
|
|
jpayne@69
|
34112 __Pyx_PyHeapTypeObject_GC_Del(m);
|
|
jpayne@69
|
34113 }
|
|
jpayne@69
|
34114 static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
|
|
jpayne@69
|
34115 {
|
|
jpayne@69
|
34116 PyObject_GC_UnTrack(m);
|
|
jpayne@69
|
34117 __Pyx__CyFunction_dealloc(m);
|
|
jpayne@69
|
34118 }
|
|
jpayne@69
|
34119 static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
|
|
jpayne@69
|
34120 {
|
|
jpayne@69
|
34121 Py_VISIT(m->func_closure);
|
|
jpayne@69
|
34122 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34123 Py_VISIT(m->func);
|
|
jpayne@69
|
34124 #else
|
|
jpayne@69
|
34125 Py_VISIT(((PyCFunctionObject*)m)->m_module);
|
|
jpayne@69
|
34126 #endif
|
|
jpayne@69
|
34127 Py_VISIT(m->func_dict);
|
|
jpayne@69
|
34128 Py_VISIT(m->func_name);
|
|
jpayne@69
|
34129 Py_VISIT(m->func_qualname);
|
|
jpayne@69
|
34130 Py_VISIT(m->func_doc);
|
|
jpayne@69
|
34131 Py_VISIT(m->func_globals);
|
|
jpayne@69
|
34132 Py_VISIT(m->func_code);
|
|
jpayne@69
|
34133 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34134 Py_VISIT(__Pyx_CyFunction_GetClassObj(m));
|
|
jpayne@69
|
34135 #endif
|
|
jpayne@69
|
34136 Py_VISIT(m->defaults_tuple);
|
|
jpayne@69
|
34137 Py_VISIT(m->defaults_kwdict);
|
|
jpayne@69
|
34138 Py_VISIT(m->func_is_coroutine);
|
|
jpayne@69
|
34139 if (m->defaults) {
|
|
jpayne@69
|
34140 PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
|
|
jpayne@69
|
34141 int i;
|
|
jpayne@69
|
34142 for (i = 0; i < m->defaults_pyobjects; i++)
|
|
jpayne@69
|
34143 Py_VISIT(pydefaults[i]);
|
|
jpayne@69
|
34144 }
|
|
jpayne@69
|
34145 return 0;
|
|
jpayne@69
|
34146 }
|
|
jpayne@69
|
34147 static PyObject*
|
|
jpayne@69
|
34148 __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
|
|
jpayne@69
|
34149 {
|
|
jpayne@69
|
34150 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
34151 return PyUnicode_FromFormat("<cyfunction %U at %p>",
|
|
jpayne@69
|
34152 op->func_qualname, (void *)op);
|
|
jpayne@69
|
34153 #else
|
|
jpayne@69
|
34154 return PyString_FromFormat("<cyfunction %s at %p>",
|
|
jpayne@69
|
34155 PyString_AsString(op->func_qualname), (void *)op);
|
|
jpayne@69
|
34156 #endif
|
|
jpayne@69
|
34157 }
|
|
jpayne@69
|
34158 static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) {
|
|
jpayne@69
|
34159 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34160 PyObject *f = ((__pyx_CyFunctionObject*)func)->func;
|
|
jpayne@69
|
34161 PyObject *py_name = NULL;
|
|
jpayne@69
|
34162 PyCFunction meth;
|
|
jpayne@69
|
34163 int flags;
|
|
jpayne@69
|
34164 meth = PyCFunction_GetFunction(f);
|
|
jpayne@69
|
34165 if (unlikely(!meth)) return NULL;
|
|
jpayne@69
|
34166 flags = PyCFunction_GetFlags(f);
|
|
jpayne@69
|
34167 if (unlikely(flags < 0)) return NULL;
|
|
jpayne@69
|
34168 #else
|
|
jpayne@69
|
34169 PyCFunctionObject* f = (PyCFunctionObject*)func;
|
|
jpayne@69
|
34170 PyCFunction meth = f->m_ml->ml_meth;
|
|
jpayne@69
|
34171 int flags = f->m_ml->ml_flags;
|
|
jpayne@69
|
34172 #endif
|
|
jpayne@69
|
34173 Py_ssize_t size;
|
|
jpayne@69
|
34174 switch (flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) {
|
|
jpayne@69
|
34175 case METH_VARARGS:
|
|
jpayne@69
|
34176 if (likely(kw == NULL || PyDict_Size(kw) == 0))
|
|
jpayne@69
|
34177 return (*meth)(self, arg);
|
|
jpayne@69
|
34178 break;
|
|
jpayne@69
|
34179 case METH_VARARGS | METH_KEYWORDS:
|
|
jpayne@69
|
34180 return (*(PyCFunctionWithKeywords)(void*)meth)(self, arg, kw);
|
|
jpayne@69
|
34181 case METH_NOARGS:
|
|
jpayne@69
|
34182 if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
|
|
jpayne@69
|
34183 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
34184 size = PyTuple_GET_SIZE(arg);
|
|
jpayne@69
|
34185 #else
|
|
jpayne@69
|
34186 size = PyTuple_Size(arg);
|
|
jpayne@69
|
34187 if (unlikely(size < 0)) return NULL;
|
|
jpayne@69
|
34188 #endif
|
|
jpayne@69
|
34189 if (likely(size == 0))
|
|
jpayne@69
|
34190 return (*meth)(self, NULL);
|
|
jpayne@69
|
34191 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34192 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
|
|
jpayne@69
|
34193 if (!py_name) return NULL;
|
|
jpayne@69
|
34194 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34195 "%.200S() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
34196 py_name, size);
|
|
jpayne@69
|
34197 Py_DECREF(py_name);
|
|
jpayne@69
|
34198 #else
|
|
jpayne@69
|
34199 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34200 "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
34201 f->m_ml->ml_name, size);
|
|
jpayne@69
|
34202 #endif
|
|
jpayne@69
|
34203 return NULL;
|
|
jpayne@69
|
34204 }
|
|
jpayne@69
|
34205 break;
|
|
jpayne@69
|
34206 case METH_O:
|
|
jpayne@69
|
34207 if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
|
|
jpayne@69
|
34208 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
34209 size = PyTuple_GET_SIZE(arg);
|
|
jpayne@69
|
34210 #else
|
|
jpayne@69
|
34211 size = PyTuple_Size(arg);
|
|
jpayne@69
|
34212 if (unlikely(size < 0)) return NULL;
|
|
jpayne@69
|
34213 #endif
|
|
jpayne@69
|
34214 if (likely(size == 1)) {
|
|
jpayne@69
|
34215 PyObject *result, *arg0;
|
|
jpayne@69
|
34216 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
34217 arg0 = PyTuple_GET_ITEM(arg, 0);
|
|
jpayne@69
|
34218 #else
|
|
jpayne@69
|
34219 arg0 = __Pyx_PySequence_ITEM(arg, 0); if (unlikely(!arg0)) return NULL;
|
|
jpayne@69
|
34220 #endif
|
|
jpayne@69
|
34221 result = (*meth)(self, arg0);
|
|
jpayne@69
|
34222 #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS)
|
|
jpayne@69
|
34223 Py_DECREF(arg0);
|
|
jpayne@69
|
34224 #endif
|
|
jpayne@69
|
34225 return result;
|
|
jpayne@69
|
34226 }
|
|
jpayne@69
|
34227 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34228 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
|
|
jpayne@69
|
34229 if (!py_name) return NULL;
|
|
jpayne@69
|
34230 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34231 "%.200S() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
34232 py_name, size);
|
|
jpayne@69
|
34233 Py_DECREF(py_name);
|
|
jpayne@69
|
34234 #else
|
|
jpayne@69
|
34235 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34236 "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
34237 f->m_ml->ml_name, size);
|
|
jpayne@69
|
34238 #endif
|
|
jpayne@69
|
34239 return NULL;
|
|
jpayne@69
|
34240 }
|
|
jpayne@69
|
34241 break;
|
|
jpayne@69
|
34242 default:
|
|
jpayne@69
|
34243 PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction");
|
|
jpayne@69
|
34244 return NULL;
|
|
jpayne@69
|
34245 }
|
|
jpayne@69
|
34246 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34247 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
|
|
jpayne@69
|
34248 if (!py_name) return NULL;
|
|
jpayne@69
|
34249 PyErr_Format(PyExc_TypeError, "%.200S() takes no keyword arguments",
|
|
jpayne@69
|
34250 py_name);
|
|
jpayne@69
|
34251 Py_DECREF(py_name);
|
|
jpayne@69
|
34252 #else
|
|
jpayne@69
|
34253 PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
|
|
jpayne@69
|
34254 f->m_ml->ml_name);
|
|
jpayne@69
|
34255 #endif
|
|
jpayne@69
|
34256 return NULL;
|
|
jpayne@69
|
34257 }
|
|
jpayne@69
|
34258 static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
|
|
jpayne@69
|
34259 PyObject *self, *result;
|
|
jpayne@69
|
34260 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34261 self = PyCFunction_GetSelf(((__pyx_CyFunctionObject*)func)->func);
|
|
jpayne@69
|
34262 if (unlikely(!self) && PyErr_Occurred()) return NULL;
|
|
jpayne@69
|
34263 #else
|
|
jpayne@69
|
34264 self = ((PyCFunctionObject*)func)->m_self;
|
|
jpayne@69
|
34265 #endif
|
|
jpayne@69
|
34266 result = __Pyx_CyFunction_CallMethod(func, self, arg, kw);
|
|
jpayne@69
|
34267 return result;
|
|
jpayne@69
|
34268 }
|
|
jpayne@69
|
34269 static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) {
|
|
jpayne@69
|
34270 PyObject *result;
|
|
jpayne@69
|
34271 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
34272 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
34273 __pyx_vectorcallfunc vc = __Pyx_CyFunction_func_vectorcall(cyfunc);
|
|
jpayne@69
|
34274 if (vc) {
|
|
jpayne@69
|
34275 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
34276 return __Pyx_PyVectorcall_FastCallDict(func, vc, &PyTuple_GET_ITEM(args, 0), (size_t)PyTuple_GET_SIZE(args), kw);
|
|
jpayne@69
|
34277 #else
|
|
jpayne@69
|
34278 (void) &__Pyx_PyVectorcall_FastCallDict;
|
|
jpayne@69
|
34279 return PyVectorcall_Call(func, args, kw);
|
|
jpayne@69
|
34280 #endif
|
|
jpayne@69
|
34281 }
|
|
jpayne@69
|
34282 #endif
|
|
jpayne@69
|
34283 if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) {
|
|
jpayne@69
|
34284 Py_ssize_t argc;
|
|
jpayne@69
|
34285 PyObject *new_args;
|
|
jpayne@69
|
34286 PyObject *self;
|
|
jpayne@69
|
34287 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
34288 argc = PyTuple_GET_SIZE(args);
|
|
jpayne@69
|
34289 #else
|
|
jpayne@69
|
34290 argc = PyTuple_Size(args);
|
|
jpayne@69
|
34291 if (unlikely(!argc) < 0) return NULL;
|
|
jpayne@69
|
34292 #endif
|
|
jpayne@69
|
34293 new_args = PyTuple_GetSlice(args, 1, argc);
|
|
jpayne@69
|
34294 if (unlikely(!new_args))
|
|
jpayne@69
|
34295 return NULL;
|
|
jpayne@69
|
34296 self = PyTuple_GetItem(args, 0);
|
|
jpayne@69
|
34297 if (unlikely(!self)) {
|
|
jpayne@69
|
34298 Py_DECREF(new_args);
|
|
jpayne@69
|
34299 #if PY_MAJOR_VERSION > 2
|
|
jpayne@69
|
34300 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34301 "unbound method %.200S() needs an argument",
|
|
jpayne@69
|
34302 cyfunc->func_qualname);
|
|
jpayne@69
|
34303 #else
|
|
jpayne@69
|
34304 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
34305 "unbound method needs an argument");
|
|
jpayne@69
|
34306 #endif
|
|
jpayne@69
|
34307 return NULL;
|
|
jpayne@69
|
34308 }
|
|
jpayne@69
|
34309 result = __Pyx_CyFunction_CallMethod(func, self, new_args, kw);
|
|
jpayne@69
|
34310 Py_DECREF(new_args);
|
|
jpayne@69
|
34311 } else {
|
|
jpayne@69
|
34312 result = __Pyx_CyFunction_Call(func, args, kw);
|
|
jpayne@69
|
34313 }
|
|
jpayne@69
|
34314 return result;
|
|
jpayne@69
|
34315 }
|
|
jpayne@69
|
34316 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
34317 static CYTHON_INLINE int __Pyx_CyFunction_Vectorcall_CheckArgs(__pyx_CyFunctionObject *cyfunc, Py_ssize_t nargs, PyObject *kwnames)
|
|
jpayne@69
|
34318 {
|
|
jpayne@69
|
34319 int ret = 0;
|
|
jpayne@69
|
34320 if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) {
|
|
jpayne@69
|
34321 if (unlikely(nargs < 1)) {
|
|
jpayne@69
|
34322 PyErr_Format(PyExc_TypeError, "%.200s() needs an argument",
|
|
jpayne@69
|
34323 ((PyCFunctionObject*)cyfunc)->m_ml->ml_name);
|
|
jpayne@69
|
34324 return -1;
|
|
jpayne@69
|
34325 }
|
|
jpayne@69
|
34326 ret = 1;
|
|
jpayne@69
|
34327 }
|
|
jpayne@69
|
34328 if (unlikely(kwnames) && unlikely(PyTuple_GET_SIZE(kwnames))) {
|
|
jpayne@69
|
34329 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34330 "%.200s() takes no keyword arguments", ((PyCFunctionObject*)cyfunc)->m_ml->ml_name);
|
|
jpayne@69
|
34331 return -1;
|
|
jpayne@69
|
34332 }
|
|
jpayne@69
|
34333 return ret;
|
|
jpayne@69
|
34334 }
|
|
jpayne@69
|
34335 static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
34336 {
|
|
jpayne@69
|
34337 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
34338 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
34339 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
34340 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
34341 #else
|
|
jpayne@69
|
34342 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
34343 #endif
|
|
jpayne@69
|
34344 PyObject *self;
|
|
jpayne@69
|
34345 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) {
|
|
jpayne@69
|
34346 case 1:
|
|
jpayne@69
|
34347 self = args[0];
|
|
jpayne@69
|
34348 args += 1;
|
|
jpayne@69
|
34349 nargs -= 1;
|
|
jpayne@69
|
34350 break;
|
|
jpayne@69
|
34351 case 0:
|
|
jpayne@69
|
34352 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
34353 break;
|
|
jpayne@69
|
34354 default:
|
|
jpayne@69
|
34355 return NULL;
|
|
jpayne@69
|
34356 }
|
|
jpayne@69
|
34357 if (unlikely(nargs != 0)) {
|
|
jpayne@69
|
34358 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34359 "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
34360 def->ml_name, nargs);
|
|
jpayne@69
|
34361 return NULL;
|
|
jpayne@69
|
34362 }
|
|
jpayne@69
|
34363 return def->ml_meth(self, NULL);
|
|
jpayne@69
|
34364 }
|
|
jpayne@69
|
34365 static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
34366 {
|
|
jpayne@69
|
34367 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
34368 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
34369 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
34370 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
34371 #else
|
|
jpayne@69
|
34372 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
34373 #endif
|
|
jpayne@69
|
34374 PyObject *self;
|
|
jpayne@69
|
34375 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) {
|
|
jpayne@69
|
34376 case 1:
|
|
jpayne@69
|
34377 self = args[0];
|
|
jpayne@69
|
34378 args += 1;
|
|
jpayne@69
|
34379 nargs -= 1;
|
|
jpayne@69
|
34380 break;
|
|
jpayne@69
|
34381 case 0:
|
|
jpayne@69
|
34382 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
34383 break;
|
|
jpayne@69
|
34384 default:
|
|
jpayne@69
|
34385 return NULL;
|
|
jpayne@69
|
34386 }
|
|
jpayne@69
|
34387 if (unlikely(nargs != 1)) {
|
|
jpayne@69
|
34388 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
34389 "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
34390 def->ml_name, nargs);
|
|
jpayne@69
|
34391 return NULL;
|
|
jpayne@69
|
34392 }
|
|
jpayne@69
|
34393 return def->ml_meth(self, args[0]);
|
|
jpayne@69
|
34394 }
|
|
jpayne@69
|
34395 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
34396 {
|
|
jpayne@69
|
34397 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
34398 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
34399 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
34400 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
34401 #else
|
|
jpayne@69
|
34402 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
34403 #endif
|
|
jpayne@69
|
34404 PyObject *self;
|
|
jpayne@69
|
34405 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) {
|
|
jpayne@69
|
34406 case 1:
|
|
jpayne@69
|
34407 self = args[0];
|
|
jpayne@69
|
34408 args += 1;
|
|
jpayne@69
|
34409 nargs -= 1;
|
|
jpayne@69
|
34410 break;
|
|
jpayne@69
|
34411 case 0:
|
|
jpayne@69
|
34412 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
34413 break;
|
|
jpayne@69
|
34414 default:
|
|
jpayne@69
|
34415 return NULL;
|
|
jpayne@69
|
34416 }
|
|
jpayne@69
|
34417 return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
|
|
jpayne@69
|
34418 }
|
|
jpayne@69
|
34419 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
34420 {
|
|
jpayne@69
|
34421 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
34422 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
34423 PyTypeObject *cls = (PyTypeObject *) __Pyx_CyFunction_GetClassObj(cyfunc);
|
|
jpayne@69
|
34424 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
34425 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
34426 #else
|
|
jpayne@69
|
34427 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
34428 #endif
|
|
jpayne@69
|
34429 PyObject *self;
|
|
jpayne@69
|
34430 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) {
|
|
jpayne@69
|
34431 case 1:
|
|
jpayne@69
|
34432 self = args[0];
|
|
jpayne@69
|
34433 args += 1;
|
|
jpayne@69
|
34434 nargs -= 1;
|
|
jpayne@69
|
34435 break;
|
|
jpayne@69
|
34436 case 0:
|
|
jpayne@69
|
34437 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
34438 break;
|
|
jpayne@69
|
34439 default:
|
|
jpayne@69
|
34440 return NULL;
|
|
jpayne@69
|
34441 }
|
|
jpayne@69
|
34442 return ((__Pyx_PyCMethod)(void(*)(void))def->ml_meth)(self, cls, args, (size_t)nargs, kwnames);
|
|
jpayne@69
|
34443 }
|
|
jpayne@69
|
34444 #endif
|
|
jpayne@69
|
34445 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
34446 static PyType_Slot __pyx_CyFunctionType_slots[] = {
|
|
jpayne@69
|
34447 {Py_tp_dealloc, (void *)__Pyx_CyFunction_dealloc},
|
|
jpayne@69
|
34448 {Py_tp_repr, (void *)__Pyx_CyFunction_repr},
|
|
jpayne@69
|
34449 {Py_tp_call, (void *)__Pyx_CyFunction_CallAsMethod},
|
|
jpayne@69
|
34450 {Py_tp_traverse, (void *)__Pyx_CyFunction_traverse},
|
|
jpayne@69
|
34451 {Py_tp_clear, (void *)__Pyx_CyFunction_clear},
|
|
jpayne@69
|
34452 {Py_tp_methods, (void *)__pyx_CyFunction_methods},
|
|
jpayne@69
|
34453 {Py_tp_members, (void *)__pyx_CyFunction_members},
|
|
jpayne@69
|
34454 {Py_tp_getset, (void *)__pyx_CyFunction_getsets},
|
|
jpayne@69
|
34455 {Py_tp_descr_get, (void *)__Pyx_PyMethod_New},
|
|
jpayne@69
|
34456 {0, 0},
|
|
jpayne@69
|
34457 };
|
|
jpayne@69
|
34458 static PyType_Spec __pyx_CyFunctionType_spec = {
|
|
jpayne@69
|
34459 __PYX_TYPE_MODULE_PREFIX "cython_function_or_method",
|
|
jpayne@69
|
34460 sizeof(__pyx_CyFunctionObject),
|
|
jpayne@69
|
34461 0,
|
|
jpayne@69
|
34462 #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR
|
|
jpayne@69
|
34463 Py_TPFLAGS_METHOD_DESCRIPTOR |
|
|
jpayne@69
|
34464 #endif
|
|
jpayne@69
|
34465 #if (defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL)
|
|
jpayne@69
|
34466 _Py_TPFLAGS_HAVE_VECTORCALL |
|
|
jpayne@69
|
34467 #endif
|
|
jpayne@69
|
34468 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE,
|
|
jpayne@69
|
34469 __pyx_CyFunctionType_slots
|
|
jpayne@69
|
34470 };
|
|
jpayne@69
|
34471 #else
|
|
jpayne@69
|
34472 static PyTypeObject __pyx_CyFunctionType_type = {
|
|
jpayne@69
|
34473 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
34474 __PYX_TYPE_MODULE_PREFIX "cython_function_or_method",
|
|
jpayne@69
|
34475 sizeof(__pyx_CyFunctionObject),
|
|
jpayne@69
|
34476 0,
|
|
jpayne@69
|
34477 (destructor) __Pyx_CyFunction_dealloc,
|
|
jpayne@69
|
34478 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
34479 0,
|
|
jpayne@69
|
34480 #elif CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
34481 (printfunc)offsetof(__pyx_CyFunctionObject, func_vectorcall),
|
|
jpayne@69
|
34482 #else
|
|
jpayne@69
|
34483 offsetof(PyCFunctionObject, vectorcall),
|
|
jpayne@69
|
34484 #endif
|
|
jpayne@69
|
34485 0,
|
|
jpayne@69
|
34486 0,
|
|
jpayne@69
|
34487 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
34488 0,
|
|
jpayne@69
|
34489 #else
|
|
jpayne@69
|
34490 0,
|
|
jpayne@69
|
34491 #endif
|
|
jpayne@69
|
34492 (reprfunc) __Pyx_CyFunction_repr,
|
|
jpayne@69
|
34493 0,
|
|
jpayne@69
|
34494 0,
|
|
jpayne@69
|
34495 0,
|
|
jpayne@69
|
34496 0,
|
|
jpayne@69
|
34497 __Pyx_CyFunction_CallAsMethod,
|
|
jpayne@69
|
34498 0,
|
|
jpayne@69
|
34499 0,
|
|
jpayne@69
|
34500 0,
|
|
jpayne@69
|
34501 0,
|
|
jpayne@69
|
34502 #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR
|
|
jpayne@69
|
34503 Py_TPFLAGS_METHOD_DESCRIPTOR |
|
|
jpayne@69
|
34504 #endif
|
|
jpayne@69
|
34505 #if defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL
|
|
jpayne@69
|
34506 _Py_TPFLAGS_HAVE_VECTORCALL |
|
|
jpayne@69
|
34507 #endif
|
|
jpayne@69
|
34508 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE,
|
|
jpayne@69
|
34509 0,
|
|
jpayne@69
|
34510 (traverseproc) __Pyx_CyFunction_traverse,
|
|
jpayne@69
|
34511 (inquiry) __Pyx_CyFunction_clear,
|
|
jpayne@69
|
34512 0,
|
|
jpayne@69
|
34513 #if PY_VERSION_HEX < 0x030500A0
|
|
jpayne@69
|
34514 offsetof(__pyx_CyFunctionObject, func_weakreflist),
|
|
jpayne@69
|
34515 #else
|
|
jpayne@69
|
34516 offsetof(PyCFunctionObject, m_weakreflist),
|
|
jpayne@69
|
34517 #endif
|
|
jpayne@69
|
34518 0,
|
|
jpayne@69
|
34519 0,
|
|
jpayne@69
|
34520 __pyx_CyFunction_methods,
|
|
jpayne@69
|
34521 __pyx_CyFunction_members,
|
|
jpayne@69
|
34522 __pyx_CyFunction_getsets,
|
|
jpayne@69
|
34523 0,
|
|
jpayne@69
|
34524 0,
|
|
jpayne@69
|
34525 __Pyx_PyMethod_New,
|
|
jpayne@69
|
34526 0,
|
|
jpayne@69
|
34527 offsetof(__pyx_CyFunctionObject, func_dict),
|
|
jpayne@69
|
34528 0,
|
|
jpayne@69
|
34529 0,
|
|
jpayne@69
|
34530 0,
|
|
jpayne@69
|
34531 0,
|
|
jpayne@69
|
34532 0,
|
|
jpayne@69
|
34533 0,
|
|
jpayne@69
|
34534 0,
|
|
jpayne@69
|
34535 0,
|
|
jpayne@69
|
34536 0,
|
|
jpayne@69
|
34537 0,
|
|
jpayne@69
|
34538 0,
|
|
jpayne@69
|
34539 0,
|
|
jpayne@69
|
34540 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
34541 0,
|
|
jpayne@69
|
34542 #endif
|
|
jpayne@69
|
34543 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
34544 0,
|
|
jpayne@69
|
34545 #endif
|
|
jpayne@69
|
34546 #if __PYX_NEED_TP_PRINT_SLOT
|
|
jpayne@69
|
34547 0,
|
|
jpayne@69
|
34548 #endif
|
|
jpayne@69
|
34549 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
34550 0,
|
|
jpayne@69
|
34551 #endif
|
|
jpayne@69
|
34552 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
34553 0,
|
|
jpayne@69
|
34554 #endif
|
|
jpayne@69
|
34555 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
34556 0,
|
|
jpayne@69
|
34557 #endif
|
|
jpayne@69
|
34558 };
|
|
jpayne@69
|
34559 #endif
|
|
jpayne@69
|
34560 static int __pyx_CyFunction_init(PyObject *module) {
|
|
jpayne@69
|
34561 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
34562 __pyx_CyFunctionType = __Pyx_FetchCommonTypeFromSpec(module, &__pyx_CyFunctionType_spec, NULL);
|
|
jpayne@69
|
34563 #else
|
|
jpayne@69
|
34564 CYTHON_UNUSED_VAR(module);
|
|
jpayne@69
|
34565 __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
|
|
jpayne@69
|
34566 #endif
|
|
jpayne@69
|
34567 if (unlikely(__pyx_CyFunctionType == NULL)) {
|
|
jpayne@69
|
34568 return -1;
|
|
jpayne@69
|
34569 }
|
|
jpayne@69
|
34570 return 0;
|
|
jpayne@69
|
34571 }
|
|
jpayne@69
|
34572 static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
|
|
jpayne@69
|
34573 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
34574 m->defaults = PyObject_Malloc(size);
|
|
jpayne@69
|
34575 if (unlikely(!m->defaults))
|
|
jpayne@69
|
34576 return PyErr_NoMemory();
|
|
jpayne@69
|
34577 memset(m->defaults, 0, size);
|
|
jpayne@69
|
34578 m->defaults_pyobjects = pyobjects;
|
|
jpayne@69
|
34579 m->defaults_size = size;
|
|
jpayne@69
|
34580 return m->defaults;
|
|
jpayne@69
|
34581 }
|
|
jpayne@69
|
34582 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
|
|
jpayne@69
|
34583 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
34584 m->defaults_tuple = tuple;
|
|
jpayne@69
|
34585 Py_INCREF(tuple);
|
|
jpayne@69
|
34586 }
|
|
jpayne@69
|
34587 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
|
|
jpayne@69
|
34588 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
34589 m->defaults_kwdict = dict;
|
|
jpayne@69
|
34590 Py_INCREF(dict);
|
|
jpayne@69
|
34591 }
|
|
jpayne@69
|
34592 static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
|
|
jpayne@69
|
34593 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
34594 m->func_annotations = dict;
|
|
jpayne@69
|
34595 Py_INCREF(dict);
|
|
jpayne@69
|
34596 }
|
|
jpayne@69
|
34597
|
|
jpayne@69
|
34598 /* CythonFunction */
|
|
jpayne@69
|
34599 static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, int flags, PyObject* qualname,
|
|
jpayne@69
|
34600 PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
|
|
jpayne@69
|
34601 PyObject *op = __Pyx_CyFunction_Init(
|
|
jpayne@69
|
34602 PyObject_GC_New(__pyx_CyFunctionObject, __pyx_CyFunctionType),
|
|
jpayne@69
|
34603 ml, flags, qualname, closure, module, globals, code
|
|
jpayne@69
|
34604 );
|
|
jpayne@69
|
34605 if (likely(op)) {
|
|
jpayne@69
|
34606 PyObject_GC_Track(op);
|
|
jpayne@69
|
34607 }
|
|
jpayne@69
|
34608 return op;
|
|
jpayne@69
|
34609 }
|
|
jpayne@69
|
34610
|
|
jpayne@69
|
34611 /* CalculateMetaclass */
|
|
jpayne@69
|
34612 static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
|
|
jpayne@69
|
34613 Py_ssize_t i, nbases;
|
|
jpayne@69
|
34614 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
34615 nbases = PyTuple_GET_SIZE(bases);
|
|
jpayne@69
|
34616 #else
|
|
jpayne@69
|
34617 nbases = PyTuple_Size(bases);
|
|
jpayne@69
|
34618 if (nbases < 0) return NULL;
|
|
jpayne@69
|
34619 #endif
|
|
jpayne@69
|
34620 for (i=0; i < nbases; i++) {
|
|
jpayne@69
|
34621 PyTypeObject *tmptype;
|
|
jpayne@69
|
34622 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
34623 PyObject *tmp = PyTuple_GET_ITEM(bases, i);
|
|
jpayne@69
|
34624 #else
|
|
jpayne@69
|
34625 PyObject *tmp = PyTuple_GetItem(bases, i);
|
|
jpayne@69
|
34626 if (!tmp) return NULL;
|
|
jpayne@69
|
34627 #endif
|
|
jpayne@69
|
34628 tmptype = Py_TYPE(tmp);
|
|
jpayne@69
|
34629 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
34630 if (tmptype == &PyClass_Type)
|
|
jpayne@69
|
34631 continue;
|
|
jpayne@69
|
34632 #endif
|
|
jpayne@69
|
34633 if (!metaclass) {
|
|
jpayne@69
|
34634 metaclass = tmptype;
|
|
jpayne@69
|
34635 continue;
|
|
jpayne@69
|
34636 }
|
|
jpayne@69
|
34637 if (PyType_IsSubtype(metaclass, tmptype))
|
|
jpayne@69
|
34638 continue;
|
|
jpayne@69
|
34639 if (PyType_IsSubtype(tmptype, metaclass)) {
|
|
jpayne@69
|
34640 metaclass = tmptype;
|
|
jpayne@69
|
34641 continue;
|
|
jpayne@69
|
34642 }
|
|
jpayne@69
|
34643 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
34644 "metaclass conflict: "
|
|
jpayne@69
|
34645 "the metaclass of a derived class "
|
|
jpayne@69
|
34646 "must be a (non-strict) subclass "
|
|
jpayne@69
|
34647 "of the metaclasses of all its bases");
|
|
jpayne@69
|
34648 return NULL;
|
|
jpayne@69
|
34649 }
|
|
jpayne@69
|
34650 if (!metaclass) {
|
|
jpayne@69
|
34651 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
34652 metaclass = &PyClass_Type;
|
|
jpayne@69
|
34653 #else
|
|
jpayne@69
|
34654 metaclass = &PyType_Type;
|
|
jpayne@69
|
34655 #endif
|
|
jpayne@69
|
34656 }
|
|
jpayne@69
|
34657 Py_INCREF((PyObject*) metaclass);
|
|
jpayne@69
|
34658 return (PyObject*) metaclass;
|
|
jpayne@69
|
34659 }
|
|
jpayne@69
|
34660
|
|
jpayne@69
|
34661 /* PyObjectCall2Args */
|
|
jpayne@69
|
34662 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) {
|
|
jpayne@69
|
34663 PyObject *args[3] = {NULL, arg1, arg2};
|
|
jpayne@69
|
34664 return __Pyx_PyObject_FastCall(function, args+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
|
|
jpayne@69
|
34665 }
|
|
jpayne@69
|
34666
|
|
jpayne@69
|
34667 /* PyObjectLookupSpecial */
|
|
jpayne@69
|
34668 #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
34669 static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error) {
|
|
jpayne@69
|
34670 PyObject *res;
|
|
jpayne@69
|
34671 PyTypeObject *tp = Py_TYPE(obj);
|
|
jpayne@69
|
34672 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
34673 if (unlikely(PyInstance_Check(obj)))
|
|
jpayne@69
|
34674 return with_error ? __Pyx_PyObject_GetAttrStr(obj, attr_name) : __Pyx_PyObject_GetAttrStrNoError(obj, attr_name);
|
|
jpayne@69
|
34675 #endif
|
|
jpayne@69
|
34676 res = _PyType_Lookup(tp, attr_name);
|
|
jpayne@69
|
34677 if (likely(res)) {
|
|
jpayne@69
|
34678 descrgetfunc f = Py_TYPE(res)->tp_descr_get;
|
|
jpayne@69
|
34679 if (!f) {
|
|
jpayne@69
|
34680 Py_INCREF(res);
|
|
jpayne@69
|
34681 } else {
|
|
jpayne@69
|
34682 res = f(res, obj, (PyObject *)tp);
|
|
jpayne@69
|
34683 }
|
|
jpayne@69
|
34684 } else if (with_error) {
|
|
jpayne@69
|
34685 PyErr_SetObject(PyExc_AttributeError, attr_name);
|
|
jpayne@69
|
34686 }
|
|
jpayne@69
|
34687 return res;
|
|
jpayne@69
|
34688 }
|
|
jpayne@69
|
34689 #endif
|
|
jpayne@69
|
34690
|
|
jpayne@69
|
34691 /* Py3ClassCreate */
|
|
jpayne@69
|
34692 static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
|
|
jpayne@69
|
34693 PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
|
|
jpayne@69
|
34694 PyObject *ns;
|
|
jpayne@69
|
34695 if (metaclass) {
|
|
jpayne@69
|
34696 PyObject *prep = __Pyx_PyObject_GetAttrStrNoError(metaclass, __pyx_n_s_prepare);
|
|
jpayne@69
|
34697 if (prep) {
|
|
jpayne@69
|
34698 PyObject *pargs[3] = {NULL, name, bases};
|
|
jpayne@69
|
34699 ns = __Pyx_PyObject_FastCallDict(prep, pargs+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, mkw);
|
|
jpayne@69
|
34700 Py_DECREF(prep);
|
|
jpayne@69
|
34701 } else {
|
|
jpayne@69
|
34702 if (unlikely(PyErr_Occurred()))
|
|
jpayne@69
|
34703 return NULL;
|
|
jpayne@69
|
34704 ns = PyDict_New();
|
|
jpayne@69
|
34705 }
|
|
jpayne@69
|
34706 } else {
|
|
jpayne@69
|
34707 ns = PyDict_New();
|
|
jpayne@69
|
34708 }
|
|
jpayne@69
|
34709 if (unlikely(!ns))
|
|
jpayne@69
|
34710 return NULL;
|
|
jpayne@69
|
34711 if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad;
|
|
jpayne@69
|
34712 #if PY_VERSION_HEX >= 0x03030000
|
|
jpayne@69
|
34713 if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad;
|
|
jpayne@69
|
34714 #else
|
|
jpayne@69
|
34715 CYTHON_MAYBE_UNUSED_VAR(qualname);
|
|
jpayne@69
|
34716 #endif
|
|
jpayne@69
|
34717 if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad;
|
|
jpayne@69
|
34718 return ns;
|
|
jpayne@69
|
34719 bad:
|
|
jpayne@69
|
34720 Py_DECREF(ns);
|
|
jpayne@69
|
34721 return NULL;
|
|
jpayne@69
|
34722 }
|
|
jpayne@69
|
34723 #if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS
|
|
jpayne@69
|
34724 static int __Pyx_SetNamesPEP487(PyObject *type_obj) {
|
|
jpayne@69
|
34725 PyTypeObject *type = (PyTypeObject*) type_obj;
|
|
jpayne@69
|
34726 PyObject *names_to_set, *key, *value, *set_name, *tmp;
|
|
jpayne@69
|
34727 Py_ssize_t i = 0;
|
|
jpayne@69
|
34728 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
34729 names_to_set = PyDict_Copy(type->tp_dict);
|
|
jpayne@69
|
34730 #else
|
|
jpayne@69
|
34731 {
|
|
jpayne@69
|
34732 PyObject *d = PyObject_GetAttr(type_obj, __pyx_n_s_dict);
|
|
jpayne@69
|
34733 names_to_set = NULL;
|
|
jpayne@69
|
34734 if (likely(d)) {
|
|
jpayne@69
|
34735 PyObject *names_to_set = PyDict_New();
|
|
jpayne@69
|
34736 int ret = likely(names_to_set) ? PyDict_Update(names_to_set, d) : -1;
|
|
jpayne@69
|
34737 Py_DECREF(d);
|
|
jpayne@69
|
34738 if (unlikely(ret < 0))
|
|
jpayne@69
|
34739 Py_CLEAR(names_to_set);
|
|
jpayne@69
|
34740 }
|
|
jpayne@69
|
34741 }
|
|
jpayne@69
|
34742 #endif
|
|
jpayne@69
|
34743 if (unlikely(names_to_set == NULL))
|
|
jpayne@69
|
34744 goto bad;
|
|
jpayne@69
|
34745 while (PyDict_Next(names_to_set, &i, &key, &value)) {
|
|
jpayne@69
|
34746 set_name = __Pyx_PyObject_LookupSpecialNoError(value, __pyx_n_s_set_name);
|
|
jpayne@69
|
34747 if (unlikely(set_name != NULL)) {
|
|
jpayne@69
|
34748 tmp = __Pyx_PyObject_Call2Args(set_name, type_obj, key);
|
|
jpayne@69
|
34749 Py_DECREF(set_name);
|
|
jpayne@69
|
34750 if (unlikely(tmp == NULL)) {
|
|
jpayne@69
|
34751 __Pyx_TypeName value_type_name =
|
|
jpayne@69
|
34752 __Pyx_PyType_GetName(Py_TYPE(value));
|
|
jpayne@69
|
34753 __Pyx_TypeName type_name = __Pyx_PyType_GetName(type);
|
|
jpayne@69
|
34754 PyErr_Format(PyExc_RuntimeError,
|
|
jpayne@69
|
34755 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
34756 "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %R " "in '" __Pyx_FMT_TYPENAME "'",
|
|
jpayne@69
|
34757 value_type_name, key, type_name);
|
|
jpayne@69
|
34758 #else
|
|
jpayne@69
|
34759 "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %.100s in '" __Pyx_FMT_TYPENAME "'",
|
|
jpayne@69
|
34760 value_type_name,
|
|
jpayne@69
|
34761 PyString_Check(key) ? PyString_AS_STRING(key) : "?",
|
|
jpayne@69
|
34762 type_name);
|
|
jpayne@69
|
34763 #endif
|
|
jpayne@69
|
34764 goto bad;
|
|
jpayne@69
|
34765 } else {
|
|
jpayne@69
|
34766 Py_DECREF(tmp);
|
|
jpayne@69
|
34767 }
|
|
jpayne@69
|
34768 }
|
|
jpayne@69
|
34769 else if (unlikely(PyErr_Occurred())) {
|
|
jpayne@69
|
34770 goto bad;
|
|
jpayne@69
|
34771 }
|
|
jpayne@69
|
34772 }
|
|
jpayne@69
|
34773 Py_DECREF(names_to_set);
|
|
jpayne@69
|
34774 return 0;
|
|
jpayne@69
|
34775 bad:
|
|
jpayne@69
|
34776 Py_XDECREF(names_to_set);
|
|
jpayne@69
|
34777 return -1;
|
|
jpayne@69
|
34778 }
|
|
jpayne@69
|
34779 static PyObject *__Pyx_InitSubclassPEP487(PyObject *type_obj, PyObject *mkw) {
|
|
jpayne@69
|
34780 #if CYTHON_USE_TYPE_SLOTS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
34781 PyTypeObject *type = (PyTypeObject*) type_obj;
|
|
jpayne@69
|
34782 PyObject *mro = type->tp_mro;
|
|
jpayne@69
|
34783 Py_ssize_t i, nbases;
|
|
jpayne@69
|
34784 if (unlikely(!mro)) goto done;
|
|
jpayne@69
|
34785 (void) &__Pyx_GetBuiltinName;
|
|
jpayne@69
|
34786 Py_INCREF(mro);
|
|
jpayne@69
|
34787 nbases = PyTuple_GET_SIZE(mro);
|
|
jpayne@69
|
34788 assert(PyTuple_GET_ITEM(mro, 0) == type_obj);
|
|
jpayne@69
|
34789 for (i = 1; i < nbases-1; i++) {
|
|
jpayne@69
|
34790 PyObject *base, *dict, *meth;
|
|
jpayne@69
|
34791 base = PyTuple_GET_ITEM(mro, i);
|
|
jpayne@69
|
34792 dict = ((PyTypeObject *)base)->tp_dict;
|
|
jpayne@69
|
34793 meth = __Pyx_PyDict_GetItemStrWithError(dict, __pyx_n_s_init_subclass);
|
|
jpayne@69
|
34794 if (unlikely(meth)) {
|
|
jpayne@69
|
34795 descrgetfunc f = Py_TYPE(meth)->tp_descr_get;
|
|
jpayne@69
|
34796 PyObject *res;
|
|
jpayne@69
|
34797 Py_INCREF(meth);
|
|
jpayne@69
|
34798 if (likely(f)) {
|
|
jpayne@69
|
34799 res = f(meth, NULL, type_obj);
|
|
jpayne@69
|
34800 Py_DECREF(meth);
|
|
jpayne@69
|
34801 if (unlikely(!res)) goto bad;
|
|
jpayne@69
|
34802 meth = res;
|
|
jpayne@69
|
34803 }
|
|
jpayne@69
|
34804 res = __Pyx_PyObject_FastCallDict(meth, NULL, 0, mkw);
|
|
jpayne@69
|
34805 Py_DECREF(meth);
|
|
jpayne@69
|
34806 if (unlikely(!res)) goto bad;
|
|
jpayne@69
|
34807 Py_DECREF(res);
|
|
jpayne@69
|
34808 goto done;
|
|
jpayne@69
|
34809 } else if (unlikely(PyErr_Occurred())) {
|
|
jpayne@69
|
34810 goto bad;
|
|
jpayne@69
|
34811 }
|
|
jpayne@69
|
34812 }
|
|
jpayne@69
|
34813 done:
|
|
jpayne@69
|
34814 Py_XDECREF(mro);
|
|
jpayne@69
|
34815 return type_obj;
|
|
jpayne@69
|
34816 bad:
|
|
jpayne@69
|
34817 Py_XDECREF(mro);
|
|
jpayne@69
|
34818 Py_DECREF(type_obj);
|
|
jpayne@69
|
34819 return NULL;
|
|
jpayne@69
|
34820 #else
|
|
jpayne@69
|
34821 PyObject *super_type, *super, *func, *res;
|
|
jpayne@69
|
34822 #if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type)
|
|
jpayne@69
|
34823 super_type = __Pyx_GetBuiltinName(__pyx_n_s_super);
|
|
jpayne@69
|
34824 #else
|
|
jpayne@69
|
34825 super_type = (PyObject*) &PySuper_Type;
|
|
jpayne@69
|
34826 (void) &__Pyx_GetBuiltinName;
|
|
jpayne@69
|
34827 #endif
|
|
jpayne@69
|
34828 super = likely(super_type) ? __Pyx_PyObject_Call2Args(super_type, type_obj, type_obj) : NULL;
|
|
jpayne@69
|
34829 #if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type)
|
|
jpayne@69
|
34830 Py_XDECREF(super_type);
|
|
jpayne@69
|
34831 #endif
|
|
jpayne@69
|
34832 if (unlikely(!super)) {
|
|
jpayne@69
|
34833 Py_CLEAR(type_obj);
|
|
jpayne@69
|
34834 goto done;
|
|
jpayne@69
|
34835 }
|
|
jpayne@69
|
34836 func = __Pyx_PyObject_GetAttrStrNoError(super, __pyx_n_s_init_subclass);
|
|
jpayne@69
|
34837 Py_DECREF(super);
|
|
jpayne@69
|
34838 if (likely(!func)) {
|
|
jpayne@69
|
34839 if (unlikely(PyErr_Occurred()))
|
|
jpayne@69
|
34840 Py_CLEAR(type_obj);
|
|
jpayne@69
|
34841 goto done;
|
|
jpayne@69
|
34842 }
|
|
jpayne@69
|
34843 res = __Pyx_PyObject_FastCallDict(func, NULL, 0, mkw);
|
|
jpayne@69
|
34844 Py_DECREF(func);
|
|
jpayne@69
|
34845 if (unlikely(!res))
|
|
jpayne@69
|
34846 Py_CLEAR(type_obj);
|
|
jpayne@69
|
34847 Py_XDECREF(res);
|
|
jpayne@69
|
34848 done:
|
|
jpayne@69
|
34849 return type_obj;
|
|
jpayne@69
|
34850 #endif
|
|
jpayne@69
|
34851 }
|
|
jpayne@69
|
34852 #endif
|
|
jpayne@69
|
34853 static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases,
|
|
jpayne@69
|
34854 PyObject *dict, PyObject *mkw,
|
|
jpayne@69
|
34855 int calculate_metaclass, int allow_py2_metaclass) {
|
|
jpayne@69
|
34856 PyObject *result;
|
|
jpayne@69
|
34857 PyObject *owned_metaclass = NULL;
|
|
jpayne@69
|
34858 PyObject *margs[4] = {NULL, name, bases, dict};
|
|
jpayne@69
|
34859 if (allow_py2_metaclass) {
|
|
jpayne@69
|
34860 owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass);
|
|
jpayne@69
|
34861 if (owned_metaclass) {
|
|
jpayne@69
|
34862 metaclass = owned_metaclass;
|
|
jpayne@69
|
34863 } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) {
|
|
jpayne@69
|
34864 PyErr_Clear();
|
|
jpayne@69
|
34865 } else {
|
|
jpayne@69
|
34866 return NULL;
|
|
jpayne@69
|
34867 }
|
|
jpayne@69
|
34868 }
|
|
jpayne@69
|
34869 if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) {
|
|
jpayne@69
|
34870 metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases);
|
|
jpayne@69
|
34871 Py_XDECREF(owned_metaclass);
|
|
jpayne@69
|
34872 if (unlikely(!metaclass))
|
|
jpayne@69
|
34873 return NULL;
|
|
jpayne@69
|
34874 owned_metaclass = metaclass;
|
|
jpayne@69
|
34875 }
|
|
jpayne@69
|
34876 result = __Pyx_PyObject_FastCallDict(metaclass, margs+1, 3 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET,
|
|
jpayne@69
|
34877 #if PY_VERSION_HEX < 0x030600A4
|
|
jpayne@69
|
34878 (metaclass == (PyObject*)&PyType_Type) ? NULL : mkw
|
|
jpayne@69
|
34879 #else
|
|
jpayne@69
|
34880 mkw
|
|
jpayne@69
|
34881 #endif
|
|
jpayne@69
|
34882 );
|
|
jpayne@69
|
34883 Py_XDECREF(owned_metaclass);
|
|
jpayne@69
|
34884 #if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS
|
|
jpayne@69
|
34885 if (likely(result) && likely(PyType_Check(result))) {
|
|
jpayne@69
|
34886 if (unlikely(__Pyx_SetNamesPEP487(result) < 0)) {
|
|
jpayne@69
|
34887 Py_CLEAR(result);
|
|
jpayne@69
|
34888 } else {
|
|
jpayne@69
|
34889 result = __Pyx_InitSubclassPEP487(result, mkw);
|
|
jpayne@69
|
34890 }
|
|
jpayne@69
|
34891 }
|
|
jpayne@69
|
34892 #else
|
|
jpayne@69
|
34893 (void) &__Pyx_GetBuiltinName;
|
|
jpayne@69
|
34894 #endif
|
|
jpayne@69
|
34895 return result;
|
|
jpayne@69
|
34896 }
|
|
jpayne@69
|
34897
|
|
jpayne@69
|
34898 /* CLineInTraceback */
|
|
jpayne@69
|
34899 #ifndef CYTHON_CLINE_IN_TRACEBACK
|
|
jpayne@69
|
34900 static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) {
|
|
jpayne@69
|
34901 PyObject *use_cline;
|
|
jpayne@69
|
34902 PyObject *ptype, *pvalue, *ptraceback;
|
|
jpayne@69
|
34903 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
34904 PyObject **cython_runtime_dict;
|
|
jpayne@69
|
34905 #endif
|
|
jpayne@69
|
34906 CYTHON_MAYBE_UNUSED_VAR(tstate);
|
|
jpayne@69
|
34907 if (unlikely(!__pyx_cython_runtime)) {
|
|
jpayne@69
|
34908 return c_line;
|
|
jpayne@69
|
34909 }
|
|
jpayne@69
|
34910 __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
|
|
jpayne@69
|
34911 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
34912 cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
|
|
jpayne@69
|
34913 if (likely(cython_runtime_dict)) {
|
|
jpayne@69
|
34914 __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
|
|
jpayne@69
|
34915 use_cline, *cython_runtime_dict,
|
|
jpayne@69
|
34916 __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback))
|
|
jpayne@69
|
34917 } else
|
|
jpayne@69
|
34918 #endif
|
|
jpayne@69
|
34919 {
|
|
jpayne@69
|
34920 PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStrNoError(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
|
|
jpayne@69
|
34921 if (use_cline_obj) {
|
|
jpayne@69
|
34922 use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
|
|
jpayne@69
|
34923 Py_DECREF(use_cline_obj);
|
|
jpayne@69
|
34924 } else {
|
|
jpayne@69
|
34925 PyErr_Clear();
|
|
jpayne@69
|
34926 use_cline = NULL;
|
|
jpayne@69
|
34927 }
|
|
jpayne@69
|
34928 }
|
|
jpayne@69
|
34929 if (!use_cline) {
|
|
jpayne@69
|
34930 c_line = 0;
|
|
jpayne@69
|
34931 (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
|
|
jpayne@69
|
34932 }
|
|
jpayne@69
|
34933 else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
|
|
jpayne@69
|
34934 c_line = 0;
|
|
jpayne@69
|
34935 }
|
|
jpayne@69
|
34936 __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
|
|
jpayne@69
|
34937 return c_line;
|
|
jpayne@69
|
34938 }
|
|
jpayne@69
|
34939 #endif
|
|
jpayne@69
|
34940
|
|
jpayne@69
|
34941 /* CodeObjectCache */
|
|
jpayne@69
|
34942 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
34943 static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
|
|
jpayne@69
|
34944 int start = 0, mid = 0, end = count - 1;
|
|
jpayne@69
|
34945 if (end >= 0 && code_line > entries[end].code_line) {
|
|
jpayne@69
|
34946 return count;
|
|
jpayne@69
|
34947 }
|
|
jpayne@69
|
34948 while (start < end) {
|
|
jpayne@69
|
34949 mid = start + (end - start) / 2;
|
|
jpayne@69
|
34950 if (code_line < entries[mid].code_line) {
|
|
jpayne@69
|
34951 end = mid;
|
|
jpayne@69
|
34952 } else if (code_line > entries[mid].code_line) {
|
|
jpayne@69
|
34953 start = mid + 1;
|
|
jpayne@69
|
34954 } else {
|
|
jpayne@69
|
34955 return mid;
|
|
jpayne@69
|
34956 }
|
|
jpayne@69
|
34957 }
|
|
jpayne@69
|
34958 if (code_line <= entries[mid].code_line) {
|
|
jpayne@69
|
34959 return mid;
|
|
jpayne@69
|
34960 } else {
|
|
jpayne@69
|
34961 return mid + 1;
|
|
jpayne@69
|
34962 }
|
|
jpayne@69
|
34963 }
|
|
jpayne@69
|
34964 static PyCodeObject *__pyx_find_code_object(int code_line) {
|
|
jpayne@69
|
34965 PyCodeObject* code_object;
|
|
jpayne@69
|
34966 int pos;
|
|
jpayne@69
|
34967 if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
|
|
jpayne@69
|
34968 return NULL;
|
|
jpayne@69
|
34969 }
|
|
jpayne@69
|
34970 pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
|
|
jpayne@69
|
34971 if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
|
|
jpayne@69
|
34972 return NULL;
|
|
jpayne@69
|
34973 }
|
|
jpayne@69
|
34974 code_object = __pyx_code_cache.entries[pos].code_object;
|
|
jpayne@69
|
34975 Py_INCREF(code_object);
|
|
jpayne@69
|
34976 return code_object;
|
|
jpayne@69
|
34977 }
|
|
jpayne@69
|
34978 static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
|
|
jpayne@69
|
34979 int pos, i;
|
|
jpayne@69
|
34980 __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
|
|
jpayne@69
|
34981 if (unlikely(!code_line)) {
|
|
jpayne@69
|
34982 return;
|
|
jpayne@69
|
34983 }
|
|
jpayne@69
|
34984 if (unlikely(!entries)) {
|
|
jpayne@69
|
34985 entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
|
|
jpayne@69
|
34986 if (likely(entries)) {
|
|
jpayne@69
|
34987 __pyx_code_cache.entries = entries;
|
|
jpayne@69
|
34988 __pyx_code_cache.max_count = 64;
|
|
jpayne@69
|
34989 __pyx_code_cache.count = 1;
|
|
jpayne@69
|
34990 entries[0].code_line = code_line;
|
|
jpayne@69
|
34991 entries[0].code_object = code_object;
|
|
jpayne@69
|
34992 Py_INCREF(code_object);
|
|
jpayne@69
|
34993 }
|
|
jpayne@69
|
34994 return;
|
|
jpayne@69
|
34995 }
|
|
jpayne@69
|
34996 pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
|
|
jpayne@69
|
34997 if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
|
|
jpayne@69
|
34998 PyCodeObject* tmp = entries[pos].code_object;
|
|
jpayne@69
|
34999 entries[pos].code_object = code_object;
|
|
jpayne@69
|
35000 Py_DECREF(tmp);
|
|
jpayne@69
|
35001 return;
|
|
jpayne@69
|
35002 }
|
|
jpayne@69
|
35003 if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
|
|
jpayne@69
|
35004 int new_max = __pyx_code_cache.max_count + 64;
|
|
jpayne@69
|
35005 entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
|
|
jpayne@69
|
35006 __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry));
|
|
jpayne@69
|
35007 if (unlikely(!entries)) {
|
|
jpayne@69
|
35008 return;
|
|
jpayne@69
|
35009 }
|
|
jpayne@69
|
35010 __pyx_code_cache.entries = entries;
|
|
jpayne@69
|
35011 __pyx_code_cache.max_count = new_max;
|
|
jpayne@69
|
35012 }
|
|
jpayne@69
|
35013 for (i=__pyx_code_cache.count; i>pos; i--) {
|
|
jpayne@69
|
35014 entries[i] = entries[i-1];
|
|
jpayne@69
|
35015 }
|
|
jpayne@69
|
35016 entries[pos].code_line = code_line;
|
|
jpayne@69
|
35017 entries[pos].code_object = code_object;
|
|
jpayne@69
|
35018 __pyx_code_cache.count++;
|
|
jpayne@69
|
35019 Py_INCREF(code_object);
|
|
jpayne@69
|
35020 }
|
|
jpayne@69
|
35021 #endif
|
|
jpayne@69
|
35022
|
|
jpayne@69
|
35023 /* AddTraceback */
|
|
jpayne@69
|
35024 #include "compile.h"
|
|
jpayne@69
|
35025 #include "frameobject.h"
|
|
jpayne@69
|
35026 #include "traceback.h"
|
|
jpayne@69
|
35027 #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
35028 #ifndef Py_BUILD_CORE
|
|
jpayne@69
|
35029 #define Py_BUILD_CORE 1
|
|
jpayne@69
|
35030 #endif
|
|
jpayne@69
|
35031 #include "internal/pycore_frame.h"
|
|
jpayne@69
|
35032 #endif
|
|
jpayne@69
|
35033 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
35034 static PyObject *__Pyx_PyCode_Replace_For_AddTraceback(PyObject *code, PyObject *scratch_dict,
|
|
jpayne@69
|
35035 PyObject *firstlineno, PyObject *name) {
|
|
jpayne@69
|
35036 PyObject *replace = NULL;
|
|
jpayne@69
|
35037 if (unlikely(PyDict_SetItemString(scratch_dict, "co_firstlineno", firstlineno))) return NULL;
|
|
jpayne@69
|
35038 if (unlikely(PyDict_SetItemString(scratch_dict, "co_name", name))) return NULL;
|
|
jpayne@69
|
35039 replace = PyObject_GetAttrString(code, "replace");
|
|
jpayne@69
|
35040 if (likely(replace)) {
|
|
jpayne@69
|
35041 PyObject *result;
|
|
jpayne@69
|
35042 result = PyObject_Call(replace, __pyx_empty_tuple, scratch_dict);
|
|
jpayne@69
|
35043 Py_DECREF(replace);
|
|
jpayne@69
|
35044 return result;
|
|
jpayne@69
|
35045 }
|
|
jpayne@69
|
35046 PyErr_Clear();
|
|
jpayne@69
|
35047 #if __PYX_LIMITED_VERSION_HEX < 0x030780000
|
|
jpayne@69
|
35048 {
|
|
jpayne@69
|
35049 PyObject *compiled = NULL, *result = NULL;
|
|
jpayne@69
|
35050 if (unlikely(PyDict_SetItemString(scratch_dict, "code", code))) return NULL;
|
|
jpayne@69
|
35051 if (unlikely(PyDict_SetItemString(scratch_dict, "type", (PyObject*)(&PyType_Type)))) return NULL;
|
|
jpayne@69
|
35052 compiled = Py_CompileString(
|
|
jpayne@69
|
35053 "out = type(code)(\n"
|
|
jpayne@69
|
35054 " code.co_argcount, code.co_kwonlyargcount, code.co_nlocals, code.co_stacksize,\n"
|
|
jpayne@69
|
35055 " code.co_flags, code.co_code, code.co_consts, code.co_names,\n"
|
|
jpayne@69
|
35056 " code.co_varnames, code.co_filename, co_name, co_firstlineno,\n"
|
|
jpayne@69
|
35057 " code.co_lnotab)\n", "<dummy>", Py_file_input);
|
|
jpayne@69
|
35058 if (!compiled) return NULL;
|
|
jpayne@69
|
35059 result = PyEval_EvalCode(compiled, scratch_dict, scratch_dict);
|
|
jpayne@69
|
35060 Py_DECREF(compiled);
|
|
jpayne@69
|
35061 if (!result) PyErr_Print();
|
|
jpayne@69
|
35062 Py_DECREF(result);
|
|
jpayne@69
|
35063 result = PyDict_GetItemString(scratch_dict, "out");
|
|
jpayne@69
|
35064 if (result) Py_INCREF(result);
|
|
jpayne@69
|
35065 return result;
|
|
jpayne@69
|
35066 }
|
|
jpayne@69
|
35067 #else
|
|
jpayne@69
|
35068 return NULL;
|
|
jpayne@69
|
35069 #endif
|
|
jpayne@69
|
35070 }
|
|
jpayne@69
|
35071 static void __Pyx_AddTraceback(const char *funcname, int c_line,
|
|
jpayne@69
|
35072 int py_line, const char *filename) {
|
|
jpayne@69
|
35073 PyObject *code_object = NULL, *py_py_line = NULL, *py_funcname = NULL, *dict = NULL;
|
|
jpayne@69
|
35074 PyObject *replace = NULL, *getframe = NULL, *frame = NULL;
|
|
jpayne@69
|
35075 PyObject *exc_type, *exc_value, *exc_traceback;
|
|
jpayne@69
|
35076 int success = 0;
|
|
jpayne@69
|
35077 if (c_line) {
|
|
jpayne@69
|
35078 (void) __pyx_cfilenm;
|
|
jpayne@69
|
35079 (void) __Pyx_CLineForTraceback(__Pyx_PyThreadState_Current, c_line);
|
|
jpayne@69
|
35080 }
|
|
jpayne@69
|
35081 PyErr_Fetch(&exc_type, &exc_value, &exc_traceback);
|
|
jpayne@69
|
35082 code_object = Py_CompileString("_getframe()", filename, Py_eval_input);
|
|
jpayne@69
|
35083 if (unlikely(!code_object)) goto bad;
|
|
jpayne@69
|
35084 py_py_line = PyLong_FromLong(py_line);
|
|
jpayne@69
|
35085 if (unlikely(!py_py_line)) goto bad;
|
|
jpayne@69
|
35086 py_funcname = PyUnicode_FromString(funcname);
|
|
jpayne@69
|
35087 if (unlikely(!py_funcname)) goto bad;
|
|
jpayne@69
|
35088 dict = PyDict_New();
|
|
jpayne@69
|
35089 if (unlikely(!dict)) goto bad;
|
|
jpayne@69
|
35090 {
|
|
jpayne@69
|
35091 PyObject *old_code_object = code_object;
|
|
jpayne@69
|
35092 code_object = __Pyx_PyCode_Replace_For_AddTraceback(code_object, dict, py_py_line, py_funcname);
|
|
jpayne@69
|
35093 Py_DECREF(old_code_object);
|
|
jpayne@69
|
35094 }
|
|
jpayne@69
|
35095 if (unlikely(!code_object)) goto bad;
|
|
jpayne@69
|
35096 getframe = PySys_GetObject("_getframe");
|
|
jpayne@69
|
35097 if (unlikely(!getframe)) goto bad;
|
|
jpayne@69
|
35098 if (unlikely(PyDict_SetItemString(dict, "_getframe", getframe))) goto bad;
|
|
jpayne@69
|
35099 frame = PyEval_EvalCode(code_object, dict, dict);
|
|
jpayne@69
|
35100 if (unlikely(!frame) || frame == Py_None) goto bad;
|
|
jpayne@69
|
35101 success = 1;
|
|
jpayne@69
|
35102 bad:
|
|
jpayne@69
|
35103 PyErr_Restore(exc_type, exc_value, exc_traceback);
|
|
jpayne@69
|
35104 Py_XDECREF(code_object);
|
|
jpayne@69
|
35105 Py_XDECREF(py_py_line);
|
|
jpayne@69
|
35106 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
35107 Py_XDECREF(dict);
|
|
jpayne@69
|
35108 Py_XDECREF(replace);
|
|
jpayne@69
|
35109 if (success) {
|
|
jpayne@69
|
35110 PyTraceBack_Here(
|
|
jpayne@69
|
35111 (struct _frame*)frame);
|
|
jpayne@69
|
35112 }
|
|
jpayne@69
|
35113 Py_XDECREF(frame);
|
|
jpayne@69
|
35114 }
|
|
jpayne@69
|
35115 #else
|
|
jpayne@69
|
35116 static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
|
|
jpayne@69
|
35117 const char *funcname, int c_line,
|
|
jpayne@69
|
35118 int py_line, const char *filename) {
|
|
jpayne@69
|
35119 PyCodeObject *py_code = NULL;
|
|
jpayne@69
|
35120 PyObject *py_funcname = NULL;
|
|
jpayne@69
|
35121 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35122 PyObject *py_srcfile = NULL;
|
|
jpayne@69
|
35123 py_srcfile = PyString_FromString(filename);
|
|
jpayne@69
|
35124 if (!py_srcfile) goto bad;
|
|
jpayne@69
|
35125 #endif
|
|
jpayne@69
|
35126 if (c_line) {
|
|
jpayne@69
|
35127 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35128 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
|
|
jpayne@69
|
35129 if (!py_funcname) goto bad;
|
|
jpayne@69
|
35130 #else
|
|
jpayne@69
|
35131 py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
|
|
jpayne@69
|
35132 if (!py_funcname) goto bad;
|
|
jpayne@69
|
35133 funcname = PyUnicode_AsUTF8(py_funcname);
|
|
jpayne@69
|
35134 if (!funcname) goto bad;
|
|
jpayne@69
|
35135 #endif
|
|
jpayne@69
|
35136 }
|
|
jpayne@69
|
35137 else {
|
|
jpayne@69
|
35138 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35139 py_funcname = PyString_FromString(funcname);
|
|
jpayne@69
|
35140 if (!py_funcname) goto bad;
|
|
jpayne@69
|
35141 #endif
|
|
jpayne@69
|
35142 }
|
|
jpayne@69
|
35143 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35144 py_code = __Pyx_PyCode_New(
|
|
jpayne@69
|
35145 0,
|
|
jpayne@69
|
35146 0,
|
|
jpayne@69
|
35147 0,
|
|
jpayne@69
|
35148 0,
|
|
jpayne@69
|
35149 0,
|
|
jpayne@69
|
35150 0,
|
|
jpayne@69
|
35151 __pyx_empty_bytes, /*PyObject *code,*/
|
|
jpayne@69
|
35152 __pyx_empty_tuple, /*PyObject *consts,*/
|
|
jpayne@69
|
35153 __pyx_empty_tuple, /*PyObject *names,*/
|
|
jpayne@69
|
35154 __pyx_empty_tuple, /*PyObject *varnames,*/
|
|
jpayne@69
|
35155 __pyx_empty_tuple, /*PyObject *freevars,*/
|
|
jpayne@69
|
35156 __pyx_empty_tuple, /*PyObject *cellvars,*/
|
|
jpayne@69
|
35157 py_srcfile, /*PyObject *filename,*/
|
|
jpayne@69
|
35158 py_funcname, /*PyObject *name,*/
|
|
jpayne@69
|
35159 py_line,
|
|
jpayne@69
|
35160 __pyx_empty_bytes /*PyObject *lnotab*/
|
|
jpayne@69
|
35161 );
|
|
jpayne@69
|
35162 Py_DECREF(py_srcfile);
|
|
jpayne@69
|
35163 #else
|
|
jpayne@69
|
35164 py_code = PyCode_NewEmpty(filename, funcname, py_line);
|
|
jpayne@69
|
35165 #endif
|
|
jpayne@69
|
35166 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
35167 return py_code;
|
|
jpayne@69
|
35168 bad:
|
|
jpayne@69
|
35169 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
35170 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35171 Py_XDECREF(py_srcfile);
|
|
jpayne@69
|
35172 #endif
|
|
jpayne@69
|
35173 return NULL;
|
|
jpayne@69
|
35174 }
|
|
jpayne@69
|
35175 static void __Pyx_AddTraceback(const char *funcname, int c_line,
|
|
jpayne@69
|
35176 int py_line, const char *filename) {
|
|
jpayne@69
|
35177 PyCodeObject *py_code = 0;
|
|
jpayne@69
|
35178 PyFrameObject *py_frame = 0;
|
|
jpayne@69
|
35179 PyThreadState *tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
35180 PyObject *ptype, *pvalue, *ptraceback;
|
|
jpayne@69
|
35181 if (c_line) {
|
|
jpayne@69
|
35182 c_line = __Pyx_CLineForTraceback(tstate, c_line);
|
|
jpayne@69
|
35183 }
|
|
jpayne@69
|
35184 py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
|
|
jpayne@69
|
35185 if (!py_code) {
|
|
jpayne@69
|
35186 __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
|
|
jpayne@69
|
35187 py_code = __Pyx_CreateCodeObjectForTraceback(
|
|
jpayne@69
|
35188 funcname, c_line, py_line, filename);
|
|
jpayne@69
|
35189 if (!py_code) {
|
|
jpayne@69
|
35190 /* If the code object creation fails, then we should clear the
|
|
jpayne@69
|
35191 fetched exception references and propagate the new exception */
|
|
jpayne@69
|
35192 Py_XDECREF(ptype);
|
|
jpayne@69
|
35193 Py_XDECREF(pvalue);
|
|
jpayne@69
|
35194 Py_XDECREF(ptraceback);
|
|
jpayne@69
|
35195 goto bad;
|
|
jpayne@69
|
35196 }
|
|
jpayne@69
|
35197 __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
|
|
jpayne@69
|
35198 __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
|
|
jpayne@69
|
35199 }
|
|
jpayne@69
|
35200 py_frame = PyFrame_New(
|
|
jpayne@69
|
35201 tstate, /*PyThreadState *tstate,*/
|
|
jpayne@69
|
35202 py_code, /*PyCodeObject *code,*/
|
|
jpayne@69
|
35203 __pyx_d, /*PyObject *globals,*/
|
|
jpayne@69
|
35204 0 /*PyObject *locals*/
|
|
jpayne@69
|
35205 );
|
|
jpayne@69
|
35206 if (!py_frame) goto bad;
|
|
jpayne@69
|
35207 __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
|
|
jpayne@69
|
35208 PyTraceBack_Here(py_frame);
|
|
jpayne@69
|
35209 bad:
|
|
jpayne@69
|
35210 Py_XDECREF(py_code);
|
|
jpayne@69
|
35211 Py_XDECREF(py_frame);
|
|
jpayne@69
|
35212 }
|
|
jpayne@69
|
35213 #endif
|
|
jpayne@69
|
35214
|
|
jpayne@69
|
35215 /* CIntFromPyVerify */
|
|
jpayne@69
|
35216 #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
|
|
jpayne@69
|
35217 __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
|
|
jpayne@69
|
35218 #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
|
|
jpayne@69
|
35219 __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
|
|
jpayne@69
|
35220 #define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
|
|
jpayne@69
|
35221 {\
|
|
jpayne@69
|
35222 func_type value = func_value;\
|
|
jpayne@69
|
35223 if (sizeof(target_type) < sizeof(func_type)) {\
|
|
jpayne@69
|
35224 if (unlikely(value != (func_type) (target_type) value)) {\
|
|
jpayne@69
|
35225 func_type zero = 0;\
|
|
jpayne@69
|
35226 if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
|
|
jpayne@69
|
35227 return (target_type) -1;\
|
|
jpayne@69
|
35228 if (is_unsigned && unlikely(value < zero))\
|
|
jpayne@69
|
35229 goto raise_neg_overflow;\
|
|
jpayne@69
|
35230 else\
|
|
jpayne@69
|
35231 goto raise_overflow;\
|
|
jpayne@69
|
35232 }\
|
|
jpayne@69
|
35233 }\
|
|
jpayne@69
|
35234 return (target_type) value;\
|
|
jpayne@69
|
35235 }
|
|
jpayne@69
|
35236
|
|
jpayne@69
|
35237 /* CIntFromPy */
|
|
jpayne@69
|
35238 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
|
|
jpayne@69
|
35239 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35240 #pragma GCC diagnostic push
|
|
jpayne@69
|
35241 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
35242 #endif
|
|
jpayne@69
|
35243 const int neg_one = (int) -1, const_zero = (int) 0;
|
|
jpayne@69
|
35244 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35245 #pragma GCC diagnostic pop
|
|
jpayne@69
|
35246 #endif
|
|
jpayne@69
|
35247 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
35248 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35249 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
35250 if ((sizeof(int) < sizeof(long))) {
|
|
jpayne@69
|
35251 __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
35252 } else {
|
|
jpayne@69
|
35253 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
35254 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
35255 goto raise_neg_overflow;
|
|
jpayne@69
|
35256 }
|
|
jpayne@69
|
35257 return (int) val;
|
|
jpayne@69
|
35258 }
|
|
jpayne@69
|
35259 }
|
|
jpayne@69
|
35260 #endif
|
|
jpayne@69
|
35261 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
35262 int val;
|
|
jpayne@69
|
35263 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
35264 if (!tmp) return (int) -1;
|
|
jpayne@69
|
35265 val = __Pyx_PyInt_As_int(tmp);
|
|
jpayne@69
|
35266 Py_DECREF(tmp);
|
|
jpayne@69
|
35267 return val;
|
|
jpayne@69
|
35268 }
|
|
jpayne@69
|
35269 if (is_unsigned) {
|
|
jpayne@69
|
35270 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
35271 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
35272 goto raise_neg_overflow;
|
|
jpayne@69
|
35273 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
35274 __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
35275 } else {
|
|
jpayne@69
|
35276 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
35277 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
35278 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
35279 case 2:
|
|
jpayne@69
|
35280 if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35281 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35282 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35283 } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35284 return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
|
|
jpayne@69
|
35285 }
|
|
jpayne@69
|
35286 }
|
|
jpayne@69
|
35287 break;
|
|
jpayne@69
|
35288 case 3:
|
|
jpayne@69
|
35289 if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35290 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35291 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35292 } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35293 return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
|
|
jpayne@69
|
35294 }
|
|
jpayne@69
|
35295 }
|
|
jpayne@69
|
35296 break;
|
|
jpayne@69
|
35297 case 4:
|
|
jpayne@69
|
35298 if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35299 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35300 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35301 } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35302 return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
|
|
jpayne@69
|
35303 }
|
|
jpayne@69
|
35304 }
|
|
jpayne@69
|
35305 break;
|
|
jpayne@69
|
35306 }
|
|
jpayne@69
|
35307 }
|
|
jpayne@69
|
35308 #endif
|
|
jpayne@69
|
35309 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
35310 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
35311 goto raise_neg_overflow;
|
|
jpayne@69
|
35312 }
|
|
jpayne@69
|
35313 #else
|
|
jpayne@69
|
35314 {
|
|
jpayne@69
|
35315 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
35316 if (unlikely(result < 0))
|
|
jpayne@69
|
35317 return (int) -1;
|
|
jpayne@69
|
35318 if (unlikely(result == 1))
|
|
jpayne@69
|
35319 goto raise_neg_overflow;
|
|
jpayne@69
|
35320 }
|
|
jpayne@69
|
35321 #endif
|
|
jpayne@69
|
35322 if ((sizeof(int) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
35323 __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
35324 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35325 } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
35326 __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
35327 #endif
|
|
jpayne@69
|
35328 }
|
|
jpayne@69
|
35329 } else {
|
|
jpayne@69
|
35330 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
35331 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
35332 __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
35333 } else {
|
|
jpayne@69
|
35334 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
35335 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
35336 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
35337 case -2:
|
|
jpayne@69
|
35338 if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35339 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35340 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35341 } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35342 return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
35343 }
|
|
jpayne@69
|
35344 }
|
|
jpayne@69
|
35345 break;
|
|
jpayne@69
|
35346 case 2:
|
|
jpayne@69
|
35347 if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35348 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35349 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35350 } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35351 return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
35352 }
|
|
jpayne@69
|
35353 }
|
|
jpayne@69
|
35354 break;
|
|
jpayne@69
|
35355 case -3:
|
|
jpayne@69
|
35356 if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35357 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35358 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35359 } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35360 return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
35361 }
|
|
jpayne@69
|
35362 }
|
|
jpayne@69
|
35363 break;
|
|
jpayne@69
|
35364 case 3:
|
|
jpayne@69
|
35365 if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35366 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35367 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35368 } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35369 return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
35370 }
|
|
jpayne@69
|
35371 }
|
|
jpayne@69
|
35372 break;
|
|
jpayne@69
|
35373 case -4:
|
|
jpayne@69
|
35374 if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35375 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35376 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35377 } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35378 return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
35379 }
|
|
jpayne@69
|
35380 }
|
|
jpayne@69
|
35381 break;
|
|
jpayne@69
|
35382 case 4:
|
|
jpayne@69
|
35383 if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35384 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35385 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35386 } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35387 return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
35388 }
|
|
jpayne@69
|
35389 }
|
|
jpayne@69
|
35390 break;
|
|
jpayne@69
|
35391 }
|
|
jpayne@69
|
35392 }
|
|
jpayne@69
|
35393 #endif
|
|
jpayne@69
|
35394 if ((sizeof(int) <= sizeof(long))) {
|
|
jpayne@69
|
35395 __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
|
|
jpayne@69
|
35396 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35397 } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
35398 __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
35399 #endif
|
|
jpayne@69
|
35400 }
|
|
jpayne@69
|
35401 }
|
|
jpayne@69
|
35402 {
|
|
jpayne@69
|
35403 int val;
|
|
jpayne@69
|
35404 int ret = -1;
|
|
jpayne@69
|
35405 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
35406 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
35407 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
35408 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
35409 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
35410 goto raise_overflow;
|
|
jpayne@69
|
35411 } else {
|
|
jpayne@69
|
35412 ret = 0;
|
|
jpayne@69
|
35413 }
|
|
jpayne@69
|
35414 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
35415 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
35416 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
35417 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
35418 bytes, sizeof(val),
|
|
jpayne@69
|
35419 is_little, !is_unsigned);
|
|
jpayne@69
|
35420 #else
|
|
jpayne@69
|
35421 PyObject *v;
|
|
jpayne@69
|
35422 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
35423 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
35424 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
35425 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
35426 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
35427 } else {
|
|
jpayne@69
|
35428 v = PyNumber_Long(x);
|
|
jpayne@69
|
35429 if (unlikely(!v)) return (int) -1;
|
|
jpayne@69
|
35430 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
35431 }
|
|
jpayne@69
|
35432 {
|
|
jpayne@69
|
35433 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
35434 if (unlikely(result < 0)) {
|
|
jpayne@69
|
35435 Py_DECREF(v);
|
|
jpayne@69
|
35436 return (int) -1;
|
|
jpayne@69
|
35437 }
|
|
jpayne@69
|
35438 is_negative = result == 1;
|
|
jpayne@69
|
35439 }
|
|
jpayne@69
|
35440 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
35441 Py_DECREF(v);
|
|
jpayne@69
|
35442 goto raise_neg_overflow;
|
|
jpayne@69
|
35443 } else if (is_negative) {
|
|
jpayne@69
|
35444 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
35445 Py_DECREF(v);
|
|
jpayne@69
|
35446 if (unlikely(!stepval))
|
|
jpayne@69
|
35447 return (int) -1;
|
|
jpayne@69
|
35448 } else {
|
|
jpayne@69
|
35449 stepval = v;
|
|
jpayne@69
|
35450 }
|
|
jpayne@69
|
35451 v = NULL;
|
|
jpayne@69
|
35452 val = (int) 0;
|
|
jpayne@69
|
35453 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
35454 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
35455 for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
35456 PyObject *tmp, *digit;
|
|
jpayne@69
|
35457 long idigit;
|
|
jpayne@69
|
35458 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
35459 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
35460 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
35461 Py_DECREF(digit);
|
|
jpayne@69
|
35462 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
35463 val |= ((int) idigit) << bits;
|
|
jpayne@69
|
35464 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
35465 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
35466 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
35467 }
|
|
jpayne@69
|
35468 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
35469 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
35470 {
|
|
jpayne@69
|
35471 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
35472 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
35473 remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
35474 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
35475 goto raise_overflow;
|
|
jpayne@69
|
35476 val |= ((int) idigit) << bits;
|
|
jpayne@69
|
35477 }
|
|
jpayne@69
|
35478 if (!is_unsigned) {
|
|
jpayne@69
|
35479 if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1))))
|
|
jpayne@69
|
35480 goto raise_overflow;
|
|
jpayne@69
|
35481 if (is_negative)
|
|
jpayne@69
|
35482 val = ~val;
|
|
jpayne@69
|
35483 }
|
|
jpayne@69
|
35484 ret = 0;
|
|
jpayne@69
|
35485 done:
|
|
jpayne@69
|
35486 Py_XDECREF(shift);
|
|
jpayne@69
|
35487 Py_XDECREF(mask);
|
|
jpayne@69
|
35488 Py_XDECREF(stepval);
|
|
jpayne@69
|
35489 #endif
|
|
jpayne@69
|
35490 if (unlikely(ret))
|
|
jpayne@69
|
35491 return (int) -1;
|
|
jpayne@69
|
35492 return val;
|
|
jpayne@69
|
35493 }
|
|
jpayne@69
|
35494 raise_overflow:
|
|
jpayne@69
|
35495 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
35496 "value too large to convert to int");
|
|
jpayne@69
|
35497 return (int) -1;
|
|
jpayne@69
|
35498 raise_neg_overflow:
|
|
jpayne@69
|
35499 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
35500 "can't convert negative value to int");
|
|
jpayne@69
|
35501 return (int) -1;
|
|
jpayne@69
|
35502 }
|
|
jpayne@69
|
35503
|
|
jpayne@69
|
35504 /* CIntToPy */
|
|
jpayne@69
|
35505 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
|
|
jpayne@69
|
35506 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35507 #pragma GCC diagnostic push
|
|
jpayne@69
|
35508 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
35509 #endif
|
|
jpayne@69
|
35510 const int neg_one = (int) -1, const_zero = (int) 0;
|
|
jpayne@69
|
35511 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35512 #pragma GCC diagnostic pop
|
|
jpayne@69
|
35513 #endif
|
|
jpayne@69
|
35514 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
35515 if (is_unsigned) {
|
|
jpayne@69
|
35516 if (sizeof(int) < sizeof(long)) {
|
|
jpayne@69
|
35517 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
35518 } else if (sizeof(int) <= sizeof(unsigned long)) {
|
|
jpayne@69
|
35519 return PyLong_FromUnsignedLong((unsigned long) value);
|
|
jpayne@69
|
35520 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35521 } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
|
|
jpayne@69
|
35522 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
|
|
jpayne@69
|
35523 #endif
|
|
jpayne@69
|
35524 }
|
|
jpayne@69
|
35525 } else {
|
|
jpayne@69
|
35526 if (sizeof(int) <= sizeof(long)) {
|
|
jpayne@69
|
35527 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
35528 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35529 } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
|
|
jpayne@69
|
35530 return PyLong_FromLongLong((PY_LONG_LONG) value);
|
|
jpayne@69
|
35531 #endif
|
|
jpayne@69
|
35532 }
|
|
jpayne@69
|
35533 }
|
|
jpayne@69
|
35534 {
|
|
jpayne@69
|
35535 unsigned char *bytes = (unsigned char *)&value;
|
|
jpayne@69
|
35536 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
35537 if (is_unsigned) {
|
|
jpayne@69
|
35538 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
35539 } else {
|
|
jpayne@69
|
35540 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
35541 }
|
|
jpayne@69
|
35542 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
35543 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
35544 return _PyLong_FromByteArray(bytes, sizeof(int),
|
|
jpayne@69
|
35545 little, !is_unsigned);
|
|
jpayne@69
|
35546 #else
|
|
jpayne@69
|
35547 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
35548 PyObject *from_bytes, *result = NULL;
|
|
jpayne@69
|
35549 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
|
|
jpayne@69
|
35550 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
|
|
jpayne@69
|
35551 if (!from_bytes) return NULL;
|
|
jpayne@69
|
35552 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int));
|
|
jpayne@69
|
35553 if (!py_bytes) goto limited_bad;
|
|
jpayne@69
|
35554 order_str = PyUnicode_FromString(little ? "little" : "big");
|
|
jpayne@69
|
35555 if (!order_str) goto limited_bad;
|
|
jpayne@69
|
35556 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
|
|
jpayne@69
|
35557 if (!arg_tuple) goto limited_bad;
|
|
jpayne@69
|
35558 if (!is_unsigned) {
|
|
jpayne@69
|
35559 kwds = PyDict_New();
|
|
jpayne@69
|
35560 if (!kwds) goto limited_bad;
|
|
jpayne@69
|
35561 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
|
|
jpayne@69
|
35562 }
|
|
jpayne@69
|
35563 result = PyObject_Call(from_bytes, arg_tuple, kwds);
|
|
jpayne@69
|
35564 limited_bad:
|
|
jpayne@69
|
35565 Py_XDECREF(kwds);
|
|
jpayne@69
|
35566 Py_XDECREF(arg_tuple);
|
|
jpayne@69
|
35567 Py_XDECREF(order_str);
|
|
jpayne@69
|
35568 Py_XDECREF(py_bytes);
|
|
jpayne@69
|
35569 Py_XDECREF(from_bytes);
|
|
jpayne@69
|
35570 return result;
|
|
jpayne@69
|
35571 #endif
|
|
jpayne@69
|
35572 }
|
|
jpayne@69
|
35573 }
|
|
jpayne@69
|
35574
|
|
jpayne@69
|
35575 /* CIntFromPy */
|
|
jpayne@69
|
35576 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
|
|
jpayne@69
|
35577 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35578 #pragma GCC diagnostic push
|
|
jpayne@69
|
35579 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
35580 #endif
|
|
jpayne@69
|
35581 const long neg_one = (long) -1, const_zero = (long) 0;
|
|
jpayne@69
|
35582 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35583 #pragma GCC diagnostic pop
|
|
jpayne@69
|
35584 #endif
|
|
jpayne@69
|
35585 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
35586 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35587 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
35588 if ((sizeof(long) < sizeof(long))) {
|
|
jpayne@69
|
35589 __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
35590 } else {
|
|
jpayne@69
|
35591 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
35592 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
35593 goto raise_neg_overflow;
|
|
jpayne@69
|
35594 }
|
|
jpayne@69
|
35595 return (long) val;
|
|
jpayne@69
|
35596 }
|
|
jpayne@69
|
35597 }
|
|
jpayne@69
|
35598 #endif
|
|
jpayne@69
|
35599 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
35600 long val;
|
|
jpayne@69
|
35601 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
35602 if (!tmp) return (long) -1;
|
|
jpayne@69
|
35603 val = __Pyx_PyInt_As_long(tmp);
|
|
jpayne@69
|
35604 Py_DECREF(tmp);
|
|
jpayne@69
|
35605 return val;
|
|
jpayne@69
|
35606 }
|
|
jpayne@69
|
35607 if (is_unsigned) {
|
|
jpayne@69
|
35608 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
35609 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
35610 goto raise_neg_overflow;
|
|
jpayne@69
|
35611 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
35612 __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
35613 } else {
|
|
jpayne@69
|
35614 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
35615 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
35616 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
35617 case 2:
|
|
jpayne@69
|
35618 if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35619 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35620 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35621 } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35622 return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
|
|
jpayne@69
|
35623 }
|
|
jpayne@69
|
35624 }
|
|
jpayne@69
|
35625 break;
|
|
jpayne@69
|
35626 case 3:
|
|
jpayne@69
|
35627 if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35628 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35629 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35630 } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35631 return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
|
|
jpayne@69
|
35632 }
|
|
jpayne@69
|
35633 }
|
|
jpayne@69
|
35634 break;
|
|
jpayne@69
|
35635 case 4:
|
|
jpayne@69
|
35636 if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35637 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35638 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35639 } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35640 return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
|
|
jpayne@69
|
35641 }
|
|
jpayne@69
|
35642 }
|
|
jpayne@69
|
35643 break;
|
|
jpayne@69
|
35644 }
|
|
jpayne@69
|
35645 }
|
|
jpayne@69
|
35646 #endif
|
|
jpayne@69
|
35647 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
35648 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
35649 goto raise_neg_overflow;
|
|
jpayne@69
|
35650 }
|
|
jpayne@69
|
35651 #else
|
|
jpayne@69
|
35652 {
|
|
jpayne@69
|
35653 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
35654 if (unlikely(result < 0))
|
|
jpayne@69
|
35655 return (long) -1;
|
|
jpayne@69
|
35656 if (unlikely(result == 1))
|
|
jpayne@69
|
35657 goto raise_neg_overflow;
|
|
jpayne@69
|
35658 }
|
|
jpayne@69
|
35659 #endif
|
|
jpayne@69
|
35660 if ((sizeof(long) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
35661 __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
35662 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35663 } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
35664 __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
35665 #endif
|
|
jpayne@69
|
35666 }
|
|
jpayne@69
|
35667 } else {
|
|
jpayne@69
|
35668 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
35669 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
35670 __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
35671 } else {
|
|
jpayne@69
|
35672 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
35673 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
35674 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
35675 case -2:
|
|
jpayne@69
|
35676 if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35677 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35678 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35679 } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35680 return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
35681 }
|
|
jpayne@69
|
35682 }
|
|
jpayne@69
|
35683 break;
|
|
jpayne@69
|
35684 case 2:
|
|
jpayne@69
|
35685 if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35686 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35687 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35688 } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35689 return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
35690 }
|
|
jpayne@69
|
35691 }
|
|
jpayne@69
|
35692 break;
|
|
jpayne@69
|
35693 case -3:
|
|
jpayne@69
|
35694 if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35695 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35696 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35697 } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35698 return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
35699 }
|
|
jpayne@69
|
35700 }
|
|
jpayne@69
|
35701 break;
|
|
jpayne@69
|
35702 case 3:
|
|
jpayne@69
|
35703 if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35704 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35705 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35706 } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35707 return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
35708 }
|
|
jpayne@69
|
35709 }
|
|
jpayne@69
|
35710 break;
|
|
jpayne@69
|
35711 case -4:
|
|
jpayne@69
|
35712 if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35713 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35714 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35715 } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35716 return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
35717 }
|
|
jpayne@69
|
35718 }
|
|
jpayne@69
|
35719 break;
|
|
jpayne@69
|
35720 case 4:
|
|
jpayne@69
|
35721 if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35722 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35723 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35724 } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35725 return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
35726 }
|
|
jpayne@69
|
35727 }
|
|
jpayne@69
|
35728 break;
|
|
jpayne@69
|
35729 }
|
|
jpayne@69
|
35730 }
|
|
jpayne@69
|
35731 #endif
|
|
jpayne@69
|
35732 if ((sizeof(long) <= sizeof(long))) {
|
|
jpayne@69
|
35733 __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
|
|
jpayne@69
|
35734 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35735 } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
35736 __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
35737 #endif
|
|
jpayne@69
|
35738 }
|
|
jpayne@69
|
35739 }
|
|
jpayne@69
|
35740 {
|
|
jpayne@69
|
35741 long val;
|
|
jpayne@69
|
35742 int ret = -1;
|
|
jpayne@69
|
35743 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
35744 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
35745 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
35746 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
35747 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
35748 goto raise_overflow;
|
|
jpayne@69
|
35749 } else {
|
|
jpayne@69
|
35750 ret = 0;
|
|
jpayne@69
|
35751 }
|
|
jpayne@69
|
35752 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
35753 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
35754 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
35755 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
35756 bytes, sizeof(val),
|
|
jpayne@69
|
35757 is_little, !is_unsigned);
|
|
jpayne@69
|
35758 #else
|
|
jpayne@69
|
35759 PyObject *v;
|
|
jpayne@69
|
35760 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
35761 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
35762 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
35763 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
35764 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
35765 } else {
|
|
jpayne@69
|
35766 v = PyNumber_Long(x);
|
|
jpayne@69
|
35767 if (unlikely(!v)) return (long) -1;
|
|
jpayne@69
|
35768 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
35769 }
|
|
jpayne@69
|
35770 {
|
|
jpayne@69
|
35771 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
35772 if (unlikely(result < 0)) {
|
|
jpayne@69
|
35773 Py_DECREF(v);
|
|
jpayne@69
|
35774 return (long) -1;
|
|
jpayne@69
|
35775 }
|
|
jpayne@69
|
35776 is_negative = result == 1;
|
|
jpayne@69
|
35777 }
|
|
jpayne@69
|
35778 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
35779 Py_DECREF(v);
|
|
jpayne@69
|
35780 goto raise_neg_overflow;
|
|
jpayne@69
|
35781 } else if (is_negative) {
|
|
jpayne@69
|
35782 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
35783 Py_DECREF(v);
|
|
jpayne@69
|
35784 if (unlikely(!stepval))
|
|
jpayne@69
|
35785 return (long) -1;
|
|
jpayne@69
|
35786 } else {
|
|
jpayne@69
|
35787 stepval = v;
|
|
jpayne@69
|
35788 }
|
|
jpayne@69
|
35789 v = NULL;
|
|
jpayne@69
|
35790 val = (long) 0;
|
|
jpayne@69
|
35791 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
35792 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
35793 for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
35794 PyObject *tmp, *digit;
|
|
jpayne@69
|
35795 long idigit;
|
|
jpayne@69
|
35796 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
35797 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
35798 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
35799 Py_DECREF(digit);
|
|
jpayne@69
|
35800 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
35801 val |= ((long) idigit) << bits;
|
|
jpayne@69
|
35802 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
35803 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
35804 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
35805 }
|
|
jpayne@69
|
35806 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
35807 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
35808 {
|
|
jpayne@69
|
35809 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
35810 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
35811 remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
35812 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
35813 goto raise_overflow;
|
|
jpayne@69
|
35814 val |= ((long) idigit) << bits;
|
|
jpayne@69
|
35815 }
|
|
jpayne@69
|
35816 if (!is_unsigned) {
|
|
jpayne@69
|
35817 if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1))))
|
|
jpayne@69
|
35818 goto raise_overflow;
|
|
jpayne@69
|
35819 if (is_negative)
|
|
jpayne@69
|
35820 val = ~val;
|
|
jpayne@69
|
35821 }
|
|
jpayne@69
|
35822 ret = 0;
|
|
jpayne@69
|
35823 done:
|
|
jpayne@69
|
35824 Py_XDECREF(shift);
|
|
jpayne@69
|
35825 Py_XDECREF(mask);
|
|
jpayne@69
|
35826 Py_XDECREF(stepval);
|
|
jpayne@69
|
35827 #endif
|
|
jpayne@69
|
35828 if (unlikely(ret))
|
|
jpayne@69
|
35829 return (long) -1;
|
|
jpayne@69
|
35830 return val;
|
|
jpayne@69
|
35831 }
|
|
jpayne@69
|
35832 raise_overflow:
|
|
jpayne@69
|
35833 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
35834 "value too large to convert to long");
|
|
jpayne@69
|
35835 return (long) -1;
|
|
jpayne@69
|
35836 raise_neg_overflow:
|
|
jpayne@69
|
35837 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
35838 "can't convert negative value to long");
|
|
jpayne@69
|
35839 return (long) -1;
|
|
jpayne@69
|
35840 }
|
|
jpayne@69
|
35841
|
|
jpayne@69
|
35842 /* CIntFromPy */
|
|
jpayne@69
|
35843 static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) {
|
|
jpayne@69
|
35844 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35845 #pragma GCC diagnostic push
|
|
jpayne@69
|
35846 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
35847 #endif
|
|
jpayne@69
|
35848 const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0;
|
|
jpayne@69
|
35849 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
35850 #pragma GCC diagnostic pop
|
|
jpayne@69
|
35851 #endif
|
|
jpayne@69
|
35852 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
35853 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
35854 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
35855 if ((sizeof(int64_t) < sizeof(long))) {
|
|
jpayne@69
|
35856 __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
35857 } else {
|
|
jpayne@69
|
35858 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
35859 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
35860 goto raise_neg_overflow;
|
|
jpayne@69
|
35861 }
|
|
jpayne@69
|
35862 return (int64_t) val;
|
|
jpayne@69
|
35863 }
|
|
jpayne@69
|
35864 }
|
|
jpayne@69
|
35865 #endif
|
|
jpayne@69
|
35866 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
35867 int64_t val;
|
|
jpayne@69
|
35868 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
35869 if (!tmp) return (int64_t) -1;
|
|
jpayne@69
|
35870 val = __Pyx_PyInt_As_int64_t(tmp);
|
|
jpayne@69
|
35871 Py_DECREF(tmp);
|
|
jpayne@69
|
35872 return val;
|
|
jpayne@69
|
35873 }
|
|
jpayne@69
|
35874 if (is_unsigned) {
|
|
jpayne@69
|
35875 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
35876 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
35877 goto raise_neg_overflow;
|
|
jpayne@69
|
35878 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
35879 __PYX_VERIFY_RETURN_INT(int64_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
35880 } else {
|
|
jpayne@69
|
35881 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
35882 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
35883 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
35884 case 2:
|
|
jpayne@69
|
35885 if ((8 * sizeof(int64_t) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35886 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35887 __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35888 } else if ((8 * sizeof(int64_t) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35889 return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]));
|
|
jpayne@69
|
35890 }
|
|
jpayne@69
|
35891 }
|
|
jpayne@69
|
35892 break;
|
|
jpayne@69
|
35893 case 3:
|
|
jpayne@69
|
35894 if ((8 * sizeof(int64_t) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35895 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35896 __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35897 } else if ((8 * sizeof(int64_t) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35898 return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]));
|
|
jpayne@69
|
35899 }
|
|
jpayne@69
|
35900 }
|
|
jpayne@69
|
35901 break;
|
|
jpayne@69
|
35902 case 4:
|
|
jpayne@69
|
35903 if ((8 * sizeof(int64_t) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35904 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35905 __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35906 } else if ((8 * sizeof(int64_t) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35907 return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]));
|
|
jpayne@69
|
35908 }
|
|
jpayne@69
|
35909 }
|
|
jpayne@69
|
35910 break;
|
|
jpayne@69
|
35911 }
|
|
jpayne@69
|
35912 }
|
|
jpayne@69
|
35913 #endif
|
|
jpayne@69
|
35914 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
35915 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
35916 goto raise_neg_overflow;
|
|
jpayne@69
|
35917 }
|
|
jpayne@69
|
35918 #else
|
|
jpayne@69
|
35919 {
|
|
jpayne@69
|
35920 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
35921 if (unlikely(result < 0))
|
|
jpayne@69
|
35922 return (int64_t) -1;
|
|
jpayne@69
|
35923 if (unlikely(result == 1))
|
|
jpayne@69
|
35924 goto raise_neg_overflow;
|
|
jpayne@69
|
35925 }
|
|
jpayne@69
|
35926 #endif
|
|
jpayne@69
|
35927 if ((sizeof(int64_t) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
35928 __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
35929 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
35930 } else if ((sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
35931 __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
35932 #endif
|
|
jpayne@69
|
35933 }
|
|
jpayne@69
|
35934 } else {
|
|
jpayne@69
|
35935 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
35936 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
35937 __PYX_VERIFY_RETURN_INT(int64_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
35938 } else {
|
|
jpayne@69
|
35939 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
35940 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
35941 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
35942 case -2:
|
|
jpayne@69
|
35943 if ((8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35944 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35945 __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35946 } else if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35947 return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])));
|
|
jpayne@69
|
35948 }
|
|
jpayne@69
|
35949 }
|
|
jpayne@69
|
35950 break;
|
|
jpayne@69
|
35951 case 2:
|
|
jpayne@69
|
35952 if ((8 * sizeof(int64_t) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35953 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35954 __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35955 } else if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35956 return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])));
|
|
jpayne@69
|
35957 }
|
|
jpayne@69
|
35958 }
|
|
jpayne@69
|
35959 break;
|
|
jpayne@69
|
35960 case -3:
|
|
jpayne@69
|
35961 if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35962 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35963 __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35964 } else if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35965 return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])));
|
|
jpayne@69
|
35966 }
|
|
jpayne@69
|
35967 }
|
|
jpayne@69
|
35968 break;
|
|
jpayne@69
|
35969 case 3:
|
|
jpayne@69
|
35970 if ((8 * sizeof(int64_t) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35971 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35972 __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35973 } else if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35974 return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])));
|
|
jpayne@69
|
35975 }
|
|
jpayne@69
|
35976 }
|
|
jpayne@69
|
35977 break;
|
|
jpayne@69
|
35978 case -4:
|
|
jpayne@69
|
35979 if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35980 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35981 __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35982 } else if ((8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35983 return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])));
|
|
jpayne@69
|
35984 }
|
|
jpayne@69
|
35985 }
|
|
jpayne@69
|
35986 break;
|
|
jpayne@69
|
35987 case 4:
|
|
jpayne@69
|
35988 if ((8 * sizeof(int64_t) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35989 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35990 __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
35991 } else if ((8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
35992 return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])));
|
|
jpayne@69
|
35993 }
|
|
jpayne@69
|
35994 }
|
|
jpayne@69
|
35995 break;
|
|
jpayne@69
|
35996 }
|
|
jpayne@69
|
35997 }
|
|
jpayne@69
|
35998 #endif
|
|
jpayne@69
|
35999 if ((sizeof(int64_t) <= sizeof(long))) {
|
|
jpayne@69
|
36000 __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x))
|
|
jpayne@69
|
36001 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36002 } else if ((sizeof(int64_t) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
36003 __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
36004 #endif
|
|
jpayne@69
|
36005 }
|
|
jpayne@69
|
36006 }
|
|
jpayne@69
|
36007 {
|
|
jpayne@69
|
36008 int64_t val;
|
|
jpayne@69
|
36009 int ret = -1;
|
|
jpayne@69
|
36010 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
36011 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
36012 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
36013 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
36014 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
36015 goto raise_overflow;
|
|
jpayne@69
|
36016 } else {
|
|
jpayne@69
|
36017 ret = 0;
|
|
jpayne@69
|
36018 }
|
|
jpayne@69
|
36019 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
36020 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
36021 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
36022 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
36023 bytes, sizeof(val),
|
|
jpayne@69
|
36024 is_little, !is_unsigned);
|
|
jpayne@69
|
36025 #else
|
|
jpayne@69
|
36026 PyObject *v;
|
|
jpayne@69
|
36027 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
36028 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
36029 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
36030 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
36031 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
36032 } else {
|
|
jpayne@69
|
36033 v = PyNumber_Long(x);
|
|
jpayne@69
|
36034 if (unlikely(!v)) return (int64_t) -1;
|
|
jpayne@69
|
36035 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
36036 }
|
|
jpayne@69
|
36037 {
|
|
jpayne@69
|
36038 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
36039 if (unlikely(result < 0)) {
|
|
jpayne@69
|
36040 Py_DECREF(v);
|
|
jpayne@69
|
36041 return (int64_t) -1;
|
|
jpayne@69
|
36042 }
|
|
jpayne@69
|
36043 is_negative = result == 1;
|
|
jpayne@69
|
36044 }
|
|
jpayne@69
|
36045 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
36046 Py_DECREF(v);
|
|
jpayne@69
|
36047 goto raise_neg_overflow;
|
|
jpayne@69
|
36048 } else if (is_negative) {
|
|
jpayne@69
|
36049 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
36050 Py_DECREF(v);
|
|
jpayne@69
|
36051 if (unlikely(!stepval))
|
|
jpayne@69
|
36052 return (int64_t) -1;
|
|
jpayne@69
|
36053 } else {
|
|
jpayne@69
|
36054 stepval = v;
|
|
jpayne@69
|
36055 }
|
|
jpayne@69
|
36056 v = NULL;
|
|
jpayne@69
|
36057 val = (int64_t) 0;
|
|
jpayne@69
|
36058 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
36059 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
36060 for (bits = 0; bits < (int) sizeof(int64_t) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
36061 PyObject *tmp, *digit;
|
|
jpayne@69
|
36062 long idigit;
|
|
jpayne@69
|
36063 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
36064 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
36065 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
36066 Py_DECREF(digit);
|
|
jpayne@69
|
36067 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
36068 val |= ((int64_t) idigit) << bits;
|
|
jpayne@69
|
36069 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
36070 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
36071 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
36072 }
|
|
jpayne@69
|
36073 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
36074 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
36075 {
|
|
jpayne@69
|
36076 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
36077 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
36078 remaining_bits = ((int) sizeof(int64_t) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
36079 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
36080 goto raise_overflow;
|
|
jpayne@69
|
36081 val |= ((int64_t) idigit) << bits;
|
|
jpayne@69
|
36082 }
|
|
jpayne@69
|
36083 if (!is_unsigned) {
|
|
jpayne@69
|
36084 if (unlikely(val & (((int64_t) 1) << (sizeof(int64_t) * 8 - 1))))
|
|
jpayne@69
|
36085 goto raise_overflow;
|
|
jpayne@69
|
36086 if (is_negative)
|
|
jpayne@69
|
36087 val = ~val;
|
|
jpayne@69
|
36088 }
|
|
jpayne@69
|
36089 ret = 0;
|
|
jpayne@69
|
36090 done:
|
|
jpayne@69
|
36091 Py_XDECREF(shift);
|
|
jpayne@69
|
36092 Py_XDECREF(mask);
|
|
jpayne@69
|
36093 Py_XDECREF(stepval);
|
|
jpayne@69
|
36094 #endif
|
|
jpayne@69
|
36095 if (unlikely(ret))
|
|
jpayne@69
|
36096 return (int64_t) -1;
|
|
jpayne@69
|
36097 return val;
|
|
jpayne@69
|
36098 }
|
|
jpayne@69
|
36099 raise_overflow:
|
|
jpayne@69
|
36100 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
36101 "value too large to convert to int64_t");
|
|
jpayne@69
|
36102 return (int64_t) -1;
|
|
jpayne@69
|
36103 raise_neg_overflow:
|
|
jpayne@69
|
36104 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
36105 "can't convert negative value to int64_t");
|
|
jpayne@69
|
36106 return (int64_t) -1;
|
|
jpayne@69
|
36107 }
|
|
jpayne@69
|
36108
|
|
jpayne@69
|
36109 /* CIntToPy */
|
|
jpayne@69
|
36110 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) {
|
|
jpayne@69
|
36111 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
36112 #pragma GCC diagnostic push
|
|
jpayne@69
|
36113 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
36114 #endif
|
|
jpayne@69
|
36115 const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0;
|
|
jpayne@69
|
36116 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
36117 #pragma GCC diagnostic pop
|
|
jpayne@69
|
36118 #endif
|
|
jpayne@69
|
36119 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
36120 if (is_unsigned) {
|
|
jpayne@69
|
36121 if (sizeof(int32_t) < sizeof(long)) {
|
|
jpayne@69
|
36122 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
36123 } else if (sizeof(int32_t) <= sizeof(unsigned long)) {
|
|
jpayne@69
|
36124 return PyLong_FromUnsignedLong((unsigned long) value);
|
|
jpayne@69
|
36125 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36126 } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) {
|
|
jpayne@69
|
36127 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
|
|
jpayne@69
|
36128 #endif
|
|
jpayne@69
|
36129 }
|
|
jpayne@69
|
36130 } else {
|
|
jpayne@69
|
36131 if (sizeof(int32_t) <= sizeof(long)) {
|
|
jpayne@69
|
36132 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
36133 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36134 } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) {
|
|
jpayne@69
|
36135 return PyLong_FromLongLong((PY_LONG_LONG) value);
|
|
jpayne@69
|
36136 #endif
|
|
jpayne@69
|
36137 }
|
|
jpayne@69
|
36138 }
|
|
jpayne@69
|
36139 {
|
|
jpayne@69
|
36140 unsigned char *bytes = (unsigned char *)&value;
|
|
jpayne@69
|
36141 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
36142 if (is_unsigned) {
|
|
jpayne@69
|
36143 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
36144 } else {
|
|
jpayne@69
|
36145 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
36146 }
|
|
jpayne@69
|
36147 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
36148 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
36149 return _PyLong_FromByteArray(bytes, sizeof(int32_t),
|
|
jpayne@69
|
36150 little, !is_unsigned);
|
|
jpayne@69
|
36151 #else
|
|
jpayne@69
|
36152 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
36153 PyObject *from_bytes, *result = NULL;
|
|
jpayne@69
|
36154 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
|
|
jpayne@69
|
36155 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
|
|
jpayne@69
|
36156 if (!from_bytes) return NULL;
|
|
jpayne@69
|
36157 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int32_t));
|
|
jpayne@69
|
36158 if (!py_bytes) goto limited_bad;
|
|
jpayne@69
|
36159 order_str = PyUnicode_FromString(little ? "little" : "big");
|
|
jpayne@69
|
36160 if (!order_str) goto limited_bad;
|
|
jpayne@69
|
36161 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
|
|
jpayne@69
|
36162 if (!arg_tuple) goto limited_bad;
|
|
jpayne@69
|
36163 if (!is_unsigned) {
|
|
jpayne@69
|
36164 kwds = PyDict_New();
|
|
jpayne@69
|
36165 if (!kwds) goto limited_bad;
|
|
jpayne@69
|
36166 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
|
|
jpayne@69
|
36167 }
|
|
jpayne@69
|
36168 result = PyObject_Call(from_bytes, arg_tuple, kwds);
|
|
jpayne@69
|
36169 limited_bad:
|
|
jpayne@69
|
36170 Py_XDECREF(kwds);
|
|
jpayne@69
|
36171 Py_XDECREF(arg_tuple);
|
|
jpayne@69
|
36172 Py_XDECREF(order_str);
|
|
jpayne@69
|
36173 Py_XDECREF(py_bytes);
|
|
jpayne@69
|
36174 Py_XDECREF(from_bytes);
|
|
jpayne@69
|
36175 return result;
|
|
jpayne@69
|
36176 #endif
|
|
jpayne@69
|
36177 }
|
|
jpayne@69
|
36178 }
|
|
jpayne@69
|
36179
|
|
jpayne@69
|
36180 /* CIntToPy */
|
|
jpayne@69
|
36181 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
|
|
jpayne@69
|
36182 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
36183 #pragma GCC diagnostic push
|
|
jpayne@69
|
36184 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
36185 #endif
|
|
jpayne@69
|
36186 const long neg_one = (long) -1, const_zero = (long) 0;
|
|
jpayne@69
|
36187 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
36188 #pragma GCC diagnostic pop
|
|
jpayne@69
|
36189 #endif
|
|
jpayne@69
|
36190 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
36191 if (is_unsigned) {
|
|
jpayne@69
|
36192 if (sizeof(long) < sizeof(long)) {
|
|
jpayne@69
|
36193 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
36194 } else if (sizeof(long) <= sizeof(unsigned long)) {
|
|
jpayne@69
|
36195 return PyLong_FromUnsignedLong((unsigned long) value);
|
|
jpayne@69
|
36196 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36197 } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
|
|
jpayne@69
|
36198 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
|
|
jpayne@69
|
36199 #endif
|
|
jpayne@69
|
36200 }
|
|
jpayne@69
|
36201 } else {
|
|
jpayne@69
|
36202 if (sizeof(long) <= sizeof(long)) {
|
|
jpayne@69
|
36203 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
36204 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36205 } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
|
|
jpayne@69
|
36206 return PyLong_FromLongLong((PY_LONG_LONG) value);
|
|
jpayne@69
|
36207 #endif
|
|
jpayne@69
|
36208 }
|
|
jpayne@69
|
36209 }
|
|
jpayne@69
|
36210 {
|
|
jpayne@69
|
36211 unsigned char *bytes = (unsigned char *)&value;
|
|
jpayne@69
|
36212 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
36213 if (is_unsigned) {
|
|
jpayne@69
|
36214 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
36215 } else {
|
|
jpayne@69
|
36216 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
36217 }
|
|
jpayne@69
|
36218 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
36219 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
36220 return _PyLong_FromByteArray(bytes, sizeof(long),
|
|
jpayne@69
|
36221 little, !is_unsigned);
|
|
jpayne@69
|
36222 #else
|
|
jpayne@69
|
36223 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
36224 PyObject *from_bytes, *result = NULL;
|
|
jpayne@69
|
36225 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
|
|
jpayne@69
|
36226 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
|
|
jpayne@69
|
36227 if (!from_bytes) return NULL;
|
|
jpayne@69
|
36228 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(long));
|
|
jpayne@69
|
36229 if (!py_bytes) goto limited_bad;
|
|
jpayne@69
|
36230 order_str = PyUnicode_FromString(little ? "little" : "big");
|
|
jpayne@69
|
36231 if (!order_str) goto limited_bad;
|
|
jpayne@69
|
36232 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
|
|
jpayne@69
|
36233 if (!arg_tuple) goto limited_bad;
|
|
jpayne@69
|
36234 if (!is_unsigned) {
|
|
jpayne@69
|
36235 kwds = PyDict_New();
|
|
jpayne@69
|
36236 if (!kwds) goto limited_bad;
|
|
jpayne@69
|
36237 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
|
|
jpayne@69
|
36238 }
|
|
jpayne@69
|
36239 result = PyObject_Call(from_bytes, arg_tuple, kwds);
|
|
jpayne@69
|
36240 limited_bad:
|
|
jpayne@69
|
36241 Py_XDECREF(kwds);
|
|
jpayne@69
|
36242 Py_XDECREF(arg_tuple);
|
|
jpayne@69
|
36243 Py_XDECREF(order_str);
|
|
jpayne@69
|
36244 Py_XDECREF(py_bytes);
|
|
jpayne@69
|
36245 Py_XDECREF(from_bytes);
|
|
jpayne@69
|
36246 return result;
|
|
jpayne@69
|
36247 #endif
|
|
jpayne@69
|
36248 }
|
|
jpayne@69
|
36249 }
|
|
jpayne@69
|
36250
|
|
jpayne@69
|
36251 /* CIntFromPy */
|
|
jpayne@69
|
36252 static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) {
|
|
jpayne@69
|
36253 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
36254 #pragma GCC diagnostic push
|
|
jpayne@69
|
36255 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
36256 #endif
|
|
jpayne@69
|
36257 const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0;
|
|
jpayne@69
|
36258 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
36259 #pragma GCC diagnostic pop
|
|
jpayne@69
|
36260 #endif
|
|
jpayne@69
|
36261 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
36262 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
36263 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
36264 if ((sizeof(int32_t) < sizeof(long))) {
|
|
jpayne@69
|
36265 __PYX_VERIFY_RETURN_INT(int32_t, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
36266 } else {
|
|
jpayne@69
|
36267 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
36268 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
36269 goto raise_neg_overflow;
|
|
jpayne@69
|
36270 }
|
|
jpayne@69
|
36271 return (int32_t) val;
|
|
jpayne@69
|
36272 }
|
|
jpayne@69
|
36273 }
|
|
jpayne@69
|
36274 #endif
|
|
jpayne@69
|
36275 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
36276 int32_t val;
|
|
jpayne@69
|
36277 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
36278 if (!tmp) return (int32_t) -1;
|
|
jpayne@69
|
36279 val = __Pyx_PyInt_As_int32_t(tmp);
|
|
jpayne@69
|
36280 Py_DECREF(tmp);
|
|
jpayne@69
|
36281 return val;
|
|
jpayne@69
|
36282 }
|
|
jpayne@69
|
36283 if (is_unsigned) {
|
|
jpayne@69
|
36284 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
36285 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
36286 goto raise_neg_overflow;
|
|
jpayne@69
|
36287 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
36288 __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
36289 } else {
|
|
jpayne@69
|
36290 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
36291 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
36292 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
36293 case 2:
|
|
jpayne@69
|
36294 if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36295 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36296 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36297 } else if ((8 * sizeof(int32_t) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36298 return (int32_t) (((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
|
|
jpayne@69
|
36299 }
|
|
jpayne@69
|
36300 }
|
|
jpayne@69
|
36301 break;
|
|
jpayne@69
|
36302 case 3:
|
|
jpayne@69
|
36303 if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36304 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36305 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36306 } else if ((8 * sizeof(int32_t) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36307 return (int32_t) (((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
|
|
jpayne@69
|
36308 }
|
|
jpayne@69
|
36309 }
|
|
jpayne@69
|
36310 break;
|
|
jpayne@69
|
36311 case 4:
|
|
jpayne@69
|
36312 if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36313 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36314 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36315 } else if ((8 * sizeof(int32_t) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36316 return (int32_t) (((((((((int32_t)digits[3]) << PyLong_SHIFT) | (int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
|
|
jpayne@69
|
36317 }
|
|
jpayne@69
|
36318 }
|
|
jpayne@69
|
36319 break;
|
|
jpayne@69
|
36320 }
|
|
jpayne@69
|
36321 }
|
|
jpayne@69
|
36322 #endif
|
|
jpayne@69
|
36323 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
36324 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
36325 goto raise_neg_overflow;
|
|
jpayne@69
|
36326 }
|
|
jpayne@69
|
36327 #else
|
|
jpayne@69
|
36328 {
|
|
jpayne@69
|
36329 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
36330 if (unlikely(result < 0))
|
|
jpayne@69
|
36331 return (int32_t) -1;
|
|
jpayne@69
|
36332 if (unlikely(result == 1))
|
|
jpayne@69
|
36333 goto raise_neg_overflow;
|
|
jpayne@69
|
36334 }
|
|
jpayne@69
|
36335 #endif
|
|
jpayne@69
|
36336 if ((sizeof(int32_t) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
36337 __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
36338 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36339 } else if ((sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
36340 __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
36341 #endif
|
|
jpayne@69
|
36342 }
|
|
jpayne@69
|
36343 } else {
|
|
jpayne@69
|
36344 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
36345 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
36346 __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
36347 } else {
|
|
jpayne@69
|
36348 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
36349 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
36350 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
36351 case -2:
|
|
jpayne@69
|
36352 if ((8 * sizeof(int32_t) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36353 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36354 __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36355 } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36356 return (int32_t) (((int32_t)-1)*(((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
36357 }
|
|
jpayne@69
|
36358 }
|
|
jpayne@69
|
36359 break;
|
|
jpayne@69
|
36360 case 2:
|
|
jpayne@69
|
36361 if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36362 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36363 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36364 } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36365 return (int32_t) ((((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
36366 }
|
|
jpayne@69
|
36367 }
|
|
jpayne@69
|
36368 break;
|
|
jpayne@69
|
36369 case -3:
|
|
jpayne@69
|
36370 if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36371 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36372 __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36373 } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36374 return (int32_t) (((int32_t)-1)*(((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
36375 }
|
|
jpayne@69
|
36376 }
|
|
jpayne@69
|
36377 break;
|
|
jpayne@69
|
36378 case 3:
|
|
jpayne@69
|
36379 if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36380 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36381 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36382 } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36383 return (int32_t) ((((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
36384 }
|
|
jpayne@69
|
36385 }
|
|
jpayne@69
|
36386 break;
|
|
jpayne@69
|
36387 case -4:
|
|
jpayne@69
|
36388 if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36389 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36390 __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36391 } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36392 return (int32_t) (((int32_t)-1)*(((((((((int32_t)digits[3]) << PyLong_SHIFT) | (int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
36393 }
|
|
jpayne@69
|
36394 }
|
|
jpayne@69
|
36395 break;
|
|
jpayne@69
|
36396 case 4:
|
|
jpayne@69
|
36397 if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36398 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36399 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
36400 } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
36401 return (int32_t) ((((((((((int32_t)digits[3]) << PyLong_SHIFT) | (int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
36402 }
|
|
jpayne@69
|
36403 }
|
|
jpayne@69
|
36404 break;
|
|
jpayne@69
|
36405 }
|
|
jpayne@69
|
36406 }
|
|
jpayne@69
|
36407 #endif
|
|
jpayne@69
|
36408 if ((sizeof(int32_t) <= sizeof(long))) {
|
|
jpayne@69
|
36409 __PYX_VERIFY_RETURN_INT_EXC(int32_t, long, PyLong_AsLong(x))
|
|
jpayne@69
|
36410 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
36411 } else if ((sizeof(int32_t) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
36412 __PYX_VERIFY_RETURN_INT_EXC(int32_t, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
36413 #endif
|
|
jpayne@69
|
36414 }
|
|
jpayne@69
|
36415 }
|
|
jpayne@69
|
36416 {
|
|
jpayne@69
|
36417 int32_t val;
|
|
jpayne@69
|
36418 int ret = -1;
|
|
jpayne@69
|
36419 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
36420 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
36421 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
36422 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
36423 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
36424 goto raise_overflow;
|
|
jpayne@69
|
36425 } else {
|
|
jpayne@69
|
36426 ret = 0;
|
|
jpayne@69
|
36427 }
|
|
jpayne@69
|
36428 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
36429 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
36430 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
36431 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
36432 bytes, sizeof(val),
|
|
jpayne@69
|
36433 is_little, !is_unsigned);
|
|
jpayne@69
|
36434 #else
|
|
jpayne@69
|
36435 PyObject *v;
|
|
jpayne@69
|
36436 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
36437 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
36438 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
36439 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
36440 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
36441 } else {
|
|
jpayne@69
|
36442 v = PyNumber_Long(x);
|
|
jpayne@69
|
36443 if (unlikely(!v)) return (int32_t) -1;
|
|
jpayne@69
|
36444 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
36445 }
|
|
jpayne@69
|
36446 {
|
|
jpayne@69
|
36447 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
36448 if (unlikely(result < 0)) {
|
|
jpayne@69
|
36449 Py_DECREF(v);
|
|
jpayne@69
|
36450 return (int32_t) -1;
|
|
jpayne@69
|
36451 }
|
|
jpayne@69
|
36452 is_negative = result == 1;
|
|
jpayne@69
|
36453 }
|
|
jpayne@69
|
36454 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
36455 Py_DECREF(v);
|
|
jpayne@69
|
36456 goto raise_neg_overflow;
|
|
jpayne@69
|
36457 } else if (is_negative) {
|
|
jpayne@69
|
36458 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
36459 Py_DECREF(v);
|
|
jpayne@69
|
36460 if (unlikely(!stepval))
|
|
jpayne@69
|
36461 return (int32_t) -1;
|
|
jpayne@69
|
36462 } else {
|
|
jpayne@69
|
36463 stepval = v;
|
|
jpayne@69
|
36464 }
|
|
jpayne@69
|
36465 v = NULL;
|
|
jpayne@69
|
36466 val = (int32_t) 0;
|
|
jpayne@69
|
36467 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
36468 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
36469 for (bits = 0; bits < (int) sizeof(int32_t) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
36470 PyObject *tmp, *digit;
|
|
jpayne@69
|
36471 long idigit;
|
|
jpayne@69
|
36472 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
36473 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
36474 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
36475 Py_DECREF(digit);
|
|
jpayne@69
|
36476 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
36477 val |= ((int32_t) idigit) << bits;
|
|
jpayne@69
|
36478 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
36479 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
36480 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
36481 }
|
|
jpayne@69
|
36482 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
36483 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
36484 {
|
|
jpayne@69
|
36485 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
36486 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
36487 remaining_bits = ((int) sizeof(int32_t) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
36488 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
36489 goto raise_overflow;
|
|
jpayne@69
|
36490 val |= ((int32_t) idigit) << bits;
|
|
jpayne@69
|
36491 }
|
|
jpayne@69
|
36492 if (!is_unsigned) {
|
|
jpayne@69
|
36493 if (unlikely(val & (((int32_t) 1) << (sizeof(int32_t) * 8 - 1))))
|
|
jpayne@69
|
36494 goto raise_overflow;
|
|
jpayne@69
|
36495 if (is_negative)
|
|
jpayne@69
|
36496 val = ~val;
|
|
jpayne@69
|
36497 }
|
|
jpayne@69
|
36498 ret = 0;
|
|
jpayne@69
|
36499 done:
|
|
jpayne@69
|
36500 Py_XDECREF(shift);
|
|
jpayne@69
|
36501 Py_XDECREF(mask);
|
|
jpayne@69
|
36502 Py_XDECREF(stepval);
|
|
jpayne@69
|
36503 #endif
|
|
jpayne@69
|
36504 if (unlikely(ret))
|
|
jpayne@69
|
36505 return (int32_t) -1;
|
|
jpayne@69
|
36506 return val;
|
|
jpayne@69
|
36507 }
|
|
jpayne@69
|
36508 raise_overflow:
|
|
jpayne@69
|
36509 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
36510 "value too large to convert to int32_t");
|
|
jpayne@69
|
36511 return (int32_t) -1;
|
|
jpayne@69
|
36512 raise_neg_overflow:
|
|
jpayne@69
|
36513 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
36514 "can't convert negative value to int32_t");
|
|
jpayne@69
|
36515 return (int32_t) -1;
|
|
jpayne@69
|
36516 }
|
|
jpayne@69
|
36517
|
|
jpayne@69
|
36518 /* FormatTypeName */
|
|
jpayne@69
|
36519 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
36520 static __Pyx_TypeName
|
|
jpayne@69
|
36521 __Pyx_PyType_GetName(PyTypeObject* tp)
|
|
jpayne@69
|
36522 {
|
|
jpayne@69
|
36523 PyObject *name = __Pyx_PyObject_GetAttrStr((PyObject *)tp,
|
|
jpayne@69
|
36524 __pyx_n_s_name);
|
|
jpayne@69
|
36525 if (unlikely(name == NULL) || unlikely(!PyUnicode_Check(name))) {
|
|
jpayne@69
|
36526 PyErr_Clear();
|
|
jpayne@69
|
36527 Py_XDECREF(name);
|
|
jpayne@69
|
36528 name = __Pyx_NewRef(__pyx_n_s__78);
|
|
jpayne@69
|
36529 }
|
|
jpayne@69
|
36530 return name;
|
|
jpayne@69
|
36531 }
|
|
jpayne@69
|
36532 #endif
|
|
jpayne@69
|
36533
|
|
jpayne@69
|
36534 /* FastTypeChecks */
|
|
jpayne@69
|
36535 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
36536 static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) {
|
|
jpayne@69
|
36537 while (a) {
|
|
jpayne@69
|
36538 a = __Pyx_PyType_GetSlot(a, tp_base, PyTypeObject*);
|
|
jpayne@69
|
36539 if (a == b)
|
|
jpayne@69
|
36540 return 1;
|
|
jpayne@69
|
36541 }
|
|
jpayne@69
|
36542 return b == &PyBaseObject_Type;
|
|
jpayne@69
|
36543 }
|
|
jpayne@69
|
36544 static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) {
|
|
jpayne@69
|
36545 PyObject *mro;
|
|
jpayne@69
|
36546 if (a == b) return 1;
|
|
jpayne@69
|
36547 mro = a->tp_mro;
|
|
jpayne@69
|
36548 if (likely(mro)) {
|
|
jpayne@69
|
36549 Py_ssize_t i, n;
|
|
jpayne@69
|
36550 n = PyTuple_GET_SIZE(mro);
|
|
jpayne@69
|
36551 for (i = 0; i < n; i++) {
|
|
jpayne@69
|
36552 if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b)
|
|
jpayne@69
|
36553 return 1;
|
|
jpayne@69
|
36554 }
|
|
jpayne@69
|
36555 return 0;
|
|
jpayne@69
|
36556 }
|
|
jpayne@69
|
36557 return __Pyx_InBases(a, b);
|
|
jpayne@69
|
36558 }
|
|
jpayne@69
|
36559 static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b) {
|
|
jpayne@69
|
36560 PyObject *mro;
|
|
jpayne@69
|
36561 if (cls == a || cls == b) return 1;
|
|
jpayne@69
|
36562 mro = cls->tp_mro;
|
|
jpayne@69
|
36563 if (likely(mro)) {
|
|
jpayne@69
|
36564 Py_ssize_t i, n;
|
|
jpayne@69
|
36565 n = PyTuple_GET_SIZE(mro);
|
|
jpayne@69
|
36566 for (i = 0; i < n; i++) {
|
|
jpayne@69
|
36567 PyObject *base = PyTuple_GET_ITEM(mro, i);
|
|
jpayne@69
|
36568 if (base == (PyObject *)a || base == (PyObject *)b)
|
|
jpayne@69
|
36569 return 1;
|
|
jpayne@69
|
36570 }
|
|
jpayne@69
|
36571 return 0;
|
|
jpayne@69
|
36572 }
|
|
jpayne@69
|
36573 return __Pyx_InBases(cls, a) || __Pyx_InBases(cls, b);
|
|
jpayne@69
|
36574 }
|
|
jpayne@69
|
36575 #if PY_MAJOR_VERSION == 2
|
|
jpayne@69
|
36576 static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) {
|
|
jpayne@69
|
36577 PyObject *exception, *value, *tb;
|
|
jpayne@69
|
36578 int res;
|
|
jpayne@69
|
36579 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
36580 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
36581 __Pyx_ErrFetch(&exception, &value, &tb);
|
|
jpayne@69
|
36582 res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0;
|
|
jpayne@69
|
36583 if (unlikely(res == -1)) {
|
|
jpayne@69
|
36584 PyErr_WriteUnraisable(err);
|
|
jpayne@69
|
36585 res = 0;
|
|
jpayne@69
|
36586 }
|
|
jpayne@69
|
36587 if (!res) {
|
|
jpayne@69
|
36588 res = PyObject_IsSubclass(err, exc_type2);
|
|
jpayne@69
|
36589 if (unlikely(res == -1)) {
|
|
jpayne@69
|
36590 PyErr_WriteUnraisable(err);
|
|
jpayne@69
|
36591 res = 0;
|
|
jpayne@69
|
36592 }
|
|
jpayne@69
|
36593 }
|
|
jpayne@69
|
36594 __Pyx_ErrRestore(exception, value, tb);
|
|
jpayne@69
|
36595 return res;
|
|
jpayne@69
|
36596 }
|
|
jpayne@69
|
36597 #else
|
|
jpayne@69
|
36598 static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) {
|
|
jpayne@69
|
36599 if (exc_type1) {
|
|
jpayne@69
|
36600 return __Pyx_IsAnySubtype2((PyTypeObject*)err, (PyTypeObject*)exc_type1, (PyTypeObject*)exc_type2);
|
|
jpayne@69
|
36601 } else {
|
|
jpayne@69
|
36602 return __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2);
|
|
jpayne@69
|
36603 }
|
|
jpayne@69
|
36604 }
|
|
jpayne@69
|
36605 #endif
|
|
jpayne@69
|
36606 static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
|
|
jpayne@69
|
36607 Py_ssize_t i, n;
|
|
jpayne@69
|
36608 assert(PyExceptionClass_Check(exc_type));
|
|
jpayne@69
|
36609 n = PyTuple_GET_SIZE(tuple);
|
|
jpayne@69
|
36610 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
36611 for (i=0; i<n; i++) {
|
|
jpayne@69
|
36612 if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
|
|
jpayne@69
|
36613 }
|
|
jpayne@69
|
36614 #endif
|
|
jpayne@69
|
36615 for (i=0; i<n; i++) {
|
|
jpayne@69
|
36616 PyObject *t = PyTuple_GET_ITEM(tuple, i);
|
|
jpayne@69
|
36617 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
36618 if (likely(exc_type == t)) return 1;
|
|
jpayne@69
|
36619 #endif
|
|
jpayne@69
|
36620 if (likely(PyExceptionClass_Check(t))) {
|
|
jpayne@69
|
36621 if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1;
|
|
jpayne@69
|
36622 } else {
|
|
jpayne@69
|
36623 }
|
|
jpayne@69
|
36624 }
|
|
jpayne@69
|
36625 return 0;
|
|
jpayne@69
|
36626 }
|
|
jpayne@69
|
36627 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) {
|
|
jpayne@69
|
36628 if (likely(err == exc_type)) return 1;
|
|
jpayne@69
|
36629 if (likely(PyExceptionClass_Check(err))) {
|
|
jpayne@69
|
36630 if (likely(PyExceptionClass_Check(exc_type))) {
|
|
jpayne@69
|
36631 return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type);
|
|
jpayne@69
|
36632 } else if (likely(PyTuple_Check(exc_type))) {
|
|
jpayne@69
|
36633 return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type);
|
|
jpayne@69
|
36634 } else {
|
|
jpayne@69
|
36635 }
|
|
jpayne@69
|
36636 }
|
|
jpayne@69
|
36637 return PyErr_GivenExceptionMatches(err, exc_type);
|
|
jpayne@69
|
36638 }
|
|
jpayne@69
|
36639 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) {
|
|
jpayne@69
|
36640 assert(PyExceptionClass_Check(exc_type1));
|
|
jpayne@69
|
36641 assert(PyExceptionClass_Check(exc_type2));
|
|
jpayne@69
|
36642 if (likely(err == exc_type1 || err == exc_type2)) return 1;
|
|
jpayne@69
|
36643 if (likely(PyExceptionClass_Check(err))) {
|
|
jpayne@69
|
36644 return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2);
|
|
jpayne@69
|
36645 }
|
|
jpayne@69
|
36646 return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2));
|
|
jpayne@69
|
36647 }
|
|
jpayne@69
|
36648 #endif
|
|
jpayne@69
|
36649
|
|
jpayne@69
|
36650 /* CheckBinaryVersion */
|
|
jpayne@69
|
36651 static unsigned long __Pyx_get_runtime_version(void) {
|
|
jpayne@69
|
36652 #if __PYX_LIMITED_VERSION_HEX >= 0x030B00A4
|
|
jpayne@69
|
36653 return Py_Version & ~0xFFUL;
|
|
jpayne@69
|
36654 #else
|
|
jpayne@69
|
36655 const char* rt_version = Py_GetVersion();
|
|
jpayne@69
|
36656 unsigned long version = 0;
|
|
jpayne@69
|
36657 unsigned long factor = 0x01000000UL;
|
|
jpayne@69
|
36658 unsigned int digit = 0;
|
|
jpayne@69
|
36659 int i = 0;
|
|
jpayne@69
|
36660 while (factor) {
|
|
jpayne@69
|
36661 while ('0' <= rt_version[i] && rt_version[i] <= '9') {
|
|
jpayne@69
|
36662 digit = digit * 10 + (unsigned int) (rt_version[i] - '0');
|
|
jpayne@69
|
36663 ++i;
|
|
jpayne@69
|
36664 }
|
|
jpayne@69
|
36665 version += factor * digit;
|
|
jpayne@69
|
36666 if (rt_version[i] != '.')
|
|
jpayne@69
|
36667 break;
|
|
jpayne@69
|
36668 digit = 0;
|
|
jpayne@69
|
36669 factor >>= 8;
|
|
jpayne@69
|
36670 ++i;
|
|
jpayne@69
|
36671 }
|
|
jpayne@69
|
36672 return version;
|
|
jpayne@69
|
36673 #endif
|
|
jpayne@69
|
36674 }
|
|
jpayne@69
|
36675 static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer) {
|
|
jpayne@69
|
36676 const unsigned long MAJOR_MINOR = 0xFFFF0000UL;
|
|
jpayne@69
|
36677 if ((rt_version & MAJOR_MINOR) == (ct_version & MAJOR_MINOR))
|
|
jpayne@69
|
36678 return 0;
|
|
jpayne@69
|
36679 if (likely(allow_newer && (rt_version & MAJOR_MINOR) > (ct_version & MAJOR_MINOR)))
|
|
jpayne@69
|
36680 return 1;
|
|
jpayne@69
|
36681 {
|
|
jpayne@69
|
36682 char message[200];
|
|
jpayne@69
|
36683 PyOS_snprintf(message, sizeof(message),
|
|
jpayne@69
|
36684 "compile time Python version %d.%d "
|
|
jpayne@69
|
36685 "of module '%.100s' "
|
|
jpayne@69
|
36686 "%s "
|
|
jpayne@69
|
36687 "runtime version %d.%d",
|
|
jpayne@69
|
36688 (int) (ct_version >> 24), (int) ((ct_version >> 16) & 0xFF),
|
|
jpayne@69
|
36689 __Pyx_MODULE_NAME,
|
|
jpayne@69
|
36690 (allow_newer) ? "was newer than" : "does not match",
|
|
jpayne@69
|
36691 (int) (rt_version >> 24), (int) ((rt_version >> 16) & 0xFF)
|
|
jpayne@69
|
36692 );
|
|
jpayne@69
|
36693 return PyErr_WarnEx(NULL, message, 1);
|
|
jpayne@69
|
36694 }
|
|
jpayne@69
|
36695 }
|
|
jpayne@69
|
36696
|
|
jpayne@69
|
36697 /* FunctionImport */
|
|
jpayne@69
|
36698 #ifndef __PYX_HAVE_RT_ImportFunction_3_0_11
|
|
jpayne@69
|
36699 #define __PYX_HAVE_RT_ImportFunction_3_0_11
|
|
jpayne@69
|
36700 static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig) {
|
|
jpayne@69
|
36701 PyObject *d = 0;
|
|
jpayne@69
|
36702 PyObject *cobj = 0;
|
|
jpayne@69
|
36703 union {
|
|
jpayne@69
|
36704 void (*fp)(void);
|
|
jpayne@69
|
36705 void *p;
|
|
jpayne@69
|
36706 } tmp;
|
|
jpayne@69
|
36707 d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
|
|
jpayne@69
|
36708 if (!d)
|
|
jpayne@69
|
36709 goto bad;
|
|
jpayne@69
|
36710 cobj = PyDict_GetItemString(d, funcname);
|
|
jpayne@69
|
36711 if (!cobj) {
|
|
jpayne@69
|
36712 PyErr_Format(PyExc_ImportError,
|
|
jpayne@69
|
36713 "%.200s does not export expected C function %.200s",
|
|
jpayne@69
|
36714 PyModule_GetName(module), funcname);
|
|
jpayne@69
|
36715 goto bad;
|
|
jpayne@69
|
36716 }
|
|
jpayne@69
|
36717 if (!PyCapsule_IsValid(cobj, sig)) {
|
|
jpayne@69
|
36718 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
36719 "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
|
|
jpayne@69
|
36720 PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj));
|
|
jpayne@69
|
36721 goto bad;
|
|
jpayne@69
|
36722 }
|
|
jpayne@69
|
36723 tmp.p = PyCapsule_GetPointer(cobj, sig);
|
|
jpayne@69
|
36724 *f = tmp.fp;
|
|
jpayne@69
|
36725 if (!(*f))
|
|
jpayne@69
|
36726 goto bad;
|
|
jpayne@69
|
36727 Py_DECREF(d);
|
|
jpayne@69
|
36728 return 0;
|
|
jpayne@69
|
36729 bad:
|
|
jpayne@69
|
36730 Py_XDECREF(d);
|
|
jpayne@69
|
36731 return -1;
|
|
jpayne@69
|
36732 }
|
|
jpayne@69
|
36733 #endif
|
|
jpayne@69
|
36734
|
|
jpayne@69
|
36735 /* InitStrings */
|
|
jpayne@69
|
36736 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
36737 static int __Pyx_InitString(__Pyx_StringTabEntry t, PyObject **str) {
|
|
jpayne@69
|
36738 if (t.is_unicode | t.is_str) {
|
|
jpayne@69
|
36739 if (t.intern) {
|
|
jpayne@69
|
36740 *str = PyUnicode_InternFromString(t.s);
|
|
jpayne@69
|
36741 } else if (t.encoding) {
|
|
jpayne@69
|
36742 *str = PyUnicode_Decode(t.s, t.n - 1, t.encoding, NULL);
|
|
jpayne@69
|
36743 } else {
|
|
jpayne@69
|
36744 *str = PyUnicode_FromStringAndSize(t.s, t.n - 1);
|
|
jpayne@69
|
36745 }
|
|
jpayne@69
|
36746 } else {
|
|
jpayne@69
|
36747 *str = PyBytes_FromStringAndSize(t.s, t.n - 1);
|
|
jpayne@69
|
36748 }
|
|
jpayne@69
|
36749 if (!*str)
|
|
jpayne@69
|
36750 return -1;
|
|
jpayne@69
|
36751 if (PyObject_Hash(*str) == -1)
|
|
jpayne@69
|
36752 return -1;
|
|
jpayne@69
|
36753 return 0;
|
|
jpayne@69
|
36754 }
|
|
jpayne@69
|
36755 #endif
|
|
jpayne@69
|
36756 static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
|
|
jpayne@69
|
36757 while (t->p) {
|
|
jpayne@69
|
36758 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
36759 __Pyx_InitString(*t, t->p);
|
|
jpayne@69
|
36760 #else
|
|
jpayne@69
|
36761 if (t->is_unicode) {
|
|
jpayne@69
|
36762 *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
|
|
jpayne@69
|
36763 } else if (t->intern) {
|
|
jpayne@69
|
36764 *t->p = PyString_InternFromString(t->s);
|
|
jpayne@69
|
36765 } else {
|
|
jpayne@69
|
36766 *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
|
|
jpayne@69
|
36767 }
|
|
jpayne@69
|
36768 if (!*t->p)
|
|
jpayne@69
|
36769 return -1;
|
|
jpayne@69
|
36770 if (PyObject_Hash(*t->p) == -1)
|
|
jpayne@69
|
36771 return -1;
|
|
jpayne@69
|
36772 #endif
|
|
jpayne@69
|
36773 ++t;
|
|
jpayne@69
|
36774 }
|
|
jpayne@69
|
36775 return 0;
|
|
jpayne@69
|
36776 }
|
|
jpayne@69
|
36777
|
|
jpayne@69
|
36778 #include <string.h>
|
|
jpayne@69
|
36779 static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s) {
|
|
jpayne@69
|
36780 size_t len = strlen(s);
|
|
jpayne@69
|
36781 if (unlikely(len > (size_t) PY_SSIZE_T_MAX)) {
|
|
jpayne@69
|
36782 PyErr_SetString(PyExc_OverflowError, "byte string is too long");
|
|
jpayne@69
|
36783 return -1;
|
|
jpayne@69
|
36784 }
|
|
jpayne@69
|
36785 return (Py_ssize_t) len;
|
|
jpayne@69
|
36786 }
|
|
jpayne@69
|
36787 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
|
|
jpayne@69
|
36788 Py_ssize_t len = __Pyx_ssize_strlen(c_str);
|
|
jpayne@69
|
36789 if (unlikely(len < 0)) return NULL;
|
|
jpayne@69
|
36790 return __Pyx_PyUnicode_FromStringAndSize(c_str, len);
|
|
jpayne@69
|
36791 }
|
|
jpayne@69
|
36792 static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char* c_str) {
|
|
jpayne@69
|
36793 Py_ssize_t len = __Pyx_ssize_strlen(c_str);
|
|
jpayne@69
|
36794 if (unlikely(len < 0)) return NULL;
|
|
jpayne@69
|
36795 return PyByteArray_FromStringAndSize(c_str, len);
|
|
jpayne@69
|
36796 }
|
|
jpayne@69
|
36797 static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
|
|
jpayne@69
|
36798 Py_ssize_t ignore;
|
|
jpayne@69
|
36799 return __Pyx_PyObject_AsStringAndSize(o, &ignore);
|
|
jpayne@69
|
36800 }
|
|
jpayne@69
|
36801 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
|
|
jpayne@69
|
36802 #if !CYTHON_PEP393_ENABLED
|
|
jpayne@69
|
36803 static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
|
|
jpayne@69
|
36804 char* defenc_c;
|
|
jpayne@69
|
36805 PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
|
|
jpayne@69
|
36806 if (!defenc) return NULL;
|
|
jpayne@69
|
36807 defenc_c = PyBytes_AS_STRING(defenc);
|
|
jpayne@69
|
36808 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
36809 {
|
|
jpayne@69
|
36810 char* end = defenc_c + PyBytes_GET_SIZE(defenc);
|
|
jpayne@69
|
36811 char* c;
|
|
jpayne@69
|
36812 for (c = defenc_c; c < end; c++) {
|
|
jpayne@69
|
36813 if ((unsigned char) (*c) >= 128) {
|
|
jpayne@69
|
36814 PyUnicode_AsASCIIString(o);
|
|
jpayne@69
|
36815 return NULL;
|
|
jpayne@69
|
36816 }
|
|
jpayne@69
|
36817 }
|
|
jpayne@69
|
36818 }
|
|
jpayne@69
|
36819 #endif
|
|
jpayne@69
|
36820 *length = PyBytes_GET_SIZE(defenc);
|
|
jpayne@69
|
36821 return defenc_c;
|
|
jpayne@69
|
36822 }
|
|
jpayne@69
|
36823 #else
|
|
jpayne@69
|
36824 static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
|
|
jpayne@69
|
36825 if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL;
|
|
jpayne@69
|
36826 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
36827 if (likely(PyUnicode_IS_ASCII(o))) {
|
|
jpayne@69
|
36828 *length = PyUnicode_GET_LENGTH(o);
|
|
jpayne@69
|
36829 return PyUnicode_AsUTF8(o);
|
|
jpayne@69
|
36830 } else {
|
|
jpayne@69
|
36831 PyUnicode_AsASCIIString(o);
|
|
jpayne@69
|
36832 return NULL;
|
|
jpayne@69
|
36833 }
|
|
jpayne@69
|
36834 #else
|
|
jpayne@69
|
36835 return PyUnicode_AsUTF8AndSize(o, length);
|
|
jpayne@69
|
36836 #endif
|
|
jpayne@69
|
36837 }
|
|
jpayne@69
|
36838 #endif
|
|
jpayne@69
|
36839 #endif
|
|
jpayne@69
|
36840 static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
|
|
jpayne@69
|
36841 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
|
|
jpayne@69
|
36842 if (
|
|
jpayne@69
|
36843 #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
36844 __Pyx_sys_getdefaultencoding_not_ascii &&
|
|
jpayne@69
|
36845 #endif
|
|
jpayne@69
|
36846 PyUnicode_Check(o)) {
|
|
jpayne@69
|
36847 return __Pyx_PyUnicode_AsStringAndSize(o, length);
|
|
jpayne@69
|
36848 } else
|
|
jpayne@69
|
36849 #endif
|
|
jpayne@69
|
36850 #if (!CYTHON_COMPILING_IN_PYPY && !CYTHON_COMPILING_IN_LIMITED_API) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
|
|
jpayne@69
|
36851 if (PyByteArray_Check(o)) {
|
|
jpayne@69
|
36852 *length = PyByteArray_GET_SIZE(o);
|
|
jpayne@69
|
36853 return PyByteArray_AS_STRING(o);
|
|
jpayne@69
|
36854 } else
|
|
jpayne@69
|
36855 #endif
|
|
jpayne@69
|
36856 {
|
|
jpayne@69
|
36857 char* result;
|
|
jpayne@69
|
36858 int r = PyBytes_AsStringAndSize(o, &result, length);
|
|
jpayne@69
|
36859 if (unlikely(r < 0)) {
|
|
jpayne@69
|
36860 return NULL;
|
|
jpayne@69
|
36861 } else {
|
|
jpayne@69
|
36862 return result;
|
|
jpayne@69
|
36863 }
|
|
jpayne@69
|
36864 }
|
|
jpayne@69
|
36865 }
|
|
jpayne@69
|
36866 static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
|
|
jpayne@69
|
36867 int is_true = x == Py_True;
|
|
jpayne@69
|
36868 if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
|
|
jpayne@69
|
36869 else return PyObject_IsTrue(x);
|
|
jpayne@69
|
36870 }
|
|
jpayne@69
|
36871 static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) {
|
|
jpayne@69
|
36872 int retval;
|
|
jpayne@69
|
36873 if (unlikely(!x)) return -1;
|
|
jpayne@69
|
36874 retval = __Pyx_PyObject_IsTrue(x);
|
|
jpayne@69
|
36875 Py_DECREF(x);
|
|
jpayne@69
|
36876 return retval;
|
|
jpayne@69
|
36877 }
|
|
jpayne@69
|
36878 static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) {
|
|
jpayne@69
|
36879 __Pyx_TypeName result_type_name = __Pyx_PyType_GetName(Py_TYPE(result));
|
|
jpayne@69
|
36880 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
36881 if (PyLong_Check(result)) {
|
|
jpayne@69
|
36882 if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1,
|
|
jpayne@69
|
36883 "__int__ returned non-int (type " __Pyx_FMT_TYPENAME "). "
|
|
jpayne@69
|
36884 "The ability to return an instance of a strict subclass of int is deprecated, "
|
|
jpayne@69
|
36885 "and may be removed in a future version of Python.",
|
|
jpayne@69
|
36886 result_type_name)) {
|
|
jpayne@69
|
36887 __Pyx_DECREF_TypeName(result_type_name);
|
|
jpayne@69
|
36888 Py_DECREF(result);
|
|
jpayne@69
|
36889 return NULL;
|
|
jpayne@69
|
36890 }
|
|
jpayne@69
|
36891 __Pyx_DECREF_TypeName(result_type_name);
|
|
jpayne@69
|
36892 return result;
|
|
jpayne@69
|
36893 }
|
|
jpayne@69
|
36894 #endif
|
|
jpayne@69
|
36895 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
36896 "__%.4s__ returned non-%.4s (type " __Pyx_FMT_TYPENAME ")",
|
|
jpayne@69
|
36897 type_name, type_name, result_type_name);
|
|
jpayne@69
|
36898 __Pyx_DECREF_TypeName(result_type_name);
|
|
jpayne@69
|
36899 Py_DECREF(result);
|
|
jpayne@69
|
36900 return NULL;
|
|
jpayne@69
|
36901 }
|
|
jpayne@69
|
36902 static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
|
|
jpayne@69
|
36903 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
36904 PyNumberMethods *m;
|
|
jpayne@69
|
36905 #endif
|
|
jpayne@69
|
36906 const char *name = NULL;
|
|
jpayne@69
|
36907 PyObject *res = NULL;
|
|
jpayne@69
|
36908 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
36909 if (likely(PyInt_Check(x) || PyLong_Check(x)))
|
|
jpayne@69
|
36910 #else
|
|
jpayne@69
|
36911 if (likely(PyLong_Check(x)))
|
|
jpayne@69
|
36912 #endif
|
|
jpayne@69
|
36913 return __Pyx_NewRef(x);
|
|
jpayne@69
|
36914 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
36915 m = Py_TYPE(x)->tp_as_number;
|
|
jpayne@69
|
36916 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
36917 if (m && m->nb_int) {
|
|
jpayne@69
|
36918 name = "int";
|
|
jpayne@69
|
36919 res = m->nb_int(x);
|
|
jpayne@69
|
36920 }
|
|
jpayne@69
|
36921 else if (m && m->nb_long) {
|
|
jpayne@69
|
36922 name = "long";
|
|
jpayne@69
|
36923 res = m->nb_long(x);
|
|
jpayne@69
|
36924 }
|
|
jpayne@69
|
36925 #else
|
|
jpayne@69
|
36926 if (likely(m && m->nb_int)) {
|
|
jpayne@69
|
36927 name = "int";
|
|
jpayne@69
|
36928 res = m->nb_int(x);
|
|
jpayne@69
|
36929 }
|
|
jpayne@69
|
36930 #endif
|
|
jpayne@69
|
36931 #else
|
|
jpayne@69
|
36932 if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) {
|
|
jpayne@69
|
36933 res = PyNumber_Int(x);
|
|
jpayne@69
|
36934 }
|
|
jpayne@69
|
36935 #endif
|
|
jpayne@69
|
36936 if (likely(res)) {
|
|
jpayne@69
|
36937 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
36938 if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) {
|
|
jpayne@69
|
36939 #else
|
|
jpayne@69
|
36940 if (unlikely(!PyLong_CheckExact(res))) {
|
|
jpayne@69
|
36941 #endif
|
|
jpayne@69
|
36942 return __Pyx_PyNumber_IntOrLongWrongResultType(res, name);
|
|
jpayne@69
|
36943 }
|
|
jpayne@69
|
36944 }
|
|
jpayne@69
|
36945 else if (!PyErr_Occurred()) {
|
|
jpayne@69
|
36946 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
36947 "an integer is required");
|
|
jpayne@69
|
36948 }
|
|
jpayne@69
|
36949 return res;
|
|
jpayne@69
|
36950 }
|
|
jpayne@69
|
36951 static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
|
|
jpayne@69
|
36952 Py_ssize_t ival;
|
|
jpayne@69
|
36953 PyObject *x;
|
|
jpayne@69
|
36954 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
36955 if (likely(PyInt_CheckExact(b))) {
|
|
jpayne@69
|
36956 if (sizeof(Py_ssize_t) >= sizeof(long))
|
|
jpayne@69
|
36957 return PyInt_AS_LONG(b);
|
|
jpayne@69
|
36958 else
|
|
jpayne@69
|
36959 return PyInt_AsSsize_t(b);
|
|
jpayne@69
|
36960 }
|
|
jpayne@69
|
36961 #endif
|
|
jpayne@69
|
36962 if (likely(PyLong_CheckExact(b))) {
|
|
jpayne@69
|
36963 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
36964 if (likely(__Pyx_PyLong_IsCompact(b))) {
|
|
jpayne@69
|
36965 return __Pyx_PyLong_CompactValue(b);
|
|
jpayne@69
|
36966 } else {
|
|
jpayne@69
|
36967 const digit* digits = __Pyx_PyLong_Digits(b);
|
|
jpayne@69
|
36968 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(b);
|
|
jpayne@69
|
36969 switch (size) {
|
|
jpayne@69
|
36970 case 2:
|
|
jpayne@69
|
36971 if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
36972 return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
36973 }
|
|
jpayne@69
|
36974 break;
|
|
jpayne@69
|
36975 case -2:
|
|
jpayne@69
|
36976 if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
36977 return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
36978 }
|
|
jpayne@69
|
36979 break;
|
|
jpayne@69
|
36980 case 3:
|
|
jpayne@69
|
36981 if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
36982 return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
36983 }
|
|
jpayne@69
|
36984 break;
|
|
jpayne@69
|
36985 case -3:
|
|
jpayne@69
|
36986 if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
36987 return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
36988 }
|
|
jpayne@69
|
36989 break;
|
|
jpayne@69
|
36990 case 4:
|
|
jpayne@69
|
36991 if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
36992 return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
36993 }
|
|
jpayne@69
|
36994 break;
|
|
jpayne@69
|
36995 case -4:
|
|
jpayne@69
|
36996 if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
36997 return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
36998 }
|
|
jpayne@69
|
36999 break;
|
|
jpayne@69
|
37000 }
|
|
jpayne@69
|
37001 }
|
|
jpayne@69
|
37002 #endif
|
|
jpayne@69
|
37003 return PyLong_AsSsize_t(b);
|
|
jpayne@69
|
37004 }
|
|
jpayne@69
|
37005 x = PyNumber_Index(b);
|
|
jpayne@69
|
37006 if (!x) return -1;
|
|
jpayne@69
|
37007 ival = PyInt_AsSsize_t(x);
|
|
jpayne@69
|
37008 Py_DECREF(x);
|
|
jpayne@69
|
37009 return ival;
|
|
jpayne@69
|
37010 }
|
|
jpayne@69
|
37011 static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
|
|
jpayne@69
|
37012 if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
|
|
jpayne@69
|
37013 return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
|
|
jpayne@69
|
37014 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
37015 } else if (likely(PyInt_CheckExact(o))) {
|
|
jpayne@69
|
37016 return PyInt_AS_LONG(o);
|
|
jpayne@69
|
37017 #endif
|
|
jpayne@69
|
37018 } else {
|
|
jpayne@69
|
37019 Py_ssize_t ival;
|
|
jpayne@69
|
37020 PyObject *x;
|
|
jpayne@69
|
37021 x = PyNumber_Index(o);
|
|
jpayne@69
|
37022 if (!x) return -1;
|
|
jpayne@69
|
37023 ival = PyInt_AsLong(x);
|
|
jpayne@69
|
37024 Py_DECREF(x);
|
|
jpayne@69
|
37025 return ival;
|
|
jpayne@69
|
37026 }
|
|
jpayne@69
|
37027 }
|
|
jpayne@69
|
37028 static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
|
|
jpayne@69
|
37029 return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
|
|
jpayne@69
|
37030 }
|
|
jpayne@69
|
37031 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
|
|
jpayne@69
|
37032 return PyInt_FromSize_t(ival);
|
|
jpayne@69
|
37033 }
|
|
jpayne@69
|
37034
|
|
jpayne@69
|
37035
|
|
jpayne@69
|
37036 /* #### Code section: utility_code_pragmas_end ### */
|
|
jpayne@69
|
37037 #ifdef _MSC_VER
|
|
jpayne@69
|
37038 #pragma warning( pop )
|
|
jpayne@69
|
37039 #endif
|
|
jpayne@69
|
37040
|
|
jpayne@69
|
37041
|
|
jpayne@69
|
37042
|
|
jpayne@69
|
37043 /* #### Code section: end ### */
|
|
jpayne@69
|
37044 #endif /* Py_PYTHON_H */
|
