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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
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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/bcftools/bcftools.pysam.h",
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jpayne@69
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14 "/project/samtools/samtools.pysam.h"
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jpayne@69
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15 ],
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jpayne@69
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16 "extra_compile_args": [
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jpayne@69
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17 "-Wno-unused",
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jpayne@69
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18 "-Wno-strict-prototypes",
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jpayne@69
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19 "-Wno-sign-compare",
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jpayne@69
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20 "-Wno-error=declaration-after-statement"
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jpayne@69
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21 ],
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jpayne@69
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22 "extra_link_args": [
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jpayne@69
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23 "-Wl,-rpath,$ORIGIN"
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jpayne@69
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24 ],
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jpayne@69
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25 "include_dirs": [
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jpayne@69
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26 "/project/pysam",
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jpayne@69
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27 "/project/htslib",
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jpayne@69
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28 "/project/samtools",
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jpayne@69
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29 "/project/samtools/lz4",
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jpayne@69
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30 "/project/bcftools",
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jpayne@69
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31 "/project"
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jpayne@69
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32 ],
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jpayne@69
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33 "language": "c",
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jpayne@69
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34 "libraries": [
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jpayne@69
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35 "z",
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jpayne@69
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36 "lzma",
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jpayne@69
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37 "bz2",
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jpayne@69
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38 "z",
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jpayne@69
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39 "m",
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jpayne@69
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40 "curl",
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jpayne@69
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41 "crypto",
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jpayne@69
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42 "chtslib.cpython-37m-x86_64-linux-gnu",
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jpayne@69
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43 "csamtools.cpython-37m-x86_64-linux-gnu",
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jpayne@69
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44 "cbcftools.cpython-37m-x86_64-linux-gnu"
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jpayne@69
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45 ],
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jpayne@69
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46 "library_dirs": [
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jpayne@69
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47 "/project/pysam",
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jpayne@69
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48 "/project",
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jpayne@69
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49 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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50 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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51 "build/lib.linux-x86_64-cpython-37/pysam",
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jpayne@69
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52 "build/lib.linux-x86_64-cpython-37/pysam"
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jpayne@69
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53 ],
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jpayne@69
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54 "name": "pysam.libcutils",
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jpayne@69
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55 "sources": [
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jpayne@69
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56 "pysam/libcutils.pyx",
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jpayne@69
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57 "pysam/pysam_util.c"
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jpayne@69
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58 ]
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jpayne@69
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59 },
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jpayne@69
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60 "module_name": "pysam.libcutils"
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jpayne@69
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61 }
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jpayne@69
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62 END: Cython Metadata */
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jpayne@69
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63
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jpayne@69
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64 #ifndef PY_SSIZE_T_CLEAN
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jpayne@69
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65 #define PY_SSIZE_T_CLEAN
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jpayne@69
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66 #endif /* PY_SSIZE_T_CLEAN */
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jpayne@69
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67 #if defined(CYTHON_LIMITED_API) && 0
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jpayne@69
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68 #ifndef Py_LIMITED_API
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jpayne@69
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69 #if CYTHON_LIMITED_API+0 > 0x03030000
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jpayne@69
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70 #define Py_LIMITED_API CYTHON_LIMITED_API
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jpayne@69
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71 #else
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jpayne@69
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72 #define Py_LIMITED_API 0x03030000
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jpayne@69
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73 #endif
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jpayne@69
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74 #endif
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jpayne@69
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75 #endif
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jpayne@69
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76
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jpayne@69
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77 #include "Python.h"
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jpayne@69
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78
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jpayne@69
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79 #if PY_MAJOR_VERSION >= 3
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jpayne@69
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80 #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj)
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jpayne@69
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81 #else
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jpayne@69
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82 #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj, NULL)
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jpayne@69
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83 #endif
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jpayne@69
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84
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jpayne@69
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85
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jpayne@69
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86 #if PY_MAJOR_VERSION <= 2
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jpayne@69
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87 #define PyDict_GetItemWithError _PyDict_GetItemWithError
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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
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jpayne@69
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91 #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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92 #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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93 #endif
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jpayne@69
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94
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jpayne@69
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95 #ifndef Py_PYTHON_H
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jpayne@69
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96 #error Python headers needed to compile C extensions, please install development version of Python.
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jpayne@69
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97 #elif PY_VERSION_HEX < 0x02070000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
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jpayne@69
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98 #error Cython requires Python 2.7+ or Python 3.3+.
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jpayne@69
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99 #else
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jpayne@69
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100 #if defined(CYTHON_LIMITED_API) && CYTHON_LIMITED_API
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jpayne@69
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101 #define __PYX_EXTRA_ABI_MODULE_NAME "limited"
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jpayne@69
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102 #else
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jpayne@69
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103 #define __PYX_EXTRA_ABI_MODULE_NAME ""
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jpayne@69
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104 #endif
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jpayne@69
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105 #define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME
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jpayne@69
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106 #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI
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jpayne@69
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107 #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "."
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jpayne@69
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108 #define CYTHON_HEX_VERSION 0x03000BF0
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jpayne@69
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109 #define CYTHON_FUTURE_DIVISION 1
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jpayne@69
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110 #include <stddef.h>
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jpayne@69
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111 #ifndef offsetof
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jpayne@69
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112 #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
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jpayne@69
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113 #endif
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jpayne@69
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114 #if !defined(_WIN32) && !defined(WIN32) && !defined(MS_WINDOWS)
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jpayne@69
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115 #ifndef __stdcall
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jpayne@69
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116 #define __stdcall
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jpayne@69
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117 #endif
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jpayne@69
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118 #ifndef __cdecl
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jpayne@69
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119 #define __cdecl
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jpayne@69
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120 #endif
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jpayne@69
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121 #ifndef __fastcall
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jpayne@69
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122 #define __fastcall
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jpayne@69
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123 #endif
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jpayne@69
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124 #endif
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jpayne@69
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125 #ifndef DL_IMPORT
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jpayne@69
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126 #define DL_IMPORT(t) t
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jpayne@69
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127 #endif
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jpayne@69
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128 #ifndef DL_EXPORT
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jpayne@69
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129 #define DL_EXPORT(t) t
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jpayne@69
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130 #endif
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jpayne@69
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131 #define __PYX_COMMA ,
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jpayne@69
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132 #ifndef HAVE_LONG_LONG
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jpayne@69
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133 #define HAVE_LONG_LONG
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jpayne@69
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134 #endif
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jpayne@69
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135 #ifndef PY_LONG_LONG
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jpayne@69
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136 #define PY_LONG_LONG LONG_LONG
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jpayne@69
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137 #endif
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jpayne@69
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138 #ifndef Py_HUGE_VAL
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jpayne@69
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139 #define Py_HUGE_VAL HUGE_VAL
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jpayne@69
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140 #endif
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jpayne@69
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141 #define __PYX_LIMITED_VERSION_HEX PY_VERSION_HEX
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jpayne@69
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142 #if defined(GRAALVM_PYTHON)
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jpayne@69
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143 /* For very preliminary testing purposes. Most variables are set the same as PyPy.
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jpayne@69
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144 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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145 #define CYTHON_COMPILING_IN_PYPY 0
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jpayne@69
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146 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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147 #define CYTHON_COMPILING_IN_LIMITED_API 0
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jpayne@69
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148 #define CYTHON_COMPILING_IN_GRAAL 1
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jpayne@69
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149 #define CYTHON_COMPILING_IN_NOGIL 0
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jpayne@69
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150 #undef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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151 #define CYTHON_USE_TYPE_SLOTS 0
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jpayne@69
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152 #undef CYTHON_USE_TYPE_SPECS
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jpayne@69
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153 #define CYTHON_USE_TYPE_SPECS 0
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jpayne@69
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154 #undef CYTHON_USE_PYTYPE_LOOKUP
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jpayne@69
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155 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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156 #if PY_VERSION_HEX < 0x03050000
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jpayne@69
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157 #undef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
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158 #define CYTHON_USE_ASYNC_SLOTS 0
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jpayne@69
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159 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
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jpayne@69
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160 #define CYTHON_USE_ASYNC_SLOTS 1
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jpayne@69
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161 #endif
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jpayne@69
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162 #undef CYTHON_USE_PYLIST_INTERNALS
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jpayne@69
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163 #define CYTHON_USE_PYLIST_INTERNALS 0
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jpayne@69
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164 #undef CYTHON_USE_UNICODE_INTERNALS
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jpayne@69
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165 #define CYTHON_USE_UNICODE_INTERNALS 0
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jpayne@69
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166 #undef CYTHON_USE_UNICODE_WRITER
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jpayne@69
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167 #define CYTHON_USE_UNICODE_WRITER 0
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jpayne@69
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168 #undef CYTHON_USE_PYLONG_INTERNALS
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jpayne@69
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169 #define CYTHON_USE_PYLONG_INTERNALS 0
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jpayne@69
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170 #undef CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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171 #define CYTHON_AVOID_BORROWED_REFS 1
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jpayne@69
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172 #undef CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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173 #define CYTHON_ASSUME_SAFE_MACROS 0
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jpayne@69
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174 #undef CYTHON_UNPACK_METHODS
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jpayne@69
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175 #define CYTHON_UNPACK_METHODS 0
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jpayne@69
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176 #undef CYTHON_FAST_THREAD_STATE
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jpayne@69
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177 #define CYTHON_FAST_THREAD_STATE 0
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jpayne@69
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178 #undef CYTHON_FAST_GIL
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jpayne@69
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179 #define CYTHON_FAST_GIL 0
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jpayne@69
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180 #undef CYTHON_METH_FASTCALL
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jpayne@69
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181 #define CYTHON_METH_FASTCALL 0
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jpayne@69
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182 #undef CYTHON_FAST_PYCALL
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jpayne@69
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183 #define CYTHON_FAST_PYCALL 0
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jpayne@69
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184 #ifndef CYTHON_PEP487_INIT_SUBCLASS
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jpayne@69
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185 #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3)
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jpayne@69
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186 #endif
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jpayne@69
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187 #undef CYTHON_PEP489_MULTI_PHASE_INIT
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jpayne@69
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188 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
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jpayne@69
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189 #undef CYTHON_USE_MODULE_STATE
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jpayne@69
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190 #define CYTHON_USE_MODULE_STATE 0
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jpayne@69
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191 #undef CYTHON_USE_TP_FINALIZE
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jpayne@69
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192 #define CYTHON_USE_TP_FINALIZE 0
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jpayne@69
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193 #undef CYTHON_USE_DICT_VERSIONS
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jpayne@69
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194 #define CYTHON_USE_DICT_VERSIONS 0
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jpayne@69
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195 #undef CYTHON_USE_EXC_INFO_STACK
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jpayne@69
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196 #define CYTHON_USE_EXC_INFO_STACK 0
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jpayne@69
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197 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
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jpayne@69
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198 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
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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_USE_FREELISTS
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jpayne@69
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201 #define CYTHON_USE_FREELISTS 0
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jpayne@69
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202 #elif defined(PYPY_VERSION)
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jpayne@69
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203 #define CYTHON_COMPILING_IN_PYPY 1
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jpayne@69
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204 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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205 #define CYTHON_COMPILING_IN_LIMITED_API 0
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jpayne@69
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206 #define CYTHON_COMPILING_IN_GRAAL 0
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jpayne@69
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207 #define CYTHON_COMPILING_IN_NOGIL 0
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jpayne@69
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208 #undef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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209 #define CYTHON_USE_TYPE_SLOTS 0
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jpayne@69
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210 #ifndef CYTHON_USE_TYPE_SPECS
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jpayne@69
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211 #define CYTHON_USE_TYPE_SPECS 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_PYTYPE_LOOKUP
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jpayne@69
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214 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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215 #if PY_VERSION_HEX < 0x03050000
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jpayne@69
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216 #undef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
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217 #define CYTHON_USE_ASYNC_SLOTS 0
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jpayne@69
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218 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
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jpayne@69
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219 #define CYTHON_USE_ASYNC_SLOTS 1
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jpayne@69
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220 #endif
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jpayne@69
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221 #undef CYTHON_USE_PYLIST_INTERNALS
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jpayne@69
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222 #define CYTHON_USE_PYLIST_INTERNALS 0
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jpayne@69
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223 #undef CYTHON_USE_UNICODE_INTERNALS
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jpayne@69
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224 #define CYTHON_USE_UNICODE_INTERNALS 0
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jpayne@69
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225 #undef CYTHON_USE_UNICODE_WRITER
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jpayne@69
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226 #define CYTHON_USE_UNICODE_WRITER 0
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jpayne@69
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227 #undef CYTHON_USE_PYLONG_INTERNALS
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jpayne@69
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228 #define CYTHON_USE_PYLONG_INTERNALS 0
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jpayne@69
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229 #undef CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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230 #define CYTHON_AVOID_BORROWED_REFS 1
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jpayne@69
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231 #undef CYTHON_ASSUME_SAFE_MACROS
|
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jpayne@69
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232 #define CYTHON_ASSUME_SAFE_MACROS 0
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jpayne@69
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233 #undef CYTHON_UNPACK_METHODS
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jpayne@69
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234 #define CYTHON_UNPACK_METHODS 0
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jpayne@69
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235 #undef CYTHON_FAST_THREAD_STATE
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jpayne@69
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236 #define CYTHON_FAST_THREAD_STATE 0
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jpayne@69
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237 #undef CYTHON_FAST_GIL
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jpayne@69
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238 #define CYTHON_FAST_GIL 0
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jpayne@69
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239 #undef CYTHON_METH_FASTCALL
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jpayne@69
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240 #define CYTHON_METH_FASTCALL 0
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jpayne@69
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241 #undef CYTHON_FAST_PYCALL
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jpayne@69
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242 #define CYTHON_FAST_PYCALL 0
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jpayne@69
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243 #ifndef CYTHON_PEP487_INIT_SUBCLASS
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jpayne@69
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244 #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3)
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jpayne@69
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245 #endif
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jpayne@69
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246 #if PY_VERSION_HEX < 0x03090000
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jpayne@69
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247 #undef CYTHON_PEP489_MULTI_PHASE_INIT
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jpayne@69
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248 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
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jpayne@69
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249 #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
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jpayne@69
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250 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
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jpayne@69
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251 #endif
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jpayne@69
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252 #undef CYTHON_USE_MODULE_STATE
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jpayne@69
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253 #define CYTHON_USE_MODULE_STATE 0
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jpayne@69
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254 #undef CYTHON_USE_TP_FINALIZE
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jpayne@69
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255 #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1 && PYPY_VERSION_NUM >= 0x07030C00)
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jpayne@69
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256 #undef CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
257 #define CYTHON_USE_DICT_VERSIONS 0
|
|
jpayne@69
|
258 #undef CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
259 #define CYTHON_USE_EXC_INFO_STACK 0
|
|
jpayne@69
|
260 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
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|
jpayne@69
|
261 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
|
|
jpayne@69
|
262 #endif
|
|
jpayne@69
|
263 #undef CYTHON_USE_FREELISTS
|
|
jpayne@69
|
264 #define CYTHON_USE_FREELISTS 0
|
|
jpayne@69
|
265 #elif defined(CYTHON_LIMITED_API)
|
|
jpayne@69
|
266 #ifdef Py_LIMITED_API
|
|
jpayne@69
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267 #undef __PYX_LIMITED_VERSION_HEX
|
|
jpayne@69
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268 #define __PYX_LIMITED_VERSION_HEX Py_LIMITED_API
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jpayne@69
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269 #endif
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jpayne@69
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270 #define CYTHON_COMPILING_IN_PYPY 0
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|
jpayne@69
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271 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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272 #define CYTHON_COMPILING_IN_LIMITED_API 1
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jpayne@69
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273 #define CYTHON_COMPILING_IN_GRAAL 0
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jpayne@69
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274 #define CYTHON_COMPILING_IN_NOGIL 0
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jpayne@69
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275 #undef CYTHON_CLINE_IN_TRACEBACK
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jpayne@69
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276 #define CYTHON_CLINE_IN_TRACEBACK 0
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jpayne@69
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277 #undef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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278 #define CYTHON_USE_TYPE_SLOTS 0
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jpayne@69
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279 #undef CYTHON_USE_TYPE_SPECS
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jpayne@69
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280 #define CYTHON_USE_TYPE_SPECS 1
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jpayne@69
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281 #undef CYTHON_USE_PYTYPE_LOOKUP
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jpayne@69
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282 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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283 #undef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
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284 #define CYTHON_USE_ASYNC_SLOTS 0
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jpayne@69
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285 #undef CYTHON_USE_PYLIST_INTERNALS
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jpayne@69
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286 #define CYTHON_USE_PYLIST_INTERNALS 0
|
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jpayne@69
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287 #undef CYTHON_USE_UNICODE_INTERNALS
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jpayne@69
|
288 #define CYTHON_USE_UNICODE_INTERNALS 0
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jpayne@69
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289 #ifndef CYTHON_USE_UNICODE_WRITER
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jpayne@69
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290 #define CYTHON_USE_UNICODE_WRITER 0
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jpayne@69
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291 #endif
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jpayne@69
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292 #undef CYTHON_USE_PYLONG_INTERNALS
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jpayne@69
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293 #define CYTHON_USE_PYLONG_INTERNALS 0
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jpayne@69
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294 #ifndef CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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295 #define CYTHON_AVOID_BORROWED_REFS 0
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jpayne@69
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296 #endif
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jpayne@69
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297 #undef CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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298 #define CYTHON_ASSUME_SAFE_MACROS 0
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jpayne@69
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299 #undef CYTHON_UNPACK_METHODS
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jpayne@69
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300 #define CYTHON_UNPACK_METHODS 0
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jpayne@69
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301 #undef CYTHON_FAST_THREAD_STATE
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jpayne@69
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302 #define CYTHON_FAST_THREAD_STATE 0
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jpayne@69
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303 #undef CYTHON_FAST_GIL
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jpayne@69
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304 #define CYTHON_FAST_GIL 0
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jpayne@69
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305 #undef CYTHON_METH_FASTCALL
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jpayne@69
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306 #define CYTHON_METH_FASTCALL 0
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jpayne@69
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307 #undef CYTHON_FAST_PYCALL
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jpayne@69
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308 #define CYTHON_FAST_PYCALL 0
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jpayne@69
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309 #ifndef CYTHON_PEP487_INIT_SUBCLASS
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jpayne@69
|
310 #define CYTHON_PEP487_INIT_SUBCLASS 1
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jpayne@69
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311 #endif
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jpayne@69
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312 #undef CYTHON_PEP489_MULTI_PHASE_INIT
|
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jpayne@69
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313 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
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jpayne@69
|
314 #undef CYTHON_USE_MODULE_STATE
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jpayne@69
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315 #define CYTHON_USE_MODULE_STATE 1
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jpayne@69
|
316 #ifndef CYTHON_USE_TP_FINALIZE
|
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jpayne@69
|
317 #define CYTHON_USE_TP_FINALIZE 0
|
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jpayne@69
|
318 #endif
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jpayne@69
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319 #undef CYTHON_USE_DICT_VERSIONS
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jpayne@69
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320 #define CYTHON_USE_DICT_VERSIONS 0
|
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jpayne@69
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321 #undef CYTHON_USE_EXC_INFO_STACK
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jpayne@69
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322 #define CYTHON_USE_EXC_INFO_STACK 0
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jpayne@69
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323 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
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jpayne@69
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324 #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
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jpayne@69
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325 #endif
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jpayne@69
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326 #undef CYTHON_USE_FREELISTS
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jpayne@69
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327 #define CYTHON_USE_FREELISTS 0
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jpayne@69
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328 #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL)
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jpayne@69
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329 #define CYTHON_COMPILING_IN_PYPY 0
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jpayne@69
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330 #define CYTHON_COMPILING_IN_CPYTHON 0
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jpayne@69
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331 #define CYTHON_COMPILING_IN_LIMITED_API 0
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jpayne@69
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332 #define CYTHON_COMPILING_IN_GRAAL 0
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jpayne@69
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333 #define CYTHON_COMPILING_IN_NOGIL 1
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jpayne@69
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334 #ifndef CYTHON_USE_TYPE_SLOTS
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jpayne@69
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335 #define CYTHON_USE_TYPE_SLOTS 1
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jpayne@69
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336 #endif
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jpayne@69
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337 #ifndef CYTHON_USE_TYPE_SPECS
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jpayne@69
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338 #define CYTHON_USE_TYPE_SPECS 0
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jpayne@69
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339 #endif
|
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jpayne@69
|
340 #undef CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
341 #define CYTHON_USE_PYTYPE_LOOKUP 0
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jpayne@69
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342 #ifndef CYTHON_USE_ASYNC_SLOTS
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jpayne@69
|
343 #define CYTHON_USE_ASYNC_SLOTS 1
|
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jpayne@69
|
344 #endif
|
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jpayne@69
|
345 #ifndef CYTHON_USE_PYLONG_INTERNALS
|
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jpayne@69
|
346 #define CYTHON_USE_PYLONG_INTERNALS 0
|
|
jpayne@69
|
347 #endif
|
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jpayne@69
|
348 #undef CYTHON_USE_PYLIST_INTERNALS
|
|
jpayne@69
|
349 #define CYTHON_USE_PYLIST_INTERNALS 0
|
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jpayne@69
|
350 #ifndef CYTHON_USE_UNICODE_INTERNALS
|
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jpayne@69
|
351 #define CYTHON_USE_UNICODE_INTERNALS 1
|
|
jpayne@69
|
352 #endif
|
|
jpayne@69
|
353 #undef CYTHON_USE_UNICODE_WRITER
|
|
jpayne@69
|
354 #define CYTHON_USE_UNICODE_WRITER 0
|
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jpayne@69
|
355 #ifndef CYTHON_AVOID_BORROWED_REFS
|
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jpayne@69
|
356 #define CYTHON_AVOID_BORROWED_REFS 0
|
|
jpayne@69
|
357 #endif
|
|
jpayne@69
|
358 #ifndef CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
359 #define CYTHON_ASSUME_SAFE_MACROS 1
|
|
jpayne@69
|
360 #endif
|
|
jpayne@69
|
361 #ifndef CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
362 #define CYTHON_UNPACK_METHODS 1
|
|
jpayne@69
|
363 #endif
|
|
jpayne@69
|
364 #undef CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
365 #define CYTHON_FAST_THREAD_STATE 0
|
|
jpayne@69
|
366 #undef CYTHON_FAST_GIL
|
|
jpayne@69
|
367 #define CYTHON_FAST_GIL 0
|
|
jpayne@69
|
368 #ifndef CYTHON_METH_FASTCALL
|
|
jpayne@69
|
369 #define CYTHON_METH_FASTCALL 1
|
|
jpayne@69
|
370 #endif
|
|
jpayne@69
|
371 #undef CYTHON_FAST_PYCALL
|
|
jpayne@69
|
372 #define CYTHON_FAST_PYCALL 0
|
|
jpayne@69
|
373 #ifndef CYTHON_PEP487_INIT_SUBCLASS
|
|
jpayne@69
|
374 #define CYTHON_PEP487_INIT_SUBCLASS 1
|
|
jpayne@69
|
375 #endif
|
|
jpayne@69
|
376 #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
377 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
|
|
jpayne@69
|
378 #endif
|
|
jpayne@69
|
379 #ifndef CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
380 #define CYTHON_USE_MODULE_STATE 0
|
|
jpayne@69
|
381 #endif
|
|
jpayne@69
|
382 #ifndef CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
383 #define CYTHON_USE_TP_FINALIZE 1
|
|
jpayne@69
|
384 #endif
|
|
jpayne@69
|
385 #undef CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
386 #define CYTHON_USE_DICT_VERSIONS 0
|
|
jpayne@69
|
387 #undef CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
388 #define CYTHON_USE_EXC_INFO_STACK 0
|
|
jpayne@69
|
389 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
390 #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
|
|
jpayne@69
|
391 #endif
|
|
jpayne@69
|
392 #ifndef CYTHON_USE_FREELISTS
|
|
jpayne@69
|
393 #define CYTHON_USE_FREELISTS 0
|
|
jpayne@69
|
394 #endif
|
|
jpayne@69
|
395 #else
|
|
jpayne@69
|
396 #define CYTHON_COMPILING_IN_PYPY 0
|
|
jpayne@69
|
397 #define CYTHON_COMPILING_IN_CPYTHON 1
|
|
jpayne@69
|
398 #define CYTHON_COMPILING_IN_LIMITED_API 0
|
|
jpayne@69
|
399 #define CYTHON_COMPILING_IN_GRAAL 0
|
|
jpayne@69
|
400 #define CYTHON_COMPILING_IN_NOGIL 0
|
|
jpayne@69
|
401 #ifndef CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
402 #define CYTHON_USE_TYPE_SLOTS 1
|
|
jpayne@69
|
403 #endif
|
|
jpayne@69
|
404 #ifndef CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
405 #define CYTHON_USE_TYPE_SPECS 0
|
|
jpayne@69
|
406 #endif
|
|
jpayne@69
|
407 #ifndef CYTHON_USE_PYTYPE_LOOKUP
|
|
jpayne@69
|
408 #define CYTHON_USE_PYTYPE_LOOKUP 1
|
|
jpayne@69
|
409 #endif
|
|
jpayne@69
|
410 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
411 #undef CYTHON_USE_ASYNC_SLOTS
|
|
jpayne@69
|
412 #define CYTHON_USE_ASYNC_SLOTS 0
|
|
jpayne@69
|
413 #elif !defined(CYTHON_USE_ASYNC_SLOTS)
|
|
jpayne@69
|
414 #define CYTHON_USE_ASYNC_SLOTS 1
|
|
jpayne@69
|
415 #endif
|
|
jpayne@69
|
416 #ifndef CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
417 #define CYTHON_USE_PYLONG_INTERNALS 1
|
|
jpayne@69
|
418 #endif
|
|
jpayne@69
|
419 #ifndef CYTHON_USE_PYLIST_INTERNALS
|
|
jpayne@69
|
420 #define CYTHON_USE_PYLIST_INTERNALS 1
|
|
jpayne@69
|
421 #endif
|
|
jpayne@69
|
422 #ifndef CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
423 #define CYTHON_USE_UNICODE_INTERNALS 1
|
|
jpayne@69
|
424 #endif
|
|
jpayne@69
|
425 #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
|
|
jpayne@69
|
426 #undef CYTHON_USE_UNICODE_WRITER
|
|
jpayne@69
|
427 #define CYTHON_USE_UNICODE_WRITER 0
|
|
jpayne@69
|
428 #elif !defined(CYTHON_USE_UNICODE_WRITER)
|
|
jpayne@69
|
429 #define CYTHON_USE_UNICODE_WRITER 1
|
|
jpayne@69
|
430 #endif
|
|
jpayne@69
|
431 #ifndef CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
432 #define CYTHON_AVOID_BORROWED_REFS 0
|
|
jpayne@69
|
433 #endif
|
|
jpayne@69
|
434 #ifndef CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
435 #define CYTHON_ASSUME_SAFE_MACROS 1
|
|
jpayne@69
|
436 #endif
|
|
jpayne@69
|
437 #ifndef CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
438 #define CYTHON_UNPACK_METHODS 1
|
|
jpayne@69
|
439 #endif
|
|
jpayne@69
|
440 #ifndef CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
441 #define CYTHON_FAST_THREAD_STATE 1
|
|
jpayne@69
|
442 #endif
|
|
jpayne@69
|
443 #ifndef CYTHON_FAST_GIL
|
|
jpayne@69
|
444 #define CYTHON_FAST_GIL (PY_MAJOR_VERSION < 3 || PY_VERSION_HEX >= 0x03060000 && PY_VERSION_HEX < 0x030C00A6)
|
|
jpayne@69
|
445 #endif
|
|
jpayne@69
|
446 #ifndef CYTHON_METH_FASTCALL
|
|
jpayne@69
|
447 #define CYTHON_METH_FASTCALL (PY_VERSION_HEX >= 0x030700A1)
|
|
jpayne@69
|
448 #endif
|
|
jpayne@69
|
449 #ifndef CYTHON_FAST_PYCALL
|
|
jpayne@69
|
450 #define CYTHON_FAST_PYCALL 1
|
|
jpayne@69
|
451 #endif
|
|
jpayne@69
|
452 #ifndef CYTHON_PEP487_INIT_SUBCLASS
|
|
jpayne@69
|
453 #define CYTHON_PEP487_INIT_SUBCLASS 1
|
|
jpayne@69
|
454 #endif
|
|
jpayne@69
|
455 #if PY_VERSION_HEX < 0x03050000
|
|
jpayne@69
|
456 #undef CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
457 #define CYTHON_PEP489_MULTI_PHASE_INIT 0
|
|
jpayne@69
|
458 #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT)
|
|
jpayne@69
|
459 #define CYTHON_PEP489_MULTI_PHASE_INIT 1
|
|
jpayne@69
|
460 #endif
|
|
jpayne@69
|
461 #ifndef CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
462 #define CYTHON_USE_MODULE_STATE 0
|
|
jpayne@69
|
463 #endif
|
|
jpayne@69
|
464 #if PY_VERSION_HEX < 0x030400a1
|
|
jpayne@69
|
465 #undef CYTHON_USE_TP_FINALIZE
|
|
jpayne@69
|
466 #define CYTHON_USE_TP_FINALIZE 0
|
|
jpayne@69
|
467 #elif !defined(CYTHON_USE_TP_FINALIZE)
|
|
jpayne@69
|
468 #define CYTHON_USE_TP_FINALIZE 1
|
|
jpayne@69
|
469 #endif
|
|
jpayne@69
|
470 #if PY_VERSION_HEX < 0x030600B1
|
|
jpayne@69
|
471 #undef CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
472 #define CYTHON_USE_DICT_VERSIONS 0
|
|
jpayne@69
|
473 #elif !defined(CYTHON_USE_DICT_VERSIONS)
|
|
jpayne@69
|
474 #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX < 0x030C00A5)
|
|
jpayne@69
|
475 #endif
|
|
jpayne@69
|
476 #if PY_VERSION_HEX < 0x030700A3
|
|
jpayne@69
|
477 #undef CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
478 #define CYTHON_USE_EXC_INFO_STACK 0
|
|
jpayne@69
|
479 #elif !defined(CYTHON_USE_EXC_INFO_STACK)
|
|
jpayne@69
|
480 #define CYTHON_USE_EXC_INFO_STACK 1
|
|
jpayne@69
|
481 #endif
|
|
jpayne@69
|
482 #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
|
|
jpayne@69
|
483 #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
|
|
jpayne@69
|
484 #endif
|
|
jpayne@69
|
485 #ifndef CYTHON_USE_FREELISTS
|
|
jpayne@69
|
486 #define CYTHON_USE_FREELISTS 1
|
|
jpayne@69
|
487 #endif
|
|
jpayne@69
|
488 #endif
|
|
jpayne@69
|
489 #if !defined(CYTHON_FAST_PYCCALL)
|
|
jpayne@69
|
490 #define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
|
|
jpayne@69
|
491 #endif
|
|
jpayne@69
|
492 #if !defined(CYTHON_VECTORCALL)
|
|
jpayne@69
|
493 #define CYTHON_VECTORCALL (CYTHON_FAST_PYCCALL && PY_VERSION_HEX >= 0x030800B1)
|
|
jpayne@69
|
494 #endif
|
|
jpayne@69
|
495 #define CYTHON_BACKPORT_VECTORCALL (CYTHON_METH_FASTCALL && PY_VERSION_HEX < 0x030800B1)
|
|
jpayne@69
|
496 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
497 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
498 #include "longintrepr.h"
|
|
jpayne@69
|
499 #endif
|
|
jpayne@69
|
500 #undef SHIFT
|
|
jpayne@69
|
501 #undef BASE
|
|
jpayne@69
|
502 #undef MASK
|
|
jpayne@69
|
503 #ifdef SIZEOF_VOID_P
|
|
jpayne@69
|
504 enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) };
|
|
jpayne@69
|
505 #endif
|
|
jpayne@69
|
506 #endif
|
|
jpayne@69
|
507 #ifndef __has_attribute
|
|
jpayne@69
|
508 #define __has_attribute(x) 0
|
|
jpayne@69
|
509 #endif
|
|
jpayne@69
|
510 #ifndef __has_cpp_attribute
|
|
jpayne@69
|
511 #define __has_cpp_attribute(x) 0
|
|
jpayne@69
|
512 #endif
|
|
jpayne@69
|
513 #ifndef CYTHON_RESTRICT
|
|
jpayne@69
|
514 #if defined(__GNUC__)
|
|
jpayne@69
|
515 #define CYTHON_RESTRICT __restrict__
|
|
jpayne@69
|
516 #elif defined(_MSC_VER) && _MSC_VER >= 1400
|
|
jpayne@69
|
517 #define CYTHON_RESTRICT __restrict
|
|
jpayne@69
|
518 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
|
|
jpayne@69
|
519 #define CYTHON_RESTRICT restrict
|
|
jpayne@69
|
520 #else
|
|
jpayne@69
|
521 #define CYTHON_RESTRICT
|
|
jpayne@69
|
522 #endif
|
|
jpayne@69
|
523 #endif
|
|
jpayne@69
|
524 #ifndef CYTHON_UNUSED
|
|
jpayne@69
|
525 #if defined(__cplusplus)
|
|
jpayne@69
|
526 /* for clang __has_cpp_attribute(maybe_unused) is true even before C++17
|
|
jpayne@69
|
527 * but leads to warnings with -pedantic, since it is a C++17 feature */
|
|
jpayne@69
|
528 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
|
|
jpayne@69
|
529 #if __has_cpp_attribute(maybe_unused)
|
|
jpayne@69
|
530 #define CYTHON_UNUSED [[maybe_unused]]
|
|
jpayne@69
|
531 #endif
|
|
jpayne@69
|
532 #endif
|
|
jpayne@69
|
533 #endif
|
|
jpayne@69
|
534 #endif
|
|
jpayne@69
|
535 #ifndef CYTHON_UNUSED
|
|
jpayne@69
|
536 # if defined(__GNUC__)
|
|
jpayne@69
|
537 # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
|
|
jpayne@69
|
538 # define CYTHON_UNUSED __attribute__ ((__unused__))
|
|
jpayne@69
|
539 # else
|
|
jpayne@69
|
540 # define CYTHON_UNUSED
|
|
jpayne@69
|
541 # endif
|
|
jpayne@69
|
542 # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
|
|
jpayne@69
|
543 # define CYTHON_UNUSED __attribute__ ((__unused__))
|
|
jpayne@69
|
544 # else
|
|
jpayne@69
|
545 # define CYTHON_UNUSED
|
|
jpayne@69
|
546 # endif
|
|
jpayne@69
|
547 #endif
|
|
jpayne@69
|
548 #ifndef CYTHON_UNUSED_VAR
|
|
jpayne@69
|
549 # if defined(__cplusplus)
|
|
jpayne@69
|
550 template<class T> void CYTHON_UNUSED_VAR( const T& ) { }
|
|
jpayne@69
|
551 # else
|
|
jpayne@69
|
552 # define CYTHON_UNUSED_VAR(x) (void)(x)
|
|
jpayne@69
|
553 # endif
|
|
jpayne@69
|
554 #endif
|
|
jpayne@69
|
555 #ifndef CYTHON_MAYBE_UNUSED_VAR
|
|
jpayne@69
|
556 #define CYTHON_MAYBE_UNUSED_VAR(x) CYTHON_UNUSED_VAR(x)
|
|
jpayne@69
|
557 #endif
|
|
jpayne@69
|
558 #ifndef CYTHON_NCP_UNUSED
|
|
jpayne@69
|
559 # if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
560 # define CYTHON_NCP_UNUSED
|
|
jpayne@69
|
561 # else
|
|
jpayne@69
|
562 # define CYTHON_NCP_UNUSED CYTHON_UNUSED
|
|
jpayne@69
|
563 # endif
|
|
jpayne@69
|
564 #endif
|
|
jpayne@69
|
565 #ifndef CYTHON_USE_CPP_STD_MOVE
|
|
jpayne@69
|
566 #if defined(__cplusplus) && (\
|
|
jpayne@69
|
567 __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600))
|
|
jpayne@69
|
568 #define CYTHON_USE_CPP_STD_MOVE 1
|
|
jpayne@69
|
569 #else
|
|
jpayne@69
|
570 #define CYTHON_USE_CPP_STD_MOVE 0
|
|
jpayne@69
|
571 #endif
|
|
jpayne@69
|
572 #endif
|
|
jpayne@69
|
573 #define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
|
|
jpayne@69
|
574 #ifdef _MSC_VER
|
|
jpayne@69
|
575 #ifndef _MSC_STDINT_H_
|
|
jpayne@69
|
576 #if _MSC_VER < 1300
|
|
jpayne@69
|
577 typedef unsigned char uint8_t;
|
|
jpayne@69
|
578 typedef unsigned short uint16_t;
|
|
jpayne@69
|
579 typedef unsigned int uint32_t;
|
|
jpayne@69
|
580 #else
|
|
jpayne@69
|
581 typedef unsigned __int8 uint8_t;
|
|
jpayne@69
|
582 typedef unsigned __int16 uint16_t;
|
|
jpayne@69
|
583 typedef unsigned __int32 uint32_t;
|
|
jpayne@69
|
584 #endif
|
|
jpayne@69
|
585 #endif
|
|
jpayne@69
|
586 #if _MSC_VER < 1300
|
|
jpayne@69
|
587 #ifdef _WIN64
|
|
jpayne@69
|
588 typedef unsigned long long __pyx_uintptr_t;
|
|
jpayne@69
|
589 #else
|
|
jpayne@69
|
590 typedef unsigned int __pyx_uintptr_t;
|
|
jpayne@69
|
591 #endif
|
|
jpayne@69
|
592 #else
|
|
jpayne@69
|
593 #ifdef _WIN64
|
|
jpayne@69
|
594 typedef unsigned __int64 __pyx_uintptr_t;
|
|
jpayne@69
|
595 #else
|
|
jpayne@69
|
596 typedef unsigned __int32 __pyx_uintptr_t;
|
|
jpayne@69
|
597 #endif
|
|
jpayne@69
|
598 #endif
|
|
jpayne@69
|
599 #else
|
|
jpayne@69
|
600 #include <stdint.h>
|
|
jpayne@69
|
601 typedef uintptr_t __pyx_uintptr_t;
|
|
jpayne@69
|
602 #endif
|
|
jpayne@69
|
603 #ifndef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
604 #if defined(__cplusplus)
|
|
jpayne@69
|
605 /* for clang __has_cpp_attribute(fallthrough) is true even before C++17
|
|
jpayne@69
|
606 * but leads to warnings with -pedantic, since it is a C++17 feature */
|
|
jpayne@69
|
607 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
|
|
jpayne@69
|
608 #if __has_cpp_attribute(fallthrough)
|
|
jpayne@69
|
609 #define CYTHON_FALLTHROUGH [[fallthrough]]
|
|
jpayne@69
|
610 #endif
|
|
jpayne@69
|
611 #endif
|
|
jpayne@69
|
612 #ifndef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
613 #if __has_cpp_attribute(clang::fallthrough)
|
|
jpayne@69
|
614 #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
|
|
jpayne@69
|
615 #elif __has_cpp_attribute(gnu::fallthrough)
|
|
jpayne@69
|
616 #define CYTHON_FALLTHROUGH [[gnu::fallthrough]]
|
|
jpayne@69
|
617 #endif
|
|
jpayne@69
|
618 #endif
|
|
jpayne@69
|
619 #endif
|
|
jpayne@69
|
620 #ifndef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
621 #if __has_attribute(fallthrough)
|
|
jpayne@69
|
622 #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
|
|
jpayne@69
|
623 #else
|
|
jpayne@69
|
624 #define CYTHON_FALLTHROUGH
|
|
jpayne@69
|
625 #endif
|
|
jpayne@69
|
626 #endif
|
|
jpayne@69
|
627 #if defined(__clang__) && defined(__apple_build_version__)
|
|
jpayne@69
|
628 #if __apple_build_version__ < 7000000
|
|
jpayne@69
|
629 #undef CYTHON_FALLTHROUGH
|
|
jpayne@69
|
630 #define CYTHON_FALLTHROUGH
|
|
jpayne@69
|
631 #endif
|
|
jpayne@69
|
632 #endif
|
|
jpayne@69
|
633 #endif
|
|
jpayne@69
|
634 #ifdef __cplusplus
|
|
jpayne@69
|
635 template <typename T>
|
|
jpayne@69
|
636 struct __PYX_IS_UNSIGNED_IMPL {static const bool value = T(0) < T(-1);};
|
|
jpayne@69
|
637 #define __PYX_IS_UNSIGNED(type) (__PYX_IS_UNSIGNED_IMPL<type>::value)
|
|
jpayne@69
|
638 #else
|
|
jpayne@69
|
639 #define __PYX_IS_UNSIGNED(type) (((type)-1) > 0)
|
|
jpayne@69
|
640 #endif
|
|
jpayne@69
|
641 #if CYTHON_COMPILING_IN_PYPY == 1
|
|
jpayne@69
|
642 #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x030A0000)
|
|
jpayne@69
|
643 #else
|
|
jpayne@69
|
644 #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000)
|
|
jpayne@69
|
645 #endif
|
|
jpayne@69
|
646 #define __PYX_REINTERPRET_FUNCION(func_pointer, other_pointer) ((func_pointer)(void(*)(void))(other_pointer))
|
|
jpayne@69
|
647
|
|
jpayne@69
|
648 #ifndef CYTHON_INLINE
|
|
jpayne@69
|
649 #if defined(__clang__)
|
|
jpayne@69
|
650 #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
|
|
jpayne@69
|
651 #elif defined(__GNUC__)
|
|
jpayne@69
|
652 #define CYTHON_INLINE __inline__
|
|
jpayne@69
|
653 #elif defined(_MSC_VER)
|
|
jpayne@69
|
654 #define CYTHON_INLINE __inline
|
|
jpayne@69
|
655 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
|
|
jpayne@69
|
656 #define CYTHON_INLINE inline
|
|
jpayne@69
|
657 #else
|
|
jpayne@69
|
658 #define CYTHON_INLINE
|
|
jpayne@69
|
659 #endif
|
|
jpayne@69
|
660 #endif
|
|
jpayne@69
|
661
|
|
jpayne@69
|
662 #define __PYX_BUILD_PY_SSIZE_T "n"
|
|
jpayne@69
|
663 #define CYTHON_FORMAT_SSIZE_T "z"
|
|
jpayne@69
|
664 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
665 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
|
|
jpayne@69
|
666 #define __Pyx_DefaultClassType PyClass_Type
|
|
jpayne@69
|
667 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
|
|
jpayne@69
|
668 PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
|
|
jpayne@69
|
669 #else
|
|
jpayne@69
|
670 #define __Pyx_BUILTIN_MODULE_NAME "builtins"
|
|
jpayne@69
|
671 #define __Pyx_DefaultClassType PyType_Type
|
|
jpayne@69
|
672 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
673 static CYTHON_INLINE PyObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f,
|
|
jpayne@69
|
674 PyObject *code, PyObject *c, PyObject* n, PyObject *v,
|
|
jpayne@69
|
675 PyObject *fv, PyObject *cell, PyObject* fn,
|
|
jpayne@69
|
676 PyObject *name, int fline, PyObject *lnos) {
|
|
jpayne@69
|
677 PyObject *exception_table = NULL;
|
|
jpayne@69
|
678 PyObject *types_module=NULL, *code_type=NULL, *result=NULL;
|
|
jpayne@69
|
679 #if __PYX_LIMITED_VERSION_HEX < 0x030B0000
|
|
jpayne@69
|
680 PyObject *version_info;
|
|
jpayne@69
|
681 PyObject *py_minor_version = NULL;
|
|
jpayne@69
|
682 #endif
|
|
jpayne@69
|
683 long minor_version = 0;
|
|
jpayne@69
|
684 PyObject *type, *value, *traceback;
|
|
jpayne@69
|
685 PyErr_Fetch(&type, &value, &traceback);
|
|
jpayne@69
|
686 #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000
|
|
jpayne@69
|
687 minor_version = 11;
|
|
jpayne@69
|
688 #else
|
|
jpayne@69
|
689 if (!(version_info = PySys_GetObject("version_info"))) goto end;
|
|
jpayne@69
|
690 if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end;
|
|
jpayne@69
|
691 minor_version = PyLong_AsLong(py_minor_version);
|
|
jpayne@69
|
692 Py_DECREF(py_minor_version);
|
|
jpayne@69
|
693 if (minor_version == -1 && PyErr_Occurred()) goto end;
|
|
jpayne@69
|
694 #endif
|
|
jpayne@69
|
695 if (!(types_module = PyImport_ImportModule("types"))) goto end;
|
|
jpayne@69
|
696 if (!(code_type = PyObject_GetAttrString(types_module, "CodeType"))) goto end;
|
|
jpayne@69
|
697 if (minor_version <= 7) {
|
|
jpayne@69
|
698 (void)p;
|
|
jpayne@69
|
699 result = PyObject_CallFunction(code_type, "iiiiiOOOOOOiOO", a, k, l, s, f, code,
|
|
jpayne@69
|
700 c, n, v, fn, name, fline, lnos, fv, cell);
|
|
jpayne@69
|
701 } else if (minor_version <= 10) {
|
|
jpayne@69
|
702 result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOiOO", a,p, k, l, s, f, code,
|
|
jpayne@69
|
703 c, n, v, fn, name, fline, lnos, fv, cell);
|
|
jpayne@69
|
704 } else {
|
|
jpayne@69
|
705 if (!(exception_table = PyBytes_FromStringAndSize(NULL, 0))) goto end;
|
|
jpayne@69
|
706 result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOOiOO", a,p, k, l, s, f, code,
|
|
jpayne@69
|
707 c, n, v, fn, name, name, fline, lnos, exception_table, fv, cell);
|
|
jpayne@69
|
708 }
|
|
jpayne@69
|
709 end:
|
|
jpayne@69
|
710 Py_XDECREF(code_type);
|
|
jpayne@69
|
711 Py_XDECREF(exception_table);
|
|
jpayne@69
|
712 Py_XDECREF(types_module);
|
|
jpayne@69
|
713 if (type) {
|
|
jpayne@69
|
714 PyErr_Restore(type, value, traceback);
|
|
jpayne@69
|
715 }
|
|
jpayne@69
|
716 return result;
|
|
jpayne@69
|
717 }
|
|
jpayne@69
|
718 #ifndef CO_OPTIMIZED
|
|
jpayne@69
|
719 #define CO_OPTIMIZED 0x0001
|
|
jpayne@69
|
720 #endif
|
|
jpayne@69
|
721 #ifndef CO_NEWLOCALS
|
|
jpayne@69
|
722 #define CO_NEWLOCALS 0x0002
|
|
jpayne@69
|
723 #endif
|
|
jpayne@69
|
724 #ifndef CO_VARARGS
|
|
jpayne@69
|
725 #define CO_VARARGS 0x0004
|
|
jpayne@69
|
726 #endif
|
|
jpayne@69
|
727 #ifndef CO_VARKEYWORDS
|
|
jpayne@69
|
728 #define CO_VARKEYWORDS 0x0008
|
|
jpayne@69
|
729 #endif
|
|
jpayne@69
|
730 #ifndef CO_ASYNC_GENERATOR
|
|
jpayne@69
|
731 #define CO_ASYNC_GENERATOR 0x0200
|
|
jpayne@69
|
732 #endif
|
|
jpayne@69
|
733 #ifndef CO_GENERATOR
|
|
jpayne@69
|
734 #define CO_GENERATOR 0x0020
|
|
jpayne@69
|
735 #endif
|
|
jpayne@69
|
736 #ifndef CO_COROUTINE
|
|
jpayne@69
|
737 #define CO_COROUTINE 0x0080
|
|
jpayne@69
|
738 #endif
|
|
jpayne@69
|
739 #elif PY_VERSION_HEX >= 0x030B0000
|
|
jpayne@69
|
740 static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f,
|
|
jpayne@69
|
741 PyObject *code, PyObject *c, PyObject* n, PyObject *v,
|
|
jpayne@69
|
742 PyObject *fv, PyObject *cell, PyObject* fn,
|
|
jpayne@69
|
743 PyObject *name, int fline, PyObject *lnos) {
|
|
jpayne@69
|
744 PyCodeObject *result;
|
|
jpayne@69
|
745 PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);
|
|
jpayne@69
|
746 if (!empty_bytes) return NULL;
|
|
jpayne@69
|
747 result =
|
|
jpayne@69
|
748 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
749 PyUnstable_Code_NewWithPosOnlyArgs
|
|
jpayne@69
|
750 #else
|
|
jpayne@69
|
751 PyCode_NewWithPosOnlyArgs
|
|
jpayne@69
|
752 #endif
|
|
jpayne@69
|
753 (a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, name, fline, lnos, empty_bytes);
|
|
jpayne@69
|
754 Py_DECREF(empty_bytes);
|
|
jpayne@69
|
755 return result;
|
|
jpayne@69
|
756 }
|
|
jpayne@69
|
757 #elif PY_VERSION_HEX >= 0x030800B2 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
758 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
|
|
jpayne@69
|
759 PyCode_NewWithPosOnlyArgs(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
|
|
jpayne@69
|
760 #else
|
|
jpayne@69
|
761 #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
|
|
jpayne@69
|
762 PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
|
|
jpayne@69
|
763 #endif
|
|
jpayne@69
|
764 #endif
|
|
jpayne@69
|
765 #if PY_VERSION_HEX >= 0x030900A4 || defined(Py_IS_TYPE)
|
|
jpayne@69
|
766 #define __Pyx_IS_TYPE(ob, type) Py_IS_TYPE(ob, type)
|
|
jpayne@69
|
767 #else
|
|
jpayne@69
|
768 #define __Pyx_IS_TYPE(ob, type) (((const PyObject*)ob)->ob_type == (type))
|
|
jpayne@69
|
769 #endif
|
|
jpayne@69
|
770 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_Is)
|
|
jpayne@69
|
771 #define __Pyx_Py_Is(x, y) Py_Is(x, y)
|
|
jpayne@69
|
772 #else
|
|
jpayne@69
|
773 #define __Pyx_Py_Is(x, y) ((x) == (y))
|
|
jpayne@69
|
774 #endif
|
|
jpayne@69
|
775 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsNone)
|
|
jpayne@69
|
776 #define __Pyx_Py_IsNone(ob) Py_IsNone(ob)
|
|
jpayne@69
|
777 #else
|
|
jpayne@69
|
778 #define __Pyx_Py_IsNone(ob) __Pyx_Py_Is((ob), Py_None)
|
|
jpayne@69
|
779 #endif
|
|
jpayne@69
|
780 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsTrue)
|
|
jpayne@69
|
781 #define __Pyx_Py_IsTrue(ob) Py_IsTrue(ob)
|
|
jpayne@69
|
782 #else
|
|
jpayne@69
|
783 #define __Pyx_Py_IsTrue(ob) __Pyx_Py_Is((ob), Py_True)
|
|
jpayne@69
|
784 #endif
|
|
jpayne@69
|
785 #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsFalse)
|
|
jpayne@69
|
786 #define __Pyx_Py_IsFalse(ob) Py_IsFalse(ob)
|
|
jpayne@69
|
787 #else
|
|
jpayne@69
|
788 #define __Pyx_Py_IsFalse(ob) __Pyx_Py_Is((ob), Py_False)
|
|
jpayne@69
|
789 #endif
|
|
jpayne@69
|
790 #define __Pyx_NoneAsNull(obj) (__Pyx_Py_IsNone(obj) ? NULL : (obj))
|
|
jpayne@69
|
791 #if PY_VERSION_HEX >= 0x030900F0 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
792 #define __Pyx_PyObject_GC_IsFinalized(o) PyObject_GC_IsFinalized(o)
|
|
jpayne@69
|
793 #else
|
|
jpayne@69
|
794 #define __Pyx_PyObject_GC_IsFinalized(o) _PyGC_FINALIZED(o)
|
|
jpayne@69
|
795 #endif
|
|
jpayne@69
|
796 #ifndef CO_COROUTINE
|
|
jpayne@69
|
797 #define CO_COROUTINE 0x80
|
|
jpayne@69
|
798 #endif
|
|
jpayne@69
|
799 #ifndef CO_ASYNC_GENERATOR
|
|
jpayne@69
|
800 #define CO_ASYNC_GENERATOR 0x200
|
|
jpayne@69
|
801 #endif
|
|
jpayne@69
|
802 #ifndef Py_TPFLAGS_CHECKTYPES
|
|
jpayne@69
|
803 #define Py_TPFLAGS_CHECKTYPES 0
|
|
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|
804 #endif
|
|
jpayne@69
|
805 #ifndef Py_TPFLAGS_HAVE_INDEX
|
|
jpayne@69
|
806 #define Py_TPFLAGS_HAVE_INDEX 0
|
|
jpayne@69
|
807 #endif
|
|
jpayne@69
|
808 #ifndef Py_TPFLAGS_HAVE_NEWBUFFER
|
|
jpayne@69
|
809 #define Py_TPFLAGS_HAVE_NEWBUFFER 0
|
|
jpayne@69
|
810 #endif
|
|
jpayne@69
|
811 #ifndef Py_TPFLAGS_HAVE_FINALIZE
|
|
jpayne@69
|
812 #define Py_TPFLAGS_HAVE_FINALIZE 0
|
|
jpayne@69
|
813 #endif
|
|
jpayne@69
|
814 #ifndef Py_TPFLAGS_SEQUENCE
|
|
jpayne@69
|
815 #define Py_TPFLAGS_SEQUENCE 0
|
|
jpayne@69
|
816 #endif
|
|
jpayne@69
|
817 #ifndef Py_TPFLAGS_MAPPING
|
|
jpayne@69
|
818 #define Py_TPFLAGS_MAPPING 0
|
|
jpayne@69
|
819 #endif
|
|
jpayne@69
|
820 #ifndef METH_STACKLESS
|
|
jpayne@69
|
821 #define METH_STACKLESS 0
|
|
jpayne@69
|
822 #endif
|
|
jpayne@69
|
823 #if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL)
|
|
jpayne@69
|
824 #ifndef METH_FASTCALL
|
|
jpayne@69
|
825 #define METH_FASTCALL 0x80
|
|
jpayne@69
|
826 #endif
|
|
jpayne@69
|
827 typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs);
|
|
jpayne@69
|
828 typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
|
|
jpayne@69
|
829 Py_ssize_t nargs, PyObject *kwnames);
|
|
jpayne@69
|
830 #else
|
|
jpayne@69
|
831 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
832 # define __Pyx_PyCFunctionFast PyCFunctionFast
|
|
jpayne@69
|
833 # define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords
|
|
jpayne@69
|
834 #else
|
|
jpayne@69
|
835 # define __Pyx_PyCFunctionFast _PyCFunctionFast
|
|
jpayne@69
|
836 # define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
|
|
jpayne@69
|
837 #endif
|
|
jpayne@69
|
838 #endif
|
|
jpayne@69
|
839 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
840 #define __Pyx_METH_FASTCALL METH_FASTCALL
|
|
jpayne@69
|
841 #define __Pyx_PyCFunction_FastCall __Pyx_PyCFunctionFast
|
|
jpayne@69
|
842 #define __Pyx_PyCFunction_FastCallWithKeywords __Pyx_PyCFunctionFastWithKeywords
|
|
jpayne@69
|
843 #else
|
|
jpayne@69
|
844 #define __Pyx_METH_FASTCALL METH_VARARGS
|
|
jpayne@69
|
845 #define __Pyx_PyCFunction_FastCall PyCFunction
|
|
jpayne@69
|
846 #define __Pyx_PyCFunction_FastCallWithKeywords PyCFunctionWithKeywords
|
|
jpayne@69
|
847 #endif
|
|
jpayne@69
|
848 #if CYTHON_VECTORCALL
|
|
jpayne@69
|
849 #define __pyx_vectorcallfunc vectorcallfunc
|
|
jpayne@69
|
850 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET PY_VECTORCALL_ARGUMENTS_OFFSET
|
|
jpayne@69
|
851 #define __Pyx_PyVectorcall_NARGS(n) PyVectorcall_NARGS((size_t)(n))
|
|
jpayne@69
|
852 #elif CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
853 typedef PyObject *(*__pyx_vectorcallfunc)(PyObject *callable, PyObject *const *args,
|
|
jpayne@69
|
854 size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
855 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET ((size_t)1 << (8 * sizeof(size_t) - 1))
|
|
jpayne@69
|
856 #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(((size_t)(n)) & ~__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET))
|
|
jpayne@69
|
857 #else
|
|
jpayne@69
|
858 #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET 0
|
|
jpayne@69
|
859 #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(n))
|
|
jpayne@69
|
860 #endif
|
|
jpayne@69
|
861 #if PY_MAJOR_VERSION >= 0x030900B1
|
|
jpayne@69
|
862 #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_CheckExact(func)
|
|
jpayne@69
|
863 #else
|
|
jpayne@69
|
864 #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_Check(func)
|
|
jpayne@69
|
865 #endif
|
|
jpayne@69
|
866 #define __Pyx_CyOrPyCFunction_Check(func) PyCFunction_Check(func)
|
|
jpayne@69
|
867 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
868 #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) (((PyCFunctionObject*)(func))->m_ml->ml_meth)
|
|
jpayne@69
|
869 #elif !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
870 #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) PyCFunction_GET_FUNCTION(func)
|
|
jpayne@69
|
871 #endif
|
|
jpayne@69
|
872 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
873 #define __Pyx_CyOrPyCFunction_GET_FLAGS(func) (((PyCFunctionObject*)(func))->m_ml->ml_flags)
|
|
jpayne@69
|
874 static CYTHON_INLINE PyObject* __Pyx_CyOrPyCFunction_GET_SELF(PyObject *func) {
|
|
jpayne@69
|
875 return (__Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_STATIC) ? NULL : ((PyCFunctionObject*)func)->m_self;
|
|
jpayne@69
|
876 }
|
|
jpayne@69
|
877 #endif
|
|
jpayne@69
|
878 static CYTHON_INLINE int __Pyx__IsSameCFunction(PyObject *func, void *cfunc) {
|
|
jpayne@69
|
879 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
880 return PyCFunction_Check(func) && PyCFunction_GetFunction(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
881 #else
|
|
jpayne@69
|
882 return PyCFunction_Check(func) && PyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
883 #endif
|
|
jpayne@69
|
884 }
|
|
jpayne@69
|
885 #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCFunction(func, cfunc)
|
|
jpayne@69
|
886 #if __PYX_LIMITED_VERSION_HEX < 0x030900B1
|
|
jpayne@69
|
887 #define __Pyx_PyType_FromModuleAndSpec(m, s, b) ((void)m, PyType_FromSpecWithBases(s, b))
|
|
jpayne@69
|
888 typedef PyObject *(*__Pyx_PyCMethod)(PyObject *, PyTypeObject *, PyObject *const *, size_t, PyObject *);
|
|
jpayne@69
|
889 #else
|
|
jpayne@69
|
890 #define __Pyx_PyType_FromModuleAndSpec(m, s, b) PyType_FromModuleAndSpec(m, s, b)
|
|
jpayne@69
|
891 #define __Pyx_PyCMethod PyCMethod
|
|
jpayne@69
|
892 #endif
|
|
jpayne@69
|
893 #ifndef METH_METHOD
|
|
jpayne@69
|
894 #define METH_METHOD 0x200
|
|
jpayne@69
|
895 #endif
|
|
jpayne@69
|
896 #if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc)
|
|
jpayne@69
|
897 #define PyObject_Malloc(s) PyMem_Malloc(s)
|
|
jpayne@69
|
898 #define PyObject_Free(p) PyMem_Free(p)
|
|
jpayne@69
|
899 #define PyObject_Realloc(p) PyMem_Realloc(p)
|
|
jpayne@69
|
900 #endif
|
|
jpayne@69
|
901 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
902 #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
|
|
jpayne@69
|
903 #define __Pyx_PyFrame_SetLineNumber(frame, lineno)
|
|
jpayne@69
|
904 #else
|
|
jpayne@69
|
905 #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
|
|
jpayne@69
|
906 #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
|
|
jpayne@69
|
907 #endif
|
|
jpayne@69
|
908 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
909 #define __Pyx_PyThreadState_Current PyThreadState_Get()
|
|
jpayne@69
|
910 #elif !CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
911 #define __Pyx_PyThreadState_Current PyThreadState_GET()
|
|
jpayne@69
|
912 #elif PY_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
913 #define __Pyx_PyThreadState_Current PyThreadState_GetUnchecked()
|
|
jpayne@69
|
914 #elif PY_VERSION_HEX >= 0x03060000
|
|
jpayne@69
|
915 #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet()
|
|
jpayne@69
|
916 #elif PY_VERSION_HEX >= 0x03000000
|
|
jpayne@69
|
917 #define __Pyx_PyThreadState_Current PyThreadState_GET()
|
|
jpayne@69
|
918 #else
|
|
jpayne@69
|
919 #define __Pyx_PyThreadState_Current _PyThreadState_Current
|
|
jpayne@69
|
920 #endif
|
|
jpayne@69
|
921 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
922 static CYTHON_INLINE void *__Pyx_PyModule_GetState(PyObject *op)
|
|
jpayne@69
|
923 {
|
|
jpayne@69
|
924 void *result;
|
|
jpayne@69
|
925 result = PyModule_GetState(op);
|
|
jpayne@69
|
926 if (!result)
|
|
jpayne@69
|
927 Py_FatalError("Couldn't find the module state");
|
|
jpayne@69
|
928 return result;
|
|
jpayne@69
|
929 }
|
|
jpayne@69
|
930 #endif
|
|
jpayne@69
|
931 #define __Pyx_PyObject_GetSlot(obj, name, func_ctype) __Pyx_PyType_GetSlot(Py_TYPE(obj), name, func_ctype)
|
|
jpayne@69
|
932 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
933 #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((func_ctype) PyType_GetSlot((type), Py_##name))
|
|
jpayne@69
|
934 #else
|
|
jpayne@69
|
935 #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((type)->name)
|
|
jpayne@69
|
936 #endif
|
|
jpayne@69
|
937 #if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT)
|
|
jpayne@69
|
938 #include "pythread.h"
|
|
jpayne@69
|
939 #define Py_tss_NEEDS_INIT 0
|
|
jpayne@69
|
940 typedef int Py_tss_t;
|
|
jpayne@69
|
941 static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) {
|
|
jpayne@69
|
942 *key = PyThread_create_key();
|
|
jpayne@69
|
943 return 0;
|
|
jpayne@69
|
944 }
|
|
jpayne@69
|
945 static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) {
|
|
jpayne@69
|
946 Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t));
|
|
jpayne@69
|
947 *key = Py_tss_NEEDS_INIT;
|
|
jpayne@69
|
948 return key;
|
|
jpayne@69
|
949 }
|
|
jpayne@69
|
950 static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) {
|
|
jpayne@69
|
951 PyObject_Free(key);
|
|
jpayne@69
|
952 }
|
|
jpayne@69
|
953 static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) {
|
|
jpayne@69
|
954 return *key != Py_tss_NEEDS_INIT;
|
|
jpayne@69
|
955 }
|
|
jpayne@69
|
956 static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) {
|
|
jpayne@69
|
957 PyThread_delete_key(*key);
|
|
jpayne@69
|
958 *key = Py_tss_NEEDS_INIT;
|
|
jpayne@69
|
959 }
|
|
jpayne@69
|
960 static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) {
|
|
jpayne@69
|
961 return PyThread_set_key_value(*key, value);
|
|
jpayne@69
|
962 }
|
|
jpayne@69
|
963 static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
|
|
jpayne@69
|
964 return PyThread_get_key_value(*key);
|
|
jpayne@69
|
965 }
|
|
jpayne@69
|
966 #endif
|
|
jpayne@69
|
967 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
968 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
969 #if PYPY_VERSION_NUM < 0x07030600
|
|
jpayne@69
|
970 #if defined(__cplusplus) && __cplusplus >= 201402L
|
|
jpayne@69
|
971 [[deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")]]
|
|
jpayne@69
|
972 #elif defined(__GNUC__) || defined(__clang__)
|
|
jpayne@69
|
973 __attribute__ ((__deprecated__("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")))
|
|
jpayne@69
|
974 #elif defined(_MSC_VER)
|
|
jpayne@69
|
975 __declspec(deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6"))
|
|
jpayne@69
|
976 #endif
|
|
jpayne@69
|
977 static CYTHON_INLINE int PyGILState_Check(void) {
|
|
jpayne@69
|
978 return 0;
|
|
jpayne@69
|
979 }
|
|
jpayne@69
|
980 #else // PYPY_VERSION_NUM < 0x07030600
|
|
jpayne@69
|
981 #endif // PYPY_VERSION_NUM < 0x07030600
|
|
jpayne@69
|
982 #else
|
|
jpayne@69
|
983 static CYTHON_INLINE int PyGILState_Check(void) {
|
|
jpayne@69
|
984 PyThreadState * tstate = _PyThreadState_Current;
|
|
jpayne@69
|
985 return tstate && (tstate == PyGILState_GetThisThreadState());
|
|
jpayne@69
|
986 }
|
|
jpayne@69
|
987 #endif
|
|
jpayne@69
|
988 #endif
|
|
jpayne@69
|
989 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030d0000 || defined(_PyDict_NewPresized)
|
|
jpayne@69
|
990 #define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n))
|
|
jpayne@69
|
991 #else
|
|
jpayne@69
|
992 #define __Pyx_PyDict_NewPresized(n) PyDict_New()
|
|
jpayne@69
|
993 #endif
|
|
jpayne@69
|
994 #if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION
|
|
jpayne@69
|
995 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
|
|
jpayne@69
|
996 #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
|
|
jpayne@69
|
997 #else
|
|
jpayne@69
|
998 #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
|
|
jpayne@69
|
999 #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
|
|
jpayne@69
|
1000 #endif
|
|
jpayne@69
|
1001 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX > 0x030600B4 && PY_VERSION_HEX < 0x030d0000 && CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
1002 #define __Pyx_PyDict_GetItemStrWithError(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash)
|
|
jpayne@69
|
1003 static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStr(PyObject *dict, PyObject *name) {
|
|
jpayne@69
|
1004 PyObject *res = __Pyx_PyDict_GetItemStrWithError(dict, name);
|
|
jpayne@69
|
1005 if (res == NULL) PyErr_Clear();
|
|
jpayne@69
|
1006 return res;
|
|
jpayne@69
|
1007 }
|
|
jpayne@69
|
1008 #elif PY_MAJOR_VERSION >= 3 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07020000)
|
|
jpayne@69
|
1009 #define __Pyx_PyDict_GetItemStrWithError PyDict_GetItemWithError
|
|
jpayne@69
|
1010 #define __Pyx_PyDict_GetItemStr PyDict_GetItem
|
|
jpayne@69
|
1011 #else
|
|
jpayne@69
|
1012 static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict, PyObject *name) {
|
|
jpayne@69
|
1013 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1014 return PyDict_GetItem(dict, name);
|
|
jpayne@69
|
1015 #else
|
|
jpayne@69
|
1016 PyDictEntry *ep;
|
|
jpayne@69
|
1017 PyDictObject *mp = (PyDictObject*) dict;
|
|
jpayne@69
|
1018 long hash = ((PyStringObject *) name)->ob_shash;
|
|
jpayne@69
|
1019 assert(hash != -1);
|
|
jpayne@69
|
1020 ep = (mp->ma_lookup)(mp, name, hash);
|
|
jpayne@69
|
1021 if (ep == NULL) {
|
|
jpayne@69
|
1022 return NULL;
|
|
jpayne@69
|
1023 }
|
|
jpayne@69
|
1024 return ep->me_value;
|
|
jpayne@69
|
1025 #endif
|
|
jpayne@69
|
1026 }
|
|
jpayne@69
|
1027 #define __Pyx_PyDict_GetItemStr PyDict_GetItem
|
|
jpayne@69
|
1028 #endif
|
|
jpayne@69
|
1029 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
1030 #define __Pyx_PyType_GetFlags(tp) (((PyTypeObject *)tp)->tp_flags)
|
|
jpayne@69
|
1031 #define __Pyx_PyType_HasFeature(type, feature) ((__Pyx_PyType_GetFlags(type) & (feature)) != 0)
|
|
jpayne@69
|
1032 #define __Pyx_PyObject_GetIterNextFunc(obj) (Py_TYPE(obj)->tp_iternext)
|
|
jpayne@69
|
1033 #else
|
|
jpayne@69
|
1034 #define __Pyx_PyType_GetFlags(tp) (PyType_GetFlags((PyTypeObject *)tp))
|
|
jpayne@69
|
1035 #define __Pyx_PyType_HasFeature(type, feature) PyType_HasFeature(type, feature)
|
|
jpayne@69
|
1036 #define __Pyx_PyObject_GetIterNextFunc(obj) PyIter_Next
|
|
jpayne@69
|
1037 #endif
|
|
jpayne@69
|
1038 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
1039 #define __Pyx_SetItemOnTypeDict(tp, k, v) PyObject_GenericSetAttr((PyObject*)tp, k, v)
|
|
jpayne@69
|
1040 #else
|
|
jpayne@69
|
1041 #define __Pyx_SetItemOnTypeDict(tp, k, v) PyDict_SetItem(tp->tp_dict, k, v)
|
|
jpayne@69
|
1042 #endif
|
|
jpayne@69
|
1043 #if CYTHON_USE_TYPE_SPECS && PY_VERSION_HEX >= 0x03080000
|
|
jpayne@69
|
1044 #define __Pyx_PyHeapTypeObject_GC_Del(obj) {\
|
|
jpayne@69
|
1045 PyTypeObject *type = Py_TYPE((PyObject*)obj);\
|
|
jpayne@69
|
1046 assert(__Pyx_PyType_HasFeature(type, Py_TPFLAGS_HEAPTYPE));\
|
|
jpayne@69
|
1047 PyObject_GC_Del(obj);\
|
|
jpayne@69
|
1048 Py_DECREF(type);\
|
|
jpayne@69
|
1049 }
|
|
jpayne@69
|
1050 #else
|
|
jpayne@69
|
1051 #define __Pyx_PyHeapTypeObject_GC_Del(obj) PyObject_GC_Del(obj)
|
|
jpayne@69
|
1052 #endif
|
|
jpayne@69
|
1053 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
1054 #define CYTHON_PEP393_ENABLED 1
|
|
jpayne@69
|
1055 #define __Pyx_PyUnicode_READY(op) (0)
|
|
jpayne@69
|
1056 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GetLength(u)
|
|
jpayne@69
|
1057 #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_ReadChar(u, i)
|
|
jpayne@69
|
1058 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((void)u, 1114111U)
|
|
jpayne@69
|
1059 #define __Pyx_PyUnicode_KIND(u) ((void)u, (0))
|
|
jpayne@69
|
1060 #define __Pyx_PyUnicode_DATA(u) ((void*)u)
|
|
jpayne@69
|
1061 #define __Pyx_PyUnicode_READ(k, d, i) ((void)k, PyUnicode_ReadChar((PyObject*)(d), i))
|
|
jpayne@69
|
1062 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GetLength(u))
|
|
jpayne@69
|
1063 #elif PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
|
|
jpayne@69
|
1064 #define CYTHON_PEP393_ENABLED 1
|
|
jpayne@69
|
1065 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
1066 #define __Pyx_PyUnicode_READY(op) (0)
|
|
jpayne@69
|
1067 #else
|
|
jpayne@69
|
1068 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
|
|
jpayne@69
|
1069 0 : _PyUnicode_Ready((PyObject *)(op)))
|
|
jpayne@69
|
1070 #endif
|
|
jpayne@69
|
1071 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
|
|
jpayne@69
|
1072 #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
|
|
jpayne@69
|
1073 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
|
|
jpayne@69
|
1074 #define __Pyx_PyUnicode_KIND(u) ((int)PyUnicode_KIND(u))
|
|
jpayne@69
|
1075 #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
|
|
jpayne@69
|
1076 #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
|
|
jpayne@69
|
1077 #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, (Py_UCS4) ch)
|
|
jpayne@69
|
1078 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
1079 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u))
|
|
jpayne@69
|
1080 #else
|
|
jpayne@69
|
1081 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000
|
|
jpayne@69
|
1082 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length))
|
|
jpayne@69
|
1083 #else
|
|
jpayne@69
|
1084 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
|
|
jpayne@69
|
1085 #endif
|
|
jpayne@69
|
1086 #endif
|
|
jpayne@69
|
1087 #else
|
|
jpayne@69
|
1088 #define CYTHON_PEP393_ENABLED 0
|
|
jpayne@69
|
1089 #define PyUnicode_1BYTE_KIND 1
|
|
jpayne@69
|
1090 #define PyUnicode_2BYTE_KIND 2
|
|
jpayne@69
|
1091 #define PyUnicode_4BYTE_KIND 4
|
|
jpayne@69
|
1092 #define __Pyx_PyUnicode_READY(op) (0)
|
|
jpayne@69
|
1093 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
|
|
jpayne@69
|
1094 #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
|
|
jpayne@69
|
1095 #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535U : 1114111U)
|
|
jpayne@69
|
1096 #define __Pyx_PyUnicode_KIND(u) ((int)sizeof(Py_UNICODE))
|
|
jpayne@69
|
1097 #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
|
|
jpayne@69
|
1098 #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
|
|
jpayne@69
|
1099 #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = (Py_UNICODE) ch)
|
|
jpayne@69
|
1100 #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
|
|
jpayne@69
|
1101 #endif
|
|
jpayne@69
|
1102 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1103 #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
|
|
jpayne@69
|
1104 #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
|
|
jpayne@69
|
1105 #else
|
|
jpayne@69
|
1106 #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
|
|
jpayne@69
|
1107 #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\
|
|
jpayne@69
|
1108 PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
|
|
jpayne@69
|
1109 #endif
|
|
jpayne@69
|
1110 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1111 #if !defined(PyUnicode_DecodeUnicodeEscape)
|
|
jpayne@69
|
1112 #define PyUnicode_DecodeUnicodeEscape(s, size, errors) PyUnicode_Decode(s, size, "unicode_escape", errors)
|
|
jpayne@69
|
1113 #endif
|
|
jpayne@69
|
1114 #if !defined(PyUnicode_Contains) || (PY_MAJOR_VERSION == 2 && PYPY_VERSION_NUM < 0x07030500)
|
|
jpayne@69
|
1115 #undef PyUnicode_Contains
|
|
jpayne@69
|
1116 #define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
|
|
jpayne@69
|
1117 #endif
|
|
jpayne@69
|
1118 #if !defined(PyByteArray_Check)
|
|
jpayne@69
|
1119 #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type)
|
|
jpayne@69
|
1120 #endif
|
|
jpayne@69
|
1121 #if !defined(PyObject_Format)
|
|
jpayne@69
|
1122 #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt)
|
|
jpayne@69
|
1123 #endif
|
|
jpayne@69
|
1124 #endif
|
|
jpayne@69
|
1125 #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
|
1126 #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
|
1127 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1128 #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
|
|
jpayne@69
|
1129 #else
|
|
jpayne@69
|
1130 #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
|
|
jpayne@69
|
1131 #endif
|
|
jpayne@69
|
1132 #if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII)
|
|
jpayne@69
|
1133 #define PyObject_ASCII(o) PyObject_Repr(o)
|
|
jpayne@69
|
1134 #endif
|
|
jpayne@69
|
1135 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1136 #define PyBaseString_Type PyUnicode_Type
|
|
jpayne@69
|
1137 #define PyStringObject PyUnicodeObject
|
|
jpayne@69
|
1138 #define PyString_Type PyUnicode_Type
|
|
jpayne@69
|
1139 #define PyString_Check PyUnicode_Check
|
|
jpayne@69
|
1140 #define PyString_CheckExact PyUnicode_CheckExact
|
|
jpayne@69
|
1141 #ifndef PyObject_Unicode
|
|
jpayne@69
|
1142 #define PyObject_Unicode PyObject_Str
|
|
jpayne@69
|
1143 #endif
|
|
jpayne@69
|
1144 #endif
|
|
jpayne@69
|
1145 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1146 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
|
|
jpayne@69
|
1147 #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
|
|
jpayne@69
|
1148 #else
|
|
jpayne@69
|
1149 #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
|
|
jpayne@69
|
1150 #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
|
|
jpayne@69
|
1151 #endif
|
|
jpayne@69
|
1152 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
1153 #define __Pyx_PySequence_ListKeepNew(obj)\
|
|
jpayne@69
|
1154 (likely(PyList_CheckExact(obj) && Py_REFCNT(obj) == 1) ? __Pyx_NewRef(obj) : PySequence_List(obj))
|
|
jpayne@69
|
1155 #else
|
|
jpayne@69
|
1156 #define __Pyx_PySequence_ListKeepNew(obj) PySequence_List(obj)
|
|
jpayne@69
|
1157 #endif
|
|
jpayne@69
|
1158 #ifndef PySet_CheckExact
|
|
jpayne@69
|
1159 #define PySet_CheckExact(obj) __Pyx_IS_TYPE(obj, &PySet_Type)
|
|
jpayne@69
|
1160 #endif
|
|
jpayne@69
|
1161 #if PY_VERSION_HEX >= 0x030900A4
|
|
jpayne@69
|
1162 #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt)
|
|
jpayne@69
|
1163 #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size)
|
|
jpayne@69
|
1164 #else
|
|
jpayne@69
|
1165 #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt)
|
|
jpayne@69
|
1166 #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size)
|
|
jpayne@69
|
1167 #endif
|
|
jpayne@69
|
1168 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
1169 #define __Pyx_PySequence_ITEM(o, i) PySequence_ITEM(o, i)
|
|
jpayne@69
|
1170 #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq)
|
|
jpayne@69
|
1171 #define __Pyx_PyTuple_SET_ITEM(o, i, v) (PyTuple_SET_ITEM(o, i, v), (0))
|
|
jpayne@69
|
1172 #define __Pyx_PyList_SET_ITEM(o, i, v) (PyList_SET_ITEM(o, i, v), (0))
|
|
jpayne@69
|
1173 #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_GET_SIZE(o)
|
|
jpayne@69
|
1174 #define __Pyx_PyList_GET_SIZE(o) PyList_GET_SIZE(o)
|
|
jpayne@69
|
1175 #define __Pyx_PySet_GET_SIZE(o) PySet_GET_SIZE(o)
|
|
jpayne@69
|
1176 #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_GET_SIZE(o)
|
|
jpayne@69
|
1177 #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_GET_SIZE(o)
|
|
jpayne@69
|
1178 #else
|
|
jpayne@69
|
1179 #define __Pyx_PySequence_ITEM(o, i) PySequence_GetItem(o, i)
|
|
jpayne@69
|
1180 #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq)
|
|
jpayne@69
|
1181 #define __Pyx_PyTuple_SET_ITEM(o, i, v) PyTuple_SetItem(o, i, v)
|
|
jpayne@69
|
1182 #define __Pyx_PyList_SET_ITEM(o, i, v) PyList_SetItem(o, i, v)
|
|
jpayne@69
|
1183 #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_Size(o)
|
|
jpayne@69
|
1184 #define __Pyx_PyList_GET_SIZE(o) PyList_Size(o)
|
|
jpayne@69
|
1185 #define __Pyx_PySet_GET_SIZE(o) PySet_Size(o)
|
|
jpayne@69
|
1186 #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o)
|
|
jpayne@69
|
1187 #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o)
|
|
jpayne@69
|
1188 #endif
|
|
jpayne@69
|
1189 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
1190 #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name)
|
|
jpayne@69
|
1191 #else
|
|
jpayne@69
|
1192 static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) {
|
|
jpayne@69
|
1193 PyObject *module = PyImport_AddModule(name);
|
|
jpayne@69
|
1194 Py_XINCREF(module);
|
|
jpayne@69
|
1195 return module;
|
|
jpayne@69
|
1196 }
|
|
jpayne@69
|
1197 #endif
|
|
jpayne@69
|
1198 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1199 #define PyIntObject PyLongObject
|
|
jpayne@69
|
1200 #define PyInt_Type PyLong_Type
|
|
jpayne@69
|
1201 #define PyInt_Check(op) PyLong_Check(op)
|
|
jpayne@69
|
1202 #define PyInt_CheckExact(op) PyLong_CheckExact(op)
|
|
jpayne@69
|
1203 #define __Pyx_Py3Int_Check(op) PyLong_Check(op)
|
|
jpayne@69
|
1204 #define __Pyx_Py3Int_CheckExact(op) PyLong_CheckExact(op)
|
|
jpayne@69
|
1205 #define PyInt_FromString PyLong_FromString
|
|
jpayne@69
|
1206 #define PyInt_FromUnicode PyLong_FromUnicode
|
|
jpayne@69
|
1207 #define PyInt_FromLong PyLong_FromLong
|
|
jpayne@69
|
1208 #define PyInt_FromSize_t PyLong_FromSize_t
|
|
jpayne@69
|
1209 #define PyInt_FromSsize_t PyLong_FromSsize_t
|
|
jpayne@69
|
1210 #define PyInt_AsLong PyLong_AsLong
|
|
jpayne@69
|
1211 #define PyInt_AS_LONG PyLong_AS_LONG
|
|
jpayne@69
|
1212 #define PyInt_AsSsize_t PyLong_AsSsize_t
|
|
jpayne@69
|
1213 #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
|
|
jpayne@69
|
1214 #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
|
|
jpayne@69
|
1215 #define PyNumber_Int PyNumber_Long
|
|
jpayne@69
|
1216 #else
|
|
jpayne@69
|
1217 #define __Pyx_Py3Int_Check(op) (PyLong_Check(op) || PyInt_Check(op))
|
|
jpayne@69
|
1218 #define __Pyx_Py3Int_CheckExact(op) (PyLong_CheckExact(op) || PyInt_CheckExact(op))
|
|
jpayne@69
|
1219 #endif
|
|
jpayne@69
|
1220 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1221 #define PyBoolObject PyLongObject
|
|
jpayne@69
|
1222 #endif
|
|
jpayne@69
|
1223 #if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1224 #ifndef PyUnicode_InternFromString
|
|
jpayne@69
|
1225 #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
|
|
jpayne@69
|
1226 #endif
|
|
jpayne@69
|
1227 #endif
|
|
jpayne@69
|
1228 #if PY_VERSION_HEX < 0x030200A4
|
|
jpayne@69
|
1229 typedef long Py_hash_t;
|
|
jpayne@69
|
1230 #define __Pyx_PyInt_FromHash_t PyInt_FromLong
|
|
jpayne@69
|
1231 #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t
|
|
jpayne@69
|
1232 #else
|
|
jpayne@69
|
1233 #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
|
|
jpayne@69
|
1234 #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t
|
|
jpayne@69
|
1235 #endif
|
|
jpayne@69
|
1236 #if CYTHON_USE_ASYNC_SLOTS
|
|
jpayne@69
|
1237 #if PY_VERSION_HEX >= 0x030500B1
|
|
jpayne@69
|
1238 #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
|
|
jpayne@69
|
1239 #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
|
|
jpayne@69
|
1240 #else
|
|
jpayne@69
|
1241 #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
|
|
jpayne@69
|
1242 #endif
|
|
jpayne@69
|
1243 #else
|
|
jpayne@69
|
1244 #define __Pyx_PyType_AsAsync(obj) NULL
|
|
jpayne@69
|
1245 #endif
|
|
jpayne@69
|
1246 #ifndef __Pyx_PyAsyncMethodsStruct
|
|
jpayne@69
|
1247 typedef struct {
|
|
jpayne@69
|
1248 unaryfunc am_await;
|
|
jpayne@69
|
1249 unaryfunc am_aiter;
|
|
jpayne@69
|
1250 unaryfunc am_anext;
|
|
jpayne@69
|
1251 } __Pyx_PyAsyncMethodsStruct;
|
|
jpayne@69
|
1252 #endif
|
|
jpayne@69
|
1253
|
|
jpayne@69
|
1254 #if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
|
|
jpayne@69
|
1255 #if !defined(_USE_MATH_DEFINES)
|
|
jpayne@69
|
1256 #define _USE_MATH_DEFINES
|
|
jpayne@69
|
1257 #endif
|
|
jpayne@69
|
1258 #endif
|
|
jpayne@69
|
1259 #include <math.h>
|
|
jpayne@69
|
1260 #ifdef NAN
|
|
jpayne@69
|
1261 #define __PYX_NAN() ((float) NAN)
|
|
jpayne@69
|
1262 #else
|
|
jpayne@69
|
1263 static CYTHON_INLINE float __PYX_NAN() {
|
|
jpayne@69
|
1264 float value;
|
|
jpayne@69
|
1265 memset(&value, 0xFF, sizeof(value));
|
|
jpayne@69
|
1266 return value;
|
|
jpayne@69
|
1267 }
|
|
jpayne@69
|
1268 #endif
|
|
jpayne@69
|
1269 #if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
|
|
jpayne@69
|
1270 #define __Pyx_truncl trunc
|
|
jpayne@69
|
1271 #else
|
|
jpayne@69
|
1272 #define __Pyx_truncl truncl
|
|
jpayne@69
|
1273 #endif
|
|
jpayne@69
|
1274
|
|
jpayne@69
|
1275 #define __PYX_MARK_ERR_POS(f_index, lineno) \
|
|
jpayne@69
|
1276 { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
|
|
jpayne@69
|
1277 #define __PYX_ERR(f_index, lineno, Ln_error) \
|
|
jpayne@69
|
1278 { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }
|
|
jpayne@69
|
1279
|
|
jpayne@69
|
1280 #ifdef CYTHON_EXTERN_C
|
|
jpayne@69
|
1281 #undef __PYX_EXTERN_C
|
|
jpayne@69
|
1282 #define __PYX_EXTERN_C CYTHON_EXTERN_C
|
|
jpayne@69
|
1283 #elif defined(__PYX_EXTERN_C)
|
|
jpayne@69
|
1284 #ifdef _MSC_VER
|
|
jpayne@69
|
1285 #pragma message ("Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.")
|
|
jpayne@69
|
1286 #else
|
|
jpayne@69
|
1287 #warning Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.
|
|
jpayne@69
|
1288 #endif
|
|
jpayne@69
|
1289 #else
|
|
jpayne@69
|
1290 #ifdef __cplusplus
|
|
jpayne@69
|
1291 #define __PYX_EXTERN_C extern "C"
|
|
jpayne@69
|
1292 #else
|
|
jpayne@69
|
1293 #define __PYX_EXTERN_C extern
|
|
jpayne@69
|
1294 #endif
|
|
jpayne@69
|
1295 #endif
|
|
jpayne@69
|
1296
|
|
jpayne@69
|
1297 #define __PYX_HAVE__pysam__libcutils
|
|
jpayne@69
|
1298 #define __PYX_HAVE_API__pysam__libcutils
|
|
jpayne@69
|
1299 /* Early includes */
|
|
jpayne@69
|
1300 #include <string.h>
|
|
jpayne@69
|
1301 #include <stdio.h>
|
|
jpayne@69
|
1302 #include <stddef.h>
|
|
jpayne@69
|
1303 #include "pythread.h"
|
|
jpayne@69
|
1304
|
|
jpayne@69
|
1305 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
1306 #ifdef _MSC_VER
|
|
jpayne@69
|
1307 #pragma message ("This module uses CPython specific internals of 'array.array', which are not available in PyPy.")
|
|
jpayne@69
|
1308 #else
|
|
jpayne@69
|
1309 #warning This module uses CPython specific internals of 'array.array', which are not available in PyPy.
|
|
jpayne@69
|
1310 #endif
|
|
jpayne@69
|
1311 #endif
|
|
jpayne@69
|
1312
|
|
jpayne@69
|
1313 #include <errno.h>
|
|
jpayne@69
|
1314 #include <stdlib.h>
|
|
jpayne@69
|
1315 #include <stdint.h>
|
|
jpayne@69
|
1316 #include <sys/types.h>
|
|
jpayne@69
|
1317 #include <fcntl.h>
|
|
jpayne@69
|
1318 #include <unistd.h>
|
|
jpayne@69
|
1319 #include "samtools.pysam.h"
|
|
jpayne@69
|
1320 #include "bcftools.pysam.h"
|
|
jpayne@69
|
1321 #ifdef _OPENMP
|
|
jpayne@69
|
1322 #include <omp.h>
|
|
jpayne@69
|
1323 #endif /* _OPENMP */
|
|
jpayne@69
|
1324
|
|
jpayne@69
|
1325 #if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
|
|
jpayne@69
|
1326 #define CYTHON_WITHOUT_ASSERTIONS
|
|
jpayne@69
|
1327 #endif
|
|
jpayne@69
|
1328
|
|
jpayne@69
|
1329 typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
|
|
jpayne@69
|
1330 const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
|
|
jpayne@69
|
1331
|
|
jpayne@69
|
1332 #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
|
|
jpayne@69
|
1333 #define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0
|
|
jpayne@69
|
1334 #define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8)
|
|
jpayne@69
|
1335 #define __PYX_DEFAULT_STRING_ENCODING ""
|
|
jpayne@69
|
1336 #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
|
|
jpayne@69
|
1337 #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
|
|
jpayne@69
|
1338 #define __Pyx_uchar_cast(c) ((unsigned char)c)
|
|
jpayne@69
|
1339 #define __Pyx_long_cast(x) ((long)x)
|
|
jpayne@69
|
1340 #define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\
|
|
jpayne@69
|
1341 (sizeof(type) < sizeof(Py_ssize_t)) ||\
|
|
jpayne@69
|
1342 (sizeof(type) > sizeof(Py_ssize_t) &&\
|
|
jpayne@69
|
1343 likely(v < (type)PY_SSIZE_T_MAX ||\
|
|
jpayne@69
|
1344 v == (type)PY_SSIZE_T_MAX) &&\
|
|
jpayne@69
|
1345 (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
|
|
jpayne@69
|
1346 v == (type)PY_SSIZE_T_MIN))) ||\
|
|
jpayne@69
|
1347 (sizeof(type) == sizeof(Py_ssize_t) &&\
|
|
jpayne@69
|
1348 (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
|
|
jpayne@69
|
1349 v == (type)PY_SSIZE_T_MAX))) )
|
|
jpayne@69
|
1350 static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) {
|
|
jpayne@69
|
1351 return (size_t) i < (size_t) limit;
|
|
jpayne@69
|
1352 }
|
|
jpayne@69
|
1353 #if defined (__cplusplus) && __cplusplus >= 201103L
|
|
jpayne@69
|
1354 #include <cstdlib>
|
|
jpayne@69
|
1355 #define __Pyx_sst_abs(value) std::abs(value)
|
|
jpayne@69
|
1356 #elif SIZEOF_INT >= SIZEOF_SIZE_T
|
|
jpayne@69
|
1357 #define __Pyx_sst_abs(value) abs(value)
|
|
jpayne@69
|
1358 #elif SIZEOF_LONG >= SIZEOF_SIZE_T
|
|
jpayne@69
|
1359 #define __Pyx_sst_abs(value) labs(value)
|
|
jpayne@69
|
1360 #elif defined (_MSC_VER)
|
|
jpayne@69
|
1361 #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
|
|
jpayne@69
|
1362 #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
|
|
jpayne@69
|
1363 #define __Pyx_sst_abs(value) llabs(value)
|
|
jpayne@69
|
1364 #elif defined (__GNUC__)
|
|
jpayne@69
|
1365 #define __Pyx_sst_abs(value) __builtin_llabs(value)
|
|
jpayne@69
|
1366 #else
|
|
jpayne@69
|
1367 #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
|
|
jpayne@69
|
1368 #endif
|
|
jpayne@69
|
1369 static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s);
|
|
jpayne@69
|
1370 static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
|
|
jpayne@69
|
1371 static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
|
|
jpayne@69
|
1372 static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char*);
|
|
jpayne@69
|
1373 #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
|
|
jpayne@69
|
1374 #define __Pyx_PyBytes_FromString PyBytes_FromString
|
|
jpayne@69
|
1375 #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
|
|
jpayne@69
|
1376 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
|
|
jpayne@69
|
1377 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
1378 #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
|
|
jpayne@69
|
1379 #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
|
|
jpayne@69
|
1380 #else
|
|
jpayne@69
|
1381 #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
|
|
jpayne@69
|
1382 #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
|
|
jpayne@69
|
1383 #endif
|
|
jpayne@69
|
1384 #define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1385 #define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1386 #define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1387 #define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1388 #define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1389 #define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s))
|
|
jpayne@69
|
1390 #define __Pyx_PyObject_AsWritableString(s) ((char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1391 #define __Pyx_PyObject_AsWritableSString(s) ((signed char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1392 #define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1393 #define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1394 #define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s))
|
|
jpayne@69
|
1395 #define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
|
|
jpayne@69
|
1396 #define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
|
|
jpayne@69
|
1397 #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
|
|
jpayne@69
|
1398 #define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
|
|
jpayne@69
|
1399 #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
|
|
jpayne@69
|
1400 #define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o)
|
|
jpayne@69
|
1401 #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
|
|
jpayne@69
|
1402 #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
|
|
jpayne@69
|
1403 #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
|
|
jpayne@69
|
1404 static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
|
|
jpayne@69
|
1405 static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
|
|
jpayne@69
|
1406 static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
|
|
jpayne@69
|
1407 static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
|
|
jpayne@69
|
1408 #define __Pyx_PySequence_Tuple(obj)\
|
|
jpayne@69
|
1409 (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
|
|
jpayne@69
|
1410 static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
|
|
jpayne@69
|
1411 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
|
|
jpayne@69
|
1412 static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
|
|
jpayne@69
|
1413 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
1414 #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
|
|
jpayne@69
|
1415 #else
|
|
jpayne@69
|
1416 #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
|
|
jpayne@69
|
1417 #endif
|
|
jpayne@69
|
1418 #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
|
|
jpayne@69
|
1419 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1420 #define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
|
|
jpayne@69
|
1421 #else
|
|
jpayne@69
|
1422 #define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
|
|
jpayne@69
|
1423 #endif
|
|
jpayne@69
|
1424 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
1425 #if PY_VERSION_HEX >= 0x030C00A7
|
|
jpayne@69
|
1426 #ifndef _PyLong_SIGN_MASK
|
|
jpayne@69
|
1427 #define _PyLong_SIGN_MASK 3
|
|
jpayne@69
|
1428 #endif
|
|
jpayne@69
|
1429 #ifndef _PyLong_NON_SIZE_BITS
|
|
jpayne@69
|
1430 #define _PyLong_NON_SIZE_BITS 3
|
|
jpayne@69
|
1431 #endif
|
|
jpayne@69
|
1432 #define __Pyx_PyLong_Sign(x) (((PyLongObject*)x)->long_value.lv_tag & _PyLong_SIGN_MASK)
|
|
jpayne@69
|
1433 #define __Pyx_PyLong_IsNeg(x) ((__Pyx_PyLong_Sign(x) & 2) != 0)
|
|
jpayne@69
|
1434 #define __Pyx_PyLong_IsNonNeg(x) (!__Pyx_PyLong_IsNeg(x))
|
|
jpayne@69
|
1435 #define __Pyx_PyLong_IsZero(x) (__Pyx_PyLong_Sign(x) & 1)
|
|
jpayne@69
|
1436 #define __Pyx_PyLong_IsPos(x) (__Pyx_PyLong_Sign(x) == 0)
|
|
jpayne@69
|
1437 #define __Pyx_PyLong_CompactValueUnsigned(x) (__Pyx_PyLong_Digits(x)[0])
|
|
jpayne@69
|
1438 #define __Pyx_PyLong_DigitCount(x) ((Py_ssize_t) (((PyLongObject*)x)->long_value.lv_tag >> _PyLong_NON_SIZE_BITS))
|
|
jpayne@69
|
1439 #define __Pyx_PyLong_SignedDigitCount(x)\
|
|
jpayne@69
|
1440 ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * __Pyx_PyLong_DigitCount(x))
|
|
jpayne@69
|
1441 #if defined(PyUnstable_Long_IsCompact) && defined(PyUnstable_Long_CompactValue)
|
|
jpayne@69
|
1442 #define __Pyx_PyLong_IsCompact(x) PyUnstable_Long_IsCompact((PyLongObject*) x)
|
|
jpayne@69
|
1443 #define __Pyx_PyLong_CompactValue(x) PyUnstable_Long_CompactValue((PyLongObject*) x)
|
|
jpayne@69
|
1444 #else
|
|
jpayne@69
|
1445 #define __Pyx_PyLong_IsCompact(x) (((PyLongObject*)x)->long_value.lv_tag < (2 << _PyLong_NON_SIZE_BITS))
|
|
jpayne@69
|
1446 #define __Pyx_PyLong_CompactValue(x) ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * (Py_ssize_t) __Pyx_PyLong_Digits(x)[0])
|
|
jpayne@69
|
1447 #endif
|
|
jpayne@69
|
1448 typedef Py_ssize_t __Pyx_compact_pylong;
|
|
jpayne@69
|
1449 typedef size_t __Pyx_compact_upylong;
|
|
jpayne@69
|
1450 #else
|
|
jpayne@69
|
1451 #define __Pyx_PyLong_IsNeg(x) (Py_SIZE(x) < 0)
|
|
jpayne@69
|
1452 #define __Pyx_PyLong_IsNonNeg(x) (Py_SIZE(x) >= 0)
|
|
jpayne@69
|
1453 #define __Pyx_PyLong_IsZero(x) (Py_SIZE(x) == 0)
|
|
jpayne@69
|
1454 #define __Pyx_PyLong_IsPos(x) (Py_SIZE(x) > 0)
|
|
jpayne@69
|
1455 #define __Pyx_PyLong_CompactValueUnsigned(x) ((Py_SIZE(x) == 0) ? 0 : __Pyx_PyLong_Digits(x)[0])
|
|
jpayne@69
|
1456 #define __Pyx_PyLong_DigitCount(x) __Pyx_sst_abs(Py_SIZE(x))
|
|
jpayne@69
|
1457 #define __Pyx_PyLong_SignedDigitCount(x) Py_SIZE(x)
|
|
jpayne@69
|
1458 #define __Pyx_PyLong_IsCompact(x) (Py_SIZE(x) == 0 || Py_SIZE(x) == 1 || Py_SIZE(x) == -1)
|
|
jpayne@69
|
1459 #define __Pyx_PyLong_CompactValue(x)\
|
|
jpayne@69
|
1460 ((Py_SIZE(x) == 0) ? (sdigit) 0 : ((Py_SIZE(x) < 0) ? -(sdigit)__Pyx_PyLong_Digits(x)[0] : (sdigit)__Pyx_PyLong_Digits(x)[0]))
|
|
jpayne@69
|
1461 typedef sdigit __Pyx_compact_pylong;
|
|
jpayne@69
|
1462 typedef digit __Pyx_compact_upylong;
|
|
jpayne@69
|
1463 #endif
|
|
jpayne@69
|
1464 #if PY_VERSION_HEX >= 0x030C00A5
|
|
jpayne@69
|
1465 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->long_value.ob_digit)
|
|
jpayne@69
|
1466 #else
|
|
jpayne@69
|
1467 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->ob_digit)
|
|
jpayne@69
|
1468 #endif
|
|
jpayne@69
|
1469 #endif
|
|
jpayne@69
|
1470 #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
1471 #include <string.h>
|
|
jpayne@69
|
1472 static int __Pyx_sys_getdefaultencoding_not_ascii;
|
|
jpayne@69
|
1473 static int __Pyx_init_sys_getdefaultencoding_params(void) {
|
|
jpayne@69
|
1474 PyObject* sys;
|
|
jpayne@69
|
1475 PyObject* default_encoding = NULL;
|
|
jpayne@69
|
1476 PyObject* ascii_chars_u = NULL;
|
|
jpayne@69
|
1477 PyObject* ascii_chars_b = NULL;
|
|
jpayne@69
|
1478 const char* default_encoding_c;
|
|
jpayne@69
|
1479 sys = PyImport_ImportModule("sys");
|
|
jpayne@69
|
1480 if (!sys) goto bad;
|
|
jpayne@69
|
1481 default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
|
|
jpayne@69
|
1482 Py_DECREF(sys);
|
|
jpayne@69
|
1483 if (!default_encoding) goto bad;
|
|
jpayne@69
|
1484 default_encoding_c = PyBytes_AsString(default_encoding);
|
|
jpayne@69
|
1485 if (!default_encoding_c) goto bad;
|
|
jpayne@69
|
1486 if (strcmp(default_encoding_c, "ascii") == 0) {
|
|
jpayne@69
|
1487 __Pyx_sys_getdefaultencoding_not_ascii = 0;
|
|
jpayne@69
|
1488 } else {
|
|
jpayne@69
|
1489 char ascii_chars[128];
|
|
jpayne@69
|
1490 int c;
|
|
jpayne@69
|
1491 for (c = 0; c < 128; c++) {
|
|
jpayne@69
|
1492 ascii_chars[c] = (char) c;
|
|
jpayne@69
|
1493 }
|
|
jpayne@69
|
1494 __Pyx_sys_getdefaultencoding_not_ascii = 1;
|
|
jpayne@69
|
1495 ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
|
|
jpayne@69
|
1496 if (!ascii_chars_u) goto bad;
|
|
jpayne@69
|
1497 ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
|
|
jpayne@69
|
1498 if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
|
|
jpayne@69
|
1499 PyErr_Format(
|
|
jpayne@69
|
1500 PyExc_ValueError,
|
|
jpayne@69
|
1501 "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
|
|
jpayne@69
|
1502 default_encoding_c);
|
|
jpayne@69
|
1503 goto bad;
|
|
jpayne@69
|
1504 }
|
|
jpayne@69
|
1505 Py_DECREF(ascii_chars_u);
|
|
jpayne@69
|
1506 Py_DECREF(ascii_chars_b);
|
|
jpayne@69
|
1507 }
|
|
jpayne@69
|
1508 Py_DECREF(default_encoding);
|
|
jpayne@69
|
1509 return 0;
|
|
jpayne@69
|
1510 bad:
|
|
jpayne@69
|
1511 Py_XDECREF(default_encoding);
|
|
jpayne@69
|
1512 Py_XDECREF(ascii_chars_u);
|
|
jpayne@69
|
1513 Py_XDECREF(ascii_chars_b);
|
|
jpayne@69
|
1514 return -1;
|
|
jpayne@69
|
1515 }
|
|
jpayne@69
|
1516 #endif
|
|
jpayne@69
|
1517 #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
1518 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
|
|
jpayne@69
|
1519 #else
|
|
jpayne@69
|
1520 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
|
|
jpayne@69
|
1521 #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
|
|
jpayne@69
|
1522 #include <string.h>
|
|
jpayne@69
|
1523 static char* __PYX_DEFAULT_STRING_ENCODING;
|
|
jpayne@69
|
1524 static int __Pyx_init_sys_getdefaultencoding_params(void) {
|
|
jpayne@69
|
1525 PyObject* sys;
|
|
jpayne@69
|
1526 PyObject* default_encoding = NULL;
|
|
jpayne@69
|
1527 char* default_encoding_c;
|
|
jpayne@69
|
1528 sys = PyImport_ImportModule("sys");
|
|
jpayne@69
|
1529 if (!sys) goto bad;
|
|
jpayne@69
|
1530 default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
|
|
jpayne@69
|
1531 Py_DECREF(sys);
|
|
jpayne@69
|
1532 if (!default_encoding) goto bad;
|
|
jpayne@69
|
1533 default_encoding_c = PyBytes_AsString(default_encoding);
|
|
jpayne@69
|
1534 if (!default_encoding_c) goto bad;
|
|
jpayne@69
|
1535 __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
|
|
jpayne@69
|
1536 if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
|
|
jpayne@69
|
1537 strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
|
|
jpayne@69
|
1538 Py_DECREF(default_encoding);
|
|
jpayne@69
|
1539 return 0;
|
|
jpayne@69
|
1540 bad:
|
|
jpayne@69
|
1541 Py_XDECREF(default_encoding);
|
|
jpayne@69
|
1542 return -1;
|
|
jpayne@69
|
1543 }
|
|
jpayne@69
|
1544 #endif
|
|
jpayne@69
|
1545 #endif
|
|
jpayne@69
|
1546
|
|
jpayne@69
|
1547
|
|
jpayne@69
|
1548 /* Test for GCC > 2.95 */
|
|
jpayne@69
|
1549 #if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
|
|
jpayne@69
|
1550 #define likely(x) __builtin_expect(!!(x), 1)
|
|
jpayne@69
|
1551 #define unlikely(x) __builtin_expect(!!(x), 0)
|
|
jpayne@69
|
1552 #else /* !__GNUC__ or GCC < 2.95 */
|
|
jpayne@69
|
1553 #define likely(x) (x)
|
|
jpayne@69
|
1554 #define unlikely(x) (x)
|
|
jpayne@69
|
1555 #endif /* __GNUC__ */
|
|
jpayne@69
|
1556 static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }
|
|
jpayne@69
|
1557
|
|
jpayne@69
|
1558 #if !CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
1559 static PyObject *__pyx_m = NULL;
|
|
jpayne@69
|
1560 #endif
|
|
jpayne@69
|
1561 static int __pyx_lineno;
|
|
jpayne@69
|
1562 static int __pyx_clineno = 0;
|
|
jpayne@69
|
1563 static const char * __pyx_cfilenm = __FILE__;
|
|
jpayne@69
|
1564 static const char *__pyx_filename;
|
|
jpayne@69
|
1565
|
|
jpayne@69
|
1566 /* #### Code section: filename_table ### */
|
|
jpayne@69
|
1567
|
|
jpayne@69
|
1568 static const char *__pyx_f[] = {
|
|
jpayne@69
|
1569 "pysam/libcutils.pyx",
|
|
jpayne@69
|
1570 "contextvars.pxd",
|
|
jpayne@69
|
1571 "array.pxd",
|
|
jpayne@69
|
1572 "type.pxd",
|
|
jpayne@69
|
1573 "bool.pxd",
|
|
jpayne@69
|
1574 "complex.pxd",
|
|
jpayne@69
|
1575 };
|
|
jpayne@69
|
1576 /* #### Code section: utility_code_proto_before_types ### */
|
|
jpayne@69
|
1577 /* ForceInitThreads.proto */
|
|
jpayne@69
|
1578 #ifndef __PYX_FORCE_INIT_THREADS
|
|
jpayne@69
|
1579 #define __PYX_FORCE_INIT_THREADS 0
|
|
jpayne@69
|
1580 #endif
|
|
jpayne@69
|
1581
|
|
jpayne@69
|
1582 /* #### Code section: numeric_typedefs ### */
|
|
jpayne@69
|
1583 /* #### Code section: complex_type_declarations ### */
|
|
jpayne@69
|
1584 /* #### Code section: type_declarations ### */
|
|
jpayne@69
|
1585
|
|
jpayne@69
|
1586 /*--- Type declarations ---*/
|
|
jpayne@69
|
1587 #ifndef _ARRAYARRAY_H
|
|
jpayne@69
|
1588 struct arrayobject;
|
|
jpayne@69
|
1589 typedef struct arrayobject arrayobject;
|
|
jpayne@69
|
1590 #endif
|
|
jpayne@69
|
1591 struct __pyx_opt_args_7cpython_11contextvars_get_value;
|
|
jpayne@69
|
1592 struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default;
|
|
jpayne@69
|
1593
|
|
jpayne@69
|
1594 /* "cpython/contextvars.pxd":112
|
|
jpayne@69
|
1595 *
|
|
jpayne@69
|
1596 *
|
|
jpayne@69
|
1597 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1598 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
1599 * or the default value of the context variable,
|
|
jpayne@69
|
1600 */
|
|
jpayne@69
|
1601 struct __pyx_opt_args_7cpython_11contextvars_get_value {
|
|
jpayne@69
|
1602 int __pyx_n;
|
|
jpayne@69
|
1603 PyObject *default_value;
|
|
jpayne@69
|
1604 };
|
|
jpayne@69
|
1605
|
|
jpayne@69
|
1606 /* "cpython/contextvars.pxd":129
|
|
jpayne@69
|
1607 *
|
|
jpayne@69
|
1608 *
|
|
jpayne@69
|
1609 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1610 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
1611 * or the provided default value if no such value was found.
|
|
jpayne@69
|
1612 */
|
|
jpayne@69
|
1613 struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default {
|
|
jpayne@69
|
1614 int __pyx_n;
|
|
jpayne@69
|
1615 PyObject *default_value;
|
|
jpayne@69
|
1616 };
|
|
jpayne@69
|
1617 struct __pyx_opt_args_5pysam_9libcutils_parse_region;
|
|
jpayne@69
|
1618 struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array;
|
|
jpayne@69
|
1619 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring;
|
|
jpayne@69
|
1620 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring;
|
|
jpayne@69
|
1621 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str;
|
|
jpayne@69
|
1622 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes;
|
|
jpayne@69
|
1623 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len;
|
|
jpayne@69
|
1624 struct __pyx_opt_args_5pysam_9libcutils_force_str;
|
|
jpayne@69
|
1625 struct __pyx_opt_args_5pysam_9libcutils_force_bytes;
|
|
jpayne@69
|
1626 struct __pyx_opt_args_5pysam_9libcutils_decode_bytes;
|
|
jpayne@69
|
1627
|
|
jpayne@69
|
1628 /* "pysam/libcutils.pxd":8
|
|
jpayne@69
|
1629 * from cpython cimport array as c_array
|
|
jpayne@69
|
1630 *
|
|
jpayne@69
|
1631 * cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1632 *
|
|
jpayne@69
|
1633 * cdef int libc_whence_from_io(int whence)
|
|
jpayne@69
|
1634 */
|
|
jpayne@69
|
1635 struct __pyx_opt_args_5pysam_9libcutils_parse_region {
|
|
jpayne@69
|
1636 int __pyx_n;
|
|
jpayne@69
|
1637 PyObject *contig;
|
|
jpayne@69
|
1638 PyObject *start;
|
|
jpayne@69
|
1639 PyObject *stop;
|
|
jpayne@69
|
1640 PyObject *region;
|
|
jpayne@69
|
1641 PyObject *reference;
|
|
jpayne@69
|
1642 PyObject *end;
|
|
jpayne@69
|
1643 };
|
|
jpayne@69
|
1644
|
|
jpayne@69
|
1645 /* "pysam/libcutils.pxd":15
|
|
jpayne@69
|
1646 * # Utility functions for quality string conversions
|
|
jpayne@69
|
1647 *
|
|
jpayne@69
|
1648 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1649 * cpdef array_to_qualitystring(c_array.array arr, int offset=*)
|
|
jpayne@69
|
1650 * cpdef qualities_to_qualitystring(qualities, int offset=*)
|
|
jpayne@69
|
1651 */
|
|
jpayne@69
|
1652 struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array {
|
|
jpayne@69
|
1653 int __pyx_n;
|
|
jpayne@69
|
1654 int offset;
|
|
jpayne@69
|
1655 };
|
|
jpayne@69
|
1656
|
|
jpayne@69
|
1657 /* "pysam/libcutils.pxd":16
|
|
jpayne@69
|
1658 *
|
|
jpayne@69
|
1659 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
|
|
jpayne@69
|
1660 * cpdef array_to_qualitystring(c_array.array arr, int offset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1661 * cpdef qualities_to_qualitystring(qualities, int offset=*)
|
|
jpayne@69
|
1662 *
|
|
jpayne@69
|
1663 */
|
|
jpayne@69
|
1664 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring {
|
|
jpayne@69
|
1665 int __pyx_n;
|
|
jpayne@69
|
1666 int offset;
|
|
jpayne@69
|
1667 };
|
|
jpayne@69
|
1668
|
|
jpayne@69
|
1669 /* "pysam/libcutils.pxd":17
|
|
jpayne@69
|
1670 * cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
|
|
jpayne@69
|
1671 * cpdef array_to_qualitystring(c_array.array arr, int offset=*)
|
|
jpayne@69
|
1672 * cpdef qualities_to_qualitystring(qualities, int offset=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1673 *
|
|
jpayne@69
|
1674 * ########################################################################
|
|
jpayne@69
|
1675 */
|
|
jpayne@69
|
1676 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring {
|
|
jpayne@69
|
1677 int __pyx_n;
|
|
jpayne@69
|
1678 int offset;
|
|
jpayne@69
|
1679 };
|
|
jpayne@69
|
1680
|
|
jpayne@69
|
1681 /* "pysam/libcutils.pxd":29
|
|
jpayne@69
|
1682 * ## Python 3 compatibility functions
|
|
jpayne@69
|
1683 * ########################################################################
|
|
jpayne@69
|
1684 * cdef charptr_to_str(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1685 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1686 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1687 */
|
|
jpayne@69
|
1688 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str {
|
|
jpayne@69
|
1689 int __pyx_n;
|
|
jpayne@69
|
1690 PyObject *encoding;
|
|
jpayne@69
|
1691 PyObject *errors;
|
|
jpayne@69
|
1692 };
|
|
jpayne@69
|
1693
|
|
jpayne@69
|
1694 /* "pysam/libcutils.pxd":30
|
|
jpayne@69
|
1695 * ########################################################################
|
|
jpayne@69
|
1696 * cdef charptr_to_str(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1697 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1698 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1699 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1700 */
|
|
jpayne@69
|
1701 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes {
|
|
jpayne@69
|
1702 int __pyx_n;
|
|
jpayne@69
|
1703 PyObject *encoding;
|
|
jpayne@69
|
1704 PyObject *errors;
|
|
jpayne@69
|
1705 };
|
|
jpayne@69
|
1706
|
|
jpayne@69
|
1707 /* "pysam/libcutils.pxd":31
|
|
jpayne@69
|
1708 * cdef charptr_to_str(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1709 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1710 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1711 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1712 * cdef bytes force_bytes(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1713 */
|
|
jpayne@69
|
1714 struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len {
|
|
jpayne@69
|
1715 int __pyx_n;
|
|
jpayne@69
|
1716 PyObject *encoding;
|
|
jpayne@69
|
1717 PyObject *errors;
|
|
jpayne@69
|
1718 };
|
|
jpayne@69
|
1719
|
|
jpayne@69
|
1720 /* "pysam/libcutils.pxd":32
|
|
jpayne@69
|
1721 * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
|
|
jpayne@69
|
1722 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1723 * cdef force_str(object s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1724 * cdef bytes force_bytes(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1725 * cdef decode_bytes(bytes s, encoding=*, errors=*)
|
|
jpayne@69
|
1726 */
|
|
jpayne@69
|
1727 struct __pyx_opt_args_5pysam_9libcutils_force_str {
|
|
jpayne@69
|
1728 int __pyx_n;
|
|
jpayne@69
|
1729 PyObject *encoding;
|
|
jpayne@69
|
1730 PyObject *errors;
|
|
jpayne@69
|
1731 };
|
|
jpayne@69
|
1732
|
|
jpayne@69
|
1733 /* "pysam/libcutils.pxd":33
|
|
jpayne@69
|
1734 * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
|
|
jpayne@69
|
1735 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1736 * cdef bytes force_bytes(object s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1737 * cdef decode_bytes(bytes s, encoding=*, errors=*)
|
|
jpayne@69
|
1738 * cdef bytes encode_filename(object filename)
|
|
jpayne@69
|
1739 */
|
|
jpayne@69
|
1740 struct __pyx_opt_args_5pysam_9libcutils_force_bytes {
|
|
jpayne@69
|
1741 int __pyx_n;
|
|
jpayne@69
|
1742 PyObject *encoding;
|
|
jpayne@69
|
1743 PyObject *errors;
|
|
jpayne@69
|
1744 };
|
|
jpayne@69
|
1745
|
|
jpayne@69
|
1746 /* "pysam/libcutils.pxd":34
|
|
jpayne@69
|
1747 * cdef force_str(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1748 * cdef bytes force_bytes(object s, encoding=*, errors=*)
|
|
jpayne@69
|
1749 * cdef decode_bytes(bytes s, encoding=*, errors=*) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
1750 * cdef bytes encode_filename(object filename)
|
|
jpayne@69
|
1751 * cdef from_string_and_size(const char *s, size_t length)
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|
jpayne@69
|
1752 */
|
|
jpayne@69
|
1753 struct __pyx_opt_args_5pysam_9libcutils_decode_bytes {
|
|
jpayne@69
|
1754 int __pyx_n;
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|
jpayne@69
|
1755 PyObject *encoding;
|
|
jpayne@69
|
1756 PyObject *errors;
|
|
jpayne@69
|
1757 };
|
|
jpayne@69
|
1758 /* #### Code section: utility_code_proto ### */
|
|
jpayne@69
|
1759
|
|
jpayne@69
|
1760 /* --- Runtime support code (head) --- */
|
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jpayne@69
|
1761 /* Refnanny.proto */
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|
jpayne@69
|
1762 #ifndef CYTHON_REFNANNY
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jpayne@69
|
1763 #define CYTHON_REFNANNY 0
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jpayne@69
|
1764 #endif
|
|
jpayne@69
|
1765 #if CYTHON_REFNANNY
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jpayne@69
|
1766 typedef struct {
|
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jpayne@69
|
1767 void (*INCREF)(void*, PyObject*, Py_ssize_t);
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|
jpayne@69
|
1768 void (*DECREF)(void*, PyObject*, Py_ssize_t);
|
|
jpayne@69
|
1769 void (*GOTREF)(void*, PyObject*, Py_ssize_t);
|
|
jpayne@69
|
1770 void (*GIVEREF)(void*, PyObject*, Py_ssize_t);
|
|
jpayne@69
|
1771 void* (*SetupContext)(const char*, Py_ssize_t, const char*);
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jpayne@69
|
1772 void (*FinishContext)(void**);
|
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jpayne@69
|
1773 } __Pyx_RefNannyAPIStruct;
|
|
jpayne@69
|
1774 static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
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|
jpayne@69
|
1775 static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname);
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|
jpayne@69
|
1776 #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
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jpayne@69
|
1777 #ifdef WITH_THREAD
|
|
jpayne@69
|
1778 #define __Pyx_RefNannySetupContext(name, acquire_gil)\
|
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jpayne@69
|
1779 if (acquire_gil) {\
|
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jpayne@69
|
1780 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
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jpayne@69
|
1781 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\
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jpayne@69
|
1782 PyGILState_Release(__pyx_gilstate_save);\
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jpayne@69
|
1783 } else {\
|
|
jpayne@69
|
1784 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\
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jpayne@69
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1785 }
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|
jpayne@69
|
1786 #define __Pyx_RefNannyFinishContextNogil() {\
|
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jpayne@69
|
1787 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
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jpayne@69
|
1788 __Pyx_RefNannyFinishContext();\
|
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jpayne@69
|
1789 PyGILState_Release(__pyx_gilstate_save);\
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jpayne@69
|
1790 }
|
|
jpayne@69
|
1791 #else
|
|
jpayne@69
|
1792 #define __Pyx_RefNannySetupContext(name, acquire_gil)\
|
|
jpayne@69
|
1793 __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__))
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|
jpayne@69
|
1794 #define __Pyx_RefNannyFinishContextNogil() __Pyx_RefNannyFinishContext()
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|
jpayne@69
|
1795 #endif
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jpayne@69
|
1796 #define __Pyx_RefNannyFinishContextNogil() {\
|
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jpayne@69
|
1797 PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\
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jpayne@69
|
1798 __Pyx_RefNannyFinishContext();\
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jpayne@69
|
1799 PyGILState_Release(__pyx_gilstate_save);\
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jpayne@69
|
1800 }
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jpayne@69
|
1801 #define __Pyx_RefNannyFinishContext()\
|
|
jpayne@69
|
1802 __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
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jpayne@69
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1803 #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
|
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jpayne@69
|
1804 #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
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jpayne@69
|
1805 #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
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jpayne@69
|
1806 #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), (__LINE__))
|
|
jpayne@69
|
1807 #define __Pyx_XINCREF(r) do { if((r) == NULL); else {__Pyx_INCREF(r); }} while(0)
|
|
jpayne@69
|
1808 #define __Pyx_XDECREF(r) do { if((r) == NULL); else {__Pyx_DECREF(r); }} while(0)
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|
jpayne@69
|
1809 #define __Pyx_XGOTREF(r) do { if((r) == NULL); else {__Pyx_GOTREF(r); }} while(0)
|
|
jpayne@69
|
1810 #define __Pyx_XGIVEREF(r) do { if((r) == NULL); else {__Pyx_GIVEREF(r);}} while(0)
|
|
jpayne@69
|
1811 #else
|
|
jpayne@69
|
1812 #define __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
1813 #define __Pyx_RefNannySetupContext(name, acquire_gil)
|
|
jpayne@69
|
1814 #define __Pyx_RefNannyFinishContextNogil()
|
|
jpayne@69
|
1815 #define __Pyx_RefNannyFinishContext()
|
|
jpayne@69
|
1816 #define __Pyx_INCREF(r) Py_INCREF(r)
|
|
jpayne@69
|
1817 #define __Pyx_DECREF(r) Py_DECREF(r)
|
|
jpayne@69
|
1818 #define __Pyx_GOTREF(r)
|
|
jpayne@69
|
1819 #define __Pyx_GIVEREF(r)
|
|
jpayne@69
|
1820 #define __Pyx_XINCREF(r) Py_XINCREF(r)
|
|
jpayne@69
|
1821 #define __Pyx_XDECREF(r) Py_XDECREF(r)
|
|
jpayne@69
|
1822 #define __Pyx_XGOTREF(r)
|
|
jpayne@69
|
1823 #define __Pyx_XGIVEREF(r)
|
|
jpayne@69
|
1824 #endif
|
|
jpayne@69
|
1825 #define __Pyx_Py_XDECREF_SET(r, v) do {\
|
|
jpayne@69
|
1826 PyObject *tmp = (PyObject *) r;\
|
|
jpayne@69
|
1827 r = v; Py_XDECREF(tmp);\
|
|
jpayne@69
|
1828 } while (0)
|
|
jpayne@69
|
1829 #define __Pyx_XDECREF_SET(r, v) do {\
|
|
jpayne@69
|
1830 PyObject *tmp = (PyObject *) r;\
|
|
jpayne@69
|
1831 r = v; __Pyx_XDECREF(tmp);\
|
|
jpayne@69
|
1832 } while (0)
|
|
jpayne@69
|
1833 #define __Pyx_DECREF_SET(r, v) do {\
|
|
jpayne@69
|
1834 PyObject *tmp = (PyObject *) r;\
|
|
jpayne@69
|
1835 r = v; __Pyx_DECREF(tmp);\
|
|
jpayne@69
|
1836 } while (0)
|
|
jpayne@69
|
1837 #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
|
|
jpayne@69
|
1838 #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
|
|
jpayne@69
|
1839
|
|
jpayne@69
|
1840 /* PyErrExceptionMatches.proto */
|
|
jpayne@69
|
1841 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
1842 #define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
|
|
jpayne@69
|
1843 static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
|
|
jpayne@69
|
1844 #else
|
|
jpayne@69
|
1845 #define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
|
|
jpayne@69
|
1846 #endif
|
|
jpayne@69
|
1847
|
|
jpayne@69
|
1848 /* PyThreadStateGet.proto */
|
|
jpayne@69
|
1849 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
1850 #define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
|
|
jpayne@69
|
1851 #define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
1852 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
1853 #define __Pyx_PyErr_Occurred() (__pyx_tstate->current_exception != NULL)
|
|
jpayne@69
|
1854 #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->current_exception ? (PyObject*) Py_TYPE(__pyx_tstate->current_exception) : (PyObject*) NULL)
|
|
jpayne@69
|
1855 #else
|
|
jpayne@69
|
1856 #define __Pyx_PyErr_Occurred() (__pyx_tstate->curexc_type != NULL)
|
|
jpayne@69
|
1857 #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->curexc_type)
|
|
jpayne@69
|
1858 #endif
|
|
jpayne@69
|
1859 #else
|
|
jpayne@69
|
1860 #define __Pyx_PyThreadState_declare
|
|
jpayne@69
|
1861 #define __Pyx_PyThreadState_assign
|
|
jpayne@69
|
1862 #define __Pyx_PyErr_Occurred() (PyErr_Occurred() != NULL)
|
|
jpayne@69
|
1863 #define __Pyx_PyErr_CurrentExceptionType() PyErr_Occurred()
|
|
jpayne@69
|
1864 #endif
|
|
jpayne@69
|
1865
|
|
jpayne@69
|
1866 /* PyErrFetchRestore.proto */
|
|
jpayne@69
|
1867 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
1868 #define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL)
|
|
jpayne@69
|
1869 #define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
|
|
jpayne@69
|
1870 #define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
|
|
jpayne@69
|
1871 #define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
1872 #define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
1873 static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
|
|
jpayne@69
|
1874 static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
1875 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A6
|
|
jpayne@69
|
1876 #define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL))
|
|
jpayne@69
|
1877 #else
|
|
jpayne@69
|
1878 #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
|
|
jpayne@69
|
1879 #endif
|
|
jpayne@69
|
1880 #else
|
|
jpayne@69
|
1881 #define __Pyx_PyErr_Clear() PyErr_Clear()
|
|
jpayne@69
|
1882 #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
|
|
jpayne@69
|
1883 #define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb)
|
|
jpayne@69
|
1884 #define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb)
|
|
jpayne@69
|
1885 #define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb)
|
|
jpayne@69
|
1886 #define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb)
|
|
jpayne@69
|
1887 #define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb)
|
|
jpayne@69
|
1888 #define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb)
|
|
jpayne@69
|
1889 #endif
|
|
jpayne@69
|
1890
|
|
jpayne@69
|
1891 /* PyObjectGetAttrStr.proto */
|
|
jpayne@69
|
1892 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
1893 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name);
|
|
jpayne@69
|
1894 #else
|
|
jpayne@69
|
1895 #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
|
|
jpayne@69
|
1896 #endif
|
|
jpayne@69
|
1897
|
|
jpayne@69
|
1898 /* PyObjectGetAttrStrNoError.proto */
|
|
jpayne@69
|
1899 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name);
|
|
jpayne@69
|
1900
|
|
jpayne@69
|
1901 /* GetBuiltinName.proto */
|
|
jpayne@69
|
1902 static PyObject *__Pyx_GetBuiltinName(PyObject *name);
|
|
jpayne@69
|
1903
|
|
jpayne@69
|
1904 /* TupleAndListFromArray.proto */
|
|
jpayne@69
|
1905 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
1906 static CYTHON_INLINE PyObject* __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n);
|
|
jpayne@69
|
1907 static CYTHON_INLINE PyObject* __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n);
|
|
jpayne@69
|
1908 #endif
|
|
jpayne@69
|
1909
|
|
jpayne@69
|
1910 /* IncludeStringH.proto */
|
|
jpayne@69
|
1911 #include <string.h>
|
|
jpayne@69
|
1912
|
|
jpayne@69
|
1913 /* BytesEquals.proto */
|
|
jpayne@69
|
1914 static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);
|
|
jpayne@69
|
1915
|
|
jpayne@69
|
1916 /* UnicodeEquals.proto */
|
|
jpayne@69
|
1917 static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);
|
|
jpayne@69
|
1918
|
|
jpayne@69
|
1919 /* fastcall.proto */
|
|
jpayne@69
|
1920 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
1921 #define __Pyx_Arg_VARARGS(args, i) PySequence_GetItem(args, i)
|
|
jpayne@69
|
1922 #elif CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
1923 #define __Pyx_Arg_VARARGS(args, i) PyTuple_GET_ITEM(args, i)
|
|
jpayne@69
|
1924 #else
|
|
jpayne@69
|
1925 #define __Pyx_Arg_VARARGS(args, i) PyTuple_GetItem(args, i)
|
|
jpayne@69
|
1926 #endif
|
|
jpayne@69
|
1927 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
1928 #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg)
|
|
jpayne@69
|
1929 #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg)
|
|
jpayne@69
|
1930 #else
|
|
jpayne@69
|
1931 #define __Pyx_Arg_NewRef_VARARGS(arg) arg
|
|
jpayne@69
|
1932 #define __Pyx_Arg_XDECREF_VARARGS(arg)
|
|
jpayne@69
|
1933 #endif
|
|
jpayne@69
|
1934 #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds)
|
|
jpayne@69
|
1935 #define __Pyx_KwValues_VARARGS(args, nargs) NULL
|
|
jpayne@69
|
1936 #define __Pyx_GetKwValue_VARARGS(kw, kwvalues, s) __Pyx_PyDict_GetItemStrWithError(kw, s)
|
|
jpayne@69
|
1937 #define __Pyx_KwargsAsDict_VARARGS(kw, kwvalues) PyDict_Copy(kw)
|
|
jpayne@69
|
1938 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
1939 #define __Pyx_Arg_FASTCALL(args, i) args[i]
|
|
jpayne@69
|
1940 #define __Pyx_NumKwargs_FASTCALL(kwds) PyTuple_GET_SIZE(kwds)
|
|
jpayne@69
|
1941 #define __Pyx_KwValues_FASTCALL(args, nargs) ((args) + (nargs))
|
|
jpayne@69
|
1942 static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s);
|
|
jpayne@69
|
1943 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
1944 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues);
|
|
jpayne@69
|
1945 #else
|
|
jpayne@69
|
1946 #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw)
|
|
jpayne@69
|
1947 #endif
|
|
jpayne@69
|
1948 #define __Pyx_Arg_NewRef_FASTCALL(arg) arg /* no-op, __Pyx_Arg_FASTCALL is direct and this needs
|
|
jpayne@69
|
1949 to have the same reference counting */
|
|
jpayne@69
|
1950 #define __Pyx_Arg_XDECREF_FASTCALL(arg)
|
|
jpayne@69
|
1951 #else
|
|
jpayne@69
|
1952 #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS
|
|
jpayne@69
|
1953 #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS
|
|
jpayne@69
|
1954 #define __Pyx_KwValues_FASTCALL __Pyx_KwValues_VARARGS
|
|
jpayne@69
|
1955 #define __Pyx_GetKwValue_FASTCALL __Pyx_GetKwValue_VARARGS
|
|
jpayne@69
|
1956 #define __Pyx_KwargsAsDict_FASTCALL __Pyx_KwargsAsDict_VARARGS
|
|
jpayne@69
|
1957 #define __Pyx_Arg_NewRef_FASTCALL(arg) __Pyx_Arg_NewRef_VARARGS(arg)
|
|
jpayne@69
|
1958 #define __Pyx_Arg_XDECREF_FASTCALL(arg) __Pyx_Arg_XDECREF_VARARGS(arg)
|
|
jpayne@69
|
1959 #endif
|
|
jpayne@69
|
1960 #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
1961 #define __Pyx_ArgsSlice_VARARGS(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_VARARGS(args, start), stop - start)
|
|
jpayne@69
|
1962 #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_FASTCALL(args, start), stop - start)
|
|
jpayne@69
|
1963 #else
|
|
jpayne@69
|
1964 #define __Pyx_ArgsSlice_VARARGS(args, start, stop) PyTuple_GetSlice(args, start, stop)
|
|
jpayne@69
|
1965 #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) PyTuple_GetSlice(args, start, stop)
|
|
jpayne@69
|
1966 #endif
|
|
jpayne@69
|
1967
|
|
jpayne@69
|
1968 /* ListCompAppend.proto */
|
|
jpayne@69
|
1969 #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
1970 static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
|
|
jpayne@69
|
1971 PyListObject* L = (PyListObject*) list;
|
|
jpayne@69
|
1972 Py_ssize_t len = Py_SIZE(list);
|
|
jpayne@69
|
1973 if (likely(L->allocated > len)) {
|
|
jpayne@69
|
1974 Py_INCREF(x);
|
|
jpayne@69
|
1975 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
1976 L->ob_item[len] = x;
|
|
jpayne@69
|
1977 #else
|
|
jpayne@69
|
1978 PyList_SET_ITEM(list, len, x);
|
|
jpayne@69
|
1979 #endif
|
|
jpayne@69
|
1980 __Pyx_SET_SIZE(list, len + 1);
|
|
jpayne@69
|
1981 return 0;
|
|
jpayne@69
|
1982 }
|
|
jpayne@69
|
1983 return PyList_Append(list, x);
|
|
jpayne@69
|
1984 }
|
|
jpayne@69
|
1985 #else
|
|
jpayne@69
|
1986 #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
|
|
jpayne@69
|
1987 #endif
|
|
jpayne@69
|
1988
|
|
jpayne@69
|
1989 /* PyObjectCall.proto */
|
|
jpayne@69
|
1990 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
1991 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
|
|
jpayne@69
|
1992 #else
|
|
jpayne@69
|
1993 #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
|
|
jpayne@69
|
1994 #endif
|
|
jpayne@69
|
1995
|
|
jpayne@69
|
1996 /* RaiseDoubleKeywords.proto */
|
|
jpayne@69
|
1997 static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
|
|
jpayne@69
|
1998
|
|
jpayne@69
|
1999 /* ParseKeywords.proto */
|
|
jpayne@69
|
2000 static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject *const *kwvalues,
|
|
jpayne@69
|
2001 PyObject **argnames[],
|
|
jpayne@69
|
2002 PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,
|
|
jpayne@69
|
2003 const char* function_name);
|
|
jpayne@69
|
2004
|
|
jpayne@69
|
2005 /* RaiseArgTupleInvalid.proto */
|
|
jpayne@69
|
2006 static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
|
|
jpayne@69
|
2007 Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
|
|
jpayne@69
|
2008
|
|
jpayne@69
|
2009 /* GetItemInt.proto */
|
|
jpayne@69
|
2010 #define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
2011 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
2012 __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\
|
|
jpayne@69
|
2013 (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\
|
|
jpayne@69
|
2014 __Pyx_GetItemInt_Generic(o, to_py_func(i))))
|
|
jpayne@69
|
2015 #define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
2016 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
2017 __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
|
|
jpayne@69
|
2018 (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
|
|
jpayne@69
|
2019 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
2020 int wraparound, int boundscheck);
|
|
jpayne@69
|
2021 #define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
2022 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
2023 __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\
|
|
jpayne@69
|
2024 (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
|
|
jpayne@69
|
2025 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
2026 int wraparound, int boundscheck);
|
|
jpayne@69
|
2027 static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
|
|
jpayne@69
|
2028 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
2029 int is_list, int wraparound, int boundscheck);
|
|
jpayne@69
|
2030
|
|
jpayne@69
|
2031 /* SetItemInt.proto */
|
|
jpayne@69
|
2032 #define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\
|
|
jpayne@69
|
2033 (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\
|
|
jpayne@69
|
2034 __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\
|
|
jpayne@69
|
2035 (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\
|
|
jpayne@69
|
2036 __Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
|
|
jpayne@69
|
2037 static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
|
|
jpayne@69
|
2038 static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
|
|
jpayne@69
|
2039 int is_list, int wraparound, int boundscheck);
|
|
jpayne@69
|
2040
|
|
jpayne@69
|
2041 /* PyFunctionFastCall.proto */
|
|
jpayne@69
|
2042 #if CYTHON_FAST_PYCALL
|
|
jpayne@69
|
2043 #if !CYTHON_VECTORCALL
|
|
jpayne@69
|
2044 #define __Pyx_PyFunction_FastCall(func, args, nargs)\
|
|
jpayne@69
|
2045 __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
|
|
jpayne@69
|
2046 static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs);
|
|
jpayne@69
|
2047 #endif
|
|
jpayne@69
|
2048 #define __Pyx_BUILD_ASSERT_EXPR(cond)\
|
|
jpayne@69
|
2049 (sizeof(char [1 - 2*!(cond)]) - 1)
|
|
jpayne@69
|
2050 #ifndef Py_MEMBER_SIZE
|
|
jpayne@69
|
2051 #define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
|
|
jpayne@69
|
2052 #endif
|
|
jpayne@69
|
2053 #if !CYTHON_VECTORCALL
|
|
jpayne@69
|
2054 #if PY_VERSION_HEX >= 0x03080000
|
|
jpayne@69
|
2055 #include "frameobject.h"
|
|
jpayne@69
|
2056 #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2057 #ifndef Py_BUILD_CORE
|
|
jpayne@69
|
2058 #define Py_BUILD_CORE 1
|
|
jpayne@69
|
2059 #endif
|
|
jpayne@69
|
2060 #include "internal/pycore_frame.h"
|
|
jpayne@69
|
2061 #endif
|
|
jpayne@69
|
2062 #define __Pxy_PyFrame_Initialize_Offsets()
|
|
jpayne@69
|
2063 #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus)
|
|
jpayne@69
|
2064 #else
|
|
jpayne@69
|
2065 static size_t __pyx_pyframe_localsplus_offset = 0;
|
|
jpayne@69
|
2066 #include "frameobject.h"
|
|
jpayne@69
|
2067 #define __Pxy_PyFrame_Initialize_Offsets()\
|
|
jpayne@69
|
2068 ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
|
|
jpayne@69
|
2069 (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
|
|
jpayne@69
|
2070 #define __Pyx_PyFrame_GetLocalsplus(frame)\
|
|
jpayne@69
|
2071 (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
|
|
jpayne@69
|
2072 #endif
|
|
jpayne@69
|
2073 #endif
|
|
jpayne@69
|
2074 #endif
|
|
jpayne@69
|
2075
|
|
jpayne@69
|
2076 /* PyObjectCallMethO.proto */
|
|
jpayne@69
|
2077 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
2078 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
|
|
jpayne@69
|
2079 #endif
|
|
jpayne@69
|
2080
|
|
jpayne@69
|
2081 /* PyObjectFastCall.proto */
|
|
jpayne@69
|
2082 #define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL)
|
|
jpayne@69
|
2083 static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs);
|
|
jpayne@69
|
2084
|
|
jpayne@69
|
2085 /* ArgTypeTest.proto */
|
|
jpayne@69
|
2086 #define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\
|
|
jpayne@69
|
2087 ((likely(__Pyx_IS_TYPE(obj, type) | (none_allowed && (obj == Py_None)))) ? 1 :\
|
|
jpayne@69
|
2088 __Pyx__ArgTypeTest(obj, type, name, exact))
|
|
jpayne@69
|
2089 static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact);
|
|
jpayne@69
|
2090
|
|
jpayne@69
|
2091 /* ExtTypeTest.proto */
|
|
jpayne@69
|
2092 static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
|
|
jpayne@69
|
2093
|
|
jpayne@69
|
2094 /* PyObjectCallOneArg.proto */
|
|
jpayne@69
|
2095 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
|
|
jpayne@69
|
2096
|
|
jpayne@69
|
2097 /* ObjectGetItem.proto */
|
|
jpayne@69
|
2098 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
2099 static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject *key);
|
|
jpayne@69
|
2100 #else
|
|
jpayne@69
|
2101 #define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key)
|
|
jpayne@69
|
2102 #endif
|
|
jpayne@69
|
2103
|
|
jpayne@69
|
2104 /* RaiseUnexpectedTypeError.proto */
|
|
jpayne@69
|
2105 static int __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj);
|
|
jpayne@69
|
2106
|
|
jpayne@69
|
2107 /* PyDictVersioning.proto */
|
|
jpayne@69
|
2108 #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
2109 #define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1)
|
|
jpayne@69
|
2110 #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag)
|
|
jpayne@69
|
2111 #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\
|
|
jpayne@69
|
2112 (version_var) = __PYX_GET_DICT_VERSION(dict);\
|
|
jpayne@69
|
2113 (cache_var) = (value);
|
|
jpayne@69
|
2114 #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\
|
|
jpayne@69
|
2115 static PY_UINT64_T __pyx_dict_version = 0;\
|
|
jpayne@69
|
2116 static PyObject *__pyx_dict_cached_value = NULL;\
|
|
jpayne@69
|
2117 if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\
|
|
jpayne@69
|
2118 (VAR) = __pyx_dict_cached_value;\
|
|
jpayne@69
|
2119 } else {\
|
|
jpayne@69
|
2120 (VAR) = __pyx_dict_cached_value = (LOOKUP);\
|
|
jpayne@69
|
2121 __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\
|
|
jpayne@69
|
2122 }\
|
|
jpayne@69
|
2123 }
|
|
jpayne@69
|
2124 static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj);
|
|
jpayne@69
|
2125 static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj);
|
|
jpayne@69
|
2126 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
|
2127 #else
|
|
jpayne@69
|
2128 #define __PYX_GET_DICT_VERSION(dict) (0)
|
|
jpayne@69
|
2129 #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)
|
|
jpayne@69
|
2130 #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP);
|
|
jpayne@69
|
2131 #endif
|
|
jpayne@69
|
2132
|
|
jpayne@69
|
2133 /* GetModuleGlobalName.proto */
|
|
jpayne@69
|
2134 #if CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
2135 #define __Pyx_GetModuleGlobalName(var, name) do {\
|
|
jpayne@69
|
2136 static PY_UINT64_T __pyx_dict_version = 0;\
|
|
jpayne@69
|
2137 static PyObject *__pyx_dict_cached_value = NULL;\
|
|
jpayne@69
|
2138 (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\
|
|
jpayne@69
|
2139 (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\
|
|
jpayne@69
|
2140 __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
|
|
jpayne@69
|
2141 } while(0)
|
|
jpayne@69
|
2142 #define __Pyx_GetModuleGlobalNameUncached(var, name) do {\
|
|
jpayne@69
|
2143 PY_UINT64_T __pyx_dict_version;\
|
|
jpayne@69
|
2144 PyObject *__pyx_dict_cached_value;\
|
|
jpayne@69
|
2145 (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\
|
|
jpayne@69
|
2146 } while(0)
|
|
jpayne@69
|
2147 static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value);
|
|
jpayne@69
|
2148 #else
|
|
jpayne@69
|
2149 #define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name)
|
|
jpayne@69
|
2150 #define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name)
|
|
jpayne@69
|
2151 static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name);
|
|
jpayne@69
|
2152 #endif
|
|
jpayne@69
|
2153
|
|
jpayne@69
|
2154 /* RaiseException.proto */
|
|
jpayne@69
|
2155 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
|
|
jpayne@69
|
2156
|
|
jpayne@69
|
2157 /* GetTopmostException.proto */
|
|
jpayne@69
|
2158 #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2159 static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate);
|
|
jpayne@69
|
2160 #endif
|
|
jpayne@69
|
2161
|
|
jpayne@69
|
2162 /* SaveResetException.proto */
|
|
jpayne@69
|
2163 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2164 #define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
2165 static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
2166 #define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
2167 static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
|
|
jpayne@69
|
2168 #else
|
|
jpayne@69
|
2169 #define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb)
|
|
jpayne@69
|
2170 #define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
|
|
jpayne@69
|
2171 #endif
|
|
jpayne@69
|
2172
|
|
jpayne@69
|
2173 /* GetException.proto */
|
|
jpayne@69
|
2174 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2175 #define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
2176 static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
2177 #else
|
|
jpayne@69
|
2178 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
2179 #endif
|
|
jpayne@69
|
2180
|
|
jpayne@69
|
2181 /* PySequenceContains.proto */
|
|
jpayne@69
|
2182 static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) {
|
|
jpayne@69
|
2183 int result = PySequence_Contains(seq, item);
|
|
jpayne@69
|
2184 return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
|
|
jpayne@69
|
2185 }
|
|
jpayne@69
|
2186
|
|
jpayne@69
|
2187 /* RaiseTooManyValuesToUnpack.proto */
|
|
jpayne@69
|
2188 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
|
|
jpayne@69
|
2189
|
|
jpayne@69
|
2190 /* RaiseNeedMoreValuesToUnpack.proto */
|
|
jpayne@69
|
2191 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
|
|
jpayne@69
|
2192
|
|
jpayne@69
|
2193 /* IterFinish.proto */
|
|
jpayne@69
|
2194 static CYTHON_INLINE int __Pyx_IterFinish(void);
|
|
jpayne@69
|
2195
|
|
jpayne@69
|
2196 /* UnpackItemEndCheck.proto */
|
|
jpayne@69
|
2197 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
|
|
jpayne@69
|
2198
|
|
jpayne@69
|
2199 /* PyIntBinop.proto */
|
|
jpayne@69
|
2200 #if !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
2201 static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check);
|
|
jpayne@69
|
2202 #else
|
|
jpayne@69
|
2203 #define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\
|
|
jpayne@69
|
2204 (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2))
|
|
jpayne@69
|
2205 #endif
|
|
jpayne@69
|
2206
|
|
jpayne@69
|
2207 /* PyObjectLookupSpecial.proto */
|
|
jpayne@69
|
2208 #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
2209 #define __Pyx_PyObject_LookupSpecialNoError(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 0)
|
|
jpayne@69
|
2210 #define __Pyx_PyObject_LookupSpecial(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 1)
|
|
jpayne@69
|
2211 static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error);
|
|
jpayne@69
|
2212 #else
|
|
jpayne@69
|
2213 #define __Pyx_PyObject_LookupSpecialNoError(o,n) __Pyx_PyObject_GetAttrStrNoError(o,n)
|
|
jpayne@69
|
2214 #define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n)
|
|
jpayne@69
|
2215 #endif
|
|
jpayne@69
|
2216
|
|
jpayne@69
|
2217 /* SwapException.proto */
|
|
jpayne@69
|
2218 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
2219 #define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb)
|
|
jpayne@69
|
2220 static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
2221 #else
|
|
jpayne@69
|
2222 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb);
|
|
jpayne@69
|
2223 #endif
|
|
jpayne@69
|
2224
|
|
jpayne@69
|
2225 /* PyIntCompare.proto */
|
|
jpayne@69
|
2226 static CYTHON_INLINE int __Pyx_PyInt_BoolEqObjC(PyObject *op1, PyObject *op2, long intval, long inplace);
|
|
jpayne@69
|
2227
|
|
jpayne@69
|
2228 /* DictGetItem.proto */
|
|
jpayne@69
|
2229 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
2230 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key);
|
|
jpayne@69
|
2231 #define __Pyx_PyObject_Dict_GetItem(obj, name)\
|
|
jpayne@69
|
2232 (likely(PyDict_CheckExact(obj)) ?\
|
|
jpayne@69
|
2233 __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name))
|
|
jpayne@69
|
2234 #else
|
|
jpayne@69
|
2235 #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
|
|
jpayne@69
|
2236 #define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name)
|
|
jpayne@69
|
2237 #endif
|
|
jpayne@69
|
2238
|
|
jpayne@69
|
2239 /* IncludeStructmemberH.proto */
|
|
jpayne@69
|
2240 #include <structmember.h>
|
|
jpayne@69
|
2241
|
|
jpayne@69
|
2242 /* FixUpExtensionType.proto */
|
|
jpayne@69
|
2243 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
2244 static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type);
|
|
jpayne@69
|
2245 #endif
|
|
jpayne@69
|
2246
|
|
jpayne@69
|
2247 /* FetchSharedCythonModule.proto */
|
|
jpayne@69
|
2248 static PyObject *__Pyx_FetchSharedCythonABIModule(void);
|
|
jpayne@69
|
2249
|
|
jpayne@69
|
2250 /* FetchCommonType.proto */
|
|
jpayne@69
|
2251 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
2252 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
|
|
jpayne@69
|
2253 #else
|
|
jpayne@69
|
2254 static PyTypeObject* __Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases);
|
|
jpayne@69
|
2255 #endif
|
|
jpayne@69
|
2256
|
|
jpayne@69
|
2257 /* PyMethodNew.proto */
|
|
jpayne@69
|
2258 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2259 static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) {
|
|
jpayne@69
|
2260 PyObject *typesModule=NULL, *methodType=NULL, *result=NULL;
|
|
jpayne@69
|
2261 CYTHON_UNUSED_VAR(typ);
|
|
jpayne@69
|
2262 if (!self)
|
|
jpayne@69
|
2263 return __Pyx_NewRef(func);
|
|
jpayne@69
|
2264 typesModule = PyImport_ImportModule("types");
|
|
jpayne@69
|
2265 if (!typesModule) return NULL;
|
|
jpayne@69
|
2266 methodType = PyObject_GetAttrString(typesModule, "MethodType");
|
|
jpayne@69
|
2267 Py_DECREF(typesModule);
|
|
jpayne@69
|
2268 if (!methodType) return NULL;
|
|
jpayne@69
|
2269 result = PyObject_CallFunctionObjArgs(methodType, func, self, NULL);
|
|
jpayne@69
|
2270 Py_DECREF(methodType);
|
|
jpayne@69
|
2271 return result;
|
|
jpayne@69
|
2272 }
|
|
jpayne@69
|
2273 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
2274 static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) {
|
|
jpayne@69
|
2275 CYTHON_UNUSED_VAR(typ);
|
|
jpayne@69
|
2276 if (!self)
|
|
jpayne@69
|
2277 return __Pyx_NewRef(func);
|
|
jpayne@69
|
2278 return PyMethod_New(func, self);
|
|
jpayne@69
|
2279 }
|
|
jpayne@69
|
2280 #else
|
|
jpayne@69
|
2281 #define __Pyx_PyMethod_New PyMethod_New
|
|
jpayne@69
|
2282 #endif
|
|
jpayne@69
|
2283
|
|
jpayne@69
|
2284 /* PyVectorcallFastCallDict.proto */
|
|
jpayne@69
|
2285 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
2286 static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw);
|
|
jpayne@69
|
2287 #endif
|
|
jpayne@69
|
2288
|
|
jpayne@69
|
2289 /* CythonFunctionShared.proto */
|
|
jpayne@69
|
2290 #define __Pyx_CyFunction_USED
|
|
jpayne@69
|
2291 #define __Pyx_CYFUNCTION_STATICMETHOD 0x01
|
|
jpayne@69
|
2292 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
|
|
jpayne@69
|
2293 #define __Pyx_CYFUNCTION_CCLASS 0x04
|
|
jpayne@69
|
2294 #define __Pyx_CYFUNCTION_COROUTINE 0x08
|
|
jpayne@69
|
2295 #define __Pyx_CyFunction_GetClosure(f)\
|
|
jpayne@69
|
2296 (((__pyx_CyFunctionObject *) (f))->func_closure)
|
|
jpayne@69
|
2297 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2298 #define __Pyx_CyFunction_GetClassObj(f)\
|
|
jpayne@69
|
2299 (((__pyx_CyFunctionObject *) (f))->func_classobj)
|
|
jpayne@69
|
2300 #else
|
|
jpayne@69
|
2301 #define __Pyx_CyFunction_GetClassObj(f)\
|
|
jpayne@69
|
2302 ((PyObject*) ((PyCMethodObject *) (f))->mm_class)
|
|
jpayne@69
|
2303 #endif
|
|
jpayne@69
|
2304 #define __Pyx_CyFunction_SetClassObj(f, classobj)\
|
|
jpayne@69
|
2305 __Pyx__CyFunction_SetClassObj((__pyx_CyFunctionObject *) (f), (classobj))
|
|
jpayne@69
|
2306 #define __Pyx_CyFunction_Defaults(type, f)\
|
|
jpayne@69
|
2307 ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
|
|
jpayne@69
|
2308 #define __Pyx_CyFunction_SetDefaultsGetter(f, g)\
|
|
jpayne@69
|
2309 ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
|
|
jpayne@69
|
2310 typedef struct {
|
|
jpayne@69
|
2311 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2312 PyObject_HEAD
|
|
jpayne@69
|
2313 PyObject *func;
|
|
jpayne@69
|
2314 #elif PY_VERSION_HEX < 0x030900B1
|
|
jpayne@69
|
2315 PyCFunctionObject func;
|
|
jpayne@69
|
2316 #else
|
|
jpayne@69
|
2317 PyCMethodObject func;
|
|
jpayne@69
|
2318 #endif
|
|
jpayne@69
|
2319 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
2320 __pyx_vectorcallfunc func_vectorcall;
|
|
jpayne@69
|
2321 #endif
|
|
jpayne@69
|
2322 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2323 PyObject *func_weakreflist;
|
|
jpayne@69
|
2324 #endif
|
|
jpayne@69
|
2325 PyObject *func_dict;
|
|
jpayne@69
|
2326 PyObject *func_name;
|
|
jpayne@69
|
2327 PyObject *func_qualname;
|
|
jpayne@69
|
2328 PyObject *func_doc;
|
|
jpayne@69
|
2329 PyObject *func_globals;
|
|
jpayne@69
|
2330 PyObject *func_code;
|
|
jpayne@69
|
2331 PyObject *func_closure;
|
|
jpayne@69
|
2332 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2333 PyObject *func_classobj;
|
|
jpayne@69
|
2334 #endif
|
|
jpayne@69
|
2335 void *defaults;
|
|
jpayne@69
|
2336 int defaults_pyobjects;
|
|
jpayne@69
|
2337 size_t defaults_size;
|
|
jpayne@69
|
2338 int flags;
|
|
jpayne@69
|
2339 PyObject *defaults_tuple;
|
|
jpayne@69
|
2340 PyObject *defaults_kwdict;
|
|
jpayne@69
|
2341 PyObject *(*defaults_getter)(PyObject *);
|
|
jpayne@69
|
2342 PyObject *func_annotations;
|
|
jpayne@69
|
2343 PyObject *func_is_coroutine;
|
|
jpayne@69
|
2344 } __pyx_CyFunctionObject;
|
|
jpayne@69
|
2345 #undef __Pyx_CyOrPyCFunction_Check
|
|
jpayne@69
|
2346 #define __Pyx_CyFunction_Check(obj) __Pyx_TypeCheck(obj, __pyx_CyFunctionType)
|
|
jpayne@69
|
2347 #define __Pyx_CyOrPyCFunction_Check(obj) __Pyx_TypeCheck2(obj, __pyx_CyFunctionType, &PyCFunction_Type)
|
|
jpayne@69
|
2348 #define __Pyx_CyFunction_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_CyFunctionType)
|
|
jpayne@69
|
2349 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc);
|
|
jpayne@69
|
2350 #undef __Pyx_IsSameCFunction
|
|
jpayne@69
|
2351 #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCyOrCFunction(func, cfunc)
|
|
jpayne@69
|
2352 static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml,
|
|
jpayne@69
|
2353 int flags, PyObject* qualname,
|
|
jpayne@69
|
2354 PyObject *closure,
|
|
jpayne@69
|
2355 PyObject *module, PyObject *globals,
|
|
jpayne@69
|
2356 PyObject* code);
|
|
jpayne@69
|
2357 static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj);
|
|
jpayne@69
|
2358 static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
|
|
jpayne@69
|
2359 size_t size,
|
|
jpayne@69
|
2360 int pyobjects);
|
|
jpayne@69
|
2361 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
|
|
jpayne@69
|
2362 PyObject *tuple);
|
|
jpayne@69
|
2363 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m,
|
|
jpayne@69
|
2364 PyObject *dict);
|
|
jpayne@69
|
2365 static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m,
|
|
jpayne@69
|
2366 PyObject *dict);
|
|
jpayne@69
|
2367 static int __pyx_CyFunction_init(PyObject *module);
|
|
jpayne@69
|
2368 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
2369 static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
2370 static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
2371 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
2372 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames);
|
|
jpayne@69
|
2373 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
2374 #define __Pyx_CyFunction_func_vectorcall(f) (((__pyx_CyFunctionObject*)f)->func_vectorcall)
|
|
jpayne@69
|
2375 #else
|
|
jpayne@69
|
2376 #define __Pyx_CyFunction_func_vectorcall(f) (((PyCFunctionObject*)f)->vectorcall)
|
|
jpayne@69
|
2377 #endif
|
|
jpayne@69
|
2378 #endif
|
|
jpayne@69
|
2379
|
|
jpayne@69
|
2380 /* CythonFunction.proto */
|
|
jpayne@69
|
2381 static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml,
|
|
jpayne@69
|
2382 int flags, PyObject* qualname,
|
|
jpayne@69
|
2383 PyObject *closure,
|
|
jpayne@69
|
2384 PyObject *module, PyObject *globals,
|
|
jpayne@69
|
2385 PyObject* code);
|
|
jpayne@69
|
2386
|
|
jpayne@69
|
2387 /* RaiseUnboundLocalError.proto */
|
|
jpayne@69
|
2388 static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
|
|
jpayne@69
|
2389
|
|
jpayne@69
|
2390 /* TypeImport.proto */
|
|
jpayne@69
|
2391 #ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11
|
|
jpayne@69
|
2392 #define __PYX_HAVE_RT_ImportType_proto_3_0_11
|
|
jpayne@69
|
2393 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L
|
|
jpayne@69
|
2394 #include <stdalign.h>
|
|
jpayne@69
|
2395 #endif
|
|
jpayne@69
|
2396 #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L
|
|
jpayne@69
|
2397 #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s)
|
|
jpayne@69
|
2398 #else
|
|
jpayne@69
|
2399 #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*)
|
|
jpayne@69
|
2400 #endif
|
|
jpayne@69
|
2401 enum __Pyx_ImportType_CheckSize_3_0_11 {
|
|
jpayne@69
|
2402 __Pyx_ImportType_CheckSize_Error_3_0_11 = 0,
|
|
jpayne@69
|
2403 __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1,
|
|
jpayne@69
|
2404 __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2
|
|
jpayne@69
|
2405 };
|
|
jpayne@69
|
2406 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
|
2407 #endif
|
|
jpayne@69
|
2408
|
|
jpayne@69
|
2409 /* Import.proto */
|
|
jpayne@69
|
2410 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
|
|
jpayne@69
|
2411
|
|
jpayne@69
|
2412 /* ImportDottedModule.proto */
|
|
jpayne@69
|
2413 static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple);
|
|
jpayne@69
|
2414 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
2415 static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple);
|
|
jpayne@69
|
2416 #endif
|
|
jpayne@69
|
2417
|
|
jpayne@69
|
2418 /* ImportFrom.proto */
|
|
jpayne@69
|
2419 static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name);
|
|
jpayne@69
|
2420
|
|
jpayne@69
|
2421 /* PyObjectCallNoArg.proto */
|
|
jpayne@69
|
2422 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
|
|
jpayne@69
|
2423
|
|
jpayne@69
|
2424 /* CLineInTraceback.proto */
|
|
jpayne@69
|
2425 #ifdef CYTHON_CLINE_IN_TRACEBACK
|
|
jpayne@69
|
2426 #define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
|
|
jpayne@69
|
2427 #else
|
|
jpayne@69
|
2428 static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
|
|
jpayne@69
|
2429 #endif
|
|
jpayne@69
|
2430
|
|
jpayne@69
|
2431 /* CodeObjectCache.proto */
|
|
jpayne@69
|
2432 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2433 typedef struct {
|
|
jpayne@69
|
2434 PyCodeObject* code_object;
|
|
jpayne@69
|
2435 int code_line;
|
|
jpayne@69
|
2436 } __Pyx_CodeObjectCacheEntry;
|
|
jpayne@69
|
2437 struct __Pyx_CodeObjectCache {
|
|
jpayne@69
|
2438 int count;
|
|
jpayne@69
|
2439 int max_count;
|
|
jpayne@69
|
2440 __Pyx_CodeObjectCacheEntry* entries;
|
|
jpayne@69
|
2441 };
|
|
jpayne@69
|
2442 static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
|
|
jpayne@69
|
2443 static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
|
|
jpayne@69
|
2444 static PyCodeObject *__pyx_find_code_object(int code_line);
|
|
jpayne@69
|
2445 static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
|
|
jpayne@69
|
2446 #endif
|
|
jpayne@69
|
2447
|
|
jpayne@69
|
2448 /* AddTraceback.proto */
|
|
jpayne@69
|
2449 static void __Pyx_AddTraceback(const char *funcname, int c_line,
|
|
jpayne@69
|
2450 int py_line, const char *filename);
|
|
jpayne@69
|
2451
|
|
jpayne@69
|
2452 /* ArrayAPI.proto */
|
|
jpayne@69
|
2453 #ifndef _ARRAYARRAY_H
|
|
jpayne@69
|
2454 #define _ARRAYARRAY_H
|
|
jpayne@69
|
2455 typedef struct arraydescr {
|
|
jpayne@69
|
2456 int typecode;
|
|
jpayne@69
|
2457 int itemsize;
|
|
jpayne@69
|
2458 PyObject * (*getitem)(struct arrayobject *, Py_ssize_t);
|
|
jpayne@69
|
2459 int (*setitem)(struct arrayobject *, Py_ssize_t, PyObject *);
|
|
jpayne@69
|
2460 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
2461 char *formats;
|
|
jpayne@69
|
2462 #endif
|
|
jpayne@69
|
2463 } arraydescr;
|
|
jpayne@69
|
2464 struct arrayobject {
|
|
jpayne@69
|
2465 PyObject_HEAD
|
|
jpayne@69
|
2466 Py_ssize_t ob_size;
|
|
jpayne@69
|
2467 union {
|
|
jpayne@69
|
2468 char *ob_item;
|
|
jpayne@69
|
2469 float *as_floats;
|
|
jpayne@69
|
2470 double *as_doubles;
|
|
jpayne@69
|
2471 int *as_ints;
|
|
jpayne@69
|
2472 unsigned int *as_uints;
|
|
jpayne@69
|
2473 unsigned char *as_uchars;
|
|
jpayne@69
|
2474 signed char *as_schars;
|
|
jpayne@69
|
2475 char *as_chars;
|
|
jpayne@69
|
2476 unsigned long *as_ulongs;
|
|
jpayne@69
|
2477 long *as_longs;
|
|
jpayne@69
|
2478 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
2479 unsigned long long *as_ulonglongs;
|
|
jpayne@69
|
2480 long long *as_longlongs;
|
|
jpayne@69
|
2481 #endif
|
|
jpayne@69
|
2482 short *as_shorts;
|
|
jpayne@69
|
2483 unsigned short *as_ushorts;
|
|
jpayne@69
|
2484 Py_UNICODE *as_pyunicodes;
|
|
jpayne@69
|
2485 void *as_voidptr;
|
|
jpayne@69
|
2486 } data;
|
|
jpayne@69
|
2487 Py_ssize_t allocated;
|
|
jpayne@69
|
2488 struct arraydescr *ob_descr;
|
|
jpayne@69
|
2489 PyObject *weakreflist;
|
|
jpayne@69
|
2490 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
2491 int ob_exports;
|
|
jpayne@69
|
2492 #endif
|
|
jpayne@69
|
2493 };
|
|
jpayne@69
|
2494 #ifndef NO_NEWARRAY_INLINE
|
|
jpayne@69
|
2495 static CYTHON_INLINE PyObject * newarrayobject(PyTypeObject *type, Py_ssize_t size,
|
|
jpayne@69
|
2496 struct arraydescr *descr) {
|
|
jpayne@69
|
2497 arrayobject *op;
|
|
jpayne@69
|
2498 size_t nbytes;
|
|
jpayne@69
|
2499 if (size < 0) {
|
|
jpayne@69
|
2500 PyErr_BadInternalCall();
|
|
jpayne@69
|
2501 return NULL;
|
|
jpayne@69
|
2502 }
|
|
jpayne@69
|
2503 nbytes = size * descr->itemsize;
|
|
jpayne@69
|
2504 if (nbytes / descr->itemsize != (size_t)size) {
|
|
jpayne@69
|
2505 return PyErr_NoMemory();
|
|
jpayne@69
|
2506 }
|
|
jpayne@69
|
2507 op = (arrayobject *) type->tp_alloc(type, 0);
|
|
jpayne@69
|
2508 if (op == NULL) {
|
|
jpayne@69
|
2509 return NULL;
|
|
jpayne@69
|
2510 }
|
|
jpayne@69
|
2511 op->ob_descr = descr;
|
|
jpayne@69
|
2512 op->allocated = size;
|
|
jpayne@69
|
2513 op->weakreflist = NULL;
|
|
jpayne@69
|
2514 __Pyx_SET_SIZE(op, size);
|
|
jpayne@69
|
2515 if (size <= 0) {
|
|
jpayne@69
|
2516 op->data.ob_item = NULL;
|
|
jpayne@69
|
2517 }
|
|
jpayne@69
|
2518 else {
|
|
jpayne@69
|
2519 op->data.ob_item = PyMem_NEW(char, nbytes);
|
|
jpayne@69
|
2520 if (op->data.ob_item == NULL) {
|
|
jpayne@69
|
2521 Py_DECREF(op);
|
|
jpayne@69
|
2522 return PyErr_NoMemory();
|
|
jpayne@69
|
2523 }
|
|
jpayne@69
|
2524 }
|
|
jpayne@69
|
2525 return (PyObject *) op;
|
|
jpayne@69
|
2526 }
|
|
jpayne@69
|
2527 #else
|
|
jpayne@69
|
2528 PyObject* newarrayobject(PyTypeObject *type, Py_ssize_t size,
|
|
jpayne@69
|
2529 struct arraydescr *descr);
|
|
jpayne@69
|
2530 #endif
|
|
jpayne@69
|
2531 static CYTHON_INLINE int resize(arrayobject *self, Py_ssize_t n) {
|
|
jpayne@69
|
2532 void *items = (void*) self->data.ob_item;
|
|
jpayne@69
|
2533 PyMem_Resize(items, char, (size_t)(n * self->ob_descr->itemsize));
|
|
jpayne@69
|
2534 if (items == NULL) {
|
|
jpayne@69
|
2535 PyErr_NoMemory();
|
|
jpayne@69
|
2536 return -1;
|
|
jpayne@69
|
2537 }
|
|
jpayne@69
|
2538 self->data.ob_item = (char*) items;
|
|
jpayne@69
|
2539 __Pyx_SET_SIZE(self, n);
|
|
jpayne@69
|
2540 self->allocated = n;
|
|
jpayne@69
|
2541 return 0;
|
|
jpayne@69
|
2542 }
|
|
jpayne@69
|
2543 static CYTHON_INLINE int resize_smart(arrayobject *self, Py_ssize_t n) {
|
|
jpayne@69
|
2544 void *items = (void*) self->data.ob_item;
|
|
jpayne@69
|
2545 Py_ssize_t newsize;
|
|
jpayne@69
|
2546 if (n < self->allocated && n*4 > self->allocated) {
|
|
jpayne@69
|
2547 __Pyx_SET_SIZE(self, n);
|
|
jpayne@69
|
2548 return 0;
|
|
jpayne@69
|
2549 }
|
|
jpayne@69
|
2550 newsize = n + (n / 2) + 1;
|
|
jpayne@69
|
2551 if (newsize <= n) {
|
|
jpayne@69
|
2552 PyErr_NoMemory();
|
|
jpayne@69
|
2553 return -1;
|
|
jpayne@69
|
2554 }
|
|
jpayne@69
|
2555 PyMem_Resize(items, char, (size_t)(newsize * self->ob_descr->itemsize));
|
|
jpayne@69
|
2556 if (items == NULL) {
|
|
jpayne@69
|
2557 PyErr_NoMemory();
|
|
jpayne@69
|
2558 return -1;
|
|
jpayne@69
|
2559 }
|
|
jpayne@69
|
2560 self->data.ob_item = (char*) items;
|
|
jpayne@69
|
2561 __Pyx_SET_SIZE(self, n);
|
|
jpayne@69
|
2562 self->allocated = newsize;
|
|
jpayne@69
|
2563 return 0;
|
|
jpayne@69
|
2564 }
|
|
jpayne@69
|
2565 #endif
|
|
jpayne@69
|
2566
|
|
jpayne@69
|
2567 /* GCCDiagnostics.proto */
|
|
jpayne@69
|
2568 #if !defined(__INTEL_COMPILER) && defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
|
|
jpayne@69
|
2569 #define __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
2570 #endif
|
|
jpayne@69
|
2571
|
|
jpayne@69
|
2572 /* CIntFromPy.proto */
|
|
jpayne@69
|
2573 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
|
|
jpayne@69
|
2574
|
|
jpayne@69
|
2575 /* CIntFromPy.proto */
|
|
jpayne@69
|
2576 static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *);
|
|
jpayne@69
|
2577
|
|
jpayne@69
|
2578 /* CIntToPy.proto */
|
|
jpayne@69
|
2579 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
|
|
jpayne@69
|
2580
|
|
jpayne@69
|
2581 /* CIntFromPy.proto */
|
|
jpayne@69
|
2582 static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *);
|
|
jpayne@69
|
2583
|
|
jpayne@69
|
2584 /* CIntToPy.proto */
|
|
jpayne@69
|
2585 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
|
|
jpayne@69
|
2586
|
|
jpayne@69
|
2587 /* CIntToPy.proto */
|
|
jpayne@69
|
2588 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value);
|
|
jpayne@69
|
2589
|
|
jpayne@69
|
2590 /* FormatTypeName.proto */
|
|
jpayne@69
|
2591 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
2592 typedef PyObject *__Pyx_TypeName;
|
|
jpayne@69
|
2593 #define __Pyx_FMT_TYPENAME "%U"
|
|
jpayne@69
|
2594 static __Pyx_TypeName __Pyx_PyType_GetName(PyTypeObject* tp);
|
|
jpayne@69
|
2595 #define __Pyx_DECREF_TypeName(obj) Py_XDECREF(obj)
|
|
jpayne@69
|
2596 #else
|
|
jpayne@69
|
2597 typedef const char *__Pyx_TypeName;
|
|
jpayne@69
|
2598 #define __Pyx_FMT_TYPENAME "%.200s"
|
|
jpayne@69
|
2599 #define __Pyx_PyType_GetName(tp) ((tp)->tp_name)
|
|
jpayne@69
|
2600 #define __Pyx_DECREF_TypeName(obj)
|
|
jpayne@69
|
2601 #endif
|
|
jpayne@69
|
2602
|
|
jpayne@69
|
2603 /* CIntFromPy.proto */
|
|
jpayne@69
|
2604 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
|
|
jpayne@69
|
2605
|
|
jpayne@69
|
2606 /* FastTypeChecks.proto */
|
|
jpayne@69
|
2607 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
2608 #define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
|
|
jpayne@69
|
2609 #define __Pyx_TypeCheck2(obj, type1, type2) __Pyx_IsAnySubtype2(Py_TYPE(obj), (PyTypeObject *)type1, (PyTypeObject *)type2)
|
|
jpayne@69
|
2610 static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
|
|
jpayne@69
|
2611 static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b);
|
|
jpayne@69
|
2612 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
|
|
jpayne@69
|
2613 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
|
|
jpayne@69
|
2614 #else
|
|
jpayne@69
|
2615 #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
|
|
jpayne@69
|
2616 #define __Pyx_TypeCheck2(obj, type1, type2) (PyObject_TypeCheck(obj, (PyTypeObject *)type1) || PyObject_TypeCheck(obj, (PyTypeObject *)type2))
|
|
jpayne@69
|
2617 #define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
|
|
jpayne@69
|
2618 #define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
|
|
jpayne@69
|
2619 #endif
|
|
jpayne@69
|
2620 #define __Pyx_PyErr_ExceptionMatches2(err1, err2) __Pyx_PyErr_GivenExceptionMatches2(__Pyx_PyErr_CurrentExceptionType(), err1, err2)
|
|
jpayne@69
|
2621 #define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
|
|
jpayne@69
|
2622
|
|
jpayne@69
|
2623 /* CheckBinaryVersion.proto */
|
|
jpayne@69
|
2624 static unsigned long __Pyx_get_runtime_version(void);
|
|
jpayne@69
|
2625 static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer);
|
|
jpayne@69
|
2626
|
|
jpayne@69
|
2627 /* FunctionExport.proto */
|
|
jpayne@69
|
2628 static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig);
|
|
jpayne@69
|
2629
|
|
jpayne@69
|
2630 /* InitStrings.proto */
|
|
jpayne@69
|
2631 static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
|
|
jpayne@69
|
2632
|
|
jpayne@69
|
2633 /* #### Code section: module_declarations ### */
|
|
jpayne@69
|
2634 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
2635 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self); /* proto*/
|
|
jpayne@69
|
2636
|
|
jpayne@69
|
2637 /* Module declarations from "cython" */
|
|
jpayne@69
|
2638
|
|
jpayne@69
|
2639 /* Module declarations from "cpython.version" */
|
|
jpayne@69
|
2640
|
|
jpayne@69
|
2641 /* Module declarations from "__builtin__" */
|
|
jpayne@69
|
2642
|
|
jpayne@69
|
2643 /* Module declarations from "cpython.type" */
|
|
jpayne@69
|
2644
|
|
jpayne@69
|
2645 /* Module declarations from "libc.string" */
|
|
jpayne@69
|
2646
|
|
jpayne@69
|
2647 /* Module declarations from "libc.stdio" */
|
|
jpayne@69
|
2648
|
|
jpayne@69
|
2649 /* Module declarations from "cpython.object" */
|
|
jpayne@69
|
2650
|
|
jpayne@69
|
2651 /* Module declarations from "cpython.ref" */
|
|
jpayne@69
|
2652
|
|
jpayne@69
|
2653 /* Module declarations from "cpython.exc" */
|
|
jpayne@69
|
2654
|
|
jpayne@69
|
2655 /* Module declarations from "cpython.module" */
|
|
jpayne@69
|
2656
|
|
jpayne@69
|
2657 /* Module declarations from "cpython.mem" */
|
|
jpayne@69
|
2658
|
|
jpayne@69
|
2659 /* Module declarations from "cpython.tuple" */
|
|
jpayne@69
|
2660
|
|
jpayne@69
|
2661 /* Module declarations from "cpython.list" */
|
|
jpayne@69
|
2662
|
|
jpayne@69
|
2663 /* Module declarations from "cpython.sequence" */
|
|
jpayne@69
|
2664
|
|
jpayne@69
|
2665 /* Module declarations from "cpython.mapping" */
|
|
jpayne@69
|
2666
|
|
jpayne@69
|
2667 /* Module declarations from "cpython.iterator" */
|
|
jpayne@69
|
2668
|
|
jpayne@69
|
2669 /* Module declarations from "cpython.number" */
|
|
jpayne@69
|
2670
|
|
jpayne@69
|
2671 /* Module declarations from "cpython.int" */
|
|
jpayne@69
|
2672
|
|
jpayne@69
|
2673 /* Module declarations from "__builtin__" */
|
|
jpayne@69
|
2674
|
|
jpayne@69
|
2675 /* Module declarations from "cpython.bool" */
|
|
jpayne@69
|
2676
|
|
jpayne@69
|
2677 /* Module declarations from "cpython.long" */
|
|
jpayne@69
|
2678
|
|
jpayne@69
|
2679 /* Module declarations from "cpython.float" */
|
|
jpayne@69
|
2680
|
|
jpayne@69
|
2681 /* Module declarations from "__builtin__" */
|
|
jpayne@69
|
2682
|
|
jpayne@69
|
2683 /* Module declarations from "cpython.complex" */
|
|
jpayne@69
|
2684
|
|
jpayne@69
|
2685 /* Module declarations from "cpython.string" */
|
|
jpayne@69
|
2686
|
|
jpayne@69
|
2687 /* Module declarations from "libc.stddef" */
|
|
jpayne@69
|
2688
|
|
jpayne@69
|
2689 /* Module declarations from "cpython.unicode" */
|
|
jpayne@69
|
2690
|
|
jpayne@69
|
2691 /* Module declarations from "cpython.pyport" */
|
|
jpayne@69
|
2692
|
|
jpayne@69
|
2693 /* Module declarations from "cpython.dict" */
|
|
jpayne@69
|
2694
|
|
jpayne@69
|
2695 /* Module declarations from "cpython.instance" */
|
|
jpayne@69
|
2696
|
|
jpayne@69
|
2697 /* Module declarations from "cpython.function" */
|
|
jpayne@69
|
2698
|
|
jpayne@69
|
2699 /* Module declarations from "cpython.method" */
|
|
jpayne@69
|
2700
|
|
jpayne@69
|
2701 /* Module declarations from "cpython.weakref" */
|
|
jpayne@69
|
2702
|
|
jpayne@69
|
2703 /* Module declarations from "cpython.getargs" */
|
|
jpayne@69
|
2704
|
|
jpayne@69
|
2705 /* Module declarations from "cpython.pythread" */
|
|
jpayne@69
|
2706
|
|
jpayne@69
|
2707 /* Module declarations from "cpython.pystate" */
|
|
jpayne@69
|
2708
|
|
jpayne@69
|
2709 /* Module declarations from "cpython.cobject" */
|
|
jpayne@69
|
2710
|
|
jpayne@69
|
2711 /* Module declarations from "cpython.oldbuffer" */
|
|
jpayne@69
|
2712
|
|
jpayne@69
|
2713 /* Module declarations from "cpython.set" */
|
|
jpayne@69
|
2714
|
|
jpayne@69
|
2715 /* Module declarations from "cpython.buffer" */
|
|
jpayne@69
|
2716
|
|
jpayne@69
|
2717 /* Module declarations from "cpython.bytes" */
|
|
jpayne@69
|
2718
|
|
jpayne@69
|
2719 /* Module declarations from "cpython.pycapsule" */
|
|
jpayne@69
|
2720
|
|
jpayne@69
|
2721 /* Module declarations from "cpython.contextvars" */
|
|
jpayne@69
|
2722
|
|
jpayne@69
|
2723 /* Module declarations from "cpython" */
|
|
jpayne@69
|
2724
|
|
jpayne@69
|
2725 /* Module declarations from "array" */
|
|
jpayne@69
|
2726
|
|
jpayne@69
|
2727 /* Module declarations from "cpython.array" */
|
|
jpayne@69
|
2728 static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_clone(arrayobject *, Py_ssize_t, int); /*proto*/
|
|
jpayne@69
|
2729 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *, char *, Py_ssize_t); /*proto*/
|
|
jpayne@69
|
2730
|
|
jpayne@69
|
2731 /* Module declarations from "libc.errno" */
|
|
jpayne@69
|
2732
|
|
jpayne@69
|
2733 /* Module declarations from "libc.stdlib" */
|
|
jpayne@69
|
2734
|
|
jpayne@69
|
2735 /* Module declarations from "libc.stdint" */
|
|
jpayne@69
|
2736
|
|
jpayne@69
|
2737 /* Module declarations from "posix.types" */
|
|
jpayne@69
|
2738
|
|
jpayne@69
|
2739 /* Module declarations from "posix.fcntl" */
|
|
jpayne@69
|
2740
|
|
jpayne@69
|
2741 /* Module declarations from "posix.unistd" */
|
|
jpayne@69
|
2742
|
|
jpayne@69
|
2743 /* Module declarations from "pysam.libcsamtools" */
|
|
jpayne@69
|
2744
|
|
jpayne@69
|
2745 /* Module declarations from "pysam.libcbcftools" */
|
|
jpayne@69
|
2746
|
|
jpayne@69
|
2747 /* Module declarations from "pysam.libcutils" */
|
|
jpayne@69
|
2748 static int __pyx_v_5pysam_9libcutils_MAX_POS;
|
|
jpayne@69
|
2749 static PyObject *__pyx_v_5pysam_9libcutils_ERROR_HANDLER = 0;
|
|
jpayne@69
|
2750 static PyObject *__pyx_v_5pysam_9libcutils_FILENAME_ENCODING = 0;
|
|
jpayne@69
|
2751 static PyObject *__pyx_v_5pysam_9libcutils_TEXT_ENCODING = 0;
|
|
jpayne@69
|
2752 static PyObject *__pyx_f_5pysam_9libcutils_parse_region(int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_parse_region *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
2753 static arrayobject *__pyx_f_5pysam_9libcutils_qualitystring_to_array(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
2754 static PyObject *__pyx_f_5pysam_9libcutils_array_to_qualitystring(arrayobject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
2755 static PyObject *__pyx_f_5pysam_9libcutils_qualities_to_qualitystring(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
2756 static PyObject *__pyx_f_5pysam_9libcutils_get_encoding_error_handler(int __pyx_skip_dispatch); /*proto*/
|
|
jpayne@69
|
2757 static PyObject *__pyx_f_5pysam_9libcutils_set_encoding_error_handler(PyObject *, int __pyx_skip_dispatch); /*proto*/
|
|
jpayne@69
|
2758 static PyObject *__pyx_f_5pysam_9libcutils_force_str(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
2759 static PyObject *__pyx_f_5pysam_9libcutils_force_bytes(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_bytes *__pyx_optional_args); /*proto*/
|
|
jpayne@69
|
2760 /* #### Code section: typeinfo ### */
|
|
jpayne@69
|
2761 /* #### Code section: before_global_var ### */
|
|
jpayne@69
|
2762 #define __Pyx_MODULE_NAME "pysam.libcutils"
|
|
jpayne@69
|
2763 extern int __pyx_module_is_main_pysam__libcutils;
|
|
jpayne@69
|
2764 int __pyx_module_is_main_pysam__libcutils = 0;
|
|
jpayne@69
|
2765
|
|
jpayne@69
|
2766 /* Implementation of "pysam.libcutils" */
|
|
jpayne@69
|
2767 /* #### Code section: global_var ### */
|
|
jpayne@69
|
2768 static PyObject *__pyx_builtin_chr;
|
|
jpayne@69
|
2769 static PyObject *__pyx_builtin_TypeError;
|
|
jpayne@69
|
2770 static PyObject *__pyx_builtin_ValueError;
|
|
jpayne@69
|
2771 static PyObject *__pyx_builtin_OverflowError;
|
|
jpayne@69
|
2772 static PyObject *__pyx_builtin_IOError;
|
|
jpayne@69
|
2773 static PyObject *__pyx_builtin_OSError;
|
|
jpayne@69
|
2774 static PyObject *__pyx_builtin_open;
|
|
jpayne@69
|
2775 static PyObject *__pyx_builtin_UnicodeDecodeError;
|
|
jpayne@69
|
2776 static PyObject *__pyx_builtin_MemoryError;
|
|
jpayne@69
|
2777 /* #### Code section: string_decls ### */
|
|
jpayne@69
|
2778 static const char __pyx_k_[] = "";
|
|
jpayne@69
|
2779 static const char __pyx_k_B[] = "B";
|
|
jpayne@69
|
2780 static const char __pyx_k_a[] = "a";
|
|
jpayne@69
|
2781 static const char __pyx_k_c[] = "-c";
|
|
jpayne@69
|
2782 static const char __pyx_k_i[] = "i";
|
|
jpayne@69
|
2783 static const char __pyx_k_l[] = "l";
|
|
jpayne@69
|
2784 static const char __pyx_k_m[] = "-m";
|
|
jpayne@69
|
2785 static const char __pyx_k_n[] = "n";
|
|
jpayne@69
|
2786 static const char __pyx_k_o[] = "-o";
|
|
jpayne@69
|
2787 static const char __pyx_k_r[] = "r";
|
|
jpayne@69
|
2788 static const char __pyx_k__7[] = ":";
|
|
jpayne@69
|
2789 static const char __pyx_k__8[] = "-";
|
|
jpayne@69
|
2790 static const char __pyx_k_fn[] = "fn";
|
|
jpayne@69
|
2791 static const char __pyx_k_io[] = "io";
|
|
jpayne@69
|
2792 static const char __pyx_k_os[] = "os";
|
|
jpayne@69
|
2793 static const char __pyx_k_rb[] = "rb";
|
|
jpayne@69
|
2794 static const char __pyx_k_re[] = "re";
|
|
jpayne@69
|
2795 static const char __pyx_k__10[] = "-@";
|
|
jpayne@69
|
2796 static const char __pyx_k__11[] = " ";
|
|
jpayne@69
|
2797 static const char __pyx_k__14[] = "*";
|
|
jpayne@69
|
2798 static const char __pyx_k__15[] = ".";
|
|
jpayne@69
|
2799 static const char __pyx_k__33[] = "?";
|
|
jpayne@69
|
2800 static const char __pyx_k_all[] = "__all__";
|
|
jpayne@69
|
2801 static const char __pyx_k_arg[] = "arg";
|
|
jpayne@69
|
2802 static const char __pyx_k_chr[] = "chr";
|
|
jpayne@69
|
2803 static const char __pyx_k_end[] = "end";
|
|
jpayne@69
|
2804 static const char __pyx_k_inf[] = "inf";
|
|
jpayne@69
|
2805 static const char __pyx_k_o_2[] = "-o {}";
|
|
jpayne@69
|
2806 static const char __pyx_k_out[] = "out";
|
|
jpayne@69
|
2807 static const char __pyx_k_roh[] = "roh";
|
|
jpayne@69
|
2808 static const char __pyx_k_sys[] = "sys";
|
|
jpayne@69
|
2809 static const char __pyx_k_args[] = "args";
|
|
jpayne@69
|
2810 static const char __pyx_k_exit[] = "__exit__";
|
|
jpayne@69
|
2811 static const char __pyx_k_head[] = "head";
|
|
jpayne@69
|
2812 static const char __pyx_k_main[] = "__main__";
|
|
jpayne@69
|
2813 static const char __pyx_k_name[] = "name";
|
|
jpayne@69
|
2814 static const char __pyx_k_open[] = "open";
|
|
jpayne@69
|
2815 static const char __pyx_k_path[] = "path";
|
|
jpayne@69
|
2816 static const char __pyx_k_read[] = "read";
|
|
jpayne@69
|
2817 static const char __pyx_k_spec[] = "__spec__";
|
|
jpayne@69
|
2818 static const char __pyx_k_stop[] = "stop";
|
|
jpayne@69
|
2819 static const char __pyx_k_test[] = "__test__";
|
|
jpayne@69
|
2820 static const char __pyx_k_view[] = "view";
|
|
jpayne@69
|
2821 static const char __pyx_k_ascii[] = "ascii";
|
|
jpayne@69
|
2822 static const char __pyx_k_calmd[] = "calmd";
|
|
jpayne@69
|
2823 static const char __pyx_k_cargs[] = "cargs";
|
|
jpayne@69
|
2824 static const char __pyx_k_close[] = "close";
|
|
jpayne@69
|
2825 static const char __pyx_k_depad[] = "depad";
|
|
jpayne@69
|
2826 static const char __pyx_k_enter[] = "__enter__";
|
|
jpayne@69
|
2827 static const char __pyx_k_index[] = "index";
|
|
jpayne@69
|
2828 static const char __pyx_k_split[] = "split";
|
|
jpayne@69
|
2829 static const char __pyx_k_start[] = "start";
|
|
jpayne@69
|
2830 static const char __pyx_k_stats[] = "stats";
|
|
jpayne@69
|
2831 static const char __pyx_k_types[] = "types";
|
|
jpayne@69
|
2832 static const char __pyx_k_utf_8[] = "utf-8";
|
|
jpayne@69
|
2833 static const char __pyx_k_codecs[] = "codecs";
|
|
jpayne@69
|
2834 static const char __pyx_k_contig[] = "contig";
|
|
jpayne@69
|
2835 static const char __pyx_k_decode[] = "decode";
|
|
jpayne@69
|
2836 static const char __pyx_k_encode[] = "encode";
|
|
jpayne@69
|
2837 static const char __pyx_k_exists[] = "exists";
|
|
jpayne@69
|
2838 static const char __pyx_k_extend[] = "extend";
|
|
jpayne@69
|
2839 static const char __pyx_k_format[] = "format";
|
|
jpayne@69
|
2840 static const char __pyx_k_import[] = "__import__";
|
|
jpayne@69
|
2841 static const char __pyx_k_method[] = "method";
|
|
jpayne@69
|
2842 static const char __pyx_k_name_2[] = "__name__";
|
|
jpayne@69
|
2843 static const char __pyx_k_object[] = "object";
|
|
jpayne@69
|
2844 static const char __pyx_k_offset[] = "offset";
|
|
jpayne@69
|
2845 static const char __pyx_k_output[] = "--output";
|
|
jpayne@69
|
2846 static const char __pyx_k_region[] = "region";
|
|
jpayne@69
|
2847 static const char __pyx_k_remove[] = "remove";
|
|
jpayne@69
|
2848 static const char __pyx_k_retval[] = "retval";
|
|
jpayne@69
|
2849 static const char __pyx_k_strict[] = "strict";
|
|
jpayne@69
|
2850 static const char __pyx_k_string[] = "string";
|
|
jpayne@69
|
2851 static const char __pyx_k_IOError[] = "IOError";
|
|
jpayne@69
|
2852 static const char __pyx_k_OSError[] = "OSError";
|
|
jpayne@69
|
2853 static const char __pyx_k_collect[] = "_collect";
|
|
jpayne@69
|
2854 static const char __pyx_k_mkstemp[] = "mkstemp";
|
|
jpayne@69
|
2855 static const char __pyx_k_mpileup[] = "mpileup";
|
|
jpayne@69
|
2856 static const char __pyx_k_threads[] = "--threads";
|
|
jpayne@69
|
2857 static const char __pyx_k_tobytes[] = "tobytes";
|
|
jpayne@69
|
2858 static const char __pyx_k_bcftools[] = "bcftools";
|
|
jpayne@69
|
2859 static const char __pyx_k_fsencode[] = "fsencode";
|
|
jpayne@69
|
2860 static const char __pyx_k_is_usage[] = "is_usage";
|
|
jpayne@69
|
2861 static const char __pyx_k_samtools[] = "samtools";
|
|
jpayne@69
|
2862 static const char __pyx_k_stderr_f[] = "stderr_f";
|
|
jpayne@69
|
2863 static const char __pyx_k_stderr_h[] = "stderr_h";
|
|
jpayne@69
|
2864 static const char __pyx_k_stdout_f[] = "stdout_f";
|
|
jpayne@69
|
2865 static const char __pyx_k_stdout_h[] = "stdout_h";
|
|
jpayne@69
|
2866 static const char __pyx_k_tempfile[] = "tempfile";
|
|
jpayne@69
|
2867 static const char __pyx_k_ARGUMENTS[] = "ARGUMENTS";
|
|
jpayne@69
|
2868 static const char __pyx_k_TypeError[] = "TypeError";
|
|
jpayne@69
|
2869 static const char __pyx_k_exception[] = "exception";
|
|
jpayne@69
|
2870 static const char __pyx_k_input_str[] = "input_str";
|
|
jpayne@69
|
2871 static const char __pyx_k_min_shift[] = "--min-shift";
|
|
jpayne@69
|
2872 static const char __pyx_k_qualities[] = "qualities";
|
|
jpayne@69
|
2873 static const char __pyx_k_reference[] = "reference";
|
|
jpayne@69
|
2874 static const char __pyx_k_skip_next[] = "skip_next";
|
|
jpayne@69
|
2875 static const char __pyx_k_ValueError[] = "ValueError";
|
|
jpayne@69
|
2876 static const char __pyx_k_collection[] = "collection";
|
|
jpayne@69
|
2877 static const char __pyx_k_contextlib[] = "contextlib";
|
|
jpayne@69
|
2878 static const char __pyx_k_extra_args[] = "extra_args";
|
|
jpayne@69
|
2879 static const char __pyx_k_out_stderr[] = "out_stderr";
|
|
jpayne@69
|
2880 static const char __pyx_k_out_stdout[] = "out_stdout";
|
|
jpayne@69
|
2881 static const char __pyx_k_startswith[] = "startswith";
|
|
jpayne@69
|
2882 static const char __pyx_k_MemoryError[] = "MemoryError";
|
|
jpayne@69
|
2883 static const char __pyx_k_output_file[] = "--output-file";
|
|
jpayne@69
|
2884 static const char __pyx_k_save_stdout[] = "save_stdout";
|
|
jpayne@69
|
2885 static const char __pyx_k_catch_stdout[] = "catch_stdout";
|
|
jpayne@69
|
2886 static const char __pyx_k_initializing[] = "_initializing";
|
|
jpayne@69
|
2887 static const char __pyx_k_is_coroutine[] = "_is_coroutine";
|
|
jpayne@69
|
2888 static const char __pyx_k_parse_region[] = "parse_region";
|
|
jpayne@69
|
2889 static const char __pyx_k_OverflowError[] = "OverflowError";
|
|
jpayne@69
|
2890 static const char __pyx_k_class_getitem[] = "__class_getitem__";
|
|
jpayne@69
|
2891 static const char __pyx_k_stdout_option[] = "stdout_option";
|
|
jpayne@69
|
2892 static const char __pyx_k_contextmanager[] = "contextmanager";
|
|
jpayne@69
|
2893 static const char __pyx_k_latin1_replace[] = "latin1_replace";
|
|
jpayne@69
|
2894 static const char __pyx_k_pysam_dispatch[] = "_pysam_dispatch";
|
|
jpayne@69
|
2895 static const char __pyx_k_register_error[] = "register_error";
|
|
jpayne@69
|
2896 static const char __pyx_k_pysam_libcutils[] = "pysam.libcutils";
|
|
jpayne@69
|
2897 static const char __pyx_k_MAP_STDOUT_OPTIONS[] = "MAP_STDOUT_OPTIONS";
|
|
jpayne@69
|
2898 static const char __pyx_k_UnicodeDecodeError[] = "UnicodeDecodeError";
|
|
jpayne@69
|
2899 static const char __pyx_k_asyncio_coroutines[] = "asyncio.coroutines";
|
|
jpayne@69
|
2900 static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
|
|
jpayne@69
|
2901 static const char __pyx_k_getdefaultencoding[] = "getdefaultencoding";
|
|
jpayne@69
|
2902 static const char __pyx_k_pysam_latin1replace[] = "pysam.latin1replace";
|
|
jpayne@69
|
2903 static const char __pyx_k_pysam_libcutils_pyx[] = "pysam/libcutils.pyx";
|
|
jpayne@69
|
2904 static const char __pyx_k_stop_out_of_range_i[] = "stop out of range (%i)";
|
|
jpayne@69
|
2905 static const char __pyx_k_start_out_of_range_i[] = "start out of range (%i)";
|
|
jpayne@69
|
2906 static const char __pyx_k_getfilesystemencoding[] = "getfilesystemencoding";
|
|
jpayne@69
|
2907 static const char __pyx_k_array_to_qualitystring[] = "array_to_qualitystring";
|
|
jpayne@69
|
2908 static const char __pyx_k_qualitystring_to_array[] = "qualitystring_to_array";
|
|
jpayne@69
|
2909 static const char __pyx_k_get_encoding_error_handler[] = "get_encoding_error_handler";
|
|
jpayne@69
|
2910 static const char __pyx_k_qualities_to_qualitystring[] = "qualities_to_qualitystring";
|
|
jpayne@69
|
2911 static const char __pyx_k_set_encoding_error_handler[] = "set_encoding_error_handler";
|
|
jpayne@69
|
2912 static const char __pyx_k_No_such_file_or_directory_s[] = "No such file or directory: '%s'";
|
|
jpayne@69
|
2913 static const char __pyx_k_pysam_dispatch_locals__collect[] = "_pysam_dispatch.<locals>._collect";
|
|
jpayne@69
|
2914 static const char __pyx_k_contig_and_reference_should_not[] = "contig and reference should not both be specified";
|
|
jpayne@69
|
2915 static const char __pyx_k_stop_and_end_should_not_both_be[] = "stop and end should not both be specified";
|
|
jpayne@69
|
2916 static const char __pyx_k_Argument_must_be_string_bytes_or[] = "Argument must be string, bytes or unicode.";
|
|
jpayne@69
|
2917 static const char __pyx_k_contig_reference_and_region_shou[] = "contig/reference and region should not both be specified";
|
|
jpayne@69
|
2918 static const char __pyx_k_error_while_opening_file_for_wri[] = "error while opening file for writing";
|
|
jpayne@69
|
2919 static const char __pyx_k_invalid_coordinates_start_i_stop[] = "invalid coordinates: start (%i) > stop (%i)";
|
|
jpayne@69
|
2920 static const char __pyx_k_neither_contig_nor_region_are_gi[] = "neither contig nor region are given";
|
|
jpayne@69
|
2921 /* #### Code section: decls ### */
|
|
jpayne@69
|
2922 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
|
2923 static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
|
|
jpayne@69
|
2924 static PyObject *__pyx_pf_5pysam_9libcutils_qualitystring_to_array(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_input_str, int __pyx_v_offset); /* proto */
|
|
jpayne@69
|
2925 static PyObject *__pyx_pf_5pysam_9libcutils_2array_to_qualitystring(CYTHON_UNUSED PyObject *__pyx_self, arrayobject *__pyx_v_qualities, int __pyx_v_offset); /* proto */
|
|
jpayne@69
|
2926 static PyObject *__pyx_pf_5pysam_9libcutils_4qualities_to_qualitystring(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_qualities, int __pyx_v_offset); /* proto */
|
|
jpayne@69
|
2927 static PyObject *__pyx_pf_5pysam_9libcutils_6latin1_replace(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_exception); /* proto */
|
|
jpayne@69
|
2928 static PyObject *__pyx_pf_5pysam_9libcutils_8get_encoding_error_handler(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
|
|
jpayne@69
|
2929 static PyObject *__pyx_pf_5pysam_9libcutils_10set_encoding_error_handler(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_name); /* proto */
|
|
jpayne@69
|
2930 static PyObject *__pyx_pf_5pysam_9libcutils_12parse_region(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_reference, PyObject *__pyx_v_end); /* proto */
|
|
jpayne@69
|
2931 static PyObject *__pyx_pf_5pysam_9libcutils_15_pysam_dispatch__collect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fn); /* proto */
|
|
jpayne@69
|
2932 static PyObject *__pyx_pf_5pysam_9libcutils_14_pysam_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_collection, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout, PyObject *__pyx_v_is_usage, PyObject *__pyx_v_save_stdout); /* proto */
|
|
jpayne@69
|
2933 /* #### Code section: late_includes ### */
|
|
jpayne@69
|
2934 /* #### Code section: module_state ### */
|
|
jpayne@69
|
2935 typedef struct {
|
|
jpayne@69
|
2936 PyObject *__pyx_d;
|
|
jpayne@69
|
2937 PyObject *__pyx_b;
|
|
jpayne@69
|
2938 PyObject *__pyx_cython_runtime;
|
|
jpayne@69
|
2939 PyObject *__pyx_empty_tuple;
|
|
jpayne@69
|
2940 PyObject *__pyx_empty_bytes;
|
|
jpayne@69
|
2941 PyObject *__pyx_empty_unicode;
|
|
jpayne@69
|
2942 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
2943 PyTypeObject *__pyx_CyFunctionType;
|
|
jpayne@69
|
2944 #endif
|
|
jpayne@69
|
2945 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
2946 PyTypeObject *__pyx_FusedFunctionType;
|
|
jpayne@69
|
2947 #endif
|
|
jpayne@69
|
2948 #ifdef __Pyx_Generator_USED
|
|
jpayne@69
|
2949 PyTypeObject *__pyx_GeneratorType;
|
|
jpayne@69
|
2950 #endif
|
|
jpayne@69
|
2951 #ifdef __Pyx_IterableCoroutine_USED
|
|
jpayne@69
|
2952 PyTypeObject *__pyx_IterableCoroutineType;
|
|
jpayne@69
|
2953 #endif
|
|
jpayne@69
|
2954 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
2955 PyTypeObject *__pyx_CoroutineAwaitType;
|
|
jpayne@69
|
2956 #endif
|
|
jpayne@69
|
2957 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
2958 PyTypeObject *__pyx_CoroutineType;
|
|
jpayne@69
|
2959 #endif
|
|
jpayne@69
|
2960 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2961 #endif
|
|
jpayne@69
|
2962 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2963 #endif
|
|
jpayne@69
|
2964 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2965 #endif
|
|
jpayne@69
|
2966 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2967 #endif
|
|
jpayne@69
|
2968 PyTypeObject *__pyx_ptype_7cpython_4type_type;
|
|
jpayne@69
|
2969 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2970 #endif
|
|
jpayne@69
|
2971 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2972 #endif
|
|
jpayne@69
|
2973 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2974 #endif
|
|
jpayne@69
|
2975 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2976 #endif
|
|
jpayne@69
|
2977 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2978 #endif
|
|
jpayne@69
|
2979 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2980 #endif
|
|
jpayne@69
|
2981 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2982 #endif
|
|
jpayne@69
|
2983 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2984 #endif
|
|
jpayne@69
|
2985 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2986 #endif
|
|
jpayne@69
|
2987 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2988 #endif
|
|
jpayne@69
|
2989 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2990 #endif
|
|
jpayne@69
|
2991 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2992 #endif
|
|
jpayne@69
|
2993 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2994 #endif
|
|
jpayne@69
|
2995 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2996 #endif
|
|
jpayne@69
|
2997 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
2998 #endif
|
|
jpayne@69
|
2999 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3000 #endif
|
|
jpayne@69
|
3001 PyTypeObject *__pyx_ptype_7cpython_4bool_bool;
|
|
jpayne@69
|
3002 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3003 #endif
|
|
jpayne@69
|
3004 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3005 #endif
|
|
jpayne@69
|
3006 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3007 #endif
|
|
jpayne@69
|
3008 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3009 #endif
|
|
jpayne@69
|
3010 PyTypeObject *__pyx_ptype_7cpython_7complex_complex;
|
|
jpayne@69
|
3011 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3012 #endif
|
|
jpayne@69
|
3013 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3014 #endif
|
|
jpayne@69
|
3015 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3016 #endif
|
|
jpayne@69
|
3017 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3018 #endif
|
|
jpayne@69
|
3019 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3020 #endif
|
|
jpayne@69
|
3021 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3022 #endif
|
|
jpayne@69
|
3023 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3024 #endif
|
|
jpayne@69
|
3025 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3026 #endif
|
|
jpayne@69
|
3027 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3028 #endif
|
|
jpayne@69
|
3029 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3030 #endif
|
|
jpayne@69
|
3031 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3032 #endif
|
|
jpayne@69
|
3033 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3034 #endif
|
|
jpayne@69
|
3035 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3036 #endif
|
|
jpayne@69
|
3037 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3038 #endif
|
|
jpayne@69
|
3039 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3040 #endif
|
|
jpayne@69
|
3041 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3042 #endif
|
|
jpayne@69
|
3043 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3044 #endif
|
|
jpayne@69
|
3045 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3046 #endif
|
|
jpayne@69
|
3047 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3048 #endif
|
|
jpayne@69
|
3049 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3050 #endif
|
|
jpayne@69
|
3051 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3052 #endif
|
|
jpayne@69
|
3053 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3054 #endif
|
|
jpayne@69
|
3055 PyTypeObject *__pyx_ptype_7cpython_5array_array;
|
|
jpayne@69
|
3056 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3057 #endif
|
|
jpayne@69
|
3058 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3059 #endif
|
|
jpayne@69
|
3060 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3061 #endif
|
|
jpayne@69
|
3062 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3063 #endif
|
|
jpayne@69
|
3064 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3065 #endif
|
|
jpayne@69
|
3066 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3067 #endif
|
|
jpayne@69
|
3068 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3069 #endif
|
|
jpayne@69
|
3070 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3071 #endif
|
|
jpayne@69
|
3072 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3073 #endif
|
|
jpayne@69
|
3074 PyObject *__pyx_kp_u_;
|
|
jpayne@69
|
3075 PyObject *__pyx_n_s_ARGUMENTS;
|
|
jpayne@69
|
3076 PyObject *__pyx_kp_u_Argument_must_be_string_bytes_or;
|
|
jpayne@69
|
3077 PyObject *__pyx_n_u_B;
|
|
jpayne@69
|
3078 PyObject *__pyx_n_s_IOError;
|
|
jpayne@69
|
3079 PyObject *__pyx_n_s_MAP_STDOUT_OPTIONS;
|
|
jpayne@69
|
3080 PyObject *__pyx_n_s_MemoryError;
|
|
jpayne@69
|
3081 PyObject *__pyx_kp_u_No_such_file_or_directory_s;
|
|
jpayne@69
|
3082 PyObject *__pyx_n_s_OSError;
|
|
jpayne@69
|
3083 PyObject *__pyx_n_s_OverflowError;
|
|
jpayne@69
|
3084 PyObject *__pyx_n_s_TypeError;
|
|
jpayne@69
|
3085 PyObject *__pyx_n_s_UnicodeDecodeError;
|
|
jpayne@69
|
3086 PyObject *__pyx_n_s_ValueError;
|
|
jpayne@69
|
3087 PyObject *__pyx_kp_u__10;
|
|
jpayne@69
|
3088 PyObject *__pyx_kp_u__11;
|
|
jpayne@69
|
3089 PyObject *__pyx_n_s__14;
|
|
jpayne@69
|
3090 PyObject *__pyx_kp_u__15;
|
|
jpayne@69
|
3091 PyObject *__pyx_n_s__33;
|
|
jpayne@69
|
3092 PyObject *__pyx_kp_u__7;
|
|
jpayne@69
|
3093 PyObject *__pyx_kp_u__8;
|
|
jpayne@69
|
3094 PyObject *__pyx_n_s_a;
|
|
jpayne@69
|
3095 PyObject *__pyx_n_s_all;
|
|
jpayne@69
|
3096 PyObject *__pyx_n_s_arg;
|
|
jpayne@69
|
3097 PyObject *__pyx_n_s_args;
|
|
jpayne@69
|
3098 PyObject *__pyx_n_s_array_to_qualitystring;
|
|
jpayne@69
|
3099 PyObject *__pyx_n_u_array_to_qualitystring;
|
|
jpayne@69
|
3100 PyObject *__pyx_n_u_ascii;
|
|
jpayne@69
|
3101 PyObject *__pyx_n_s_asyncio_coroutines;
|
|
jpayne@69
|
3102 PyObject *__pyx_n_b_bcftools;
|
|
jpayne@69
|
3103 PyObject *__pyx_n_u_bcftools;
|
|
jpayne@69
|
3104 PyObject *__pyx_kp_u_c;
|
|
jpayne@69
|
3105 PyObject *__pyx_n_u_calmd;
|
|
jpayne@69
|
3106 PyObject *__pyx_n_s_cargs;
|
|
jpayne@69
|
3107 PyObject *__pyx_n_s_catch_stdout;
|
|
jpayne@69
|
3108 PyObject *__pyx_n_s_chr;
|
|
jpayne@69
|
3109 PyObject *__pyx_n_s_class_getitem;
|
|
jpayne@69
|
3110 PyObject *__pyx_n_s_cline_in_traceback;
|
|
jpayne@69
|
3111 PyObject *__pyx_n_s_close;
|
|
jpayne@69
|
3112 PyObject *__pyx_n_s_codecs;
|
|
jpayne@69
|
3113 PyObject *__pyx_n_s_collect;
|
|
jpayne@69
|
3114 PyObject *__pyx_n_s_collection;
|
|
jpayne@69
|
3115 PyObject *__pyx_n_s_contextlib;
|
|
jpayne@69
|
3116 PyObject *__pyx_n_s_contextmanager;
|
|
jpayne@69
|
3117 PyObject *__pyx_n_s_contig;
|
|
jpayne@69
|
3118 PyObject *__pyx_kp_u_contig_and_reference_should_not;
|
|
jpayne@69
|
3119 PyObject *__pyx_kp_u_contig_reference_and_region_shou;
|
|
jpayne@69
|
3120 PyObject *__pyx_n_s_decode;
|
|
jpayne@69
|
3121 PyObject *__pyx_n_u_depad;
|
|
jpayne@69
|
3122 PyObject *__pyx_n_s_encode;
|
|
jpayne@69
|
3123 PyObject *__pyx_n_s_end;
|
|
jpayne@69
|
3124 PyObject *__pyx_n_s_enter;
|
|
jpayne@69
|
3125 PyObject *__pyx_kp_u_error_while_opening_file_for_wri;
|
|
jpayne@69
|
3126 PyObject *__pyx_n_s_exception;
|
|
jpayne@69
|
3127 PyObject *__pyx_n_s_exists;
|
|
jpayne@69
|
3128 PyObject *__pyx_n_s_exit;
|
|
jpayne@69
|
3129 PyObject *__pyx_n_s_extend;
|
|
jpayne@69
|
3130 PyObject *__pyx_n_s_extra_args;
|
|
jpayne@69
|
3131 PyObject *__pyx_n_s_fn;
|
|
jpayne@69
|
3132 PyObject *__pyx_n_s_format;
|
|
jpayne@69
|
3133 PyObject *__pyx_n_s_fsencode;
|
|
jpayne@69
|
3134 PyObject *__pyx_n_s_get_encoding_error_handler;
|
|
jpayne@69
|
3135 PyObject *__pyx_n_u_get_encoding_error_handler;
|
|
jpayne@69
|
3136 PyObject *__pyx_n_s_getdefaultencoding;
|
|
jpayne@69
|
3137 PyObject *__pyx_n_s_getfilesystemencoding;
|
|
jpayne@69
|
3138 PyObject *__pyx_n_u_head;
|
|
jpayne@69
|
3139 PyObject *__pyx_n_s_i;
|
|
jpayne@69
|
3140 PyObject *__pyx_n_s_import;
|
|
jpayne@69
|
3141 PyObject *__pyx_n_b_index;
|
|
jpayne@69
|
3142 PyObject *__pyx_n_u_index;
|
|
jpayne@69
|
3143 PyObject *__pyx_n_s_inf;
|
|
jpayne@69
|
3144 PyObject *__pyx_n_s_initializing;
|
|
jpayne@69
|
3145 PyObject *__pyx_n_s_input_str;
|
|
jpayne@69
|
3146 PyObject *__pyx_kp_u_invalid_coordinates_start_i_stop;
|
|
jpayne@69
|
3147 PyObject *__pyx_n_s_io;
|
|
jpayne@69
|
3148 PyObject *__pyx_n_s_is_coroutine;
|
|
jpayne@69
|
3149 PyObject *__pyx_n_s_is_usage;
|
|
jpayne@69
|
3150 PyObject *__pyx_n_s_l;
|
|
jpayne@69
|
3151 PyObject *__pyx_n_s_latin1_replace;
|
|
jpayne@69
|
3152 PyObject *__pyx_kp_u_m;
|
|
jpayne@69
|
3153 PyObject *__pyx_n_s_main;
|
|
jpayne@69
|
3154 PyObject *__pyx_n_s_method;
|
|
jpayne@69
|
3155 PyObject *__pyx_kp_u_min_shift;
|
|
jpayne@69
|
3156 PyObject *__pyx_n_s_mkstemp;
|
|
jpayne@69
|
3157 PyObject *__pyx_n_u_mpileup;
|
|
jpayne@69
|
3158 PyObject *__pyx_n_s_n;
|
|
jpayne@69
|
3159 PyObject *__pyx_n_s_name;
|
|
jpayne@69
|
3160 PyObject *__pyx_n_s_name_2;
|
|
jpayne@69
|
3161 PyObject *__pyx_kp_u_neither_contig_nor_region_are_gi;
|
|
jpayne@69
|
3162 PyObject *__pyx_kp_u_o;
|
|
jpayne@69
|
3163 PyObject *__pyx_kp_u_o_2;
|
|
jpayne@69
|
3164 PyObject *__pyx_n_s_object;
|
|
jpayne@69
|
3165 PyObject *__pyx_n_s_offset;
|
|
jpayne@69
|
3166 PyObject *__pyx_n_s_open;
|
|
jpayne@69
|
3167 PyObject *__pyx_n_s_os;
|
|
jpayne@69
|
3168 PyObject *__pyx_n_s_out;
|
|
jpayne@69
|
3169 PyObject *__pyx_n_s_out_stderr;
|
|
jpayne@69
|
3170 PyObject *__pyx_n_s_out_stdout;
|
|
jpayne@69
|
3171 PyObject *__pyx_kp_u_output;
|
|
jpayne@69
|
3172 PyObject *__pyx_kp_u_output_file;
|
|
jpayne@69
|
3173 PyObject *__pyx_n_s_parse_region;
|
|
jpayne@69
|
3174 PyObject *__pyx_n_s_path;
|
|
jpayne@69
|
3175 PyObject *__pyx_n_s_pysam_dispatch;
|
|
jpayne@69
|
3176 PyObject *__pyx_n_s_pysam_dispatch_locals__collect;
|
|
jpayne@69
|
3177 PyObject *__pyx_kp_u_pysam_latin1replace;
|
|
jpayne@69
|
3178 PyObject *__pyx_n_s_pysam_libcutils;
|
|
jpayne@69
|
3179 PyObject *__pyx_kp_s_pysam_libcutils_pyx;
|
|
jpayne@69
|
3180 PyObject *__pyx_n_s_qualities;
|
|
jpayne@69
|
3181 PyObject *__pyx_n_s_qualities_to_qualitystring;
|
|
jpayne@69
|
3182 PyObject *__pyx_n_u_qualities_to_qualitystring;
|
|
jpayne@69
|
3183 PyObject *__pyx_n_s_qualitystring_to_array;
|
|
jpayne@69
|
3184 PyObject *__pyx_n_u_qualitystring_to_array;
|
|
jpayne@69
|
3185 PyObject *__pyx_n_u_r;
|
|
jpayne@69
|
3186 PyObject *__pyx_n_u_rb;
|
|
jpayne@69
|
3187 PyObject *__pyx_n_s_re;
|
|
jpayne@69
|
3188 PyObject *__pyx_n_s_read;
|
|
jpayne@69
|
3189 PyObject *__pyx_n_s_reference;
|
|
jpayne@69
|
3190 PyObject *__pyx_n_s_region;
|
|
jpayne@69
|
3191 PyObject *__pyx_n_s_register_error;
|
|
jpayne@69
|
3192 PyObject *__pyx_n_s_remove;
|
|
jpayne@69
|
3193 PyObject *__pyx_n_s_retval;
|
|
jpayne@69
|
3194 PyObject *__pyx_n_u_roh;
|
|
jpayne@69
|
3195 PyObject *__pyx_n_b_samtools;
|
|
jpayne@69
|
3196 PyObject *__pyx_n_u_samtools;
|
|
jpayne@69
|
3197 PyObject *__pyx_n_s_save_stdout;
|
|
jpayne@69
|
3198 PyObject *__pyx_n_s_set_encoding_error_handler;
|
|
jpayne@69
|
3199 PyObject *__pyx_n_u_set_encoding_error_handler;
|
|
jpayne@69
|
3200 PyObject *__pyx_n_s_skip_next;
|
|
jpayne@69
|
3201 PyObject *__pyx_n_s_spec;
|
|
jpayne@69
|
3202 PyObject *__pyx_n_s_split;
|
|
jpayne@69
|
3203 PyObject *__pyx_n_s_start;
|
|
jpayne@69
|
3204 PyObject *__pyx_kp_u_start_out_of_range_i;
|
|
jpayne@69
|
3205 PyObject *__pyx_n_s_startswith;
|
|
jpayne@69
|
3206 PyObject *__pyx_n_u_stats;
|
|
jpayne@69
|
3207 PyObject *__pyx_n_s_stderr_f;
|
|
jpayne@69
|
3208 PyObject *__pyx_n_s_stderr_h;
|
|
jpayne@69
|
3209 PyObject *__pyx_n_s_stdout_f;
|
|
jpayne@69
|
3210 PyObject *__pyx_n_s_stdout_h;
|
|
jpayne@69
|
3211 PyObject *__pyx_n_s_stdout_option;
|
|
jpayne@69
|
3212 PyObject *__pyx_n_s_stop;
|
|
jpayne@69
|
3213 PyObject *__pyx_kp_u_stop_and_end_should_not_both_be;
|
|
jpayne@69
|
3214 PyObject *__pyx_kp_u_stop_out_of_range_i;
|
|
jpayne@69
|
3215 PyObject *__pyx_n_u_strict;
|
|
jpayne@69
|
3216 PyObject *__pyx_n_s_string;
|
|
jpayne@69
|
3217 PyObject *__pyx_n_s_sys;
|
|
jpayne@69
|
3218 PyObject *__pyx_n_s_tempfile;
|
|
jpayne@69
|
3219 PyObject *__pyx_n_s_test;
|
|
jpayne@69
|
3220 PyObject *__pyx_kp_u_threads;
|
|
jpayne@69
|
3221 PyObject *__pyx_n_s_tobytes;
|
|
jpayne@69
|
3222 PyObject *__pyx_n_s_types;
|
|
jpayne@69
|
3223 PyObject *__pyx_kp_u_utf_8;
|
|
jpayne@69
|
3224 PyObject *__pyx_n_u_view;
|
|
jpayne@69
|
3225 PyObject *__pyx_int_1;
|
|
jpayne@69
|
3226 PyObject *__pyx_int_33;
|
|
jpayne@69
|
3227 PyObject *__pyx_int_neg_1;
|
|
jpayne@69
|
3228 PyObject *__pyx_tuple__2;
|
|
jpayne@69
|
3229 PyObject *__pyx_tuple__3;
|
|
jpayne@69
|
3230 PyObject *__pyx_tuple__4;
|
|
jpayne@69
|
3231 PyObject *__pyx_tuple__5;
|
|
jpayne@69
|
3232 PyObject *__pyx_tuple__6;
|
|
jpayne@69
|
3233 PyObject *__pyx_tuple__9;
|
|
jpayne@69
|
3234 PyObject *__pyx_tuple__12;
|
|
jpayne@69
|
3235 PyObject *__pyx_tuple__16;
|
|
jpayne@69
|
3236 PyObject *__pyx_tuple__18;
|
|
jpayne@69
|
3237 PyObject *__pyx_tuple__19;
|
|
jpayne@69
|
3238 PyObject *__pyx_tuple__22;
|
|
jpayne@69
|
3239 PyObject *__pyx_tuple__25;
|
|
jpayne@69
|
3240 PyObject *__pyx_tuple__27;
|
|
jpayne@69
|
3241 PyObject *__pyx_tuple__29;
|
|
jpayne@69
|
3242 PyObject *__pyx_tuple__30;
|
|
jpayne@69
|
3243 PyObject *__pyx_tuple__32;
|
|
jpayne@69
|
3244 PyObject *__pyx_codeobj__13;
|
|
jpayne@69
|
3245 PyObject *__pyx_codeobj__17;
|
|
jpayne@69
|
3246 PyObject *__pyx_codeobj__20;
|
|
jpayne@69
|
3247 PyObject *__pyx_codeobj__21;
|
|
jpayne@69
|
3248 PyObject *__pyx_codeobj__23;
|
|
jpayne@69
|
3249 PyObject *__pyx_codeobj__24;
|
|
jpayne@69
|
3250 PyObject *__pyx_codeobj__26;
|
|
jpayne@69
|
3251 PyObject *__pyx_codeobj__28;
|
|
jpayne@69
|
3252 PyObject *__pyx_codeobj__31;
|
|
jpayne@69
|
3253 } __pyx_mstate;
|
|
jpayne@69
|
3254
|
|
jpayne@69
|
3255 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3256 #ifdef __cplusplus
|
|
jpayne@69
|
3257 namespace {
|
|
jpayne@69
|
3258 extern struct PyModuleDef __pyx_moduledef;
|
|
jpayne@69
|
3259 } /* anonymous namespace */
|
|
jpayne@69
|
3260 #else
|
|
jpayne@69
|
3261 static struct PyModuleDef __pyx_moduledef;
|
|
jpayne@69
|
3262 #endif
|
|
jpayne@69
|
3263
|
|
jpayne@69
|
3264 #define __pyx_mstate(o) ((__pyx_mstate *)__Pyx_PyModule_GetState(o))
|
|
jpayne@69
|
3265
|
|
jpayne@69
|
3266 #define __pyx_mstate_global (__pyx_mstate(PyState_FindModule(&__pyx_moduledef)))
|
|
jpayne@69
|
3267
|
|
jpayne@69
|
3268 #define __pyx_m (PyState_FindModule(&__pyx_moduledef))
|
|
jpayne@69
|
3269 #else
|
|
jpayne@69
|
3270 static __pyx_mstate __pyx_mstate_global_static =
|
|
jpayne@69
|
3271 #ifdef __cplusplus
|
|
jpayne@69
|
3272 {};
|
|
jpayne@69
|
3273 #else
|
|
jpayne@69
|
3274 {0};
|
|
jpayne@69
|
3275 #endif
|
|
jpayne@69
|
3276 static __pyx_mstate *__pyx_mstate_global = &__pyx_mstate_global_static;
|
|
jpayne@69
|
3277 #endif
|
|
jpayne@69
|
3278 /* #### Code section: module_state_clear ### */
|
|
jpayne@69
|
3279 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3280 static int __pyx_m_clear(PyObject *m) {
|
|
jpayne@69
|
3281 __pyx_mstate *clear_module_state = __pyx_mstate(m);
|
|
jpayne@69
|
3282 if (!clear_module_state) return 0;
|
|
jpayne@69
|
3283 Py_CLEAR(clear_module_state->__pyx_d);
|
|
jpayne@69
|
3284 Py_CLEAR(clear_module_state->__pyx_b);
|
|
jpayne@69
|
3285 Py_CLEAR(clear_module_state->__pyx_cython_runtime);
|
|
jpayne@69
|
3286 Py_CLEAR(clear_module_state->__pyx_empty_tuple);
|
|
jpayne@69
|
3287 Py_CLEAR(clear_module_state->__pyx_empty_bytes);
|
|
jpayne@69
|
3288 Py_CLEAR(clear_module_state->__pyx_empty_unicode);
|
|
jpayne@69
|
3289 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
3290 Py_CLEAR(clear_module_state->__pyx_CyFunctionType);
|
|
jpayne@69
|
3291 #endif
|
|
jpayne@69
|
3292 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
3293 Py_CLEAR(clear_module_state->__pyx_FusedFunctionType);
|
|
jpayne@69
|
3294 #endif
|
|
jpayne@69
|
3295 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4type_type);
|
|
jpayne@69
|
3296 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4bool_bool);
|
|
jpayne@69
|
3297 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_7complex_complex);
|
|
jpayne@69
|
3298 Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_5array_array);
|
|
jpayne@69
|
3299 Py_CLEAR(clear_module_state->__pyx_kp_u_);
|
|
jpayne@69
|
3300 Py_CLEAR(clear_module_state->__pyx_n_s_ARGUMENTS);
|
|
jpayne@69
|
3301 Py_CLEAR(clear_module_state->__pyx_kp_u_Argument_must_be_string_bytes_or);
|
|
jpayne@69
|
3302 Py_CLEAR(clear_module_state->__pyx_n_u_B);
|
|
jpayne@69
|
3303 Py_CLEAR(clear_module_state->__pyx_n_s_IOError);
|
|
jpayne@69
|
3304 Py_CLEAR(clear_module_state->__pyx_n_s_MAP_STDOUT_OPTIONS);
|
|
jpayne@69
|
3305 Py_CLEAR(clear_module_state->__pyx_n_s_MemoryError);
|
|
jpayne@69
|
3306 Py_CLEAR(clear_module_state->__pyx_kp_u_No_such_file_or_directory_s);
|
|
jpayne@69
|
3307 Py_CLEAR(clear_module_state->__pyx_n_s_OSError);
|
|
jpayne@69
|
3308 Py_CLEAR(clear_module_state->__pyx_n_s_OverflowError);
|
|
jpayne@69
|
3309 Py_CLEAR(clear_module_state->__pyx_n_s_TypeError);
|
|
jpayne@69
|
3310 Py_CLEAR(clear_module_state->__pyx_n_s_UnicodeDecodeError);
|
|
jpayne@69
|
3311 Py_CLEAR(clear_module_state->__pyx_n_s_ValueError);
|
|
jpayne@69
|
3312 Py_CLEAR(clear_module_state->__pyx_kp_u__10);
|
|
jpayne@69
|
3313 Py_CLEAR(clear_module_state->__pyx_kp_u__11);
|
|
jpayne@69
|
3314 Py_CLEAR(clear_module_state->__pyx_n_s__14);
|
|
jpayne@69
|
3315 Py_CLEAR(clear_module_state->__pyx_kp_u__15);
|
|
jpayne@69
|
3316 Py_CLEAR(clear_module_state->__pyx_n_s__33);
|
|
jpayne@69
|
3317 Py_CLEAR(clear_module_state->__pyx_kp_u__7);
|
|
jpayne@69
|
3318 Py_CLEAR(clear_module_state->__pyx_kp_u__8);
|
|
jpayne@69
|
3319 Py_CLEAR(clear_module_state->__pyx_n_s_a);
|
|
jpayne@69
|
3320 Py_CLEAR(clear_module_state->__pyx_n_s_all);
|
|
jpayne@69
|
3321 Py_CLEAR(clear_module_state->__pyx_n_s_arg);
|
|
jpayne@69
|
3322 Py_CLEAR(clear_module_state->__pyx_n_s_args);
|
|
jpayne@69
|
3323 Py_CLEAR(clear_module_state->__pyx_n_s_array_to_qualitystring);
|
|
jpayne@69
|
3324 Py_CLEAR(clear_module_state->__pyx_n_u_array_to_qualitystring);
|
|
jpayne@69
|
3325 Py_CLEAR(clear_module_state->__pyx_n_u_ascii);
|
|
jpayne@69
|
3326 Py_CLEAR(clear_module_state->__pyx_n_s_asyncio_coroutines);
|
|
jpayne@69
|
3327 Py_CLEAR(clear_module_state->__pyx_n_b_bcftools);
|
|
jpayne@69
|
3328 Py_CLEAR(clear_module_state->__pyx_n_u_bcftools);
|
|
jpayne@69
|
3329 Py_CLEAR(clear_module_state->__pyx_kp_u_c);
|
|
jpayne@69
|
3330 Py_CLEAR(clear_module_state->__pyx_n_u_calmd);
|
|
jpayne@69
|
3331 Py_CLEAR(clear_module_state->__pyx_n_s_cargs);
|
|
jpayne@69
|
3332 Py_CLEAR(clear_module_state->__pyx_n_s_catch_stdout);
|
|
jpayne@69
|
3333 Py_CLEAR(clear_module_state->__pyx_n_s_chr);
|
|
jpayne@69
|
3334 Py_CLEAR(clear_module_state->__pyx_n_s_class_getitem);
|
|
jpayne@69
|
3335 Py_CLEAR(clear_module_state->__pyx_n_s_cline_in_traceback);
|
|
jpayne@69
|
3336 Py_CLEAR(clear_module_state->__pyx_n_s_close);
|
|
jpayne@69
|
3337 Py_CLEAR(clear_module_state->__pyx_n_s_codecs);
|
|
jpayne@69
|
3338 Py_CLEAR(clear_module_state->__pyx_n_s_collect);
|
|
jpayne@69
|
3339 Py_CLEAR(clear_module_state->__pyx_n_s_collection);
|
|
jpayne@69
|
3340 Py_CLEAR(clear_module_state->__pyx_n_s_contextlib);
|
|
jpayne@69
|
3341 Py_CLEAR(clear_module_state->__pyx_n_s_contextmanager);
|
|
jpayne@69
|
3342 Py_CLEAR(clear_module_state->__pyx_n_s_contig);
|
|
jpayne@69
|
3343 Py_CLEAR(clear_module_state->__pyx_kp_u_contig_and_reference_should_not);
|
|
jpayne@69
|
3344 Py_CLEAR(clear_module_state->__pyx_kp_u_contig_reference_and_region_shou);
|
|
jpayne@69
|
3345 Py_CLEAR(clear_module_state->__pyx_n_s_decode);
|
|
jpayne@69
|
3346 Py_CLEAR(clear_module_state->__pyx_n_u_depad);
|
|
jpayne@69
|
3347 Py_CLEAR(clear_module_state->__pyx_n_s_encode);
|
|
jpayne@69
|
3348 Py_CLEAR(clear_module_state->__pyx_n_s_end);
|
|
jpayne@69
|
3349 Py_CLEAR(clear_module_state->__pyx_n_s_enter);
|
|
jpayne@69
|
3350 Py_CLEAR(clear_module_state->__pyx_kp_u_error_while_opening_file_for_wri);
|
|
jpayne@69
|
3351 Py_CLEAR(clear_module_state->__pyx_n_s_exception);
|
|
jpayne@69
|
3352 Py_CLEAR(clear_module_state->__pyx_n_s_exists);
|
|
jpayne@69
|
3353 Py_CLEAR(clear_module_state->__pyx_n_s_exit);
|
|
jpayne@69
|
3354 Py_CLEAR(clear_module_state->__pyx_n_s_extend);
|
|
jpayne@69
|
3355 Py_CLEAR(clear_module_state->__pyx_n_s_extra_args);
|
|
jpayne@69
|
3356 Py_CLEAR(clear_module_state->__pyx_n_s_fn);
|
|
jpayne@69
|
3357 Py_CLEAR(clear_module_state->__pyx_n_s_format);
|
|
jpayne@69
|
3358 Py_CLEAR(clear_module_state->__pyx_n_s_fsencode);
|
|
jpayne@69
|
3359 Py_CLEAR(clear_module_state->__pyx_n_s_get_encoding_error_handler);
|
|
jpayne@69
|
3360 Py_CLEAR(clear_module_state->__pyx_n_u_get_encoding_error_handler);
|
|
jpayne@69
|
3361 Py_CLEAR(clear_module_state->__pyx_n_s_getdefaultencoding);
|
|
jpayne@69
|
3362 Py_CLEAR(clear_module_state->__pyx_n_s_getfilesystemencoding);
|
|
jpayne@69
|
3363 Py_CLEAR(clear_module_state->__pyx_n_u_head);
|
|
jpayne@69
|
3364 Py_CLEAR(clear_module_state->__pyx_n_s_i);
|
|
jpayne@69
|
3365 Py_CLEAR(clear_module_state->__pyx_n_s_import);
|
|
jpayne@69
|
3366 Py_CLEAR(clear_module_state->__pyx_n_b_index);
|
|
jpayne@69
|
3367 Py_CLEAR(clear_module_state->__pyx_n_u_index);
|
|
jpayne@69
|
3368 Py_CLEAR(clear_module_state->__pyx_n_s_inf);
|
|
jpayne@69
|
3369 Py_CLEAR(clear_module_state->__pyx_n_s_initializing);
|
|
jpayne@69
|
3370 Py_CLEAR(clear_module_state->__pyx_n_s_input_str);
|
|
jpayne@69
|
3371 Py_CLEAR(clear_module_state->__pyx_kp_u_invalid_coordinates_start_i_stop);
|
|
jpayne@69
|
3372 Py_CLEAR(clear_module_state->__pyx_n_s_io);
|
|
jpayne@69
|
3373 Py_CLEAR(clear_module_state->__pyx_n_s_is_coroutine);
|
|
jpayne@69
|
3374 Py_CLEAR(clear_module_state->__pyx_n_s_is_usage);
|
|
jpayne@69
|
3375 Py_CLEAR(clear_module_state->__pyx_n_s_l);
|
|
jpayne@69
|
3376 Py_CLEAR(clear_module_state->__pyx_n_s_latin1_replace);
|
|
jpayne@69
|
3377 Py_CLEAR(clear_module_state->__pyx_kp_u_m);
|
|
jpayne@69
|
3378 Py_CLEAR(clear_module_state->__pyx_n_s_main);
|
|
jpayne@69
|
3379 Py_CLEAR(clear_module_state->__pyx_n_s_method);
|
|
jpayne@69
|
3380 Py_CLEAR(clear_module_state->__pyx_kp_u_min_shift);
|
|
jpayne@69
|
3381 Py_CLEAR(clear_module_state->__pyx_n_s_mkstemp);
|
|
jpayne@69
|
3382 Py_CLEAR(clear_module_state->__pyx_n_u_mpileup);
|
|
jpayne@69
|
3383 Py_CLEAR(clear_module_state->__pyx_n_s_n);
|
|
jpayne@69
|
3384 Py_CLEAR(clear_module_state->__pyx_n_s_name);
|
|
jpayne@69
|
3385 Py_CLEAR(clear_module_state->__pyx_n_s_name_2);
|
|
jpayne@69
|
3386 Py_CLEAR(clear_module_state->__pyx_kp_u_neither_contig_nor_region_are_gi);
|
|
jpayne@69
|
3387 Py_CLEAR(clear_module_state->__pyx_kp_u_o);
|
|
jpayne@69
|
3388 Py_CLEAR(clear_module_state->__pyx_kp_u_o_2);
|
|
jpayne@69
|
3389 Py_CLEAR(clear_module_state->__pyx_n_s_object);
|
|
jpayne@69
|
3390 Py_CLEAR(clear_module_state->__pyx_n_s_offset);
|
|
jpayne@69
|
3391 Py_CLEAR(clear_module_state->__pyx_n_s_open);
|
|
jpayne@69
|
3392 Py_CLEAR(clear_module_state->__pyx_n_s_os);
|
|
jpayne@69
|
3393 Py_CLEAR(clear_module_state->__pyx_n_s_out);
|
|
jpayne@69
|
3394 Py_CLEAR(clear_module_state->__pyx_n_s_out_stderr);
|
|
jpayne@69
|
3395 Py_CLEAR(clear_module_state->__pyx_n_s_out_stdout);
|
|
jpayne@69
|
3396 Py_CLEAR(clear_module_state->__pyx_kp_u_output);
|
|
jpayne@69
|
3397 Py_CLEAR(clear_module_state->__pyx_kp_u_output_file);
|
|
jpayne@69
|
3398 Py_CLEAR(clear_module_state->__pyx_n_s_parse_region);
|
|
jpayne@69
|
3399 Py_CLEAR(clear_module_state->__pyx_n_s_path);
|
|
jpayne@69
|
3400 Py_CLEAR(clear_module_state->__pyx_n_s_pysam_dispatch);
|
|
jpayne@69
|
3401 Py_CLEAR(clear_module_state->__pyx_n_s_pysam_dispatch_locals__collect);
|
|
jpayne@69
|
3402 Py_CLEAR(clear_module_state->__pyx_kp_u_pysam_latin1replace);
|
|
jpayne@69
|
3403 Py_CLEAR(clear_module_state->__pyx_n_s_pysam_libcutils);
|
|
jpayne@69
|
3404 Py_CLEAR(clear_module_state->__pyx_kp_s_pysam_libcutils_pyx);
|
|
jpayne@69
|
3405 Py_CLEAR(clear_module_state->__pyx_n_s_qualities);
|
|
jpayne@69
|
3406 Py_CLEAR(clear_module_state->__pyx_n_s_qualities_to_qualitystring);
|
|
jpayne@69
|
3407 Py_CLEAR(clear_module_state->__pyx_n_u_qualities_to_qualitystring);
|
|
jpayne@69
|
3408 Py_CLEAR(clear_module_state->__pyx_n_s_qualitystring_to_array);
|
|
jpayne@69
|
3409 Py_CLEAR(clear_module_state->__pyx_n_u_qualitystring_to_array);
|
|
jpayne@69
|
3410 Py_CLEAR(clear_module_state->__pyx_n_u_r);
|
|
jpayne@69
|
3411 Py_CLEAR(clear_module_state->__pyx_n_u_rb);
|
|
jpayne@69
|
3412 Py_CLEAR(clear_module_state->__pyx_n_s_re);
|
|
jpayne@69
|
3413 Py_CLEAR(clear_module_state->__pyx_n_s_read);
|
|
jpayne@69
|
3414 Py_CLEAR(clear_module_state->__pyx_n_s_reference);
|
|
jpayne@69
|
3415 Py_CLEAR(clear_module_state->__pyx_n_s_region);
|
|
jpayne@69
|
3416 Py_CLEAR(clear_module_state->__pyx_n_s_register_error);
|
|
jpayne@69
|
3417 Py_CLEAR(clear_module_state->__pyx_n_s_remove);
|
|
jpayne@69
|
3418 Py_CLEAR(clear_module_state->__pyx_n_s_retval);
|
|
jpayne@69
|
3419 Py_CLEAR(clear_module_state->__pyx_n_u_roh);
|
|
jpayne@69
|
3420 Py_CLEAR(clear_module_state->__pyx_n_b_samtools);
|
|
jpayne@69
|
3421 Py_CLEAR(clear_module_state->__pyx_n_u_samtools);
|
|
jpayne@69
|
3422 Py_CLEAR(clear_module_state->__pyx_n_s_save_stdout);
|
|
jpayne@69
|
3423 Py_CLEAR(clear_module_state->__pyx_n_s_set_encoding_error_handler);
|
|
jpayne@69
|
3424 Py_CLEAR(clear_module_state->__pyx_n_u_set_encoding_error_handler);
|
|
jpayne@69
|
3425 Py_CLEAR(clear_module_state->__pyx_n_s_skip_next);
|
|
jpayne@69
|
3426 Py_CLEAR(clear_module_state->__pyx_n_s_spec);
|
|
jpayne@69
|
3427 Py_CLEAR(clear_module_state->__pyx_n_s_split);
|
|
jpayne@69
|
3428 Py_CLEAR(clear_module_state->__pyx_n_s_start);
|
|
jpayne@69
|
3429 Py_CLEAR(clear_module_state->__pyx_kp_u_start_out_of_range_i);
|
|
jpayne@69
|
3430 Py_CLEAR(clear_module_state->__pyx_n_s_startswith);
|
|
jpayne@69
|
3431 Py_CLEAR(clear_module_state->__pyx_n_u_stats);
|
|
jpayne@69
|
3432 Py_CLEAR(clear_module_state->__pyx_n_s_stderr_f);
|
|
jpayne@69
|
3433 Py_CLEAR(clear_module_state->__pyx_n_s_stderr_h);
|
|
jpayne@69
|
3434 Py_CLEAR(clear_module_state->__pyx_n_s_stdout_f);
|
|
jpayne@69
|
3435 Py_CLEAR(clear_module_state->__pyx_n_s_stdout_h);
|
|
jpayne@69
|
3436 Py_CLEAR(clear_module_state->__pyx_n_s_stdout_option);
|
|
jpayne@69
|
3437 Py_CLEAR(clear_module_state->__pyx_n_s_stop);
|
|
jpayne@69
|
3438 Py_CLEAR(clear_module_state->__pyx_kp_u_stop_and_end_should_not_both_be);
|
|
jpayne@69
|
3439 Py_CLEAR(clear_module_state->__pyx_kp_u_stop_out_of_range_i);
|
|
jpayne@69
|
3440 Py_CLEAR(clear_module_state->__pyx_n_u_strict);
|
|
jpayne@69
|
3441 Py_CLEAR(clear_module_state->__pyx_n_s_string);
|
|
jpayne@69
|
3442 Py_CLEAR(clear_module_state->__pyx_n_s_sys);
|
|
jpayne@69
|
3443 Py_CLEAR(clear_module_state->__pyx_n_s_tempfile);
|
|
jpayne@69
|
3444 Py_CLEAR(clear_module_state->__pyx_n_s_test);
|
|
jpayne@69
|
3445 Py_CLEAR(clear_module_state->__pyx_kp_u_threads);
|
|
jpayne@69
|
3446 Py_CLEAR(clear_module_state->__pyx_n_s_tobytes);
|
|
jpayne@69
|
3447 Py_CLEAR(clear_module_state->__pyx_n_s_types);
|
|
jpayne@69
|
3448 Py_CLEAR(clear_module_state->__pyx_kp_u_utf_8);
|
|
jpayne@69
|
3449 Py_CLEAR(clear_module_state->__pyx_n_u_view);
|
|
jpayne@69
|
3450 Py_CLEAR(clear_module_state->__pyx_int_1);
|
|
jpayne@69
|
3451 Py_CLEAR(clear_module_state->__pyx_int_33);
|
|
jpayne@69
|
3452 Py_CLEAR(clear_module_state->__pyx_int_neg_1);
|
|
jpayne@69
|
3453 Py_CLEAR(clear_module_state->__pyx_tuple__2);
|
|
jpayne@69
|
3454 Py_CLEAR(clear_module_state->__pyx_tuple__3);
|
|
jpayne@69
|
3455 Py_CLEAR(clear_module_state->__pyx_tuple__4);
|
|
jpayne@69
|
3456 Py_CLEAR(clear_module_state->__pyx_tuple__5);
|
|
jpayne@69
|
3457 Py_CLEAR(clear_module_state->__pyx_tuple__6);
|
|
jpayne@69
|
3458 Py_CLEAR(clear_module_state->__pyx_tuple__9);
|
|
jpayne@69
|
3459 Py_CLEAR(clear_module_state->__pyx_tuple__12);
|
|
jpayne@69
|
3460 Py_CLEAR(clear_module_state->__pyx_tuple__16);
|
|
jpayne@69
|
3461 Py_CLEAR(clear_module_state->__pyx_tuple__18);
|
|
jpayne@69
|
3462 Py_CLEAR(clear_module_state->__pyx_tuple__19);
|
|
jpayne@69
|
3463 Py_CLEAR(clear_module_state->__pyx_tuple__22);
|
|
jpayne@69
|
3464 Py_CLEAR(clear_module_state->__pyx_tuple__25);
|
|
jpayne@69
|
3465 Py_CLEAR(clear_module_state->__pyx_tuple__27);
|
|
jpayne@69
|
3466 Py_CLEAR(clear_module_state->__pyx_tuple__29);
|
|
jpayne@69
|
3467 Py_CLEAR(clear_module_state->__pyx_tuple__30);
|
|
jpayne@69
|
3468 Py_CLEAR(clear_module_state->__pyx_tuple__32);
|
|
jpayne@69
|
3469 Py_CLEAR(clear_module_state->__pyx_codeobj__13);
|
|
jpayne@69
|
3470 Py_CLEAR(clear_module_state->__pyx_codeobj__17);
|
|
jpayne@69
|
3471 Py_CLEAR(clear_module_state->__pyx_codeobj__20);
|
|
jpayne@69
|
3472 Py_CLEAR(clear_module_state->__pyx_codeobj__21);
|
|
jpayne@69
|
3473 Py_CLEAR(clear_module_state->__pyx_codeobj__23);
|
|
jpayne@69
|
3474 Py_CLEAR(clear_module_state->__pyx_codeobj__24);
|
|
jpayne@69
|
3475 Py_CLEAR(clear_module_state->__pyx_codeobj__26);
|
|
jpayne@69
|
3476 Py_CLEAR(clear_module_state->__pyx_codeobj__28);
|
|
jpayne@69
|
3477 Py_CLEAR(clear_module_state->__pyx_codeobj__31);
|
|
jpayne@69
|
3478 return 0;
|
|
jpayne@69
|
3479 }
|
|
jpayne@69
|
3480 #endif
|
|
jpayne@69
|
3481 /* #### Code section: module_state_traverse ### */
|
|
jpayne@69
|
3482 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3483 static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) {
|
|
jpayne@69
|
3484 __pyx_mstate *traverse_module_state = __pyx_mstate(m);
|
|
jpayne@69
|
3485 if (!traverse_module_state) return 0;
|
|
jpayne@69
|
3486 Py_VISIT(traverse_module_state->__pyx_d);
|
|
jpayne@69
|
3487 Py_VISIT(traverse_module_state->__pyx_b);
|
|
jpayne@69
|
3488 Py_VISIT(traverse_module_state->__pyx_cython_runtime);
|
|
jpayne@69
|
3489 Py_VISIT(traverse_module_state->__pyx_empty_tuple);
|
|
jpayne@69
|
3490 Py_VISIT(traverse_module_state->__pyx_empty_bytes);
|
|
jpayne@69
|
3491 Py_VISIT(traverse_module_state->__pyx_empty_unicode);
|
|
jpayne@69
|
3492 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
3493 Py_VISIT(traverse_module_state->__pyx_CyFunctionType);
|
|
jpayne@69
|
3494 #endif
|
|
jpayne@69
|
3495 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
3496 Py_VISIT(traverse_module_state->__pyx_FusedFunctionType);
|
|
jpayne@69
|
3497 #endif
|
|
jpayne@69
|
3498 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4type_type);
|
|
jpayne@69
|
3499 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4bool_bool);
|
|
jpayne@69
|
3500 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_7complex_complex);
|
|
jpayne@69
|
3501 Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_5array_array);
|
|
jpayne@69
|
3502 Py_VISIT(traverse_module_state->__pyx_kp_u_);
|
|
jpayne@69
|
3503 Py_VISIT(traverse_module_state->__pyx_n_s_ARGUMENTS);
|
|
jpayne@69
|
3504 Py_VISIT(traverse_module_state->__pyx_kp_u_Argument_must_be_string_bytes_or);
|
|
jpayne@69
|
3505 Py_VISIT(traverse_module_state->__pyx_n_u_B);
|
|
jpayne@69
|
3506 Py_VISIT(traverse_module_state->__pyx_n_s_IOError);
|
|
jpayne@69
|
3507 Py_VISIT(traverse_module_state->__pyx_n_s_MAP_STDOUT_OPTIONS);
|
|
jpayne@69
|
3508 Py_VISIT(traverse_module_state->__pyx_n_s_MemoryError);
|
|
jpayne@69
|
3509 Py_VISIT(traverse_module_state->__pyx_kp_u_No_such_file_or_directory_s);
|
|
jpayne@69
|
3510 Py_VISIT(traverse_module_state->__pyx_n_s_OSError);
|
|
jpayne@69
|
3511 Py_VISIT(traverse_module_state->__pyx_n_s_OverflowError);
|
|
jpayne@69
|
3512 Py_VISIT(traverse_module_state->__pyx_n_s_TypeError);
|
|
jpayne@69
|
3513 Py_VISIT(traverse_module_state->__pyx_n_s_UnicodeDecodeError);
|
|
jpayne@69
|
3514 Py_VISIT(traverse_module_state->__pyx_n_s_ValueError);
|
|
jpayne@69
|
3515 Py_VISIT(traverse_module_state->__pyx_kp_u__10);
|
|
jpayne@69
|
3516 Py_VISIT(traverse_module_state->__pyx_kp_u__11);
|
|
jpayne@69
|
3517 Py_VISIT(traverse_module_state->__pyx_n_s__14);
|
|
jpayne@69
|
3518 Py_VISIT(traverse_module_state->__pyx_kp_u__15);
|
|
jpayne@69
|
3519 Py_VISIT(traverse_module_state->__pyx_n_s__33);
|
|
jpayne@69
|
3520 Py_VISIT(traverse_module_state->__pyx_kp_u__7);
|
|
jpayne@69
|
3521 Py_VISIT(traverse_module_state->__pyx_kp_u__8);
|
|
jpayne@69
|
3522 Py_VISIT(traverse_module_state->__pyx_n_s_a);
|
|
jpayne@69
|
3523 Py_VISIT(traverse_module_state->__pyx_n_s_all);
|
|
jpayne@69
|
3524 Py_VISIT(traverse_module_state->__pyx_n_s_arg);
|
|
jpayne@69
|
3525 Py_VISIT(traverse_module_state->__pyx_n_s_args);
|
|
jpayne@69
|
3526 Py_VISIT(traverse_module_state->__pyx_n_s_array_to_qualitystring);
|
|
jpayne@69
|
3527 Py_VISIT(traverse_module_state->__pyx_n_u_array_to_qualitystring);
|
|
jpayne@69
|
3528 Py_VISIT(traverse_module_state->__pyx_n_u_ascii);
|
|
jpayne@69
|
3529 Py_VISIT(traverse_module_state->__pyx_n_s_asyncio_coroutines);
|
|
jpayne@69
|
3530 Py_VISIT(traverse_module_state->__pyx_n_b_bcftools);
|
|
jpayne@69
|
3531 Py_VISIT(traverse_module_state->__pyx_n_u_bcftools);
|
|
jpayne@69
|
3532 Py_VISIT(traverse_module_state->__pyx_kp_u_c);
|
|
jpayne@69
|
3533 Py_VISIT(traverse_module_state->__pyx_n_u_calmd);
|
|
jpayne@69
|
3534 Py_VISIT(traverse_module_state->__pyx_n_s_cargs);
|
|
jpayne@69
|
3535 Py_VISIT(traverse_module_state->__pyx_n_s_catch_stdout);
|
|
jpayne@69
|
3536 Py_VISIT(traverse_module_state->__pyx_n_s_chr);
|
|
jpayne@69
|
3537 Py_VISIT(traverse_module_state->__pyx_n_s_class_getitem);
|
|
jpayne@69
|
3538 Py_VISIT(traverse_module_state->__pyx_n_s_cline_in_traceback);
|
|
jpayne@69
|
3539 Py_VISIT(traverse_module_state->__pyx_n_s_close);
|
|
jpayne@69
|
3540 Py_VISIT(traverse_module_state->__pyx_n_s_codecs);
|
|
jpayne@69
|
3541 Py_VISIT(traverse_module_state->__pyx_n_s_collect);
|
|
jpayne@69
|
3542 Py_VISIT(traverse_module_state->__pyx_n_s_collection);
|
|
jpayne@69
|
3543 Py_VISIT(traverse_module_state->__pyx_n_s_contextlib);
|
|
jpayne@69
|
3544 Py_VISIT(traverse_module_state->__pyx_n_s_contextmanager);
|
|
jpayne@69
|
3545 Py_VISIT(traverse_module_state->__pyx_n_s_contig);
|
|
jpayne@69
|
3546 Py_VISIT(traverse_module_state->__pyx_kp_u_contig_and_reference_should_not);
|
|
jpayne@69
|
3547 Py_VISIT(traverse_module_state->__pyx_kp_u_contig_reference_and_region_shou);
|
|
jpayne@69
|
3548 Py_VISIT(traverse_module_state->__pyx_n_s_decode);
|
|
jpayne@69
|
3549 Py_VISIT(traverse_module_state->__pyx_n_u_depad);
|
|
jpayne@69
|
3550 Py_VISIT(traverse_module_state->__pyx_n_s_encode);
|
|
jpayne@69
|
3551 Py_VISIT(traverse_module_state->__pyx_n_s_end);
|
|
jpayne@69
|
3552 Py_VISIT(traverse_module_state->__pyx_n_s_enter);
|
|
jpayne@69
|
3553 Py_VISIT(traverse_module_state->__pyx_kp_u_error_while_opening_file_for_wri);
|
|
jpayne@69
|
3554 Py_VISIT(traverse_module_state->__pyx_n_s_exception);
|
|
jpayne@69
|
3555 Py_VISIT(traverse_module_state->__pyx_n_s_exists);
|
|
jpayne@69
|
3556 Py_VISIT(traverse_module_state->__pyx_n_s_exit);
|
|
jpayne@69
|
3557 Py_VISIT(traverse_module_state->__pyx_n_s_extend);
|
|
jpayne@69
|
3558 Py_VISIT(traverse_module_state->__pyx_n_s_extra_args);
|
|
jpayne@69
|
3559 Py_VISIT(traverse_module_state->__pyx_n_s_fn);
|
|
jpayne@69
|
3560 Py_VISIT(traverse_module_state->__pyx_n_s_format);
|
|
jpayne@69
|
3561 Py_VISIT(traverse_module_state->__pyx_n_s_fsencode);
|
|
jpayne@69
|
3562 Py_VISIT(traverse_module_state->__pyx_n_s_get_encoding_error_handler);
|
|
jpayne@69
|
3563 Py_VISIT(traverse_module_state->__pyx_n_u_get_encoding_error_handler);
|
|
jpayne@69
|
3564 Py_VISIT(traverse_module_state->__pyx_n_s_getdefaultencoding);
|
|
jpayne@69
|
3565 Py_VISIT(traverse_module_state->__pyx_n_s_getfilesystemencoding);
|
|
jpayne@69
|
3566 Py_VISIT(traverse_module_state->__pyx_n_u_head);
|
|
jpayne@69
|
3567 Py_VISIT(traverse_module_state->__pyx_n_s_i);
|
|
jpayne@69
|
3568 Py_VISIT(traverse_module_state->__pyx_n_s_import);
|
|
jpayne@69
|
3569 Py_VISIT(traverse_module_state->__pyx_n_b_index);
|
|
jpayne@69
|
3570 Py_VISIT(traverse_module_state->__pyx_n_u_index);
|
|
jpayne@69
|
3571 Py_VISIT(traverse_module_state->__pyx_n_s_inf);
|
|
jpayne@69
|
3572 Py_VISIT(traverse_module_state->__pyx_n_s_initializing);
|
|
jpayne@69
|
3573 Py_VISIT(traverse_module_state->__pyx_n_s_input_str);
|
|
jpayne@69
|
3574 Py_VISIT(traverse_module_state->__pyx_kp_u_invalid_coordinates_start_i_stop);
|
|
jpayne@69
|
3575 Py_VISIT(traverse_module_state->__pyx_n_s_io);
|
|
jpayne@69
|
3576 Py_VISIT(traverse_module_state->__pyx_n_s_is_coroutine);
|
|
jpayne@69
|
3577 Py_VISIT(traverse_module_state->__pyx_n_s_is_usage);
|
|
jpayne@69
|
3578 Py_VISIT(traverse_module_state->__pyx_n_s_l);
|
|
jpayne@69
|
3579 Py_VISIT(traverse_module_state->__pyx_n_s_latin1_replace);
|
|
jpayne@69
|
3580 Py_VISIT(traverse_module_state->__pyx_kp_u_m);
|
|
jpayne@69
|
3581 Py_VISIT(traverse_module_state->__pyx_n_s_main);
|
|
jpayne@69
|
3582 Py_VISIT(traverse_module_state->__pyx_n_s_method);
|
|
jpayne@69
|
3583 Py_VISIT(traverse_module_state->__pyx_kp_u_min_shift);
|
|
jpayne@69
|
3584 Py_VISIT(traverse_module_state->__pyx_n_s_mkstemp);
|
|
jpayne@69
|
3585 Py_VISIT(traverse_module_state->__pyx_n_u_mpileup);
|
|
jpayne@69
|
3586 Py_VISIT(traverse_module_state->__pyx_n_s_n);
|
|
jpayne@69
|
3587 Py_VISIT(traverse_module_state->__pyx_n_s_name);
|
|
jpayne@69
|
3588 Py_VISIT(traverse_module_state->__pyx_n_s_name_2);
|
|
jpayne@69
|
3589 Py_VISIT(traverse_module_state->__pyx_kp_u_neither_contig_nor_region_are_gi);
|
|
jpayne@69
|
3590 Py_VISIT(traverse_module_state->__pyx_kp_u_o);
|
|
jpayne@69
|
3591 Py_VISIT(traverse_module_state->__pyx_kp_u_o_2);
|
|
jpayne@69
|
3592 Py_VISIT(traverse_module_state->__pyx_n_s_object);
|
|
jpayne@69
|
3593 Py_VISIT(traverse_module_state->__pyx_n_s_offset);
|
|
jpayne@69
|
3594 Py_VISIT(traverse_module_state->__pyx_n_s_open);
|
|
jpayne@69
|
3595 Py_VISIT(traverse_module_state->__pyx_n_s_os);
|
|
jpayne@69
|
3596 Py_VISIT(traverse_module_state->__pyx_n_s_out);
|
|
jpayne@69
|
3597 Py_VISIT(traverse_module_state->__pyx_n_s_out_stderr);
|
|
jpayne@69
|
3598 Py_VISIT(traverse_module_state->__pyx_n_s_out_stdout);
|
|
jpayne@69
|
3599 Py_VISIT(traverse_module_state->__pyx_kp_u_output);
|
|
jpayne@69
|
3600 Py_VISIT(traverse_module_state->__pyx_kp_u_output_file);
|
|
jpayne@69
|
3601 Py_VISIT(traverse_module_state->__pyx_n_s_parse_region);
|
|
jpayne@69
|
3602 Py_VISIT(traverse_module_state->__pyx_n_s_path);
|
|
jpayne@69
|
3603 Py_VISIT(traverse_module_state->__pyx_n_s_pysam_dispatch);
|
|
jpayne@69
|
3604 Py_VISIT(traverse_module_state->__pyx_n_s_pysam_dispatch_locals__collect);
|
|
jpayne@69
|
3605 Py_VISIT(traverse_module_state->__pyx_kp_u_pysam_latin1replace);
|
|
jpayne@69
|
3606 Py_VISIT(traverse_module_state->__pyx_n_s_pysam_libcutils);
|
|
jpayne@69
|
3607 Py_VISIT(traverse_module_state->__pyx_kp_s_pysam_libcutils_pyx);
|
|
jpayne@69
|
3608 Py_VISIT(traverse_module_state->__pyx_n_s_qualities);
|
|
jpayne@69
|
3609 Py_VISIT(traverse_module_state->__pyx_n_s_qualities_to_qualitystring);
|
|
jpayne@69
|
3610 Py_VISIT(traverse_module_state->__pyx_n_u_qualities_to_qualitystring);
|
|
jpayne@69
|
3611 Py_VISIT(traverse_module_state->__pyx_n_s_qualitystring_to_array);
|
|
jpayne@69
|
3612 Py_VISIT(traverse_module_state->__pyx_n_u_qualitystring_to_array);
|
|
jpayne@69
|
3613 Py_VISIT(traverse_module_state->__pyx_n_u_r);
|
|
jpayne@69
|
3614 Py_VISIT(traverse_module_state->__pyx_n_u_rb);
|
|
jpayne@69
|
3615 Py_VISIT(traverse_module_state->__pyx_n_s_re);
|
|
jpayne@69
|
3616 Py_VISIT(traverse_module_state->__pyx_n_s_read);
|
|
jpayne@69
|
3617 Py_VISIT(traverse_module_state->__pyx_n_s_reference);
|
|
jpayne@69
|
3618 Py_VISIT(traverse_module_state->__pyx_n_s_region);
|
|
jpayne@69
|
3619 Py_VISIT(traverse_module_state->__pyx_n_s_register_error);
|
|
jpayne@69
|
3620 Py_VISIT(traverse_module_state->__pyx_n_s_remove);
|
|
jpayne@69
|
3621 Py_VISIT(traverse_module_state->__pyx_n_s_retval);
|
|
jpayne@69
|
3622 Py_VISIT(traverse_module_state->__pyx_n_u_roh);
|
|
jpayne@69
|
3623 Py_VISIT(traverse_module_state->__pyx_n_b_samtools);
|
|
jpayne@69
|
3624 Py_VISIT(traverse_module_state->__pyx_n_u_samtools);
|
|
jpayne@69
|
3625 Py_VISIT(traverse_module_state->__pyx_n_s_save_stdout);
|
|
jpayne@69
|
3626 Py_VISIT(traverse_module_state->__pyx_n_s_set_encoding_error_handler);
|
|
jpayne@69
|
3627 Py_VISIT(traverse_module_state->__pyx_n_u_set_encoding_error_handler);
|
|
jpayne@69
|
3628 Py_VISIT(traverse_module_state->__pyx_n_s_skip_next);
|
|
jpayne@69
|
3629 Py_VISIT(traverse_module_state->__pyx_n_s_spec);
|
|
jpayne@69
|
3630 Py_VISIT(traverse_module_state->__pyx_n_s_split);
|
|
jpayne@69
|
3631 Py_VISIT(traverse_module_state->__pyx_n_s_start);
|
|
jpayne@69
|
3632 Py_VISIT(traverse_module_state->__pyx_kp_u_start_out_of_range_i);
|
|
jpayne@69
|
3633 Py_VISIT(traverse_module_state->__pyx_n_s_startswith);
|
|
jpayne@69
|
3634 Py_VISIT(traverse_module_state->__pyx_n_u_stats);
|
|
jpayne@69
|
3635 Py_VISIT(traverse_module_state->__pyx_n_s_stderr_f);
|
|
jpayne@69
|
3636 Py_VISIT(traverse_module_state->__pyx_n_s_stderr_h);
|
|
jpayne@69
|
3637 Py_VISIT(traverse_module_state->__pyx_n_s_stdout_f);
|
|
jpayne@69
|
3638 Py_VISIT(traverse_module_state->__pyx_n_s_stdout_h);
|
|
jpayne@69
|
3639 Py_VISIT(traverse_module_state->__pyx_n_s_stdout_option);
|
|
jpayne@69
|
3640 Py_VISIT(traverse_module_state->__pyx_n_s_stop);
|
|
jpayne@69
|
3641 Py_VISIT(traverse_module_state->__pyx_kp_u_stop_and_end_should_not_both_be);
|
|
jpayne@69
|
3642 Py_VISIT(traverse_module_state->__pyx_kp_u_stop_out_of_range_i);
|
|
jpayne@69
|
3643 Py_VISIT(traverse_module_state->__pyx_n_u_strict);
|
|
jpayne@69
|
3644 Py_VISIT(traverse_module_state->__pyx_n_s_string);
|
|
jpayne@69
|
3645 Py_VISIT(traverse_module_state->__pyx_n_s_sys);
|
|
jpayne@69
|
3646 Py_VISIT(traverse_module_state->__pyx_n_s_tempfile);
|
|
jpayne@69
|
3647 Py_VISIT(traverse_module_state->__pyx_n_s_test);
|
|
jpayne@69
|
3648 Py_VISIT(traverse_module_state->__pyx_kp_u_threads);
|
|
jpayne@69
|
3649 Py_VISIT(traverse_module_state->__pyx_n_s_tobytes);
|
|
jpayne@69
|
3650 Py_VISIT(traverse_module_state->__pyx_n_s_types);
|
|
jpayne@69
|
3651 Py_VISIT(traverse_module_state->__pyx_kp_u_utf_8);
|
|
jpayne@69
|
3652 Py_VISIT(traverse_module_state->__pyx_n_u_view);
|
|
jpayne@69
|
3653 Py_VISIT(traverse_module_state->__pyx_int_1);
|
|
jpayne@69
|
3654 Py_VISIT(traverse_module_state->__pyx_int_33);
|
|
jpayne@69
|
3655 Py_VISIT(traverse_module_state->__pyx_int_neg_1);
|
|
jpayne@69
|
3656 Py_VISIT(traverse_module_state->__pyx_tuple__2);
|
|
jpayne@69
|
3657 Py_VISIT(traverse_module_state->__pyx_tuple__3);
|
|
jpayne@69
|
3658 Py_VISIT(traverse_module_state->__pyx_tuple__4);
|
|
jpayne@69
|
3659 Py_VISIT(traverse_module_state->__pyx_tuple__5);
|
|
jpayne@69
|
3660 Py_VISIT(traverse_module_state->__pyx_tuple__6);
|
|
jpayne@69
|
3661 Py_VISIT(traverse_module_state->__pyx_tuple__9);
|
|
jpayne@69
|
3662 Py_VISIT(traverse_module_state->__pyx_tuple__12);
|
|
jpayne@69
|
3663 Py_VISIT(traverse_module_state->__pyx_tuple__16);
|
|
jpayne@69
|
3664 Py_VISIT(traverse_module_state->__pyx_tuple__18);
|
|
jpayne@69
|
3665 Py_VISIT(traverse_module_state->__pyx_tuple__19);
|
|
jpayne@69
|
3666 Py_VISIT(traverse_module_state->__pyx_tuple__22);
|
|
jpayne@69
|
3667 Py_VISIT(traverse_module_state->__pyx_tuple__25);
|
|
jpayne@69
|
3668 Py_VISIT(traverse_module_state->__pyx_tuple__27);
|
|
jpayne@69
|
3669 Py_VISIT(traverse_module_state->__pyx_tuple__29);
|
|
jpayne@69
|
3670 Py_VISIT(traverse_module_state->__pyx_tuple__30);
|
|
jpayne@69
|
3671 Py_VISIT(traverse_module_state->__pyx_tuple__32);
|
|
jpayne@69
|
3672 Py_VISIT(traverse_module_state->__pyx_codeobj__13);
|
|
jpayne@69
|
3673 Py_VISIT(traverse_module_state->__pyx_codeobj__17);
|
|
jpayne@69
|
3674 Py_VISIT(traverse_module_state->__pyx_codeobj__20);
|
|
jpayne@69
|
3675 Py_VISIT(traverse_module_state->__pyx_codeobj__21);
|
|
jpayne@69
|
3676 Py_VISIT(traverse_module_state->__pyx_codeobj__23);
|
|
jpayne@69
|
3677 Py_VISIT(traverse_module_state->__pyx_codeobj__24);
|
|
jpayne@69
|
3678 Py_VISIT(traverse_module_state->__pyx_codeobj__26);
|
|
jpayne@69
|
3679 Py_VISIT(traverse_module_state->__pyx_codeobj__28);
|
|
jpayne@69
|
3680 Py_VISIT(traverse_module_state->__pyx_codeobj__31);
|
|
jpayne@69
|
3681 return 0;
|
|
jpayne@69
|
3682 }
|
|
jpayne@69
|
3683 #endif
|
|
jpayne@69
|
3684 /* #### Code section: module_state_defines ### */
|
|
jpayne@69
|
3685 #define __pyx_d __pyx_mstate_global->__pyx_d
|
|
jpayne@69
|
3686 #define __pyx_b __pyx_mstate_global->__pyx_b
|
|
jpayne@69
|
3687 #define __pyx_cython_runtime __pyx_mstate_global->__pyx_cython_runtime
|
|
jpayne@69
|
3688 #define __pyx_empty_tuple __pyx_mstate_global->__pyx_empty_tuple
|
|
jpayne@69
|
3689 #define __pyx_empty_bytes __pyx_mstate_global->__pyx_empty_bytes
|
|
jpayne@69
|
3690 #define __pyx_empty_unicode __pyx_mstate_global->__pyx_empty_unicode
|
|
jpayne@69
|
3691 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
3692 #define __pyx_CyFunctionType __pyx_mstate_global->__pyx_CyFunctionType
|
|
jpayne@69
|
3693 #endif
|
|
jpayne@69
|
3694 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
3695 #define __pyx_FusedFunctionType __pyx_mstate_global->__pyx_FusedFunctionType
|
|
jpayne@69
|
3696 #endif
|
|
jpayne@69
|
3697 #ifdef __Pyx_Generator_USED
|
|
jpayne@69
|
3698 #define __pyx_GeneratorType __pyx_mstate_global->__pyx_GeneratorType
|
|
jpayne@69
|
3699 #endif
|
|
jpayne@69
|
3700 #ifdef __Pyx_IterableCoroutine_USED
|
|
jpayne@69
|
3701 #define __pyx_IterableCoroutineType __pyx_mstate_global->__pyx_IterableCoroutineType
|
|
jpayne@69
|
3702 #endif
|
|
jpayne@69
|
3703 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
3704 #define __pyx_CoroutineAwaitType __pyx_mstate_global->__pyx_CoroutineAwaitType
|
|
jpayne@69
|
3705 #endif
|
|
jpayne@69
|
3706 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
3707 #define __pyx_CoroutineType __pyx_mstate_global->__pyx_CoroutineType
|
|
jpayne@69
|
3708 #endif
|
|
jpayne@69
|
3709 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3710 #endif
|
|
jpayne@69
|
3711 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3712 #endif
|
|
jpayne@69
|
3713 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3714 #endif
|
|
jpayne@69
|
3715 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3716 #endif
|
|
jpayne@69
|
3717 #define __pyx_ptype_7cpython_4type_type __pyx_mstate_global->__pyx_ptype_7cpython_4type_type
|
|
jpayne@69
|
3718 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3719 #endif
|
|
jpayne@69
|
3720 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3721 #endif
|
|
jpayne@69
|
3722 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3723 #endif
|
|
jpayne@69
|
3724 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3725 #endif
|
|
jpayne@69
|
3726 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3727 #endif
|
|
jpayne@69
|
3728 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3729 #endif
|
|
jpayne@69
|
3730 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3731 #endif
|
|
jpayne@69
|
3732 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3733 #endif
|
|
jpayne@69
|
3734 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3735 #endif
|
|
jpayne@69
|
3736 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3737 #endif
|
|
jpayne@69
|
3738 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3739 #endif
|
|
jpayne@69
|
3740 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3741 #endif
|
|
jpayne@69
|
3742 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3743 #endif
|
|
jpayne@69
|
3744 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3745 #endif
|
|
jpayne@69
|
3746 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3747 #endif
|
|
jpayne@69
|
3748 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3749 #endif
|
|
jpayne@69
|
3750 #define __pyx_ptype_7cpython_4bool_bool __pyx_mstate_global->__pyx_ptype_7cpython_4bool_bool
|
|
jpayne@69
|
3751 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3752 #endif
|
|
jpayne@69
|
3753 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3754 #endif
|
|
jpayne@69
|
3755 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3756 #endif
|
|
jpayne@69
|
3757 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3758 #endif
|
|
jpayne@69
|
3759 #define __pyx_ptype_7cpython_7complex_complex __pyx_mstate_global->__pyx_ptype_7cpython_7complex_complex
|
|
jpayne@69
|
3760 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3761 #endif
|
|
jpayne@69
|
3762 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3763 #endif
|
|
jpayne@69
|
3764 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3765 #endif
|
|
jpayne@69
|
3766 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3767 #endif
|
|
jpayne@69
|
3768 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3769 #endif
|
|
jpayne@69
|
3770 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3771 #endif
|
|
jpayne@69
|
3772 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3773 #endif
|
|
jpayne@69
|
3774 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3775 #endif
|
|
jpayne@69
|
3776 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3777 #endif
|
|
jpayne@69
|
3778 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3779 #endif
|
|
jpayne@69
|
3780 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3781 #endif
|
|
jpayne@69
|
3782 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3783 #endif
|
|
jpayne@69
|
3784 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3785 #endif
|
|
jpayne@69
|
3786 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3787 #endif
|
|
jpayne@69
|
3788 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3789 #endif
|
|
jpayne@69
|
3790 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3791 #endif
|
|
jpayne@69
|
3792 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3793 #endif
|
|
jpayne@69
|
3794 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3795 #endif
|
|
jpayne@69
|
3796 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3797 #endif
|
|
jpayne@69
|
3798 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3799 #endif
|
|
jpayne@69
|
3800 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3801 #endif
|
|
jpayne@69
|
3802 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3803 #endif
|
|
jpayne@69
|
3804 #define __pyx_ptype_7cpython_5array_array __pyx_mstate_global->__pyx_ptype_7cpython_5array_array
|
|
jpayne@69
|
3805 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3806 #endif
|
|
jpayne@69
|
3807 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3808 #endif
|
|
jpayne@69
|
3809 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3810 #endif
|
|
jpayne@69
|
3811 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3812 #endif
|
|
jpayne@69
|
3813 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3814 #endif
|
|
jpayne@69
|
3815 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3816 #endif
|
|
jpayne@69
|
3817 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3818 #endif
|
|
jpayne@69
|
3819 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3820 #endif
|
|
jpayne@69
|
3821 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
3822 #endif
|
|
jpayne@69
|
3823 #define __pyx_kp_u_ __pyx_mstate_global->__pyx_kp_u_
|
|
jpayne@69
|
3824 #define __pyx_n_s_ARGUMENTS __pyx_mstate_global->__pyx_n_s_ARGUMENTS
|
|
jpayne@69
|
3825 #define __pyx_kp_u_Argument_must_be_string_bytes_or __pyx_mstate_global->__pyx_kp_u_Argument_must_be_string_bytes_or
|
|
jpayne@69
|
3826 #define __pyx_n_u_B __pyx_mstate_global->__pyx_n_u_B
|
|
jpayne@69
|
3827 #define __pyx_n_s_IOError __pyx_mstate_global->__pyx_n_s_IOError
|
|
jpayne@69
|
3828 #define __pyx_n_s_MAP_STDOUT_OPTIONS __pyx_mstate_global->__pyx_n_s_MAP_STDOUT_OPTIONS
|
|
jpayne@69
|
3829 #define __pyx_n_s_MemoryError __pyx_mstate_global->__pyx_n_s_MemoryError
|
|
jpayne@69
|
3830 #define __pyx_kp_u_No_such_file_or_directory_s __pyx_mstate_global->__pyx_kp_u_No_such_file_or_directory_s
|
|
jpayne@69
|
3831 #define __pyx_n_s_OSError __pyx_mstate_global->__pyx_n_s_OSError
|
|
jpayne@69
|
3832 #define __pyx_n_s_OverflowError __pyx_mstate_global->__pyx_n_s_OverflowError
|
|
jpayne@69
|
3833 #define __pyx_n_s_TypeError __pyx_mstate_global->__pyx_n_s_TypeError
|
|
jpayne@69
|
3834 #define __pyx_n_s_UnicodeDecodeError __pyx_mstate_global->__pyx_n_s_UnicodeDecodeError
|
|
jpayne@69
|
3835 #define __pyx_n_s_ValueError __pyx_mstate_global->__pyx_n_s_ValueError
|
|
jpayne@69
|
3836 #define __pyx_kp_u__10 __pyx_mstate_global->__pyx_kp_u__10
|
|
jpayne@69
|
3837 #define __pyx_kp_u__11 __pyx_mstate_global->__pyx_kp_u__11
|
|
jpayne@69
|
3838 #define __pyx_n_s__14 __pyx_mstate_global->__pyx_n_s__14
|
|
jpayne@69
|
3839 #define __pyx_kp_u__15 __pyx_mstate_global->__pyx_kp_u__15
|
|
jpayne@69
|
3840 #define __pyx_n_s__33 __pyx_mstate_global->__pyx_n_s__33
|
|
jpayne@69
|
3841 #define __pyx_kp_u__7 __pyx_mstate_global->__pyx_kp_u__7
|
|
jpayne@69
|
3842 #define __pyx_kp_u__8 __pyx_mstate_global->__pyx_kp_u__8
|
|
jpayne@69
|
3843 #define __pyx_n_s_a __pyx_mstate_global->__pyx_n_s_a
|
|
jpayne@69
|
3844 #define __pyx_n_s_all __pyx_mstate_global->__pyx_n_s_all
|
|
jpayne@69
|
3845 #define __pyx_n_s_arg __pyx_mstate_global->__pyx_n_s_arg
|
|
jpayne@69
|
3846 #define __pyx_n_s_args __pyx_mstate_global->__pyx_n_s_args
|
|
jpayne@69
|
3847 #define __pyx_n_s_array_to_qualitystring __pyx_mstate_global->__pyx_n_s_array_to_qualitystring
|
|
jpayne@69
|
3848 #define __pyx_n_u_array_to_qualitystring __pyx_mstate_global->__pyx_n_u_array_to_qualitystring
|
|
jpayne@69
|
3849 #define __pyx_n_u_ascii __pyx_mstate_global->__pyx_n_u_ascii
|
|
jpayne@69
|
3850 #define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines
|
|
jpayne@69
|
3851 #define __pyx_n_b_bcftools __pyx_mstate_global->__pyx_n_b_bcftools
|
|
jpayne@69
|
3852 #define __pyx_n_u_bcftools __pyx_mstate_global->__pyx_n_u_bcftools
|
|
jpayne@69
|
3853 #define __pyx_kp_u_c __pyx_mstate_global->__pyx_kp_u_c
|
|
jpayne@69
|
3854 #define __pyx_n_u_calmd __pyx_mstate_global->__pyx_n_u_calmd
|
|
jpayne@69
|
3855 #define __pyx_n_s_cargs __pyx_mstate_global->__pyx_n_s_cargs
|
|
jpayne@69
|
3856 #define __pyx_n_s_catch_stdout __pyx_mstate_global->__pyx_n_s_catch_stdout
|
|
jpayne@69
|
3857 #define __pyx_n_s_chr __pyx_mstate_global->__pyx_n_s_chr
|
|
jpayne@69
|
3858 #define __pyx_n_s_class_getitem __pyx_mstate_global->__pyx_n_s_class_getitem
|
|
jpayne@69
|
3859 #define __pyx_n_s_cline_in_traceback __pyx_mstate_global->__pyx_n_s_cline_in_traceback
|
|
jpayne@69
|
3860 #define __pyx_n_s_close __pyx_mstate_global->__pyx_n_s_close
|
|
jpayne@69
|
3861 #define __pyx_n_s_codecs __pyx_mstate_global->__pyx_n_s_codecs
|
|
jpayne@69
|
3862 #define __pyx_n_s_collect __pyx_mstate_global->__pyx_n_s_collect
|
|
jpayne@69
|
3863 #define __pyx_n_s_collection __pyx_mstate_global->__pyx_n_s_collection
|
|
jpayne@69
|
3864 #define __pyx_n_s_contextlib __pyx_mstate_global->__pyx_n_s_contextlib
|
|
jpayne@69
|
3865 #define __pyx_n_s_contextmanager __pyx_mstate_global->__pyx_n_s_contextmanager
|
|
jpayne@69
|
3866 #define __pyx_n_s_contig __pyx_mstate_global->__pyx_n_s_contig
|
|
jpayne@69
|
3867 #define __pyx_kp_u_contig_and_reference_should_not __pyx_mstate_global->__pyx_kp_u_contig_and_reference_should_not
|
|
jpayne@69
|
3868 #define __pyx_kp_u_contig_reference_and_region_shou __pyx_mstate_global->__pyx_kp_u_contig_reference_and_region_shou
|
|
jpayne@69
|
3869 #define __pyx_n_s_decode __pyx_mstate_global->__pyx_n_s_decode
|
|
jpayne@69
|
3870 #define __pyx_n_u_depad __pyx_mstate_global->__pyx_n_u_depad
|
|
jpayne@69
|
3871 #define __pyx_n_s_encode __pyx_mstate_global->__pyx_n_s_encode
|
|
jpayne@69
|
3872 #define __pyx_n_s_end __pyx_mstate_global->__pyx_n_s_end
|
|
jpayne@69
|
3873 #define __pyx_n_s_enter __pyx_mstate_global->__pyx_n_s_enter
|
|
jpayne@69
|
3874 #define __pyx_kp_u_error_while_opening_file_for_wri __pyx_mstate_global->__pyx_kp_u_error_while_opening_file_for_wri
|
|
jpayne@69
|
3875 #define __pyx_n_s_exception __pyx_mstate_global->__pyx_n_s_exception
|
|
jpayne@69
|
3876 #define __pyx_n_s_exists __pyx_mstate_global->__pyx_n_s_exists
|
|
jpayne@69
|
3877 #define __pyx_n_s_exit __pyx_mstate_global->__pyx_n_s_exit
|
|
jpayne@69
|
3878 #define __pyx_n_s_extend __pyx_mstate_global->__pyx_n_s_extend
|
|
jpayne@69
|
3879 #define __pyx_n_s_extra_args __pyx_mstate_global->__pyx_n_s_extra_args
|
|
jpayne@69
|
3880 #define __pyx_n_s_fn __pyx_mstate_global->__pyx_n_s_fn
|
|
jpayne@69
|
3881 #define __pyx_n_s_format __pyx_mstate_global->__pyx_n_s_format
|
|
jpayne@69
|
3882 #define __pyx_n_s_fsencode __pyx_mstate_global->__pyx_n_s_fsencode
|
|
jpayne@69
|
3883 #define __pyx_n_s_get_encoding_error_handler __pyx_mstate_global->__pyx_n_s_get_encoding_error_handler
|
|
jpayne@69
|
3884 #define __pyx_n_u_get_encoding_error_handler __pyx_mstate_global->__pyx_n_u_get_encoding_error_handler
|
|
jpayne@69
|
3885 #define __pyx_n_s_getdefaultencoding __pyx_mstate_global->__pyx_n_s_getdefaultencoding
|
|
jpayne@69
|
3886 #define __pyx_n_s_getfilesystemencoding __pyx_mstate_global->__pyx_n_s_getfilesystemencoding
|
|
jpayne@69
|
3887 #define __pyx_n_u_head __pyx_mstate_global->__pyx_n_u_head
|
|
jpayne@69
|
3888 #define __pyx_n_s_i __pyx_mstate_global->__pyx_n_s_i
|
|
jpayne@69
|
3889 #define __pyx_n_s_import __pyx_mstate_global->__pyx_n_s_import
|
|
jpayne@69
|
3890 #define __pyx_n_b_index __pyx_mstate_global->__pyx_n_b_index
|
|
jpayne@69
|
3891 #define __pyx_n_u_index __pyx_mstate_global->__pyx_n_u_index
|
|
jpayne@69
|
3892 #define __pyx_n_s_inf __pyx_mstate_global->__pyx_n_s_inf
|
|
jpayne@69
|
3893 #define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing
|
|
jpayne@69
|
3894 #define __pyx_n_s_input_str __pyx_mstate_global->__pyx_n_s_input_str
|
|
jpayne@69
|
3895 #define __pyx_kp_u_invalid_coordinates_start_i_stop __pyx_mstate_global->__pyx_kp_u_invalid_coordinates_start_i_stop
|
|
jpayne@69
|
3896 #define __pyx_n_s_io __pyx_mstate_global->__pyx_n_s_io
|
|
jpayne@69
|
3897 #define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine
|
|
jpayne@69
|
3898 #define __pyx_n_s_is_usage __pyx_mstate_global->__pyx_n_s_is_usage
|
|
jpayne@69
|
3899 #define __pyx_n_s_l __pyx_mstate_global->__pyx_n_s_l
|
|
jpayne@69
|
3900 #define __pyx_n_s_latin1_replace __pyx_mstate_global->__pyx_n_s_latin1_replace
|
|
jpayne@69
|
3901 #define __pyx_kp_u_m __pyx_mstate_global->__pyx_kp_u_m
|
|
jpayne@69
|
3902 #define __pyx_n_s_main __pyx_mstate_global->__pyx_n_s_main
|
|
jpayne@69
|
3903 #define __pyx_n_s_method __pyx_mstate_global->__pyx_n_s_method
|
|
jpayne@69
|
3904 #define __pyx_kp_u_min_shift __pyx_mstate_global->__pyx_kp_u_min_shift
|
|
jpayne@69
|
3905 #define __pyx_n_s_mkstemp __pyx_mstate_global->__pyx_n_s_mkstemp
|
|
jpayne@69
|
3906 #define __pyx_n_u_mpileup __pyx_mstate_global->__pyx_n_u_mpileup
|
|
jpayne@69
|
3907 #define __pyx_n_s_n __pyx_mstate_global->__pyx_n_s_n
|
|
jpayne@69
|
3908 #define __pyx_n_s_name __pyx_mstate_global->__pyx_n_s_name
|
|
jpayne@69
|
3909 #define __pyx_n_s_name_2 __pyx_mstate_global->__pyx_n_s_name_2
|
|
jpayne@69
|
3910 #define __pyx_kp_u_neither_contig_nor_region_are_gi __pyx_mstate_global->__pyx_kp_u_neither_contig_nor_region_are_gi
|
|
jpayne@69
|
3911 #define __pyx_kp_u_o __pyx_mstate_global->__pyx_kp_u_o
|
|
jpayne@69
|
3912 #define __pyx_kp_u_o_2 __pyx_mstate_global->__pyx_kp_u_o_2
|
|
jpayne@69
|
3913 #define __pyx_n_s_object __pyx_mstate_global->__pyx_n_s_object
|
|
jpayne@69
|
3914 #define __pyx_n_s_offset __pyx_mstate_global->__pyx_n_s_offset
|
|
jpayne@69
|
3915 #define __pyx_n_s_open __pyx_mstate_global->__pyx_n_s_open
|
|
jpayne@69
|
3916 #define __pyx_n_s_os __pyx_mstate_global->__pyx_n_s_os
|
|
jpayne@69
|
3917 #define __pyx_n_s_out __pyx_mstate_global->__pyx_n_s_out
|
|
jpayne@69
|
3918 #define __pyx_n_s_out_stderr __pyx_mstate_global->__pyx_n_s_out_stderr
|
|
jpayne@69
|
3919 #define __pyx_n_s_out_stdout __pyx_mstate_global->__pyx_n_s_out_stdout
|
|
jpayne@69
|
3920 #define __pyx_kp_u_output __pyx_mstate_global->__pyx_kp_u_output
|
|
jpayne@69
|
3921 #define __pyx_kp_u_output_file __pyx_mstate_global->__pyx_kp_u_output_file
|
|
jpayne@69
|
3922 #define __pyx_n_s_parse_region __pyx_mstate_global->__pyx_n_s_parse_region
|
|
jpayne@69
|
3923 #define __pyx_n_s_path __pyx_mstate_global->__pyx_n_s_path
|
|
jpayne@69
|
3924 #define __pyx_n_s_pysam_dispatch __pyx_mstate_global->__pyx_n_s_pysam_dispatch
|
|
jpayne@69
|
3925 #define __pyx_n_s_pysam_dispatch_locals__collect __pyx_mstate_global->__pyx_n_s_pysam_dispatch_locals__collect
|
|
jpayne@69
|
3926 #define __pyx_kp_u_pysam_latin1replace __pyx_mstate_global->__pyx_kp_u_pysam_latin1replace
|
|
jpayne@69
|
3927 #define __pyx_n_s_pysam_libcutils __pyx_mstate_global->__pyx_n_s_pysam_libcutils
|
|
jpayne@69
|
3928 #define __pyx_kp_s_pysam_libcutils_pyx __pyx_mstate_global->__pyx_kp_s_pysam_libcutils_pyx
|
|
jpayne@69
|
3929 #define __pyx_n_s_qualities __pyx_mstate_global->__pyx_n_s_qualities
|
|
jpayne@69
|
3930 #define __pyx_n_s_qualities_to_qualitystring __pyx_mstate_global->__pyx_n_s_qualities_to_qualitystring
|
|
jpayne@69
|
3931 #define __pyx_n_u_qualities_to_qualitystring __pyx_mstate_global->__pyx_n_u_qualities_to_qualitystring
|
|
jpayne@69
|
3932 #define __pyx_n_s_qualitystring_to_array __pyx_mstate_global->__pyx_n_s_qualitystring_to_array
|
|
jpayne@69
|
3933 #define __pyx_n_u_qualitystring_to_array __pyx_mstate_global->__pyx_n_u_qualitystring_to_array
|
|
jpayne@69
|
3934 #define __pyx_n_u_r __pyx_mstate_global->__pyx_n_u_r
|
|
jpayne@69
|
3935 #define __pyx_n_u_rb __pyx_mstate_global->__pyx_n_u_rb
|
|
jpayne@69
|
3936 #define __pyx_n_s_re __pyx_mstate_global->__pyx_n_s_re
|
|
jpayne@69
|
3937 #define __pyx_n_s_read __pyx_mstate_global->__pyx_n_s_read
|
|
jpayne@69
|
3938 #define __pyx_n_s_reference __pyx_mstate_global->__pyx_n_s_reference
|
|
jpayne@69
|
3939 #define __pyx_n_s_region __pyx_mstate_global->__pyx_n_s_region
|
|
jpayne@69
|
3940 #define __pyx_n_s_register_error __pyx_mstate_global->__pyx_n_s_register_error
|
|
jpayne@69
|
3941 #define __pyx_n_s_remove __pyx_mstate_global->__pyx_n_s_remove
|
|
jpayne@69
|
3942 #define __pyx_n_s_retval __pyx_mstate_global->__pyx_n_s_retval
|
|
jpayne@69
|
3943 #define __pyx_n_u_roh __pyx_mstate_global->__pyx_n_u_roh
|
|
jpayne@69
|
3944 #define __pyx_n_b_samtools __pyx_mstate_global->__pyx_n_b_samtools
|
|
jpayne@69
|
3945 #define __pyx_n_u_samtools __pyx_mstate_global->__pyx_n_u_samtools
|
|
jpayne@69
|
3946 #define __pyx_n_s_save_stdout __pyx_mstate_global->__pyx_n_s_save_stdout
|
|
jpayne@69
|
3947 #define __pyx_n_s_set_encoding_error_handler __pyx_mstate_global->__pyx_n_s_set_encoding_error_handler
|
|
jpayne@69
|
3948 #define __pyx_n_u_set_encoding_error_handler __pyx_mstate_global->__pyx_n_u_set_encoding_error_handler
|
|
jpayne@69
|
3949 #define __pyx_n_s_skip_next __pyx_mstate_global->__pyx_n_s_skip_next
|
|
jpayne@69
|
3950 #define __pyx_n_s_spec __pyx_mstate_global->__pyx_n_s_spec
|
|
jpayne@69
|
3951 #define __pyx_n_s_split __pyx_mstate_global->__pyx_n_s_split
|
|
jpayne@69
|
3952 #define __pyx_n_s_start __pyx_mstate_global->__pyx_n_s_start
|
|
jpayne@69
|
3953 #define __pyx_kp_u_start_out_of_range_i __pyx_mstate_global->__pyx_kp_u_start_out_of_range_i
|
|
jpayne@69
|
3954 #define __pyx_n_s_startswith __pyx_mstate_global->__pyx_n_s_startswith
|
|
jpayne@69
|
3955 #define __pyx_n_u_stats __pyx_mstate_global->__pyx_n_u_stats
|
|
jpayne@69
|
3956 #define __pyx_n_s_stderr_f __pyx_mstate_global->__pyx_n_s_stderr_f
|
|
jpayne@69
|
3957 #define __pyx_n_s_stderr_h __pyx_mstate_global->__pyx_n_s_stderr_h
|
|
jpayne@69
|
3958 #define __pyx_n_s_stdout_f __pyx_mstate_global->__pyx_n_s_stdout_f
|
|
jpayne@69
|
3959 #define __pyx_n_s_stdout_h __pyx_mstate_global->__pyx_n_s_stdout_h
|
|
jpayne@69
|
3960 #define __pyx_n_s_stdout_option __pyx_mstate_global->__pyx_n_s_stdout_option
|
|
jpayne@69
|
3961 #define __pyx_n_s_stop __pyx_mstate_global->__pyx_n_s_stop
|
|
jpayne@69
|
3962 #define __pyx_kp_u_stop_and_end_should_not_both_be __pyx_mstate_global->__pyx_kp_u_stop_and_end_should_not_both_be
|
|
jpayne@69
|
3963 #define __pyx_kp_u_stop_out_of_range_i __pyx_mstate_global->__pyx_kp_u_stop_out_of_range_i
|
|
jpayne@69
|
3964 #define __pyx_n_u_strict __pyx_mstate_global->__pyx_n_u_strict
|
|
jpayne@69
|
3965 #define __pyx_n_s_string __pyx_mstate_global->__pyx_n_s_string
|
|
jpayne@69
|
3966 #define __pyx_n_s_sys __pyx_mstate_global->__pyx_n_s_sys
|
|
jpayne@69
|
3967 #define __pyx_n_s_tempfile __pyx_mstate_global->__pyx_n_s_tempfile
|
|
jpayne@69
|
3968 #define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test
|
|
jpayne@69
|
3969 #define __pyx_kp_u_threads __pyx_mstate_global->__pyx_kp_u_threads
|
|
jpayne@69
|
3970 #define __pyx_n_s_tobytes __pyx_mstate_global->__pyx_n_s_tobytes
|
|
jpayne@69
|
3971 #define __pyx_n_s_types __pyx_mstate_global->__pyx_n_s_types
|
|
jpayne@69
|
3972 #define __pyx_kp_u_utf_8 __pyx_mstate_global->__pyx_kp_u_utf_8
|
|
jpayne@69
|
3973 #define __pyx_n_u_view __pyx_mstate_global->__pyx_n_u_view
|
|
jpayne@69
|
3974 #define __pyx_int_1 __pyx_mstate_global->__pyx_int_1
|
|
jpayne@69
|
3975 #define __pyx_int_33 __pyx_mstate_global->__pyx_int_33
|
|
jpayne@69
|
3976 #define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1
|
|
jpayne@69
|
3977 #define __pyx_tuple__2 __pyx_mstate_global->__pyx_tuple__2
|
|
jpayne@69
|
3978 #define __pyx_tuple__3 __pyx_mstate_global->__pyx_tuple__3
|
|
jpayne@69
|
3979 #define __pyx_tuple__4 __pyx_mstate_global->__pyx_tuple__4
|
|
jpayne@69
|
3980 #define __pyx_tuple__5 __pyx_mstate_global->__pyx_tuple__5
|
|
jpayne@69
|
3981 #define __pyx_tuple__6 __pyx_mstate_global->__pyx_tuple__6
|
|
jpayne@69
|
3982 #define __pyx_tuple__9 __pyx_mstate_global->__pyx_tuple__9
|
|
jpayne@69
|
3983 #define __pyx_tuple__12 __pyx_mstate_global->__pyx_tuple__12
|
|
jpayne@69
|
3984 #define __pyx_tuple__16 __pyx_mstate_global->__pyx_tuple__16
|
|
jpayne@69
|
3985 #define __pyx_tuple__18 __pyx_mstate_global->__pyx_tuple__18
|
|
jpayne@69
|
3986 #define __pyx_tuple__19 __pyx_mstate_global->__pyx_tuple__19
|
|
jpayne@69
|
3987 #define __pyx_tuple__22 __pyx_mstate_global->__pyx_tuple__22
|
|
jpayne@69
|
3988 #define __pyx_tuple__25 __pyx_mstate_global->__pyx_tuple__25
|
|
jpayne@69
|
3989 #define __pyx_tuple__27 __pyx_mstate_global->__pyx_tuple__27
|
|
jpayne@69
|
3990 #define __pyx_tuple__29 __pyx_mstate_global->__pyx_tuple__29
|
|
jpayne@69
|
3991 #define __pyx_tuple__30 __pyx_mstate_global->__pyx_tuple__30
|
|
jpayne@69
|
3992 #define __pyx_tuple__32 __pyx_mstate_global->__pyx_tuple__32
|
|
jpayne@69
|
3993 #define __pyx_codeobj__13 __pyx_mstate_global->__pyx_codeobj__13
|
|
jpayne@69
|
3994 #define __pyx_codeobj__17 __pyx_mstate_global->__pyx_codeobj__17
|
|
jpayne@69
|
3995 #define __pyx_codeobj__20 __pyx_mstate_global->__pyx_codeobj__20
|
|
jpayne@69
|
3996 #define __pyx_codeobj__21 __pyx_mstate_global->__pyx_codeobj__21
|
|
jpayne@69
|
3997 #define __pyx_codeobj__23 __pyx_mstate_global->__pyx_codeobj__23
|
|
jpayne@69
|
3998 #define __pyx_codeobj__24 __pyx_mstate_global->__pyx_codeobj__24
|
|
jpayne@69
|
3999 #define __pyx_codeobj__26 __pyx_mstate_global->__pyx_codeobj__26
|
|
jpayne@69
|
4000 #define __pyx_codeobj__28 __pyx_mstate_global->__pyx_codeobj__28
|
|
jpayne@69
|
4001 #define __pyx_codeobj__31 __pyx_mstate_global->__pyx_codeobj__31
|
|
jpayne@69
|
4002 /* #### Code section: module_code ### */
|
|
jpayne@69
|
4003
|
|
jpayne@69
|
4004 /* "cpython/complex.pxd":19
|
|
jpayne@69
|
4005 *
|
|
jpayne@69
|
4006 * @property
|
|
jpayne@69
|
4007 * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4008 * return self.cval.real
|
|
jpayne@69
|
4009 *
|
|
jpayne@69
|
4010 */
|
|
jpayne@69
|
4011
|
|
jpayne@69
|
4012 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self) {
|
|
jpayne@69
|
4013 double __pyx_r;
|
|
jpayne@69
|
4014
|
|
jpayne@69
|
4015 /* "cpython/complex.pxd":20
|
|
jpayne@69
|
4016 * @property
|
|
jpayne@69
|
4017 * cdef inline double real(self) noexcept:
|
|
jpayne@69
|
4018 * return self.cval.real # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4019 *
|
|
jpayne@69
|
4020 * @property
|
|
jpayne@69
|
4021 */
|
|
jpayne@69
|
4022 __pyx_r = __pyx_v_self->cval.real;
|
|
jpayne@69
|
4023 goto __pyx_L0;
|
|
jpayne@69
|
4024
|
|
jpayne@69
|
4025 /* "cpython/complex.pxd":19
|
|
jpayne@69
|
4026 *
|
|
jpayne@69
|
4027 * @property
|
|
jpayne@69
|
4028 * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4029 * return self.cval.real
|
|
jpayne@69
|
4030 *
|
|
jpayne@69
|
4031 */
|
|
jpayne@69
|
4032
|
|
jpayne@69
|
4033 /* function exit code */
|
|
jpayne@69
|
4034 __pyx_L0:;
|
|
jpayne@69
|
4035 return __pyx_r;
|
|
jpayne@69
|
4036 }
|
|
jpayne@69
|
4037
|
|
jpayne@69
|
4038 /* "cpython/complex.pxd":23
|
|
jpayne@69
|
4039 *
|
|
jpayne@69
|
4040 * @property
|
|
jpayne@69
|
4041 * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4042 * return self.cval.imag
|
|
jpayne@69
|
4043 *
|
|
jpayne@69
|
4044 */
|
|
jpayne@69
|
4045
|
|
jpayne@69
|
4046 static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self) {
|
|
jpayne@69
|
4047 double __pyx_r;
|
|
jpayne@69
|
4048
|
|
jpayne@69
|
4049 /* "cpython/complex.pxd":24
|
|
jpayne@69
|
4050 * @property
|
|
jpayne@69
|
4051 * cdef inline double imag(self) noexcept:
|
|
jpayne@69
|
4052 * return self.cval.imag # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4053 *
|
|
jpayne@69
|
4054 * # PyTypeObject PyComplex_Type
|
|
jpayne@69
|
4055 */
|
|
jpayne@69
|
4056 __pyx_r = __pyx_v_self->cval.imag;
|
|
jpayne@69
|
4057 goto __pyx_L0;
|
|
jpayne@69
|
4058
|
|
jpayne@69
|
4059 /* "cpython/complex.pxd":23
|
|
jpayne@69
|
4060 *
|
|
jpayne@69
|
4061 * @property
|
|
jpayne@69
|
4062 * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4063 * return self.cval.imag
|
|
jpayne@69
|
4064 *
|
|
jpayne@69
|
4065 */
|
|
jpayne@69
|
4066
|
|
jpayne@69
|
4067 /* function exit code */
|
|
jpayne@69
|
4068 __pyx_L0:;
|
|
jpayne@69
|
4069 return __pyx_r;
|
|
jpayne@69
|
4070 }
|
|
jpayne@69
|
4071
|
|
jpayne@69
|
4072 /* "cpython/contextvars.pxd":112
|
|
jpayne@69
|
4073 *
|
|
jpayne@69
|
4074 *
|
|
jpayne@69
|
4075 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4076 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
4077 * or the default value of the context variable,
|
|
jpayne@69
|
4078 */
|
|
jpayne@69
|
4079
|
|
jpayne@69
|
4080 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
|
4081 PyObject *__pyx_v_default_value = ((PyObject *)Py_None);
|
|
jpayne@69
|
4082 PyObject *__pyx_v_value;
|
|
jpayne@69
|
4083 PyObject *__pyx_v_pyvalue = NULL;
|
|
jpayne@69
|
4084 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
4085 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
4086 int __pyx_t_1;
|
|
jpayne@69
|
4087 int __pyx_t_2;
|
|
jpayne@69
|
4088 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
4089 int __pyx_lineno = 0;
|
|
jpayne@69
|
4090 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4091 int __pyx_clineno = 0;
|
|
jpayne@69
|
4092 __Pyx_RefNannySetupContext("get_value", 1);
|
|
jpayne@69
|
4093 if (__pyx_optional_args) {
|
|
jpayne@69
|
4094 if (__pyx_optional_args->__pyx_n > 0) {
|
|
jpayne@69
|
4095 __pyx_v_default_value = __pyx_optional_args->default_value;
|
|
jpayne@69
|
4096 }
|
|
jpayne@69
|
4097 }
|
|
jpayne@69
|
4098
|
|
jpayne@69
|
4099 /* "cpython/contextvars.pxd":117
|
|
jpayne@69
|
4100 * or None if no such value or default was found.
|
|
jpayne@69
|
4101 * """
|
|
jpayne@69
|
4102 * cdef PyObject *value = NULL # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4103 * PyContextVar_Get(var, NULL, &value)
|
|
jpayne@69
|
4104 * if value is NULL:
|
|
jpayne@69
|
4105 */
|
|
jpayne@69
|
4106 __pyx_v_value = NULL;
|
|
jpayne@69
|
4107
|
|
jpayne@69
|
4108 /* "cpython/contextvars.pxd":118
|
|
jpayne@69
|
4109 * """
|
|
jpayne@69
|
4110 * cdef PyObject *value = NULL
|
|
jpayne@69
|
4111 * PyContextVar_Get(var, NULL, &value) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4112 * if value is NULL:
|
|
jpayne@69
|
4113 * # context variable does not have a default
|
|
jpayne@69
|
4114 */
|
|
jpayne@69
|
4115 __pyx_t_1 = PyContextVar_Get(__pyx_v_var, NULL, (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(1, 118, __pyx_L1_error)
|
|
jpayne@69
|
4116
|
|
jpayne@69
|
4117 /* "cpython/contextvars.pxd":119
|
|
jpayne@69
|
4118 * cdef PyObject *value = NULL
|
|
jpayne@69
|
4119 * PyContextVar_Get(var, NULL, &value)
|
|
jpayne@69
|
4120 * if value is NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4121 * # context variable does not have a default
|
|
jpayne@69
|
4122 * pyvalue = default_value
|
|
jpayne@69
|
4123 */
|
|
jpayne@69
|
4124 __pyx_t_2 = (__pyx_v_value == NULL);
|
|
jpayne@69
|
4125 if (__pyx_t_2) {
|
|
jpayne@69
|
4126
|
|
jpayne@69
|
4127 /* "cpython/contextvars.pxd":121
|
|
jpayne@69
|
4128 * if value is NULL:
|
|
jpayne@69
|
4129 * # context variable does not have a default
|
|
jpayne@69
|
4130 * pyvalue = default_value # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4131 * else:
|
|
jpayne@69
|
4132 * # value or default value of context variable
|
|
jpayne@69
|
4133 */
|
|
jpayne@69
|
4134 __Pyx_INCREF(__pyx_v_default_value);
|
|
jpayne@69
|
4135 __pyx_v_pyvalue = __pyx_v_default_value;
|
|
jpayne@69
|
4136
|
|
jpayne@69
|
4137 /* "cpython/contextvars.pxd":119
|
|
jpayne@69
|
4138 * cdef PyObject *value = NULL
|
|
jpayne@69
|
4139 * PyContextVar_Get(var, NULL, &value)
|
|
jpayne@69
|
4140 * if value is NULL: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4141 * # context variable does not have a default
|
|
jpayne@69
|
4142 * pyvalue = default_value
|
|
jpayne@69
|
4143 */
|
|
jpayne@69
|
4144 goto __pyx_L3;
|
|
jpayne@69
|
4145 }
|
|
jpayne@69
|
4146
|
|
jpayne@69
|
4147 /* "cpython/contextvars.pxd":124
|
|
jpayne@69
|
4148 * else:
|
|
jpayne@69
|
4149 * # value or default value of context variable
|
|
jpayne@69
|
4150 * pyvalue = <object>value # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4151 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
4152 * return pyvalue
|
|
jpayne@69
|
4153 */
|
|
jpayne@69
|
4154 /*else*/ {
|
|
jpayne@69
|
4155 __pyx_t_3 = ((PyObject *)__pyx_v_value);
|
|
jpayne@69
|
4156 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
4157 __pyx_v_pyvalue = __pyx_t_3;
|
|
jpayne@69
|
4158 __pyx_t_3 = 0;
|
|
jpayne@69
|
4159
|
|
jpayne@69
|
4160 /* "cpython/contextvars.pxd":125
|
|
jpayne@69
|
4161 * # value or default value of context variable
|
|
jpayne@69
|
4162 * pyvalue = <object>value
|
|
jpayne@69
|
4163 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4164 * return pyvalue
|
|
jpayne@69
|
4165 *
|
|
jpayne@69
|
4166 */
|
|
jpayne@69
|
4167 Py_XDECREF(__pyx_v_value);
|
|
jpayne@69
|
4168 }
|
|
jpayne@69
|
4169 __pyx_L3:;
|
|
jpayne@69
|
4170
|
|
jpayne@69
|
4171 /* "cpython/contextvars.pxd":126
|
|
jpayne@69
|
4172 * pyvalue = <object>value
|
|
jpayne@69
|
4173 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
4174 * return pyvalue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4175 *
|
|
jpayne@69
|
4176 *
|
|
jpayne@69
|
4177 */
|
|
jpayne@69
|
4178 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
4179 __Pyx_INCREF(__pyx_v_pyvalue);
|
|
jpayne@69
|
4180 __pyx_r = __pyx_v_pyvalue;
|
|
jpayne@69
|
4181 goto __pyx_L0;
|
|
jpayne@69
|
4182
|
|
jpayne@69
|
4183 /* "cpython/contextvars.pxd":112
|
|
jpayne@69
|
4184 *
|
|
jpayne@69
|
4185 *
|
|
jpayne@69
|
4186 * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4187 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
4188 * or the default value of the context variable,
|
|
jpayne@69
|
4189 */
|
|
jpayne@69
|
4190
|
|
jpayne@69
|
4191 /* function exit code */
|
|
jpayne@69
|
4192 __pyx_L1_error:;
|
|
jpayne@69
|
4193 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
4194 __Pyx_AddTraceback("cpython.contextvars.get_value", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
4195 __pyx_r = 0;
|
|
jpayne@69
|
4196 __pyx_L0:;
|
|
jpayne@69
|
4197 __Pyx_XDECREF(__pyx_v_pyvalue);
|
|
jpayne@69
|
4198 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
4199 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
4200 return __pyx_r;
|
|
jpayne@69
|
4201 }
|
|
jpayne@69
|
4202
|
|
jpayne@69
|
4203 /* "cpython/contextvars.pxd":129
|
|
jpayne@69
|
4204 *
|
|
jpayne@69
|
4205 *
|
|
jpayne@69
|
4206 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4207 * """Return a new reference to the value of the context variable,
|
|
jpayne@69
|
4208 * or the provided default value if no such value was found.
|
|
jpayne@69
|
4209 */
|
|
jpayne@69
|
4210
|
|
jpayne@69
|
4211 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
|
4212 PyObject *__pyx_v_default_value = ((PyObject *)Py_None);
|
|
jpayne@69
|
4213 PyObject *__pyx_v_value;
|
|
jpayne@69
|
4214 PyObject *__pyx_v_pyvalue = NULL;
|
|
jpayne@69
|
4215 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
4216 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
4217 int __pyx_t_1;
|
|
jpayne@69
|
4218 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
4219 int __pyx_lineno = 0;
|
|
jpayne@69
|
4220 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4221 int __pyx_clineno = 0;
|
|
jpayne@69
|
4222 __Pyx_RefNannySetupContext("get_value_no_default", 1);
|
|
jpayne@69
|
4223 if (__pyx_optional_args) {
|
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jpayne@69
|
4224 if (__pyx_optional_args->__pyx_n > 0) {
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jpayne@69
|
4225 __pyx_v_default_value = __pyx_optional_args->default_value;
|
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jpayne@69
|
4226 }
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|
jpayne@69
|
4227 }
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|
jpayne@69
|
4228
|
|
jpayne@69
|
4229 /* "cpython/contextvars.pxd":135
|
|
jpayne@69
|
4230 * Ignores the default value of the context variable, if any.
|
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jpayne@69
|
4231 * """
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jpayne@69
|
4232 * cdef PyObject *value = NULL # <<<<<<<<<<<<<<
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|
jpayne@69
|
4233 * PyContextVar_Get(var, <PyObject*>default_value, &value)
|
|
jpayne@69
|
4234 * # value of context variable or 'default_value'
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jpayne@69
|
4235 */
|
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jpayne@69
|
4236 __pyx_v_value = NULL;
|
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jpayne@69
|
4237
|
|
jpayne@69
|
4238 /* "cpython/contextvars.pxd":136
|
|
jpayne@69
|
4239 * """
|
|
jpayne@69
|
4240 * cdef PyObject *value = NULL
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jpayne@69
|
4241 * PyContextVar_Get(var, <PyObject*>default_value, &value) # <<<<<<<<<<<<<<
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jpayne@69
|
4242 * # value of context variable or 'default_value'
|
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jpayne@69
|
4243 * pyvalue = <object>value
|
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jpayne@69
|
4244 */
|
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jpayne@69
|
4245 __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(1, 136, __pyx_L1_error)
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jpayne@69
|
4246
|
|
jpayne@69
|
4247 /* "cpython/contextvars.pxd":138
|
|
jpayne@69
|
4248 * PyContextVar_Get(var, <PyObject*>default_value, &value)
|
|
jpayne@69
|
4249 * # value of context variable or 'default_value'
|
|
jpayne@69
|
4250 * pyvalue = <object>value # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4251 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
|
|
jpayne@69
|
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|
|
jpayne@69
|
4253 */
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|
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jpayne@69
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4257 __pyx_t_2 = 0;
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jpayne@69
|
4258
|
|
jpayne@69
|
4259 /* "cpython/contextvars.pxd":139
|
|
jpayne@69
|
4260 * # value of context variable or 'default_value'
|
|
jpayne@69
|
4261 * pyvalue = <object>value
|
|
jpayne@69
|
4262 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<<
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|
jpayne@69
|
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|
|
jpayne@69
|
4264 */
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jpayne@69
|
4265 Py_XDECREF(__pyx_v_value);
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jpayne@69
|
4266
|
|
jpayne@69
|
4267 /* "cpython/contextvars.pxd":140
|
|
jpayne@69
|
4268 * pyvalue = <object>value
|
|
jpayne@69
|
4269 * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*'
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jpayne@69
|
4270 * return pyvalue # <<<<<<<<<<<<<<
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jpayne@69
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4271 */
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jpayne@69
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4272 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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4273 __Pyx_INCREF(__pyx_v_pyvalue);
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jpayne@69
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jpayne@69
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4275 goto __pyx_L0;
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jpayne@69
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4276
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jpayne@69
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4277 /* "cpython/contextvars.pxd":129
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jpayne@69
|
4278 *
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|
jpayne@69
|
4279 *
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jpayne@69
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4280 * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<<
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jpayne@69
|
4281 * """Return a new reference to the value of the context variable,
|
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jpayne@69
|
4282 * or the provided default value if no such value was found.
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jpayne@69
|
4283 */
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jpayne@69
|
4284
|
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jpayne@69
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4285 /* function exit code */
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jpayne@69
|
4286 __pyx_L1_error:;
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jpayne@69
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4287 __Pyx_XDECREF(__pyx_t_2);
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jpayne@69
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4288 __Pyx_AddTraceback("cpython.contextvars.get_value_no_default", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
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4289 __pyx_r = 0;
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jpayne@69
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4290 __pyx_L0:;
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jpayne@69
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4293 __Pyx_RefNannyFinishContext();
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jpayne@69
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4294 return __pyx_r;
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jpayne@69
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4295 }
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jpayne@69
|
4296
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jpayne@69
|
4297 /* "array.pxd":104
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jpayne@69
|
4298 * __data_union data
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jpayne@69
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4299 *
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jpayne@69
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4300 * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
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jpayne@69
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4301 * # This implementation of getbuffer is geared towards Cython
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jpayne@69
|
4302 * # requirements, and does not yet fulfill the PEP.
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jpayne@69
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4303 */
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jpayne@69
|
4304
|
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jpayne@69
|
4305 /* Python wrapper */
|
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jpayne@69
|
4306 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*/
|
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jpayne@69
|
4307 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
|
4308 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
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jpayne@69
|
4309 int __pyx_r;
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jpayne@69
|
4310 __Pyx_RefNannyDeclarations
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jpayne@69
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4311 __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0);
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jpayne@69
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jpayne@69
|
4313 __pyx_r = __pyx_pf_7cpython_5array_5array___getbuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags));
|
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jpayne@69
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4314
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jpayne@69
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4315 /* function exit code */
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jpayne@69
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4316 __Pyx_RefNannyFinishContext();
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jpayne@69
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4317 return __pyx_r;
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jpayne@69
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4318 }
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jpayne@69
|
4319
|
|
jpayne@69
|
4320 static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags) {
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jpayne@69
|
4321 PyObject *__pyx_v_item_count = NULL;
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jpayne@69
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4322 int __pyx_r;
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jpayne@69
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4323 __Pyx_RefNannyDeclarations
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jpayne@69
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4324 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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4325 char *__pyx_t_2;
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jpayne@69
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4326 int __pyx_t_3;
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jpayne@69
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4327 PyObject *__pyx_t_4 = NULL;
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jpayne@69
|
4328 Py_ssize_t __pyx_t_5;
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jpayne@69
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4329 int __pyx_t_6;
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jpayne@69
|
4330 char __pyx_t_7;
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jpayne@69
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4331 int __pyx_lineno = 0;
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jpayne@69
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4332 const char *__pyx_filename = NULL;
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jpayne@69
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4333 int __pyx_clineno = 0;
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jpayne@69
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4334 if (unlikely(__pyx_v_info == NULL)) {
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jpayne@69
|
4335 PyErr_SetString(PyExc_BufferError, "PyObject_GetBuffer: view==NULL argument is obsolete");
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jpayne@69
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4336 return -1;
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jpayne@69
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4337 }
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jpayne@69
|
4338 __Pyx_RefNannySetupContext("__getbuffer__", 0);
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jpayne@69
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4339 __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None);
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jpayne@69
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4340 __Pyx_GIVEREF(__pyx_v_info->obj);
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jpayne@69
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4341
|
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jpayne@69
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4342 /* "array.pxd":109
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jpayne@69
|
4343 * # In particular strided access is always provided regardless
|
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jpayne@69
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4344 * # of flags
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jpayne@69
|
4345 * item_count = Py_SIZE(self) # <<<<<<<<<<<<<<
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jpayne@69
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4346 *
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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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4352 __pyx_t_1 = 0;
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jpayne@69
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4353
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jpayne@69
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4354 /* "array.pxd":111
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jpayne@69
|
4355 * item_count = Py_SIZE(self)
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jpayne@69
|
4356 *
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jpayne@69
|
4357 * info.suboffsets = NULL # <<<<<<<<<<<<<<
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jpayne@69
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4358 * info.buf = self.data.as_chars
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jpayne@69
|
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jpayne@69
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4360 */
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jpayne@69
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4361 __pyx_v_info->suboffsets = NULL;
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jpayne@69
|
4362
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jpayne@69
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4363 /* "array.pxd":112
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jpayne@69
|
4364 *
|
|
jpayne@69
|
4365 * info.suboffsets = NULL
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jpayne@69
|
4366 * info.buf = self.data.as_chars # <<<<<<<<<<<<<<
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jpayne@69
|
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jpayne@69
|
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jpayne@69
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4369 */
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jpayne@69
|
4370 __pyx_t_2 = __pyx_v_self->data.as_chars;
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jpayne@69
|
4371 __pyx_v_info->buf = __pyx_t_2;
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jpayne@69
|
4372
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jpayne@69
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4373 /* "array.pxd":113
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|
jpayne@69
|
4374 * info.suboffsets = NULL
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jpayne@69
|
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|
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jpayne@69
|
4376 * info.readonly = 0 # <<<<<<<<<<<<<<
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jpayne@69
|
4377 * info.ndim = 1
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jpayne@69
|
4378 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
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jpayne@69
|
4379 */
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jpayne@69
|
4380 __pyx_v_info->readonly = 0;
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jpayne@69
|
4381
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jpayne@69
|
4382 /* "array.pxd":114
|
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jpayne@69
|
4383 * info.buf = self.data.as_chars
|
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jpayne@69
|
4384 * info.readonly = 0
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jpayne@69
|
4385 * info.ndim = 1 # <<<<<<<<<<<<<<
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jpayne@69
|
4386 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
|
|
jpayne@69
|
4387 * info.len = info.itemsize * item_count
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jpayne@69
|
4388 */
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jpayne@69
|
4389 __pyx_v_info->ndim = 1;
|
|
jpayne@69
|
4390
|
|
jpayne@69
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4391 /* "array.pxd":115
|
|
jpayne@69
|
4392 * info.readonly = 0
|
|
jpayne@69
|
4393 * info.ndim = 1
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|
jpayne@69
|
4394 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4395 * info.len = info.itemsize * item_count
|
|
jpayne@69
|
4396 *
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|
jpayne@69
|
4397 */
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jpayne@69
|
4398 __pyx_t_3 = __pyx_v_self->ob_descr->itemsize;
|
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jpayne@69
|
4399 __pyx_v_info->itemsize = __pyx_t_3;
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jpayne@69
|
4400
|
|
jpayne@69
|
4401 /* "array.pxd":116
|
|
jpayne@69
|
4402 * info.ndim = 1
|
|
jpayne@69
|
4403 * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float)
|
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jpayne@69
|
4404 * info.len = info.itemsize * item_count # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4405 *
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|
jpayne@69
|
4406 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
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jpayne@69
|
4407 */
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jpayne@69
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jpayne@69
|
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jpayne@69
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4410 __pyx_t_4 = PyNumber_Multiply(__pyx_t_1, __pyx_v_item_count); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 116, __pyx_L1_error)
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jpayne@69
|
4411 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
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4412 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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4413 __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 116, __pyx_L1_error)
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jpayne@69
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4414 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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jpayne@69
|
4415 __pyx_v_info->len = __pyx_t_5;
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jpayne@69
|
4416
|
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jpayne@69
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4417 /* "array.pxd":118
|
|
jpayne@69
|
4418 * info.len = info.itemsize * item_count
|
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jpayne@69
|
4419 *
|
|
jpayne@69
|
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jpayne@69
|
4421 * if not info.shape:
|
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jpayne@69
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|
|
jpayne@69
|
4423 */
|
|
jpayne@69
|
4424 __pyx_v_info->shape = ((Py_ssize_t *)PyObject_Malloc(((sizeof(Py_ssize_t)) + 2)));
|
|
jpayne@69
|
4425
|
|
jpayne@69
|
4426 /* "array.pxd":119
|
|
jpayne@69
|
4427 *
|
|
jpayne@69
|
4428 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
|
jpayne@69
|
4429 * if not info.shape: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4430 * raise MemoryError()
|
|
jpayne@69
|
4431 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
4432 */
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|
jpayne@69
|
4433 __pyx_t_6 = (!(__pyx_v_info->shape != 0));
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|
jpayne@69
|
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|
|
jpayne@69
|
4435
|
|
jpayne@69
|
4436 /* "array.pxd":120
|
|
jpayne@69
|
4437 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
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|
jpayne@69
|
4438 * if not info.shape:
|
|
jpayne@69
|
4439 * raise MemoryError() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4440 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
4441 * info.strides = &info.itemsize
|
|
jpayne@69
|
4442 */
|
|
jpayne@69
|
4443 PyErr_NoMemory(); __PYX_ERR(2, 120, __pyx_L1_error)
|
|
jpayne@69
|
4444
|
|
jpayne@69
|
4445 /* "array.pxd":119
|
|
jpayne@69
|
4446 *
|
|
jpayne@69
|
4447 * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2)
|
|
jpayne@69
|
4448 * if not info.shape: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4449 * raise MemoryError()
|
|
jpayne@69
|
4450 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
4451 */
|
|
jpayne@69
|
4452 }
|
|
jpayne@69
|
4453
|
|
jpayne@69
|
4454 /* "array.pxd":121
|
|
jpayne@69
|
4455 * if not info.shape:
|
|
jpayne@69
|
4456 * raise MemoryError()
|
|
jpayne@69
|
4457 * info.shape[0] = item_count # constant regardless of resizing # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4458 * info.strides = &info.itemsize
|
|
jpayne@69
|
4459 *
|
|
jpayne@69
|
4460 */
|
|
jpayne@69
|
4461 __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_item_count); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(2, 121, __pyx_L1_error)
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|
jpayne@69
|
4462 (__pyx_v_info->shape[0]) = __pyx_t_5;
|
|
jpayne@69
|
4463
|
|
jpayne@69
|
4464 /* "array.pxd":122
|
|
jpayne@69
|
4465 * raise MemoryError()
|
|
jpayne@69
|
4466 * info.shape[0] = item_count # constant regardless of resizing
|
|
jpayne@69
|
4467 * info.strides = &info.itemsize # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4468 *
|
|
jpayne@69
|
4469 * info.format = <char*> (info.shape + 1)
|
|
jpayne@69
|
4470 */
|
|
jpayne@69
|
4471 __pyx_v_info->strides = (&__pyx_v_info->itemsize);
|
|
jpayne@69
|
4472
|
|
jpayne@69
|
4473 /* "array.pxd":124
|
|
jpayne@69
|
4474 * info.strides = &info.itemsize
|
|
jpayne@69
|
4475 *
|
|
jpayne@69
|
4476 * info.format = <char*> (info.shape + 1) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4477 * info.format[0] = self.ob_descr.typecode
|
|
jpayne@69
|
4478 * info.format[1] = 0
|
|
jpayne@69
|
4479 */
|
|
jpayne@69
|
4480 __pyx_v_info->format = ((char *)(__pyx_v_info->shape + 1));
|
|
jpayne@69
|
4481
|
|
jpayne@69
|
4482 /* "array.pxd":125
|
|
jpayne@69
|
4483 *
|
|
jpayne@69
|
4484 * info.format = <char*> (info.shape + 1)
|
|
jpayne@69
|
4485 * info.format[0] = self.ob_descr.typecode # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4486 * info.format[1] = 0
|
|
jpayne@69
|
4487 * info.obj = self
|
|
jpayne@69
|
4488 */
|
|
jpayne@69
|
4489 __pyx_t_7 = __pyx_v_self->ob_descr->typecode;
|
|
jpayne@69
|
4490 (__pyx_v_info->format[0]) = __pyx_t_7;
|
|
jpayne@69
|
4491
|
|
jpayne@69
|
4492 /* "array.pxd":126
|
|
jpayne@69
|
4493 * info.format = <char*> (info.shape + 1)
|
|
jpayne@69
|
4494 * info.format[0] = self.ob_descr.typecode
|
|
jpayne@69
|
4495 * info.format[1] = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4496 * info.obj = self
|
|
jpayne@69
|
4497 *
|
|
jpayne@69
|
4498 */
|
|
jpayne@69
|
4499 (__pyx_v_info->format[1]) = 0;
|
|
jpayne@69
|
4500
|
|
jpayne@69
|
4501 /* "array.pxd":127
|
|
jpayne@69
|
4502 * info.format[0] = self.ob_descr.typecode
|
|
jpayne@69
|
4503 * info.format[1] = 0
|
|
jpayne@69
|
4504 * info.obj = self # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4505 *
|
|
jpayne@69
|
4506 * def __releasebuffer__(self, Py_buffer* info):
|
|
jpayne@69
|
4507 */
|
|
jpayne@69
|
4508 __Pyx_INCREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
4509 __Pyx_GIVEREF((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
4510 __Pyx_GOTREF(__pyx_v_info->obj);
|
|
jpayne@69
|
4511 __Pyx_DECREF(__pyx_v_info->obj);
|
|
jpayne@69
|
4512 __pyx_v_info->obj = ((PyObject *)__pyx_v_self);
|
|
jpayne@69
|
4513
|
|
jpayne@69
|
4514 /* "array.pxd":104
|
|
jpayne@69
|
4515 * __data_union data
|
|
jpayne@69
|
4516 *
|
|
jpayne@69
|
4517 * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4518 * # This implementation of getbuffer is geared towards Cython
|
|
jpayne@69
|
4519 * # requirements, and does not yet fulfill the PEP.
|
|
jpayne@69
|
4520 */
|
|
jpayne@69
|
4521
|
|
jpayne@69
|
4522 /* function exit code */
|
|
jpayne@69
|
4523 __pyx_r = 0;
|
|
jpayne@69
|
4524 goto __pyx_L0;
|
|
jpayne@69
|
4525 __pyx_L1_error:;
|
|
jpayne@69
|
4526 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
4527 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
4528 __Pyx_AddTraceback("cpython.array.array.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
4529 __pyx_r = -1;
|
|
jpayne@69
|
4530 if (__pyx_v_info->obj != NULL) {
|
|
jpayne@69
|
4531 __Pyx_GOTREF(__pyx_v_info->obj);
|
|
jpayne@69
|
4532 __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0;
|
|
jpayne@69
|
4533 }
|
|
jpayne@69
|
4534 goto __pyx_L2;
|
|
jpayne@69
|
4535 __pyx_L0:;
|
|
jpayne@69
|
4536 if (__pyx_v_info->obj == Py_None) {
|
|
jpayne@69
|
4537 __Pyx_GOTREF(__pyx_v_info->obj);
|
|
jpayne@69
|
4538 __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0;
|
|
jpayne@69
|
4539 }
|
|
jpayne@69
|
4540 __pyx_L2:;
|
|
jpayne@69
|
4541 __Pyx_XDECREF(__pyx_v_item_count);
|
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jpayne@69
|
4542 __Pyx_RefNannyFinishContext();
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jpayne@69
|
4543 return __pyx_r;
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jpayne@69
|
4544 }
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jpayne@69
|
4545
|
|
jpayne@69
|
4546 /* "array.pxd":129
|
|
jpayne@69
|
4547 * info.obj = self
|
|
jpayne@69
|
4548 *
|
|
jpayne@69
|
4549 * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4550 * PyObject_Free(info.shape)
|
|
jpayne@69
|
4551 *
|
|
jpayne@69
|
4552 */
|
|
jpayne@69
|
4553
|
|
jpayne@69
|
4554 /* Python wrapper */
|
|
jpayne@69
|
4555 CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/
|
|
jpayne@69
|
4556 CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) {
|
|
jpayne@69
|
4557 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
4558 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
4559 __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0);
|
|
jpayne@69
|
4560 __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
4561 __pyx_pf_7cpython_5array_5array_2__releasebuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info));
|
|
jpayne@69
|
4562
|
|
jpayne@69
|
4563 /* function exit code */
|
|
jpayne@69
|
4564 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
4565 }
|
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jpayne@69
|
4566
|
|
jpayne@69
|
4567 static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info) {
|
|
jpayne@69
|
4568
|
|
jpayne@69
|
4569 /* "array.pxd":130
|
|
jpayne@69
|
4570 *
|
|
jpayne@69
|
4571 * def __releasebuffer__(self, Py_buffer* info):
|
|
jpayne@69
|
4572 * PyObject_Free(info.shape) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4573 *
|
|
jpayne@69
|
4574 * array newarrayobject(PyTypeObject* type, Py_ssize_t size, arraydescr *descr)
|
|
jpayne@69
|
4575 */
|
|
jpayne@69
|
4576 PyObject_Free(__pyx_v_info->shape);
|
|
jpayne@69
|
4577
|
|
jpayne@69
|
4578 /* "array.pxd":129
|
|
jpayne@69
|
4579 * info.obj = self
|
|
jpayne@69
|
4580 *
|
|
jpayne@69
|
4581 * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4582 * PyObject_Free(info.shape)
|
|
jpayne@69
|
4583 *
|
|
jpayne@69
|
4584 */
|
|
jpayne@69
|
4585
|
|
jpayne@69
|
4586 /* function exit code */
|
|
jpayne@69
|
4587 }
|
|
jpayne@69
|
4588
|
|
jpayne@69
|
4589 /* "array.pxd":141
|
|
jpayne@69
|
4590 *
|
|
jpayne@69
|
4591 *
|
|
jpayne@69
|
4592 * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4593 * """ fast creation of a new array, given a template array.
|
|
jpayne@69
|
4594 * type will be same as template.
|
|
jpayne@69
|
4595 */
|
|
jpayne@69
|
4596
|
|
jpayne@69
|
4597 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
|
4598 arrayobject *__pyx_v_op = 0;
|
|
jpayne@69
|
4599 arrayobject *__pyx_r = NULL;
|
|
jpayne@69
|
4600 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
4601 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
4602 int __pyx_t_2;
|
|
jpayne@69
|
4603 int __pyx_t_3;
|
|
jpayne@69
|
4604 int __pyx_lineno = 0;
|
|
jpayne@69
|
4605 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4606 int __pyx_clineno = 0;
|
|
jpayne@69
|
4607 __Pyx_RefNannySetupContext("clone", 1);
|
|
jpayne@69
|
4608
|
|
jpayne@69
|
4609 /* "array.pxd":145
|
|
jpayne@69
|
4610 * type will be same as template.
|
|
jpayne@69
|
4611 * if zero is true, new array will be initialized with zeroes."""
|
|
jpayne@69
|
4612 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4613 * if zero and op is not None:
|
|
jpayne@69
|
4614 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
4615 */
|
|
jpayne@69
|
4616 __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(2, 145, __pyx_L1_error)
|
|
jpayne@69
|
4617 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
4618 __pyx_v_op = ((arrayobject *)__pyx_t_1);
|
|
jpayne@69
|
4619 __pyx_t_1 = 0;
|
|
jpayne@69
|
4620
|
|
jpayne@69
|
4621 /* "array.pxd":146
|
|
jpayne@69
|
4622 * if zero is true, new array will be initialized with zeroes."""
|
|
jpayne@69
|
4623 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
|
|
jpayne@69
|
4624 * if zero and op is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4625 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
4626 * return op
|
|
jpayne@69
|
4627 */
|
|
jpayne@69
|
4628 if (__pyx_v_zero) {
|
|
jpayne@69
|
4629 } else {
|
|
jpayne@69
|
4630 __pyx_t_2 = __pyx_v_zero;
|
|
jpayne@69
|
4631 goto __pyx_L4_bool_binop_done;
|
|
jpayne@69
|
4632 }
|
|
jpayne@69
|
4633 __pyx_t_3 = (((PyObject *)__pyx_v_op) != Py_None);
|
|
jpayne@69
|
4634 __pyx_t_2 = __pyx_t_3;
|
|
jpayne@69
|
4635 __pyx_L4_bool_binop_done:;
|
|
jpayne@69
|
4636 if (__pyx_t_2) {
|
|
jpayne@69
|
4637
|
|
jpayne@69
|
4638 /* "array.pxd":147
|
|
jpayne@69
|
4639 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
|
|
jpayne@69
|
4640 * if zero and op is not None:
|
|
jpayne@69
|
4641 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4642 * return op
|
|
jpayne@69
|
4643 *
|
|
jpayne@69
|
4644 */
|
|
jpayne@69
|
4645 (void)(memset(__pyx_v_op->data.as_chars, 0, (__pyx_v_length * __pyx_v_op->ob_descr->itemsize)));
|
|
jpayne@69
|
4646
|
|
jpayne@69
|
4647 /* "array.pxd":146
|
|
jpayne@69
|
4648 * if zero is true, new array will be initialized with zeroes."""
|
|
jpayne@69
|
4649 * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr)
|
|
jpayne@69
|
4650 * if zero and op is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4651 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
4652 * return op
|
|
jpayne@69
|
4653 */
|
|
jpayne@69
|
4654 }
|
|
jpayne@69
|
4655
|
|
jpayne@69
|
4656 /* "array.pxd":148
|
|
jpayne@69
|
4657 * if zero and op is not None:
|
|
jpayne@69
|
4658 * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize)
|
|
jpayne@69
|
4659 * return op # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4660 *
|
|
jpayne@69
|
4661 * cdef inline array copy(array self):
|
|
jpayne@69
|
4662 */
|
|
jpayne@69
|
4663 __Pyx_XDECREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
4664 __Pyx_INCREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
4665 __pyx_r = __pyx_v_op;
|
|
jpayne@69
|
4666 goto __pyx_L0;
|
|
jpayne@69
|
4667
|
|
jpayne@69
|
4668 /* "array.pxd":141
|
|
jpayne@69
|
4669 *
|
|
jpayne@69
|
4670 *
|
|
jpayne@69
|
4671 * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4672 * """ fast creation of a new array, given a template array.
|
|
jpayne@69
|
4673 * type will be same as template.
|
|
jpayne@69
|
4674 */
|
|
jpayne@69
|
4675
|
|
jpayne@69
|
4676 /* function exit code */
|
|
jpayne@69
|
4677 __pyx_L1_error:;
|
|
jpayne@69
|
4678 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
4679 __Pyx_AddTraceback("cpython.array.clone", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
4680 __pyx_r = 0;
|
|
jpayne@69
|
4681 __pyx_L0:;
|
|
jpayne@69
|
4682 __Pyx_XDECREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
4683 __Pyx_XGIVEREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
4684 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
4685 return __pyx_r;
|
|
jpayne@69
|
4686 }
|
|
jpayne@69
|
4687
|
|
jpayne@69
|
4688 /* "array.pxd":150
|
|
jpayne@69
|
4689 * return op
|
|
jpayne@69
|
4690 *
|
|
jpayne@69
|
4691 * cdef inline array copy(array self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4692 * """ make a copy of an array. """
|
|
jpayne@69
|
4693 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
4694 */
|
|
jpayne@69
|
4695
|
|
jpayne@69
|
4696 static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_copy(arrayobject *__pyx_v_self) {
|
|
jpayne@69
|
4697 arrayobject *__pyx_v_op = 0;
|
|
jpayne@69
|
4698 arrayobject *__pyx_r = NULL;
|
|
jpayne@69
|
4699 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
4700 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
4701 int __pyx_lineno = 0;
|
|
jpayne@69
|
4702 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4703 int __pyx_clineno = 0;
|
|
jpayne@69
|
4704 __Pyx_RefNannySetupContext("copy", 1);
|
|
jpayne@69
|
4705
|
|
jpayne@69
|
4706 /* "array.pxd":152
|
|
jpayne@69
|
4707 * cdef inline array copy(array self):
|
|
jpayne@69
|
4708 * """ make a copy of an array. """
|
|
jpayne@69
|
4709 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4710 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize)
|
|
jpayne@69
|
4711 * return op
|
|
jpayne@69
|
4712 */
|
|
jpayne@69
|
4713 __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(2, 152, __pyx_L1_error)
|
|
jpayne@69
|
4714 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
4715 __pyx_v_op = ((arrayobject *)__pyx_t_1);
|
|
jpayne@69
|
4716 __pyx_t_1 = 0;
|
|
jpayne@69
|
4717
|
|
jpayne@69
|
4718 /* "array.pxd":153
|
|
jpayne@69
|
4719 * """ make a copy of an array. """
|
|
jpayne@69
|
4720 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
4721 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4722 * return op
|
|
jpayne@69
|
4723 *
|
|
jpayne@69
|
4724 */
|
|
jpayne@69
|
4725 (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
|
4726
|
|
jpayne@69
|
4727 /* "array.pxd":154
|
|
jpayne@69
|
4728 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
4729 * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize)
|
|
jpayne@69
|
4730 * return op # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4731 *
|
|
jpayne@69
|
4732 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1:
|
|
jpayne@69
|
4733 */
|
|
jpayne@69
|
4734 __Pyx_XDECREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
4735 __Pyx_INCREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
4736 __pyx_r = __pyx_v_op;
|
|
jpayne@69
|
4737 goto __pyx_L0;
|
|
jpayne@69
|
4738
|
|
jpayne@69
|
4739 /* "array.pxd":150
|
|
jpayne@69
|
4740 * return op
|
|
jpayne@69
|
4741 *
|
|
jpayne@69
|
4742 * cdef inline array copy(array self): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4743 * """ make a copy of an array. """
|
|
jpayne@69
|
4744 * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr)
|
|
jpayne@69
|
4745 */
|
|
jpayne@69
|
4746
|
|
jpayne@69
|
4747 /* function exit code */
|
|
jpayne@69
|
4748 __pyx_L1_error:;
|
|
jpayne@69
|
4749 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
4750 __Pyx_AddTraceback("cpython.array.copy", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
4751 __pyx_r = 0;
|
|
jpayne@69
|
4752 __pyx_L0:;
|
|
jpayne@69
|
4753 __Pyx_XDECREF((PyObject *)__pyx_v_op);
|
|
jpayne@69
|
4754 __Pyx_XGIVEREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
4755 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
4756 return __pyx_r;
|
|
jpayne@69
|
4757 }
|
|
jpayne@69
|
4758
|
|
jpayne@69
|
4759 /* "array.pxd":156
|
|
jpayne@69
|
4760 * return op
|
|
jpayne@69
|
4761 *
|
|
jpayne@69
|
4762 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4763 * """ efficient appending of new stuff of same type
|
|
jpayne@69
|
4764 * (e.g. of same array type)
|
|
jpayne@69
|
4765 */
|
|
jpayne@69
|
4766
|
|
jpayne@69
|
4767 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
|
4768 Py_ssize_t __pyx_v_itemsize;
|
|
jpayne@69
|
4769 Py_ssize_t __pyx_v_origsize;
|
|
jpayne@69
|
4770 int __pyx_r;
|
|
jpayne@69
|
4771 int __pyx_t_1;
|
|
jpayne@69
|
4772 int __pyx_lineno = 0;
|
|
jpayne@69
|
4773 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4774 int __pyx_clineno = 0;
|
|
jpayne@69
|
4775
|
|
jpayne@69
|
4776 /* "array.pxd":160
|
|
jpayne@69
|
4777 * (e.g. of same array type)
|
|
jpayne@69
|
4778 * n: number of elements (not number of bytes!) """
|
|
jpayne@69
|
4779 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4780 * cdef Py_ssize_t origsize = Py_SIZE(self)
|
|
jpayne@69
|
4781 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
4782 */
|
|
jpayne@69
|
4783 __pyx_t_1 = __pyx_v_self->ob_descr->itemsize;
|
|
jpayne@69
|
4784 __pyx_v_itemsize = __pyx_t_1;
|
|
jpayne@69
|
4785
|
|
jpayne@69
|
4786 /* "array.pxd":161
|
|
jpayne@69
|
4787 * n: number of elements (not number of bytes!) """
|
|
jpayne@69
|
4788 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize
|
|
jpayne@69
|
4789 * cdef Py_ssize_t origsize = Py_SIZE(self) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4790 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
4791 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
|
|
jpayne@69
|
4792 */
|
|
jpayne@69
|
4793 __pyx_v_origsize = Py_SIZE(((PyObject *)__pyx_v_self));
|
|
jpayne@69
|
4794
|
|
jpayne@69
|
4795 /* "array.pxd":162
|
|
jpayne@69
|
4796 * cdef Py_ssize_t itemsize = self.ob_descr.itemsize
|
|
jpayne@69
|
4797 * cdef Py_ssize_t origsize = Py_SIZE(self)
|
|
jpayne@69
|
4798 * resize_smart(self, origsize + n) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4799 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
|
|
jpayne@69
|
4800 * return 0
|
|
jpayne@69
|
4801 */
|
|
jpayne@69
|
4802 __pyx_t_1 = resize_smart(__pyx_v_self, (__pyx_v_origsize + __pyx_v_n)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 162, __pyx_L1_error)
|
|
jpayne@69
|
4803
|
|
jpayne@69
|
4804 /* "array.pxd":163
|
|
jpayne@69
|
4805 * cdef Py_ssize_t origsize = Py_SIZE(self)
|
|
jpayne@69
|
4806 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
4807 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4808 * return 0
|
|
jpayne@69
|
4809 *
|
|
jpayne@69
|
4810 */
|
|
jpayne@69
|
4811 (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
|
4812
|
|
jpayne@69
|
4813 /* "array.pxd":164
|
|
jpayne@69
|
4814 * resize_smart(self, origsize + n)
|
|
jpayne@69
|
4815 * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize)
|
|
jpayne@69
|
4816 * return 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4817 *
|
|
jpayne@69
|
4818 * cdef inline int extend(array self, array other) except -1:
|
|
jpayne@69
|
4819 */
|
|
jpayne@69
|
4820 __pyx_r = 0;
|
|
jpayne@69
|
4821 goto __pyx_L0;
|
|
jpayne@69
|
4822
|
|
jpayne@69
|
4823 /* "array.pxd":156
|
|
jpayne@69
|
4824 * return op
|
|
jpayne@69
|
4825 *
|
|
jpayne@69
|
4826 * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4827 * """ efficient appending of new stuff of same type
|
|
jpayne@69
|
4828 * (e.g. of same array type)
|
|
jpayne@69
|
4829 */
|
|
jpayne@69
|
4830
|
|
jpayne@69
|
4831 /* function exit code */
|
|
jpayne@69
|
4832 __pyx_L1_error:;
|
|
jpayne@69
|
4833 __Pyx_AddTraceback("cpython.array.extend_buffer", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
4834 __pyx_r = -1;
|
|
jpayne@69
|
4835 __pyx_L0:;
|
|
jpayne@69
|
4836 return __pyx_r;
|
|
jpayne@69
|
4837 }
|
|
jpayne@69
|
4838
|
|
jpayne@69
|
4839 /* "array.pxd":166
|
|
jpayne@69
|
4840 * return 0
|
|
jpayne@69
|
4841 *
|
|
jpayne@69
|
4842 * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4843 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
4844 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
4845 */
|
|
jpayne@69
|
4846
|
|
jpayne@69
|
4847 static CYTHON_INLINE int __pyx_f_7cpython_5array_extend(arrayobject *__pyx_v_self, arrayobject *__pyx_v_other) {
|
|
jpayne@69
|
4848 int __pyx_r;
|
|
jpayne@69
|
4849 int __pyx_t_1;
|
|
jpayne@69
|
4850 int __pyx_t_2;
|
|
jpayne@69
|
4851 int __pyx_lineno = 0;
|
|
jpayne@69
|
4852 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4853 int __pyx_clineno = 0;
|
|
jpayne@69
|
4854
|
|
jpayne@69
|
4855 /* "array.pxd":168
|
|
jpayne@69
|
4856 * cdef inline int extend(array self, array other) except -1:
|
|
jpayne@69
|
4857 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
4858 * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4859 * PyErr_BadArgument()
|
|
jpayne@69
|
4860 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
4861 */
|
|
jpayne@69
|
4862 __pyx_t_1 = (__pyx_v_self->ob_descr->typecode != __pyx_v_other->ob_descr->typecode);
|
|
jpayne@69
|
4863 if (__pyx_t_1) {
|
|
jpayne@69
|
4864
|
|
jpayne@69
|
4865 /* "array.pxd":169
|
|
jpayne@69
|
4866 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
4867 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
4868 * PyErr_BadArgument() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4869 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
4870 *
|
|
jpayne@69
|
4871 */
|
|
jpayne@69
|
4872 __pyx_t_2 = PyErr_BadArgument(); if (unlikely(__pyx_t_2 == ((int)0))) __PYX_ERR(2, 169, __pyx_L1_error)
|
|
jpayne@69
|
4873
|
|
jpayne@69
|
4874 /* "array.pxd":168
|
|
jpayne@69
|
4875 * cdef inline int extend(array self, array other) except -1:
|
|
jpayne@69
|
4876 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
4877 * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4878 * PyErr_BadArgument()
|
|
jpayne@69
|
4879 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
4880 */
|
|
jpayne@69
|
4881 }
|
|
jpayne@69
|
4882
|
|
jpayne@69
|
4883 /* "array.pxd":170
|
|
jpayne@69
|
4884 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
4885 * PyErr_BadArgument()
|
|
jpayne@69
|
4886 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4887 *
|
|
jpayne@69
|
4888 * cdef inline void zero(array self) noexcept:
|
|
jpayne@69
|
4889 */
|
|
jpayne@69
|
4890 __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(2, 170, __pyx_L1_error)
|
|
jpayne@69
|
4891 __pyx_r = __pyx_t_2;
|
|
jpayne@69
|
4892 goto __pyx_L0;
|
|
jpayne@69
|
4893
|
|
jpayne@69
|
4894 /* "array.pxd":166
|
|
jpayne@69
|
4895 * return 0
|
|
jpayne@69
|
4896 *
|
|
jpayne@69
|
4897 * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4898 * """ extend array with data from another array; types must match. """
|
|
jpayne@69
|
4899 * if self.ob_descr.typecode != other.ob_descr.typecode:
|
|
jpayne@69
|
4900 */
|
|
jpayne@69
|
4901
|
|
jpayne@69
|
4902 /* function exit code */
|
|
jpayne@69
|
4903 __pyx_L1_error:;
|
|
jpayne@69
|
4904 __Pyx_AddTraceback("cpython.array.extend", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
4905 __pyx_r = -1;
|
|
jpayne@69
|
4906 __pyx_L0:;
|
|
jpayne@69
|
4907 return __pyx_r;
|
|
jpayne@69
|
4908 }
|
|
jpayne@69
|
4909
|
|
jpayne@69
|
4910 /* "array.pxd":172
|
|
jpayne@69
|
4911 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
4912 *
|
|
jpayne@69
|
4913 * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4914 * """ set all elements of array to zero. """
|
|
jpayne@69
|
4915 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize)
|
|
jpayne@69
|
4916 */
|
|
jpayne@69
|
4917
|
|
jpayne@69
|
4918 static CYTHON_INLINE void __pyx_f_7cpython_5array_zero(arrayobject *__pyx_v_self) {
|
|
jpayne@69
|
4919
|
|
jpayne@69
|
4920 /* "array.pxd":174
|
|
jpayne@69
|
4921 * cdef inline void zero(array self) noexcept:
|
|
jpayne@69
|
4922 * """ set all elements of array to zero. """
|
|
jpayne@69
|
4923 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4924 */
|
|
jpayne@69
|
4925 (void)(memset(__pyx_v_self->data.as_chars, 0, (Py_SIZE(((PyObject *)__pyx_v_self)) * __pyx_v_self->ob_descr->itemsize)));
|
|
jpayne@69
|
4926
|
|
jpayne@69
|
4927 /* "array.pxd":172
|
|
jpayne@69
|
4928 * return extend_buffer(self, other.data.as_chars, Py_SIZE(other))
|
|
jpayne@69
|
4929 *
|
|
jpayne@69
|
4930 * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4931 * """ set all elements of array to zero. """
|
|
jpayne@69
|
4932 * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize)
|
|
jpayne@69
|
4933 */
|
|
jpayne@69
|
4934
|
|
jpayne@69
|
4935 /* function exit code */
|
|
jpayne@69
|
4936 }
|
|
jpayne@69
|
4937
|
|
jpayne@69
|
4938 /* "pysam/libcutils.pyx":36
|
|
jpayne@69
|
4939 * #################################################################
|
|
jpayne@69
|
4940 * # Utility functions for quality string conversions
|
|
jpayne@69
|
4941 * cpdef c_array.array qualitystring_to_array(input_str, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4942 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
4943 * if input_str is None:
|
|
jpayne@69
|
4944 */
|
|
jpayne@69
|
4945
|
|
jpayne@69
|
4946 static PyObject *__pyx_pw_5pysam_9libcutils_1qualitystring_to_array(PyObject *__pyx_self,
|
|
jpayne@69
|
4947 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
4948 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
4949 #else
|
|
jpayne@69
|
4950 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
4951 #endif
|
|
jpayne@69
|
4952 ); /*proto*/
|
|
jpayne@69
|
4953 static arrayobject *__pyx_f_5pysam_9libcutils_qualitystring_to_array(PyObject *__pyx_v_input_str, CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array *__pyx_optional_args) {
|
|
jpayne@69
|
4954 int __pyx_v_offset = ((int)33);
|
|
jpayne@69
|
4955 PyObject *__pyx_v_qs = NULL;
|
|
jpayne@69
|
4956 char __pyx_7genexpr__pyx_v_i;
|
|
jpayne@69
|
4957 arrayobject *__pyx_r = NULL;
|
|
jpayne@69
|
4958 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
4959 int __pyx_t_1;
|
|
jpayne@69
|
4960 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
4961 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
4962 char *__pyx_t_4;
|
|
jpayne@69
|
4963 char *__pyx_t_5;
|
|
jpayne@69
|
4964 char *__pyx_t_6;
|
|
jpayne@69
|
4965 char *__pyx_t_7;
|
|
jpayne@69
|
4966 PyObject *__pyx_t_8 = NULL;
|
|
jpayne@69
|
4967 int __pyx_lineno = 0;
|
|
jpayne@69
|
4968 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
4969 int __pyx_clineno = 0;
|
|
jpayne@69
|
4970 __Pyx_RefNannySetupContext("qualitystring_to_array", 1);
|
|
jpayne@69
|
4971 if (__pyx_optional_args) {
|
|
jpayne@69
|
4972 if (__pyx_optional_args->__pyx_n > 0) {
|
|
jpayne@69
|
4973 __pyx_v_offset = __pyx_optional_args->offset;
|
|
jpayne@69
|
4974 }
|
|
jpayne@69
|
4975 }
|
|
jpayne@69
|
4976
|
|
jpayne@69
|
4977 /* "pysam/libcutils.pyx":38
|
|
jpayne@69
|
4978 * cpdef c_array.array qualitystring_to_array(input_str, int offset=33):
|
|
jpayne@69
|
4979 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
4980 * if input_str is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4981 * return None
|
|
jpayne@69
|
4982 * qs = force_bytes(input_str)
|
|
jpayne@69
|
4983 */
|
|
jpayne@69
|
4984 __pyx_t_1 = (__pyx_v_input_str == Py_None);
|
|
jpayne@69
|
4985 if (__pyx_t_1) {
|
|
jpayne@69
|
4986
|
|
jpayne@69
|
4987 /* "pysam/libcutils.pyx":39
|
|
jpayne@69
|
4988 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
4989 * if input_str is None:
|
|
jpayne@69
|
4990 * return None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
4991 * qs = force_bytes(input_str)
|
|
jpayne@69
|
4992 * cdef char i
|
|
jpayne@69
|
4993 */
|
|
jpayne@69
|
4994 __Pyx_XDECREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
4995 __pyx_r = ((arrayobject *)Py_None); __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
4996 goto __pyx_L0;
|
|
jpayne@69
|
4997
|
|
jpayne@69
|
4998 /* "pysam/libcutils.pyx":38
|
|
jpayne@69
|
4999 * cpdef c_array.array qualitystring_to_array(input_str, int offset=33):
|
|
jpayne@69
|
5000 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
5001 * if input_str is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5002 * return None
|
|
jpayne@69
|
5003 * qs = force_bytes(input_str)
|
|
jpayne@69
|
5004 */
|
|
jpayne@69
|
5005 }
|
|
jpayne@69
|
5006
|
|
jpayne@69
|
5007 /* "pysam/libcutils.pyx":40
|
|
jpayne@69
|
5008 * if input_str is None:
|
|
jpayne@69
|
5009 * return None
|
|
jpayne@69
|
5010 * qs = force_bytes(input_str) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5011 * cdef char i
|
|
jpayne@69
|
5012 * return c_array.array('B', [i - offset for i in qs])
|
|
jpayne@69
|
5013 */
|
|
jpayne@69
|
5014 __pyx_t_2 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_input_str, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 40, __pyx_L1_error)
|
|
jpayne@69
|
5015 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
5016 __pyx_v_qs = ((PyObject*)__pyx_t_2);
|
|
jpayne@69
|
5017 __pyx_t_2 = 0;
|
|
jpayne@69
|
5018
|
|
jpayne@69
|
5019 /* "pysam/libcutils.pyx":42
|
|
jpayne@69
|
5020 * qs = force_bytes(input_str)
|
|
jpayne@69
|
5021 * cdef char i
|
|
jpayne@69
|
5022 * return c_array.array('B', [i - offset for i in qs]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5023 *
|
|
jpayne@69
|
5024 *
|
|
jpayne@69
|
5025 */
|
|
jpayne@69
|
5026 __Pyx_XDECREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
5027 { /* enter inner scope */
|
|
jpayne@69
|
5028 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 42, __pyx_L1_error)
|
|
jpayne@69
|
5029 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
5030 if (unlikely(__pyx_v_qs == Py_None)) {
|
|
jpayne@69
|
5031 PyErr_SetString(PyExc_TypeError, "'NoneType' is not iterable");
|
|
jpayne@69
|
5032 __PYX_ERR(0, 42, __pyx_L1_error)
|
|
jpayne@69
|
5033 }
|
|
jpayne@69
|
5034 __Pyx_INCREF(__pyx_v_qs);
|
|
jpayne@69
|
5035 __pyx_t_3 = __pyx_v_qs;
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jpayne@69
|
5036 __pyx_t_5 = PyBytes_AS_STRING(__pyx_t_3);
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jpayne@69
|
5037 __pyx_t_6 = (__pyx_t_5 + PyBytes_GET_SIZE(__pyx_t_3));
|
|
jpayne@69
|
5038 for (__pyx_t_7 = __pyx_t_5; __pyx_t_7 < __pyx_t_6; __pyx_t_7++) {
|
|
jpayne@69
|
5039 __pyx_t_4 = __pyx_t_7;
|
|
jpayne@69
|
5040 __pyx_7genexpr__pyx_v_i = (__pyx_t_4[0]);
|
|
jpayne@69
|
5041 __pyx_t_8 = __Pyx_PyInt_From_int((__pyx_7genexpr__pyx_v_i - __pyx_v_offset)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 42, __pyx_L1_error)
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jpayne@69
|
5042 __Pyx_GOTREF(__pyx_t_8);
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jpayne@69
|
5043 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_8))) __PYX_ERR(0, 42, __pyx_L1_error)
|
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jpayne@69
|
5044 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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jpayne@69
|
5045 }
|
|
jpayne@69
|
5046 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
5047 } /* exit inner scope */
|
|
jpayne@69
|
5048 __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 42, __pyx_L1_error)
|
|
jpayne@69
|
5049 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
5050 __Pyx_INCREF(__pyx_n_u_B);
|
|
jpayne@69
|
5051 __Pyx_GIVEREF(__pyx_n_u_B);
|
|
jpayne@69
|
5052 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_n_u_B)) __PYX_ERR(0, 42, __pyx_L1_error);
|
|
jpayne@69
|
5053 __Pyx_GIVEREF(__pyx_t_2);
|
|
jpayne@69
|
5054 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_2)) __PYX_ERR(0, 42, __pyx_L1_error);
|
|
jpayne@69
|
5055 __pyx_t_2 = 0;
|
|
jpayne@69
|
5056 __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_7cpython_5array_array), __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 42, __pyx_L1_error)
|
|
jpayne@69
|
5057 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
5058 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
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jpayne@69
|
5059 __pyx_r = ((arrayobject *)__pyx_t_2);
|
|
jpayne@69
|
5060 __pyx_t_2 = 0;
|
|
jpayne@69
|
5061 goto __pyx_L0;
|
|
jpayne@69
|
5062
|
|
jpayne@69
|
5063 /* "pysam/libcutils.pyx":36
|
|
jpayne@69
|
5064 * #################################################################
|
|
jpayne@69
|
5065 * # Utility functions for quality string conversions
|
|
jpayne@69
|
5066 * cpdef c_array.array qualitystring_to_array(input_str, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5067 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
5068 * if input_str is None:
|
|
jpayne@69
|
5069 */
|
|
jpayne@69
|
5070
|
|
jpayne@69
|
5071 /* function exit code */
|
|
jpayne@69
|
5072 __pyx_L1_error:;
|
|
jpayne@69
|
5073 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
5074 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
5075 __Pyx_XDECREF(__pyx_t_8);
|
|
jpayne@69
|
5076 __Pyx_AddTraceback("pysam.libcutils.qualitystring_to_array", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
5077 __pyx_r = 0;
|
|
jpayne@69
|
5078 __pyx_L0:;
|
|
jpayne@69
|
5079 __Pyx_XDECREF(__pyx_v_qs);
|
|
jpayne@69
|
5080 __Pyx_XGIVEREF((PyObject *)__pyx_r);
|
|
jpayne@69
|
5081 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
5082 return __pyx_r;
|
|
jpayne@69
|
5083 }
|
|
jpayne@69
|
5084
|
|
jpayne@69
|
5085 /* Python wrapper */
|
|
jpayne@69
|
5086 static PyObject *__pyx_pw_5pysam_9libcutils_1qualitystring_to_array(PyObject *__pyx_self,
|
|
jpayne@69
|
5087 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5088 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5089 #else
|
|
jpayne@69
|
5090 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5091 #endif
|
|
jpayne@69
|
5092 ); /*proto*/
|
|
jpayne@69
|
5093 PyDoc_STRVAR(__pyx_doc_5pysam_9libcutils_qualitystring_to_array, "convert a qualitystring to an array of quality values.");
|
|
jpayne@69
|
5094 static PyMethodDef __pyx_mdef_5pysam_9libcutils_1qualitystring_to_array = {"qualitystring_to_array", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_1qualitystring_to_array, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libcutils_qualitystring_to_array};
|
|
jpayne@69
|
5095 static PyObject *__pyx_pw_5pysam_9libcutils_1qualitystring_to_array(PyObject *__pyx_self,
|
|
jpayne@69
|
5096 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5097 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5098 #else
|
|
jpayne@69
|
5099 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5100 #endif
|
|
jpayne@69
|
5101 ) {
|
|
jpayne@69
|
5102 PyObject *__pyx_v_input_str = 0;
|
|
jpayne@69
|
5103 int __pyx_v_offset;
|
|
jpayne@69
|
5104 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5105 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
5106 #endif
|
|
jpayne@69
|
5107 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
5108 PyObject* values[2] = {0,0};
|
|
jpayne@69
|
5109 int __pyx_lineno = 0;
|
|
jpayne@69
|
5110 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
5111 int __pyx_clineno = 0;
|
|
jpayne@69
|
5112 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
5113 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
5114 __Pyx_RefNannySetupContext("qualitystring_to_array (wrapper)", 0);
|
|
jpayne@69
|
5115 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5116 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
5117 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
5118 #else
|
|
jpayne@69
|
5119 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
5120 #endif
|
|
jpayne@69
|
5121 #endif
|
|
jpayne@69
|
5122 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
5123 {
|
|
jpayne@69
|
5124 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_input_str,&__pyx_n_s_offset,0};
|
|
jpayne@69
|
5125 if (__pyx_kwds) {
|
|
jpayne@69
|
5126 Py_ssize_t kw_args;
|
|
jpayne@69
|
5127 switch (__pyx_nargs) {
|
|
jpayne@69
|
5128 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
5129 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5130 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5131 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5132 case 0: break;
|
|
jpayne@69
|
5133 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5134 }
|
|
jpayne@69
|
5135 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
5136 switch (__pyx_nargs) {
|
|
jpayne@69
|
5137 case 0:
|
|
jpayne@69
|
5138 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_input_str)) != 0)) {
|
|
jpayne@69
|
5139 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
5140 kw_args--;
|
|
jpayne@69
|
5141 }
|
|
jpayne@69
|
5142 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 36, __pyx_L3_error)
|
|
jpayne@69
|
5143 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5144 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5145 case 1:
|
|
jpayne@69
|
5146 if (kw_args > 0) {
|
|
jpayne@69
|
5147 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_offset);
|
|
jpayne@69
|
5148 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
5149 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 36, __pyx_L3_error)
|
|
jpayne@69
|
5150 }
|
|
jpayne@69
|
5151 }
|
|
jpayne@69
|
5152 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
5153 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
5154 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "qualitystring_to_array") < 0)) __PYX_ERR(0, 36, __pyx_L3_error)
|
|
jpayne@69
|
5155 }
|
|
jpayne@69
|
5156 } else {
|
|
jpayne@69
|
5157 switch (__pyx_nargs) {
|
|
jpayne@69
|
5158 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
5159 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5160 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5161 break;
|
|
jpayne@69
|
5162 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5163 }
|
|
jpayne@69
|
5164 }
|
|
jpayne@69
|
5165 __pyx_v_input_str = values[0];
|
|
jpayne@69
|
5166 if (values[1]) {
|
|
jpayne@69
|
5167 __pyx_v_offset = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_offset == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 36, __pyx_L3_error)
|
|
jpayne@69
|
5168 } else {
|
|
jpayne@69
|
5169 __pyx_v_offset = ((int)33);
|
|
jpayne@69
|
5170 }
|
|
jpayne@69
|
5171 }
|
|
jpayne@69
|
5172 goto __pyx_L6_skip;
|
|
jpayne@69
|
5173 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
5174 __Pyx_RaiseArgtupleInvalid("qualitystring_to_array", 0, 1, 2, __pyx_nargs); __PYX_ERR(0, 36, __pyx_L3_error)
|
|
jpayne@69
|
5175 __pyx_L6_skip:;
|
|
jpayne@69
|
5176 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
5177 __pyx_L3_error:;
|
|
jpayne@69
|
5178 {
|
|
jpayne@69
|
5179 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
5180 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
5181 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
5182 }
|
|
jpayne@69
|
5183 }
|
|
jpayne@69
|
5184 __Pyx_AddTraceback("pysam.libcutils.qualitystring_to_array", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
5185 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
5186 return NULL;
|
|
jpayne@69
|
5187 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
5188 __pyx_r = __pyx_pf_5pysam_9libcutils_qualitystring_to_array(__pyx_self, __pyx_v_input_str, __pyx_v_offset);
|
|
jpayne@69
|
5189
|
|
jpayne@69
|
5190 /* function exit code */
|
|
jpayne@69
|
5191 {
|
|
jpayne@69
|
5192 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
5193 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
5194 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
5195 }
|
|
jpayne@69
|
5196 }
|
|
jpayne@69
|
5197 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
5198 return __pyx_r;
|
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jpayne@69
|
5199 }
|
|
jpayne@69
|
5200
|
|
jpayne@69
|
5201 static PyObject *__pyx_pf_5pysam_9libcutils_qualitystring_to_array(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_input_str, int __pyx_v_offset) {
|
|
jpayne@69
|
5202 PyObject *__pyx_r = NULL;
|
|
jpayne@69
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jpayne@69
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jpayne@69
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5208 int __pyx_clineno = 0;
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jpayne@69
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jpayne@69
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5213 __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9libcutils_qualitystring_to_array(__pyx_v_input_str, 0, &__pyx_t_2)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 36, __pyx_L1_error)
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5216 __pyx_t_1 = 0;
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jpayne@69
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5217 goto __pyx_L0;
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jpayne@69
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5218
|
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jpayne@69
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5219 /* function exit code */
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jpayne@69
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jpayne@69
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jpayne@69
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jpayne@69
|
5229
|
|
jpayne@69
|
5230 /* "pysam/libcutils.pyx":45
|
|
jpayne@69
|
5231 *
|
|
jpayne@69
|
5232 *
|
|
jpayne@69
|
5233 * cpdef array_to_qualitystring(c_array.array qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5234 * """convert an array of quality values to a string."""
|
|
jpayne@69
|
5235 * if qualities is None:
|
|
jpayne@69
|
5236 */
|
|
jpayne@69
|
5237
|
|
jpayne@69
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5238 static PyObject *__pyx_pw_5pysam_9libcutils_3array_to_qualitystring(PyObject *__pyx_self,
|
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jpayne@69
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5239 #if CYTHON_METH_FASTCALL
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jpayne@69
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5240 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
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5241 #else
|
|
jpayne@69
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5242 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
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5243 #endif
|
|
jpayne@69
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5244 ); /*proto*/
|
|
jpayne@69
|
5245 static PyObject *__pyx_f_5pysam_9libcutils_array_to_qualitystring(arrayobject *__pyx_v_qualities, CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring *__pyx_optional_args) {
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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
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jpayne@69
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5259 int __pyx_clineno = 0;
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jpayne@69
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5260 __Pyx_RefNannySetupContext("array_to_qualitystring", 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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5264 }
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jpayne@69
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5265 }
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jpayne@69
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5266
|
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jpayne@69
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5267 /* "pysam/libcutils.pyx":47
|
|
jpayne@69
|
5268 * cpdef array_to_qualitystring(c_array.array qualities, int offset=33):
|
|
jpayne@69
|
5269 * """convert an array of quality values to a string."""
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jpayne@69
|
5270 * if qualities is None: # <<<<<<<<<<<<<<
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jpayne@69
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5271 * return None
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jpayne@69
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5272 * cdef int x
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jpayne@69
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5273 */
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jpayne@69
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5274 __pyx_t_1 = (((PyObject *)__pyx_v_qualities) == Py_None);
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jpayne@69
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5275 if (__pyx_t_1) {
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jpayne@69
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5276
|
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jpayne@69
|
5277 /* "pysam/libcutils.pyx":48
|
|
jpayne@69
|
5278 * """convert an array of quality values to a string."""
|
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jpayne@69
|
5279 * if qualities is None:
|
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jpayne@69
|
5280 * return None # <<<<<<<<<<<<<<
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jpayne@69
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5281 * cdef int x
|
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jpayne@69
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jpayne@69
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5286 goto __pyx_L0;
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jpayne@69
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5287
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jpayne@69
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5288 /* "pysam/libcutils.pyx":47
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jpayne@69
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5289 * cpdef array_to_qualitystring(c_array.array qualities, int offset=33):
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jpayne@69
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5290 * """convert an array of quality values to a string."""
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jpayne@69
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5291 * if qualities is None: # <<<<<<<<<<<<<<
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jpayne@69
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5292 * return None
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jpayne@69
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5293 * cdef int x
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jpayne@69
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jpayne@69
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5295 }
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jpayne@69
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5296
|
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jpayne@69
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5297 /* "pysam/libcutils.pyx":52
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jpayne@69
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5298 *
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jpayne@69
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5299 * cdef c_array.array result
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jpayne@69
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jpayne@69
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5301 *
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jpayne@69
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5302 * for x from 0 <= x < len(qualities):
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jpayne@69
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5303 */
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jpayne@69
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jpayne@69
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jpayne@69
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5307 }
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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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5313
|
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jpayne@69
|
5314 /* "pysam/libcutils.pyx":54
|
|
jpayne@69
|
5315 * result = c_array.clone(qualities, len(qualities), zero=False)
|
|
jpayne@69
|
5316 *
|
|
jpayne@69
|
5317 * for x from 0 <= x < len(qualities): # <<<<<<<<<<<<<<
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jpayne@69
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5318 * result[x] = qualities[x] + offset
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jpayne@69
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5320 */
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jpayne@69
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5321 if (unlikely(((PyObject *)__pyx_v_qualities) == Py_None)) {
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jpayne@69
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jpayne@69
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5323 __PYX_ERR(0, 54, __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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jpayne@69
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5327
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jpayne@69
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5328 /* "pysam/libcutils.pyx":55
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jpayne@69
|
5329 *
|
|
jpayne@69
|
5330 * for x from 0 <= x < len(qualities):
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jpayne@69
|
5331 * result[x] = qualities[x] + offset # <<<<<<<<<<<<<<
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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
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|
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jpayne@69
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5347 /* "pysam/libcutils.pyx":56
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|
jpayne@69
|
5348 * for x from 0 <= x < len(qualities):
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jpayne@69
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5349 * result[x] = qualities[x] + offset
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5350 * return force_str(result.tobytes()) # <<<<<<<<<<<<<<
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jpayne@69
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5351 *
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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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5360 if (likely(PyMethod_Check(__pyx_t_4))) {
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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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5371 {
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5383 __pyx_t_4 = 0;
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jpayne@69
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jpayne@69
|
5385
|
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jpayne@69
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5386 /* "pysam/libcutils.pyx":45
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jpayne@69
|
5387 *
|
|
jpayne@69
|
5388 *
|
|
jpayne@69
|
5389 * cpdef array_to_qualitystring(c_array.array qualities, int offset=33): # <<<<<<<<<<<<<<
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jpayne@69
|
5390 * """convert an array of quality values to a string."""
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jpayne@69
|
5391 * if qualities is None:
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jpayne@69
|
5392 */
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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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jpayne@69
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5404 __Pyx_RefNannyFinishContext();
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jpayne@69
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5405 return __pyx_r;
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jpayne@69
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5406 }
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jpayne@69
|
5407
|
|
jpayne@69
|
5408 /* Python wrapper */
|
|
jpayne@69
|
5409 static PyObject *__pyx_pw_5pysam_9libcutils_3array_to_qualitystring(PyObject *__pyx_self,
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jpayne@69
|
5410 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5411 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
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5412 #else
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jpayne@69
|
5413 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
|
5414 #endif
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jpayne@69
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5415 ); /*proto*/
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jpayne@69
|
5416 PyDoc_STRVAR(__pyx_doc_5pysam_9libcutils_2array_to_qualitystring, "convert an array of quality values to a string.");
|
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jpayne@69
|
5417 static PyMethodDef __pyx_mdef_5pysam_9libcutils_3array_to_qualitystring = {"array_to_qualitystring", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_3array_to_qualitystring, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libcutils_2array_to_qualitystring};
|
|
jpayne@69
|
5418 static PyObject *__pyx_pw_5pysam_9libcutils_3array_to_qualitystring(PyObject *__pyx_self,
|
|
jpayne@69
|
5419 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5420 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
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5421 #else
|
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jpayne@69
|
5422 PyObject *__pyx_args, PyObject *__pyx_kwds
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jpayne@69
|
5423 #endif
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jpayne@69
|
5424 ) {
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jpayne@69
|
5425 arrayobject *__pyx_v_qualities = 0;
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jpayne@69
|
5426 int __pyx_v_offset;
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jpayne@69
|
5427 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5428 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
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|
jpayne@69
|
5429 #endif
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|
jpayne@69
|
5430 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
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jpayne@69
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5431 PyObject* values[2] = {0,0};
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jpayne@69
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|
|
jpayne@69
|
5433 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
5434 int __pyx_clineno = 0;
|
|
jpayne@69
|
5435 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
5436 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
5437 __Pyx_RefNannySetupContext("array_to_qualitystring (wrapper)", 0);
|
|
jpayne@69
|
5438 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5439 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
5440 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
5441 #else
|
|
jpayne@69
|
5442 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
5443 #endif
|
|
jpayne@69
|
5444 #endif
|
|
jpayne@69
|
5445 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
5446 {
|
|
jpayne@69
|
5447 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_qualities,&__pyx_n_s_offset,0};
|
|
jpayne@69
|
5448 if (__pyx_kwds) {
|
|
jpayne@69
|
5449 Py_ssize_t kw_args;
|
|
jpayne@69
|
5450 switch (__pyx_nargs) {
|
|
jpayne@69
|
5451 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
5452 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5453 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5454 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5455 case 0: break;
|
|
jpayne@69
|
5456 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5457 }
|
|
jpayne@69
|
5458 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
5459 switch (__pyx_nargs) {
|
|
jpayne@69
|
5460 case 0:
|
|
jpayne@69
|
5461 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_qualities)) != 0)) {
|
|
jpayne@69
|
5462 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
5463 kw_args--;
|
|
jpayne@69
|
5464 }
|
|
jpayne@69
|
5465 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 45, __pyx_L3_error)
|
|
jpayne@69
|
5466 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5467 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5468 case 1:
|
|
jpayne@69
|
5469 if (kw_args > 0) {
|
|
jpayne@69
|
5470 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_offset);
|
|
jpayne@69
|
5471 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
5472 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 45, __pyx_L3_error)
|
|
jpayne@69
|
5473 }
|
|
jpayne@69
|
5474 }
|
|
jpayne@69
|
5475 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
5476 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
5477 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "array_to_qualitystring") < 0)) __PYX_ERR(0, 45, __pyx_L3_error)
|
|
jpayne@69
|
5478 }
|
|
jpayne@69
|
5479 } else {
|
|
jpayne@69
|
5480 switch (__pyx_nargs) {
|
|
jpayne@69
|
5481 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
5482 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5483 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5484 break;
|
|
jpayne@69
|
5485 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5486 }
|
|
jpayne@69
|
5487 }
|
|
jpayne@69
|
5488 __pyx_v_qualities = ((arrayobject *)values[0]);
|
|
jpayne@69
|
5489 if (values[1]) {
|
|
jpayne@69
|
5490 __pyx_v_offset = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_offset == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 45, __pyx_L3_error)
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jpayne@69
|
5491 } else {
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jpayne@69
|
5492 __pyx_v_offset = ((int)33);
|
|
jpayne@69
|
5493 }
|
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jpayne@69
|
5494 }
|
|
jpayne@69
|
5495 goto __pyx_L6_skip;
|
|
jpayne@69
|
5496 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
5497 __Pyx_RaiseArgtupleInvalid("array_to_qualitystring", 0, 1, 2, __pyx_nargs); __PYX_ERR(0, 45, __pyx_L3_error)
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jpayne@69
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5498 __pyx_L6_skip:;
|
|
jpayne@69
|
5499 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
5500 __pyx_L3_error:;
|
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jpayne@69
|
5501 {
|
|
jpayne@69
|
5502 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
5503 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
5504 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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|
jpayne@69
|
5505 }
|
|
jpayne@69
|
5506 }
|
|
jpayne@69
|
5507 __Pyx_AddTraceback("pysam.libcutils.array_to_qualitystring", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
5508 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
5509 return NULL;
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jpayne@69
|
5510 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
5511 if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_qualities), __pyx_ptype_7cpython_5array_array, 1, "qualities", 0))) __PYX_ERR(0, 45, __pyx_L1_error)
|
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jpayne@69
|
5512 __pyx_r = __pyx_pf_5pysam_9libcutils_2array_to_qualitystring(__pyx_self, __pyx_v_qualities, __pyx_v_offset);
|
|
jpayne@69
|
5513
|
|
jpayne@69
|
5514 /* function exit code */
|
|
jpayne@69
|
5515 goto __pyx_L0;
|
|
jpayne@69
|
5516 __pyx_L1_error:;
|
|
jpayne@69
|
5517 __pyx_r = NULL;
|
|
jpayne@69
|
5518 __pyx_L0:;
|
|
jpayne@69
|
5519 {
|
|
jpayne@69
|
5520 Py_ssize_t __pyx_temp;
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jpayne@69
|
5521 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
5522 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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jpayne@69
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5523 }
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jpayne@69
|
5524 }
|
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jpayne@69
|
5525 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
5526 return __pyx_r;
|
|
jpayne@69
|
5527 }
|
|
jpayne@69
|
5528
|
|
jpayne@69
|
5529 static PyObject *__pyx_pf_5pysam_9libcutils_2array_to_qualitystring(CYTHON_UNUSED PyObject *__pyx_self, arrayobject *__pyx_v_qualities, int __pyx_v_offset) {
|
|
jpayne@69
|
5530 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
5531 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
5532 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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5533 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring __pyx_t_2;
|
|
jpayne@69
|
5534 int __pyx_lineno = 0;
|
|
jpayne@69
|
5535 const char *__pyx_filename = NULL;
|
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jpayne@69
|
5536 int __pyx_clineno = 0;
|
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jpayne@69
|
5537 __Pyx_RefNannySetupContext("array_to_qualitystring", 1);
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jpayne@69
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5538 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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5539 __pyx_t_2.__pyx_n = 1;
|
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jpayne@69
|
5540 __pyx_t_2.offset = __pyx_v_offset;
|
|
jpayne@69
|
5541 __pyx_t_1 = __pyx_f_5pysam_9libcutils_array_to_qualitystring(__pyx_v_qualities, 0, &__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 45, __pyx_L1_error)
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jpayne@69
|
5542 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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5543 __pyx_r = __pyx_t_1;
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jpayne@69
|
5544 __pyx_t_1 = 0;
|
|
jpayne@69
|
5545 goto __pyx_L0;
|
|
jpayne@69
|
5546
|
|
jpayne@69
|
5547 /* function exit code */
|
|
jpayne@69
|
5548 __pyx_L1_error:;
|
|
jpayne@69
|
5549 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
5550 __Pyx_AddTraceback("pysam.libcutils.array_to_qualitystring", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
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jpayne@69
|
5551 __pyx_r = NULL;
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jpayne@69
|
5552 __pyx_L0:;
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jpayne@69
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5553 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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5554 __Pyx_RefNannyFinishContext();
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jpayne@69
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5555 return __pyx_r;
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jpayne@69
|
5556 }
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|
jpayne@69
|
5557
|
|
jpayne@69
|
5558 /* "pysam/libcutils.pyx":59
|
|
jpayne@69
|
5559 *
|
|
jpayne@69
|
5560 *
|
|
jpayne@69
|
5561 * cpdef qualities_to_qualitystring(qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5562 * """convert a list or array of quality scores to the string
|
|
jpayne@69
|
5563 * representation used in the SAM format.
|
|
jpayne@69
|
5564 */
|
|
jpayne@69
|
5565
|
|
jpayne@69
|
5566 static PyObject *__pyx_pw_5pysam_9libcutils_5qualities_to_qualitystring(PyObject *__pyx_self,
|
|
jpayne@69
|
5567 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5568 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5569 #else
|
|
jpayne@69
|
5570 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5571 #endif
|
|
jpayne@69
|
5572 ); /*proto*/
|
|
jpayne@69
|
5573 static PyObject *__pyx_f_5pysam_9libcutils_qualities_to_qualitystring(PyObject *__pyx_v_qualities, CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring *__pyx_optional_args) {
|
|
jpayne@69
|
5574 int __pyx_v_offset = ((int)33);
|
|
jpayne@69
|
5575 char __pyx_8genexpr1__pyx_v_x;
|
|
jpayne@69
|
5576 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
5577 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
5578 int __pyx_t_1;
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|
jpayne@69
|
5579 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
5580 struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring __pyx_t_3;
|
|
jpayne@69
|
5581 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
5582 Py_ssize_t __pyx_t_5;
|
|
jpayne@69
|
5583 PyObject *(*__pyx_t_6)(PyObject *);
|
|
jpayne@69
|
5584 PyObject *__pyx_t_7 = NULL;
|
|
jpayne@69
|
5585 char __pyx_t_8;
|
|
jpayne@69
|
5586 PyObject *__pyx_t_9 = NULL;
|
|
jpayne@69
|
5587 int __pyx_lineno = 0;
|
|
jpayne@69
|
5588 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
5589 int __pyx_clineno = 0;
|
|
jpayne@69
|
5590 __Pyx_RefNannySetupContext("qualities_to_qualitystring", 1);
|
|
jpayne@69
|
5591 if (__pyx_optional_args) {
|
|
jpayne@69
|
5592 if (__pyx_optional_args->__pyx_n > 0) {
|
|
jpayne@69
|
5593 __pyx_v_offset = __pyx_optional_args->offset;
|
|
jpayne@69
|
5594 }
|
|
jpayne@69
|
5595 }
|
|
jpayne@69
|
5596
|
|
jpayne@69
|
5597 /* "pysam/libcutils.pyx":76
|
|
jpayne@69
|
5598 * """
|
|
jpayne@69
|
5599 * cdef char x
|
|
jpayne@69
|
5600 * if qualities is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5601 * return None
|
|
jpayne@69
|
5602 * elif isinstance(qualities, c_array.array):
|
|
jpayne@69
|
5603 */
|
|
jpayne@69
|
5604 __pyx_t_1 = (__pyx_v_qualities == Py_None);
|
|
jpayne@69
|
5605 if (__pyx_t_1) {
|
|
jpayne@69
|
5606
|
|
jpayne@69
|
5607 /* "pysam/libcutils.pyx":77
|
|
jpayne@69
|
5608 * cdef char x
|
|
jpayne@69
|
5609 * if qualities is None:
|
|
jpayne@69
|
5610 * return None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5611 * elif isinstance(qualities, c_array.array):
|
|
jpayne@69
|
5612 * return array_to_qualitystring(qualities, offset=offset)
|
|
jpayne@69
|
5613 */
|
|
jpayne@69
|
5614 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
5615 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
5616 goto __pyx_L0;
|
|
jpayne@69
|
5617
|
|
jpayne@69
|
5618 /* "pysam/libcutils.pyx":76
|
|
jpayne@69
|
5619 * """
|
|
jpayne@69
|
5620 * cdef char x
|
|
jpayne@69
|
5621 * if qualities is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5622 * return None
|
|
jpayne@69
|
5623 * elif isinstance(qualities, c_array.array):
|
|
jpayne@69
|
5624 */
|
|
jpayne@69
|
5625 }
|
|
jpayne@69
|
5626
|
|
jpayne@69
|
5627 /* "pysam/libcutils.pyx":78
|
|
jpayne@69
|
5628 * if qualities is None:
|
|
jpayne@69
|
5629 * return None
|
|
jpayne@69
|
5630 * elif isinstance(qualities, c_array.array): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5631 * return array_to_qualitystring(qualities, offset=offset)
|
|
jpayne@69
|
5632 * else:
|
|
jpayne@69
|
5633 */
|
|
jpayne@69
|
5634 __pyx_t_1 = __Pyx_TypeCheck(__pyx_v_qualities, __pyx_ptype_7cpython_5array_array);
|
|
jpayne@69
|
5635 if (__pyx_t_1) {
|
|
jpayne@69
|
5636
|
|
jpayne@69
|
5637 /* "pysam/libcutils.pyx":79
|
|
jpayne@69
|
5638 * return None
|
|
jpayne@69
|
5639 * elif isinstance(qualities, c_array.array):
|
|
jpayne@69
|
5640 * return array_to_qualitystring(qualities, offset=offset) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5641 * else:
|
|
jpayne@69
|
5642 * # tuples and lists
|
|
jpayne@69
|
5643 */
|
|
jpayne@69
|
5644 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
5645 if (!(likely(((__pyx_v_qualities) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_qualities, __pyx_ptype_7cpython_5array_array))))) __PYX_ERR(0, 79, __pyx_L1_error)
|
|
jpayne@69
|
5646 __pyx_t_3.__pyx_n = 1;
|
|
jpayne@69
|
5647 __pyx_t_3.offset = __pyx_v_offset;
|
|
jpayne@69
|
5648 __pyx_t_2 = __pyx_f_5pysam_9libcutils_array_to_qualitystring(((arrayobject *)__pyx_v_qualities), 0, &__pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 79, __pyx_L1_error)
|
|
jpayne@69
|
5649 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
5650 __pyx_r = __pyx_t_2;
|
|
jpayne@69
|
5651 __pyx_t_2 = 0;
|
|
jpayne@69
|
5652 goto __pyx_L0;
|
|
jpayne@69
|
5653
|
|
jpayne@69
|
5654 /* "pysam/libcutils.pyx":78
|
|
jpayne@69
|
5655 * if qualities is None:
|
|
jpayne@69
|
5656 * return None
|
|
jpayne@69
|
5657 * elif isinstance(qualities, c_array.array): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5658 * return array_to_qualitystring(qualities, offset=offset)
|
|
jpayne@69
|
5659 * else:
|
|
jpayne@69
|
5660 */
|
|
jpayne@69
|
5661 }
|
|
jpayne@69
|
5662
|
|
jpayne@69
|
5663 /* "pysam/libcutils.pyx":82
|
|
jpayne@69
|
5664 * else:
|
|
jpayne@69
|
5665 * # tuples and lists
|
|
jpayne@69
|
5666 * return force_str("".join([chr(x + offset) for x in qualities])) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5667 *
|
|
jpayne@69
|
5668 *
|
|
jpayne@69
|
5669 */
|
|
jpayne@69
|
5670 /*else*/ {
|
|
jpayne@69
|
5671 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
5672 { /* enter inner scope */
|
|
jpayne@69
|
5673 __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 82, __pyx_L1_error)
|
|
jpayne@69
|
5674 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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5675 if (likely(PyList_CheckExact(__pyx_v_qualities)) || PyTuple_CheckExact(__pyx_v_qualities)) {
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jpayne@69
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jpayne@69
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5677 __pyx_t_5 = 0;
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jpayne@69
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5678 __pyx_t_6 = NULL;
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jpayne@69
|
5679 } else {
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jpayne@69
|
5680 __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_qualities); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5681 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
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5682 __pyx_t_6 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_4); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5683 }
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jpayne@69
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5684 for (;;) {
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jpayne@69
|
5685 if (likely(!__pyx_t_6)) {
|
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jpayne@69
|
5686 if (likely(PyList_CheckExact(__pyx_t_4))) {
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jpayne@69
|
5687 {
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jpayne@69
|
5688 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_4);
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jpayne@69
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5689 #if !CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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5690 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5691 #endif
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jpayne@69
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5692 if (__pyx_t_5 >= __pyx_temp) break;
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jpayne@69
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5693 }
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jpayne@69
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5694 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
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jpayne@69
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5695 __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5696 #else
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jpayne@69
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5697 __pyx_t_7 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5698 __Pyx_GOTREF(__pyx_t_7);
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jpayne@69
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5699 #endif
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jpayne@69
|
5700 } else {
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jpayne@69
|
5701 {
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jpayne@69
|
5702 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_4);
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jpayne@69
|
5703 #if !CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
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5704 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
|
5705 #endif
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jpayne@69
|
5706 if (__pyx_t_5 >= __pyx_temp) break;
|
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jpayne@69
|
5707 }
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jpayne@69
|
5708 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
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|
jpayne@69
|
5709 __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely((0 < 0))) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5710 #else
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jpayne@69
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5711 __pyx_t_7 = __Pyx_PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5712 __Pyx_GOTREF(__pyx_t_7);
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jpayne@69
|
5713 #endif
|
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jpayne@69
|
5714 }
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jpayne@69
|
5715 } else {
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jpayne@69
|
5716 __pyx_t_7 = __pyx_t_6(__pyx_t_4);
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jpayne@69
|
5717 if (unlikely(!__pyx_t_7)) {
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jpayne@69
|
5718 PyObject* exc_type = PyErr_Occurred();
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jpayne@69
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5719 if (exc_type) {
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jpayne@69
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5720 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
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jpayne@69
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5721 else __PYX_ERR(0, 82, __pyx_L1_error)
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jpayne@69
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5722 }
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jpayne@69
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5723 break;
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jpayne@69
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5724 }
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jpayne@69
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5725 __Pyx_GOTREF(__pyx_t_7);
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jpayne@69
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5726 }
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5728 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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jpayne@69
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5729 __pyx_8genexpr1__pyx_v_x = __pyx_t_8;
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jpayne@69
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5730 __pyx_t_7 = __Pyx_PyInt_From_int((__pyx_8genexpr1__pyx_v_x + __pyx_v_offset)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 82, __pyx_L1_error)
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5733 __Pyx_GOTREF(__pyx_t_9);
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5734 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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5735 if (unlikely(__Pyx_ListComp_Append(__pyx_t_2, (PyObject*)__pyx_t_9))) __PYX_ERR(0, 82, __pyx_L1_error)
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5736 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
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5737 }
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5738 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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jpayne@69
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5739 } /* exit inner scope */
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jpayne@69
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5740 __pyx_t_4 = PyUnicode_Join(__pyx_kp_u_, __pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 82, __pyx_L1_error)
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5741 __Pyx_GOTREF(__pyx_t_4);
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5742 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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5743 __pyx_t_2 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 82, __pyx_L1_error)
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5744 __Pyx_GOTREF(__pyx_t_2);
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5746 __pyx_r = __pyx_t_2;
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jpayne@69
|
5747 __pyx_t_2 = 0;
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jpayne@69
|
5748 goto __pyx_L0;
|
|
jpayne@69
|
5749 }
|
|
jpayne@69
|
5750
|
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jpayne@69
|
5751 /* "pysam/libcutils.pyx":59
|
|
jpayne@69
|
5752 *
|
|
jpayne@69
|
5753 *
|
|
jpayne@69
|
5754 * cpdef qualities_to_qualitystring(qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5755 * """convert a list or array of quality scores to the string
|
|
jpayne@69
|
5756 * representation used in the SAM format.
|
|
jpayne@69
|
5757 */
|
|
jpayne@69
|
5758
|
|
jpayne@69
|
5759 /* function exit code */
|
|
jpayne@69
|
5760 __pyx_L1_error:;
|
|
jpayne@69
|
5761 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
5762 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
5763 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
5764 __Pyx_XDECREF(__pyx_t_9);
|
|
jpayne@69
|
5765 __Pyx_AddTraceback("pysam.libcutils.qualities_to_qualitystring", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
5766 __pyx_r = 0;
|
|
jpayne@69
|
5767 __pyx_L0:;
|
|
jpayne@69
|
5768 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
5769 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
5770 return __pyx_r;
|
|
jpayne@69
|
5771 }
|
|
jpayne@69
|
5772
|
|
jpayne@69
|
5773 /* Python wrapper */
|
|
jpayne@69
|
5774 static PyObject *__pyx_pw_5pysam_9libcutils_5qualities_to_qualitystring(PyObject *__pyx_self,
|
|
jpayne@69
|
5775 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5776 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5777 #else
|
|
jpayne@69
|
5778 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5779 #endif
|
|
jpayne@69
|
5780 ); /*proto*/
|
|
jpayne@69
|
5781 PyDoc_STRVAR(__pyx_doc_5pysam_9libcutils_4qualities_to_qualitystring, "convert a list or array of quality scores to the string\n representation used in the SAM format.\n\n Parameters\n ----------\n offset : int\n offset to be added to the quality scores to arrive at\n the characters of the quality string (default=33).\n\n Returns\n -------\n string\n a quality string\n\n ");
|
|
jpayne@69
|
5782 static PyMethodDef __pyx_mdef_5pysam_9libcutils_5qualities_to_qualitystring = {"qualities_to_qualitystring", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_5qualities_to_qualitystring, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libcutils_4qualities_to_qualitystring};
|
|
jpayne@69
|
5783 static PyObject *__pyx_pw_5pysam_9libcutils_5qualities_to_qualitystring(PyObject *__pyx_self,
|
|
jpayne@69
|
5784 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5785 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5786 #else
|
|
jpayne@69
|
5787 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5788 #endif
|
|
jpayne@69
|
5789 ) {
|
|
jpayne@69
|
5790 PyObject *__pyx_v_qualities = 0;
|
|
jpayne@69
|
5791 int __pyx_v_offset;
|
|
jpayne@69
|
5792 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5793 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
5794 #endif
|
|
jpayne@69
|
5795 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
5796 PyObject* values[2] = {0,0};
|
|
jpayne@69
|
5797 int __pyx_lineno = 0;
|
|
jpayne@69
|
5798 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
5799 int __pyx_clineno = 0;
|
|
jpayne@69
|
5800 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
5801 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
5802 __Pyx_RefNannySetupContext("qualities_to_qualitystring (wrapper)", 0);
|
|
jpayne@69
|
5803 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5804 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
5805 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
5806 #else
|
|
jpayne@69
|
5807 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
5808 #endif
|
|
jpayne@69
|
5809 #endif
|
|
jpayne@69
|
5810 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
5811 {
|
|
jpayne@69
|
5812 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_qualities,&__pyx_n_s_offset,0};
|
|
jpayne@69
|
5813 if (__pyx_kwds) {
|
|
jpayne@69
|
5814 Py_ssize_t kw_args;
|
|
jpayne@69
|
5815 switch (__pyx_nargs) {
|
|
jpayne@69
|
5816 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
5817 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5818 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5819 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5820 case 0: break;
|
|
jpayne@69
|
5821 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5822 }
|
|
jpayne@69
|
5823 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
5824 switch (__pyx_nargs) {
|
|
jpayne@69
|
5825 case 0:
|
|
jpayne@69
|
5826 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_qualities)) != 0)) {
|
|
jpayne@69
|
5827 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
5828 kw_args--;
|
|
jpayne@69
|
5829 }
|
|
jpayne@69
|
5830 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 59, __pyx_L3_error)
|
|
jpayne@69
|
5831 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5832 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5833 case 1:
|
|
jpayne@69
|
5834 if (kw_args > 0) {
|
|
jpayne@69
|
5835 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_offset);
|
|
jpayne@69
|
5836 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
5837 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 59, __pyx_L3_error)
|
|
jpayne@69
|
5838 }
|
|
jpayne@69
|
5839 }
|
|
jpayne@69
|
5840 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
5841 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
5842 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "qualities_to_qualitystring") < 0)) __PYX_ERR(0, 59, __pyx_L3_error)
|
|
jpayne@69
|
5843 }
|
|
jpayne@69
|
5844 } else {
|
|
jpayne@69
|
5845 switch (__pyx_nargs) {
|
|
jpayne@69
|
5846 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
5847 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5848 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5849 break;
|
|
jpayne@69
|
5850 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5851 }
|
|
jpayne@69
|
5852 }
|
|
jpayne@69
|
5853 __pyx_v_qualities = values[0];
|
|
jpayne@69
|
5854 if (values[1]) {
|
|
jpayne@69
|
5855 __pyx_v_offset = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_offset == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 59, __pyx_L3_error)
|
|
jpayne@69
|
5856 } else {
|
|
jpayne@69
|
5857 __pyx_v_offset = ((int)33);
|
|
jpayne@69
|
5858 }
|
|
jpayne@69
|
5859 }
|
|
jpayne@69
|
5860 goto __pyx_L6_skip;
|
|
jpayne@69
|
5861 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
5862 __Pyx_RaiseArgtupleInvalid("qualities_to_qualitystring", 0, 1, 2, __pyx_nargs); __PYX_ERR(0, 59, __pyx_L3_error)
|
|
jpayne@69
|
5863 __pyx_L6_skip:;
|
|
jpayne@69
|
5864 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
5865 __pyx_L3_error:;
|
|
jpayne@69
|
5866 {
|
|
jpayne@69
|
5867 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
5868 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
5869 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
5870 }
|
|
jpayne@69
|
5871 }
|
|
jpayne@69
|
5872 __Pyx_AddTraceback("pysam.libcutils.qualities_to_qualitystring", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
5873 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
5874 return NULL;
|
|
jpayne@69
|
5875 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
5876 __pyx_r = __pyx_pf_5pysam_9libcutils_4qualities_to_qualitystring(__pyx_self, __pyx_v_qualities, __pyx_v_offset);
|
|
jpayne@69
|
5877
|
|
jpayne@69
|
5878 /* function exit code */
|
|
jpayne@69
|
5879 {
|
|
jpayne@69
|
5880 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
5881 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
5882 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
5883 }
|
|
jpayne@69
|
5884 }
|
|
jpayne@69
|
5885 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
5886 return __pyx_r;
|
|
jpayne@69
|
5887 }
|
|
jpayne@69
|
5888
|
|
jpayne@69
|
5889 static PyObject *__pyx_pf_5pysam_9libcutils_4qualities_to_qualitystring(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_qualities, int __pyx_v_offset) {
|
|
jpayne@69
|
5890 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
5891 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
5892 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
5893 struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring __pyx_t_2;
|
|
jpayne@69
|
5894 int __pyx_lineno = 0;
|
|
jpayne@69
|
5895 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
5896 int __pyx_clineno = 0;
|
|
jpayne@69
|
5897 __Pyx_RefNannySetupContext("qualities_to_qualitystring", 1);
|
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jpayne@69
|
5898 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
5899 __pyx_t_2.__pyx_n = 1;
|
|
jpayne@69
|
5900 __pyx_t_2.offset = __pyx_v_offset;
|
|
jpayne@69
|
5901 __pyx_t_1 = __pyx_f_5pysam_9libcutils_qualities_to_qualitystring(__pyx_v_qualities, 0, &__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 59, __pyx_L1_error)
|
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jpayne@69
|
5902 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
|
5903 __pyx_r = __pyx_t_1;
|
|
jpayne@69
|
5904 __pyx_t_1 = 0;
|
|
jpayne@69
|
5905 goto __pyx_L0;
|
|
jpayne@69
|
5906
|
|
jpayne@69
|
5907 /* function exit code */
|
|
jpayne@69
|
5908 __pyx_L1_error:;
|
|
jpayne@69
|
5909 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
5910 __Pyx_AddTraceback("pysam.libcutils.qualities_to_qualitystring", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
5911 __pyx_r = NULL;
|
|
jpayne@69
|
5912 __pyx_L0:;
|
|
jpayne@69
|
5913 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
5914 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
5915 return __pyx_r;
|
|
jpayne@69
|
5916 }
|
|
jpayne@69
|
5917
|
|
jpayne@69
|
5918 /* "pysam/libcutils.pyx":90
|
|
jpayne@69
|
5919 *
|
|
jpayne@69
|
5920 * # Codec error handler that just interprets each bad byte as ISO-8859-1.
|
|
jpayne@69
|
5921 * def latin1_replace(exception): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
5922 * return (chr(exception.object[exception.start]), exception.end)
|
|
jpayne@69
|
5923 *
|
|
jpayne@69
|
5924 */
|
|
jpayne@69
|
5925
|
|
jpayne@69
|
5926 /* Python wrapper */
|
|
jpayne@69
|
5927 static PyObject *__pyx_pw_5pysam_9libcutils_7latin1_replace(PyObject *__pyx_self,
|
|
jpayne@69
|
5928 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5929 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5930 #else
|
|
jpayne@69
|
5931 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5932 #endif
|
|
jpayne@69
|
5933 ); /*proto*/
|
|
jpayne@69
|
5934 static PyMethodDef __pyx_mdef_5pysam_9libcutils_7latin1_replace = {"latin1_replace", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_7latin1_replace, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0};
|
|
jpayne@69
|
5935 static PyObject *__pyx_pw_5pysam_9libcutils_7latin1_replace(PyObject *__pyx_self,
|
|
jpayne@69
|
5936 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5937 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
5938 #else
|
|
jpayne@69
|
5939 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
5940 #endif
|
|
jpayne@69
|
5941 ) {
|
|
jpayne@69
|
5942 PyObject *__pyx_v_exception = 0;
|
|
jpayne@69
|
5943 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5944 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
5945 #endif
|
|
jpayne@69
|
5946 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
5947 PyObject* values[1] = {0};
|
|
jpayne@69
|
5948 int __pyx_lineno = 0;
|
|
jpayne@69
|
5949 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
5950 int __pyx_clineno = 0;
|
|
jpayne@69
|
5951 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
5952 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
5953 __Pyx_RefNannySetupContext("latin1_replace (wrapper)", 0);
|
|
jpayne@69
|
5954 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
5955 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
5956 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
5957 #else
|
|
jpayne@69
|
5958 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
5959 #endif
|
|
jpayne@69
|
5960 #endif
|
|
jpayne@69
|
5961 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
5962 {
|
|
jpayne@69
|
5963 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_exception,0};
|
|
jpayne@69
|
5964 if (__pyx_kwds) {
|
|
jpayne@69
|
5965 Py_ssize_t kw_args;
|
|
jpayne@69
|
5966 switch (__pyx_nargs) {
|
|
jpayne@69
|
5967 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
5968 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
5969 case 0: break;
|
|
jpayne@69
|
5970 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
5971 }
|
|
jpayne@69
|
5972 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
5973 switch (__pyx_nargs) {
|
|
jpayne@69
|
5974 case 0:
|
|
jpayne@69
|
5975 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_exception)) != 0)) {
|
|
jpayne@69
|
5976 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
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jpayne@69
|
5977 kw_args--;
|
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jpayne@69
|
5978 }
|
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jpayne@69
|
5979 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 90, __pyx_L3_error)
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jpayne@69
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5980 else goto __pyx_L5_argtuple_error;
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jpayne@69
|
5981 }
|
|
jpayne@69
|
5982 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
5983 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
5984 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "latin1_replace") < 0)) __PYX_ERR(0, 90, __pyx_L3_error)
|
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jpayne@69
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5985 }
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jpayne@69
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5986 } else if (unlikely(__pyx_nargs != 1)) {
|
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jpayne@69
|
5987 goto __pyx_L5_argtuple_error;
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jpayne@69
|
5988 } else {
|
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jpayne@69
|
5989 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
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jpayne@69
|
5990 }
|
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jpayne@69
|
5991 __pyx_v_exception = values[0];
|
|
jpayne@69
|
5992 }
|
|
jpayne@69
|
5993 goto __pyx_L6_skip;
|
|
jpayne@69
|
5994 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
5995 __Pyx_RaiseArgtupleInvalid("latin1_replace", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 90, __pyx_L3_error)
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jpayne@69
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5996 __pyx_L6_skip:;
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jpayne@69
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5997 goto __pyx_L4_argument_unpacking_done;
|
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jpayne@69
|
5998 __pyx_L3_error:;
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jpayne@69
|
5999 {
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jpayne@69
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6000 Py_ssize_t __pyx_temp;
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jpayne@69
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6001 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
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jpayne@69
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6002 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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jpayne@69
|
6003 }
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jpayne@69
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6004 }
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jpayne@69
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6005 __Pyx_AddTraceback("pysam.libcutils.latin1_replace", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
|
6006 __Pyx_RefNannyFinishContext();
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jpayne@69
|
6007 return NULL;
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jpayne@69
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6008 __pyx_L4_argument_unpacking_done:;
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jpayne@69
|
6009 __pyx_r = __pyx_pf_5pysam_9libcutils_6latin1_replace(__pyx_self, __pyx_v_exception);
|
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jpayne@69
|
6010
|
|
jpayne@69
|
6011 /* function exit code */
|
|
jpayne@69
|
6012 {
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jpayne@69
|
6013 Py_ssize_t __pyx_temp;
|
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jpayne@69
|
6014 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
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jpayne@69
|
6015 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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jpayne@69
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6016 }
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jpayne@69
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jpayne@69
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6018 __Pyx_RefNannyFinishContext();
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jpayne@69
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6019 return __pyx_r;
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jpayne@69
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6020 }
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jpayne@69
|
6021
|
|
jpayne@69
|
6022 static PyObject *__pyx_pf_5pysam_9libcutils_6latin1_replace(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_exception) {
|
|
jpayne@69
|
6023 PyObject *__pyx_r = NULL;
|
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jpayne@69
|
6024 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
6025 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
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|
|
jpayne@69
|
6027 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
6028 int __pyx_lineno = 0;
|
|
jpayne@69
|
6029 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6030 int __pyx_clineno = 0;
|
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jpayne@69
|
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jpayne@69
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6032
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jpayne@69
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|
|
jpayne@69
|
6034 * # Codec error handler that just interprets each bad byte as ISO-8859-1.
|
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jpayne@69
|
6035 * def latin1_replace(exception):
|
|
jpayne@69
|
6036 * return (chr(exception.object[exception.start]), exception.end) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6037 *
|
|
jpayne@69
|
6038 * register_error('pysam.latin1replace', latin1_replace)
|
|
jpayne@69
|
6039 */
|
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jpayne@69
|
6040 __Pyx_XDECREF(__pyx_r);
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6041 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_exception, __pyx_n_s_object); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 91, __pyx_L1_error)
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6043 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_exception, __pyx_n_s_start); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 91, __pyx_L1_error)
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6044 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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6045 __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 91, __pyx_L1_error)
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jpayne@69
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6050 __Pyx_GOTREF(__pyx_t_2);
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6052 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_exception, __pyx_n_s_end); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 91, __pyx_L1_error)
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jpayne@69
|
6053 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
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6054 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 91, __pyx_L1_error)
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jpayne@69
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6055 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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jpayne@69
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6059 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3)) __PYX_ERR(0, 91, __pyx_L1_error);
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jpayne@69
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6060 __pyx_t_2 = 0;
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jpayne@69
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|
6062 __pyx_r = __pyx_t_1;
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jpayne@69
|
6063 __pyx_t_1 = 0;
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jpayne@69
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6064 goto __pyx_L0;
|
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jpayne@69
|
6065
|
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jpayne@69
|
6066 /* "pysam/libcutils.pyx":90
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|
jpayne@69
|
6067 *
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jpayne@69
|
6068 * # Codec error handler that just interprets each bad byte as ISO-8859-1.
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jpayne@69
|
6069 * def latin1_replace(exception): # <<<<<<<<<<<<<<
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jpayne@69
|
6070 * return (chr(exception.object[exception.start]), exception.end)
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|
jpayne@69
|
6071 *
|
|
jpayne@69
|
6072 */
|
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jpayne@69
|
6073
|
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jpayne@69
|
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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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|
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jpayne@69
|
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jpayne@69
|
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jpayne@69
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6083 __Pyx_RefNannyFinishContext();
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jpayne@69
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6084 return __pyx_r;
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jpayne@69
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6085 }
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jpayne@69
|
6086
|
|
jpayne@69
|
6087 /* "pysam/libcutils.pyx":98
|
|
jpayne@69
|
6088 * cdef str ERROR_HANDLER = 'strict'
|
|
jpayne@69
|
6089 *
|
|
jpayne@69
|
6090 * cpdef get_encoding_error_handler(): # <<<<<<<<<<<<<<
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|
jpayne@69
|
6091 * return ERROR_HANDLER
|
|
jpayne@69
|
6092 *
|
|
jpayne@69
|
6093 */
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|
jpayne@69
|
6094
|
|
jpayne@69
|
6095 static PyObject *__pyx_pw_5pysam_9libcutils_9get_encoding_error_handler(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
|
|
jpayne@69
|
6096 static PyObject *__pyx_f_5pysam_9libcutils_get_encoding_error_handler(CYTHON_UNUSED int __pyx_skip_dispatch) {
|
|
jpayne@69
|
6097 PyObject *__pyx_r = NULL;
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jpayne@69
|
6098 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
6099 __Pyx_RefNannySetupContext("get_encoding_error_handler", 1);
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jpayne@69
|
6100
|
|
jpayne@69
|
6101 /* "pysam/libcutils.pyx":99
|
|
jpayne@69
|
6102 *
|
|
jpayne@69
|
6103 * cpdef get_encoding_error_handler():
|
|
jpayne@69
|
6104 * return ERROR_HANDLER # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6105 *
|
|
jpayne@69
|
6106 * cpdef set_encoding_error_handler(name):
|
|
jpayne@69
|
6107 */
|
|
jpayne@69
|
6108 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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6109 __Pyx_INCREF(__pyx_v_5pysam_9libcutils_ERROR_HANDLER);
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jpayne@69
|
6110 __pyx_r = __pyx_v_5pysam_9libcutils_ERROR_HANDLER;
|
|
jpayne@69
|
6111 goto __pyx_L0;
|
|
jpayne@69
|
6112
|
|
jpayne@69
|
6113 /* "pysam/libcutils.pyx":98
|
|
jpayne@69
|
6114 * cdef str ERROR_HANDLER = 'strict'
|
|
jpayne@69
|
6115 *
|
|
jpayne@69
|
6116 * cpdef get_encoding_error_handler(): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6117 * return ERROR_HANDLER
|
|
jpayne@69
|
6118 *
|
|
jpayne@69
|
6119 */
|
|
jpayne@69
|
6120
|
|
jpayne@69
|
6121 /* function exit code */
|
|
jpayne@69
|
6122 __pyx_L0:;
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jpayne@69
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6123 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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6124 __Pyx_RefNannyFinishContext();
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jpayne@69
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6125 return __pyx_r;
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jpayne@69
|
6126 }
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jpayne@69
|
6127
|
|
jpayne@69
|
6128 /* Python wrapper */
|
|
jpayne@69
|
6129 static PyObject *__pyx_pw_5pysam_9libcutils_9get_encoding_error_handler(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
|
|
jpayne@69
|
6130 static PyMethodDef __pyx_mdef_5pysam_9libcutils_9get_encoding_error_handler = {"get_encoding_error_handler", (PyCFunction)__pyx_pw_5pysam_9libcutils_9get_encoding_error_handler, METH_NOARGS, 0};
|
|
jpayne@69
|
6131 static PyObject *__pyx_pw_5pysam_9libcutils_9get_encoding_error_handler(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
|
|
jpayne@69
|
6132 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
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jpayne@69
|
6133 PyObject *__pyx_r = 0;
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jpayne@69
|
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jpayne@69
|
6137 __pyx_r = __pyx_pf_5pysam_9libcutils_8get_encoding_error_handler(__pyx_self);
|
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jpayne@69
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6138
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jpayne@69
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6139 /* function exit code */
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jpayne@69
|
6140 __Pyx_RefNannyFinishContext();
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jpayne@69
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6141 return __pyx_r;
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jpayne@69
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6142 }
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|
jpayne@69
|
6143
|
|
jpayne@69
|
6144 static PyObject *__pyx_pf_5pysam_9libcutils_8get_encoding_error_handler(CYTHON_UNUSED PyObject *__pyx_self) {
|
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jpayne@69
|
6145 PyObject *__pyx_r = NULL;
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jpayne@69
|
6146 __Pyx_RefNannyDeclarations
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jpayne@69
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6147 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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jpayne@69
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6149 const char *__pyx_filename = NULL;
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jpayne@69
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6150 int __pyx_clineno = 0;
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jpayne@69
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6151 __Pyx_RefNannySetupContext("get_encoding_error_handler", 1);
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jpayne@69
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6152 __Pyx_XDECREF(__pyx_r);
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6153 __pyx_t_1 = __pyx_f_5pysam_9libcutils_get_encoding_error_handler(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 98, __pyx_L1_error)
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6154 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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6157 goto __pyx_L0;
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jpayne@69
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6158
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jpayne@69
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6159 /* function exit code */
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jpayne@69
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6160 __pyx_L1_error:;
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6161 __Pyx_XDECREF(__pyx_t_1);
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jpayne@69
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6162 __Pyx_AddTraceback("pysam.libcutils.get_encoding_error_handler", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
|
6163 __pyx_r = NULL;
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jpayne@69
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6164 __pyx_L0:;
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jpayne@69
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jpayne@69
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6166 __Pyx_RefNannyFinishContext();
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jpayne@69
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6167 return __pyx_r;
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jpayne@69
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6168 }
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jpayne@69
|
6169
|
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jpayne@69
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6170 /* "pysam/libcutils.pyx":101
|
|
jpayne@69
|
6171 * return ERROR_HANDLER
|
|
jpayne@69
|
6172 *
|
|
jpayne@69
|
6173 * cpdef set_encoding_error_handler(name): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6174 * global ERROR_HANDLER
|
|
jpayne@69
|
6175 * previous = ERROR_HANDLER
|
|
jpayne@69
|
6176 */
|
|
jpayne@69
|
6177
|
|
jpayne@69
|
6178 static PyObject *__pyx_pw_5pysam_9libcutils_11set_encoding_error_handler(PyObject *__pyx_self,
|
|
jpayne@69
|
6179 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
6180 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
|
6181 #else
|
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jpayne@69
|
6182 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
6183 #endif
|
|
jpayne@69
|
6184 ); /*proto*/
|
|
jpayne@69
|
6185 static PyObject *__pyx_f_5pysam_9libcutils_set_encoding_error_handler(PyObject *__pyx_v_name, CYTHON_UNUSED int __pyx_skip_dispatch) {
|
|
jpayne@69
|
6186 PyObject *__pyx_v_previous = NULL;
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jpayne@69
|
6187 PyObject *__pyx_r = NULL;
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jpayne@69
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6188 __Pyx_RefNannyDeclarations
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jpayne@69
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6190 int __pyx_lineno = 0;
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|
jpayne@69
|
6191 const char *__pyx_filename = NULL;
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jpayne@69
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6192 int __pyx_clineno = 0;
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jpayne@69
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6193 __Pyx_RefNannySetupContext("set_encoding_error_handler", 1);
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jpayne@69
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6194
|
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jpayne@69
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6195 /* "pysam/libcutils.pyx":103
|
|
jpayne@69
|
6196 * cpdef set_encoding_error_handler(name):
|
|
jpayne@69
|
6197 * global ERROR_HANDLER
|
|
jpayne@69
|
6198 * previous = ERROR_HANDLER # <<<<<<<<<<<<<<
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|
jpayne@69
|
6199 * ERROR_HANDLER = name
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jpayne@69
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6200 * return previous
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jpayne@69
|
6201 */
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jpayne@69
|
6202 __Pyx_INCREF(__pyx_v_5pysam_9libcutils_ERROR_HANDLER);
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jpayne@69
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6203 __pyx_v_previous = __pyx_v_5pysam_9libcutils_ERROR_HANDLER;
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|
jpayne@69
|
6204
|
|
jpayne@69
|
6205 /* "pysam/libcutils.pyx":104
|
|
jpayne@69
|
6206 * global ERROR_HANDLER
|
|
jpayne@69
|
6207 * previous = ERROR_HANDLER
|
|
jpayne@69
|
6208 * ERROR_HANDLER = name # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6209 * return previous
|
|
jpayne@69
|
6210 *
|
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jpayne@69
|
6211 */
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jpayne@69
|
6212 if (!(likely(PyUnicode_CheckExact(__pyx_v_name))||((__pyx_v_name) == Py_None) || __Pyx_RaiseUnexpectedTypeError("unicode", __pyx_v_name))) __PYX_ERR(0, 104, __pyx_L1_error)
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jpayne@69
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6213 __pyx_t_1 = __pyx_v_name;
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jpayne@69
|
6214 __Pyx_INCREF(__pyx_t_1);
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jpayne@69
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jpayne@69
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6216 __Pyx_DECREF_SET(__pyx_v_5pysam_9libcutils_ERROR_HANDLER, ((PyObject*)__pyx_t_1));
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jpayne@69
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6217 __Pyx_GIVEREF(__pyx_t_1);
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jpayne@69
|
6218 __pyx_t_1 = 0;
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jpayne@69
|
6219
|
|
jpayne@69
|
6220 /* "pysam/libcutils.pyx":105
|
|
jpayne@69
|
6221 * previous = ERROR_HANDLER
|
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jpayne@69
|
6222 * ERROR_HANDLER = name
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jpayne@69
|
6223 * return previous # <<<<<<<<<<<<<<
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jpayne@69
|
6224 *
|
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jpayne@69
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6225 * ########################################################################
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jpayne@69
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6226 */
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jpayne@69
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6227 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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6229 __pyx_r = __pyx_v_previous;
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jpayne@69
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6230 goto __pyx_L0;
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jpayne@69
|
6231
|
|
jpayne@69
|
6232 /* "pysam/libcutils.pyx":101
|
|
jpayne@69
|
6233 * return ERROR_HANDLER
|
|
jpayne@69
|
6234 *
|
|
jpayne@69
|
6235 * cpdef set_encoding_error_handler(name): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6236 * global ERROR_HANDLER
|
|
jpayne@69
|
6237 * previous = ERROR_HANDLER
|
|
jpayne@69
|
6238 */
|
|
jpayne@69
|
6239
|
|
jpayne@69
|
6240 /* function exit code */
|
|
jpayne@69
|
6241 __pyx_L1_error:;
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|
jpayne@69
|
6242 __Pyx_XDECREF(__pyx_t_1);
|
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jpayne@69
|
6243 __Pyx_AddTraceback("pysam.libcutils.set_encoding_error_handler", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6244 __pyx_r = 0;
|
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jpayne@69
|
6245 __pyx_L0:;
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|
jpayne@69
|
6246 __Pyx_XDECREF(__pyx_v_previous);
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jpayne@69
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jpayne@69
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6248 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
6249 return __pyx_r;
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jpayne@69
|
6250 }
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jpayne@69
|
6251
|
|
jpayne@69
|
6252 /* Python wrapper */
|
|
jpayne@69
|
6253 static PyObject *__pyx_pw_5pysam_9libcutils_11set_encoding_error_handler(PyObject *__pyx_self,
|
|
jpayne@69
|
6254 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
6255 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
6256 #else
|
|
jpayne@69
|
6257 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
6258 #endif
|
|
jpayne@69
|
6259 ); /*proto*/
|
|
jpayne@69
|
6260 static PyMethodDef __pyx_mdef_5pysam_9libcutils_11set_encoding_error_handler = {"set_encoding_error_handler", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_11set_encoding_error_handler, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0};
|
|
jpayne@69
|
6261 static PyObject *__pyx_pw_5pysam_9libcutils_11set_encoding_error_handler(PyObject *__pyx_self,
|
|
jpayne@69
|
6262 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
6263 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
6264 #else
|
|
jpayne@69
|
6265 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
6266 #endif
|
|
jpayne@69
|
6267 ) {
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|
jpayne@69
|
6268 PyObject *__pyx_v_name = 0;
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|
jpayne@69
|
6269 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
6270 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
6271 #endif
|
|
jpayne@69
|
6272 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
6273 PyObject* values[1] = {0};
|
|
jpayne@69
|
6274 int __pyx_lineno = 0;
|
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jpayne@69
|
6275 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
6276 int __pyx_clineno = 0;
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jpayne@69
|
6277 PyObject *__pyx_r = 0;
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jpayne@69
|
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|
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6280 #if !CYTHON_METH_FASTCALL
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|
6281 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
6282 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
6283 #else
|
|
jpayne@69
|
6284 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
6285 #endif
|
|
jpayne@69
|
6286 #endif
|
|
jpayne@69
|
6287 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
6288 {
|
|
jpayne@69
|
6289 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_name,0};
|
|
jpayne@69
|
6290 if (__pyx_kwds) {
|
|
jpayne@69
|
6291 Py_ssize_t kw_args;
|
|
jpayne@69
|
6292 switch (__pyx_nargs) {
|
|
jpayne@69
|
6293 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
6294 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
6295 case 0: break;
|
|
jpayne@69
|
6296 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
6297 }
|
|
jpayne@69
|
6298 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
6299 switch (__pyx_nargs) {
|
|
jpayne@69
|
6300 case 0:
|
|
jpayne@69
|
6301 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_name)) != 0)) {
|
|
jpayne@69
|
6302 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
6303 kw_args--;
|
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jpayne@69
|
6304 }
|
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jpayne@69
|
6305 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 101, __pyx_L3_error)
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jpayne@69
|
6306 else goto __pyx_L5_argtuple_error;
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|
jpayne@69
|
6307 }
|
|
jpayne@69
|
6308 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
6309 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
6310 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "set_encoding_error_handler") < 0)) __PYX_ERR(0, 101, __pyx_L3_error)
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jpayne@69
|
6311 }
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jpayne@69
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6312 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
6313 goto __pyx_L5_argtuple_error;
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jpayne@69
|
6314 } else {
|
|
jpayne@69
|
6315 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
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jpayne@69
|
6316 }
|
|
jpayne@69
|
6317 __pyx_v_name = values[0];
|
|
jpayne@69
|
6318 }
|
|
jpayne@69
|
6319 goto __pyx_L6_skip;
|
|
jpayne@69
|
6320 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
6321 __Pyx_RaiseArgtupleInvalid("set_encoding_error_handler", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 101, __pyx_L3_error)
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jpayne@69
|
6322 __pyx_L6_skip:;
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jpayne@69
|
6323 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
6324 __pyx_L3_error:;
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jpayne@69
|
6325 {
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|
jpayne@69
|
6326 Py_ssize_t __pyx_temp;
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jpayne@69
|
6327 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
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|
jpayne@69
|
6328 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
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jpayne@69
|
6329 }
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|
jpayne@69
|
6330 }
|
|
jpayne@69
|
6331 __Pyx_AddTraceback("pysam.libcutils.set_encoding_error_handler", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
6332 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
6333 return NULL;
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|
jpayne@69
|
6334 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
6335 __pyx_r = __pyx_pf_5pysam_9libcutils_10set_encoding_error_handler(__pyx_self, __pyx_v_name);
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|
jpayne@69
|
6336
|
|
jpayne@69
|
6337 /* function exit code */
|
|
jpayne@69
|
6338 {
|
|
jpayne@69
|
6339 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
6340 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
6341 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
6342 }
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jpayne@69
|
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jpayne@69
|
6344 __Pyx_RefNannyFinishContext();
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jpayne@69
|
6345 return __pyx_r;
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jpayne@69
|
6346 }
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jpayne@69
|
6347
|
|
jpayne@69
|
6348 static PyObject *__pyx_pf_5pysam_9libcutils_10set_encoding_error_handler(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_name) {
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jpayne@69
|
6349 PyObject *__pyx_r = NULL;
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jpayne@69
|
6350 __Pyx_RefNannyDeclarations
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jpayne@69
|
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jpayne@69
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jpayne@69
|
6353 const char *__pyx_filename = NULL;
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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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|
6603 * return None
|
|
jpayne@69
|
6604 * elif PyBytes_Check(s):
|
|
jpayne@69
|
6605 */
|
|
jpayne@69
|
6606 __pyx_t_1 = (__pyx_v_s == Py_None);
|
|
jpayne@69
|
6607 if (__pyx_t_1) {
|
|
jpayne@69
|
6608
|
|
jpayne@69
|
6609 /* "pysam/libcutils.pyx":130
|
|
jpayne@69
|
6610 * """
|
|
jpayne@69
|
6611 * if s is None:
|
|
jpayne@69
|
6612 * return None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6613 * elif PyBytes_Check(s):
|
|
jpayne@69
|
6614 * return s
|
|
jpayne@69
|
6615 */
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jpayne@69
|
6616 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
6617 __pyx_r = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
6618 goto __pyx_L0;
|
|
jpayne@69
|
6619
|
|
jpayne@69
|
6620 /* "pysam/libcutils.pyx":129
|
|
jpayne@69
|
6621 * utf8 encoding.
|
|
jpayne@69
|
6622 * """
|
|
jpayne@69
|
6623 * if s is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6624 * return None
|
|
jpayne@69
|
6625 * elif PyBytes_Check(s):
|
|
jpayne@69
|
6626 */
|
|
jpayne@69
|
6627 }
|
|
jpayne@69
|
6628
|
|
jpayne@69
|
6629 /* "pysam/libcutils.pyx":131
|
|
jpayne@69
|
6630 * if s is None:
|
|
jpayne@69
|
6631 * return None
|
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jpayne@69
|
6632 * elif PyBytes_Check(s): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6633 * return s
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|
jpayne@69
|
6634 * elif PyUnicode_Check(s):
|
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jpayne@69
|
6635 */
|
|
jpayne@69
|
6636 __pyx_t_1 = PyBytes_Check(__pyx_v_s);
|
|
jpayne@69
|
6637 if (__pyx_t_1) {
|
|
jpayne@69
|
6638
|
|
jpayne@69
|
6639 /* "pysam/libcutils.pyx":132
|
|
jpayne@69
|
6640 * return None
|
|
jpayne@69
|
6641 * elif PyBytes_Check(s):
|
|
jpayne@69
|
6642 * return s # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6643 * elif PyUnicode_Check(s):
|
|
jpayne@69
|
6644 * return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
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jpayne@69
|
6645 */
|
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jpayne@69
|
6646 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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6647 if (!(likely(PyBytes_CheckExact(__pyx_v_s))||((__pyx_v_s) == Py_None) || __Pyx_RaiseUnexpectedTypeError("bytes", __pyx_v_s))) __PYX_ERR(0, 132, __pyx_L1_error)
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jpayne@69
|
6648 __Pyx_INCREF(__pyx_v_s);
|
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jpayne@69
|
6649 __pyx_r = ((PyObject*)__pyx_v_s);
|
|
jpayne@69
|
6650 goto __pyx_L0;
|
|
jpayne@69
|
6651
|
|
jpayne@69
|
6652 /* "pysam/libcutils.pyx":131
|
|
jpayne@69
|
6653 * if s is None:
|
|
jpayne@69
|
6654 * return None
|
|
jpayne@69
|
6655 * elif PyBytes_Check(s): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6656 * return s
|
|
jpayne@69
|
6657 * elif PyUnicode_Check(s):
|
|
jpayne@69
|
6658 */
|
|
jpayne@69
|
6659 }
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|
jpayne@69
|
6660
|
|
jpayne@69
|
6661 /* "pysam/libcutils.pyx":133
|
|
jpayne@69
|
6662 * elif PyBytes_Check(s):
|
|
jpayne@69
|
6663 * return s
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jpayne@69
|
6664 * elif PyUnicode_Check(s): # <<<<<<<<<<<<<<
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jpayne@69
|
6665 * return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
|
|
jpayne@69
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6666 * else:
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jpayne@69
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6667 */
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jpayne@69
|
6668 __pyx_t_1 = PyUnicode_Check(__pyx_v_s);
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jpayne@69
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6669 if (likely(__pyx_t_1)) {
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jpayne@69
|
6670
|
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jpayne@69
|
6671 /* "pysam/libcutils.pyx":134
|
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jpayne@69
|
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jpayne@69
|
6673 * elif PyUnicode_Check(s):
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jpayne@69
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6674 * return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) # <<<<<<<<<<<<<<
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|
6675 * else:
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|
jpayne@69
|
6676 * raise TypeError("Argument must be string, bytes or unicode.")
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jpayne@69
|
6677 */
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jpayne@69
|
6678 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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6679 __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_s, __pyx_n_s_encode); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 134, __pyx_L1_error)
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jpayne@69
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6682 if (!__pyx_t_1) {
|
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jpayne@69
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6683 } else {
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jpayne@69
|
6684 __Pyx_INCREF(__pyx_v_encoding);
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jpayne@69
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6685 __pyx_t_4 = __pyx_v_encoding;
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|
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|
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jpayne@69
|
6687 }
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|
jpayne@69
|
6688 __Pyx_INCREF(__pyx_v_5pysam_9libcutils_TEXT_ENCODING);
|
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jpayne@69
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6690 __pyx_L4_bool_binop_done:;
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jpayne@69
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jpayne@69
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jpayne@69
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6693 } else {
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jpayne@69
|
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|
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jpayne@69
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|
|
jpayne@69
|
6696 goto __pyx_L6_bool_binop_done;
|
|
jpayne@69
|
6697 }
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jpayne@69
|
6698 __Pyx_INCREF(__pyx_v_5pysam_9libcutils_ERROR_HANDLER);
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jpayne@69
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|
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jpayne@69
|
6700 __pyx_L6_bool_binop_done:;
|
|
jpayne@69
|
6701 __pyx_t_6 = NULL;
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jpayne@69
|
6702 __pyx_t_7 = 0;
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jpayne@69
|
6703 #if CYTHON_UNPACK_METHODS
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|
jpayne@69
|
6704 if (likely(PyMethod_Check(__pyx_t_3))) {
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jpayne@69
|
6705 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3);
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jpayne@69
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6706 if (likely(__pyx_t_6)) {
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jpayne@69
|
6707 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
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jpayne@69
|
6708 __Pyx_INCREF(__pyx_t_6);
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jpayne@69
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jpayne@69
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jpayne@69
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6712 }
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jpayne@69
|
6713 }
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jpayne@69
|
6714 #endif
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jpayne@69
|
6715 {
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jpayne@69
|
6716 PyObject *__pyx_callargs[3] = {__pyx_t_6, __pyx_t_4, __pyx_t_5};
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jpayne@69
|
6717 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_7, 2+__pyx_t_7);
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jpayne@69
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6718 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
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jpayne@69
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jpayne@69
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6722 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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jpayne@69
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6724 }
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jpayne@69
|
6725 if (!(likely(PyBytes_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None) || __Pyx_RaiseUnexpectedTypeError("bytes", __pyx_t_2))) __PYX_ERR(0, 134, __pyx_L1_error)
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jpayne@69
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jpayne@69
|
6727 __pyx_t_2 = 0;
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jpayne@69
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6728 goto __pyx_L0;
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jpayne@69
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6729
|
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jpayne@69
|
6730 /* "pysam/libcutils.pyx":133
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jpayne@69
|
6731 * elif PyBytes_Check(s):
|
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jpayne@69
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jpayne@69
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6733 * elif PyUnicode_Check(s): # <<<<<<<<<<<<<<
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6734 * return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
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jpayne@69
|
6735 * else:
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jpayne@69
|
6736 */
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jpayne@69
|
6737 }
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jpayne@69
|
6738
|
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jpayne@69
|
6739 /* "pysam/libcutils.pyx":136
|
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jpayne@69
|
6740 * return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
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jpayne@69
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jpayne@69
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6742 * raise TypeError("Argument must be string, bytes or unicode.") # <<<<<<<<<<<<<<
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jpayne@69
|
6743 *
|
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jpayne@69
|
6744 *
|
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jpayne@69
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jpayne@69
|
6746 /*else*/ {
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jpayne@69
|
6747 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 136, __pyx_L1_error)
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jpayne@69
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6748 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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6749 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
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jpayne@69
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6750 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
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6751 __PYX_ERR(0, 136, __pyx_L1_error)
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jpayne@69
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6752 }
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jpayne@69
|
6753
|
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jpayne@69
|
6754 /* "pysam/libcutils.pyx":125
|
|
jpayne@69
|
6755 *
|
|
jpayne@69
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6756 *
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jpayne@69
|
6757 * cdef bytes force_bytes(object s, encoding=None, errors=None): # <<<<<<<<<<<<<<
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jpayne@69
|
6758 * """convert string or unicode object to bytes, assuming
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jpayne@69
|
6759 * utf8 encoding.
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jpayne@69
|
6760 */
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|
jpayne@69
|
6761
|
|
jpayne@69
|
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|
|
jpayne@69
|
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|
6764 __Pyx_XDECREF(__pyx_t_2);
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jpayne@69
|
6765 __Pyx_XDECREF(__pyx_t_3);
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jpayne@69
|
6766 __Pyx_XDECREF(__pyx_t_4);
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jpayne@69
|
6767 __Pyx_XDECREF(__pyx_t_5);
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jpayne@69
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jpayne@69
|
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jpayne@69
|
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|
|
jpayne@69
|
6771 __pyx_L0:;
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jpayne@69
|
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jpayne@69
|
6773 __Pyx_RefNannyFinishContext();
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jpayne@69
|
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|
jpayne@69
|
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jpayne@69
|
6776
|
|
jpayne@69
|
6777 /* "pysam/libcutils.pyx":139
|
|
jpayne@69
|
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|
|
jpayne@69
|
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|
jpayne@69
|
6780 * cdef charptr_to_str(const char* s, encoding=None, errors=None): # <<<<<<<<<<<<<<
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|
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|
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jpayne@69
|
6783 */
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|
jpayne@69
|
6784
|
|
jpayne@69
|
6785 static PyObject *__pyx_f_5pysam_9libcutils_charptr_to_str(char const *__pyx_v_s, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str *__pyx_optional_args) {
|
|
jpayne@69
|
6786 PyObject *__pyx_v_encoding = ((PyObject *)Py_None);
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|
jpayne@69
|
6787 PyObject *__pyx_v_errors = ((PyObject *)Py_None);
|
|
jpayne@69
|
6788 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
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|
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jpayne@69
|
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jpayne@69
|
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|
jpayne@69
|
6792 PyObject *__pyx_t_3 = NULL;
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|
jpayne@69
|
6793 PyObject *__pyx_t_4 = NULL;
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|
jpayne@69
|
6794 PyObject *__pyx_t_5 = NULL;
|
|
jpayne@69
|
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|
jpayne@69
|
6796 unsigned int __pyx_t_7;
|
|
jpayne@69
|
6797 int __pyx_lineno = 0;
|
|
jpayne@69
|
6798 const char *__pyx_filename = NULL;
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jpayne@69
|
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|
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|
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jpayne@69
|
6803 __pyx_v_encoding = __pyx_optional_args->encoding;
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jpayne@69
|
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jpayne@69
|
6805 __pyx_v_errors = __pyx_optional_args->errors;
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jpayne@69
|
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jpayne@69
|
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jpayne@69
|
6808 }
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jpayne@69
|
6809
|
|
jpayne@69
|
6810 /* "pysam/libcutils.pyx":140
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jpayne@69
|
6811 *
|
|
jpayne@69
|
6812 * cdef charptr_to_str(const char* s, encoding=None, errors=None):
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6813 * if s == NULL: # <<<<<<<<<<<<<<
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jpayne@69
|
6814 * return None
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jpayne@69
|
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jpayne@69
|
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jpayne@69
|
6817 __pyx_t_1 = (__pyx_v_s == NULL);
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|
jpayne@69
|
6818 if (__pyx_t_1) {
|
|
jpayne@69
|
6819
|
|
jpayne@69
|
6820 /* "pysam/libcutils.pyx":141
|
|
jpayne@69
|
6821 * cdef charptr_to_str(const char* s, encoding=None, errors=None):
|
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jpayne@69
|
6822 * if s == NULL:
|
|
jpayne@69
|
6823 * return None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
6824 * return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
|
|
jpayne@69
|
6825 *
|
|
jpayne@69
|
6826 */
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jpayne@69
|
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jpayne@69
|
6828 __pyx_r = Py_None; __Pyx_INCREF(Py_None);
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jpayne@69
|
6829 goto __pyx_L0;
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jpayne@69
|
6830
|
|
jpayne@69
|
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|
jpayne@69
|
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|
|
jpayne@69
|
6833 * cdef charptr_to_str(const char* s, encoding=None, errors=None):
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jpayne@69
|
6834 * if s == NULL: # <<<<<<<<<<<<<<
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jpayne@69
|
6835 * return None
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jpayne@69
|
6836 * return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
|
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jpayne@69
|
6837 */
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jpayne@69
|
6838 }
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jpayne@69
|
6839
|
|
jpayne@69
|
6840 /* "pysam/libcutils.pyx":142
|
|
jpayne@69
|
6841 * if s == NULL:
|
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jpayne@69
|
6842 * return None
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jpayne@69
|
6843 * return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER) # <<<<<<<<<<<<<<
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|
jpayne@69
|
6844 *
|
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jpayne@69
|
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jpayne@69
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7091 /* "pysam/libcutils.pyx":152
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jpayne@69
|
7092 *
|
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jpayne@69
|
7093 * cdef bytes charptr_to_bytes(const char* s, encoding=None, errors=None):
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jpayne@69
|
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|
7095 * return None
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|
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|
7098 __pyx_t_1 = (__pyx_v_s == NULL);
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jpayne@69
|
7099 if (__pyx_t_1) {
|
|
jpayne@69
|
7100
|
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jpayne@69
|
7101 /* "pysam/libcutils.pyx":153
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|
jpayne@69
|
7102 * cdef bytes charptr_to_bytes(const char* s, encoding=None, errors=None):
|
|
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|
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|
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7109 __pyx_r = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
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jpayne@69
|
7111
|
|
jpayne@69
|
7112 /* "pysam/libcutils.pyx":152
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|
jpayne@69
|
7113 *
|
|
jpayne@69
|
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|
jpayne@69
|
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|
|
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|
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|
|
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|
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|
|
jpayne@69
|
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|
|
jpayne@69
|
7119 }
|
|
jpayne@69
|
7120
|
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jpayne@69
|
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|
|
jpayne@69
|
7122 * return None
|
|
jpayne@69
|
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jpayne@69
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|
|
jpayne@69
|
7125 *
|
|
jpayne@69
|
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|
|
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|
|
jpayne@69
|
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|
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jpayne@69
|
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jpayne@69
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7130 __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_s); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 155, __pyx_L1_error)
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jpayne@69
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7131 __Pyx_GOTREF(__pyx_t_2);
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7132 __pyx_r = ((PyObject*)__pyx_t_2);
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jpayne@69
|
7133 __pyx_t_2 = 0;
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jpayne@69
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7134 goto __pyx_L0;
|
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jpayne@69
|
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jpayne@69
|
7136
|
|
jpayne@69
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7137 /* "pysam/libcutils.pyx":151
|
|
jpayne@69
|
7138 *
|
|
jpayne@69
|
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|
|
jpayne@69
|
7140 * cdef bytes charptr_to_bytes(const char* s, encoding=None, errors=None): # <<<<<<<<<<<<<<
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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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|
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jpayne@69
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|
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jpayne@69
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jpayne@69
|
7155
|
|
jpayne@69
|
7156 /* "pysam/libcutils.pyx":158
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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
|
7161 * (bytes in Py2, unicode in Py3)"""
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jpayne@69
|
7162 */
|
|
jpayne@69
|
7163
|
|
jpayne@69
|
7164 static PyObject *__pyx_f_5pysam_9libcutils_force_str(PyObject *__pyx_v_s, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args) {
|
|
jpayne@69
|
7165 PyObject *__pyx_v_encoding = ((PyObject *)Py_None);
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jpayne@69
|
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jpayne@69
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jpayne@69
|
7171 PyObject *__pyx_t_3 = NULL;
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jpayne@69
|
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|
jpayne@69
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jpayne@69
|
7174 PyObject *__pyx_t_6 = NULL;
|
|
jpayne@69
|
7175 unsigned int __pyx_t_7;
|
|
jpayne@69
|
7176 int __pyx_lineno = 0;
|
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jpayne@69
|
7177 const char *__pyx_filename = NULL;
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jpayne@69
|
7178 int __pyx_clineno = 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
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jpayne@69
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jpayne@69
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7198
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jpayne@69
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jpayne@69
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jpayne@69
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7201 * if s is None:
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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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7211 * """Return s converted to str type of current Python
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jpayne@69
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jpayne@69
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jpayne@69
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7218
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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
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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
|
7271 }
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jpayne@69
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jpayne@69
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7273 {
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jpayne@69
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7275 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_7, 2+__pyx_t_7);
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jpayne@69
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7284 __pyx_t_2 = 0;
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jpayne@69
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7286
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jpayne@69
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|
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|
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|
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|
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jpayne@69
|
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|
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jpayne@69
|
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jpayne@69
|
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jpayne@69
|
7300 *
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jpayne@69
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7307
|
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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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7330
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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
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7348 PyObject *__pyx_t_5 = NULL;
|
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jpayne@69
|
7349 PyObject *__pyx_t_6 = NULL;
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jpayne@69
|
7350 unsigned int __pyx_t_7;
|
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jpayne@69
|
7351 int __pyx_lineno = 0;
|
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jpayne@69
|
7352 const char *__pyx_filename = NULL;
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jpayne@69
|
7353 int __pyx_clineno = 0;
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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
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|
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jpayne@69
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7359 __pyx_v_errors = __pyx_optional_args->errors;
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jpayne@69
|
7360 }
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jpayne@69
|
7361 }
|
|
jpayne@69
|
7362 }
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|
jpayne@69
|
7363
|
|
jpayne@69
|
7364 /* "pysam/libcutils.pyx":172
|
|
jpayne@69
|
7365 * """Return s converted to current Python's str type,
|
|
jpayne@69
|
7366 * always decoding even in Python 2"""
|
|
jpayne@69
|
7367 * if s is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7368 * return None
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|
jpayne@69
|
7369 * else:
|
|
jpayne@69
|
7370 */
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|
jpayne@69
|
7371 __pyx_t_1 = (__pyx_v_s == ((PyObject*)Py_None));
|
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jpayne@69
|
7372 if (__pyx_t_1) {
|
|
jpayne@69
|
7373
|
|
jpayne@69
|
7374 /* "pysam/libcutils.pyx":173
|
|
jpayne@69
|
7375 * always decoding even in Python 2"""
|
|
jpayne@69
|
7376 * if s is None:
|
|
jpayne@69
|
7377 * return None # <<<<<<<<<<<<<<
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jpayne@69
|
7378 * else:
|
|
jpayne@69
|
7379 * return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
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jpayne@69
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7380 */
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jpayne@69
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7381 __Pyx_XDECREF(__pyx_r);
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jpayne@69
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7383 goto __pyx_L0;
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jpayne@69
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7384
|
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jpayne@69
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|
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jpayne@69
|
7386 * """Return s converted to current Python's str type,
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jpayne@69
|
7387 * always decoding even in Python 2"""
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|
jpayne@69
|
7388 * if s is None: # <<<<<<<<<<<<<<
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|
jpayne@69
|
7389 * return None
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jpayne@69
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|
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jpayne@69
|
7391 */
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jpayne@69
|
7392 }
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jpayne@69
|
7393
|
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jpayne@69
|
7394 /* "pysam/libcutils.pyx":175
|
|
jpayne@69
|
7395 * return None
|
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jpayne@69
|
7396 * else:
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jpayne@69
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jpayne@69
|
7398 *
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jpayne@69
|
7399 *
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jpayne@69
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7401 /*else*/ {
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jpayne@69
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7402 __Pyx_XDECREF(__pyx_r);
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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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7407 } else {
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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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7411 }
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jpayne@69
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7412 __Pyx_INCREF(__pyx_v_5pysam_9libcutils_TEXT_ENCODING);
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jpayne@69
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jpayne@69
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7414 __pyx_L4_bool_binop_done:;
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jpayne@69
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7415 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_errors); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 175, __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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7421 }
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jpayne@69
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jpayne@69
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jpayne@69
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7424 __pyx_L6_bool_binop_done:;
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jpayne@69
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7425 __pyx_t_6 = NULL;
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jpayne@69
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7426 __pyx_t_7 = 0;
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jpayne@69
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7427 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
7428 if (likely(PyMethod_Check(__pyx_t_3))) {
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jpayne@69
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7429 __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3);
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jpayne@69
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7430 if (likely(__pyx_t_6)) {
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jpayne@69
|
7431 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3);
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jpayne@69
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7432 __Pyx_INCREF(__pyx_t_6);
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jpayne@69
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7433 __Pyx_INCREF(function);
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jpayne@69
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7434 __Pyx_DECREF_SET(__pyx_t_3, function);
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jpayne@69
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7435 __pyx_t_7 = 1;
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jpayne@69
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7436 }
|
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jpayne@69
|
7437 }
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jpayne@69
|
7438 #endif
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jpayne@69
|
7439 {
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jpayne@69
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7440 PyObject *__pyx_callargs[3] = {__pyx_t_6, __pyx_t_4, __pyx_t_5};
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jpayne@69
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7441 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_7, 2+__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
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7445 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 175, __pyx_L1_error)
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jpayne@69
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7446 __Pyx_GOTREF(__pyx_t_2);
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jpayne@69
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7447 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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jpayne@69
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7448 }
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jpayne@69
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7449 __pyx_r = __pyx_t_2;
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jpayne@69
|
7450 __pyx_t_2 = 0;
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jpayne@69
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7451 goto __pyx_L0;
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jpayne@69
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7452 }
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jpayne@69
|
7453
|
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jpayne@69
|
7454 /* "pysam/libcutils.pyx":169
|
|
jpayne@69
|
7455 *
|
|
jpayne@69
|
7456 *
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|
jpayne@69
|
7457 * cdef decode_bytes(bytes s, encoding=None, errors=None): # <<<<<<<<<<<<<<
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jpayne@69
|
7458 * """Return s converted to current Python's str type,
|
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jpayne@69
|
7459 * always decoding even in Python 2"""
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jpayne@69
|
7460 */
|
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jpayne@69
|
7461
|
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jpayne@69
|
7462 /* function exit code */
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jpayne@69
|
7463 __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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jpayne@69
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7467 __Pyx_XDECREF(__pyx_t_5);
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jpayne@69
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7468 __Pyx_XDECREF(__pyx_t_6);
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jpayne@69
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7469 __Pyx_AddTraceback("pysam.libcutils.decode_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
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jpayne@69
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jpayne@69
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jpayne@69
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7475 }
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jpayne@69
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7476
|
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jpayne@69
|
7477 /* "pysam/libcutils.pyx":178
|
|
jpayne@69
|
7478 *
|
|
jpayne@69
|
7479 *
|
|
jpayne@69
|
7480 * cpdef parse_region(contig=None, # <<<<<<<<<<<<<<
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jpayne@69
|
7481 * start=None,
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jpayne@69
|
7482 * stop=None,
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jpayne@69
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7483 */
|
|
jpayne@69
|
7484
|
|
jpayne@69
|
7485 static PyObject *__pyx_pw_5pysam_9libcutils_13parse_region(PyObject *__pyx_self,
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|
jpayne@69
|
7486 #if CYTHON_METH_FASTCALL
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jpayne@69
|
7487 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
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jpayne@69
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7488 #else
|
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jpayne@69
|
7489 PyObject *__pyx_args, PyObject *__pyx_kwds
|
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jpayne@69
|
7490 #endif
|
|
jpayne@69
|
7491 ); /*proto*/
|
|
jpayne@69
|
7492 static PyObject *__pyx_f_5pysam_9libcutils_parse_region(CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_parse_region *__pyx_optional_args) {
|
|
jpayne@69
|
7493 PyObject *__pyx_v_contig = ((PyObject *)Py_None);
|
|
jpayne@69
|
7494
|
|
jpayne@69
|
7495 /* "pysam/libcutils.pyx":179
|
|
jpayne@69
|
7496 *
|
|
jpayne@69
|
7497 * cpdef parse_region(contig=None,
|
|
jpayne@69
|
7498 * start=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7499 * stop=None,
|
|
jpayne@69
|
7500 * region=None,
|
|
jpayne@69
|
7501 */
|
|
jpayne@69
|
7502 PyObject *__pyx_v_start = ((PyObject *)Py_None);
|
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jpayne@69
|
7503
|
|
jpayne@69
|
7504 /* "pysam/libcutils.pyx":180
|
|
jpayne@69
|
7505 * cpdef parse_region(contig=None,
|
|
jpayne@69
|
7506 * start=None,
|
|
jpayne@69
|
7507 * stop=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7508 * region=None,
|
|
jpayne@69
|
7509 * reference=None,
|
|
jpayne@69
|
7510 */
|
|
jpayne@69
|
7511 PyObject *__pyx_v_stop = ((PyObject *)Py_None);
|
|
jpayne@69
|
7512
|
|
jpayne@69
|
7513 /* "pysam/libcutils.pyx":181
|
|
jpayne@69
|
7514 * start=None,
|
|
jpayne@69
|
7515 * stop=None,
|
|
jpayne@69
|
7516 * region=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7517 * reference=None,
|
|
jpayne@69
|
7518 * end=None):
|
|
jpayne@69
|
7519 */
|
|
jpayne@69
|
7520 PyObject *__pyx_v_region = ((PyObject *)Py_None);
|
|
jpayne@69
|
7521
|
|
jpayne@69
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7522 /* "pysam/libcutils.pyx":182
|
|
jpayne@69
|
7523 * stop=None,
|
|
jpayne@69
|
7524 * region=None,
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|
jpayne@69
|
7525 * reference=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7526 * end=None):
|
|
jpayne@69
|
7527 * """parse alternative ways to specify a genomic region. A region can
|
|
jpayne@69
|
7528 */
|
|
jpayne@69
|
7529 PyObject *__pyx_v_reference = ((PyObject *)Py_None);
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|
jpayne@69
|
7530
|
|
jpayne@69
|
7531 /* "pysam/libcutils.pyx":183
|
|
jpayne@69
|
7532 * region=None,
|
|
jpayne@69
|
7533 * reference=None,
|
|
jpayne@69
|
7534 * end=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7535 * """parse alternative ways to specify a genomic region. A region can
|
|
jpayne@69
|
7536 * either be specified by :term:`reference`, `start` and
|
|
jpayne@69
|
7537 */
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|
jpayne@69
|
7538 PyObject *__pyx_v_end = ((PyObject *)Py_None);
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|
jpayne@69
|
7539 int32_t __pyx_v_rstart;
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jpayne@69
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7540 int32_t __pyx_v_rstop;
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jpayne@69
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7541 PyObject *__pyx_v_coord = NULL;
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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
|
7547 int __pyx_t_3;
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jpayne@69
|
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jpayne@69
|
7549 PyObject *__pyx_t_5 = NULL;
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jpayne@69
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7550 PyObject *__pyx_t_6 = NULL;
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jpayne@69
|
7551 int32_t __pyx_t_7;
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jpayne@69
|
7552 int __pyx_t_8;
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|
jpayne@69
|
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jpayne@69
|
7554 PyObject *__pyx_t_10 = NULL;
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jpayne@69
|
7555 PyObject *__pyx_t_11 = NULL;
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jpayne@69
|
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jpayne@69
|
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jpayne@69
|
7558 PyObject *(*__pyx_t_14)(PyObject *);
|
|
jpayne@69
|
7559 Py_ssize_t __pyx_t_15;
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jpayne@69
|
7560 int __pyx_lineno = 0;
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jpayne@69
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7561 const char *__pyx_filename = NULL;
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jpayne@69
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jpayne@69
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7563 __Pyx_RefNannySetupContext("parse_region", 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
|
7567 if (__pyx_optional_args->__pyx_n > 1) {
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|
jpayne@69
|
7568 __pyx_v_start = __pyx_optional_args->start;
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|
jpayne@69
|
7569 if (__pyx_optional_args->__pyx_n > 2) {
|
|
jpayne@69
|
7570 __pyx_v_stop = __pyx_optional_args->stop;
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|
jpayne@69
|
7571 if (__pyx_optional_args->__pyx_n > 3) {
|
|
jpayne@69
|
7572 __pyx_v_region = __pyx_optional_args->region;
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|
jpayne@69
|
7573 if (__pyx_optional_args->__pyx_n > 4) {
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|
jpayne@69
|
7574 __pyx_v_reference = __pyx_optional_args->reference;
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jpayne@69
|
7575 if (__pyx_optional_args->__pyx_n > 5) {
|
|
jpayne@69
|
7576 __pyx_v_end = __pyx_optional_args->end;
|
|
jpayne@69
|
7577 }
|
|
jpayne@69
|
7578 }
|
|
jpayne@69
|
7579 }
|
|
jpayne@69
|
7580 }
|
|
jpayne@69
|
7581 }
|
|
jpayne@69
|
7582 }
|
|
jpayne@69
|
7583 }
|
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jpayne@69
|
7584 __Pyx_INCREF(__pyx_v_contig);
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jpayne@69
|
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|
jpayne@69
|
7586
|
|
jpayne@69
|
7587 /* "pysam/libcutils.pyx":216
|
|
jpayne@69
|
7588 *
|
|
jpayne@69
|
7589 *
|
|
jpayne@69
|
7590 * if reference is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7591 * if contig is not None:
|
|
jpayne@69
|
7592 * raise ValueError('contig and reference should not both be specified')
|
|
jpayne@69
|
7593 */
|
|
jpayne@69
|
7594 __pyx_t_1 = (__pyx_v_reference != Py_None);
|
|
jpayne@69
|
7595 if (__pyx_t_1) {
|
|
jpayne@69
|
7596
|
|
jpayne@69
|
7597 /* "pysam/libcutils.pyx":217
|
|
jpayne@69
|
7598 *
|
|
jpayne@69
|
7599 * if reference is not None:
|
|
jpayne@69
|
7600 * if contig is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7601 * raise ValueError('contig and reference should not both be specified')
|
|
jpayne@69
|
7602 * contig = reference
|
|
jpayne@69
|
7603 */
|
|
jpayne@69
|
7604 __pyx_t_1 = (__pyx_v_contig != Py_None);
|
|
jpayne@69
|
7605 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
7606
|
|
jpayne@69
|
7607 /* "pysam/libcutils.pyx":218
|
|
jpayne@69
|
7608 * if reference is not None:
|
|
jpayne@69
|
7609 * if contig is not None:
|
|
jpayne@69
|
7610 * raise ValueError('contig and reference should not both be specified') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7611 * contig = reference
|
|
jpayne@69
|
7612 *
|
|
jpayne@69
|
7613 */
|
|
jpayne@69
|
7614 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 218, __pyx_L1_error)
|
|
jpayne@69
|
7615 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
7616 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
7617 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
7618 __PYX_ERR(0, 218, __pyx_L1_error)
|
|
jpayne@69
|
7619
|
|
jpayne@69
|
7620 /* "pysam/libcutils.pyx":217
|
|
jpayne@69
|
7621 *
|
|
jpayne@69
|
7622 * if reference is not None:
|
|
jpayne@69
|
7623 * if contig is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7624 * raise ValueError('contig and reference should not both be specified')
|
|
jpayne@69
|
7625 * contig = reference
|
|
jpayne@69
|
7626 */
|
|
jpayne@69
|
7627 }
|
|
jpayne@69
|
7628
|
|
jpayne@69
|
7629 /* "pysam/libcutils.pyx":219
|
|
jpayne@69
|
7630 * if contig is not None:
|
|
jpayne@69
|
7631 * raise ValueError('contig and reference should not both be specified')
|
|
jpayne@69
|
7632 * contig = reference # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7633 *
|
|
jpayne@69
|
7634 * if contig is not None and region is not None:
|
|
jpayne@69
|
7635 */
|
|
jpayne@69
|
7636 __Pyx_INCREF(__pyx_v_reference);
|
|
jpayne@69
|
7637 __Pyx_DECREF_SET(__pyx_v_contig, __pyx_v_reference);
|
|
jpayne@69
|
7638
|
|
jpayne@69
|
7639 /* "pysam/libcutils.pyx":216
|
|
jpayne@69
|
7640 *
|
|
jpayne@69
|
7641 *
|
|
jpayne@69
|
7642 * if reference is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7643 * if contig is not None:
|
|
jpayne@69
|
7644 * raise ValueError('contig and reference should not both be specified')
|
|
jpayne@69
|
7645 */
|
|
jpayne@69
|
7646 }
|
|
jpayne@69
|
7647
|
|
jpayne@69
|
7648 /* "pysam/libcutils.pyx":221
|
|
jpayne@69
|
7649 * contig = reference
|
|
jpayne@69
|
7650 *
|
|
jpayne@69
|
7651 * if contig is not None and region is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7652 * raise ValueError('contig/reference and region should not both be specified')
|
|
jpayne@69
|
7653 *
|
|
jpayne@69
|
7654 */
|
|
jpayne@69
|
7655 __pyx_t_3 = (__pyx_v_contig != Py_None);
|
|
jpayne@69
|
7656 if (__pyx_t_3) {
|
|
jpayne@69
|
7657 } else {
|
|
jpayne@69
|
7658 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
7659 goto __pyx_L6_bool_binop_done;
|
|
jpayne@69
|
7660 }
|
|
jpayne@69
|
7661 __pyx_t_3 = (__pyx_v_region != Py_None);
|
|
jpayne@69
|
7662 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
7663 __pyx_L6_bool_binop_done:;
|
|
jpayne@69
|
7664 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
7665
|
|
jpayne@69
|
7666 /* "pysam/libcutils.pyx":222
|
|
jpayne@69
|
7667 *
|
|
jpayne@69
|
7668 * if contig is not None and region is not None:
|
|
jpayne@69
|
7669 * raise ValueError('contig/reference and region should not both be specified') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7670 *
|
|
jpayne@69
|
7671 * if end is not None:
|
|
jpayne@69
|
7672 */
|
|
jpayne@69
|
7673 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 222, __pyx_L1_error)
|
|
jpayne@69
|
7674 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
7675 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
7676 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
7677 __PYX_ERR(0, 222, __pyx_L1_error)
|
|
jpayne@69
|
7678
|
|
jpayne@69
|
7679 /* "pysam/libcutils.pyx":221
|
|
jpayne@69
|
7680 * contig = reference
|
|
jpayne@69
|
7681 *
|
|
jpayne@69
|
7682 * if contig is not None and region is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7683 * raise ValueError('contig/reference and region should not both be specified')
|
|
jpayne@69
|
7684 *
|
|
jpayne@69
|
7685 */
|
|
jpayne@69
|
7686 }
|
|
jpayne@69
|
7687
|
|
jpayne@69
|
7688 /* "pysam/libcutils.pyx":224
|
|
jpayne@69
|
7689 * raise ValueError('contig/reference and region should not both be specified')
|
|
jpayne@69
|
7690 *
|
|
jpayne@69
|
7691 * if end is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7692 * if stop is not None:
|
|
jpayne@69
|
7693 * raise ValueError('stop and end should not both be specified')
|
|
jpayne@69
|
7694 */
|
|
jpayne@69
|
7695 __pyx_t_1 = (__pyx_v_end != Py_None);
|
|
jpayne@69
|
7696 if (__pyx_t_1) {
|
|
jpayne@69
|
7697
|
|
jpayne@69
|
7698 /* "pysam/libcutils.pyx":225
|
|
jpayne@69
|
7699 *
|
|
jpayne@69
|
7700 * if end is not None:
|
|
jpayne@69
|
7701 * if stop is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7702 * raise ValueError('stop and end should not both be specified')
|
|
jpayne@69
|
7703 * stop = end
|
|
jpayne@69
|
7704 */
|
|
jpayne@69
|
7705 __pyx_t_1 = (__pyx_v_stop != Py_None);
|
|
jpayne@69
|
7706 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
7707
|
|
jpayne@69
|
7708 /* "pysam/libcutils.pyx":226
|
|
jpayne@69
|
7709 * if end is not None:
|
|
jpayne@69
|
7710 * if stop is not None:
|
|
jpayne@69
|
7711 * raise ValueError('stop and end should not both be specified') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7712 * stop = end
|
|
jpayne@69
|
7713 *
|
|
jpayne@69
|
7714 */
|
|
jpayne@69
|
7715 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 226, __pyx_L1_error)
|
|
jpayne@69
|
7716 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
7717 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
7718 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
7719 __PYX_ERR(0, 226, __pyx_L1_error)
|
|
jpayne@69
|
7720
|
|
jpayne@69
|
7721 /* "pysam/libcutils.pyx":225
|
|
jpayne@69
|
7722 *
|
|
jpayne@69
|
7723 * if end is not None:
|
|
jpayne@69
|
7724 * if stop is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7725 * raise ValueError('stop and end should not both be specified')
|
|
jpayne@69
|
7726 * stop = end
|
|
jpayne@69
|
7727 */
|
|
jpayne@69
|
7728 }
|
|
jpayne@69
|
7729
|
|
jpayne@69
|
7730 /* "pysam/libcutils.pyx":227
|
|
jpayne@69
|
7731 * if stop is not None:
|
|
jpayne@69
|
7732 * raise ValueError('stop and end should not both be specified')
|
|
jpayne@69
|
7733 * stop = end # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7734 *
|
|
jpayne@69
|
7735 * if contig is None and region is None:
|
|
jpayne@69
|
7736 */
|
|
jpayne@69
|
7737 __Pyx_INCREF(__pyx_v_end);
|
|
jpayne@69
|
7738 __Pyx_DECREF_SET(__pyx_v_stop, __pyx_v_end);
|
|
jpayne@69
|
7739
|
|
jpayne@69
|
7740 /* "pysam/libcutils.pyx":224
|
|
jpayne@69
|
7741 * raise ValueError('contig/reference and region should not both be specified')
|
|
jpayne@69
|
7742 *
|
|
jpayne@69
|
7743 * if end is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7744 * if stop is not None:
|
|
jpayne@69
|
7745 * raise ValueError('stop and end should not both be specified')
|
|
jpayne@69
|
7746 */
|
|
jpayne@69
|
7747 }
|
|
jpayne@69
|
7748
|
|
jpayne@69
|
7749 /* "pysam/libcutils.pyx":229
|
|
jpayne@69
|
7750 * stop = end
|
|
jpayne@69
|
7751 *
|
|
jpayne@69
|
7752 * if contig is None and region is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7753 * raise ValueError("neither contig nor region are given")
|
|
jpayne@69
|
7754 *
|
|
jpayne@69
|
7755 */
|
|
jpayne@69
|
7756 __pyx_t_3 = (__pyx_v_contig == Py_None);
|
|
jpayne@69
|
7757 if (__pyx_t_3) {
|
|
jpayne@69
|
7758 } else {
|
|
jpayne@69
|
7759 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
7760 goto __pyx_L11_bool_binop_done;
|
|
jpayne@69
|
7761 }
|
|
jpayne@69
|
7762 __pyx_t_3 = (__pyx_v_region == Py_None);
|
|
jpayne@69
|
7763 __pyx_t_1 = __pyx_t_3;
|
|
jpayne@69
|
7764 __pyx_L11_bool_binop_done:;
|
|
jpayne@69
|
7765 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
7766
|
|
jpayne@69
|
7767 /* "pysam/libcutils.pyx":230
|
|
jpayne@69
|
7768 *
|
|
jpayne@69
|
7769 * if contig is None and region is None:
|
|
jpayne@69
|
7770 * raise ValueError("neither contig nor region are given") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7771 *
|
|
jpayne@69
|
7772 * rstart = 0
|
|
jpayne@69
|
7773 */
|
|
jpayne@69
|
7774 __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 230, __pyx_L1_error)
|
|
jpayne@69
|
7775 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
7776 __Pyx_Raise(__pyx_t_2, 0, 0, 0);
|
|
jpayne@69
|
7777 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
7778 __PYX_ERR(0, 230, __pyx_L1_error)
|
|
jpayne@69
|
7779
|
|
jpayne@69
|
7780 /* "pysam/libcutils.pyx":229
|
|
jpayne@69
|
7781 * stop = end
|
|
jpayne@69
|
7782 *
|
|
jpayne@69
|
7783 * if contig is None and region is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7784 * raise ValueError("neither contig nor region are given")
|
|
jpayne@69
|
7785 *
|
|
jpayne@69
|
7786 */
|
|
jpayne@69
|
7787 }
|
|
jpayne@69
|
7788
|
|
jpayne@69
|
7789 /* "pysam/libcutils.pyx":232
|
|
jpayne@69
|
7790 * raise ValueError("neither contig nor region are given")
|
|
jpayne@69
|
7791 *
|
|
jpayne@69
|
7792 * rstart = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7793 * rstop = MAX_POS
|
|
jpayne@69
|
7794 * if start is not None:
|
|
jpayne@69
|
7795 */
|
|
jpayne@69
|
7796 __pyx_v_rstart = 0;
|
|
jpayne@69
|
7797
|
|
jpayne@69
|
7798 /* "pysam/libcutils.pyx":233
|
|
jpayne@69
|
7799 *
|
|
jpayne@69
|
7800 * rstart = 0
|
|
jpayne@69
|
7801 * rstop = MAX_POS # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7802 * if start is not None:
|
|
jpayne@69
|
7803 * try:
|
|
jpayne@69
|
7804 */
|
|
jpayne@69
|
7805 __pyx_v_rstop = __pyx_v_5pysam_9libcutils_MAX_POS;
|
|
jpayne@69
|
7806
|
|
jpayne@69
|
7807 /* "pysam/libcutils.pyx":234
|
|
jpayne@69
|
7808 * rstart = 0
|
|
jpayne@69
|
7809 * rstop = MAX_POS
|
|
jpayne@69
|
7810 * if start is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7811 * try:
|
|
jpayne@69
|
7812 * rstart = start
|
|
jpayne@69
|
7813 */
|
|
jpayne@69
|
7814 __pyx_t_1 = (__pyx_v_start != Py_None);
|
|
jpayne@69
|
7815 if (__pyx_t_1) {
|
|
jpayne@69
|
7816
|
|
jpayne@69
|
7817 /* "pysam/libcutils.pyx":235
|
|
jpayne@69
|
7818 * rstop = MAX_POS
|
|
jpayne@69
|
7819 * if start is not None:
|
|
jpayne@69
|
7820 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7821 * rstart = start
|
|
jpayne@69
|
7822 * except OverflowError:
|
|
jpayne@69
|
7823 */
|
|
jpayne@69
|
7824 {
|
|
jpayne@69
|
7825 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
7826 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
7827 __Pyx_ExceptionSave(&__pyx_t_4, &__pyx_t_5, &__pyx_t_6);
|
|
jpayne@69
|
7828 __Pyx_XGOTREF(__pyx_t_4);
|
|
jpayne@69
|
7829 __Pyx_XGOTREF(__pyx_t_5);
|
|
jpayne@69
|
7830 __Pyx_XGOTREF(__pyx_t_6);
|
|
jpayne@69
|
7831 /*try:*/ {
|
|
jpayne@69
|
7832
|
|
jpayne@69
|
7833 /* "pysam/libcutils.pyx":236
|
|
jpayne@69
|
7834 * if start is not None:
|
|
jpayne@69
|
7835 * try:
|
|
jpayne@69
|
7836 * rstart = start # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7837 * except OverflowError:
|
|
jpayne@69
|
7838 * raise ValueError('start out of range (%i)' % start)
|
|
jpayne@69
|
7839 */
|
|
jpayne@69
|
7840 __pyx_t_7 = __Pyx_PyInt_As_int32_t(__pyx_v_start); if (unlikely((__pyx_t_7 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 236, __pyx_L14_error)
|
|
jpayne@69
|
7841 __pyx_v_rstart = __pyx_t_7;
|
|
jpayne@69
|
7842
|
|
jpayne@69
|
7843 /* "pysam/libcutils.pyx":235
|
|
jpayne@69
|
7844 * rstop = MAX_POS
|
|
jpayne@69
|
7845 * if start is not None:
|
|
jpayne@69
|
7846 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7847 * rstart = start
|
|
jpayne@69
|
7848 * except OverflowError:
|
|
jpayne@69
|
7849 */
|
|
jpayne@69
|
7850 }
|
|
jpayne@69
|
7851 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
7852 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
7853 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
7854 goto __pyx_L19_try_end;
|
|
jpayne@69
|
7855 __pyx_L14_error:;
|
|
jpayne@69
|
7856 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
7857
|
|
jpayne@69
|
7858 /* "pysam/libcutils.pyx":237
|
|
jpayne@69
|
7859 * try:
|
|
jpayne@69
|
7860 * rstart = start
|
|
jpayne@69
|
7861 * except OverflowError: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7862 * raise ValueError('start out of range (%i)' % start)
|
|
jpayne@69
|
7863 *
|
|
jpayne@69
|
7864 */
|
|
jpayne@69
|
7865 __pyx_t_8 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
|
|
jpayne@69
|
7866 if (__pyx_t_8) {
|
|
jpayne@69
|
7867 __Pyx_AddTraceback("pysam.libcutils.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7868 if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_9, &__pyx_t_10) < 0) __PYX_ERR(0, 237, __pyx_L16_except_error)
|
|
jpayne@69
|
7869 __Pyx_XGOTREF(__pyx_t_2);
|
|
jpayne@69
|
7870 __Pyx_XGOTREF(__pyx_t_9);
|
|
jpayne@69
|
7871 __Pyx_XGOTREF(__pyx_t_10);
|
|
jpayne@69
|
7872
|
|
jpayne@69
|
7873 /* "pysam/libcutils.pyx":238
|
|
jpayne@69
|
7874 * rstart = start
|
|
jpayne@69
|
7875 * except OverflowError:
|
|
jpayne@69
|
7876 * raise ValueError('start out of range (%i)' % start) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7877 *
|
|
jpayne@69
|
7878 * if stop is not None:
|
|
jpayne@69
|
7879 */
|
|
jpayne@69
|
7880 __pyx_t_11 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_start_out_of_range_i, __pyx_v_start); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 238, __pyx_L16_except_error)
|
|
jpayne@69
|
7881 __Pyx_GOTREF(__pyx_t_11);
|
|
jpayne@69
|
7882 __pyx_t_12 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_11); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 238, __pyx_L16_except_error)
|
|
jpayne@69
|
7883 __Pyx_GOTREF(__pyx_t_12);
|
|
jpayne@69
|
7884 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
7885 __Pyx_Raise(__pyx_t_12, 0, 0, 0);
|
|
jpayne@69
|
7886 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
7887 __PYX_ERR(0, 238, __pyx_L16_except_error)
|
|
jpayne@69
|
7888 }
|
|
jpayne@69
|
7889 goto __pyx_L16_except_error;
|
|
jpayne@69
|
7890
|
|
jpayne@69
|
7891 /* "pysam/libcutils.pyx":235
|
|
jpayne@69
|
7892 * rstop = MAX_POS
|
|
jpayne@69
|
7893 * if start is not None:
|
|
jpayne@69
|
7894 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7895 * rstart = start
|
|
jpayne@69
|
7896 * except OverflowError:
|
|
jpayne@69
|
7897 */
|
|
jpayne@69
|
7898 __pyx_L16_except_error:;
|
|
jpayne@69
|
7899 __Pyx_XGIVEREF(__pyx_t_4);
|
|
jpayne@69
|
7900 __Pyx_XGIVEREF(__pyx_t_5);
|
|
jpayne@69
|
7901 __Pyx_XGIVEREF(__pyx_t_6);
|
|
jpayne@69
|
7902 __Pyx_ExceptionReset(__pyx_t_4, __pyx_t_5, __pyx_t_6);
|
|
jpayne@69
|
7903 goto __pyx_L1_error;
|
|
jpayne@69
|
7904 __pyx_L19_try_end:;
|
|
jpayne@69
|
7905 }
|
|
jpayne@69
|
7906
|
|
jpayne@69
|
7907 /* "pysam/libcutils.pyx":234
|
|
jpayne@69
|
7908 * rstart = 0
|
|
jpayne@69
|
7909 * rstop = MAX_POS
|
|
jpayne@69
|
7910 * if start is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7911 * try:
|
|
jpayne@69
|
7912 * rstart = start
|
|
jpayne@69
|
7913 */
|
|
jpayne@69
|
7914 }
|
|
jpayne@69
|
7915
|
|
jpayne@69
|
7916 /* "pysam/libcutils.pyx":240
|
|
jpayne@69
|
7917 * raise ValueError('start out of range (%i)' % start)
|
|
jpayne@69
|
7918 *
|
|
jpayne@69
|
7919 * if stop is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7920 * try:
|
|
jpayne@69
|
7921 * rstop = stop
|
|
jpayne@69
|
7922 */
|
|
jpayne@69
|
7923 __pyx_t_1 = (__pyx_v_stop != Py_None);
|
|
jpayne@69
|
7924 if (__pyx_t_1) {
|
|
jpayne@69
|
7925
|
|
jpayne@69
|
7926 /* "pysam/libcutils.pyx":241
|
|
jpayne@69
|
7927 *
|
|
jpayne@69
|
7928 * if stop is not None:
|
|
jpayne@69
|
7929 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7930 * rstop = stop
|
|
jpayne@69
|
7931 * except OverflowError:
|
|
jpayne@69
|
7932 */
|
|
jpayne@69
|
7933 {
|
|
jpayne@69
|
7934 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
7935 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
7936 __Pyx_ExceptionSave(&__pyx_t_6, &__pyx_t_5, &__pyx_t_4);
|
|
jpayne@69
|
7937 __Pyx_XGOTREF(__pyx_t_6);
|
|
jpayne@69
|
7938 __Pyx_XGOTREF(__pyx_t_5);
|
|
jpayne@69
|
7939 __Pyx_XGOTREF(__pyx_t_4);
|
|
jpayne@69
|
7940 /*try:*/ {
|
|
jpayne@69
|
7941
|
|
jpayne@69
|
7942 /* "pysam/libcutils.pyx":242
|
|
jpayne@69
|
7943 * if stop is not None:
|
|
jpayne@69
|
7944 * try:
|
|
jpayne@69
|
7945 * rstop = stop # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7946 * except OverflowError:
|
|
jpayne@69
|
7947 * raise ValueError('stop out of range (%i)' % stop)
|
|
jpayne@69
|
7948 */
|
|
jpayne@69
|
7949 __pyx_t_7 = __Pyx_PyInt_As_int32_t(__pyx_v_stop); if (unlikely((__pyx_t_7 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 242, __pyx_L23_error)
|
|
jpayne@69
|
7950 __pyx_v_rstop = __pyx_t_7;
|
|
jpayne@69
|
7951
|
|
jpayne@69
|
7952 /* "pysam/libcutils.pyx":241
|
|
jpayne@69
|
7953 *
|
|
jpayne@69
|
7954 * if stop is not None:
|
|
jpayne@69
|
7955 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7956 * rstop = stop
|
|
jpayne@69
|
7957 * except OverflowError:
|
|
jpayne@69
|
7958 */
|
|
jpayne@69
|
7959 }
|
|
jpayne@69
|
7960 __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
7961 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
7962 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
7963 goto __pyx_L28_try_end;
|
|
jpayne@69
|
7964 __pyx_L23_error:;
|
|
jpayne@69
|
7965 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
7966 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
7967 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
7968 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
7969 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
7970
|
|
jpayne@69
|
7971 /* "pysam/libcutils.pyx":243
|
|
jpayne@69
|
7972 * try:
|
|
jpayne@69
|
7973 * rstop = stop
|
|
jpayne@69
|
7974 * except OverflowError: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7975 * raise ValueError('stop out of range (%i)' % stop)
|
|
jpayne@69
|
7976 *
|
|
jpayne@69
|
7977 */
|
|
jpayne@69
|
7978 __pyx_t_8 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
|
|
jpayne@69
|
7979 if (__pyx_t_8) {
|
|
jpayne@69
|
7980 __Pyx_AddTraceback("pysam.libcutils.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
7981 if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_2) < 0) __PYX_ERR(0, 243, __pyx_L25_except_error)
|
|
jpayne@69
|
7982 __Pyx_XGOTREF(__pyx_t_10);
|
|
jpayne@69
|
7983 __Pyx_XGOTREF(__pyx_t_9);
|
|
jpayne@69
|
7984 __Pyx_XGOTREF(__pyx_t_2);
|
|
jpayne@69
|
7985
|
|
jpayne@69
|
7986 /* "pysam/libcutils.pyx":244
|
|
jpayne@69
|
7987 * rstop = stop
|
|
jpayne@69
|
7988 * except OverflowError:
|
|
jpayne@69
|
7989 * raise ValueError('stop out of range (%i)' % stop) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
7990 *
|
|
jpayne@69
|
7991 * if region:
|
|
jpayne@69
|
7992 */
|
|
jpayne@69
|
7993 __pyx_t_12 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_stop_out_of_range_i, __pyx_v_stop); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 244, __pyx_L25_except_error)
|
|
jpayne@69
|
7994 __Pyx_GOTREF(__pyx_t_12);
|
|
jpayne@69
|
7995 __pyx_t_11 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_12); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 244, __pyx_L25_except_error)
|
|
jpayne@69
|
7996 __Pyx_GOTREF(__pyx_t_11);
|
|
jpayne@69
|
7997 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
7998 __Pyx_Raise(__pyx_t_11, 0, 0, 0);
|
|
jpayne@69
|
7999 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
8000 __PYX_ERR(0, 244, __pyx_L25_except_error)
|
|
jpayne@69
|
8001 }
|
|
jpayne@69
|
8002 goto __pyx_L25_except_error;
|
|
jpayne@69
|
8003
|
|
jpayne@69
|
8004 /* "pysam/libcutils.pyx":241
|
|
jpayne@69
|
8005 *
|
|
jpayne@69
|
8006 * if stop is not None:
|
|
jpayne@69
|
8007 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8008 * rstop = stop
|
|
jpayne@69
|
8009 * except OverflowError:
|
|
jpayne@69
|
8010 */
|
|
jpayne@69
|
8011 __pyx_L25_except_error:;
|
|
jpayne@69
|
8012 __Pyx_XGIVEREF(__pyx_t_6);
|
|
jpayne@69
|
8013 __Pyx_XGIVEREF(__pyx_t_5);
|
|
jpayne@69
|
8014 __Pyx_XGIVEREF(__pyx_t_4);
|
|
jpayne@69
|
8015 __Pyx_ExceptionReset(__pyx_t_6, __pyx_t_5, __pyx_t_4);
|
|
jpayne@69
|
8016 goto __pyx_L1_error;
|
|
jpayne@69
|
8017 __pyx_L28_try_end:;
|
|
jpayne@69
|
8018 }
|
|
jpayne@69
|
8019
|
|
jpayne@69
|
8020 /* "pysam/libcutils.pyx":240
|
|
jpayne@69
|
8021 * raise ValueError('start out of range (%i)' % start)
|
|
jpayne@69
|
8022 *
|
|
jpayne@69
|
8023 * if stop is not None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8024 * try:
|
|
jpayne@69
|
8025 * rstop = stop
|
|
jpayne@69
|
8026 */
|
|
jpayne@69
|
8027 }
|
|
jpayne@69
|
8028
|
|
jpayne@69
|
8029 /* "pysam/libcutils.pyx":246
|
|
jpayne@69
|
8030 * raise ValueError('stop out of range (%i)' % stop)
|
|
jpayne@69
|
8031 *
|
|
jpayne@69
|
8032 * if region: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8033 * if ":" in region:
|
|
jpayne@69
|
8034 * contig, coord = region.split(":")
|
|
jpayne@69
|
8035 */
|
|
jpayne@69
|
8036 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 246, __pyx_L1_error)
|
|
jpayne@69
|
8037 if (__pyx_t_1) {
|
|
jpayne@69
|
8038
|
|
jpayne@69
|
8039 /* "pysam/libcutils.pyx":247
|
|
jpayne@69
|
8040 *
|
|
jpayne@69
|
8041 * if region:
|
|
jpayne@69
|
8042 * if ":" in region: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8043 * contig, coord = region.split(":")
|
|
jpayne@69
|
8044 * parts = coord.split("-")
|
|
jpayne@69
|
8045 */
|
|
jpayne@69
|
8046 __pyx_t_1 = (__Pyx_PySequence_ContainsTF(__pyx_kp_u__7, __pyx_v_region, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 247, __pyx_L1_error)
|
|
jpayne@69
|
8047 if (__pyx_t_1) {
|
|
jpayne@69
|
8048
|
|
jpayne@69
|
8049 /* "pysam/libcutils.pyx":248
|
|
jpayne@69
|
8050 * if region:
|
|
jpayne@69
|
8051 * if ":" in region:
|
|
jpayne@69
|
8052 * contig, coord = region.split(":") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8053 * parts = coord.split("-")
|
|
jpayne@69
|
8054 * rstart = int(parts[0]) - 1
|
|
jpayne@69
|
8055 */
|
|
jpayne@69
|
8056 __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_region, __pyx_n_s_split); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8057 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8058 __pyx_t_10 = NULL;
|
|
jpayne@69
|
8059 __pyx_t_13 = 0;
|
|
jpayne@69
|
8060 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
8061 if (likely(PyMethod_Check(__pyx_t_9))) {
|
|
jpayne@69
|
8062 __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_9);
|
|
jpayne@69
|
8063 if (likely(__pyx_t_10)) {
|
|
jpayne@69
|
8064 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9);
|
|
jpayne@69
|
8065 __Pyx_INCREF(__pyx_t_10);
|
|
jpayne@69
|
8066 __Pyx_INCREF(function);
|
|
jpayne@69
|
8067 __Pyx_DECREF_SET(__pyx_t_9, function);
|
|
jpayne@69
|
8068 __pyx_t_13 = 1;
|
|
jpayne@69
|
8069 }
|
|
jpayne@69
|
8070 }
|
|
jpayne@69
|
8071 #endif
|
|
jpayne@69
|
8072 {
|
|
jpayne@69
|
8073 PyObject *__pyx_callargs[2] = {__pyx_t_10, __pyx_kp_u__7};
|
|
jpayne@69
|
8074 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13);
|
|
jpayne@69
|
8075 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
8076 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8077 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8078 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8079 }
|
|
jpayne@69
|
8080 if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
|
|
jpayne@69
|
8081 PyObject* sequence = __pyx_t_2;
|
|
jpayne@69
|
8082 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
|
|
jpayne@69
|
8083 if (unlikely(size != 2)) {
|
|
jpayne@69
|
8084 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
|
|
jpayne@69
|
8085 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
|
|
jpayne@69
|
8086 __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8087 }
|
|
jpayne@69
|
8088 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
8089 if (likely(PyTuple_CheckExact(sequence))) {
|
|
jpayne@69
|
8090 __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
8091 __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
8092 } else {
|
|
jpayne@69
|
8093 __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
8094 __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
8095 }
|
|
jpayne@69
|
8096 __Pyx_INCREF(__pyx_t_9);
|
|
jpayne@69
|
8097 __Pyx_INCREF(__pyx_t_10);
|
|
jpayne@69
|
8098 #else
|
|
jpayne@69
|
8099 __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8100 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8101 __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8102 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8103 #endif
|
|
jpayne@69
|
8104 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8105 } else {
|
|
jpayne@69
|
8106 Py_ssize_t index = -1;
|
|
jpayne@69
|
8107 __pyx_t_11 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8108 __Pyx_GOTREF(__pyx_t_11);
|
|
jpayne@69
|
8109 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8110 __pyx_t_14 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11);
|
|
jpayne@69
|
8111 index = 0; __pyx_t_9 = __pyx_t_14(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L33_unpacking_failed;
|
|
jpayne@69
|
8112 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8113 index = 1; __pyx_t_10 = __pyx_t_14(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L33_unpacking_failed;
|
|
jpayne@69
|
8114 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8115 if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_11), 2) < 0) __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8116 __pyx_t_14 = NULL;
|
|
jpayne@69
|
8117 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
8118 goto __pyx_L34_unpacking_done;
|
|
jpayne@69
|
8119 __pyx_L33_unpacking_failed:;
|
|
jpayne@69
|
8120 __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
8121 __pyx_t_14 = NULL;
|
|
jpayne@69
|
8122 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
|
|
jpayne@69
|
8123 __PYX_ERR(0, 248, __pyx_L1_error)
|
|
jpayne@69
|
8124 __pyx_L34_unpacking_done:;
|
|
jpayne@69
|
8125 }
|
|
jpayne@69
|
8126 __Pyx_DECREF_SET(__pyx_v_contig, __pyx_t_9);
|
|
jpayne@69
|
8127 __pyx_t_9 = 0;
|
|
jpayne@69
|
8128 __pyx_v_coord = __pyx_t_10;
|
|
jpayne@69
|
8129 __pyx_t_10 = 0;
|
|
jpayne@69
|
8130
|
|
jpayne@69
|
8131 /* "pysam/libcutils.pyx":249
|
|
jpayne@69
|
8132 * if ":" in region:
|
|
jpayne@69
|
8133 * contig, coord = region.split(":")
|
|
jpayne@69
|
8134 * parts = coord.split("-") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8135 * rstart = int(parts[0]) - 1
|
|
jpayne@69
|
8136 * if len(parts) >= 1:
|
|
jpayne@69
|
8137 */
|
|
jpayne@69
|
8138 __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_coord, __pyx_n_s_split); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 249, __pyx_L1_error)
|
|
jpayne@69
|
8139 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8140 __pyx_t_9 = NULL;
|
|
jpayne@69
|
8141 __pyx_t_13 = 0;
|
|
jpayne@69
|
8142 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
8143 if (likely(PyMethod_Check(__pyx_t_10))) {
|
|
jpayne@69
|
8144 __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_10);
|
|
jpayne@69
|
8145 if (likely(__pyx_t_9)) {
|
|
jpayne@69
|
8146 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
|
|
jpayne@69
|
8147 __Pyx_INCREF(__pyx_t_9);
|
|
jpayne@69
|
8148 __Pyx_INCREF(function);
|
|
jpayne@69
|
8149 __Pyx_DECREF_SET(__pyx_t_10, function);
|
|
jpayne@69
|
8150 __pyx_t_13 = 1;
|
|
jpayne@69
|
8151 }
|
|
jpayne@69
|
8152 }
|
|
jpayne@69
|
8153 #endif
|
|
jpayne@69
|
8154 {
|
|
jpayne@69
|
8155 PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_kp_u__8};
|
|
jpayne@69
|
8156 __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13);
|
|
jpayne@69
|
8157 __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8158 if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 249, __pyx_L1_error)
|
|
jpayne@69
|
8159 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8160 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
8161 }
|
|
jpayne@69
|
8162 __pyx_v_parts = __pyx_t_2;
|
|
jpayne@69
|
8163 __pyx_t_2 = 0;
|
|
jpayne@69
|
8164
|
|
jpayne@69
|
8165 /* "pysam/libcutils.pyx":250
|
|
jpayne@69
|
8166 * contig, coord = region.split(":")
|
|
jpayne@69
|
8167 * parts = coord.split("-")
|
|
jpayne@69
|
8168 * rstart = int(parts[0]) - 1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8169 * if len(parts) >= 1:
|
|
jpayne@69
|
8170 * rstop = int(parts[1])
|
|
jpayne@69
|
8171 */
|
|
jpayne@69
|
8172 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_parts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 250, __pyx_L1_error)
|
|
jpayne@69
|
8173 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8174 __pyx_t_10 = __Pyx_PyNumber_Int(__pyx_t_2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 250, __pyx_L1_error)
|
|
jpayne@69
|
8175 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8176 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8177 __pyx_t_2 = __Pyx_PyInt_SubtractObjC(__pyx_t_10, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 250, __pyx_L1_error)
|
|
jpayne@69
|
8178 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8179 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
8180 __pyx_t_7 = __Pyx_PyInt_As_int32_t(__pyx_t_2); if (unlikely((__pyx_t_7 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 250, __pyx_L1_error)
|
|
jpayne@69
|
8181 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8182 __pyx_v_rstart = __pyx_t_7;
|
|
jpayne@69
|
8183
|
|
jpayne@69
|
8184 /* "pysam/libcutils.pyx":251
|
|
jpayne@69
|
8185 * parts = coord.split("-")
|
|
jpayne@69
|
8186 * rstart = int(parts[0]) - 1
|
|
jpayne@69
|
8187 * if len(parts) >= 1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8188 * rstop = int(parts[1])
|
|
jpayne@69
|
8189 * else:
|
|
jpayne@69
|
8190 */
|
|
jpayne@69
|
8191 __pyx_t_15 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 251, __pyx_L1_error)
|
|
jpayne@69
|
8192 __pyx_t_1 = (__pyx_t_15 >= 1);
|
|
jpayne@69
|
8193 if (__pyx_t_1) {
|
|
jpayne@69
|
8194
|
|
jpayne@69
|
8195 /* "pysam/libcutils.pyx":252
|
|
jpayne@69
|
8196 * rstart = int(parts[0]) - 1
|
|
jpayne@69
|
8197 * if len(parts) >= 1:
|
|
jpayne@69
|
8198 * rstop = int(parts[1]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8199 * else:
|
|
jpayne@69
|
8200 * contig = region
|
|
jpayne@69
|
8201 */
|
|
jpayne@69
|
8202 __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_parts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 252, __pyx_L1_error)
|
|
jpayne@69
|
8203 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8204 __pyx_t_10 = __Pyx_PyNumber_Int(__pyx_t_2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 252, __pyx_L1_error)
|
|
jpayne@69
|
8205 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8206 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8207 __pyx_t_7 = __Pyx_PyInt_As_int32_t(__pyx_t_10); if (unlikely((__pyx_t_7 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 252, __pyx_L1_error)
|
|
jpayne@69
|
8208 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
8209 __pyx_v_rstop = __pyx_t_7;
|
|
jpayne@69
|
8210
|
|
jpayne@69
|
8211 /* "pysam/libcutils.pyx":251
|
|
jpayne@69
|
8212 * parts = coord.split("-")
|
|
jpayne@69
|
8213 * rstart = int(parts[0]) - 1
|
|
jpayne@69
|
8214 * if len(parts) >= 1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8215 * rstop = int(parts[1])
|
|
jpayne@69
|
8216 * else:
|
|
jpayne@69
|
8217 */
|
|
jpayne@69
|
8218 }
|
|
jpayne@69
|
8219
|
|
jpayne@69
|
8220 /* "pysam/libcutils.pyx":247
|
|
jpayne@69
|
8221 *
|
|
jpayne@69
|
8222 * if region:
|
|
jpayne@69
|
8223 * if ":" in region: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8224 * contig, coord = region.split(":")
|
|
jpayne@69
|
8225 * parts = coord.split("-")
|
|
jpayne@69
|
8226 */
|
|
jpayne@69
|
8227 goto __pyx_L32;
|
|
jpayne@69
|
8228 }
|
|
jpayne@69
|
8229
|
|
jpayne@69
|
8230 /* "pysam/libcutils.pyx":254
|
|
jpayne@69
|
8231 * rstop = int(parts[1])
|
|
jpayne@69
|
8232 * else:
|
|
jpayne@69
|
8233 * contig = region # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8234 *
|
|
jpayne@69
|
8235 * if rstart > rstop:
|
|
jpayne@69
|
8236 */
|
|
jpayne@69
|
8237 /*else*/ {
|
|
jpayne@69
|
8238 __Pyx_INCREF(__pyx_v_region);
|
|
jpayne@69
|
8239 __Pyx_DECREF_SET(__pyx_v_contig, __pyx_v_region);
|
|
jpayne@69
|
8240 }
|
|
jpayne@69
|
8241 __pyx_L32:;
|
|
jpayne@69
|
8242
|
|
jpayne@69
|
8243 /* "pysam/libcutils.pyx":246
|
|
jpayne@69
|
8244 * raise ValueError('stop out of range (%i)' % stop)
|
|
jpayne@69
|
8245 *
|
|
jpayne@69
|
8246 * if region: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8247 * if ":" in region:
|
|
jpayne@69
|
8248 * contig, coord = region.split(":")
|
|
jpayne@69
|
8249 */
|
|
jpayne@69
|
8250 }
|
|
jpayne@69
|
8251
|
|
jpayne@69
|
8252 /* "pysam/libcutils.pyx":256
|
|
jpayne@69
|
8253 * contig = region
|
|
jpayne@69
|
8254 *
|
|
jpayne@69
|
8255 * if rstart > rstop: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8256 * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
|
|
jpayne@69
|
8257 * if not 0 <= rstart < MAX_POS:
|
|
jpayne@69
|
8258 */
|
|
jpayne@69
|
8259 __pyx_t_1 = (__pyx_v_rstart > __pyx_v_rstop);
|
|
jpayne@69
|
8260 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
8261
|
|
jpayne@69
|
8262 /* "pysam/libcutils.pyx":257
|
|
jpayne@69
|
8263 *
|
|
jpayne@69
|
8264 * if rstart > rstop:
|
|
jpayne@69
|
8265 * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8266 * if not 0 <= rstart < MAX_POS:
|
|
jpayne@69
|
8267 * raise ValueError('start out of range (%i)' % rstart)
|
|
jpayne@69
|
8268 */
|
|
jpayne@69
|
8269 __pyx_t_10 = __Pyx_PyInt_From_int32_t(__pyx_v_rstart); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 257, __pyx_L1_error)
|
|
jpayne@69
|
8270 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8271 __pyx_t_2 = __Pyx_PyInt_From_int32_t(__pyx_v_rstop); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 257, __pyx_L1_error)
|
|
jpayne@69
|
8272 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8273 __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 257, __pyx_L1_error)
|
|
jpayne@69
|
8274 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8275 __Pyx_GIVEREF(__pyx_t_10);
|
|
jpayne@69
|
8276 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10)) __PYX_ERR(0, 257, __pyx_L1_error);
|
|
jpayne@69
|
8277 __Pyx_GIVEREF(__pyx_t_2);
|
|
jpayne@69
|
8278 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_2)) __PYX_ERR(0, 257, __pyx_L1_error);
|
|
jpayne@69
|
8279 __pyx_t_10 = 0;
|
|
jpayne@69
|
8280 __pyx_t_2 = 0;
|
|
jpayne@69
|
8281 __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_invalid_coordinates_start_i_stop, __pyx_t_9); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 257, __pyx_L1_error)
|
|
jpayne@69
|
8282 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8283 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8284 __pyx_t_9 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 257, __pyx_L1_error)
|
|
jpayne@69
|
8285 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8286 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8287 __Pyx_Raise(__pyx_t_9, 0, 0, 0);
|
|
jpayne@69
|
8288 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8289 __PYX_ERR(0, 257, __pyx_L1_error)
|
|
jpayne@69
|
8290
|
|
jpayne@69
|
8291 /* "pysam/libcutils.pyx":256
|
|
jpayne@69
|
8292 * contig = region
|
|
jpayne@69
|
8293 *
|
|
jpayne@69
|
8294 * if rstart > rstop: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8295 * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
|
|
jpayne@69
|
8296 * if not 0 <= rstart < MAX_POS:
|
|
jpayne@69
|
8297 */
|
|
jpayne@69
|
8298 }
|
|
jpayne@69
|
8299
|
|
jpayne@69
|
8300 /* "pysam/libcutils.pyx":258
|
|
jpayne@69
|
8301 * if rstart > rstop:
|
|
jpayne@69
|
8302 * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
|
|
jpayne@69
|
8303 * if not 0 <= rstart < MAX_POS: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8304 * raise ValueError('start out of range (%i)' % rstart)
|
|
jpayne@69
|
8305 * if not 0 <= rstop <= MAX_POS:
|
|
jpayne@69
|
8306 */
|
|
jpayne@69
|
8307 __pyx_t_1 = (0 <= __pyx_v_rstart);
|
|
jpayne@69
|
8308 if (__pyx_t_1) {
|
|
jpayne@69
|
8309 __pyx_t_1 = (__pyx_v_rstart < __pyx_v_5pysam_9libcutils_MAX_POS);
|
|
jpayne@69
|
8310 }
|
|
jpayne@69
|
8311 __pyx_t_3 = (!__pyx_t_1);
|
|
jpayne@69
|
8312 if (unlikely(__pyx_t_3)) {
|
|
jpayne@69
|
8313
|
|
jpayne@69
|
8314 /* "pysam/libcutils.pyx":259
|
|
jpayne@69
|
8315 * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
|
|
jpayne@69
|
8316 * if not 0 <= rstart < MAX_POS:
|
|
jpayne@69
|
8317 * raise ValueError('start out of range (%i)' % rstart) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8318 * if not 0 <= rstop <= MAX_POS:
|
|
jpayne@69
|
8319 * raise ValueError('stop out of range (%i)' % rstop)
|
|
jpayne@69
|
8320 */
|
|
jpayne@69
|
8321 __pyx_t_9 = __Pyx_PyInt_From_int32_t(__pyx_v_rstart); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 259, __pyx_L1_error)
|
|
jpayne@69
|
8322 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8323 __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_start_out_of_range_i, __pyx_t_9); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 259, __pyx_L1_error)
|
|
jpayne@69
|
8324 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8325 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8326 __pyx_t_9 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 259, __pyx_L1_error)
|
|
jpayne@69
|
8327 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8328 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8329 __Pyx_Raise(__pyx_t_9, 0, 0, 0);
|
|
jpayne@69
|
8330 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8331 __PYX_ERR(0, 259, __pyx_L1_error)
|
|
jpayne@69
|
8332
|
|
jpayne@69
|
8333 /* "pysam/libcutils.pyx":258
|
|
jpayne@69
|
8334 * if rstart > rstop:
|
|
jpayne@69
|
8335 * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
|
|
jpayne@69
|
8336 * if not 0 <= rstart < MAX_POS: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8337 * raise ValueError('start out of range (%i)' % rstart)
|
|
jpayne@69
|
8338 * if not 0 <= rstop <= MAX_POS:
|
|
jpayne@69
|
8339 */
|
|
jpayne@69
|
8340 }
|
|
jpayne@69
|
8341
|
|
jpayne@69
|
8342 /* "pysam/libcutils.pyx":260
|
|
jpayne@69
|
8343 * if not 0 <= rstart < MAX_POS:
|
|
jpayne@69
|
8344 * raise ValueError('start out of range (%i)' % rstart)
|
|
jpayne@69
|
8345 * if not 0 <= rstop <= MAX_POS: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8346 * raise ValueError('stop out of range (%i)' % rstop)
|
|
jpayne@69
|
8347 *
|
|
jpayne@69
|
8348 */
|
|
jpayne@69
|
8349 __pyx_t_3 = (0 <= __pyx_v_rstop);
|
|
jpayne@69
|
8350 if (__pyx_t_3) {
|
|
jpayne@69
|
8351 __pyx_t_3 = (__pyx_v_rstop <= __pyx_v_5pysam_9libcutils_MAX_POS);
|
|
jpayne@69
|
8352 }
|
|
jpayne@69
|
8353 __pyx_t_1 = (!__pyx_t_3);
|
|
jpayne@69
|
8354 if (unlikely(__pyx_t_1)) {
|
|
jpayne@69
|
8355
|
|
jpayne@69
|
8356 /* "pysam/libcutils.pyx":261
|
|
jpayne@69
|
8357 * raise ValueError('start out of range (%i)' % rstart)
|
|
jpayne@69
|
8358 * if not 0 <= rstop <= MAX_POS:
|
|
jpayne@69
|
8359 * raise ValueError('stop out of range (%i)' % rstop) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8360 *
|
|
jpayne@69
|
8361 * return contig, rstart, rstop
|
|
jpayne@69
|
8362 */
|
|
jpayne@69
|
8363 __pyx_t_9 = __Pyx_PyInt_From_int32_t(__pyx_v_rstop); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 261, __pyx_L1_error)
|
|
jpayne@69
|
8364 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8365 __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_stop_out_of_range_i, __pyx_t_9); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 261, __pyx_L1_error)
|
|
jpayne@69
|
8366 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8367 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8368 __pyx_t_9 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 261, __pyx_L1_error)
|
|
jpayne@69
|
8369 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8370 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
8371 __Pyx_Raise(__pyx_t_9, 0, 0, 0);
|
|
jpayne@69
|
8372 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
|
|
jpayne@69
|
8373 __PYX_ERR(0, 261, __pyx_L1_error)
|
|
jpayne@69
|
8374
|
|
jpayne@69
|
8375 /* "pysam/libcutils.pyx":260
|
|
jpayne@69
|
8376 * if not 0 <= rstart < MAX_POS:
|
|
jpayne@69
|
8377 * raise ValueError('start out of range (%i)' % rstart)
|
|
jpayne@69
|
8378 * if not 0 <= rstop <= MAX_POS: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8379 * raise ValueError('stop out of range (%i)' % rstop)
|
|
jpayne@69
|
8380 *
|
|
jpayne@69
|
8381 */
|
|
jpayne@69
|
8382 }
|
|
jpayne@69
|
8383
|
|
jpayne@69
|
8384 /* "pysam/libcutils.pyx":263
|
|
jpayne@69
|
8385 * raise ValueError('stop out of range (%i)' % rstop)
|
|
jpayne@69
|
8386 *
|
|
jpayne@69
|
8387 * return contig, rstart, rstop # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8388 *
|
|
jpayne@69
|
8389 *
|
|
jpayne@69
|
8390 */
|
|
jpayne@69
|
8391 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
8392 __pyx_t_9 = __Pyx_PyInt_From_int32_t(__pyx_v_rstart); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 263, __pyx_L1_error)
|
|
jpayne@69
|
8393 __Pyx_GOTREF(__pyx_t_9);
|
|
jpayne@69
|
8394 __pyx_t_2 = __Pyx_PyInt_From_int32_t(__pyx_v_rstop); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 263, __pyx_L1_error)
|
|
jpayne@69
|
8395 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
8396 __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 263, __pyx_L1_error)
|
|
jpayne@69
|
8397 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
8398 __Pyx_INCREF(__pyx_v_contig);
|
|
jpayne@69
|
8399 __Pyx_GIVEREF(__pyx_v_contig);
|
|
jpayne@69
|
8400 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_contig)) __PYX_ERR(0, 263, __pyx_L1_error);
|
|
jpayne@69
|
8401 __Pyx_GIVEREF(__pyx_t_9);
|
|
jpayne@69
|
8402 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9)) __PYX_ERR(0, 263, __pyx_L1_error);
|
|
jpayne@69
|
8403 __Pyx_GIVEREF(__pyx_t_2);
|
|
jpayne@69
|
8404 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_2)) __PYX_ERR(0, 263, __pyx_L1_error);
|
|
jpayne@69
|
8405 __pyx_t_9 = 0;
|
|
jpayne@69
|
8406 __pyx_t_2 = 0;
|
|
jpayne@69
|
8407 __pyx_r = __pyx_t_10;
|
|
jpayne@69
|
8408 __pyx_t_10 = 0;
|
|
jpayne@69
|
8409 goto __pyx_L0;
|
|
jpayne@69
|
8410
|
|
jpayne@69
|
8411 /* "pysam/libcutils.pyx":178
|
|
jpayne@69
|
8412 *
|
|
jpayne@69
|
8413 *
|
|
jpayne@69
|
8414 * cpdef parse_region(contig=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8415 * start=None,
|
|
jpayne@69
|
8416 * stop=None,
|
|
jpayne@69
|
8417 */
|
|
jpayne@69
|
8418
|
|
jpayne@69
|
8419 /* function exit code */
|
|
jpayne@69
|
8420 __pyx_L1_error:;
|
|
jpayne@69
|
8421 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
8422 __Pyx_XDECREF(__pyx_t_9);
|
|
jpayne@69
|
8423 __Pyx_XDECREF(__pyx_t_10);
|
|
jpayne@69
|
8424 __Pyx_XDECREF(__pyx_t_11);
|
|
jpayne@69
|
8425 __Pyx_XDECREF(__pyx_t_12);
|
|
jpayne@69
|
8426 __Pyx_AddTraceback("pysam.libcutils.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8427 __pyx_r = 0;
|
|
jpayne@69
|
8428 __pyx_L0:;
|
|
jpayne@69
|
8429 __Pyx_XDECREF(__pyx_v_coord);
|
|
jpayne@69
|
8430 __Pyx_XDECREF(__pyx_v_parts);
|
|
jpayne@69
|
8431 __Pyx_XDECREF(__pyx_v_contig);
|
|
jpayne@69
|
8432 __Pyx_XDECREF(__pyx_v_stop);
|
|
jpayne@69
|
8433 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
8434 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8435 return __pyx_r;
|
|
jpayne@69
|
8436 }
|
|
jpayne@69
|
8437
|
|
jpayne@69
|
8438 /* Python wrapper */
|
|
jpayne@69
|
8439 static PyObject *__pyx_pw_5pysam_9libcutils_13parse_region(PyObject *__pyx_self,
|
|
jpayne@69
|
8440 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8441 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8442 #else
|
|
jpayne@69
|
8443 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8444 #endif
|
|
jpayne@69
|
8445 ); /*proto*/
|
|
jpayne@69
|
8446 PyDoc_STRVAR(__pyx_doc_5pysam_9libcutils_12parse_region, "parse alternative ways to specify a genomic region. A region can\n either be specified by :term:`reference`, `start` and\n `end`. `start` and `end` denote 0-based, half-open intervals.\n \n :term:`reference` and `end` are also accepted for backward\n compatibility as synonyms for :term:`contig` and `stop`,\n respectively.\n\n Alternatively, a samtools :term:`region` string can be supplied.\n\n If any of the coordinates are missing they will be replaced by the\n minimum (`start`) or maximum (`end`) coordinate.\n\n Note that region strings are 1-based, while `start` and `end`\n denote an interval in python coordinates.\n\n Returns\n -------\n\n tuple : a tuple of `reference`, `start` and `end`.\n\n Raises\n ------\n\n ValueError\n for invalid or out of bounds regions.\n\n ");
|
|
jpayne@69
|
8447 static PyMethodDef __pyx_mdef_5pysam_9libcutils_13parse_region = {"parse_region", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_13parse_region, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libcutils_12parse_region};
|
|
jpayne@69
|
8448 static PyObject *__pyx_pw_5pysam_9libcutils_13parse_region(PyObject *__pyx_self,
|
|
jpayne@69
|
8449 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8450 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8451 #else
|
|
jpayne@69
|
8452 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8453 #endif
|
|
jpayne@69
|
8454 ) {
|
|
jpayne@69
|
8455 PyObject *__pyx_v_contig = 0;
|
|
jpayne@69
|
8456 PyObject *__pyx_v_start = 0;
|
|
jpayne@69
|
8457 PyObject *__pyx_v_stop = 0;
|
|
jpayne@69
|
8458 PyObject *__pyx_v_region = 0;
|
|
jpayne@69
|
8459 PyObject *__pyx_v_reference = 0;
|
|
jpayne@69
|
8460 PyObject *__pyx_v_end = 0;
|
|
jpayne@69
|
8461 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8462 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
8463 #endif
|
|
jpayne@69
|
8464 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
8465 PyObject* values[6] = {0,0,0,0,0,0};
|
|
jpayne@69
|
8466 int __pyx_lineno = 0;
|
|
jpayne@69
|
8467 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
8468 int __pyx_clineno = 0;
|
|
jpayne@69
|
8469 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
8470 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
8471 __Pyx_RefNannySetupContext("parse_region (wrapper)", 0);
|
|
jpayne@69
|
8472 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8473 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
8474 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
8475 #else
|
|
jpayne@69
|
8476 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
8477 #endif
|
|
jpayne@69
|
8478 #endif
|
|
jpayne@69
|
8479 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
8480 {
|
|
jpayne@69
|
8481 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_contig,&__pyx_n_s_start,&__pyx_n_s_stop,&__pyx_n_s_region,&__pyx_n_s_reference,&__pyx_n_s_end,0};
|
|
jpayne@69
|
8482 values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8483
|
|
jpayne@69
|
8484 /* "pysam/libcutils.pyx":179
|
|
jpayne@69
|
8485 *
|
|
jpayne@69
|
8486 * cpdef parse_region(contig=None,
|
|
jpayne@69
|
8487 * start=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8488 * stop=None,
|
|
jpayne@69
|
8489 * region=None,
|
|
jpayne@69
|
8490 */
|
|
jpayne@69
|
8491 values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8492
|
|
jpayne@69
|
8493 /* "pysam/libcutils.pyx":180
|
|
jpayne@69
|
8494 * cpdef parse_region(contig=None,
|
|
jpayne@69
|
8495 * start=None,
|
|
jpayne@69
|
8496 * stop=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8497 * region=None,
|
|
jpayne@69
|
8498 * reference=None,
|
|
jpayne@69
|
8499 */
|
|
jpayne@69
|
8500 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8501
|
|
jpayne@69
|
8502 /* "pysam/libcutils.pyx":181
|
|
jpayne@69
|
8503 * start=None,
|
|
jpayne@69
|
8504 * stop=None,
|
|
jpayne@69
|
8505 * region=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8506 * reference=None,
|
|
jpayne@69
|
8507 * end=None):
|
|
jpayne@69
|
8508 */
|
|
jpayne@69
|
8509 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8510
|
|
jpayne@69
|
8511 /* "pysam/libcutils.pyx":182
|
|
jpayne@69
|
8512 * stop=None,
|
|
jpayne@69
|
8513 * region=None,
|
|
jpayne@69
|
8514 * reference=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8515 * end=None):
|
|
jpayne@69
|
8516 * """parse alternative ways to specify a genomic region. A region can
|
|
jpayne@69
|
8517 */
|
|
jpayne@69
|
8518 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8519
|
|
jpayne@69
|
8520 /* "pysam/libcutils.pyx":183
|
|
jpayne@69
|
8521 * region=None,
|
|
jpayne@69
|
8522 * reference=None,
|
|
jpayne@69
|
8523 * end=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8524 * """parse alternative ways to specify a genomic region. A region can
|
|
jpayne@69
|
8525 * either be specified by :term:`reference`, `start` and
|
|
jpayne@69
|
8526 */
|
|
jpayne@69
|
8527 values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8528 if (__pyx_kwds) {
|
|
jpayne@69
|
8529 Py_ssize_t kw_args;
|
|
jpayne@69
|
8530 switch (__pyx_nargs) {
|
|
jpayne@69
|
8531 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
8532 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8533 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
8534 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8535 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
8536 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8537 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
8538 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8539 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
8540 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8541 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8542 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8543 case 0: break;
|
|
jpayne@69
|
8544 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8545 }
|
|
jpayne@69
|
8546 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
8547 switch (__pyx_nargs) {
|
|
jpayne@69
|
8548 case 0:
|
|
jpayne@69
|
8549 if (kw_args > 0) {
|
|
jpayne@69
|
8550 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_contig);
|
|
jpayne@69
|
8551 if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8552 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8553 }
|
|
jpayne@69
|
8554 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8555 case 1:
|
|
jpayne@69
|
8556 if (kw_args > 0) {
|
|
jpayne@69
|
8557 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start);
|
|
jpayne@69
|
8558 if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8559 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8560 }
|
|
jpayne@69
|
8561 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8562 case 2:
|
|
jpayne@69
|
8563 if (kw_args > 0) {
|
|
jpayne@69
|
8564 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stop);
|
|
jpayne@69
|
8565 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8566 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8567 }
|
|
jpayne@69
|
8568 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8569 case 3:
|
|
jpayne@69
|
8570 if (kw_args > 0) {
|
|
jpayne@69
|
8571 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_region);
|
|
jpayne@69
|
8572 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8573 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8574 }
|
|
jpayne@69
|
8575 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8576 case 4:
|
|
jpayne@69
|
8577 if (kw_args > 0) {
|
|
jpayne@69
|
8578 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_reference);
|
|
jpayne@69
|
8579 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8580 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8581 }
|
|
jpayne@69
|
8582 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8583 case 5:
|
|
jpayne@69
|
8584 if (kw_args > 0) {
|
|
jpayne@69
|
8585 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end);
|
|
jpayne@69
|
8586 if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8587 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8588 }
|
|
jpayne@69
|
8589 }
|
|
jpayne@69
|
8590 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
8591 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
8592 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_region") < 0)) __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8593 }
|
|
jpayne@69
|
8594 } else {
|
|
jpayne@69
|
8595 switch (__pyx_nargs) {
|
|
jpayne@69
|
8596 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
8597 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8598 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
8599 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8600 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
8601 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8602 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
8603 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8604 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
8605 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8606 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8607 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8608 case 0: break;
|
|
jpayne@69
|
8609 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8610 }
|
|
jpayne@69
|
8611 }
|
|
jpayne@69
|
8612 __pyx_v_contig = values[0];
|
|
jpayne@69
|
8613 __pyx_v_start = values[1];
|
|
jpayne@69
|
8614 __pyx_v_stop = values[2];
|
|
jpayne@69
|
8615 __pyx_v_region = values[3];
|
|
jpayne@69
|
8616 __pyx_v_reference = values[4];
|
|
jpayne@69
|
8617 __pyx_v_end = values[5];
|
|
jpayne@69
|
8618 }
|
|
jpayne@69
|
8619 goto __pyx_L6_skip;
|
|
jpayne@69
|
8620 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
8621 __Pyx_RaiseArgtupleInvalid("parse_region", 0, 0, 6, __pyx_nargs); __PYX_ERR(0, 178, __pyx_L3_error)
|
|
jpayne@69
|
8622 __pyx_L6_skip:;
|
|
jpayne@69
|
8623 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
8624 __pyx_L3_error:;
|
|
jpayne@69
|
8625 {
|
|
jpayne@69
|
8626 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8627 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8628 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8629 }
|
|
jpayne@69
|
8630 }
|
|
jpayne@69
|
8631 __Pyx_AddTraceback("pysam.libcutils.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8632 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8633 return NULL;
|
|
jpayne@69
|
8634 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
8635 __pyx_r = __pyx_pf_5pysam_9libcutils_12parse_region(__pyx_self, __pyx_v_contig, __pyx_v_start, __pyx_v_stop, __pyx_v_region, __pyx_v_reference, __pyx_v_end);
|
|
jpayne@69
|
8636
|
|
jpayne@69
|
8637 /* "pysam/libcutils.pyx":178
|
|
jpayne@69
|
8638 *
|
|
jpayne@69
|
8639 *
|
|
jpayne@69
|
8640 * cpdef parse_region(contig=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8641 * start=None,
|
|
jpayne@69
|
8642 * stop=None,
|
|
jpayne@69
|
8643 */
|
|
jpayne@69
|
8644
|
|
jpayne@69
|
8645 /* function exit code */
|
|
jpayne@69
|
8646 {
|
|
jpayne@69
|
8647 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8648 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8649 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8650 }
|
|
jpayne@69
|
8651 }
|
|
jpayne@69
|
8652 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8653 return __pyx_r;
|
|
jpayne@69
|
8654 }
|
|
jpayne@69
|
8655
|
|
jpayne@69
|
8656 static PyObject *__pyx_pf_5pysam_9libcutils_12parse_region(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_reference, PyObject *__pyx_v_end) {
|
|
jpayne@69
|
8657 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
8658 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
8659 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
8660 struct __pyx_opt_args_5pysam_9libcutils_parse_region __pyx_t_2;
|
|
jpayne@69
|
8661 int __pyx_lineno = 0;
|
|
jpayne@69
|
8662 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
8663 int __pyx_clineno = 0;
|
|
jpayne@69
|
8664 __Pyx_RefNannySetupContext("parse_region", 1);
|
|
jpayne@69
|
8665 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
8666 __pyx_t_2.__pyx_n = 6;
|
|
jpayne@69
|
8667 __pyx_t_2.contig = __pyx_v_contig;
|
|
jpayne@69
|
8668 __pyx_t_2.start = __pyx_v_start;
|
|
jpayne@69
|
8669 __pyx_t_2.stop = __pyx_v_stop;
|
|
jpayne@69
|
8670 __pyx_t_2.region = __pyx_v_region;
|
|
jpayne@69
|
8671 __pyx_t_2.reference = __pyx_v_reference;
|
|
jpayne@69
|
8672 __pyx_t_2.end = __pyx_v_end;
|
|
jpayne@69
|
8673 __pyx_t_1 = __pyx_f_5pysam_9libcutils_parse_region(0, &__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 178, __pyx_L1_error)
|
|
jpayne@69
|
8674 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
8675 __pyx_r = __pyx_t_1;
|
|
jpayne@69
|
8676 __pyx_t_1 = 0;
|
|
jpayne@69
|
8677 goto __pyx_L0;
|
|
jpayne@69
|
8678
|
|
jpayne@69
|
8679 /* function exit code */
|
|
jpayne@69
|
8680 __pyx_L1_error:;
|
|
jpayne@69
|
8681 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
8682 __Pyx_AddTraceback("pysam.libcutils.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8683 __pyx_r = NULL;
|
|
jpayne@69
|
8684 __pyx_L0:;
|
|
jpayne@69
|
8685 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
8686 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8687 return __pyx_r;
|
|
jpayne@69
|
8688 }
|
|
jpayne@69
|
8689
|
|
jpayne@69
|
8690 /* "pysam/libcutils.pyx":266
|
|
jpayne@69
|
8691 *
|
|
jpayne@69
|
8692 *
|
|
jpayne@69
|
8693 * cdef int libc_whence_from_io(int whence): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8694 * # io.SEEK_SET/_CUR/_END are by definition 0/1/2 but C/POSIX's equivalents
|
|
jpayne@69
|
8695 * # have unspecified values. So we must translate, but checking for 0/1/2
|
|
jpayne@69
|
8696 */
|
|
jpayne@69
|
8697
|
|
jpayne@69
|
8698 static int __pyx_f_5pysam_9libcutils_libc_whence_from_io(int __pyx_v_whence) {
|
|
jpayne@69
|
8699 int __pyx_r;
|
|
jpayne@69
|
8700 int __pyx_t_1;
|
|
jpayne@69
|
8701
|
|
jpayne@69
|
8702 /* "pysam/libcutils.pyx":270
|
|
jpayne@69
|
8703 * # have unspecified values. So we must translate, but checking for 0/1/2
|
|
jpayne@69
|
8704 * # rather than io.SEEK_SET/etc suffices.
|
|
jpayne@69
|
8705 * if whence == 0: return SEEK_SET # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8706 * if whence == 1: return SEEK_CUR
|
|
jpayne@69
|
8707 * if whence == 2: return SEEK_END
|
|
jpayne@69
|
8708 */
|
|
jpayne@69
|
8709 __pyx_t_1 = (__pyx_v_whence == 0);
|
|
jpayne@69
|
8710 if (__pyx_t_1) {
|
|
jpayne@69
|
8711 __pyx_r = SEEK_SET;
|
|
jpayne@69
|
8712 goto __pyx_L0;
|
|
jpayne@69
|
8713 }
|
|
jpayne@69
|
8714
|
|
jpayne@69
|
8715 /* "pysam/libcutils.pyx":271
|
|
jpayne@69
|
8716 * # rather than io.SEEK_SET/etc suffices.
|
|
jpayne@69
|
8717 * if whence == 0: return SEEK_SET
|
|
jpayne@69
|
8718 * if whence == 1: return SEEK_CUR # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8719 * if whence == 2: return SEEK_END
|
|
jpayne@69
|
8720 * return whence # Otherwise likely invalid, but let HTSlib or OS report it
|
|
jpayne@69
|
8721 */
|
|
jpayne@69
|
8722 __pyx_t_1 = (__pyx_v_whence == 1);
|
|
jpayne@69
|
8723 if (__pyx_t_1) {
|
|
jpayne@69
|
8724 __pyx_r = SEEK_CUR;
|
|
jpayne@69
|
8725 goto __pyx_L0;
|
|
jpayne@69
|
8726 }
|
|
jpayne@69
|
8727
|
|
jpayne@69
|
8728 /* "pysam/libcutils.pyx":272
|
|
jpayne@69
|
8729 * if whence == 0: return SEEK_SET
|
|
jpayne@69
|
8730 * if whence == 1: return SEEK_CUR
|
|
jpayne@69
|
8731 * if whence == 2: return SEEK_END # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8732 * return whence # Otherwise likely invalid, but let HTSlib or OS report it
|
|
jpayne@69
|
8733 *
|
|
jpayne@69
|
8734 */
|
|
jpayne@69
|
8735 __pyx_t_1 = (__pyx_v_whence == 2);
|
|
jpayne@69
|
8736 if (__pyx_t_1) {
|
|
jpayne@69
|
8737 __pyx_r = SEEK_END;
|
|
jpayne@69
|
8738 goto __pyx_L0;
|
|
jpayne@69
|
8739 }
|
|
jpayne@69
|
8740
|
|
jpayne@69
|
8741 /* "pysam/libcutils.pyx":273
|
|
jpayne@69
|
8742 * if whence == 1: return SEEK_CUR
|
|
jpayne@69
|
8743 * if whence == 2: return SEEK_END
|
|
jpayne@69
|
8744 * return whence # Otherwise likely invalid, but let HTSlib or OS report it # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8745 *
|
|
jpayne@69
|
8746 *
|
|
jpayne@69
|
8747 */
|
|
jpayne@69
|
8748 __pyx_r = __pyx_v_whence;
|
|
jpayne@69
|
8749 goto __pyx_L0;
|
|
jpayne@69
|
8750
|
|
jpayne@69
|
8751 /* "pysam/libcutils.pyx":266
|
|
jpayne@69
|
8752 *
|
|
jpayne@69
|
8753 *
|
|
jpayne@69
|
8754 * cdef int libc_whence_from_io(int whence): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8755 * # io.SEEK_SET/_CUR/_END are by definition 0/1/2 but C/POSIX's equivalents
|
|
jpayne@69
|
8756 * # have unspecified values. So we must translate, but checking for 0/1/2
|
|
jpayne@69
|
8757 */
|
|
jpayne@69
|
8758
|
|
jpayne@69
|
8759 /* function exit code */
|
|
jpayne@69
|
8760 __pyx_L0:;
|
|
jpayne@69
|
8761 return __pyx_r;
|
|
jpayne@69
|
8762 }
|
|
jpayne@69
|
8763
|
|
jpayne@69
|
8764 /* "pysam/libcutils.pyx":276
|
|
jpayne@69
|
8765 *
|
|
jpayne@69
|
8766 *
|
|
jpayne@69
|
8767 * def _pysam_dispatch(collection, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8768 * method,
|
|
jpayne@69
|
8769 * args=None,
|
|
jpayne@69
|
8770 */
|
|
jpayne@69
|
8771
|
|
jpayne@69
|
8772 /* Python wrapper */
|
|
jpayne@69
|
8773 static PyObject *__pyx_pw_5pysam_9libcutils_15_pysam_dispatch(PyObject *__pyx_self,
|
|
jpayne@69
|
8774 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8775 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8776 #else
|
|
jpayne@69
|
8777 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8778 #endif
|
|
jpayne@69
|
8779 ); /*proto*/
|
|
jpayne@69
|
8780 PyDoc_STRVAR(__pyx_doc_5pysam_9libcutils_14_pysam_dispatch, "call ``method`` in samtools/bcftools providing arguments in args.\n \n By default, stdout is redirected to a temporary file using the patched\n C sources except for a few commands that have an explicit output option\n (typically: -o). In these commands (such as samtools view), this explicit\n option is used. If *is_usage* is True, then these explicit output options\n will not be used.\n\n Catching of stdout can be turned off by setting *catch_stdout* to\n False.\n ");
|
|
jpayne@69
|
8781 static PyMethodDef __pyx_mdef_5pysam_9libcutils_15_pysam_dispatch = {"_pysam_dispatch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_15_pysam_dispatch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libcutils_14_pysam_dispatch};
|
|
jpayne@69
|
8782 static PyObject *__pyx_pw_5pysam_9libcutils_15_pysam_dispatch(PyObject *__pyx_self,
|
|
jpayne@69
|
8783 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8784 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8785 #else
|
|
jpayne@69
|
8786 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8787 #endif
|
|
jpayne@69
|
8788 ) {
|
|
jpayne@69
|
8789 PyObject *__pyx_v_collection = 0;
|
|
jpayne@69
|
8790 PyObject *__pyx_v_method = 0;
|
|
jpayne@69
|
8791 PyObject *__pyx_v_args = 0;
|
|
jpayne@69
|
8792 PyObject *__pyx_v_catch_stdout = 0;
|
|
jpayne@69
|
8793 PyObject *__pyx_v_is_usage = 0;
|
|
jpayne@69
|
8794 PyObject *__pyx_v_save_stdout = 0;
|
|
jpayne@69
|
8795 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8796 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
8797 #endif
|
|
jpayne@69
|
8798 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
8799 PyObject* values[6] = {0,0,0,0,0,0};
|
|
jpayne@69
|
8800 int __pyx_lineno = 0;
|
|
jpayne@69
|
8801 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
8802 int __pyx_clineno = 0;
|
|
jpayne@69
|
8803 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
8804 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
8805 __Pyx_RefNannySetupContext("_pysam_dispatch (wrapper)", 0);
|
|
jpayne@69
|
8806 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8807 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
8808 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
8809 #else
|
|
jpayne@69
|
8810 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
8811 #endif
|
|
jpayne@69
|
8812 #endif
|
|
jpayne@69
|
8813 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
8814 {
|
|
jpayne@69
|
8815 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_collection,&__pyx_n_s_method,&__pyx_n_s_args,&__pyx_n_s_catch_stdout,&__pyx_n_s_is_usage,&__pyx_n_s_save_stdout,0};
|
|
jpayne@69
|
8816
|
|
jpayne@69
|
8817 /* "pysam/libcutils.pyx":278
|
|
jpayne@69
|
8818 * def _pysam_dispatch(collection,
|
|
jpayne@69
|
8819 * method,
|
|
jpayne@69
|
8820 * args=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8821 * catch_stdout=True,
|
|
jpayne@69
|
8822 * is_usage=False,
|
|
jpayne@69
|
8823 */
|
|
jpayne@69
|
8824 values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8825
|
|
jpayne@69
|
8826 /* "pysam/libcutils.pyx":279
|
|
jpayne@69
|
8827 * method,
|
|
jpayne@69
|
8828 * args=None,
|
|
jpayne@69
|
8829 * catch_stdout=True, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8830 * is_usage=False,
|
|
jpayne@69
|
8831 * save_stdout=None):
|
|
jpayne@69
|
8832 */
|
|
jpayne@69
|
8833 values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_True)));
|
|
jpayne@69
|
8834
|
|
jpayne@69
|
8835 /* "pysam/libcutils.pyx":280
|
|
jpayne@69
|
8836 * args=None,
|
|
jpayne@69
|
8837 * catch_stdout=True,
|
|
jpayne@69
|
8838 * is_usage=False, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8839 * save_stdout=None):
|
|
jpayne@69
|
8840 * '''call ``method`` in samtools/bcftools providing arguments in args.
|
|
jpayne@69
|
8841 */
|
|
jpayne@69
|
8842 values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False)));
|
|
jpayne@69
|
8843
|
|
jpayne@69
|
8844 /* "pysam/libcutils.pyx":281
|
|
jpayne@69
|
8845 * catch_stdout=True,
|
|
jpayne@69
|
8846 * is_usage=False,
|
|
jpayne@69
|
8847 * save_stdout=None): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8848 * '''call ``method`` in samtools/bcftools providing arguments in args.
|
|
jpayne@69
|
8849 *
|
|
jpayne@69
|
8850 */
|
|
jpayne@69
|
8851 values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None));
|
|
jpayne@69
|
8852 if (__pyx_kwds) {
|
|
jpayne@69
|
8853 Py_ssize_t kw_args;
|
|
jpayne@69
|
8854 switch (__pyx_nargs) {
|
|
jpayne@69
|
8855 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
8856 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8857 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
8858 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8859 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
8860 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8861 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
8862 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8863 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
8864 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8865 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8866 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8867 case 0: break;
|
|
jpayne@69
|
8868 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8869 }
|
|
jpayne@69
|
8870 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
8871 switch (__pyx_nargs) {
|
|
jpayne@69
|
8872 case 0:
|
|
jpayne@69
|
8873 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_collection)) != 0)) {
|
|
jpayne@69
|
8874 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
8875 kw_args--;
|
|
jpayne@69
|
8876 }
|
|
jpayne@69
|
8877 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8878 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8879 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8880 case 1:
|
|
jpayne@69
|
8881 if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_method)) != 0)) {
|
|
jpayne@69
|
8882 (void)__Pyx_Arg_NewRef_FASTCALL(values[1]);
|
|
jpayne@69
|
8883 kw_args--;
|
|
jpayne@69
|
8884 }
|
|
jpayne@69
|
8885 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8886 else {
|
|
jpayne@69
|
8887 __Pyx_RaiseArgtupleInvalid("_pysam_dispatch", 0, 2, 6, 1); __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8888 }
|
|
jpayne@69
|
8889 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8890 case 2:
|
|
jpayne@69
|
8891 if (kw_args > 0) {
|
|
jpayne@69
|
8892 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_args);
|
|
jpayne@69
|
8893 if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8894 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8895 }
|
|
jpayne@69
|
8896 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8897 case 3:
|
|
jpayne@69
|
8898 if (kw_args > 0) {
|
|
jpayne@69
|
8899 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_catch_stdout);
|
|
jpayne@69
|
8900 if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8901 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8902 }
|
|
jpayne@69
|
8903 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8904 case 4:
|
|
jpayne@69
|
8905 if (kw_args > 0) {
|
|
jpayne@69
|
8906 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_is_usage);
|
|
jpayne@69
|
8907 if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8908 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8909 }
|
|
jpayne@69
|
8910 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8911 case 5:
|
|
jpayne@69
|
8912 if (kw_args > 0) {
|
|
jpayne@69
|
8913 PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_save_stdout);
|
|
jpayne@69
|
8914 if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; }
|
|
jpayne@69
|
8915 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8916 }
|
|
jpayne@69
|
8917 }
|
|
jpayne@69
|
8918 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
8919 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
8920 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_pysam_dispatch") < 0)) __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8921 }
|
|
jpayne@69
|
8922 } else {
|
|
jpayne@69
|
8923 switch (__pyx_nargs) {
|
|
jpayne@69
|
8924 case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5);
|
|
jpayne@69
|
8925 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8926 case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4);
|
|
jpayne@69
|
8927 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8928 case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3);
|
|
jpayne@69
|
8929 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8930 case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2);
|
|
jpayne@69
|
8931 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
8932 case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1);
|
|
jpayne@69
|
8933 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
8934 break;
|
|
jpayne@69
|
8935 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
8936 }
|
|
jpayne@69
|
8937 }
|
|
jpayne@69
|
8938 __pyx_v_collection = values[0];
|
|
jpayne@69
|
8939 __pyx_v_method = values[1];
|
|
jpayne@69
|
8940 __pyx_v_args = values[2];
|
|
jpayne@69
|
8941 __pyx_v_catch_stdout = values[3];
|
|
jpayne@69
|
8942 __pyx_v_is_usage = values[4];
|
|
jpayne@69
|
8943 __pyx_v_save_stdout = values[5];
|
|
jpayne@69
|
8944 }
|
|
jpayne@69
|
8945 goto __pyx_L6_skip;
|
|
jpayne@69
|
8946 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
8947 __Pyx_RaiseArgtupleInvalid("_pysam_dispatch", 0, 2, 6, __pyx_nargs); __PYX_ERR(0, 276, __pyx_L3_error)
|
|
jpayne@69
|
8948 __pyx_L6_skip:;
|
|
jpayne@69
|
8949 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
8950 __pyx_L3_error:;
|
|
jpayne@69
|
8951 {
|
|
jpayne@69
|
8952 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8953 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8954 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8955 }
|
|
jpayne@69
|
8956 }
|
|
jpayne@69
|
8957 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
8958 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8959 return NULL;
|
|
jpayne@69
|
8960 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
8961 __pyx_r = __pyx_pf_5pysam_9libcutils_14_pysam_dispatch(__pyx_self, __pyx_v_collection, __pyx_v_method, __pyx_v_args, __pyx_v_catch_stdout, __pyx_v_is_usage, __pyx_v_save_stdout);
|
|
jpayne@69
|
8962
|
|
jpayne@69
|
8963 /* "pysam/libcutils.pyx":276
|
|
jpayne@69
|
8964 *
|
|
jpayne@69
|
8965 *
|
|
jpayne@69
|
8966 * def _pysam_dispatch(collection, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8967 * method,
|
|
jpayne@69
|
8968 * args=None,
|
|
jpayne@69
|
8969 */
|
|
jpayne@69
|
8970
|
|
jpayne@69
|
8971 /* function exit code */
|
|
jpayne@69
|
8972 {
|
|
jpayne@69
|
8973 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
8974 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
8975 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
8976 }
|
|
jpayne@69
|
8977 }
|
|
jpayne@69
|
8978 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
8979 return __pyx_r;
|
|
jpayne@69
|
8980 }
|
|
jpayne@69
|
8981
|
|
jpayne@69
|
8982 /* "pysam/libcutils.pyx":413
|
|
jpayne@69
|
8983 *
|
|
jpayne@69
|
8984 * # get error messages
|
|
jpayne@69
|
8985 * def _collect(fn): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
8986 * out = []
|
|
jpayne@69
|
8987 * try:
|
|
jpayne@69
|
8988 */
|
|
jpayne@69
|
8989
|
|
jpayne@69
|
8990 /* Python wrapper */
|
|
jpayne@69
|
8991 static PyObject *__pyx_pw_5pysam_9libcutils_15_pysam_dispatch_1_collect(PyObject *__pyx_self,
|
|
jpayne@69
|
8992 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
8993 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
8994 #else
|
|
jpayne@69
|
8995 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
8996 #endif
|
|
jpayne@69
|
8997 ); /*proto*/
|
|
jpayne@69
|
8998 static PyMethodDef __pyx_mdef_5pysam_9libcutils_15_pysam_dispatch_1_collect = {"_collect", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libcutils_15_pysam_dispatch_1_collect, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0};
|
|
jpayne@69
|
8999 static PyObject *__pyx_pw_5pysam_9libcutils_15_pysam_dispatch_1_collect(PyObject *__pyx_self,
|
|
jpayne@69
|
9000 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9001 PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds
|
|
jpayne@69
|
9002 #else
|
|
jpayne@69
|
9003 PyObject *__pyx_args, PyObject *__pyx_kwds
|
|
jpayne@69
|
9004 #endif
|
|
jpayne@69
|
9005 ) {
|
|
jpayne@69
|
9006 PyObject *__pyx_v_fn = 0;
|
|
jpayne@69
|
9007 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9008 CYTHON_UNUSED Py_ssize_t __pyx_nargs;
|
|
jpayne@69
|
9009 #endif
|
|
jpayne@69
|
9010 CYTHON_UNUSED PyObject *const *__pyx_kwvalues;
|
|
jpayne@69
|
9011 PyObject* values[1] = {0};
|
|
jpayne@69
|
9012 int __pyx_lineno = 0;
|
|
jpayne@69
|
9013 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
9014 int __pyx_clineno = 0;
|
|
jpayne@69
|
9015 PyObject *__pyx_r = 0;
|
|
jpayne@69
|
9016 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
9017 __Pyx_RefNannySetupContext("_collect (wrapper)", 0);
|
|
jpayne@69
|
9018 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
9019 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
9020 __pyx_nargs = PyTuple_GET_SIZE(__pyx_args);
|
|
jpayne@69
|
9021 #else
|
|
jpayne@69
|
9022 __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL;
|
|
jpayne@69
|
9023 #endif
|
|
jpayne@69
|
9024 #endif
|
|
jpayne@69
|
9025 __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs);
|
|
jpayne@69
|
9026 {
|
|
jpayne@69
|
9027 PyObject **__pyx_pyargnames[] = {&__pyx_n_s_fn,0};
|
|
jpayne@69
|
9028 if (__pyx_kwds) {
|
|
jpayne@69
|
9029 Py_ssize_t kw_args;
|
|
jpayne@69
|
9030 switch (__pyx_nargs) {
|
|
jpayne@69
|
9031 case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
9032 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
9033 case 0: break;
|
|
jpayne@69
|
9034 default: goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9035 }
|
|
jpayne@69
|
9036 kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds);
|
|
jpayne@69
|
9037 switch (__pyx_nargs) {
|
|
jpayne@69
|
9038 case 0:
|
|
jpayne@69
|
9039 if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_fn)) != 0)) {
|
|
jpayne@69
|
9040 (void)__Pyx_Arg_NewRef_FASTCALL(values[0]);
|
|
jpayne@69
|
9041 kw_args--;
|
|
jpayne@69
|
9042 }
|
|
jpayne@69
|
9043 else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 413, __pyx_L3_error)
|
|
jpayne@69
|
9044 else goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9045 }
|
|
jpayne@69
|
9046 if (unlikely(kw_args > 0)) {
|
|
jpayne@69
|
9047 const Py_ssize_t kwd_pos_args = __pyx_nargs;
|
|
jpayne@69
|
9048 if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_collect") < 0)) __PYX_ERR(0, 413, __pyx_L3_error)
|
|
jpayne@69
|
9049 }
|
|
jpayne@69
|
9050 } else if (unlikely(__pyx_nargs != 1)) {
|
|
jpayne@69
|
9051 goto __pyx_L5_argtuple_error;
|
|
jpayne@69
|
9052 } else {
|
|
jpayne@69
|
9053 values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0);
|
|
jpayne@69
|
9054 }
|
|
jpayne@69
|
9055 __pyx_v_fn = values[0];
|
|
jpayne@69
|
9056 }
|
|
jpayne@69
|
9057 goto __pyx_L6_skip;
|
|
jpayne@69
|
9058 __pyx_L5_argtuple_error:;
|
|
jpayne@69
|
9059 __Pyx_RaiseArgtupleInvalid("_collect", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 413, __pyx_L3_error)
|
|
jpayne@69
|
9060 __pyx_L6_skip:;
|
|
jpayne@69
|
9061 goto __pyx_L4_argument_unpacking_done;
|
|
jpayne@69
|
9062 __pyx_L3_error:;
|
|
jpayne@69
|
9063 {
|
|
jpayne@69
|
9064 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
9065 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
9066 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
9067 }
|
|
jpayne@69
|
9068 }
|
|
jpayne@69
|
9069 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch._collect", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9070 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9071 return NULL;
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jpayne@69
|
9072 __pyx_L4_argument_unpacking_done:;
|
|
jpayne@69
|
9073 __pyx_r = __pyx_pf_5pysam_9libcutils_15_pysam_dispatch__collect(__pyx_self, __pyx_v_fn);
|
|
jpayne@69
|
9074
|
|
jpayne@69
|
9075 /* function exit code */
|
|
jpayne@69
|
9076 {
|
|
jpayne@69
|
9077 Py_ssize_t __pyx_temp;
|
|
jpayne@69
|
9078 for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
|
|
jpayne@69
|
9079 __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]);
|
|
jpayne@69
|
9080 }
|
|
jpayne@69
|
9081 }
|
|
jpayne@69
|
9082 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
9083 return __pyx_r;
|
|
jpayne@69
|
9084 }
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|
jpayne@69
|
9085
|
|
jpayne@69
|
9086 static PyObject *__pyx_pf_5pysam_9libcutils_15_pysam_dispatch__collect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fn) {
|
|
jpayne@69
|
9087 PyObject *__pyx_v_out = NULL;
|
|
jpayne@69
|
9088 PyObject *__pyx_v_inf = NULL;
|
|
jpayne@69
|
9089 PyObject *__pyx_r = NULL;
|
|
jpayne@69
|
9090 __Pyx_RefNannyDeclarations
|
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jpayne@69
|
9091 PyObject *__pyx_t_1 = NULL;
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jpayne@69
|
9092 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
9093 PyObject *__pyx_t_3 = NULL;
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jpayne@69
|
9094 PyObject *__pyx_t_4 = NULL;
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jpayne@69
|
9095 PyObject *__pyx_t_5 = NULL;
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jpayne@69
|
9096 PyObject *__pyx_t_6 = NULL;
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jpayne@69
|
9097 PyObject *__pyx_t_7 = NULL;
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jpayne@69
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9098 PyObject *__pyx_t_8 = NULL;
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jpayne@69
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9099 unsigned int __pyx_t_9;
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jpayne@69
|
9100 PyObject *__pyx_t_10 = NULL;
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jpayne@69
|
9101 PyObject *__pyx_t_11 = NULL;
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jpayne@69
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9102 PyObject *__pyx_t_12 = NULL;
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jpayne@69
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9103 PyObject *__pyx_t_13 = NULL;
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jpayne@69
|
9104 int __pyx_t_14;
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jpayne@69
|
9105 int __pyx_t_15;
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jpayne@69
|
9106 int __pyx_t_16;
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jpayne@69
|
9107 PyObject *__pyx_t_17 = NULL;
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jpayne@69
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9108 PyObject *__pyx_t_18 = NULL;
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jpayne@69
|
9109 PyObject *__pyx_t_19 = NULL;
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jpayne@69
|
9110 int __pyx_t_20;
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jpayne@69
|
9111 char const *__pyx_t_21;
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jpayne@69
|
9112 int __pyx_lineno = 0;
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jpayne@69
|
9113 const char *__pyx_filename = NULL;
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jpayne@69
|
9114 int __pyx_clineno = 0;
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jpayne@69
|
9115 __Pyx_RefNannySetupContext("_collect", 1);
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jpayne@69
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9116
|
|
jpayne@69
|
9117 /* "pysam/libcutils.pyx":414
|
|
jpayne@69
|
9118 * # get error messages
|
|
jpayne@69
|
9119 * def _collect(fn):
|
|
jpayne@69
|
9120 * out = [] # <<<<<<<<<<<<<<
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jpayne@69
|
9121 * try:
|
|
jpayne@69
|
9122 * with open(fn, "r") as inf:
|
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jpayne@69
|
9123 */
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jpayne@69
|
9124 __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 414, __pyx_L1_error)
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jpayne@69
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9125 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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9126 __pyx_v_out = __pyx_t_1;
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jpayne@69
|
9127 __pyx_t_1 = 0;
|
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jpayne@69
|
9128
|
|
jpayne@69
|
9129 /* "pysam/libcutils.pyx":415
|
|
jpayne@69
|
9130 * def _collect(fn):
|
|
jpayne@69
|
9131 * out = []
|
|
jpayne@69
|
9132 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
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9133 * with open(fn, "r") as inf:
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jpayne@69
|
9134 * out = inf.read()
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jpayne@69
|
9135 */
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jpayne@69
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9136 /*try:*/ {
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jpayne@69
|
9137 {
|
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jpayne@69
|
9138 __Pyx_PyThreadState_declare
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jpayne@69
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9139 __Pyx_PyThreadState_assign
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jpayne@69
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9140 __Pyx_ExceptionSave(&__pyx_t_2, &__pyx_t_3, &__pyx_t_4);
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jpayne@69
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9141 __Pyx_XGOTREF(__pyx_t_2);
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jpayne@69
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9142 __Pyx_XGOTREF(__pyx_t_3);
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jpayne@69
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9143 __Pyx_XGOTREF(__pyx_t_4);
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jpayne@69
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9144 /*try:*/ {
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jpayne@69
|
9145
|
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jpayne@69
|
9146 /* "pysam/libcutils.pyx":416
|
|
jpayne@69
|
9147 * out = []
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|
jpayne@69
|
9148 * try:
|
|
jpayne@69
|
9149 * with open(fn, "r") as inf: # <<<<<<<<<<<<<<
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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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9153 /*with:*/ {
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jpayne@69
|
9154 __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 416, __pyx_L6_error)
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jpayne@69
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9155 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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9156 __Pyx_INCREF(__pyx_v_fn);
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jpayne@69
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9157 __Pyx_GIVEREF(__pyx_v_fn);
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jpayne@69
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9158 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fn)) __PYX_ERR(0, 416, __pyx_L6_error);
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jpayne@69
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9159 __Pyx_INCREF(__pyx_n_u_r);
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jpayne@69
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9160 __Pyx_GIVEREF(__pyx_n_u_r);
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jpayne@69
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9161 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_n_u_r)) __PYX_ERR(0, 416, __pyx_L6_error);
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jpayne@69
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9162 __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_open, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 416, __pyx_L6_error)
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jpayne@69
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9163 __Pyx_GOTREF(__pyx_t_5);
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jpayne@69
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9164 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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9166 __Pyx_GOTREF(__pyx_t_6);
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jpayne@69
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9167 __pyx_t_7 = __Pyx_PyObject_LookupSpecial(__pyx_t_5, __pyx_n_s_enter); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 416, __pyx_L12_error)
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jpayne@69
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9168 __Pyx_GOTREF(__pyx_t_7);
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jpayne@69
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jpayne@69
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jpayne@69
|
9171 #if CYTHON_UNPACK_METHODS
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|
jpayne@69
|
9172 if (likely(PyMethod_Check(__pyx_t_7))) {
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jpayne@69
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9173 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_7);
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jpayne@69
|
9174 if (likely(__pyx_t_8)) {
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jpayne@69
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9175 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
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jpayne@69
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9176 __Pyx_INCREF(__pyx_t_8);
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jpayne@69
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9177 __Pyx_INCREF(function);
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jpayne@69
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9178 __Pyx_DECREF_SET(__pyx_t_7, function);
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jpayne@69
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9179 __pyx_t_9 = 1;
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jpayne@69
|
9180 }
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jpayne@69
|
9181 }
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jpayne@69
|
9182 #endif
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jpayne@69
|
9183 {
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jpayne@69
|
9184 PyObject *__pyx_callargs[2] = {__pyx_t_8, NULL};
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jpayne@69
|
9185 __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_9, 0+__pyx_t_9);
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jpayne@69
|
9186 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
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jpayne@69
|
9187 if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 416, __pyx_L12_error)
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jpayne@69
|
9188 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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9189 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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jpayne@69
|
9190 }
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jpayne@69
|
9191 __pyx_t_7 = __pyx_t_1;
|
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jpayne@69
|
9192 __pyx_t_1 = 0;
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jpayne@69
|
9193 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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jpayne@69
|
9194 /*try:*/ {
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jpayne@69
|
9195 {
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|
jpayne@69
|
9196 __Pyx_PyThreadState_declare
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jpayne@69
|
9197 __Pyx_PyThreadState_assign
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jpayne@69
|
9198 __Pyx_ExceptionSave(&__pyx_t_10, &__pyx_t_11, &__pyx_t_12);
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|
jpayne@69
|
9199 __Pyx_XGOTREF(__pyx_t_10);
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jpayne@69
|
9200 __Pyx_XGOTREF(__pyx_t_11);
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jpayne@69
|
9201 __Pyx_XGOTREF(__pyx_t_12);
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jpayne@69
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9202 /*try:*/ {
|
|
jpayne@69
|
9203 __pyx_v_inf = __pyx_t_7;
|
|
jpayne@69
|
9204 __pyx_t_7 = 0;
|
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jpayne@69
|
9205
|
|
jpayne@69
|
9206 /* "pysam/libcutils.pyx":417
|
|
jpayne@69
|
9207 * try:
|
|
jpayne@69
|
9208 * with open(fn, "r") as inf:
|
|
jpayne@69
|
9209 * out = inf.read() # <<<<<<<<<<<<<<
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jpayne@69
|
9210 * except UnicodeDecodeError:
|
|
jpayne@69
|
9211 * with open(fn, "rb") as inf:
|
|
jpayne@69
|
9212 */
|
|
jpayne@69
|
9213 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_inf, __pyx_n_s_read); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 417, __pyx_L16_error)
|
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jpayne@69
|
9214 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
9215 __pyx_t_1 = NULL;
|
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jpayne@69
|
9216 __pyx_t_9 = 0;
|
|
jpayne@69
|
9217 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
9218 if (likely(PyMethod_Check(__pyx_t_5))) {
|
|
jpayne@69
|
9219 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_5);
|
|
jpayne@69
|
9220 if (likely(__pyx_t_1)) {
|
|
jpayne@69
|
9221 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
|
|
jpayne@69
|
9222 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
9223 __Pyx_INCREF(function);
|
|
jpayne@69
|
9224 __Pyx_DECREF_SET(__pyx_t_5, function);
|
|
jpayne@69
|
9225 __pyx_t_9 = 1;
|
|
jpayne@69
|
9226 }
|
|
jpayne@69
|
9227 }
|
|
jpayne@69
|
9228 #endif
|
|
jpayne@69
|
9229 {
|
|
jpayne@69
|
9230 PyObject *__pyx_callargs[2] = {__pyx_t_1, NULL};
|
|
jpayne@69
|
9231 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_9, 0+__pyx_t_9);
|
|
jpayne@69
|
9232 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9233 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 417, __pyx_L16_error)
|
|
jpayne@69
|
9234 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
9235 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9236 }
|
|
jpayne@69
|
9237 __Pyx_DECREF_SET(__pyx_v_out, __pyx_t_7);
|
|
jpayne@69
|
9238 __pyx_t_7 = 0;
|
|
jpayne@69
|
9239
|
|
jpayne@69
|
9240 /* "pysam/libcutils.pyx":416
|
|
jpayne@69
|
9241 * out = []
|
|
jpayne@69
|
9242 * try:
|
|
jpayne@69
|
9243 * with open(fn, "r") as inf: # <<<<<<<<<<<<<<
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|
jpayne@69
|
9244 * out = inf.read()
|
|
jpayne@69
|
9245 * except UnicodeDecodeError:
|
|
jpayne@69
|
9246 */
|
|
jpayne@69
|
9247 }
|
|
jpayne@69
|
9248 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
9249 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
9250 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
9251 goto __pyx_L21_try_end;
|
|
jpayne@69
|
9252 __pyx_L16_error:;
|
|
jpayne@69
|
9253 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9254 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9255 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9256 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9257 /*except:*/ {
|
|
jpayne@69
|
9258 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch._collect", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9259 if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_5, &__pyx_t_1) < 0) __PYX_ERR(0, 416, __pyx_L18_except_error)
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jpayne@69
|
9260 __Pyx_XGOTREF(__pyx_t_7);
|
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jpayne@69
|
9261 __Pyx_XGOTREF(__pyx_t_5);
|
|
jpayne@69
|
9262 __Pyx_XGOTREF(__pyx_t_1);
|
|
jpayne@69
|
9263 __pyx_t_8 = PyTuple_Pack(3, __pyx_t_7, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 416, __pyx_L18_except_error)
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jpayne@69
|
9264 __Pyx_GOTREF(__pyx_t_8);
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jpayne@69
|
9265 __pyx_t_13 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_8, NULL);
|
|
jpayne@69
|
9266 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9267 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9268 if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 416, __pyx_L18_except_error)
|
|
jpayne@69
|
9269 __Pyx_GOTREF(__pyx_t_13);
|
|
jpayne@69
|
9270 __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_13);
|
|
jpayne@69
|
9271 __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
|
|
jpayne@69
|
9272 if (__pyx_t_14 < 0) __PYX_ERR(0, 416, __pyx_L18_except_error)
|
|
jpayne@69
|
9273 __pyx_t_15 = (!__pyx_t_14);
|
|
jpayne@69
|
9274 if (unlikely(__pyx_t_15)) {
|
|
jpayne@69
|
9275 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
9276 __Pyx_GIVEREF(__pyx_t_5);
|
|
jpayne@69
|
9277 __Pyx_XGIVEREF(__pyx_t_1);
|
|
jpayne@69
|
9278 __Pyx_ErrRestoreWithState(__pyx_t_7, __pyx_t_5, __pyx_t_1);
|
|
jpayne@69
|
9279 __pyx_t_7 = 0; __pyx_t_5 = 0; __pyx_t_1 = 0;
|
|
jpayne@69
|
9280 __PYX_ERR(0, 416, __pyx_L18_except_error)
|
|
jpayne@69
|
9281 }
|
|
jpayne@69
|
9282 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9283 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9284 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9285 goto __pyx_L17_exception_handled;
|
|
jpayne@69
|
9286 }
|
|
jpayne@69
|
9287 __pyx_L18_except_error:;
|
|
jpayne@69
|
9288 __Pyx_XGIVEREF(__pyx_t_10);
|
|
jpayne@69
|
9289 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
9290 __Pyx_XGIVEREF(__pyx_t_12);
|
|
jpayne@69
|
9291 __Pyx_ExceptionReset(__pyx_t_10, __pyx_t_11, __pyx_t_12);
|
|
jpayne@69
|
9292 goto __pyx_L6_error;
|
|
jpayne@69
|
9293 __pyx_L17_exception_handled:;
|
|
jpayne@69
|
9294 __Pyx_XGIVEREF(__pyx_t_10);
|
|
jpayne@69
|
9295 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
9296 __Pyx_XGIVEREF(__pyx_t_12);
|
|
jpayne@69
|
9297 __Pyx_ExceptionReset(__pyx_t_10, __pyx_t_11, __pyx_t_12);
|
|
jpayne@69
|
9298 __pyx_L21_try_end:;
|
|
jpayne@69
|
9299 }
|
|
jpayne@69
|
9300 }
|
|
jpayne@69
|
9301 /*finally:*/ {
|
|
jpayne@69
|
9302 /*normal exit:*/{
|
|
jpayne@69
|
9303 if (__pyx_t_6) {
|
|
jpayne@69
|
9304 __pyx_t_12 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_tuple__9, NULL);
|
|
jpayne@69
|
9305 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9306 if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 416, __pyx_L6_error)
|
|
jpayne@69
|
9307 __Pyx_GOTREF(__pyx_t_12);
|
|
jpayne@69
|
9308 __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
9309 }
|
|
jpayne@69
|
9310 goto __pyx_L15;
|
|
jpayne@69
|
9311 }
|
|
jpayne@69
|
9312 __pyx_L15:;
|
|
jpayne@69
|
9313 }
|
|
jpayne@69
|
9314 goto __pyx_L25;
|
|
jpayne@69
|
9315 __pyx_L12_error:;
|
|
jpayne@69
|
9316 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9317 goto __pyx_L6_error;
|
|
jpayne@69
|
9318 __pyx_L25:;
|
|
jpayne@69
|
9319 }
|
|
jpayne@69
|
9320
|
|
jpayne@69
|
9321 /* "pysam/libcutils.pyx":415
|
|
jpayne@69
|
9322 * def _collect(fn):
|
|
jpayne@69
|
9323 * out = []
|
|
jpayne@69
|
9324 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9325 * with open(fn, "r") as inf:
|
|
jpayne@69
|
9326 * out = inf.read()
|
|
jpayne@69
|
9327 */
|
|
jpayne@69
|
9328 }
|
|
jpayne@69
|
9329 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
9330 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
9331 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
9332 goto __pyx_L11_try_end;
|
|
jpayne@69
|
9333 __pyx_L6_error:;
|
|
jpayne@69
|
9334 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9335 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9336 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9337 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9338
|
|
jpayne@69
|
9339 /* "pysam/libcutils.pyx":418
|
|
jpayne@69
|
9340 * with open(fn, "r") as inf:
|
|
jpayne@69
|
9341 * out = inf.read()
|
|
jpayne@69
|
9342 * except UnicodeDecodeError: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9343 * with open(fn, "rb") as inf:
|
|
jpayne@69
|
9344 * # read binary output
|
|
jpayne@69
|
9345 */
|
|
jpayne@69
|
9346 __pyx_t_16 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
|
|
jpayne@69
|
9347 if (__pyx_t_16) {
|
|
jpayne@69
|
9348 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch._collect", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9349 if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_5, &__pyx_t_7) < 0) __PYX_ERR(0, 418, __pyx_L8_except_error)
|
|
jpayne@69
|
9350 __Pyx_XGOTREF(__pyx_t_1);
|
|
jpayne@69
|
9351 __Pyx_XGOTREF(__pyx_t_5);
|
|
jpayne@69
|
9352 __Pyx_XGOTREF(__pyx_t_7);
|
|
jpayne@69
|
9353
|
|
jpayne@69
|
9354 /* "pysam/libcutils.pyx":419
|
|
jpayne@69
|
9355 * out = inf.read()
|
|
jpayne@69
|
9356 * except UnicodeDecodeError:
|
|
jpayne@69
|
9357 * with open(fn, "rb") as inf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9358 * # read binary output
|
|
jpayne@69
|
9359 * out = inf.read()
|
|
jpayne@69
|
9360 */
|
|
jpayne@69
|
9361 /*with:*/ {
|
|
jpayne@69
|
9362 __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 419, __pyx_L8_except_error)
|
|
jpayne@69
|
9363 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
9364 __Pyx_INCREF(__pyx_v_fn);
|
|
jpayne@69
|
9365 __Pyx_GIVEREF(__pyx_v_fn);
|
|
jpayne@69
|
9366 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_fn)) __PYX_ERR(0, 419, __pyx_L8_except_error);
|
|
jpayne@69
|
9367 __Pyx_INCREF(__pyx_n_u_rb);
|
|
jpayne@69
|
9368 __Pyx_GIVEREF(__pyx_n_u_rb);
|
|
jpayne@69
|
9369 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_n_u_rb)) __PYX_ERR(0, 419, __pyx_L8_except_error);
|
|
jpayne@69
|
9370 __pyx_t_17 = __Pyx_PyObject_Call(__pyx_builtin_open, __pyx_t_8, NULL); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 419, __pyx_L8_except_error)
|
|
jpayne@69
|
9371 __Pyx_GOTREF(__pyx_t_17);
|
|
jpayne@69
|
9372 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9373 __pyx_t_6 = __Pyx_PyObject_LookupSpecial(__pyx_t_17, __pyx_n_s_exit); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 419, __pyx_L8_except_error)
|
|
jpayne@69
|
9374 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
9375 __pyx_t_18 = __Pyx_PyObject_LookupSpecial(__pyx_t_17, __pyx_n_s_enter); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 419, __pyx_L28_error)
|
|
jpayne@69
|
9376 __Pyx_GOTREF(__pyx_t_18);
|
|
jpayne@69
|
9377 __pyx_t_19 = NULL;
|
|
jpayne@69
|
9378 __pyx_t_9 = 0;
|
|
jpayne@69
|
9379 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
9380 if (likely(PyMethod_Check(__pyx_t_18))) {
|
|
jpayne@69
|
9381 __pyx_t_19 = PyMethod_GET_SELF(__pyx_t_18);
|
|
jpayne@69
|
9382 if (likely(__pyx_t_19)) {
|
|
jpayne@69
|
9383 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_18);
|
|
jpayne@69
|
9384 __Pyx_INCREF(__pyx_t_19);
|
|
jpayne@69
|
9385 __Pyx_INCREF(function);
|
|
jpayne@69
|
9386 __Pyx_DECREF_SET(__pyx_t_18, function);
|
|
jpayne@69
|
9387 __pyx_t_9 = 1;
|
|
jpayne@69
|
9388 }
|
|
jpayne@69
|
9389 }
|
|
jpayne@69
|
9390 #endif
|
|
jpayne@69
|
9391 {
|
|
jpayne@69
|
9392 PyObject *__pyx_callargs[2] = {__pyx_t_19, NULL};
|
|
jpayne@69
|
9393 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_18, __pyx_callargs+1-__pyx_t_9, 0+__pyx_t_9);
|
|
jpayne@69
|
9394 __Pyx_XDECREF(__pyx_t_19); __pyx_t_19 = 0;
|
|
jpayne@69
|
9395 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 419, __pyx_L28_error)
|
|
jpayne@69
|
9396 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
9397 __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
|
|
jpayne@69
|
9398 }
|
|
jpayne@69
|
9399 __pyx_t_18 = __pyx_t_8;
|
|
jpayne@69
|
9400 __pyx_t_8 = 0;
|
|
jpayne@69
|
9401 __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
|
|
jpayne@69
|
9402 /*try:*/ {
|
|
jpayne@69
|
9403 {
|
|
jpayne@69
|
9404 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
9405 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
9406 __Pyx_ExceptionSave(&__pyx_t_12, &__pyx_t_11, &__pyx_t_10);
|
|
jpayne@69
|
9407 __Pyx_XGOTREF(__pyx_t_12);
|
|
jpayne@69
|
9408 __Pyx_XGOTREF(__pyx_t_11);
|
|
jpayne@69
|
9409 __Pyx_XGOTREF(__pyx_t_10);
|
|
jpayne@69
|
9410 /*try:*/ {
|
|
jpayne@69
|
9411 __Pyx_XDECREF_SET(__pyx_v_inf, __pyx_t_18);
|
|
jpayne@69
|
9412 __pyx_t_18 = 0;
|
|
jpayne@69
|
9413
|
|
jpayne@69
|
9414 /* "pysam/libcutils.pyx":421
|
|
jpayne@69
|
9415 * with open(fn, "rb") as inf:
|
|
jpayne@69
|
9416 * # read binary output
|
|
jpayne@69
|
9417 * out = inf.read() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9418 * finally:
|
|
jpayne@69
|
9419 * os.remove(fn)
|
|
jpayne@69
|
9420 */
|
|
jpayne@69
|
9421 __pyx_t_17 = __Pyx_PyObject_GetAttrStr(__pyx_v_inf, __pyx_n_s_read); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 421, __pyx_L34_error)
|
|
jpayne@69
|
9422 __Pyx_GOTREF(__pyx_t_17);
|
|
jpayne@69
|
9423 __pyx_t_8 = NULL;
|
|
jpayne@69
|
9424 __pyx_t_9 = 0;
|
|
jpayne@69
|
9425 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
9426 if (likely(PyMethod_Check(__pyx_t_17))) {
|
|
jpayne@69
|
9427 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_17);
|
|
jpayne@69
|
9428 if (likely(__pyx_t_8)) {
|
|
jpayne@69
|
9429 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_17);
|
|
jpayne@69
|
9430 __Pyx_INCREF(__pyx_t_8);
|
|
jpayne@69
|
9431 __Pyx_INCREF(function);
|
|
jpayne@69
|
9432 __Pyx_DECREF_SET(__pyx_t_17, function);
|
|
jpayne@69
|
9433 __pyx_t_9 = 1;
|
|
jpayne@69
|
9434 }
|
|
jpayne@69
|
9435 }
|
|
jpayne@69
|
9436 #endif
|
|
jpayne@69
|
9437 {
|
|
jpayne@69
|
9438 PyObject *__pyx_callargs[2] = {__pyx_t_8, NULL};
|
|
jpayne@69
|
9439 __pyx_t_18 = __Pyx_PyObject_FastCall(__pyx_t_17, __pyx_callargs+1-__pyx_t_9, 0+__pyx_t_9);
|
|
jpayne@69
|
9440 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9441 if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 421, __pyx_L34_error)
|
|
jpayne@69
|
9442 __Pyx_GOTREF(__pyx_t_18);
|
|
jpayne@69
|
9443 __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
|
|
jpayne@69
|
9444 }
|
|
jpayne@69
|
9445 __Pyx_DECREF_SET(__pyx_v_out, __pyx_t_18);
|
|
jpayne@69
|
9446 __pyx_t_18 = 0;
|
|
jpayne@69
|
9447
|
|
jpayne@69
|
9448 /* "pysam/libcutils.pyx":419
|
|
jpayne@69
|
9449 * out = inf.read()
|
|
jpayne@69
|
9450 * except UnicodeDecodeError:
|
|
jpayne@69
|
9451 * with open(fn, "rb") as inf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9452 * # read binary output
|
|
jpayne@69
|
9453 * out = inf.read()
|
|
jpayne@69
|
9454 */
|
|
jpayne@69
|
9455 }
|
|
jpayne@69
|
9456 __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
|
|
jpayne@69
|
9457 __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
|
|
jpayne@69
|
9458 __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
9459 goto __pyx_L41_try_end;
|
|
jpayne@69
|
9460 __pyx_L34_error:;
|
|
jpayne@69
|
9461 __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
|
|
jpayne@69
|
9462 __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
|
|
jpayne@69
|
9463 __Pyx_XDECREF(__pyx_t_19); __pyx_t_19 = 0;
|
|
jpayne@69
|
9464 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9465 /*except:*/ {
|
|
jpayne@69
|
9466 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch._collect", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9467 if (__Pyx_GetException(&__pyx_t_18, &__pyx_t_17, &__pyx_t_8) < 0) __PYX_ERR(0, 419, __pyx_L36_except_error)
|
|
jpayne@69
|
9468 __Pyx_XGOTREF(__pyx_t_18);
|
|
jpayne@69
|
9469 __Pyx_XGOTREF(__pyx_t_17);
|
|
jpayne@69
|
9470 __Pyx_XGOTREF(__pyx_t_8);
|
|
jpayne@69
|
9471 __pyx_t_19 = PyTuple_Pack(3, __pyx_t_18, __pyx_t_17, __pyx_t_8); if (unlikely(!__pyx_t_19)) __PYX_ERR(0, 419, __pyx_L36_except_error)
|
|
jpayne@69
|
9472 __Pyx_GOTREF(__pyx_t_19);
|
|
jpayne@69
|
9473 __pyx_t_13 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_19, NULL);
|
|
jpayne@69
|
9474 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9475 __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
|
|
jpayne@69
|
9476 if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 419, __pyx_L36_except_error)
|
|
jpayne@69
|
9477 __Pyx_GOTREF(__pyx_t_13);
|
|
jpayne@69
|
9478 __pyx_t_15 = __Pyx_PyObject_IsTrue(__pyx_t_13);
|
|
jpayne@69
|
9479 __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
|
|
jpayne@69
|
9480 if (__pyx_t_15 < 0) __PYX_ERR(0, 419, __pyx_L36_except_error)
|
|
jpayne@69
|
9481 __pyx_t_14 = (!__pyx_t_15);
|
|
jpayne@69
|
9482 if (unlikely(__pyx_t_14)) {
|
|
jpayne@69
|
9483 __Pyx_GIVEREF(__pyx_t_18);
|
|
jpayne@69
|
9484 __Pyx_GIVEREF(__pyx_t_17);
|
|
jpayne@69
|
9485 __Pyx_XGIVEREF(__pyx_t_8);
|
|
jpayne@69
|
9486 __Pyx_ErrRestoreWithState(__pyx_t_18, __pyx_t_17, __pyx_t_8);
|
|
jpayne@69
|
9487 __pyx_t_18 = 0; __pyx_t_17 = 0; __pyx_t_8 = 0;
|
|
jpayne@69
|
9488 __PYX_ERR(0, 419, __pyx_L36_except_error)
|
|
jpayne@69
|
9489 }
|
|
jpayne@69
|
9490 __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
|
|
jpayne@69
|
9491 __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
|
|
jpayne@69
|
9492 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9493 goto __pyx_L35_exception_handled;
|
|
jpayne@69
|
9494 }
|
|
jpayne@69
|
9495 __pyx_L36_except_error:;
|
|
jpayne@69
|
9496 __Pyx_XGIVEREF(__pyx_t_12);
|
|
jpayne@69
|
9497 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
9498 __Pyx_XGIVEREF(__pyx_t_10);
|
|
jpayne@69
|
9499 __Pyx_ExceptionReset(__pyx_t_12, __pyx_t_11, __pyx_t_10);
|
|
jpayne@69
|
9500 goto __pyx_L8_except_error;
|
|
jpayne@69
|
9501 __pyx_L35_exception_handled:;
|
|
jpayne@69
|
9502 __Pyx_XGIVEREF(__pyx_t_12);
|
|
jpayne@69
|
9503 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
9504 __Pyx_XGIVEREF(__pyx_t_10);
|
|
jpayne@69
|
9505 __Pyx_ExceptionReset(__pyx_t_12, __pyx_t_11, __pyx_t_10);
|
|
jpayne@69
|
9506 __pyx_L41_try_end:;
|
|
jpayne@69
|
9507 }
|
|
jpayne@69
|
9508 }
|
|
jpayne@69
|
9509 /*finally:*/ {
|
|
jpayne@69
|
9510 /*normal exit:*/{
|
|
jpayne@69
|
9511 if (__pyx_t_6) {
|
|
jpayne@69
|
9512 __pyx_t_10 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_tuple__9, NULL);
|
|
jpayne@69
|
9513 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9514 if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 419, __pyx_L8_except_error)
|
|
jpayne@69
|
9515 __Pyx_GOTREF(__pyx_t_10);
|
|
jpayne@69
|
9516 __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
|
|
jpayne@69
|
9517 }
|
|
jpayne@69
|
9518 goto __pyx_L33;
|
|
jpayne@69
|
9519 }
|
|
jpayne@69
|
9520 __pyx_L33:;
|
|
jpayne@69
|
9521 }
|
|
jpayne@69
|
9522 goto __pyx_L45;
|
|
jpayne@69
|
9523 __pyx_L28_error:;
|
|
jpayne@69
|
9524 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9525 goto __pyx_L8_except_error;
|
|
jpayne@69
|
9526 __pyx_L45:;
|
|
jpayne@69
|
9527 }
|
|
jpayne@69
|
9528 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9529 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9530 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9531 goto __pyx_L7_exception_handled;
|
|
jpayne@69
|
9532 }
|
|
jpayne@69
|
9533 goto __pyx_L8_except_error;
|
|
jpayne@69
|
9534
|
|
jpayne@69
|
9535 /* "pysam/libcutils.pyx":415
|
|
jpayne@69
|
9536 * def _collect(fn):
|
|
jpayne@69
|
9537 * out = []
|
|
jpayne@69
|
9538 * try: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9539 * with open(fn, "r") as inf:
|
|
jpayne@69
|
9540 * out = inf.read()
|
|
jpayne@69
|
9541 */
|
|
jpayne@69
|
9542 __pyx_L8_except_error:;
|
|
jpayne@69
|
9543 __Pyx_XGIVEREF(__pyx_t_2);
|
|
jpayne@69
|
9544 __Pyx_XGIVEREF(__pyx_t_3);
|
|
jpayne@69
|
9545 __Pyx_XGIVEREF(__pyx_t_4);
|
|
jpayne@69
|
9546 __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
|
|
jpayne@69
|
9547 goto __pyx_L4_error;
|
|
jpayne@69
|
9548 __pyx_L7_exception_handled:;
|
|
jpayne@69
|
9549 __Pyx_XGIVEREF(__pyx_t_2);
|
|
jpayne@69
|
9550 __Pyx_XGIVEREF(__pyx_t_3);
|
|
jpayne@69
|
9551 __Pyx_XGIVEREF(__pyx_t_4);
|
|
jpayne@69
|
9552 __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
|
|
jpayne@69
|
9553 __pyx_L11_try_end:;
|
|
jpayne@69
|
9554 }
|
|
jpayne@69
|
9555 }
|
|
jpayne@69
|
9556
|
|
jpayne@69
|
9557 /* "pysam/libcutils.pyx":423
|
|
jpayne@69
|
9558 * out = inf.read()
|
|
jpayne@69
|
9559 * finally:
|
|
jpayne@69
|
9560 * os.remove(fn) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9561 * return out
|
|
jpayne@69
|
9562 *
|
|
jpayne@69
|
9563 */
|
|
jpayne@69
|
9564 /*finally:*/ {
|
|
jpayne@69
|
9565 /*normal exit:*/{
|
|
jpayne@69
|
9566 __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_os); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 423, __pyx_L1_error)
|
|
jpayne@69
|
9567 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
9568 __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_remove); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 423, __pyx_L1_error)
|
|
jpayne@69
|
9569 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9570 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9571 __pyx_t_5 = NULL;
|
|
jpayne@69
|
9572 __pyx_t_9 = 0;
|
|
jpayne@69
|
9573 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
9574 if (unlikely(PyMethod_Check(__pyx_t_1))) {
|
|
jpayne@69
|
9575 __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1);
|
|
jpayne@69
|
9576 if (likely(__pyx_t_5)) {
|
|
jpayne@69
|
9577 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1);
|
|
jpayne@69
|
9578 __Pyx_INCREF(__pyx_t_5);
|
|
jpayne@69
|
9579 __Pyx_INCREF(function);
|
|
jpayne@69
|
9580 __Pyx_DECREF_SET(__pyx_t_1, function);
|
|
jpayne@69
|
9581 __pyx_t_9 = 1;
|
|
jpayne@69
|
9582 }
|
|
jpayne@69
|
9583 }
|
|
jpayne@69
|
9584 #endif
|
|
jpayne@69
|
9585 {
|
|
jpayne@69
|
9586 PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_fn};
|
|
jpayne@69
|
9587 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
9588 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9589 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 423, __pyx_L1_error)
|
|
jpayne@69
|
9590 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
9591 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9592 }
|
|
jpayne@69
|
9593 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9594 goto __pyx_L5;
|
|
jpayne@69
|
9595 }
|
|
jpayne@69
|
9596 __pyx_L4_error:;
|
|
jpayne@69
|
9597 /*exception exit:*/{
|
|
jpayne@69
|
9598 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
9599 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
9600 __pyx_t_4 = 0; __pyx_t_3 = 0; __pyx_t_2 = 0; __pyx_t_6 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0;
|
|
jpayne@69
|
9601 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9602 __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
|
|
jpayne@69
|
9603 __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
|
|
jpayne@69
|
9604 __Pyx_XDECREF(__pyx_t_19); __pyx_t_19 = 0;
|
|
jpayne@69
|
9605 __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9606 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9607 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9608 if (PY_MAJOR_VERSION >= 3) __Pyx_ExceptionSwap(&__pyx_t_6, &__pyx_t_10, &__pyx_t_11);
|
|
jpayne@69
|
9609 if ((PY_MAJOR_VERSION < 3) || unlikely(__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0)) __Pyx_ErrFetch(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2);
|
|
jpayne@69
|
9610 __Pyx_XGOTREF(__pyx_t_4);
|
|
jpayne@69
|
9611 __Pyx_XGOTREF(__pyx_t_3);
|
|
jpayne@69
|
9612 __Pyx_XGOTREF(__pyx_t_2);
|
|
jpayne@69
|
9613 __Pyx_XGOTREF(__pyx_t_6);
|
|
jpayne@69
|
9614 __Pyx_XGOTREF(__pyx_t_10);
|
|
jpayne@69
|
9615 __Pyx_XGOTREF(__pyx_t_11);
|
|
jpayne@69
|
9616 __pyx_t_16 = __pyx_lineno; __pyx_t_20 = __pyx_clineno; __pyx_t_21 = __pyx_filename;
|
|
jpayne@69
|
9617 {
|
|
jpayne@69
|
9618 __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_os); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 423, __pyx_L47_error)
|
|
jpayne@69
|
9619 __Pyx_GOTREF(__pyx_t_1);
|
|
jpayne@69
|
9620 __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_remove); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 423, __pyx_L47_error)
|
|
jpayne@69
|
9621 __Pyx_GOTREF(__pyx_t_5);
|
|
jpayne@69
|
9622 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9623 __pyx_t_1 = NULL;
|
|
jpayne@69
|
9624 __pyx_t_9 = 0;
|
|
jpayne@69
|
9625 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
9626 if (unlikely(PyMethod_Check(__pyx_t_5))) {
|
|
jpayne@69
|
9627 __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_5);
|
|
jpayne@69
|
9628 if (likely(__pyx_t_1)) {
|
|
jpayne@69
|
9629 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
|
|
jpayne@69
|
9630 __Pyx_INCREF(__pyx_t_1);
|
|
jpayne@69
|
9631 __Pyx_INCREF(function);
|
|
jpayne@69
|
9632 __Pyx_DECREF_SET(__pyx_t_5, function);
|
|
jpayne@69
|
9633 __pyx_t_9 = 1;
|
|
jpayne@69
|
9634 }
|
|
jpayne@69
|
9635 }
|
|
jpayne@69
|
9636 #endif
|
|
jpayne@69
|
9637 {
|
|
jpayne@69
|
9638 PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_v_fn};
|
|
jpayne@69
|
9639 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
9640 __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
|
|
jpayne@69
|
9641 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 423, __pyx_L47_error)
|
|
jpayne@69
|
9642 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
9643 __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
|
|
jpayne@69
|
9644 }
|
|
jpayne@69
|
9645 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9646 }
|
|
jpayne@69
|
9647 if (PY_MAJOR_VERSION >= 3) {
|
|
jpayne@69
|
9648 __Pyx_XGIVEREF(__pyx_t_6);
|
|
jpayne@69
|
9649 __Pyx_XGIVEREF(__pyx_t_10);
|
|
jpayne@69
|
9650 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
9651 __Pyx_ExceptionReset(__pyx_t_6, __pyx_t_10, __pyx_t_11);
|
|
jpayne@69
|
9652 }
|
|
jpayne@69
|
9653 __Pyx_XGIVEREF(__pyx_t_4);
|
|
jpayne@69
|
9654 __Pyx_XGIVEREF(__pyx_t_3);
|
|
jpayne@69
|
9655 __Pyx_XGIVEREF(__pyx_t_2);
|
|
jpayne@69
|
9656 __Pyx_ErrRestore(__pyx_t_4, __pyx_t_3, __pyx_t_2);
|
|
jpayne@69
|
9657 __pyx_t_4 = 0; __pyx_t_3 = 0; __pyx_t_2 = 0; __pyx_t_6 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0;
|
|
jpayne@69
|
9658 __pyx_lineno = __pyx_t_16; __pyx_clineno = __pyx_t_20; __pyx_filename = __pyx_t_21;
|
|
jpayne@69
|
9659 goto __pyx_L1_error;
|
|
jpayne@69
|
9660 __pyx_L47_error:;
|
|
jpayne@69
|
9661 if (PY_MAJOR_VERSION >= 3) {
|
|
jpayne@69
|
9662 __Pyx_XGIVEREF(__pyx_t_6);
|
|
jpayne@69
|
9663 __Pyx_XGIVEREF(__pyx_t_10);
|
|
jpayne@69
|
9664 __Pyx_XGIVEREF(__pyx_t_11);
|
|
jpayne@69
|
9665 __Pyx_ExceptionReset(__pyx_t_6, __pyx_t_10, __pyx_t_11);
|
|
jpayne@69
|
9666 }
|
|
jpayne@69
|
9667 __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
9668 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
9669 __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
9670 __pyx_t_6 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0;
|
|
jpayne@69
|
9671 goto __pyx_L1_error;
|
|
jpayne@69
|
9672 }
|
|
jpayne@69
|
9673 __pyx_L5:;
|
|
jpayne@69
|
9674 }
|
|
jpayne@69
|
9675
|
|
jpayne@69
|
9676 /* "pysam/libcutils.pyx":424
|
|
jpayne@69
|
9677 * finally:
|
|
jpayne@69
|
9678 * os.remove(fn)
|
|
jpayne@69
|
9679 * return out # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9680 *
|
|
jpayne@69
|
9681 * out_stderr = _collect(stderr_f)
|
|
jpayne@69
|
9682 */
|
|
jpayne@69
|
9683 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
9684 __Pyx_INCREF(__pyx_v_out);
|
|
jpayne@69
|
9685 __pyx_r = __pyx_v_out;
|
|
jpayne@69
|
9686 goto __pyx_L0;
|
|
jpayne@69
|
9687
|
|
jpayne@69
|
9688 /* "pysam/libcutils.pyx":413
|
|
jpayne@69
|
9689 *
|
|
jpayne@69
|
9690 * # get error messages
|
|
jpayne@69
|
9691 * def _collect(fn): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9692 * out = []
|
|
jpayne@69
|
9693 * try:
|
|
jpayne@69
|
9694 */
|
|
jpayne@69
|
9695
|
|
jpayne@69
|
9696 /* function exit code */
|
|
jpayne@69
|
9697 __pyx_L1_error:;
|
|
jpayne@69
|
9698 __Pyx_XDECREF(__pyx_t_1);
|
|
jpayne@69
|
9699 __Pyx_XDECREF(__pyx_t_5);
|
|
jpayne@69
|
9700 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
9701 __Pyx_XDECREF(__pyx_t_8);
|
|
jpayne@69
|
9702 __Pyx_XDECREF(__pyx_t_17);
|
|
jpayne@69
|
9703 __Pyx_XDECREF(__pyx_t_18);
|
|
jpayne@69
|
9704 __Pyx_XDECREF(__pyx_t_19);
|
|
jpayne@69
|
9705 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch._collect", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
9706 __pyx_r = NULL;
|
|
jpayne@69
|
9707 __pyx_L0:;
|
|
jpayne@69
|
9708 __Pyx_XDECREF(__pyx_v_out);
|
|
jpayne@69
|
9709 __Pyx_XDECREF(__pyx_v_inf);
|
|
jpayne@69
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9710 __Pyx_XGIVEREF(__pyx_r);
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jpayne@69
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9711 __Pyx_RefNannyFinishContext();
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jpayne@69
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jpayne@69
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9713 }
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jpayne@69
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9714
|
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jpayne@69
|
9715 /* "pysam/libcutils.pyx":276
|
|
jpayne@69
|
9716 *
|
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jpayne@69
|
9717 *
|
|
jpayne@69
|
9718 * def _pysam_dispatch(collection, # <<<<<<<<<<<<<<
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|
jpayne@69
|
9719 * method,
|
|
jpayne@69
|
9720 * args=None,
|
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jpayne@69
|
9721 */
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|
jpayne@69
|
9722
|
|
jpayne@69
|
9723 static PyObject *__pyx_pf_5pysam_9libcutils_14_pysam_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_collection, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout, PyObject *__pyx_v_is_usage, PyObject *__pyx_v_save_stdout) {
|
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jpayne@69
|
9724 PyObject *__pyx_v_ARGUMENTS = NULL;
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jpayne@69
|
9725 int __pyx_v_skip_next;
|
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jpayne@69
|
9726 PyObject *__pyx_v_arg = NULL;
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jpayne@69
|
9727 PyObject *__pyx_v_stderr_h = NULL;
|
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jpayne@69
|
9728 PyObject *__pyx_v_stderr_f = NULL;
|
|
jpayne@69
|
9729 PyObject *__pyx_v_stdout_f = NULL;
|
|
jpayne@69
|
9730 PyObject *__pyx_v_stdout_h = NULL;
|
|
jpayne@69
|
9731 PyObject *__pyx_v_MAP_STDOUT_OPTIONS = NULL;
|
|
jpayne@69
|
9732 PyObject *__pyx_v_stdout_option = NULL;
|
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jpayne@69
|
9733 char **__pyx_v_cargs;
|
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jpayne@69
|
9734 int __pyx_v_i;
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jpayne@69
|
9735 int __pyx_v_n;
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jpayne@69
|
9736 int __pyx_v_retval;
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jpayne@69
|
9737 int __pyx_v_l;
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jpayne@69
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9738 int __pyx_v_extra_args;
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jpayne@69
|
9739 PyObject *__pyx_v__collect = 0;
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jpayne@69
|
9740 PyObject *__pyx_v_out_stderr = NULL;
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jpayne@69
|
9741 PyObject *__pyx_v_out_stdout = NULL;
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jpayne@69
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9742 PyObject *__pyx_8genexpr2__pyx_v_a = NULL;
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jpayne@69
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9743 PyObject *__pyx_r = NULL;
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jpayne@69
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9744 __Pyx_RefNannyDeclarations
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jpayne@69
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9745 int __pyx_t_1;
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jpayne@69
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9746 int __pyx_t_2;
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jpayne@69
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9747 PyObject *__pyx_t_3 = NULL;
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jpayne@69
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9748 Py_ssize_t __pyx_t_4;
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jpayne@69
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9749 PyObject *(*__pyx_t_5)(PyObject *);
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jpayne@69
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9750 PyObject *__pyx_t_6 = NULL;
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jpayne@69
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9751 PyObject *__pyx_t_7 = NULL;
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jpayne@69
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9752 PyObject *__pyx_t_8 = NULL;
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jpayne@69
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9753 unsigned int __pyx_t_9;
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jpayne@69
|
9754 PyObject *(*__pyx_t_10)(PyObject *);
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jpayne@69
|
9755 char const *__pyx_t_11;
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jpayne@69
|
9756 char const *__pyx_t_12;
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jpayne@69
|
9757 char const *__pyx_t_13;
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jpayne@69
|
9758 int __pyx_t_14;
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jpayne@69
|
9759 PyObject *__pyx_t_15 = NULL;
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jpayne@69
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9760 PyObject *__pyx_t_16 = NULL;
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jpayne@69
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9761 char *__pyx_t_17;
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jpayne@69
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9762 int __pyx_t_18;
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jpayne@69
|
9763 char const *__pyx_t_19;
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jpayne@69
|
9764 int __pyx_lineno = 0;
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jpayne@69
|
9765 const char *__pyx_filename = NULL;
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jpayne@69
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9766 int __pyx_clineno = 0;
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jpayne@69
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9767 __Pyx_RefNannySetupContext("_pysam_dispatch", 0);
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jpayne@69
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9768 __Pyx_INCREF(__pyx_v_collection);
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jpayne@69
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9769 __Pyx_INCREF(__pyx_v_method);
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jpayne@69
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9770 __Pyx_INCREF(__pyx_v_args);
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jpayne@69
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9771
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jpayne@69
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9772 /* "pysam/libcutils.pyx":294
|
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jpayne@69
|
9773 * '''
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jpayne@69
|
9774 *
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jpayne@69
|
9775 * if method == "index" and args: # <<<<<<<<<<<<<<
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jpayne@69
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9776 * # We make sure that at least the first specified input file exists,
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jpayne@69
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9777 * # and if it doesn't we raise an IOError.
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jpayne@69
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9778 */
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jpayne@69
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9779 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_v_method, __pyx_n_u_index, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 294, __pyx_L1_error)
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jpayne@69
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9780 if (__pyx_t_2) {
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jpayne@69
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9781 } else {
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jpayne@69
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9782 __pyx_t_1 = __pyx_t_2;
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jpayne@69
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9783 goto __pyx_L4_bool_binop_done;
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jpayne@69
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9784 }
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jpayne@69
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9785 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_args); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 294, __pyx_L1_error)
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jpayne@69
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9786 __pyx_t_1 = __pyx_t_2;
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jpayne@69
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9787 __pyx_L4_bool_binop_done:;
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jpayne@69
|
9788 if (__pyx_t_1) {
|
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jpayne@69
|
9789
|
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jpayne@69
|
9790 /* "pysam/libcutils.pyx":297
|
|
jpayne@69
|
9791 * # We make sure that at least the first specified input file exists,
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jpayne@69
|
9792 * # and if it doesn't we raise an IOError.
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jpayne@69
|
9793 * ARGUMENTS = ['-m', '--min-shift', '-o', '--output', '--output-file', '-@', '--threads'] # <<<<<<<<<<<<<<
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jpayne@69
|
9794 * skip_next = False
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jpayne@69
|
9795 * for arg in args:
|
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jpayne@69
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9796 */
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jpayne@69
|
9797 __pyx_t_3 = PyList_New(7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 297, __pyx_L1_error)
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jpayne@69
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9798 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
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9799 __Pyx_INCREF(__pyx_kp_u_m);
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jpayne@69
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9800 __Pyx_GIVEREF(__pyx_kp_u_m);
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jpayne@69
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9801 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_m)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9802 __Pyx_INCREF(__pyx_kp_u_min_shift);
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jpayne@69
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9803 __Pyx_GIVEREF(__pyx_kp_u_min_shift);
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jpayne@69
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9804 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 1, __pyx_kp_u_min_shift)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9805 __Pyx_INCREF(__pyx_kp_u_o);
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jpayne@69
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9806 __Pyx_GIVEREF(__pyx_kp_u_o);
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jpayne@69
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9807 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_o)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9808 __Pyx_INCREF(__pyx_kp_u_output);
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jpayne@69
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9809 __Pyx_GIVEREF(__pyx_kp_u_output);
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jpayne@69
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9810 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 3, __pyx_kp_u_output)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9811 __Pyx_INCREF(__pyx_kp_u_output_file);
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jpayne@69
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9812 __Pyx_GIVEREF(__pyx_kp_u_output_file);
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jpayne@69
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9813 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u_output_file)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9814 __Pyx_INCREF(__pyx_kp_u__10);
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jpayne@69
|
9815 __Pyx_GIVEREF(__pyx_kp_u__10);
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jpayne@69
|
9816 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 5, __pyx_kp_u__10)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9817 __Pyx_INCREF(__pyx_kp_u_threads);
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jpayne@69
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9818 __Pyx_GIVEREF(__pyx_kp_u_threads);
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jpayne@69
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9819 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 6, __pyx_kp_u_threads)) __PYX_ERR(0, 297, __pyx_L1_error);
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jpayne@69
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9820 __pyx_v_ARGUMENTS = ((PyObject*)__pyx_t_3);
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jpayne@69
|
9821 __pyx_t_3 = 0;
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jpayne@69
|
9822
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jpayne@69
|
9823 /* "pysam/libcutils.pyx":298
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|
jpayne@69
|
9824 * # and if it doesn't we raise an IOError.
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jpayne@69
|
9825 * ARGUMENTS = ['-m', '--min-shift', '-o', '--output', '--output-file', '-@', '--threads']
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jpayne@69
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9826 * skip_next = False # <<<<<<<<<<<<<<
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jpayne@69
|
9827 * for arg in args:
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|
jpayne@69
|
9828 * if skip_next:
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jpayne@69
|
9829 */
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jpayne@69
|
9830 __pyx_v_skip_next = 0;
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jpayne@69
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9831
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jpayne@69
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9832 /* "pysam/libcutils.pyx":299
|
|
jpayne@69
|
9833 * ARGUMENTS = ['-m', '--min-shift', '-o', '--output', '--output-file', '-@', '--threads']
|
|
jpayne@69
|
9834 * skip_next = False
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|
jpayne@69
|
9835 * for arg in args: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9836 * if skip_next:
|
|
jpayne@69
|
9837 * skip_next = False
|
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jpayne@69
|
9838 */
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jpayne@69
|
9839 if (likely(PyList_CheckExact(__pyx_v_args)) || PyTuple_CheckExact(__pyx_v_args)) {
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jpayne@69
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9840 __pyx_t_3 = __pyx_v_args; __Pyx_INCREF(__pyx_t_3);
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jpayne@69
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9841 __pyx_t_4 = 0;
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jpayne@69
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9842 __pyx_t_5 = NULL;
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jpayne@69
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9843 } else {
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jpayne@69
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9844 __pyx_t_4 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 299, __pyx_L1_error)
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jpayne@69
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9845 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
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9846 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 299, __pyx_L1_error)
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jpayne@69
|
9847 }
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jpayne@69
|
9848 for (;;) {
|
|
jpayne@69
|
9849 if (likely(!__pyx_t_5)) {
|
|
jpayne@69
|
9850 if (likely(PyList_CheckExact(__pyx_t_3))) {
|
|
jpayne@69
|
9851 {
|
|
jpayne@69
|
9852 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_3);
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jpayne@69
|
9853 #if !CYTHON_ASSUME_SAFE_MACROS
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jpayne@69
|
9854 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 299, __pyx_L1_error)
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|
jpayne@69
|
9855 #endif
|
|
jpayne@69
|
9856 if (__pyx_t_4 >= __pyx_temp) break;
|
|
jpayne@69
|
9857 }
|
|
jpayne@69
|
9858 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
9859 __pyx_t_6 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 299, __pyx_L1_error)
|
|
jpayne@69
|
9860 #else
|
|
jpayne@69
|
9861 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 299, __pyx_L1_error)
|
|
jpayne@69
|
9862 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
9863 #endif
|
|
jpayne@69
|
9864 } else {
|
|
jpayne@69
|
9865 {
|
|
jpayne@69
|
9866 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_3);
|
|
jpayne@69
|
9867 #if !CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
9868 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 299, __pyx_L1_error)
|
|
jpayne@69
|
9869 #endif
|
|
jpayne@69
|
9870 if (__pyx_t_4 >= __pyx_temp) break;
|
|
jpayne@69
|
9871 }
|
|
jpayne@69
|
9872 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
9873 __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 299, __pyx_L1_error)
|
|
jpayne@69
|
9874 #else
|
|
jpayne@69
|
9875 __pyx_t_6 = __Pyx_PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 299, __pyx_L1_error)
|
|
jpayne@69
|
9876 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
9877 #endif
|
|
jpayne@69
|
9878 }
|
|
jpayne@69
|
9879 } else {
|
|
jpayne@69
|
9880 __pyx_t_6 = __pyx_t_5(__pyx_t_3);
|
|
jpayne@69
|
9881 if (unlikely(!__pyx_t_6)) {
|
|
jpayne@69
|
9882 PyObject* exc_type = PyErr_Occurred();
|
|
jpayne@69
|
9883 if (exc_type) {
|
|
jpayne@69
|
9884 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
|
|
jpayne@69
|
9885 else __PYX_ERR(0, 299, __pyx_L1_error)
|
|
jpayne@69
|
9886 }
|
|
jpayne@69
|
9887 break;
|
|
jpayne@69
|
9888 }
|
|
jpayne@69
|
9889 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
9890 }
|
|
jpayne@69
|
9891 __Pyx_XDECREF_SET(__pyx_v_arg, __pyx_t_6);
|
|
jpayne@69
|
9892 __pyx_t_6 = 0;
|
|
jpayne@69
|
9893
|
|
jpayne@69
|
9894 /* "pysam/libcutils.pyx":300
|
|
jpayne@69
|
9895 * skip_next = False
|
|
jpayne@69
|
9896 * for arg in args:
|
|
jpayne@69
|
9897 * if skip_next: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9898 * skip_next = False
|
|
jpayne@69
|
9899 * continue
|
|
jpayne@69
|
9900 */
|
|
jpayne@69
|
9901 if (__pyx_v_skip_next) {
|
|
jpayne@69
|
9902
|
|
jpayne@69
|
9903 /* "pysam/libcutils.pyx":301
|
|
jpayne@69
|
9904 * for arg in args:
|
|
jpayne@69
|
9905 * if skip_next:
|
|
jpayne@69
|
9906 * skip_next = False # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9907 * continue
|
|
jpayne@69
|
9908 * if arg.startswith('-'):
|
|
jpayne@69
|
9909 */
|
|
jpayne@69
|
9910 __pyx_v_skip_next = 0;
|
|
jpayne@69
|
9911
|
|
jpayne@69
|
9912 /* "pysam/libcutils.pyx":302
|
|
jpayne@69
|
9913 * if skip_next:
|
|
jpayne@69
|
9914 * skip_next = False
|
|
jpayne@69
|
9915 * continue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9916 * if arg.startswith('-'):
|
|
jpayne@69
|
9917 * # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12'
|
|
jpayne@69
|
9918 */
|
|
jpayne@69
|
9919 goto __pyx_L6_continue;
|
|
jpayne@69
|
9920
|
|
jpayne@69
|
9921 /* "pysam/libcutils.pyx":300
|
|
jpayne@69
|
9922 * skip_next = False
|
|
jpayne@69
|
9923 * for arg in args:
|
|
jpayne@69
|
9924 * if skip_next: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9925 * skip_next = False
|
|
jpayne@69
|
9926 * continue
|
|
jpayne@69
|
9927 */
|
|
jpayne@69
|
9928 }
|
|
jpayne@69
|
9929
|
|
jpayne@69
|
9930 /* "pysam/libcutils.pyx":303
|
|
jpayne@69
|
9931 * skip_next = False
|
|
jpayne@69
|
9932 * continue
|
|
jpayne@69
|
9933 * if arg.startswith('-'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9934 * # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12'
|
|
jpayne@69
|
9935 * if arg in ARGUMENTS:
|
|
jpayne@69
|
9936 */
|
|
jpayne@69
|
9937 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_arg, __pyx_n_s_startswith); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 303, __pyx_L1_error)
|
|
jpayne@69
|
9938 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
9939 __pyx_t_8 = NULL;
|
|
jpayne@69
|
9940 __pyx_t_9 = 0;
|
|
jpayne@69
|
9941 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
9942 if (likely(PyMethod_Check(__pyx_t_7))) {
|
|
jpayne@69
|
9943 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_7);
|
|
jpayne@69
|
9944 if (likely(__pyx_t_8)) {
|
|
jpayne@69
|
9945 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
|
|
jpayne@69
|
9946 __Pyx_INCREF(__pyx_t_8);
|
|
jpayne@69
|
9947 __Pyx_INCREF(function);
|
|
jpayne@69
|
9948 __Pyx_DECREF_SET(__pyx_t_7, function);
|
|
jpayne@69
|
9949 __pyx_t_9 = 1;
|
|
jpayne@69
|
9950 }
|
|
jpayne@69
|
9951 }
|
|
jpayne@69
|
9952 #endif
|
|
jpayne@69
|
9953 {
|
|
jpayne@69
|
9954 PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_kp_u__8};
|
|
jpayne@69
|
9955 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
9956 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
9957 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 303, __pyx_L1_error)
|
|
jpayne@69
|
9958 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
9959 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
9960 }
|
|
jpayne@69
|
9961 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 303, __pyx_L1_error)
|
|
jpayne@69
|
9962 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
9963 if (__pyx_t_1) {
|
|
jpayne@69
|
9964
|
|
jpayne@69
|
9965 /* "pysam/libcutils.pyx":305
|
|
jpayne@69
|
9966 * if arg.startswith('-'):
|
|
jpayne@69
|
9967 * # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12'
|
|
jpayne@69
|
9968 * if arg in ARGUMENTS: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9969 * skip_next = True
|
|
jpayne@69
|
9970 * continue
|
|
jpayne@69
|
9971 */
|
|
jpayne@69
|
9972 __pyx_t_1 = (__Pyx_PySequence_ContainsTF(__pyx_v_arg, __pyx_v_ARGUMENTS, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 305, __pyx_L1_error)
|
|
jpayne@69
|
9973 if (__pyx_t_1) {
|
|
jpayne@69
|
9974
|
|
jpayne@69
|
9975 /* "pysam/libcutils.pyx":306
|
|
jpayne@69
|
9976 * # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12'
|
|
jpayne@69
|
9977 * if arg in ARGUMENTS:
|
|
jpayne@69
|
9978 * skip_next = True # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9979 * continue
|
|
jpayne@69
|
9980 * if not os.path.exists(arg):
|
|
jpayne@69
|
9981 */
|
|
jpayne@69
|
9982 __pyx_v_skip_next = 1;
|
|
jpayne@69
|
9983
|
|
jpayne@69
|
9984 /* "pysam/libcutils.pyx":305
|
|
jpayne@69
|
9985 * if arg.startswith('-'):
|
|
jpayne@69
|
9986 * # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12'
|
|
jpayne@69
|
9987 * if arg in ARGUMENTS: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9988 * skip_next = True
|
|
jpayne@69
|
9989 * continue
|
|
jpayne@69
|
9990 */
|
|
jpayne@69
|
9991 }
|
|
jpayne@69
|
9992
|
|
jpayne@69
|
9993 /* "pysam/libcutils.pyx":307
|
|
jpayne@69
|
9994 * if arg in ARGUMENTS:
|
|
jpayne@69
|
9995 * skip_next = True
|
|
jpayne@69
|
9996 * continue # <<<<<<<<<<<<<<
|
|
jpayne@69
|
9997 * if not os.path.exists(arg):
|
|
jpayne@69
|
9998 * raise IOError("No such file or directory: '%s'" % arg)
|
|
jpayne@69
|
9999 */
|
|
jpayne@69
|
10000 goto __pyx_L6_continue;
|
|
jpayne@69
|
10001
|
|
jpayne@69
|
10002 /* "pysam/libcutils.pyx":303
|
|
jpayne@69
|
10003 * skip_next = False
|
|
jpayne@69
|
10004 * continue
|
|
jpayne@69
|
10005 * if arg.startswith('-'): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10006 * # Skip next argument for e.g. '--min-shift' '12' or '-m' '12' but not '-m12'
|
|
jpayne@69
|
10007 * if arg in ARGUMENTS:
|
|
jpayne@69
|
10008 */
|
|
jpayne@69
|
10009 }
|
|
jpayne@69
|
10010
|
|
jpayne@69
|
10011 /* "pysam/libcutils.pyx":308
|
|
jpayne@69
|
10012 * skip_next = True
|
|
jpayne@69
|
10013 * continue
|
|
jpayne@69
|
10014 * if not os.path.exists(arg): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10015 * raise IOError("No such file or directory: '%s'" % arg)
|
|
jpayne@69
|
10016 * else:
|
|
jpayne@69
|
10017 */
|
|
jpayne@69
|
10018 __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_os); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 308, __pyx_L1_error)
|
|
jpayne@69
|
10019 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10020 __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_path); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 308, __pyx_L1_error)
|
|
jpayne@69
|
10021 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
10022 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10023 __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_exists); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 308, __pyx_L1_error)
|
|
jpayne@69
|
10024 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10025 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10026 __pyx_t_8 = NULL;
|
|
jpayne@69
|
10027 __pyx_t_9 = 0;
|
|
jpayne@69
|
10028 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10029 if (likely(PyMethod_Check(__pyx_t_7))) {
|
|
jpayne@69
|
10030 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_7);
|
|
jpayne@69
|
10031 if (likely(__pyx_t_8)) {
|
|
jpayne@69
|
10032 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
|
|
jpayne@69
|
10033 __Pyx_INCREF(__pyx_t_8);
|
|
jpayne@69
|
10034 __Pyx_INCREF(function);
|
|
jpayne@69
|
10035 __Pyx_DECREF_SET(__pyx_t_7, function);
|
|
jpayne@69
|
10036 __pyx_t_9 = 1;
|
|
jpayne@69
|
10037 }
|
|
jpayne@69
|
10038 }
|
|
jpayne@69
|
10039 #endif
|
|
jpayne@69
|
10040 {
|
|
jpayne@69
|
10041 PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_v_arg};
|
|
jpayne@69
|
10042 __pyx_t_6 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
10043 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10044 if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 308, __pyx_L1_error)
|
|
jpayne@69
|
10045 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10046 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10047 }
|
|
jpayne@69
|
10048 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 308, __pyx_L1_error)
|
|
jpayne@69
|
10049 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
10050 __pyx_t_2 = (!__pyx_t_1);
|
|
jpayne@69
|
10051 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
10052
|
|
jpayne@69
|
10053 /* "pysam/libcutils.pyx":309
|
|
jpayne@69
|
10054 * continue
|
|
jpayne@69
|
10055 * if not os.path.exists(arg):
|
|
jpayne@69
|
10056 * raise IOError("No such file or directory: '%s'" % arg) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10057 * else:
|
|
jpayne@69
|
10058 * break
|
|
jpayne@69
|
10059 */
|
|
jpayne@69
|
10060 __pyx_t_6 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_No_such_file_or_directory_s, __pyx_v_arg); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 309, __pyx_L1_error)
|
|
jpayne@69
|
10061 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10062 __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 309, __pyx_L1_error)
|
|
jpayne@69
|
10063 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10064 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
10065 __Pyx_Raise(__pyx_t_7, 0, 0, 0);
|
|
jpayne@69
|
10066 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10067 __PYX_ERR(0, 309, __pyx_L1_error)
|
|
jpayne@69
|
10068
|
|
jpayne@69
|
10069 /* "pysam/libcutils.pyx":308
|
|
jpayne@69
|
10070 * skip_next = True
|
|
jpayne@69
|
10071 * continue
|
|
jpayne@69
|
10072 * if not os.path.exists(arg): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10073 * raise IOError("No such file or directory: '%s'" % arg)
|
|
jpayne@69
|
10074 * else:
|
|
jpayne@69
|
10075 */
|
|
jpayne@69
|
10076 }
|
|
jpayne@69
|
10077
|
|
jpayne@69
|
10078 /* "pysam/libcutils.pyx":311
|
|
jpayne@69
|
10079 * raise IOError("No such file or directory: '%s'" % arg)
|
|
jpayne@69
|
10080 * else:
|
|
jpayne@69
|
10081 * break # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10082 *
|
|
jpayne@69
|
10083 * if args is None:
|
|
jpayne@69
|
10084 */
|
|
jpayne@69
|
10085 /*else*/ {
|
|
jpayne@69
|
10086 goto __pyx_L7_break;
|
|
jpayne@69
|
10087 }
|
|
jpayne@69
|
10088
|
|
jpayne@69
|
10089 /* "pysam/libcutils.pyx":299
|
|
jpayne@69
|
10090 * ARGUMENTS = ['-m', '--min-shift', '-o', '--output', '--output-file', '-@', '--threads']
|
|
jpayne@69
|
10091 * skip_next = False
|
|
jpayne@69
|
10092 * for arg in args: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10093 * if skip_next:
|
|
jpayne@69
|
10094 * skip_next = False
|
|
jpayne@69
|
10095 */
|
|
jpayne@69
|
10096 __pyx_L6_continue:;
|
|
jpayne@69
|
10097 }
|
|
jpayne@69
|
10098 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10099 goto __pyx_L12_for_end;
|
|
jpayne@69
|
10100 __pyx_L7_break:;
|
|
jpayne@69
|
10101 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10102 goto __pyx_L12_for_end;
|
|
jpayne@69
|
10103 __pyx_L12_for_end:;
|
|
jpayne@69
|
10104
|
|
jpayne@69
|
10105 /* "pysam/libcutils.pyx":294
|
|
jpayne@69
|
10106 * '''
|
|
jpayne@69
|
10107 *
|
|
jpayne@69
|
10108 * if method == "index" and args: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10109 * # We make sure that at least the first specified input file exists,
|
|
jpayne@69
|
10110 * # and if it doesn't we raise an IOError.
|
|
jpayne@69
|
10111 */
|
|
jpayne@69
|
10112 }
|
|
jpayne@69
|
10113
|
|
jpayne@69
|
10114 /* "pysam/libcutils.pyx":313
|
|
jpayne@69
|
10115 * break
|
|
jpayne@69
|
10116 *
|
|
jpayne@69
|
10117 * if args is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10118 * args = []
|
|
jpayne@69
|
10119 * else:
|
|
jpayne@69
|
10120 */
|
|
jpayne@69
|
10121 __pyx_t_2 = (__pyx_v_args == Py_None);
|
|
jpayne@69
|
10122 if (__pyx_t_2) {
|
|
jpayne@69
|
10123
|
|
jpayne@69
|
10124 /* "pysam/libcutils.pyx":314
|
|
jpayne@69
|
10125 *
|
|
jpayne@69
|
10126 * if args is None:
|
|
jpayne@69
|
10127 * args = [] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10128 * else:
|
|
jpayne@69
|
10129 * args = list(args)
|
|
jpayne@69
|
10130 */
|
|
jpayne@69
|
10131 __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 314, __pyx_L1_error)
|
|
jpayne@69
|
10132 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10133 __Pyx_DECREF_SET(__pyx_v_args, __pyx_t_3);
|
|
jpayne@69
|
10134 __pyx_t_3 = 0;
|
|
jpayne@69
|
10135
|
|
jpayne@69
|
10136 /* "pysam/libcutils.pyx":313
|
|
jpayne@69
|
10137 * break
|
|
jpayne@69
|
10138 *
|
|
jpayne@69
|
10139 * if args is None: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10140 * args = []
|
|
jpayne@69
|
10141 * else:
|
|
jpayne@69
|
10142 */
|
|
jpayne@69
|
10143 goto __pyx_L13;
|
|
jpayne@69
|
10144 }
|
|
jpayne@69
|
10145
|
|
jpayne@69
|
10146 /* "pysam/libcutils.pyx":316
|
|
jpayne@69
|
10147 * args = []
|
|
jpayne@69
|
10148 * else:
|
|
jpayne@69
|
10149 * args = list(args) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10150 *
|
|
jpayne@69
|
10151 * # redirect stderr to file
|
|
jpayne@69
|
10152 */
|
|
jpayne@69
|
10153 /*else*/ {
|
|
jpayne@69
|
10154 __pyx_t_3 = PySequence_List(__pyx_v_args); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 316, __pyx_L1_error)
|
|
jpayne@69
|
10155 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10156 __Pyx_DECREF_SET(__pyx_v_args, __pyx_t_3);
|
|
jpayne@69
|
10157 __pyx_t_3 = 0;
|
|
jpayne@69
|
10158 }
|
|
jpayne@69
|
10159 __pyx_L13:;
|
|
jpayne@69
|
10160
|
|
jpayne@69
|
10161 /* "pysam/libcutils.pyx":319
|
|
jpayne@69
|
10162 *
|
|
jpayne@69
|
10163 * # redirect stderr to file
|
|
jpayne@69
|
10164 * stderr_h, stderr_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10165 *
|
|
jpayne@69
|
10166 * # redirect stdout to file
|
|
jpayne@69
|
10167 */
|
|
jpayne@69
|
10168 __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_tempfile); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10169 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10170 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_mkstemp); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10171 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10172 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10173 __pyx_t_7 = NULL;
|
|
jpayne@69
|
10174 __pyx_t_9 = 0;
|
|
jpayne@69
|
10175 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10176 if (unlikely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
10177 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
10178 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
10179 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
10180 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
10181 __Pyx_INCREF(function);
|
|
jpayne@69
|
10182 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
10183 __pyx_t_9 = 1;
|
|
jpayne@69
|
10184 }
|
|
jpayne@69
|
10185 }
|
|
jpayne@69
|
10186 #endif
|
|
jpayne@69
|
10187 {
|
|
jpayne@69
|
10188 PyObject *__pyx_callargs[2] = {__pyx_t_7, NULL};
|
|
jpayne@69
|
10189 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_9, 0+__pyx_t_9);
|
|
jpayne@69
|
10190 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10191 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10192 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10193 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
10194 }
|
|
jpayne@69
|
10195 if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
|
|
jpayne@69
|
10196 PyObject* sequence = __pyx_t_3;
|
|
jpayne@69
|
10197 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
|
|
jpayne@69
|
10198 if (unlikely(size != 2)) {
|
|
jpayne@69
|
10199 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
|
|
jpayne@69
|
10200 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
|
|
jpayne@69
|
10201 __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10202 }
|
|
jpayne@69
|
10203 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
10204 if (likely(PyTuple_CheckExact(sequence))) {
|
|
jpayne@69
|
10205 __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
10206 __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
10207 } else {
|
|
jpayne@69
|
10208 __pyx_t_6 = PyList_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
10209 __pyx_t_7 = PyList_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
10210 }
|
|
jpayne@69
|
10211 __Pyx_INCREF(__pyx_t_6);
|
|
jpayne@69
|
10212 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
10213 #else
|
|
jpayne@69
|
10214 __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10215 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10216 __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10217 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10218 #endif
|
|
jpayne@69
|
10219 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10220 } else {
|
|
jpayne@69
|
10221 Py_ssize_t index = -1;
|
|
jpayne@69
|
10222 __pyx_t_8 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10223 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
10224 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10225 __pyx_t_10 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_8);
|
|
jpayne@69
|
10226 index = 0; __pyx_t_6 = __pyx_t_10(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L14_unpacking_failed;
|
|
jpayne@69
|
10227 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10228 index = 1; __pyx_t_7 = __pyx_t_10(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L14_unpacking_failed;
|
|
jpayne@69
|
10229 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10230 if (__Pyx_IternextUnpackEndCheck(__pyx_t_10(__pyx_t_8), 2) < 0) __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10231 __pyx_t_10 = NULL;
|
|
jpayne@69
|
10232 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10233 goto __pyx_L15_unpacking_done;
|
|
jpayne@69
|
10234 __pyx_L14_unpacking_failed:;
|
|
jpayne@69
|
10235 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10236 __pyx_t_10 = NULL;
|
|
jpayne@69
|
10237 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
|
|
jpayne@69
|
10238 __PYX_ERR(0, 319, __pyx_L1_error)
|
|
jpayne@69
|
10239 __pyx_L15_unpacking_done:;
|
|
jpayne@69
|
10240 }
|
|
jpayne@69
|
10241 __pyx_v_stderr_h = __pyx_t_6;
|
|
jpayne@69
|
10242 __pyx_t_6 = 0;
|
|
jpayne@69
|
10243 __pyx_v_stderr_f = __pyx_t_7;
|
|
jpayne@69
|
10244 __pyx_t_7 = 0;
|
|
jpayne@69
|
10245
|
|
jpayne@69
|
10246 /* "pysam/libcutils.pyx":322
|
|
jpayne@69
|
10247 *
|
|
jpayne@69
|
10248 * # redirect stdout to file
|
|
jpayne@69
|
10249 * if save_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10250 * stdout_f = save_stdout
|
|
jpayne@69
|
10251 * stdout_h = c_open(force_bytes(stdout_f),
|
|
jpayne@69
|
10252 */
|
|
jpayne@69
|
10253 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_save_stdout); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 322, __pyx_L1_error)
|
|
jpayne@69
|
10254 if (__pyx_t_2) {
|
|
jpayne@69
|
10255
|
|
jpayne@69
|
10256 /* "pysam/libcutils.pyx":323
|
|
jpayne@69
|
10257 * # redirect stdout to file
|
|
jpayne@69
|
10258 * if save_stdout:
|
|
jpayne@69
|
10259 * stdout_f = save_stdout # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10260 * stdout_h = c_open(force_bytes(stdout_f),
|
|
jpayne@69
|
10261 * O_WRONLY|O_CREAT|O_TRUNC, 0666)
|
|
jpayne@69
|
10262 */
|
|
jpayne@69
|
10263 __Pyx_INCREF(__pyx_v_save_stdout);
|
|
jpayne@69
|
10264 __pyx_v_stdout_f = __pyx_v_save_stdout;
|
|
jpayne@69
|
10265
|
|
jpayne@69
|
10266 /* "pysam/libcutils.pyx":324
|
|
jpayne@69
|
10267 * if save_stdout:
|
|
jpayne@69
|
10268 * stdout_f = save_stdout
|
|
jpayne@69
|
10269 * stdout_h = c_open(force_bytes(stdout_f), # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10270 * O_WRONLY|O_CREAT|O_TRUNC, 0666)
|
|
jpayne@69
|
10271 * if stdout_h == -1:
|
|
jpayne@69
|
10272 */
|
|
jpayne@69
|
10273 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_stdout_f, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 324, __pyx_L1_error)
|
|
jpayne@69
|
10274 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10275 if (unlikely(__pyx_t_3 == Py_None)) {
|
|
jpayne@69
|
10276 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
10277 __PYX_ERR(0, 324, __pyx_L1_error)
|
|
jpayne@69
|
10278 }
|
|
jpayne@69
|
10279 __pyx_t_11 = __Pyx_PyBytes_AsString(__pyx_t_3); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) __PYX_ERR(0, 324, __pyx_L1_error)
|
|
jpayne@69
|
10280
|
|
jpayne@69
|
10281 /* "pysam/libcutils.pyx":325
|
|
jpayne@69
|
10282 * stdout_f = save_stdout
|
|
jpayne@69
|
10283 * stdout_h = c_open(force_bytes(stdout_f),
|
|
jpayne@69
|
10284 * O_WRONLY|O_CREAT|O_TRUNC, 0666) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10285 * if stdout_h == -1:
|
|
jpayne@69
|
10286 * raise OSError(errno, "error while opening file for writing", stdout_f)
|
|
jpayne@69
|
10287 */
|
|
jpayne@69
|
10288 __pyx_t_7 = __Pyx_PyInt_From_int(open(__pyx_t_11, ((O_WRONLY | O_CREAT) | O_TRUNC), 0666)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 324, __pyx_L1_error)
|
|
jpayne@69
|
10289 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10290 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10291 __pyx_v_stdout_h = __pyx_t_7;
|
|
jpayne@69
|
10292 __pyx_t_7 = 0;
|
|
jpayne@69
|
10293
|
|
jpayne@69
|
10294 /* "pysam/libcutils.pyx":326
|
|
jpayne@69
|
10295 * stdout_h = c_open(force_bytes(stdout_f),
|
|
jpayne@69
|
10296 * O_WRONLY|O_CREAT|O_TRUNC, 0666)
|
|
jpayne@69
|
10297 * if stdout_h == -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10298 * raise OSError(errno, "error while opening file for writing", stdout_f)
|
|
jpayne@69
|
10299 *
|
|
jpayne@69
|
10300 */
|
|
jpayne@69
|
10301 __pyx_t_2 = (__Pyx_PyInt_BoolEqObjC(__pyx_v_stdout_h, __pyx_int_neg_1, -1L, 0)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 326, __pyx_L1_error)
|
|
jpayne@69
|
10302 if (unlikely(__pyx_t_2)) {
|
|
jpayne@69
|
10303
|
|
jpayne@69
|
10304 /* "pysam/libcutils.pyx":327
|
|
jpayne@69
|
10305 * O_WRONLY|O_CREAT|O_TRUNC, 0666)
|
|
jpayne@69
|
10306 * if stdout_h == -1:
|
|
jpayne@69
|
10307 * raise OSError(errno, "error while opening file for writing", stdout_f) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10308 *
|
|
jpayne@69
|
10309 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10310 */
|
|
jpayne@69
|
10311 __pyx_t_7 = __Pyx_PyInt_From_int(errno); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 327, __pyx_L1_error)
|
|
jpayne@69
|
10312 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10313 __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 327, __pyx_L1_error)
|
|
jpayne@69
|
10314 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10315 __Pyx_GIVEREF(__pyx_t_7);
|
|
jpayne@69
|
10316 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_7)) __PYX_ERR(0, 327, __pyx_L1_error);
|
|
jpayne@69
|
10317 __Pyx_INCREF(__pyx_kp_u_error_while_opening_file_for_wri);
|
|
jpayne@69
|
10318 __Pyx_GIVEREF(__pyx_kp_u_error_while_opening_file_for_wri);
|
|
jpayne@69
|
10319 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_kp_u_error_while_opening_file_for_wri)) __PYX_ERR(0, 327, __pyx_L1_error);
|
|
jpayne@69
|
10320 __Pyx_INCREF(__pyx_v_stdout_f);
|
|
jpayne@69
|
10321 __Pyx_GIVEREF(__pyx_v_stdout_f);
|
|
jpayne@69
|
10322 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_v_stdout_f)) __PYX_ERR(0, 327, __pyx_L1_error);
|
|
jpayne@69
|
10323 __pyx_t_7 = 0;
|
|
jpayne@69
|
10324 __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_OSError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 327, __pyx_L1_error)
|
|
jpayne@69
|
10325 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10326 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10327 __Pyx_Raise(__pyx_t_7, 0, 0, 0);
|
|
jpayne@69
|
10328 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10329 __PYX_ERR(0, 327, __pyx_L1_error)
|
|
jpayne@69
|
10330
|
|
jpayne@69
|
10331 /* "pysam/libcutils.pyx":326
|
|
jpayne@69
|
10332 * stdout_h = c_open(force_bytes(stdout_f),
|
|
jpayne@69
|
10333 * O_WRONLY|O_CREAT|O_TRUNC, 0666)
|
|
jpayne@69
|
10334 * if stdout_h == -1: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10335 * raise OSError(errno, "error while opening file for writing", stdout_f)
|
|
jpayne@69
|
10336 *
|
|
jpayne@69
|
10337 */
|
|
jpayne@69
|
10338 }
|
|
jpayne@69
|
10339
|
|
jpayne@69
|
10340 /* "pysam/libcutils.pyx":329
|
|
jpayne@69
|
10341 * raise OSError(errno, "error while opening file for writing", stdout_f)
|
|
jpayne@69
|
10342 *
|
|
jpayne@69
|
10343 * samtools_set_stdout_fn(force_bytes(stdout_f)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10344 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10345 *
|
|
jpayne@69
|
10346 */
|
|
jpayne@69
|
10347 __pyx_t_7 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_stdout_f, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 329, __pyx_L1_error)
|
|
jpayne@69
|
10348 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10349 if (unlikely(__pyx_t_7 == Py_None)) {
|
|
jpayne@69
|
10350 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
10351 __PYX_ERR(0, 329, __pyx_L1_error)
|
|
jpayne@69
|
10352 }
|
|
jpayne@69
|
10353 __pyx_t_12 = __Pyx_PyBytes_AsString(__pyx_t_7); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) __PYX_ERR(0, 329, __pyx_L1_error)
|
|
jpayne@69
|
10354 samtools_set_stdout_fn(__pyx_t_12);
|
|
jpayne@69
|
10355 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10356
|
|
jpayne@69
|
10357 /* "pysam/libcutils.pyx":330
|
|
jpayne@69
|
10358 *
|
|
jpayne@69
|
10359 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10360 * bcftools_set_stdout_fn(force_bytes(stdout_f)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10361 *
|
|
jpayne@69
|
10362 * elif catch_stdout:
|
|
jpayne@69
|
10363 */
|
|
jpayne@69
|
10364 __pyx_t_7 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_stdout_f, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 330, __pyx_L1_error)
|
|
jpayne@69
|
10365 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10366 if (unlikely(__pyx_t_7 == Py_None)) {
|
|
jpayne@69
|
10367 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
10368 __PYX_ERR(0, 330, __pyx_L1_error)
|
|
jpayne@69
|
10369 }
|
|
jpayne@69
|
10370 __pyx_t_13 = __Pyx_PyBytes_AsString(__pyx_t_7); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) __PYX_ERR(0, 330, __pyx_L1_error)
|
|
jpayne@69
|
10371 bcftools_set_stdout_fn(__pyx_t_13);
|
|
jpayne@69
|
10372 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10373
|
|
jpayne@69
|
10374 /* "pysam/libcutils.pyx":322
|
|
jpayne@69
|
10375 *
|
|
jpayne@69
|
10376 * # redirect stdout to file
|
|
jpayne@69
|
10377 * if save_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10378 * stdout_f = save_stdout
|
|
jpayne@69
|
10379 * stdout_h = c_open(force_bytes(stdout_f),
|
|
jpayne@69
|
10380 */
|
|
jpayne@69
|
10381 goto __pyx_L16;
|
|
jpayne@69
|
10382 }
|
|
jpayne@69
|
10383
|
|
jpayne@69
|
10384 /* "pysam/libcutils.pyx":332
|
|
jpayne@69
|
10385 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10386 *
|
|
jpayne@69
|
10387 * elif catch_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10388 * stdout_h, stdout_f = tempfile.mkstemp()
|
|
jpayne@69
|
10389 * MAP_STDOUT_OPTIONS = {
|
|
jpayne@69
|
10390 */
|
|
jpayne@69
|
10391 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 332, __pyx_L1_error)
|
|
jpayne@69
|
10392 if (__pyx_t_2) {
|
|
jpayne@69
|
10393
|
|
jpayne@69
|
10394 /* "pysam/libcutils.pyx":333
|
|
jpayne@69
|
10395 *
|
|
jpayne@69
|
10396 * elif catch_stdout:
|
|
jpayne@69
|
10397 * stdout_h, stdout_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10398 * MAP_STDOUT_OPTIONS = {
|
|
jpayne@69
|
10399 * "samtools": {
|
|
jpayne@69
|
10400 */
|
|
jpayne@69
|
10401 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_tempfile); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10402 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10403 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_mkstemp); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10404 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10405 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10406 __pyx_t_3 = NULL;
|
|
jpayne@69
|
10407 __pyx_t_9 = 0;
|
|
jpayne@69
|
10408 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10409 if (unlikely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
10410 __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
10411 if (likely(__pyx_t_3)) {
|
|
jpayne@69
|
10412 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
10413 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
10414 __Pyx_INCREF(function);
|
|
jpayne@69
|
10415 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
10416 __pyx_t_9 = 1;
|
|
jpayne@69
|
10417 }
|
|
jpayne@69
|
10418 }
|
|
jpayne@69
|
10419 #endif
|
|
jpayne@69
|
10420 {
|
|
jpayne@69
|
10421 PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL};
|
|
jpayne@69
|
10422 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_9, 0+__pyx_t_9);
|
|
jpayne@69
|
10423 __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10424 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10425 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10426 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
10427 }
|
|
jpayne@69
|
10428 if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
|
|
jpayne@69
|
10429 PyObject* sequence = __pyx_t_7;
|
|
jpayne@69
|
10430 Py_ssize_t size = __Pyx_PySequence_SIZE(sequence);
|
|
jpayne@69
|
10431 if (unlikely(size != 2)) {
|
|
jpayne@69
|
10432 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
|
|
jpayne@69
|
10433 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
|
|
jpayne@69
|
10434 __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10435 }
|
|
jpayne@69
|
10436 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
10437 if (likely(PyTuple_CheckExact(sequence))) {
|
|
jpayne@69
|
10438 __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
10439 __pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
10440 } else {
|
|
jpayne@69
|
10441 __pyx_t_6 = PyList_GET_ITEM(sequence, 0);
|
|
jpayne@69
|
10442 __pyx_t_3 = PyList_GET_ITEM(sequence, 1);
|
|
jpayne@69
|
10443 }
|
|
jpayne@69
|
10444 __Pyx_INCREF(__pyx_t_6);
|
|
jpayne@69
|
10445 __Pyx_INCREF(__pyx_t_3);
|
|
jpayne@69
|
10446 #else
|
|
jpayne@69
|
10447 __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10448 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10449 __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10450 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10451 #endif
|
|
jpayne@69
|
10452 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10453 } else {
|
|
jpayne@69
|
10454 Py_ssize_t index = -1;
|
|
jpayne@69
|
10455 __pyx_t_8 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10456 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
10457 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10458 __pyx_t_10 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_8);
|
|
jpayne@69
|
10459 index = 0; __pyx_t_6 = __pyx_t_10(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L18_unpacking_failed;
|
|
jpayne@69
|
10460 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10461 index = 1; __pyx_t_3 = __pyx_t_10(__pyx_t_8); if (unlikely(!__pyx_t_3)) goto __pyx_L18_unpacking_failed;
|
|
jpayne@69
|
10462 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10463 if (__Pyx_IternextUnpackEndCheck(__pyx_t_10(__pyx_t_8), 2) < 0) __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10464 __pyx_t_10 = NULL;
|
|
jpayne@69
|
10465 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10466 goto __pyx_L19_unpacking_done;
|
|
jpayne@69
|
10467 __pyx_L18_unpacking_failed:;
|
|
jpayne@69
|
10468 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10469 __pyx_t_10 = NULL;
|
|
jpayne@69
|
10470 if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
|
|
jpayne@69
|
10471 __PYX_ERR(0, 333, __pyx_L1_error)
|
|
jpayne@69
|
10472 __pyx_L19_unpacking_done:;
|
|
jpayne@69
|
10473 }
|
|
jpayne@69
|
10474 __pyx_v_stdout_h = __pyx_t_6;
|
|
jpayne@69
|
10475 __pyx_t_6 = 0;
|
|
jpayne@69
|
10476 __pyx_v_stdout_f = __pyx_t_3;
|
|
jpayne@69
|
10477 __pyx_t_3 = 0;
|
|
jpayne@69
|
10478
|
|
jpayne@69
|
10479 /* "pysam/libcutils.pyx":335
|
|
jpayne@69
|
10480 * stdout_h, stdout_f = tempfile.mkstemp()
|
|
jpayne@69
|
10481 * MAP_STDOUT_OPTIONS = {
|
|
jpayne@69
|
10482 * "samtools": { # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10483 * "view": "-o {}",
|
|
jpayne@69
|
10484 * "mpileup": "-o {}",
|
|
jpayne@69
|
10485 */
|
|
jpayne@69
|
10486 __pyx_t_7 = __Pyx_PyDict_NewPresized(2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 335, __pyx_L1_error)
|
|
jpayne@69
|
10487 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10488
|
|
jpayne@69
|
10489 /* "pysam/libcutils.pyx":336
|
|
jpayne@69
|
10490 * MAP_STDOUT_OPTIONS = {
|
|
jpayne@69
|
10491 * "samtools": {
|
|
jpayne@69
|
10492 * "view": "-o {}", # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10493 * "mpileup": "-o {}",
|
|
jpayne@69
|
10494 * "depad": "-o {}",
|
|
jpayne@69
|
10495 */
|
|
jpayne@69
|
10496 __pyx_t_3 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 336, __pyx_L1_error)
|
|
jpayne@69
|
10497 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10498 if (PyDict_SetItem(__pyx_t_3, __pyx_n_u_view, __pyx_kp_u_o_2) < 0) __PYX_ERR(0, 336, __pyx_L1_error)
|
|
jpayne@69
|
10499 if (PyDict_SetItem(__pyx_t_3, __pyx_n_u_mpileup, __pyx_kp_u_o_2) < 0) __PYX_ERR(0, 336, __pyx_L1_error)
|
|
jpayne@69
|
10500 if (PyDict_SetItem(__pyx_t_3, __pyx_n_u_depad, __pyx_kp_u_o_2) < 0) __PYX_ERR(0, 336, __pyx_L1_error)
|
|
jpayne@69
|
10501 if (PyDict_SetItem(__pyx_t_3, __pyx_n_u_calmd, __pyx_kp_u_) < 0) __PYX_ERR(0, 336, __pyx_L1_error)
|
|
jpayne@69
|
10502 if (PyDict_SetItem(__pyx_t_7, __pyx_n_u_samtools, __pyx_t_3) < 0) __PYX_ERR(0, 335, __pyx_L1_error)
|
|
jpayne@69
|
10503 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10504
|
|
jpayne@69
|
10505 /* "pysam/libcutils.pyx":341
|
|
jpayne@69
|
10506 * "calmd": "", # uses pysam_stdout_fn
|
|
jpayne@69
|
10507 * },
|
|
jpayne@69
|
10508 * "bcftools": {} # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10509 * }
|
|
jpayne@69
|
10510 *
|
|
jpayne@69
|
10511 */
|
|
jpayne@69
|
10512 __pyx_t_3 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 341, __pyx_L1_error)
|
|
jpayne@69
|
10513 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10514 if (PyDict_SetItem(__pyx_t_7, __pyx_n_u_bcftools, __pyx_t_3) < 0) __PYX_ERR(0, 335, __pyx_L1_error)
|
|
jpayne@69
|
10515 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10516 __pyx_v_MAP_STDOUT_OPTIONS = ((PyObject*)__pyx_t_7);
|
|
jpayne@69
|
10517 __pyx_t_7 = 0;
|
|
jpayne@69
|
10518
|
|
jpayne@69
|
10519 /* "pysam/libcutils.pyx":344
|
|
jpayne@69
|
10520 * }
|
|
jpayne@69
|
10521 *
|
|
jpayne@69
|
10522 * stdout_option = None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10523 * if collection == "bcftools":
|
|
jpayne@69
|
10524 * # in bcftools, most methods accept -o, the exceptions
|
|
jpayne@69
|
10525 */
|
|
jpayne@69
|
10526 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
10527 __pyx_v_stdout_option = Py_None;
|
|
jpayne@69
|
10528
|
|
jpayne@69
|
10529 /* "pysam/libcutils.pyx":345
|
|
jpayne@69
|
10530 *
|
|
jpayne@69
|
10531 * stdout_option = None
|
|
jpayne@69
|
10532 * if collection == "bcftools": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10533 * # in bcftools, most methods accept -o, the exceptions
|
|
jpayne@69
|
10534 * # are below:
|
|
jpayne@69
|
10535 */
|
|
jpayne@69
|
10536 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_v_collection, __pyx_n_u_bcftools, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 345, __pyx_L1_error)
|
|
jpayne@69
|
10537 if (__pyx_t_2) {
|
|
jpayne@69
|
10538
|
|
jpayne@69
|
10539 /* "pysam/libcutils.pyx":348
|
|
jpayne@69
|
10540 * # in bcftools, most methods accept -o, the exceptions
|
|
jpayne@69
|
10541 * # are below:
|
|
jpayne@69
|
10542 * if method not in ("head", "index", "roh", "stats"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10543 * stdout_option = "-o {}"
|
|
jpayne@69
|
10544 * elif method in MAP_STDOUT_OPTIONS[collection]:
|
|
jpayne@69
|
10545 */
|
|
jpayne@69
|
10546 __Pyx_INCREF(__pyx_v_method);
|
|
jpayne@69
|
10547 __pyx_t_7 = __pyx_v_method;
|
|
jpayne@69
|
10548 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_n_u_head, Py_NE)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 348, __pyx_L1_error)
|
|
jpayne@69
|
10549 if (__pyx_t_1) {
|
|
jpayne@69
|
10550 } else {
|
|
jpayne@69
|
10551 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
10552 goto __pyx_L22_bool_binop_done;
|
|
jpayne@69
|
10553 }
|
|
jpayne@69
|
10554 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_n_u_index, Py_NE)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 348, __pyx_L1_error)
|
|
jpayne@69
|
10555 if (__pyx_t_1) {
|
|
jpayne@69
|
10556 } else {
|
|
jpayne@69
|
10557 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
10558 goto __pyx_L22_bool_binop_done;
|
|
jpayne@69
|
10559 }
|
|
jpayne@69
|
10560 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_n_u_roh, Py_NE)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 348, __pyx_L1_error)
|
|
jpayne@69
|
10561 if (__pyx_t_1) {
|
|
jpayne@69
|
10562 } else {
|
|
jpayne@69
|
10563 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
10564 goto __pyx_L22_bool_binop_done;
|
|
jpayne@69
|
10565 }
|
|
jpayne@69
|
10566 __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_t_7, __pyx_n_u_stats, Py_NE)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 348, __pyx_L1_error)
|
|
jpayne@69
|
10567 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
10568 __pyx_L22_bool_binop_done:;
|
|
jpayne@69
|
10569 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10570 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
10571 if (__pyx_t_1) {
|
|
jpayne@69
|
10572
|
|
jpayne@69
|
10573 /* "pysam/libcutils.pyx":349
|
|
jpayne@69
|
10574 * # are below:
|
|
jpayne@69
|
10575 * if method not in ("head", "index", "roh", "stats"):
|
|
jpayne@69
|
10576 * stdout_option = "-o {}" # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10577 * elif method in MAP_STDOUT_OPTIONS[collection]:
|
|
jpayne@69
|
10578 * # special case - samtools view -c outputs on stdout
|
|
jpayne@69
|
10579 */
|
|
jpayne@69
|
10580 __Pyx_INCREF(__pyx_kp_u_o_2);
|
|
jpayne@69
|
10581 __Pyx_DECREF_SET(__pyx_v_stdout_option, __pyx_kp_u_o_2);
|
|
jpayne@69
|
10582
|
|
jpayne@69
|
10583 /* "pysam/libcutils.pyx":348
|
|
jpayne@69
|
10584 * # in bcftools, most methods accept -o, the exceptions
|
|
jpayne@69
|
10585 * # are below:
|
|
jpayne@69
|
10586 * if method not in ("head", "index", "roh", "stats"): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10587 * stdout_option = "-o {}"
|
|
jpayne@69
|
10588 * elif method in MAP_STDOUT_OPTIONS[collection]:
|
|
jpayne@69
|
10589 */
|
|
jpayne@69
|
10590 }
|
|
jpayne@69
|
10591
|
|
jpayne@69
|
10592 /* "pysam/libcutils.pyx":345
|
|
jpayne@69
|
10593 *
|
|
jpayne@69
|
10594 * stdout_option = None
|
|
jpayne@69
|
10595 * if collection == "bcftools": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10596 * # in bcftools, most methods accept -o, the exceptions
|
|
jpayne@69
|
10597 * # are below:
|
|
jpayne@69
|
10598 */
|
|
jpayne@69
|
10599 goto __pyx_L20;
|
|
jpayne@69
|
10600 }
|
|
jpayne@69
|
10601
|
|
jpayne@69
|
10602 /* "pysam/libcutils.pyx":350
|
|
jpayne@69
|
10603 * if method not in ("head", "index", "roh", "stats"):
|
|
jpayne@69
|
10604 * stdout_option = "-o {}"
|
|
jpayne@69
|
10605 * elif method in MAP_STDOUT_OPTIONS[collection]: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10606 * # special case - samtools view -c outputs on stdout
|
|
jpayne@69
|
10607 * if not(method == "view" and "-c" in args):
|
|
jpayne@69
|
10608 */
|
|
jpayne@69
|
10609 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_MAP_STDOUT_OPTIONS, __pyx_v_collection); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 350, __pyx_L1_error)
|
|
jpayne@69
|
10610 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10611 __pyx_t_1 = (__Pyx_PySequence_ContainsTF(__pyx_v_method, __pyx_t_7, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 350, __pyx_L1_error)
|
|
jpayne@69
|
10612 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10613 if (__pyx_t_1) {
|
|
jpayne@69
|
10614
|
|
jpayne@69
|
10615 /* "pysam/libcutils.pyx":352
|
|
jpayne@69
|
10616 * elif method in MAP_STDOUT_OPTIONS[collection]:
|
|
jpayne@69
|
10617 * # special case - samtools view -c outputs on stdout
|
|
jpayne@69
|
10618 * if not(method == "view" and "-c" in args): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10619 * stdout_option = MAP_STDOUT_OPTIONS[collection][method]
|
|
jpayne@69
|
10620 *
|
|
jpayne@69
|
10621 */
|
|
jpayne@69
|
10622 __pyx_t_2 = (__Pyx_PyUnicode_Equals(__pyx_v_method, __pyx_n_u_view, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
10623 if (__pyx_t_2) {
|
|
jpayne@69
|
10624 } else {
|
|
jpayne@69
|
10625 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
10626 goto __pyx_L27_bool_binop_done;
|
|
jpayne@69
|
10627 }
|
|
jpayne@69
|
10628 __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_kp_u_c, __pyx_v_args, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 352, __pyx_L1_error)
|
|
jpayne@69
|
10629 __pyx_t_1 = __pyx_t_2;
|
|
jpayne@69
|
10630 __pyx_L27_bool_binop_done:;
|
|
jpayne@69
|
10631 __pyx_t_2 = (!__pyx_t_1);
|
|
jpayne@69
|
10632 if (__pyx_t_2) {
|
|
jpayne@69
|
10633
|
|
jpayne@69
|
10634 /* "pysam/libcutils.pyx":353
|
|
jpayne@69
|
10635 * # special case - samtools view -c outputs on stdout
|
|
jpayne@69
|
10636 * if not(method == "view" and "-c" in args):
|
|
jpayne@69
|
10637 * stdout_option = MAP_STDOUT_OPTIONS[collection][method] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10638 *
|
|
jpayne@69
|
10639 * if stdout_option is not None and not is_usage:
|
|
jpayne@69
|
10640 */
|
|
jpayne@69
|
10641 __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_MAP_STDOUT_OPTIONS, __pyx_v_collection); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 353, __pyx_L1_error)
|
|
jpayne@69
|
10642 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10643 __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_t_7, __pyx_v_method); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 353, __pyx_L1_error)
|
|
jpayne@69
|
10644 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10645 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10646 __Pyx_DECREF_SET(__pyx_v_stdout_option, __pyx_t_3);
|
|
jpayne@69
|
10647 __pyx_t_3 = 0;
|
|
jpayne@69
|
10648
|
|
jpayne@69
|
10649 /* "pysam/libcutils.pyx":352
|
|
jpayne@69
|
10650 * elif method in MAP_STDOUT_OPTIONS[collection]:
|
|
jpayne@69
|
10651 * # special case - samtools view -c outputs on stdout
|
|
jpayne@69
|
10652 * if not(method == "view" and "-c" in args): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10653 * stdout_option = MAP_STDOUT_OPTIONS[collection][method]
|
|
jpayne@69
|
10654 *
|
|
jpayne@69
|
10655 */
|
|
jpayne@69
|
10656 }
|
|
jpayne@69
|
10657
|
|
jpayne@69
|
10658 /* "pysam/libcutils.pyx":350
|
|
jpayne@69
|
10659 * if method not in ("head", "index", "roh", "stats"):
|
|
jpayne@69
|
10660 * stdout_option = "-o {}"
|
|
jpayne@69
|
10661 * elif method in MAP_STDOUT_OPTIONS[collection]: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10662 * # special case - samtools view -c outputs on stdout
|
|
jpayne@69
|
10663 * if not(method == "view" and "-c" in args):
|
|
jpayne@69
|
10664 */
|
|
jpayne@69
|
10665 }
|
|
jpayne@69
|
10666 __pyx_L20:;
|
|
jpayne@69
|
10667
|
|
jpayne@69
|
10668 /* "pysam/libcutils.pyx":355
|
|
jpayne@69
|
10669 * stdout_option = MAP_STDOUT_OPTIONS[collection][method]
|
|
jpayne@69
|
10670 *
|
|
jpayne@69
|
10671 * if stdout_option is not None and not is_usage: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10672 * os.close(stdout_h)
|
|
jpayne@69
|
10673 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10674 */
|
|
jpayne@69
|
10675 __pyx_t_1 = (__pyx_v_stdout_option != Py_None);
|
|
jpayne@69
|
10676 if (__pyx_t_1) {
|
|
jpayne@69
|
10677 } else {
|
|
jpayne@69
|
10678 __pyx_t_2 = __pyx_t_1;
|
|
jpayne@69
|
10679 goto __pyx_L30_bool_binop_done;
|
|
jpayne@69
|
10680 }
|
|
jpayne@69
|
10681 __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_is_usage); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 355, __pyx_L1_error)
|
|
jpayne@69
|
10682 __pyx_t_14 = (!__pyx_t_1);
|
|
jpayne@69
|
10683 __pyx_t_2 = __pyx_t_14;
|
|
jpayne@69
|
10684 __pyx_L30_bool_binop_done:;
|
|
jpayne@69
|
10685 if (__pyx_t_2) {
|
|
jpayne@69
|
10686
|
|
jpayne@69
|
10687 /* "pysam/libcutils.pyx":356
|
|
jpayne@69
|
10688 *
|
|
jpayne@69
|
10689 * if stdout_option is not None and not is_usage:
|
|
jpayne@69
|
10690 * os.close(stdout_h) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10691 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10692 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10693 */
|
|
jpayne@69
|
10694 __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_os); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 356, __pyx_L1_error)
|
|
jpayne@69
|
10695 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10696 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_close); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 356, __pyx_L1_error)
|
|
jpayne@69
|
10697 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10698 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10699 __pyx_t_7 = NULL;
|
|
jpayne@69
|
10700 __pyx_t_9 = 0;
|
|
jpayne@69
|
10701 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10702 if (unlikely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
10703 __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
10704 if (likely(__pyx_t_7)) {
|
|
jpayne@69
|
10705 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
10706 __Pyx_INCREF(__pyx_t_7);
|
|
jpayne@69
|
10707 __Pyx_INCREF(function);
|
|
jpayne@69
|
10708 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
10709 __pyx_t_9 = 1;
|
|
jpayne@69
|
10710 }
|
|
jpayne@69
|
10711 }
|
|
jpayne@69
|
10712 #endif
|
|
jpayne@69
|
10713 {
|
|
jpayne@69
|
10714 PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_v_stdout_h};
|
|
jpayne@69
|
10715 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
10716 __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10717 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 356, __pyx_L1_error)
|
|
jpayne@69
|
10718 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10719 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
10720 }
|
|
jpayne@69
|
10721 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10722
|
|
jpayne@69
|
10723 /* "pysam/libcutils.pyx":357
|
|
jpayne@69
|
10724 * if stdout_option is not None and not is_usage:
|
|
jpayne@69
|
10725 * os.close(stdout_h)
|
|
jpayne@69
|
10726 * samtools_set_stdout_fn(force_bytes(stdout_f)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10727 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10728 * args.extend(stdout_option.format(stdout_f).split(" "))
|
|
jpayne@69
|
10729 */
|
|
jpayne@69
|
10730 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_stdout_f, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 357, __pyx_L1_error)
|
|
jpayne@69
|
10731 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10732 if (unlikely(__pyx_t_3 == Py_None)) {
|
|
jpayne@69
|
10733 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
10734 __PYX_ERR(0, 357, __pyx_L1_error)
|
|
jpayne@69
|
10735 }
|
|
jpayne@69
|
10736 __pyx_t_12 = __Pyx_PyBytes_AsString(__pyx_t_3); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) __PYX_ERR(0, 357, __pyx_L1_error)
|
|
jpayne@69
|
10737 samtools_set_stdout_fn(__pyx_t_12);
|
|
jpayne@69
|
10738 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10739
|
|
jpayne@69
|
10740 /* "pysam/libcutils.pyx":358
|
|
jpayne@69
|
10741 * os.close(stdout_h)
|
|
jpayne@69
|
10742 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10743 * bcftools_set_stdout_fn(force_bytes(stdout_f)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10744 * args.extend(stdout_option.format(stdout_f).split(" "))
|
|
jpayne@69
|
10745 * stdout_h = c_open(b"/dev/null", O_WRONLY)
|
|
jpayne@69
|
10746 */
|
|
jpayne@69
|
10747 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_stdout_f, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 358, __pyx_L1_error)
|
|
jpayne@69
|
10748 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10749 if (unlikely(__pyx_t_3 == Py_None)) {
|
|
jpayne@69
|
10750 PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found");
|
|
jpayne@69
|
10751 __PYX_ERR(0, 358, __pyx_L1_error)
|
|
jpayne@69
|
10752 }
|
|
jpayne@69
|
10753 __pyx_t_13 = __Pyx_PyBytes_AsString(__pyx_t_3); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) __PYX_ERR(0, 358, __pyx_L1_error)
|
|
jpayne@69
|
10754 bcftools_set_stdout_fn(__pyx_t_13);
|
|
jpayne@69
|
10755 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10756
|
|
jpayne@69
|
10757 /* "pysam/libcutils.pyx":359
|
|
jpayne@69
|
10758 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10759 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10760 * args.extend(stdout_option.format(stdout_f).split(" ")) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10761 * stdout_h = c_open(b"/dev/null", O_WRONLY)
|
|
jpayne@69
|
10762 * else:
|
|
jpayne@69
|
10763 */
|
|
jpayne@69
|
10764 __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_args, __pyx_n_s_extend); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 359, __pyx_L1_error)
|
|
jpayne@69
|
10765 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10766 __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_v_stdout_option, __pyx_n_s_format); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 359, __pyx_L1_error)
|
|
jpayne@69
|
10767 __Pyx_GOTREF(__pyx_t_15);
|
|
jpayne@69
|
10768 __pyx_t_16 = NULL;
|
|
jpayne@69
|
10769 __pyx_t_9 = 0;
|
|
jpayne@69
|
10770 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10771 if (likely(PyMethod_Check(__pyx_t_15))) {
|
|
jpayne@69
|
10772 __pyx_t_16 = PyMethod_GET_SELF(__pyx_t_15);
|
|
jpayne@69
|
10773 if (likely(__pyx_t_16)) {
|
|
jpayne@69
|
10774 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_15);
|
|
jpayne@69
|
10775 __Pyx_INCREF(__pyx_t_16);
|
|
jpayne@69
|
10776 __Pyx_INCREF(function);
|
|
jpayne@69
|
10777 __Pyx_DECREF_SET(__pyx_t_15, function);
|
|
jpayne@69
|
10778 __pyx_t_9 = 1;
|
|
jpayne@69
|
10779 }
|
|
jpayne@69
|
10780 }
|
|
jpayne@69
|
10781 #endif
|
|
jpayne@69
|
10782 {
|
|
jpayne@69
|
10783 PyObject *__pyx_callargs[2] = {__pyx_t_16, __pyx_v_stdout_f};
|
|
jpayne@69
|
10784 __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_15, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
10785 __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
|
|
jpayne@69
|
10786 if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 359, __pyx_L1_error)
|
|
jpayne@69
|
10787 __Pyx_GOTREF(__pyx_t_8);
|
|
jpayne@69
|
10788 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
|
|
jpayne@69
|
10789 }
|
|
jpayne@69
|
10790 __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_split); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 359, __pyx_L1_error)
|
|
jpayne@69
|
10791 __Pyx_GOTREF(__pyx_t_15);
|
|
jpayne@69
|
10792 __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10793 __pyx_t_8 = NULL;
|
|
jpayne@69
|
10794 __pyx_t_9 = 0;
|
|
jpayne@69
|
10795 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10796 if (likely(PyMethod_Check(__pyx_t_15))) {
|
|
jpayne@69
|
10797 __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_15);
|
|
jpayne@69
|
10798 if (likely(__pyx_t_8)) {
|
|
jpayne@69
|
10799 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_15);
|
|
jpayne@69
|
10800 __Pyx_INCREF(__pyx_t_8);
|
|
jpayne@69
|
10801 __Pyx_INCREF(function);
|
|
jpayne@69
|
10802 __Pyx_DECREF_SET(__pyx_t_15, function);
|
|
jpayne@69
|
10803 __pyx_t_9 = 1;
|
|
jpayne@69
|
10804 }
|
|
jpayne@69
|
10805 }
|
|
jpayne@69
|
10806 #endif
|
|
jpayne@69
|
10807 {
|
|
jpayne@69
|
10808 PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_kp_u__11};
|
|
jpayne@69
|
10809 __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_15, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
10810 __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
|
|
jpayne@69
|
10811 if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 359, __pyx_L1_error)
|
|
jpayne@69
|
10812 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10813 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
|
|
jpayne@69
|
10814 }
|
|
jpayne@69
|
10815 __pyx_t_15 = NULL;
|
|
jpayne@69
|
10816 __pyx_t_9 = 0;
|
|
jpayne@69
|
10817 #if CYTHON_UNPACK_METHODS
|
|
jpayne@69
|
10818 if (likely(PyMethod_Check(__pyx_t_6))) {
|
|
jpayne@69
|
10819 __pyx_t_15 = PyMethod_GET_SELF(__pyx_t_6);
|
|
jpayne@69
|
10820 if (likely(__pyx_t_15)) {
|
|
jpayne@69
|
10821 PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
|
|
jpayne@69
|
10822 __Pyx_INCREF(__pyx_t_15);
|
|
jpayne@69
|
10823 __Pyx_INCREF(function);
|
|
jpayne@69
|
10824 __Pyx_DECREF_SET(__pyx_t_6, function);
|
|
jpayne@69
|
10825 __pyx_t_9 = 1;
|
|
jpayne@69
|
10826 }
|
|
jpayne@69
|
10827 }
|
|
jpayne@69
|
10828 #endif
|
|
jpayne@69
|
10829 {
|
|
jpayne@69
|
10830 PyObject *__pyx_callargs[2] = {__pyx_t_15, __pyx_t_7};
|
|
jpayne@69
|
10831 __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9);
|
|
jpayne@69
|
10832 __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
|
|
jpayne@69
|
10833 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
10834 if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 359, __pyx_L1_error)
|
|
jpayne@69
|
10835 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10836 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
10837 }
|
|
jpayne@69
|
10838 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
10839
|
|
jpayne@69
|
10840 /* "pysam/libcutils.pyx":360
|
|
jpayne@69
|
10841 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10842 * args.extend(stdout_option.format(stdout_f).split(" "))
|
|
jpayne@69
|
10843 * stdout_h = c_open(b"/dev/null", O_WRONLY) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10844 * else:
|
|
jpayne@69
|
10845 * samtools_set_stdout_fn("-")
|
|
jpayne@69
|
10846 */
|
|
jpayne@69
|
10847 __pyx_t_3 = __Pyx_PyInt_From_int(open(((char const *)"/dev/null"), O_WRONLY)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 360, __pyx_L1_error)
|
|
jpayne@69
|
10848 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10849 __Pyx_DECREF_SET(__pyx_v_stdout_h, __pyx_t_3);
|
|
jpayne@69
|
10850 __pyx_t_3 = 0;
|
|
jpayne@69
|
10851
|
|
jpayne@69
|
10852 /* "pysam/libcutils.pyx":355
|
|
jpayne@69
|
10853 * stdout_option = MAP_STDOUT_OPTIONS[collection][method]
|
|
jpayne@69
|
10854 *
|
|
jpayne@69
|
10855 * if stdout_option is not None and not is_usage: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10856 * os.close(stdout_h)
|
|
jpayne@69
|
10857 * samtools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10858 */
|
|
jpayne@69
|
10859 }
|
|
jpayne@69
|
10860
|
|
jpayne@69
|
10861 /* "pysam/libcutils.pyx":332
|
|
jpayne@69
|
10862 * bcftools_set_stdout_fn(force_bytes(stdout_f))
|
|
jpayne@69
|
10863 *
|
|
jpayne@69
|
10864 * elif catch_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10865 * stdout_h, stdout_f = tempfile.mkstemp()
|
|
jpayne@69
|
10866 * MAP_STDOUT_OPTIONS = {
|
|
jpayne@69
|
10867 */
|
|
jpayne@69
|
10868 goto __pyx_L16;
|
|
jpayne@69
|
10869 }
|
|
jpayne@69
|
10870
|
|
jpayne@69
|
10871 /* "pysam/libcutils.pyx":362
|
|
jpayne@69
|
10872 * stdout_h = c_open(b"/dev/null", O_WRONLY)
|
|
jpayne@69
|
10873 * else:
|
|
jpayne@69
|
10874 * samtools_set_stdout_fn("-") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10875 * bcftools_set_stdout_fn("-")
|
|
jpayne@69
|
10876 * stdout_h = c_open(b"/dev/null", O_WRONLY)
|
|
jpayne@69
|
10877 */
|
|
jpayne@69
|
10878 /*else*/ {
|
|
jpayne@69
|
10879 samtools_set_stdout_fn(((char const *)"-"));
|
|
jpayne@69
|
10880
|
|
jpayne@69
|
10881 /* "pysam/libcutils.pyx":363
|
|
jpayne@69
|
10882 * else:
|
|
jpayne@69
|
10883 * samtools_set_stdout_fn("-")
|
|
jpayne@69
|
10884 * bcftools_set_stdout_fn("-") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10885 * stdout_h = c_open(b"/dev/null", O_WRONLY)
|
|
jpayne@69
|
10886 *
|
|
jpayne@69
|
10887 */
|
|
jpayne@69
|
10888 bcftools_set_stdout_fn(((char const *)"-"));
|
|
jpayne@69
|
10889
|
|
jpayne@69
|
10890 /* "pysam/libcutils.pyx":364
|
|
jpayne@69
|
10891 * samtools_set_stdout_fn("-")
|
|
jpayne@69
|
10892 * bcftools_set_stdout_fn("-")
|
|
jpayne@69
|
10893 * stdout_h = c_open(b"/dev/null", O_WRONLY) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10894 *
|
|
jpayne@69
|
10895 * # setup the function call to samtools/bcftools main
|
|
jpayne@69
|
10896 */
|
|
jpayne@69
|
10897 __pyx_t_3 = __Pyx_PyInt_From_int(open(((char const *)"/dev/null"), O_WRONLY)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 364, __pyx_L1_error)
|
|
jpayne@69
|
10898 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10899 __pyx_v_stdout_h = __pyx_t_3;
|
|
jpayne@69
|
10900 __pyx_t_3 = 0;
|
|
jpayne@69
|
10901 }
|
|
jpayne@69
|
10902 __pyx_L16:;
|
|
jpayne@69
|
10903
|
|
jpayne@69
|
10904 /* "pysam/libcutils.pyx":369
|
|
jpayne@69
|
10905 * cdef char ** cargs
|
|
jpayne@69
|
10906 * cdef int i, n, retval, l
|
|
jpayne@69
|
10907 * n = len(args) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10908 * method = force_bytes(method)
|
|
jpayne@69
|
10909 * collection = force_bytes(collection)
|
|
jpayne@69
|
10910 */
|
|
jpayne@69
|
10911 __pyx_t_4 = PyObject_Length(__pyx_v_args); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 369, __pyx_L1_error)
|
|
jpayne@69
|
10912 __pyx_v_n = __pyx_t_4;
|
|
jpayne@69
|
10913
|
|
jpayne@69
|
10914 /* "pysam/libcutils.pyx":370
|
|
jpayne@69
|
10915 * cdef int i, n, retval, l
|
|
jpayne@69
|
10916 * n = len(args)
|
|
jpayne@69
|
10917 * method = force_bytes(method) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10918 * collection = force_bytes(collection)
|
|
jpayne@69
|
10919 * args = [force_bytes(a) for a in args]
|
|
jpayne@69
|
10920 */
|
|
jpayne@69
|
10921 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_method, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 370, __pyx_L1_error)
|
|
jpayne@69
|
10922 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10923 __Pyx_DECREF_SET(__pyx_v_method, __pyx_t_3);
|
|
jpayne@69
|
10924 __pyx_t_3 = 0;
|
|
jpayne@69
|
10925
|
|
jpayne@69
|
10926 /* "pysam/libcutils.pyx":371
|
|
jpayne@69
|
10927 * n = len(args)
|
|
jpayne@69
|
10928 * method = force_bytes(method)
|
|
jpayne@69
|
10929 * collection = force_bytes(collection) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10930 * args = [force_bytes(a) for a in args]
|
|
jpayne@69
|
10931 *
|
|
jpayne@69
|
10932 */
|
|
jpayne@69
|
10933 __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_collection, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 371, __pyx_L1_error)
|
|
jpayne@69
|
10934 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10935 __Pyx_DECREF_SET(__pyx_v_collection, __pyx_t_3);
|
|
jpayne@69
|
10936 __pyx_t_3 = 0;
|
|
jpayne@69
|
10937
|
|
jpayne@69
|
10938 /* "pysam/libcutils.pyx":372
|
|
jpayne@69
|
10939 * method = force_bytes(method)
|
|
jpayne@69
|
10940 * collection = force_bytes(collection)
|
|
jpayne@69
|
10941 * args = [force_bytes(a) for a in args] # <<<<<<<<<<<<<<
|
|
jpayne@69
|
10942 *
|
|
jpayne@69
|
10943 * # allocate two more for first (dummy) argument (contains command)
|
|
jpayne@69
|
10944 */
|
|
jpayne@69
|
10945 { /* enter inner scope */
|
|
jpayne@69
|
10946 __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10947 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
10948 if (likely(PyList_CheckExact(__pyx_v_args)) || PyTuple_CheckExact(__pyx_v_args)) {
|
|
jpayne@69
|
10949 __pyx_t_6 = __pyx_v_args; __Pyx_INCREF(__pyx_t_6);
|
|
jpayne@69
|
10950 __pyx_t_4 = 0;
|
|
jpayne@69
|
10951 __pyx_t_5 = NULL;
|
|
jpayne@69
|
10952 } else {
|
|
jpayne@69
|
10953 __pyx_t_4 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10954 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
10955 __pyx_t_5 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10956 }
|
|
jpayne@69
|
10957 for (;;) {
|
|
jpayne@69
|
10958 if (likely(!__pyx_t_5)) {
|
|
jpayne@69
|
10959 if (likely(PyList_CheckExact(__pyx_t_6))) {
|
|
jpayne@69
|
10960 {
|
|
jpayne@69
|
10961 Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_6);
|
|
jpayne@69
|
10962 #if !CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
10963 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10964 #endif
|
|
jpayne@69
|
10965 if (__pyx_t_4 >= __pyx_temp) break;
|
|
jpayne@69
|
10966 }
|
|
jpayne@69
|
10967 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
10968 __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10969 #else
|
|
jpayne@69
|
10970 __pyx_t_7 = __Pyx_PySequence_ITEM(__pyx_t_6, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10971 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10972 #endif
|
|
jpayne@69
|
10973 } else {
|
|
jpayne@69
|
10974 {
|
|
jpayne@69
|
10975 Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_6);
|
|
jpayne@69
|
10976 #if !CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
10977 if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10978 #endif
|
|
jpayne@69
|
10979 if (__pyx_t_4 >= __pyx_temp) break;
|
|
jpayne@69
|
10980 }
|
|
jpayne@69
|
10981 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
10982 __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely((0 < 0))) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10983 #else
|
|
jpayne@69
|
10984 __pyx_t_7 = __Pyx_PySequence_ITEM(__pyx_t_6, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10985 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10986 #endif
|
|
jpayne@69
|
10987 }
|
|
jpayne@69
|
10988 } else {
|
|
jpayne@69
|
10989 __pyx_t_7 = __pyx_t_5(__pyx_t_6);
|
|
jpayne@69
|
10990 if (unlikely(!__pyx_t_7)) {
|
|
jpayne@69
|
10991 PyObject* exc_type = PyErr_Occurred();
|
|
jpayne@69
|
10992 if (exc_type) {
|
|
jpayne@69
|
10993 if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
|
|
jpayne@69
|
10994 else __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
10995 }
|
|
jpayne@69
|
10996 break;
|
|
jpayne@69
|
10997 }
|
|
jpayne@69
|
10998 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
10999 }
|
|
jpayne@69
|
11000 __Pyx_XDECREF_SET(__pyx_8genexpr2__pyx_v_a, __pyx_t_7);
|
|
jpayne@69
|
11001 __pyx_t_7 = 0;
|
|
jpayne@69
|
11002 __pyx_t_7 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_8genexpr2__pyx_v_a, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
11003 __Pyx_GOTREF(__pyx_t_7);
|
|
jpayne@69
|
11004 if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) __PYX_ERR(0, 372, __pyx_L34_error)
|
|
jpayne@69
|
11005 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
|
|
jpayne@69
|
11006 }
|
|
jpayne@69
|
11007 __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
|
|
jpayne@69
|
11008 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_a); __pyx_8genexpr2__pyx_v_a = 0;
|
|
jpayne@69
|
11009 goto __pyx_L38_exit_scope;
|
|
jpayne@69
|
11010 __pyx_L34_error:;
|
|
jpayne@69
|
11011 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_a); __pyx_8genexpr2__pyx_v_a = 0;
|
|
jpayne@69
|
11012 goto __pyx_L1_error;
|
|
jpayne@69
|
11013 __pyx_L38_exit_scope:;
|
|
jpayne@69
|
11014 } /* exit inner scope */
|
|
jpayne@69
|
11015 __Pyx_DECREF_SET(__pyx_v_args, __pyx_t_3);
|
|
jpayne@69
|
11016 __pyx_t_3 = 0;
|
|
jpayne@69
|
11017
|
|
jpayne@69
|
11018 /* "pysam/libcutils.pyx":375
|
|
jpayne@69
|
11019 *
|
|
jpayne@69
|
11020 * # allocate two more for first (dummy) argument (contains command)
|
|
jpayne@69
|
11021 * cdef int extra_args = 0 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11022 * if method == b"index":
|
|
jpayne@69
|
11023 * extra_args = 1
|
|
jpayne@69
|
11024 */
|
|
jpayne@69
|
11025 __pyx_v_extra_args = 0;
|
|
jpayne@69
|
11026
|
|
jpayne@69
|
11027 /* "pysam/libcutils.pyx":376
|
|
jpayne@69
|
11028 * # allocate two more for first (dummy) argument (contains command)
|
|
jpayne@69
|
11029 * cdef int extra_args = 0
|
|
jpayne@69
|
11030 * if method == b"index": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11031 * extra_args = 1
|
|
jpayne@69
|
11032 * # add extra arguments for commands accepting optional arguments
|
|
jpayne@69
|
11033 */
|
|
jpayne@69
|
11034 __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_v_method, __pyx_n_b_index, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 376, __pyx_L1_error)
|
|
jpayne@69
|
11035 if (__pyx_t_2) {
|
|
jpayne@69
|
11036
|
|
jpayne@69
|
11037 /* "pysam/libcutils.pyx":377
|
|
jpayne@69
|
11038 * cdef int extra_args = 0
|
|
jpayne@69
|
11039 * if method == b"index":
|
|
jpayne@69
|
11040 * extra_args = 1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11041 * # add extra arguments for commands accepting optional arguments
|
|
jpayne@69
|
11042 * # such as 'samtools index x.bam [out.index]'
|
|
jpayne@69
|
11043 */
|
|
jpayne@69
|
11044 __pyx_v_extra_args = 1;
|
|
jpayne@69
|
11045
|
|
jpayne@69
|
11046 /* "pysam/libcutils.pyx":376
|
|
jpayne@69
|
11047 * # allocate two more for first (dummy) argument (contains command)
|
|
jpayne@69
|
11048 * cdef int extra_args = 0
|
|
jpayne@69
|
11049 * if method == b"index": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11050 * extra_args = 1
|
|
jpayne@69
|
11051 * # add extra arguments for commands accepting optional arguments
|
|
jpayne@69
|
11052 */
|
|
jpayne@69
|
11053 }
|
|
jpayne@69
|
11054
|
|
jpayne@69
|
11055 /* "pysam/libcutils.pyx":380
|
|
jpayne@69
|
11056 * # add extra arguments for commands accepting optional arguments
|
|
jpayne@69
|
11057 * # such as 'samtools index x.bam [out.index]'
|
|
jpayne@69
|
11058 * cargs = <char**>calloc(n + 2 + extra_args, sizeof(char *)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11059 * cargs[0] = collection
|
|
jpayne@69
|
11060 * cargs[1] = method
|
|
jpayne@69
|
11061 */
|
|
jpayne@69
|
11062 __pyx_v_cargs = ((char **)calloc(((__pyx_v_n + 2) + __pyx_v_extra_args), (sizeof(char *))));
|
|
jpayne@69
|
11063
|
|
jpayne@69
|
11064 /* "pysam/libcutils.pyx":381
|
|
jpayne@69
|
11065 * # such as 'samtools index x.bam [out.index]'
|
|
jpayne@69
|
11066 * cargs = <char**>calloc(n + 2 + extra_args, sizeof(char *))
|
|
jpayne@69
|
11067 * cargs[0] = collection # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11068 * cargs[1] = method
|
|
jpayne@69
|
11069 *
|
|
jpayne@69
|
11070 */
|
|
jpayne@69
|
11071 __pyx_t_17 = __Pyx_PyObject_AsWritableString(__pyx_v_collection); if (unlikely((!__pyx_t_17) && PyErr_Occurred())) __PYX_ERR(0, 381, __pyx_L1_error)
|
|
jpayne@69
|
11072 (__pyx_v_cargs[0]) = __pyx_t_17;
|
|
jpayne@69
|
11073
|
|
jpayne@69
|
11074 /* "pysam/libcutils.pyx":382
|
|
jpayne@69
|
11075 * cargs = <char**>calloc(n + 2 + extra_args, sizeof(char *))
|
|
jpayne@69
|
11076 * cargs[0] = collection
|
|
jpayne@69
|
11077 * cargs[1] = method # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11078 *
|
|
jpayne@69
|
11079 * # create copies of strings - getopt for long options permutes
|
|
jpayne@69
|
11080 */
|
|
jpayne@69
|
11081 __pyx_t_17 = __Pyx_PyObject_AsWritableString(__pyx_v_method); if (unlikely((!__pyx_t_17) && PyErr_Occurred())) __PYX_ERR(0, 382, __pyx_L1_error)
|
|
jpayne@69
|
11082 (__pyx_v_cargs[1]) = __pyx_t_17;
|
|
jpayne@69
|
11083
|
|
jpayne@69
|
11084 /* "pysam/libcutils.pyx":386
|
|
jpayne@69
|
11085 * # create copies of strings - getopt for long options permutes
|
|
jpayne@69
|
11086 * # arguments
|
|
jpayne@69
|
11087 * for i from 0 <= i < n: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11088 * l = len(args[i])
|
|
jpayne@69
|
11089 * cargs[i + 2] = <char *>calloc(l + 1, sizeof(char))
|
|
jpayne@69
|
11090 */
|
|
jpayne@69
|
11091 __pyx_t_18 = __pyx_v_n;
|
|
jpayne@69
|
11092 for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_18; __pyx_v_i++) {
|
|
jpayne@69
|
11093
|
|
jpayne@69
|
11094 /* "pysam/libcutils.pyx":387
|
|
jpayne@69
|
11095 * # arguments
|
|
jpayne@69
|
11096 * for i from 0 <= i < n:
|
|
jpayne@69
|
11097 * l = len(args[i]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11098 * cargs[i + 2] = <char *>calloc(l + 1, sizeof(char))
|
|
jpayne@69
|
11099 * strncpy(cargs[i + 2], args[i], l)
|
|
jpayne@69
|
11100 */
|
|
jpayne@69
|
11101 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 387, __pyx_L1_error)
|
|
jpayne@69
|
11102 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11103 __pyx_t_4 = PyObject_Length(__pyx_t_3); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(0, 387, __pyx_L1_error)
|
|
jpayne@69
|
11104 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11105 __pyx_v_l = __pyx_t_4;
|
|
jpayne@69
|
11106
|
|
jpayne@69
|
11107 /* "pysam/libcutils.pyx":388
|
|
jpayne@69
|
11108 * for i from 0 <= i < n:
|
|
jpayne@69
|
11109 * l = len(args[i])
|
|
jpayne@69
|
11110 * cargs[i + 2] = <char *>calloc(l + 1, sizeof(char)) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11111 * strncpy(cargs[i + 2], args[i], l)
|
|
jpayne@69
|
11112 *
|
|
jpayne@69
|
11113 */
|
|
jpayne@69
|
11114 (__pyx_v_cargs[(__pyx_v_i + 2)]) = ((char *)calloc((__pyx_v_l + 1), (sizeof(char))));
|
|
jpayne@69
|
11115
|
|
jpayne@69
|
11116 /* "pysam/libcutils.pyx":389
|
|
jpayne@69
|
11117 * l = len(args[i])
|
|
jpayne@69
|
11118 * cargs[i + 2] = <char *>calloc(l + 1, sizeof(char))
|
|
jpayne@69
|
11119 * strncpy(cargs[i + 2], args[i], l) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11120 *
|
|
jpayne@69
|
11121 * # call samtools/bcftools
|
|
jpayne@69
|
11122 */
|
|
jpayne@69
|
11123 __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 389, __pyx_L1_error)
|
|
jpayne@69
|
11124 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11125 __pyx_t_19 = __Pyx_PyObject_AsString(__pyx_t_3); if (unlikely((!__pyx_t_19) && PyErr_Occurred())) __PYX_ERR(0, 389, __pyx_L1_error)
|
|
jpayne@69
|
11126 (void)(strncpy((__pyx_v_cargs[(__pyx_v_i + 2)]), __pyx_t_19, __pyx_v_l));
|
|
jpayne@69
|
11127 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
11128 }
|
|
jpayne@69
|
11129
|
|
jpayne@69
|
11130 /* "pysam/libcutils.pyx":392
|
|
jpayne@69
|
11131 *
|
|
jpayne@69
|
11132 * # call samtools/bcftools
|
|
jpayne@69
|
11133 * if collection == b"samtools": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11134 * samtools_set_stdout(stdout_h)
|
|
jpayne@69
|
11135 * samtools_set_stderr(stderr_h)
|
|
jpayne@69
|
11136 */
|
|
jpayne@69
|
11137 __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_v_collection, __pyx_n_b_samtools, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 392, __pyx_L1_error)
|
|
jpayne@69
|
11138 if (__pyx_t_2) {
|
|
jpayne@69
|
11139
|
|
jpayne@69
|
11140 /* "pysam/libcutils.pyx":393
|
|
jpayne@69
|
11141 * # call samtools/bcftools
|
|
jpayne@69
|
11142 * if collection == b"samtools":
|
|
jpayne@69
|
11143 * samtools_set_stdout(stdout_h) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11144 * samtools_set_stderr(stderr_h)
|
|
jpayne@69
|
11145 * retval = samtools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11146 */
|
|
jpayne@69
|
11147 __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_v_stdout_h); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 393, __pyx_L1_error)
|
|
jpayne@69
|
11148 samtools_set_stdout(__pyx_t_18);
|
|
jpayne@69
|
11149
|
|
jpayne@69
|
11150 /* "pysam/libcutils.pyx":394
|
|
jpayne@69
|
11151 * if collection == b"samtools":
|
|
jpayne@69
|
11152 * samtools_set_stdout(stdout_h)
|
|
jpayne@69
|
11153 * samtools_set_stderr(stderr_h) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11154 * retval = samtools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11155 * samtools_close_stdout()
|
|
jpayne@69
|
11156 */
|
|
jpayne@69
|
11157 __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_v_stderr_h); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 394, __pyx_L1_error)
|
|
jpayne@69
|
11158 samtools_set_stderr(__pyx_t_18);
|
|
jpayne@69
|
11159
|
|
jpayne@69
|
11160 /* "pysam/libcutils.pyx":395
|
|
jpayne@69
|
11161 * samtools_set_stdout(stdout_h)
|
|
jpayne@69
|
11162 * samtools_set_stderr(stderr_h)
|
|
jpayne@69
|
11163 * retval = samtools_dispatch(n + 2, cargs) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11164 * samtools_close_stdout()
|
|
jpayne@69
|
11165 * samtools_close_stderr()
|
|
jpayne@69
|
11166 */
|
|
jpayne@69
|
11167 __pyx_v_retval = samtools_dispatch((__pyx_v_n + 2), __pyx_v_cargs);
|
|
jpayne@69
|
11168
|
|
jpayne@69
|
11169 /* "pysam/libcutils.pyx":396
|
|
jpayne@69
|
11170 * samtools_set_stderr(stderr_h)
|
|
jpayne@69
|
11171 * retval = samtools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11172 * samtools_close_stdout() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11173 * samtools_close_stderr()
|
|
jpayne@69
|
11174 * elif collection == b"bcftools":
|
|
jpayne@69
|
11175 */
|
|
jpayne@69
|
11176 samtools_close_stdout();
|
|
jpayne@69
|
11177
|
|
jpayne@69
|
11178 /* "pysam/libcutils.pyx":397
|
|
jpayne@69
|
11179 * retval = samtools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11180 * samtools_close_stdout()
|
|
jpayne@69
|
11181 * samtools_close_stderr() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11182 * elif collection == b"bcftools":
|
|
jpayne@69
|
11183 * bcftools_set_stdout(stdout_h)
|
|
jpayne@69
|
11184 */
|
|
jpayne@69
|
11185 samtools_close_stderr();
|
|
jpayne@69
|
11186
|
|
jpayne@69
|
11187 /* "pysam/libcutils.pyx":392
|
|
jpayne@69
|
11188 *
|
|
jpayne@69
|
11189 * # call samtools/bcftools
|
|
jpayne@69
|
11190 * if collection == b"samtools": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11191 * samtools_set_stdout(stdout_h)
|
|
jpayne@69
|
11192 * samtools_set_stderr(stderr_h)
|
|
jpayne@69
|
11193 */
|
|
jpayne@69
|
11194 goto __pyx_L42;
|
|
jpayne@69
|
11195 }
|
|
jpayne@69
|
11196
|
|
jpayne@69
|
11197 /* "pysam/libcutils.pyx":398
|
|
jpayne@69
|
11198 * samtools_close_stdout()
|
|
jpayne@69
|
11199 * samtools_close_stderr()
|
|
jpayne@69
|
11200 * elif collection == b"bcftools": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11201 * bcftools_set_stdout(stdout_h)
|
|
jpayne@69
|
11202 * bcftools_set_stderr(stderr_h)
|
|
jpayne@69
|
11203 */
|
|
jpayne@69
|
11204 __pyx_t_2 = (__Pyx_PyBytes_Equals(__pyx_v_collection, __pyx_n_b_bcftools, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 398, __pyx_L1_error)
|
|
jpayne@69
|
11205 if (__pyx_t_2) {
|
|
jpayne@69
|
11206
|
|
jpayne@69
|
11207 /* "pysam/libcutils.pyx":399
|
|
jpayne@69
|
11208 * samtools_close_stderr()
|
|
jpayne@69
|
11209 * elif collection == b"bcftools":
|
|
jpayne@69
|
11210 * bcftools_set_stdout(stdout_h) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11211 * bcftools_set_stderr(stderr_h)
|
|
jpayne@69
|
11212 * retval = bcftools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11213 */
|
|
jpayne@69
|
11214 __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_v_stdout_h); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 399, __pyx_L1_error)
|
|
jpayne@69
|
11215 bcftools_set_stdout(__pyx_t_18);
|
|
jpayne@69
|
11216
|
|
jpayne@69
|
11217 /* "pysam/libcutils.pyx":400
|
|
jpayne@69
|
11218 * elif collection == b"bcftools":
|
|
jpayne@69
|
11219 * bcftools_set_stdout(stdout_h)
|
|
jpayne@69
|
11220 * bcftools_set_stderr(stderr_h) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11221 * retval = bcftools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11222 * bcftools_close_stdout()
|
|
jpayne@69
|
11223 */
|
|
jpayne@69
|
11224 __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_v_stderr_h); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 400, __pyx_L1_error)
|
|
jpayne@69
|
11225 bcftools_set_stderr(__pyx_t_18);
|
|
jpayne@69
|
11226
|
|
jpayne@69
|
11227 /* "pysam/libcutils.pyx":401
|
|
jpayne@69
|
11228 * bcftools_set_stdout(stdout_h)
|
|
jpayne@69
|
11229 * bcftools_set_stderr(stderr_h)
|
|
jpayne@69
|
11230 * retval = bcftools_dispatch(n + 2, cargs) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11231 * bcftools_close_stdout()
|
|
jpayne@69
|
11232 * bcftools_close_stderr()
|
|
jpayne@69
|
11233 */
|
|
jpayne@69
|
11234 __pyx_v_retval = bcftools_dispatch((__pyx_v_n + 2), __pyx_v_cargs);
|
|
jpayne@69
|
11235
|
|
jpayne@69
|
11236 /* "pysam/libcutils.pyx":402
|
|
jpayne@69
|
11237 * bcftools_set_stderr(stderr_h)
|
|
jpayne@69
|
11238 * retval = bcftools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11239 * bcftools_close_stdout() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11240 * bcftools_close_stderr()
|
|
jpayne@69
|
11241 * else:
|
|
jpayne@69
|
11242 */
|
|
jpayne@69
|
11243 bcftools_close_stdout();
|
|
jpayne@69
|
11244
|
|
jpayne@69
|
11245 /* "pysam/libcutils.pyx":403
|
|
jpayne@69
|
11246 * retval = bcftools_dispatch(n + 2, cargs)
|
|
jpayne@69
|
11247 * bcftools_close_stdout()
|
|
jpayne@69
|
11248 * bcftools_close_stderr() # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11249 * else:
|
|
jpayne@69
|
11250 * # unknown -- just return a Unix shell's "command not found" exit status
|
|
jpayne@69
|
11251 */
|
|
jpayne@69
|
11252 bcftools_close_stderr();
|
|
jpayne@69
|
11253
|
|
jpayne@69
|
11254 /* "pysam/libcutils.pyx":398
|
|
jpayne@69
|
11255 * samtools_close_stdout()
|
|
jpayne@69
|
11256 * samtools_close_stderr()
|
|
jpayne@69
|
11257 * elif collection == b"bcftools": # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11258 * bcftools_set_stdout(stdout_h)
|
|
jpayne@69
|
11259 * bcftools_set_stderr(stderr_h)
|
|
jpayne@69
|
11260 */
|
|
jpayne@69
|
11261 goto __pyx_L42;
|
|
jpayne@69
|
11262 }
|
|
jpayne@69
|
11263
|
|
jpayne@69
|
11264 /* "pysam/libcutils.pyx":406
|
|
jpayne@69
|
11265 * else:
|
|
jpayne@69
|
11266 * # unknown -- just return a Unix shell's "command not found" exit status
|
|
jpayne@69
|
11267 * retval = 127 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11268 *
|
|
jpayne@69
|
11269 * for i from 0 <= i < n:
|
|
jpayne@69
|
11270 */
|
|
jpayne@69
|
11271 /*else*/ {
|
|
jpayne@69
|
11272 __pyx_v_retval = 0x7F;
|
|
jpayne@69
|
11273 }
|
|
jpayne@69
|
11274 __pyx_L42:;
|
|
jpayne@69
|
11275
|
|
jpayne@69
|
11276 /* "pysam/libcutils.pyx":408
|
|
jpayne@69
|
11277 * retval = 127
|
|
jpayne@69
|
11278 *
|
|
jpayne@69
|
11279 * for i from 0 <= i < n: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11280 * free(cargs[i + 2])
|
|
jpayne@69
|
11281 * free(cargs)
|
|
jpayne@69
|
11282 */
|
|
jpayne@69
|
11283 __pyx_t_18 = __pyx_v_n;
|
|
jpayne@69
|
11284 for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_18; __pyx_v_i++) {
|
|
jpayne@69
|
11285
|
|
jpayne@69
|
11286 /* "pysam/libcutils.pyx":409
|
|
jpayne@69
|
11287 *
|
|
jpayne@69
|
11288 * for i from 0 <= i < n:
|
|
jpayne@69
|
11289 * free(cargs[i + 2]) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11290 * free(cargs)
|
|
jpayne@69
|
11291 *
|
|
jpayne@69
|
11292 */
|
|
jpayne@69
|
11293 free((__pyx_v_cargs[(__pyx_v_i + 2)]));
|
|
jpayne@69
|
11294 }
|
|
jpayne@69
|
11295
|
|
jpayne@69
|
11296 /* "pysam/libcutils.pyx":410
|
|
jpayne@69
|
11297 * for i from 0 <= i < n:
|
|
jpayne@69
|
11298 * free(cargs[i + 2])
|
|
jpayne@69
|
11299 * free(cargs) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11300 *
|
|
jpayne@69
|
11301 * # get error messages
|
|
jpayne@69
|
11302 */
|
|
jpayne@69
|
11303 free(__pyx_v_cargs);
|
|
jpayne@69
|
11304
|
|
jpayne@69
|
11305 /* "pysam/libcutils.pyx":413
|
|
jpayne@69
|
11306 *
|
|
jpayne@69
|
11307 * # get error messages
|
|
jpayne@69
|
11308 * def _collect(fn): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11309 * out = []
|
|
jpayne@69
|
11310 * try:
|
|
jpayne@69
|
11311 */
|
|
jpayne@69
|
11312 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_15_pysam_dispatch_1_collect, 0, __pyx_n_s_pysam_dispatch_locals__collect, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__13)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 413, __pyx_L1_error)
|
|
jpayne@69
|
11313 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11314 __pyx_v__collect = __pyx_t_3;
|
|
jpayne@69
|
11315 __pyx_t_3 = 0;
|
|
jpayne@69
|
11316
|
|
jpayne@69
|
11317 /* "pysam/libcutils.pyx":426
|
|
jpayne@69
|
11318 * return out
|
|
jpayne@69
|
11319 *
|
|
jpayne@69
|
11320 * out_stderr = _collect(stderr_f) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11321 * if save_stdout:
|
|
jpayne@69
|
11322 * out_stdout = None
|
|
jpayne@69
|
11323 */
|
|
jpayne@69
|
11324 __pyx_t_3 = __pyx_pf_5pysam_9libcutils_15_pysam_dispatch__collect(__pyx_v__collect, __pyx_v_stderr_f); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 426, __pyx_L1_error)
|
|
jpayne@69
|
11325 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11326 __pyx_v_out_stderr = __pyx_t_3;
|
|
jpayne@69
|
11327 __pyx_t_3 = 0;
|
|
jpayne@69
|
11328
|
|
jpayne@69
|
11329 /* "pysam/libcutils.pyx":427
|
|
jpayne@69
|
11330 *
|
|
jpayne@69
|
11331 * out_stderr = _collect(stderr_f)
|
|
jpayne@69
|
11332 * if save_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11333 * out_stdout = None
|
|
jpayne@69
|
11334 * elif catch_stdout:
|
|
jpayne@69
|
11335 */
|
|
jpayne@69
|
11336 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_save_stdout); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 427, __pyx_L1_error)
|
|
jpayne@69
|
11337 if (__pyx_t_2) {
|
|
jpayne@69
|
11338
|
|
jpayne@69
|
11339 /* "pysam/libcutils.pyx":428
|
|
jpayne@69
|
11340 * out_stderr = _collect(stderr_f)
|
|
jpayne@69
|
11341 * if save_stdout:
|
|
jpayne@69
|
11342 * out_stdout = None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11343 * elif catch_stdout:
|
|
jpayne@69
|
11344 * out_stdout = _collect(stdout_f)
|
|
jpayne@69
|
11345 */
|
|
jpayne@69
|
11346 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
11347 __pyx_v_out_stdout = Py_None;
|
|
jpayne@69
|
11348
|
|
jpayne@69
|
11349 /* "pysam/libcutils.pyx":427
|
|
jpayne@69
|
11350 *
|
|
jpayne@69
|
11351 * out_stderr = _collect(stderr_f)
|
|
jpayne@69
|
11352 * if save_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11353 * out_stdout = None
|
|
jpayne@69
|
11354 * elif catch_stdout:
|
|
jpayne@69
|
11355 */
|
|
jpayne@69
|
11356 goto __pyx_L45;
|
|
jpayne@69
|
11357 }
|
|
jpayne@69
|
11358
|
|
jpayne@69
|
11359 /* "pysam/libcutils.pyx":429
|
|
jpayne@69
|
11360 * if save_stdout:
|
|
jpayne@69
|
11361 * out_stdout = None
|
|
jpayne@69
|
11362 * elif catch_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11363 * out_stdout = _collect(stdout_f)
|
|
jpayne@69
|
11364 * else:
|
|
jpayne@69
|
11365 */
|
|
jpayne@69
|
11366 __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 429, __pyx_L1_error)
|
|
jpayne@69
|
11367 if (__pyx_t_2) {
|
|
jpayne@69
|
11368
|
|
jpayne@69
|
11369 /* "pysam/libcutils.pyx":430
|
|
jpayne@69
|
11370 * out_stdout = None
|
|
jpayne@69
|
11371 * elif catch_stdout:
|
|
jpayne@69
|
11372 * out_stdout = _collect(stdout_f) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11373 * else:
|
|
jpayne@69
|
11374 * out_stdout = None
|
|
jpayne@69
|
11375 */
|
|
jpayne@69
|
11376 if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); __PYX_ERR(0, 430, __pyx_L1_error) }
|
|
jpayne@69
|
11377 __pyx_t_3 = __pyx_pf_5pysam_9libcutils_15_pysam_dispatch__collect(__pyx_v__collect, __pyx_v_stdout_f); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 430, __pyx_L1_error)
|
|
jpayne@69
|
11378 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11379 __pyx_v_out_stdout = __pyx_t_3;
|
|
jpayne@69
|
11380 __pyx_t_3 = 0;
|
|
jpayne@69
|
11381
|
|
jpayne@69
|
11382 /* "pysam/libcutils.pyx":429
|
|
jpayne@69
|
11383 * if save_stdout:
|
|
jpayne@69
|
11384 * out_stdout = None
|
|
jpayne@69
|
11385 * elif catch_stdout: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11386 * out_stdout = _collect(stdout_f)
|
|
jpayne@69
|
11387 * else:
|
|
jpayne@69
|
11388 */
|
|
jpayne@69
|
11389 goto __pyx_L45;
|
|
jpayne@69
|
11390 }
|
|
jpayne@69
|
11391
|
|
jpayne@69
|
11392 /* "pysam/libcutils.pyx":432
|
|
jpayne@69
|
11393 * out_stdout = _collect(stdout_f)
|
|
jpayne@69
|
11394 * else:
|
|
jpayne@69
|
11395 * out_stdout = None # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11396 *
|
|
jpayne@69
|
11397 * return retval, out_stderr, out_stdout
|
|
jpayne@69
|
11398 */
|
|
jpayne@69
|
11399 /*else*/ {
|
|
jpayne@69
|
11400 __Pyx_INCREF(Py_None);
|
|
jpayne@69
|
11401 __pyx_v_out_stdout = Py_None;
|
|
jpayne@69
|
11402 }
|
|
jpayne@69
|
11403 __pyx_L45:;
|
|
jpayne@69
|
11404
|
|
jpayne@69
|
11405 /* "pysam/libcutils.pyx":434
|
|
jpayne@69
|
11406 * out_stdout = None
|
|
jpayne@69
|
11407 *
|
|
jpayne@69
|
11408 * return retval, out_stderr, out_stdout # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11409 *
|
|
jpayne@69
|
11410 *
|
|
jpayne@69
|
11411 */
|
|
jpayne@69
|
11412 __Pyx_XDECREF(__pyx_r);
|
|
jpayne@69
|
11413 __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_retval); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 434, __pyx_L1_error)
|
|
jpayne@69
|
11414 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
11415 __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 434, __pyx_L1_error)
|
|
jpayne@69
|
11416 __Pyx_GOTREF(__pyx_t_6);
|
|
jpayne@69
|
11417 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
11418 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3)) __PYX_ERR(0, 434, __pyx_L1_error);
|
|
jpayne@69
|
11419 __Pyx_INCREF(__pyx_v_out_stderr);
|
|
jpayne@69
|
11420 __Pyx_GIVEREF(__pyx_v_out_stderr);
|
|
jpayne@69
|
11421 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_out_stderr)) __PYX_ERR(0, 434, __pyx_L1_error);
|
|
jpayne@69
|
11422 __Pyx_INCREF(__pyx_v_out_stdout);
|
|
jpayne@69
|
11423 __Pyx_GIVEREF(__pyx_v_out_stdout);
|
|
jpayne@69
|
11424 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_v_out_stdout)) __PYX_ERR(0, 434, __pyx_L1_error);
|
|
jpayne@69
|
11425 __pyx_t_3 = 0;
|
|
jpayne@69
|
11426 __pyx_r = __pyx_t_6;
|
|
jpayne@69
|
11427 __pyx_t_6 = 0;
|
|
jpayne@69
|
11428 goto __pyx_L0;
|
|
jpayne@69
|
11429
|
|
jpayne@69
|
11430 /* "pysam/libcutils.pyx":276
|
|
jpayne@69
|
11431 *
|
|
jpayne@69
|
11432 *
|
|
jpayne@69
|
11433 * def _pysam_dispatch(collection, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11434 * method,
|
|
jpayne@69
|
11435 * args=None,
|
|
jpayne@69
|
11436 */
|
|
jpayne@69
|
11437
|
|
jpayne@69
|
11438 /* function exit code */
|
|
jpayne@69
|
11439 __pyx_L1_error:;
|
|
jpayne@69
|
11440 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
11441 __Pyx_XDECREF(__pyx_t_6);
|
|
jpayne@69
|
11442 __Pyx_XDECREF(__pyx_t_7);
|
|
jpayne@69
|
11443 __Pyx_XDECREF(__pyx_t_8);
|
|
jpayne@69
|
11444 __Pyx_XDECREF(__pyx_t_15);
|
|
jpayne@69
|
11445 __Pyx_XDECREF(__pyx_t_16);
|
|
jpayne@69
|
11446 __Pyx_AddTraceback("pysam.libcutils._pysam_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
11447 __pyx_r = NULL;
|
|
jpayne@69
|
11448 __pyx_L0:;
|
|
jpayne@69
|
11449 __Pyx_XDECREF(__pyx_v_ARGUMENTS);
|
|
jpayne@69
|
11450 __Pyx_XDECREF(__pyx_v_arg);
|
|
jpayne@69
|
11451 __Pyx_XDECREF(__pyx_v_stderr_h);
|
|
jpayne@69
|
11452 __Pyx_XDECREF(__pyx_v_stderr_f);
|
|
jpayne@69
|
11453 __Pyx_XDECREF(__pyx_v_stdout_f);
|
|
jpayne@69
|
11454 __Pyx_XDECREF(__pyx_v_stdout_h);
|
|
jpayne@69
|
11455 __Pyx_XDECREF(__pyx_v_MAP_STDOUT_OPTIONS);
|
|
jpayne@69
|
11456 __Pyx_XDECREF(__pyx_v_stdout_option);
|
|
jpayne@69
|
11457 __Pyx_XDECREF(__pyx_v__collect);
|
|
jpayne@69
|
11458 __Pyx_XDECREF(__pyx_v_out_stderr);
|
|
jpayne@69
|
11459 __Pyx_XDECREF(__pyx_v_out_stdout);
|
|
jpayne@69
|
11460 __Pyx_XDECREF(__pyx_8genexpr2__pyx_v_a);
|
|
jpayne@69
|
11461 __Pyx_XDECREF(__pyx_v_collection);
|
|
jpayne@69
|
11462 __Pyx_XDECREF(__pyx_v_method);
|
|
jpayne@69
|
11463 __Pyx_XDECREF(__pyx_v_args);
|
|
jpayne@69
|
11464 __Pyx_XGIVEREF(__pyx_r);
|
|
jpayne@69
|
11465 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11466 return __pyx_r;
|
|
jpayne@69
|
11467 }
|
|
jpayne@69
|
11468
|
|
jpayne@69
|
11469 static PyMethodDef __pyx_methods[] = {
|
|
jpayne@69
|
11470 {0, 0, 0, 0}
|
|
jpayne@69
|
11471 };
|
|
jpayne@69
|
11472 #ifndef CYTHON_SMALL_CODE
|
|
jpayne@69
|
11473 #if defined(__clang__)
|
|
jpayne@69
|
11474 #define CYTHON_SMALL_CODE
|
|
jpayne@69
|
11475 #elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))
|
|
jpayne@69
|
11476 #define CYTHON_SMALL_CODE __attribute__((cold))
|
|
jpayne@69
|
11477 #else
|
|
jpayne@69
|
11478 #define CYTHON_SMALL_CODE
|
|
jpayne@69
|
11479 #endif
|
|
jpayne@69
|
11480 #endif
|
|
jpayne@69
|
11481 /* #### Code section: pystring_table ### */
|
|
jpayne@69
|
11482
|
|
jpayne@69
|
11483 static int __Pyx_CreateStringTabAndInitStrings(void) {
|
|
jpayne@69
|
11484 __Pyx_StringTabEntry __pyx_string_tab[] = {
|
|
jpayne@69
|
11485 {&__pyx_kp_u_, __pyx_k_, sizeof(__pyx_k_), 0, 1, 0, 0},
|
|
jpayne@69
|
11486 {&__pyx_n_s_ARGUMENTS, __pyx_k_ARGUMENTS, sizeof(__pyx_k_ARGUMENTS), 0, 0, 1, 1},
|
|
jpayne@69
|
11487 {&__pyx_kp_u_Argument_must_be_string_bytes_or, __pyx_k_Argument_must_be_string_bytes_or, sizeof(__pyx_k_Argument_must_be_string_bytes_or), 0, 1, 0, 0},
|
|
jpayne@69
|
11488 {&__pyx_n_u_B, __pyx_k_B, sizeof(__pyx_k_B), 0, 1, 0, 1},
|
|
jpayne@69
|
11489 {&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1},
|
|
jpayne@69
|
11490 {&__pyx_n_s_MAP_STDOUT_OPTIONS, __pyx_k_MAP_STDOUT_OPTIONS, sizeof(__pyx_k_MAP_STDOUT_OPTIONS), 0, 0, 1, 1},
|
|
jpayne@69
|
11491 {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1},
|
|
jpayne@69
|
11492 {&__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
|
11493 {&__pyx_n_s_OSError, __pyx_k_OSError, sizeof(__pyx_k_OSError), 0, 0, 1, 1},
|
|
jpayne@69
|
11494 {&__pyx_n_s_OverflowError, __pyx_k_OverflowError, sizeof(__pyx_k_OverflowError), 0, 0, 1, 1},
|
|
jpayne@69
|
11495 {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1},
|
|
jpayne@69
|
11496 {&__pyx_n_s_UnicodeDecodeError, __pyx_k_UnicodeDecodeError, sizeof(__pyx_k_UnicodeDecodeError), 0, 0, 1, 1},
|
|
jpayne@69
|
11497 {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
|
|
jpayne@69
|
11498 {&__pyx_kp_u__10, __pyx_k__10, sizeof(__pyx_k__10), 0, 1, 0, 0},
|
|
jpayne@69
|
11499 {&__pyx_kp_u__11, __pyx_k__11, sizeof(__pyx_k__11), 0, 1, 0, 0},
|
|
jpayne@69
|
11500 {&__pyx_n_s__14, __pyx_k__14, sizeof(__pyx_k__14), 0, 0, 1, 1},
|
|
jpayne@69
|
11501 {&__pyx_kp_u__15, __pyx_k__15, sizeof(__pyx_k__15), 0, 1, 0, 0},
|
|
jpayne@69
|
11502 {&__pyx_n_s__33, __pyx_k__33, sizeof(__pyx_k__33), 0, 0, 1, 1},
|
|
jpayne@69
|
11503 {&__pyx_kp_u__7, __pyx_k__7, sizeof(__pyx_k__7), 0, 1, 0, 0},
|
|
jpayne@69
|
11504 {&__pyx_kp_u__8, __pyx_k__8, sizeof(__pyx_k__8), 0, 1, 0, 0},
|
|
jpayne@69
|
11505 {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1},
|
|
jpayne@69
|
11506 {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1},
|
|
jpayne@69
|
11507 {&__pyx_n_s_arg, __pyx_k_arg, sizeof(__pyx_k_arg), 0, 0, 1, 1},
|
|
jpayne@69
|
11508 {&__pyx_n_s_args, __pyx_k_args, sizeof(__pyx_k_args), 0, 0, 1, 1},
|
|
jpayne@69
|
11509 {&__pyx_n_s_array_to_qualitystring, __pyx_k_array_to_qualitystring, sizeof(__pyx_k_array_to_qualitystring), 0, 0, 1, 1},
|
|
jpayne@69
|
11510 {&__pyx_n_u_array_to_qualitystring, __pyx_k_array_to_qualitystring, sizeof(__pyx_k_array_to_qualitystring), 0, 1, 0, 1},
|
|
jpayne@69
|
11511 {&__pyx_n_u_ascii, __pyx_k_ascii, sizeof(__pyx_k_ascii), 0, 1, 0, 1},
|
|
jpayne@69
|
11512 {&__pyx_n_s_asyncio_coroutines, __pyx_k_asyncio_coroutines, sizeof(__pyx_k_asyncio_coroutines), 0, 0, 1, 1},
|
|
jpayne@69
|
11513 {&__pyx_n_b_bcftools, __pyx_k_bcftools, sizeof(__pyx_k_bcftools), 0, 0, 0, 1},
|
|
jpayne@69
|
11514 {&__pyx_n_u_bcftools, __pyx_k_bcftools, sizeof(__pyx_k_bcftools), 0, 1, 0, 1},
|
|
jpayne@69
|
11515 {&__pyx_kp_u_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 1, 0, 0},
|
|
jpayne@69
|
11516 {&__pyx_n_u_calmd, __pyx_k_calmd, sizeof(__pyx_k_calmd), 0, 1, 0, 1},
|
|
jpayne@69
|
11517 {&__pyx_n_s_cargs, __pyx_k_cargs, sizeof(__pyx_k_cargs), 0, 0, 1, 1},
|
|
jpayne@69
|
11518 {&__pyx_n_s_catch_stdout, __pyx_k_catch_stdout, sizeof(__pyx_k_catch_stdout), 0, 0, 1, 1},
|
|
jpayne@69
|
11519 {&__pyx_n_s_chr, __pyx_k_chr, sizeof(__pyx_k_chr), 0, 0, 1, 1},
|
|
jpayne@69
|
11520 {&__pyx_n_s_class_getitem, __pyx_k_class_getitem, sizeof(__pyx_k_class_getitem), 0, 0, 1, 1},
|
|
jpayne@69
|
11521 {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1},
|
|
jpayne@69
|
11522 {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
|
|
jpayne@69
|
11523 {&__pyx_n_s_codecs, __pyx_k_codecs, sizeof(__pyx_k_codecs), 0, 0, 1, 1},
|
|
jpayne@69
|
11524 {&__pyx_n_s_collect, __pyx_k_collect, sizeof(__pyx_k_collect), 0, 0, 1, 1},
|
|
jpayne@69
|
11525 {&__pyx_n_s_collection, __pyx_k_collection, sizeof(__pyx_k_collection), 0, 0, 1, 1},
|
|
jpayne@69
|
11526 {&__pyx_n_s_contextlib, __pyx_k_contextlib, sizeof(__pyx_k_contextlib), 0, 0, 1, 1},
|
|
jpayne@69
|
11527 {&__pyx_n_s_contextmanager, __pyx_k_contextmanager, sizeof(__pyx_k_contextmanager), 0, 0, 1, 1},
|
|
jpayne@69
|
11528 {&__pyx_n_s_contig, __pyx_k_contig, sizeof(__pyx_k_contig), 0, 0, 1, 1},
|
|
jpayne@69
|
11529 {&__pyx_kp_u_contig_and_reference_should_not, __pyx_k_contig_and_reference_should_not, sizeof(__pyx_k_contig_and_reference_should_not), 0, 1, 0, 0},
|
|
jpayne@69
|
11530 {&__pyx_kp_u_contig_reference_and_region_shou, __pyx_k_contig_reference_and_region_shou, sizeof(__pyx_k_contig_reference_and_region_shou), 0, 1, 0, 0},
|
|
jpayne@69
|
11531 {&__pyx_n_s_decode, __pyx_k_decode, sizeof(__pyx_k_decode), 0, 0, 1, 1},
|
|
jpayne@69
|
11532 {&__pyx_n_u_depad, __pyx_k_depad, sizeof(__pyx_k_depad), 0, 1, 0, 1},
|
|
jpayne@69
|
11533 {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1},
|
|
jpayne@69
|
11534 {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1},
|
|
jpayne@69
|
11535 {&__pyx_n_s_enter, __pyx_k_enter, sizeof(__pyx_k_enter), 0, 0, 1, 1},
|
|
jpayne@69
|
11536 {&__pyx_kp_u_error_while_opening_file_for_wri, __pyx_k_error_while_opening_file_for_wri, sizeof(__pyx_k_error_while_opening_file_for_wri), 0, 1, 0, 0},
|
|
jpayne@69
|
11537 {&__pyx_n_s_exception, __pyx_k_exception, sizeof(__pyx_k_exception), 0, 0, 1, 1},
|
|
jpayne@69
|
11538 {&__pyx_n_s_exists, __pyx_k_exists, sizeof(__pyx_k_exists), 0, 0, 1, 1},
|
|
jpayne@69
|
11539 {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1},
|
|
jpayne@69
|
11540 {&__pyx_n_s_extend, __pyx_k_extend, sizeof(__pyx_k_extend), 0, 0, 1, 1},
|
|
jpayne@69
|
11541 {&__pyx_n_s_extra_args, __pyx_k_extra_args, sizeof(__pyx_k_extra_args), 0, 0, 1, 1},
|
|
jpayne@69
|
11542 {&__pyx_n_s_fn, __pyx_k_fn, sizeof(__pyx_k_fn), 0, 0, 1, 1},
|
|
jpayne@69
|
11543 {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1},
|
|
jpayne@69
|
11544 {&__pyx_n_s_fsencode, __pyx_k_fsencode, sizeof(__pyx_k_fsencode), 0, 0, 1, 1},
|
|
jpayne@69
|
11545 {&__pyx_n_s_get_encoding_error_handler, __pyx_k_get_encoding_error_handler, sizeof(__pyx_k_get_encoding_error_handler), 0, 0, 1, 1},
|
|
jpayne@69
|
11546 {&__pyx_n_u_get_encoding_error_handler, __pyx_k_get_encoding_error_handler, sizeof(__pyx_k_get_encoding_error_handler), 0, 1, 0, 1},
|
|
jpayne@69
|
11547 {&__pyx_n_s_getdefaultencoding, __pyx_k_getdefaultencoding, sizeof(__pyx_k_getdefaultencoding), 0, 0, 1, 1},
|
|
jpayne@69
|
11548 {&__pyx_n_s_getfilesystemencoding, __pyx_k_getfilesystemencoding, sizeof(__pyx_k_getfilesystemencoding), 0, 0, 1, 1},
|
|
jpayne@69
|
11549 {&__pyx_n_u_head, __pyx_k_head, sizeof(__pyx_k_head), 0, 1, 0, 1},
|
|
jpayne@69
|
11550 {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1},
|
|
jpayne@69
|
11551 {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
|
|
jpayne@69
|
11552 {&__pyx_n_b_index, __pyx_k_index, sizeof(__pyx_k_index), 0, 0, 0, 1},
|
|
jpayne@69
|
11553 {&__pyx_n_u_index, __pyx_k_index, sizeof(__pyx_k_index), 0, 1, 0, 1},
|
|
jpayne@69
|
11554 {&__pyx_n_s_inf, __pyx_k_inf, sizeof(__pyx_k_inf), 0, 0, 1, 1},
|
|
jpayne@69
|
11555 {&__pyx_n_s_initializing, __pyx_k_initializing, sizeof(__pyx_k_initializing), 0, 0, 1, 1},
|
|
jpayne@69
|
11556 {&__pyx_n_s_input_str, __pyx_k_input_str, sizeof(__pyx_k_input_str), 0, 0, 1, 1},
|
|
jpayne@69
|
11557 {&__pyx_kp_u_invalid_coordinates_start_i_stop, __pyx_k_invalid_coordinates_start_i_stop, sizeof(__pyx_k_invalid_coordinates_start_i_stop), 0, 1, 0, 0},
|
|
jpayne@69
|
11558 {&__pyx_n_s_io, __pyx_k_io, sizeof(__pyx_k_io), 0, 0, 1, 1},
|
|
jpayne@69
|
11559 {&__pyx_n_s_is_coroutine, __pyx_k_is_coroutine, sizeof(__pyx_k_is_coroutine), 0, 0, 1, 1},
|
|
jpayne@69
|
11560 {&__pyx_n_s_is_usage, __pyx_k_is_usage, sizeof(__pyx_k_is_usage), 0, 0, 1, 1},
|
|
jpayne@69
|
11561 {&__pyx_n_s_l, __pyx_k_l, sizeof(__pyx_k_l), 0, 0, 1, 1},
|
|
jpayne@69
|
11562 {&__pyx_n_s_latin1_replace, __pyx_k_latin1_replace, sizeof(__pyx_k_latin1_replace), 0, 0, 1, 1},
|
|
jpayne@69
|
11563 {&__pyx_kp_u_m, __pyx_k_m, sizeof(__pyx_k_m), 0, 1, 0, 0},
|
|
jpayne@69
|
11564 {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
|
|
jpayne@69
|
11565 {&__pyx_n_s_method, __pyx_k_method, sizeof(__pyx_k_method), 0, 0, 1, 1},
|
|
jpayne@69
|
11566 {&__pyx_kp_u_min_shift, __pyx_k_min_shift, sizeof(__pyx_k_min_shift), 0, 1, 0, 0},
|
|
jpayne@69
|
11567 {&__pyx_n_s_mkstemp, __pyx_k_mkstemp, sizeof(__pyx_k_mkstemp), 0, 0, 1, 1},
|
|
jpayne@69
|
11568 {&__pyx_n_u_mpileup, __pyx_k_mpileup, sizeof(__pyx_k_mpileup), 0, 1, 0, 1},
|
|
jpayne@69
|
11569 {&__pyx_n_s_n, __pyx_k_n, sizeof(__pyx_k_n), 0, 0, 1, 1},
|
|
jpayne@69
|
11570 {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1},
|
|
jpayne@69
|
11571 {&__pyx_n_s_name_2, __pyx_k_name_2, sizeof(__pyx_k_name_2), 0, 0, 1, 1},
|
|
jpayne@69
|
11572 {&__pyx_kp_u_neither_contig_nor_region_are_gi, __pyx_k_neither_contig_nor_region_are_gi, sizeof(__pyx_k_neither_contig_nor_region_are_gi), 0, 1, 0, 0},
|
|
jpayne@69
|
11573 {&__pyx_kp_u_o, __pyx_k_o, sizeof(__pyx_k_o), 0, 1, 0, 0},
|
|
jpayne@69
|
11574 {&__pyx_kp_u_o_2, __pyx_k_o_2, sizeof(__pyx_k_o_2), 0, 1, 0, 0},
|
|
jpayne@69
|
11575 {&__pyx_n_s_object, __pyx_k_object, sizeof(__pyx_k_object), 0, 0, 1, 1},
|
|
jpayne@69
|
11576 {&__pyx_n_s_offset, __pyx_k_offset, sizeof(__pyx_k_offset), 0, 0, 1, 1},
|
|
jpayne@69
|
11577 {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1},
|
|
jpayne@69
|
11578 {&__pyx_n_s_os, __pyx_k_os, sizeof(__pyx_k_os), 0, 0, 1, 1},
|
|
jpayne@69
|
11579 {&__pyx_n_s_out, __pyx_k_out, sizeof(__pyx_k_out), 0, 0, 1, 1},
|
|
jpayne@69
|
11580 {&__pyx_n_s_out_stderr, __pyx_k_out_stderr, sizeof(__pyx_k_out_stderr), 0, 0, 1, 1},
|
|
jpayne@69
|
11581 {&__pyx_n_s_out_stdout, __pyx_k_out_stdout, sizeof(__pyx_k_out_stdout), 0, 0, 1, 1},
|
|
jpayne@69
|
11582 {&__pyx_kp_u_output, __pyx_k_output, sizeof(__pyx_k_output), 0, 1, 0, 0},
|
|
jpayne@69
|
11583 {&__pyx_kp_u_output_file, __pyx_k_output_file, sizeof(__pyx_k_output_file), 0, 1, 0, 0},
|
|
jpayne@69
|
11584 {&__pyx_n_s_parse_region, __pyx_k_parse_region, sizeof(__pyx_k_parse_region), 0, 0, 1, 1},
|
|
jpayne@69
|
11585 {&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1},
|
|
jpayne@69
|
11586 {&__pyx_n_s_pysam_dispatch, __pyx_k_pysam_dispatch, sizeof(__pyx_k_pysam_dispatch), 0, 0, 1, 1},
|
|
jpayne@69
|
11587 {&__pyx_n_s_pysam_dispatch_locals__collect, __pyx_k_pysam_dispatch_locals__collect, sizeof(__pyx_k_pysam_dispatch_locals__collect), 0, 0, 1, 1},
|
|
jpayne@69
|
11588 {&__pyx_kp_u_pysam_latin1replace, __pyx_k_pysam_latin1replace, sizeof(__pyx_k_pysam_latin1replace), 0, 1, 0, 0},
|
|
jpayne@69
|
11589 {&__pyx_n_s_pysam_libcutils, __pyx_k_pysam_libcutils, sizeof(__pyx_k_pysam_libcutils), 0, 0, 1, 1},
|
|
jpayne@69
|
11590 {&__pyx_kp_s_pysam_libcutils_pyx, __pyx_k_pysam_libcutils_pyx, sizeof(__pyx_k_pysam_libcutils_pyx), 0, 0, 1, 0},
|
|
jpayne@69
|
11591 {&__pyx_n_s_qualities, __pyx_k_qualities, sizeof(__pyx_k_qualities), 0, 0, 1, 1},
|
|
jpayne@69
|
11592 {&__pyx_n_s_qualities_to_qualitystring, __pyx_k_qualities_to_qualitystring, sizeof(__pyx_k_qualities_to_qualitystring), 0, 0, 1, 1},
|
|
jpayne@69
|
11593 {&__pyx_n_u_qualities_to_qualitystring, __pyx_k_qualities_to_qualitystring, sizeof(__pyx_k_qualities_to_qualitystring), 0, 1, 0, 1},
|
|
jpayne@69
|
11594 {&__pyx_n_s_qualitystring_to_array, __pyx_k_qualitystring_to_array, sizeof(__pyx_k_qualitystring_to_array), 0, 0, 1, 1},
|
|
jpayne@69
|
11595 {&__pyx_n_u_qualitystring_to_array, __pyx_k_qualitystring_to_array, sizeof(__pyx_k_qualitystring_to_array), 0, 1, 0, 1},
|
|
jpayne@69
|
11596 {&__pyx_n_u_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 1, 0, 1},
|
|
jpayne@69
|
11597 {&__pyx_n_u_rb, __pyx_k_rb, sizeof(__pyx_k_rb), 0, 1, 0, 1},
|
|
jpayne@69
|
11598 {&__pyx_n_s_re, __pyx_k_re, sizeof(__pyx_k_re), 0, 0, 1, 1},
|
|
jpayne@69
|
11599 {&__pyx_n_s_read, __pyx_k_read, sizeof(__pyx_k_read), 0, 0, 1, 1},
|
|
jpayne@69
|
11600 {&__pyx_n_s_reference, __pyx_k_reference, sizeof(__pyx_k_reference), 0, 0, 1, 1},
|
|
jpayne@69
|
11601 {&__pyx_n_s_region, __pyx_k_region, sizeof(__pyx_k_region), 0, 0, 1, 1},
|
|
jpayne@69
|
11602 {&__pyx_n_s_register_error, __pyx_k_register_error, sizeof(__pyx_k_register_error), 0, 0, 1, 1},
|
|
jpayne@69
|
11603 {&__pyx_n_s_remove, __pyx_k_remove, sizeof(__pyx_k_remove), 0, 0, 1, 1},
|
|
jpayne@69
|
11604 {&__pyx_n_s_retval, __pyx_k_retval, sizeof(__pyx_k_retval), 0, 0, 1, 1},
|
|
jpayne@69
|
11605 {&__pyx_n_u_roh, __pyx_k_roh, sizeof(__pyx_k_roh), 0, 1, 0, 1},
|
|
jpayne@69
|
11606 {&__pyx_n_b_samtools, __pyx_k_samtools, sizeof(__pyx_k_samtools), 0, 0, 0, 1},
|
|
jpayne@69
|
11607 {&__pyx_n_u_samtools, __pyx_k_samtools, sizeof(__pyx_k_samtools), 0, 1, 0, 1},
|
|
jpayne@69
|
11608 {&__pyx_n_s_save_stdout, __pyx_k_save_stdout, sizeof(__pyx_k_save_stdout), 0, 0, 1, 1},
|
|
jpayne@69
|
11609 {&__pyx_n_s_set_encoding_error_handler, __pyx_k_set_encoding_error_handler, sizeof(__pyx_k_set_encoding_error_handler), 0, 0, 1, 1},
|
|
jpayne@69
|
11610 {&__pyx_n_u_set_encoding_error_handler, __pyx_k_set_encoding_error_handler, sizeof(__pyx_k_set_encoding_error_handler), 0, 1, 0, 1},
|
|
jpayne@69
|
11611 {&__pyx_n_s_skip_next, __pyx_k_skip_next, sizeof(__pyx_k_skip_next), 0, 0, 1, 1},
|
|
jpayne@69
|
11612 {&__pyx_n_s_spec, __pyx_k_spec, sizeof(__pyx_k_spec), 0, 0, 1, 1},
|
|
jpayne@69
|
11613 {&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1},
|
|
jpayne@69
|
11614 {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
|
|
jpayne@69
|
11615 {&__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
|
11616 {&__pyx_n_s_startswith, __pyx_k_startswith, sizeof(__pyx_k_startswith), 0, 0, 1, 1},
|
|
jpayne@69
|
11617 {&__pyx_n_u_stats, __pyx_k_stats, sizeof(__pyx_k_stats), 0, 1, 0, 1},
|
|
jpayne@69
|
11618 {&__pyx_n_s_stderr_f, __pyx_k_stderr_f, sizeof(__pyx_k_stderr_f), 0, 0, 1, 1},
|
|
jpayne@69
|
11619 {&__pyx_n_s_stderr_h, __pyx_k_stderr_h, sizeof(__pyx_k_stderr_h), 0, 0, 1, 1},
|
|
jpayne@69
|
11620 {&__pyx_n_s_stdout_f, __pyx_k_stdout_f, sizeof(__pyx_k_stdout_f), 0, 0, 1, 1},
|
|
jpayne@69
|
11621 {&__pyx_n_s_stdout_h, __pyx_k_stdout_h, sizeof(__pyx_k_stdout_h), 0, 0, 1, 1},
|
|
jpayne@69
|
11622 {&__pyx_n_s_stdout_option, __pyx_k_stdout_option, sizeof(__pyx_k_stdout_option), 0, 0, 1, 1},
|
|
jpayne@69
|
11623 {&__pyx_n_s_stop, __pyx_k_stop, sizeof(__pyx_k_stop), 0, 0, 1, 1},
|
|
jpayne@69
|
11624 {&__pyx_kp_u_stop_and_end_should_not_both_be, __pyx_k_stop_and_end_should_not_both_be, sizeof(__pyx_k_stop_and_end_should_not_both_be), 0, 1, 0, 0},
|
|
jpayne@69
|
11625 {&__pyx_kp_u_stop_out_of_range_i, __pyx_k_stop_out_of_range_i, sizeof(__pyx_k_stop_out_of_range_i), 0, 1, 0, 0},
|
|
jpayne@69
|
11626 {&__pyx_n_u_strict, __pyx_k_strict, sizeof(__pyx_k_strict), 0, 1, 0, 1},
|
|
jpayne@69
|
11627 {&__pyx_n_s_string, __pyx_k_string, sizeof(__pyx_k_string), 0, 0, 1, 1},
|
|
jpayne@69
|
11628 {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1},
|
|
jpayne@69
|
11629 {&__pyx_n_s_tempfile, __pyx_k_tempfile, sizeof(__pyx_k_tempfile), 0, 0, 1, 1},
|
|
jpayne@69
|
11630 {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
|
|
jpayne@69
|
11631 {&__pyx_kp_u_threads, __pyx_k_threads, sizeof(__pyx_k_threads), 0, 1, 0, 0},
|
|
jpayne@69
|
11632 {&__pyx_n_s_tobytes, __pyx_k_tobytes, sizeof(__pyx_k_tobytes), 0, 0, 1, 1},
|
|
jpayne@69
|
11633 {&__pyx_n_s_types, __pyx_k_types, sizeof(__pyx_k_types), 0, 0, 1, 1},
|
|
jpayne@69
|
11634 {&__pyx_kp_u_utf_8, __pyx_k_utf_8, sizeof(__pyx_k_utf_8), 0, 1, 0, 0},
|
|
jpayne@69
|
11635 {&__pyx_n_u_view, __pyx_k_view, sizeof(__pyx_k_view), 0, 1, 0, 1},
|
|
jpayne@69
|
11636 {0, 0, 0, 0, 0, 0, 0}
|
|
jpayne@69
|
11637 };
|
|
jpayne@69
|
11638 return __Pyx_InitStrings(__pyx_string_tab);
|
|
jpayne@69
|
11639 }
|
|
jpayne@69
|
11640 /* #### Code section: cached_builtins ### */
|
|
jpayne@69
|
11641 static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) {
|
|
jpayne@69
|
11642 __pyx_builtin_chr = __Pyx_GetBuiltinName(__pyx_n_s_chr); if (!__pyx_builtin_chr) __PYX_ERR(0, 82, __pyx_L1_error)
|
|
jpayne@69
|
11643 __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(0, 136, __pyx_L1_error)
|
|
jpayne@69
|
11644 __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 218, __pyx_L1_error)
|
|
jpayne@69
|
11645 __pyx_builtin_OverflowError = __Pyx_GetBuiltinName(__pyx_n_s_OverflowError); if (!__pyx_builtin_OverflowError) __PYX_ERR(0, 237, __pyx_L1_error)
|
|
jpayne@69
|
11646 __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) __PYX_ERR(0, 309, __pyx_L1_error)
|
|
jpayne@69
|
11647 __pyx_builtin_OSError = __Pyx_GetBuiltinName(__pyx_n_s_OSError); if (!__pyx_builtin_OSError) __PYX_ERR(0, 327, __pyx_L1_error)
|
|
jpayne@69
|
11648 __pyx_builtin_open = __Pyx_GetBuiltinName(__pyx_n_s_open); if (!__pyx_builtin_open) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
11649 __pyx_builtin_UnicodeDecodeError = __Pyx_GetBuiltinName(__pyx_n_s_UnicodeDecodeError); if (!__pyx_builtin_UnicodeDecodeError) __PYX_ERR(0, 418, __pyx_L1_error)
|
|
jpayne@69
|
11650 __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) __PYX_ERR(2, 120, __pyx_L1_error)
|
|
jpayne@69
|
11651 return 0;
|
|
jpayne@69
|
11652 __pyx_L1_error:;
|
|
jpayne@69
|
11653 return -1;
|
|
jpayne@69
|
11654 }
|
|
jpayne@69
|
11655 /* #### Code section: cached_constants ### */
|
|
jpayne@69
|
11656
|
|
jpayne@69
|
11657 static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) {
|
|
jpayne@69
|
11658 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
11659 __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
|
|
jpayne@69
|
11660
|
|
jpayne@69
|
11661 /* "pysam/libcutils.pyx":136
|
|
jpayne@69
|
11662 * return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
|
|
jpayne@69
|
11663 * else:
|
|
jpayne@69
|
11664 * raise TypeError("Argument must be string, bytes or unicode.") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11665 *
|
|
jpayne@69
|
11666 *
|
|
jpayne@69
|
11667 */
|
|
jpayne@69
|
11668 __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_Argument_must_be_string_bytes_or); if (unlikely(!__pyx_tuple__2)) __PYX_ERR(0, 136, __pyx_L1_error)
|
|
jpayne@69
|
11669 __Pyx_GOTREF(__pyx_tuple__2);
|
|
jpayne@69
|
11670 __Pyx_GIVEREF(__pyx_tuple__2);
|
|
jpayne@69
|
11671
|
|
jpayne@69
|
11672 /* "pysam/libcutils.pyx":218
|
|
jpayne@69
|
11673 * if reference is not None:
|
|
jpayne@69
|
11674 * if contig is not None:
|
|
jpayne@69
|
11675 * raise ValueError('contig and reference should not both be specified') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11676 * contig = reference
|
|
jpayne@69
|
11677 *
|
|
jpayne@69
|
11678 */
|
|
jpayne@69
|
11679 __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_contig_and_reference_should_not); if (unlikely(!__pyx_tuple__3)) __PYX_ERR(0, 218, __pyx_L1_error)
|
|
jpayne@69
|
11680 __Pyx_GOTREF(__pyx_tuple__3);
|
|
jpayne@69
|
11681 __Pyx_GIVEREF(__pyx_tuple__3);
|
|
jpayne@69
|
11682
|
|
jpayne@69
|
11683 /* "pysam/libcutils.pyx":222
|
|
jpayne@69
|
11684 *
|
|
jpayne@69
|
11685 * if contig is not None and region is not None:
|
|
jpayne@69
|
11686 * raise ValueError('contig/reference and region should not both be specified') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11687 *
|
|
jpayne@69
|
11688 * if end is not None:
|
|
jpayne@69
|
11689 */
|
|
jpayne@69
|
11690 __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_contig_reference_and_region_shou); if (unlikely(!__pyx_tuple__4)) __PYX_ERR(0, 222, __pyx_L1_error)
|
|
jpayne@69
|
11691 __Pyx_GOTREF(__pyx_tuple__4);
|
|
jpayne@69
|
11692 __Pyx_GIVEREF(__pyx_tuple__4);
|
|
jpayne@69
|
11693
|
|
jpayne@69
|
11694 /* "pysam/libcutils.pyx":226
|
|
jpayne@69
|
11695 * if end is not None:
|
|
jpayne@69
|
11696 * if stop is not None:
|
|
jpayne@69
|
11697 * raise ValueError('stop and end should not both be specified') # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11698 * stop = end
|
|
jpayne@69
|
11699 *
|
|
jpayne@69
|
11700 */
|
|
jpayne@69
|
11701 __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_stop_and_end_should_not_both_be); if (unlikely(!__pyx_tuple__5)) __PYX_ERR(0, 226, __pyx_L1_error)
|
|
jpayne@69
|
11702 __Pyx_GOTREF(__pyx_tuple__5);
|
|
jpayne@69
|
11703 __Pyx_GIVEREF(__pyx_tuple__5);
|
|
jpayne@69
|
11704
|
|
jpayne@69
|
11705 /* "pysam/libcutils.pyx":230
|
|
jpayne@69
|
11706 *
|
|
jpayne@69
|
11707 * if contig is None and region is None:
|
|
jpayne@69
|
11708 * raise ValueError("neither contig nor region are given") # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11709 *
|
|
jpayne@69
|
11710 * rstart = 0
|
|
jpayne@69
|
11711 */
|
|
jpayne@69
|
11712 __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_neither_contig_nor_region_are_gi); if (unlikely(!__pyx_tuple__6)) __PYX_ERR(0, 230, __pyx_L1_error)
|
|
jpayne@69
|
11713 __Pyx_GOTREF(__pyx_tuple__6);
|
|
jpayne@69
|
11714 __Pyx_GIVEREF(__pyx_tuple__6);
|
|
jpayne@69
|
11715
|
|
jpayne@69
|
11716 /* "pysam/libcutils.pyx":416
|
|
jpayne@69
|
11717 * out = []
|
|
jpayne@69
|
11718 * try:
|
|
jpayne@69
|
11719 * with open(fn, "r") as inf: # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11720 * out = inf.read()
|
|
jpayne@69
|
11721 * except UnicodeDecodeError:
|
|
jpayne@69
|
11722 */
|
|
jpayne@69
|
11723 __pyx_tuple__9 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__9)) __PYX_ERR(0, 416, __pyx_L1_error)
|
|
jpayne@69
|
11724 __Pyx_GOTREF(__pyx_tuple__9);
|
|
jpayne@69
|
11725 __Pyx_GIVEREF(__pyx_tuple__9);
|
|
jpayne@69
|
11726
|
|
jpayne@69
|
11727 /* "pysam/libcutils.pyx":413
|
|
jpayne@69
|
11728 *
|
|
jpayne@69
|
11729 * # get error messages
|
|
jpayne@69
|
11730 * def _collect(fn): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11731 * out = []
|
|
jpayne@69
|
11732 * try:
|
|
jpayne@69
|
11733 */
|
|
jpayne@69
|
11734 __pyx_tuple__12 = PyTuple_Pack(3, __pyx_n_s_fn, __pyx_n_s_out, __pyx_n_s_inf); if (unlikely(!__pyx_tuple__12)) __PYX_ERR(0, 413, __pyx_L1_error)
|
|
jpayne@69
|
11735 __Pyx_GOTREF(__pyx_tuple__12);
|
|
jpayne@69
|
11736 __Pyx_GIVEREF(__pyx_tuple__12);
|
|
jpayne@69
|
11737 __pyx_codeobj__13 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__12, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_collect, 413, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__13)) __PYX_ERR(0, 413, __pyx_L1_error)
|
|
jpayne@69
|
11738
|
|
jpayne@69
|
11739 /* "pysam/libcutils.pyx":36
|
|
jpayne@69
|
11740 * #################################################################
|
|
jpayne@69
|
11741 * # Utility functions for quality string conversions
|
|
jpayne@69
|
11742 * cpdef c_array.array qualitystring_to_array(input_str, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11743 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
11744 * if input_str is None:
|
|
jpayne@69
|
11745 */
|
|
jpayne@69
|
11746 __pyx_tuple__16 = PyTuple_Pack(2, __pyx_n_s_input_str, __pyx_n_s_offset); if (unlikely(!__pyx_tuple__16)) __PYX_ERR(0, 36, __pyx_L1_error)
|
|
jpayne@69
|
11747 __Pyx_GOTREF(__pyx_tuple__16);
|
|
jpayne@69
|
11748 __Pyx_GIVEREF(__pyx_tuple__16);
|
|
jpayne@69
|
11749 __pyx_codeobj__17 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__16, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_qualitystring_to_array, 36, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) __PYX_ERR(0, 36, __pyx_L1_error)
|
|
jpayne@69
|
11750 __pyx_tuple__18 = PyTuple_Pack(1, __pyx_int_33); if (unlikely(!__pyx_tuple__18)) __PYX_ERR(0, 36, __pyx_L1_error)
|
|
jpayne@69
|
11751 __Pyx_GOTREF(__pyx_tuple__18);
|
|
jpayne@69
|
11752 __Pyx_GIVEREF(__pyx_tuple__18);
|
|
jpayne@69
|
11753
|
|
jpayne@69
|
11754 /* "pysam/libcutils.pyx":45
|
|
jpayne@69
|
11755 *
|
|
jpayne@69
|
11756 *
|
|
jpayne@69
|
11757 * cpdef array_to_qualitystring(c_array.array qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11758 * """convert an array of quality values to a string."""
|
|
jpayne@69
|
11759 * if qualities is None:
|
|
jpayne@69
|
11760 */
|
|
jpayne@69
|
11761 __pyx_tuple__19 = PyTuple_Pack(2, __pyx_n_s_qualities, __pyx_n_s_offset); if (unlikely(!__pyx_tuple__19)) __PYX_ERR(0, 45, __pyx_L1_error)
|
|
jpayne@69
|
11762 __Pyx_GOTREF(__pyx_tuple__19);
|
|
jpayne@69
|
11763 __Pyx_GIVEREF(__pyx_tuple__19);
|
|
jpayne@69
|
11764 __pyx_codeobj__20 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__19, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_array_to_qualitystring, 45, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__20)) __PYX_ERR(0, 45, __pyx_L1_error)
|
|
jpayne@69
|
11765
|
|
jpayne@69
|
11766 /* "pysam/libcutils.pyx":59
|
|
jpayne@69
|
11767 *
|
|
jpayne@69
|
11768 *
|
|
jpayne@69
|
11769 * cpdef qualities_to_qualitystring(qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11770 * """convert a list or array of quality scores to the string
|
|
jpayne@69
|
11771 * representation used in the SAM format.
|
|
jpayne@69
|
11772 */
|
|
jpayne@69
|
11773 __pyx_codeobj__21 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__19, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_qualities_to_qualitystring, 59, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__21)) __PYX_ERR(0, 59, __pyx_L1_error)
|
|
jpayne@69
|
11774
|
|
jpayne@69
|
11775 /* "pysam/libcutils.pyx":90
|
|
jpayne@69
|
11776 *
|
|
jpayne@69
|
11777 * # Codec error handler that just interprets each bad byte as ISO-8859-1.
|
|
jpayne@69
|
11778 * def latin1_replace(exception): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11779 * return (chr(exception.object[exception.start]), exception.end)
|
|
jpayne@69
|
11780 *
|
|
jpayne@69
|
11781 */
|
|
jpayne@69
|
11782 __pyx_tuple__22 = PyTuple_Pack(1, __pyx_n_s_exception); if (unlikely(!__pyx_tuple__22)) __PYX_ERR(0, 90, __pyx_L1_error)
|
|
jpayne@69
|
11783 __Pyx_GOTREF(__pyx_tuple__22);
|
|
jpayne@69
|
11784 __Pyx_GIVEREF(__pyx_tuple__22);
|
|
jpayne@69
|
11785 __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__22, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_latin1_replace, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) __PYX_ERR(0, 90, __pyx_L1_error)
|
|
jpayne@69
|
11786
|
|
jpayne@69
|
11787 /* "pysam/libcutils.pyx":98
|
|
jpayne@69
|
11788 * cdef str ERROR_HANDLER = 'strict'
|
|
jpayne@69
|
11789 *
|
|
jpayne@69
|
11790 * cpdef get_encoding_error_handler(): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11791 * return ERROR_HANDLER
|
|
jpayne@69
|
11792 *
|
|
jpayne@69
|
11793 */
|
|
jpayne@69
|
11794 __pyx_codeobj__24 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_get_encoding_error_handler, 98, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__24)) __PYX_ERR(0, 98, __pyx_L1_error)
|
|
jpayne@69
|
11795
|
|
jpayne@69
|
11796 /* "pysam/libcutils.pyx":101
|
|
jpayne@69
|
11797 * return ERROR_HANDLER
|
|
jpayne@69
|
11798 *
|
|
jpayne@69
|
11799 * cpdef set_encoding_error_handler(name): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11800 * global ERROR_HANDLER
|
|
jpayne@69
|
11801 * previous = ERROR_HANDLER
|
|
jpayne@69
|
11802 */
|
|
jpayne@69
|
11803 __pyx_tuple__25 = PyTuple_Pack(1, __pyx_n_s_name); if (unlikely(!__pyx_tuple__25)) __PYX_ERR(0, 101, __pyx_L1_error)
|
|
jpayne@69
|
11804 __Pyx_GOTREF(__pyx_tuple__25);
|
|
jpayne@69
|
11805 __Pyx_GIVEREF(__pyx_tuple__25);
|
|
jpayne@69
|
11806 __pyx_codeobj__26 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__25, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_set_encoding_error_handler, 101, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__26)) __PYX_ERR(0, 101, __pyx_L1_error)
|
|
jpayne@69
|
11807
|
|
jpayne@69
|
11808 /* "pysam/libcutils.pyx":178
|
|
jpayne@69
|
11809 *
|
|
jpayne@69
|
11810 *
|
|
jpayne@69
|
11811 * cpdef parse_region(contig=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11812 * start=None,
|
|
jpayne@69
|
11813 * stop=None,
|
|
jpayne@69
|
11814 */
|
|
jpayne@69
|
11815 __pyx_tuple__27 = PyTuple_Pack(6, __pyx_n_s_contig, __pyx_n_s_start, __pyx_n_s_stop, __pyx_n_s_region, __pyx_n_s_reference, __pyx_n_s_end); if (unlikely(!__pyx_tuple__27)) __PYX_ERR(0, 178, __pyx_L1_error)
|
|
jpayne@69
|
11816 __Pyx_GOTREF(__pyx_tuple__27);
|
|
jpayne@69
|
11817 __Pyx_GIVEREF(__pyx_tuple__27);
|
|
jpayne@69
|
11818 __pyx_codeobj__28 = (PyObject*)__Pyx_PyCode_New(6, 0, 0, 6, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__27, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_parse_region, 178, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__28)) __PYX_ERR(0, 178, __pyx_L1_error)
|
|
jpayne@69
|
11819 __pyx_tuple__29 = PyTuple_Pack(6, Py_None, Py_None, Py_None, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__29)) __PYX_ERR(0, 178, __pyx_L1_error)
|
|
jpayne@69
|
11820 __Pyx_GOTREF(__pyx_tuple__29);
|
|
jpayne@69
|
11821 __Pyx_GIVEREF(__pyx_tuple__29);
|
|
jpayne@69
|
11822
|
|
jpayne@69
|
11823 /* "pysam/libcutils.pyx":276
|
|
jpayne@69
|
11824 *
|
|
jpayne@69
|
11825 *
|
|
jpayne@69
|
11826 * def _pysam_dispatch(collection, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
11827 * method,
|
|
jpayne@69
|
11828 * args=None,
|
|
jpayne@69
|
11829 */
|
|
jpayne@69
|
11830 __pyx_tuple__30 = PyTuple_Pack(26, __pyx_n_s_collection, __pyx_n_s_method, __pyx_n_s_args, __pyx_n_s_catch_stdout, __pyx_n_s_is_usage, __pyx_n_s_save_stdout, __pyx_n_s_ARGUMENTS, __pyx_n_s_skip_next, __pyx_n_s_arg, __pyx_n_s_stderr_h, __pyx_n_s_stderr_f, __pyx_n_s_stdout_f, __pyx_n_s_stdout_h, __pyx_n_s_MAP_STDOUT_OPTIONS, __pyx_n_s_stdout_option, __pyx_n_s_cargs, __pyx_n_s_i, __pyx_n_s_n, __pyx_n_s_retval, __pyx_n_s_l, __pyx_n_s_extra_args, __pyx_n_s_collect, __pyx_n_s_collect, __pyx_n_s_out_stderr, __pyx_n_s_out_stdout, __pyx_n_s_a); if (unlikely(!__pyx_tuple__30)) __PYX_ERR(0, 276, __pyx_L1_error)
|
|
jpayne@69
|
11831 __Pyx_GOTREF(__pyx_tuple__30);
|
|
jpayne@69
|
11832 __Pyx_GIVEREF(__pyx_tuple__30);
|
|
jpayne@69
|
11833 __pyx_codeobj__31 = (PyObject*)__Pyx_PyCode_New(6, 0, 0, 26, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__30, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcutils_pyx, __pyx_n_s_pysam_dispatch, 276, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__31)) __PYX_ERR(0, 276, __pyx_L1_error)
|
|
jpayne@69
|
11834 __pyx_tuple__32 = PyTuple_Pack(4, Py_None, ((PyObject *)Py_True), ((PyObject *)Py_False), Py_None); if (unlikely(!__pyx_tuple__32)) __PYX_ERR(0, 276, __pyx_L1_error)
|
|
jpayne@69
|
11835 __Pyx_GOTREF(__pyx_tuple__32);
|
|
jpayne@69
|
11836 __Pyx_GIVEREF(__pyx_tuple__32);
|
|
jpayne@69
|
11837 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11838 return 0;
|
|
jpayne@69
|
11839 __pyx_L1_error:;
|
|
jpayne@69
|
11840 __Pyx_RefNannyFinishContext();
|
|
jpayne@69
|
11841 return -1;
|
|
jpayne@69
|
11842 }
|
|
jpayne@69
|
11843 /* #### Code section: init_constants ### */
|
|
jpayne@69
|
11844
|
|
jpayne@69
|
11845 static CYTHON_SMALL_CODE int __Pyx_InitConstants(void) {
|
|
jpayne@69
|
11846 if (__Pyx_CreateStringTabAndInitStrings() < 0) __PYX_ERR(0, 1, __pyx_L1_error);
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jpayne@69
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11847 __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11848 __pyx_int_33 = PyInt_FromLong(33); if (unlikely(!__pyx_int_33)) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11849 __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11850 return 0;
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11851 __pyx_L1_error:;
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jpayne@69
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11852 return -1;
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jpayne@69
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11853 }
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11854 /* #### Code section: init_globals ### */
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jpayne@69
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11855
|
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jpayne@69
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11856 static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) {
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jpayne@69
|
11857 return 0;
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jpayne@69
|
11858 }
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jpayne@69
|
11859 /* #### Code section: init_module ### */
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jpayne@69
|
11860
|
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jpayne@69
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11861 static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/
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jpayne@69
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11862 static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/
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jpayne@69
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11863 static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/
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jpayne@69
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11864 static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/
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jpayne@69
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11865 static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/
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jpayne@69
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11866 static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/
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jpayne@69
|
11867 static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/
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|
jpayne@69
|
11868
|
|
jpayne@69
|
11869 static int __Pyx_modinit_global_init_code(void) {
|
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jpayne@69
|
11870 __Pyx_RefNannyDeclarations
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jpayne@69
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11871 __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0);
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jpayne@69
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11872 /*--- Global init code ---*/
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jpayne@69
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jpayne@69
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11874 __pyx_v_5pysam_9libcutils_FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
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jpayne@69
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11875 __pyx_v_5pysam_9libcutils_TEXT_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
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jpayne@69
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11876 __Pyx_RefNannyFinishContext();
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jpayne@69
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11877 return 0;
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jpayne@69
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11878 }
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jpayne@69
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11879
|
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jpayne@69
|
11880 static int __Pyx_modinit_variable_export_code(void) {
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jpayne@69
|
11881 __Pyx_RefNannyDeclarations
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jpayne@69
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11882 __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0);
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11884 __Pyx_RefNannyFinishContext();
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jpayne@69
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11885 return 0;
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jpayne@69
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11886 }
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jpayne@69
|
11887
|
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jpayne@69
|
11888 static int __Pyx_modinit_function_export_code(void) {
|
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jpayne@69
|
11889 __Pyx_RefNannyDeclarations
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jpayne@69
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11890 int __pyx_lineno = 0;
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jpayne@69
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11891 const char *__pyx_filename = NULL;
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jpayne@69
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11892 int __pyx_clineno = 0;
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jpayne@69
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11893 __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0);
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jpayne@69
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11894 /*--- Function export code ---*/
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jpayne@69
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11895 if (__Pyx_ExportFunction("parse_region", (void (*)(void))__pyx_f_5pysam_9libcutils_parse_region, "PyObject *(int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_parse_region *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
|
11896 if (__Pyx_ExportFunction("libc_whence_from_io", (void (*)(void))__pyx_f_5pysam_9libcutils_libc_whence_from_io, "int (int)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
|
11897 if (__Pyx_ExportFunction("qualitystring_to_array", (void (*)(void))__pyx_f_5pysam_9libcutils_qualitystring_to_array, "arrayobject *(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
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jpayne@69
|
11898 if (__Pyx_ExportFunction("array_to_qualitystring", (void (*)(void))__pyx_f_5pysam_9libcutils_array_to_qualitystring, "PyObject *(arrayobject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
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jpayne@69
|
11899 if (__Pyx_ExportFunction("qualities_to_qualitystring", (void (*)(void))__pyx_f_5pysam_9libcutils_qualities_to_qualitystring, "PyObject *(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
|
11900 if (__Pyx_ExportFunction("get_encoding_error_handler", (void (*)(void))__pyx_f_5pysam_9libcutils_get_encoding_error_handler, "PyObject *(int __pyx_skip_dispatch)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
|
11901 if (__Pyx_ExportFunction("set_encoding_error_handler", (void (*)(void))__pyx_f_5pysam_9libcutils_set_encoding_error_handler, "PyObject *(PyObject *, int __pyx_skip_dispatch)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
|
11902 if (__Pyx_ExportFunction("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)
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jpayne@69
|
11903 if (__Pyx_ExportFunction("charptr_to_bytes", (void (*)(void))__pyx_f_5pysam_9libcutils_charptr_to_bytes, "PyObject *(char const *, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11904 if (__Pyx_ExportFunction("charptr_to_str_w_len", (void (*)(void))__pyx_f_5pysam_9libcutils_charptr_to_str_w_len, "PyObject *(char const *, size_t, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11905 if (__Pyx_ExportFunction("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)
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jpayne@69
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11906 if (__Pyx_ExportFunction("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)
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jpayne@69
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11907 if (__Pyx_ExportFunction("decode_bytes", (void (*)(void))__pyx_f_5pysam_9libcutils_decode_bytes, "PyObject *(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_decode_bytes *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11908 if (__Pyx_ExportFunction("encode_filename", (void (*)(void))__pyx_f_5pysam_9libcutils_encode_filename, "PyObject *(PyObject *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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jpayne@69
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11909 if (__Pyx_ExportFunction("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)
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jpayne@69
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11910 __Pyx_RefNannyFinishContext();
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jpayne@69
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11911 return 0;
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jpayne@69
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11912 __pyx_L1_error:;
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jpayne@69
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11913 __Pyx_RefNannyFinishContext();
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jpayne@69
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11914 return -1;
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jpayne@69
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11915 }
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jpayne@69
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11916
|
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jpayne@69
|
11917 static int __Pyx_modinit_type_init_code(void) {
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jpayne@69
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11918 __Pyx_RefNannyDeclarations
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jpayne@69
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11919 __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0);
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11920 /*--- Type init code ---*/
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11921 __Pyx_RefNannyFinishContext();
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jpayne@69
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11922 return 0;
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jpayne@69
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11923 }
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jpayne@69
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11924
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jpayne@69
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11925 static int __Pyx_modinit_type_import_code(void) {
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jpayne@69
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11926 __Pyx_RefNannyDeclarations
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jpayne@69
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11927 PyObject *__pyx_t_1 = NULL;
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jpayne@69
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11928 int __pyx_lineno = 0;
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jpayne@69
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11929 const char *__pyx_filename = NULL;
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jpayne@69
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11930 int __pyx_clineno = 0;
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jpayne@69
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11931 __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0);
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jpayne@69
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11932 /*--- Type import code ---*/
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11933 __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 9, __pyx_L1_error)
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jpayne@69
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11934 __Pyx_GOTREF(__pyx_t_1);
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jpayne@69
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11935 __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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11936 #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000
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jpayne@69
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11937 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject),
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jpayne@69
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11938 #elif CYTHON_COMPILING_IN_LIMITED_API
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jpayne@69
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11939 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject),
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jpayne@69
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11940 #else
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jpayne@69
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11941 sizeof(PyHeapTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyHeapTypeObject),
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jpayne@69
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11942 #endif
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11943 __Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(3, 9, __pyx_L1_error)
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11944 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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11945 __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 8, __pyx_L1_error)
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jpayne@69
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11946 __Pyx_GOTREF(__pyx_t_1);
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11947 __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(4, 8, __pyx_L1_error)
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jpayne@69
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11948 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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jpayne@69
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11949 __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(5, 15, __pyx_L1_error)
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jpayne@69
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11950 __Pyx_GOTREF(__pyx_t_1);
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11958 return 0;
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11962 return -1;
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jpayne@69
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11963 }
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jpayne@69
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11964
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jpayne@69
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11965 static int __Pyx_modinit_variable_import_code(void) {
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11966 __Pyx_RefNannyDeclarations
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11972
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jpayne@69
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11973 static int __Pyx_modinit_function_import_code(void) {
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11980
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jpayne@69
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11981
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jpayne@69
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11982 #if PY_MAJOR_VERSION >= 3
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jpayne@69
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11983 #if CYTHON_PEP489_MULTI_PHASE_INIT
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jpayne@69
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11984 static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/
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jpayne@69
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11985 static int __pyx_pymod_exec_libcutils(PyObject* module); /*proto*/
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jpayne@69
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11986 static PyModuleDef_Slot __pyx_moduledef_slots[] = {
|
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jpayne@69
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11987 {Py_mod_create, (void*)__pyx_pymod_create},
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jpayne@69
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11988 {Py_mod_exec, (void*)__pyx_pymod_exec_libcutils},
|
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jpayne@69
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11989 {0, NULL}
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jpayne@69
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11990 };
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jpayne@69
|
11991 #endif
|
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jpayne@69
|
11992
|
|
jpayne@69
|
11993 #ifdef __cplusplus
|
|
jpayne@69
|
11994 namespace {
|
|
jpayne@69
|
11995 struct PyModuleDef __pyx_moduledef =
|
|
jpayne@69
|
11996 #else
|
|
jpayne@69
|
11997 static struct PyModuleDef __pyx_moduledef =
|
|
jpayne@69
|
11998 #endif
|
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jpayne@69
|
11999 {
|
|
jpayne@69
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12000 PyModuleDef_HEAD_INIT,
|
|
jpayne@69
|
12001 "libcutils",
|
|
jpayne@69
|
12002 0, /* m_doc */
|
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jpayne@69
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12003 #if CYTHON_PEP489_MULTI_PHASE_INIT
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jpayne@69
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12004 0, /* m_size */
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jpayne@69
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12005 #elif CYTHON_USE_MODULE_STATE
|
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jpayne@69
|
12006 sizeof(__pyx_mstate), /* m_size */
|
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jpayne@69
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12007 #else
|
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jpayne@69
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12008 -1, /* m_size */
|
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jpayne@69
|
12009 #endif
|
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jpayne@69
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12010 __pyx_methods /* m_methods */,
|
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jpayne@69
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12011 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
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jpayne@69
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12012 __pyx_moduledef_slots, /* m_slots */
|
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jpayne@69
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12013 #else
|
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jpayne@69
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12014 NULL, /* m_reload */
|
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jpayne@69
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12015 #endif
|
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jpayne@69
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12016 #if CYTHON_USE_MODULE_STATE
|
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jpayne@69
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12017 __pyx_m_traverse, /* m_traverse */
|
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jpayne@69
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12018 __pyx_m_clear, /* m_clear */
|
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jpayne@69
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12019 NULL /* m_free */
|
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jpayne@69
|
12020 #else
|
|
jpayne@69
|
12021 NULL, /* m_traverse */
|
|
jpayne@69
|
12022 NULL, /* m_clear */
|
|
jpayne@69
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12023 NULL /* m_free */
|
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jpayne@69
|
12024 #endif
|
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jpayne@69
|
12025 };
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jpayne@69
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12026 #ifdef __cplusplus
|
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jpayne@69
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12027 } /* anonymous namespace */
|
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jpayne@69
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12028 #endif
|
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jpayne@69
|
12029 #endif
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|
jpayne@69
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12030
|
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jpayne@69
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12031 #ifndef CYTHON_NO_PYINIT_EXPORT
|
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jpayne@69
|
12032 #define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC
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|
jpayne@69
|
12033 #elif PY_MAJOR_VERSION < 3
|
|
jpayne@69
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12034 #ifdef __cplusplus
|
|
jpayne@69
|
12035 #define __Pyx_PyMODINIT_FUNC extern "C" void
|
|
jpayne@69
|
12036 #else
|
|
jpayne@69
|
12037 #define __Pyx_PyMODINIT_FUNC void
|
|
jpayne@69
|
12038 #endif
|
|
jpayne@69
|
12039 #else
|
|
jpayne@69
|
12040 #ifdef __cplusplus
|
|
jpayne@69
|
12041 #define __Pyx_PyMODINIT_FUNC extern "C" PyObject *
|
|
jpayne@69
|
12042 #else
|
|
jpayne@69
|
12043 #define __Pyx_PyMODINIT_FUNC PyObject *
|
|
jpayne@69
|
12044 #endif
|
|
jpayne@69
|
12045 #endif
|
|
jpayne@69
|
12046
|
|
jpayne@69
|
12047
|
|
jpayne@69
|
12048 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
12049 __Pyx_PyMODINIT_FUNC initlibcutils(void) CYTHON_SMALL_CODE; /*proto*/
|
|
jpayne@69
|
12050 __Pyx_PyMODINIT_FUNC initlibcutils(void)
|
|
jpayne@69
|
12051 #else
|
|
jpayne@69
|
12052 __Pyx_PyMODINIT_FUNC PyInit_libcutils(void) CYTHON_SMALL_CODE; /*proto*/
|
|
jpayne@69
|
12053 __Pyx_PyMODINIT_FUNC PyInit_libcutils(void)
|
|
jpayne@69
|
12054 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
12055 {
|
|
jpayne@69
|
12056 return PyModuleDef_Init(&__pyx_moduledef);
|
|
jpayne@69
|
12057 }
|
|
jpayne@69
|
12058 static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) {
|
|
jpayne@69
|
12059 #if PY_VERSION_HEX >= 0x030700A1
|
|
jpayne@69
|
12060 static PY_INT64_T main_interpreter_id = -1;
|
|
jpayne@69
|
12061 PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp);
|
|
jpayne@69
|
12062 if (main_interpreter_id == -1) {
|
|
jpayne@69
|
12063 main_interpreter_id = current_id;
|
|
jpayne@69
|
12064 return (unlikely(current_id == -1)) ? -1 : 0;
|
|
jpayne@69
|
12065 } else if (unlikely(main_interpreter_id != current_id))
|
|
jpayne@69
|
12066 #else
|
|
jpayne@69
|
12067 static PyInterpreterState *main_interpreter = NULL;
|
|
jpayne@69
|
12068 PyInterpreterState *current_interpreter = PyThreadState_Get()->interp;
|
|
jpayne@69
|
12069 if (!main_interpreter) {
|
|
jpayne@69
|
12070 main_interpreter = current_interpreter;
|
|
jpayne@69
|
12071 } else if (unlikely(main_interpreter != current_interpreter))
|
|
jpayne@69
|
12072 #endif
|
|
jpayne@69
|
12073 {
|
|
jpayne@69
|
12074 PyErr_SetString(
|
|
jpayne@69
|
12075 PyExc_ImportError,
|
|
jpayne@69
|
12076 "Interpreter change detected - this module can only be loaded into one interpreter per process.");
|
|
jpayne@69
|
12077 return -1;
|
|
jpayne@69
|
12078 }
|
|
jpayne@69
|
12079 return 0;
|
|
jpayne@69
|
12080 }
|
|
jpayne@69
|
12081 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
12082 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
|
12083 #else
|
|
jpayne@69
|
12084 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
|
12085 #endif
|
|
jpayne@69
|
12086 {
|
|
jpayne@69
|
12087 PyObject *value = PyObject_GetAttrString(spec, from_name);
|
|
jpayne@69
|
12088 int result = 0;
|
|
jpayne@69
|
12089 if (likely(value)) {
|
|
jpayne@69
|
12090 if (allow_none || value != Py_None) {
|
|
jpayne@69
|
12091 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
12092 result = PyModule_AddObject(module, to_name, value);
|
|
jpayne@69
|
12093 #else
|
|
jpayne@69
|
12094 result = PyDict_SetItemString(moddict, to_name, value);
|
|
jpayne@69
|
12095 #endif
|
|
jpayne@69
|
12096 }
|
|
jpayne@69
|
12097 Py_DECREF(value);
|
|
jpayne@69
|
12098 } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) {
|
|
jpayne@69
|
12099 PyErr_Clear();
|
|
jpayne@69
|
12100 } else {
|
|
jpayne@69
|
12101 result = -1;
|
|
jpayne@69
|
12102 }
|
|
jpayne@69
|
12103 return result;
|
|
jpayne@69
|
12104 }
|
|
jpayne@69
|
12105 static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def) {
|
|
jpayne@69
|
12106 PyObject *module = NULL, *moddict, *modname;
|
|
jpayne@69
|
12107 CYTHON_UNUSED_VAR(def);
|
|
jpayne@69
|
12108 if (__Pyx_check_single_interpreter())
|
|
jpayne@69
|
12109 return NULL;
|
|
jpayne@69
|
12110 if (__pyx_m)
|
|
jpayne@69
|
12111 return __Pyx_NewRef(__pyx_m);
|
|
jpayne@69
|
12112 modname = PyObject_GetAttrString(spec, "name");
|
|
jpayne@69
|
12113 if (unlikely(!modname)) goto bad;
|
|
jpayne@69
|
12114 module = PyModule_NewObject(modname);
|
|
jpayne@69
|
12115 Py_DECREF(modname);
|
|
jpayne@69
|
12116 if (unlikely(!module)) goto bad;
|
|
jpayne@69
|
12117 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
12118 moddict = module;
|
|
jpayne@69
|
12119 #else
|
|
jpayne@69
|
12120 moddict = PyModule_GetDict(module);
|
|
jpayne@69
|
12121 if (unlikely(!moddict)) goto bad;
|
|
jpayne@69
|
12122 #endif
|
|
jpayne@69
|
12123 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad;
|
|
jpayne@69
|
12124 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad;
|
|
jpayne@69
|
12125 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad;
|
|
jpayne@69
|
12126 if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad;
|
|
jpayne@69
|
12127 return module;
|
|
jpayne@69
|
12128 bad:
|
|
jpayne@69
|
12129 Py_XDECREF(module);
|
|
jpayne@69
|
12130 return NULL;
|
|
jpayne@69
|
12131 }
|
|
jpayne@69
|
12132
|
|
jpayne@69
|
12133
|
|
jpayne@69
|
12134 static CYTHON_SMALL_CODE int __pyx_pymod_exec_libcutils(PyObject *__pyx_pyinit_module)
|
|
jpayne@69
|
12135 #endif
|
|
jpayne@69
|
12136 #endif
|
|
jpayne@69
|
12137 {
|
|
jpayne@69
|
12138 int stringtab_initialized = 0;
|
|
jpayne@69
|
12139 #if CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
12140 int pystate_addmodule_run = 0;
|
|
jpayne@69
|
12141 #endif
|
|
jpayne@69
|
12142 PyObject *__pyx_t_1 = NULL;
|
|
jpayne@69
|
12143 PyObject *__pyx_t_2 = NULL;
|
|
jpayne@69
|
12144 PyObject *__pyx_t_3 = NULL;
|
|
jpayne@69
|
12145 PyObject *__pyx_t_4 = NULL;
|
|
jpayne@69
|
12146 int __pyx_t_5;
|
|
jpayne@69
|
12147 int __pyx_lineno = 0;
|
|
jpayne@69
|
12148 const char *__pyx_filename = NULL;
|
|
jpayne@69
|
12149 int __pyx_clineno = 0;
|
|
jpayne@69
|
12150 __Pyx_RefNannyDeclarations
|
|
jpayne@69
|
12151 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
12152 if (__pyx_m) {
|
|
jpayne@69
|
12153 if (__pyx_m == __pyx_pyinit_module) return 0;
|
|
jpayne@69
|
12154 PyErr_SetString(PyExc_RuntimeError, "Module 'libcutils' has already been imported. Re-initialisation is not supported.");
|
|
jpayne@69
|
12155 return -1;
|
|
jpayne@69
|
12156 }
|
|
jpayne@69
|
12157 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
12158 if (__pyx_m) return __Pyx_NewRef(__pyx_m);
|
|
jpayne@69
|
12159 #endif
|
|
jpayne@69
|
12160 /*--- Module creation code ---*/
|
|
jpayne@69
|
12161 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
12162 __pyx_m = __pyx_pyinit_module;
|
|
jpayne@69
|
12163 Py_INCREF(__pyx_m);
|
|
jpayne@69
|
12164 #else
|
|
jpayne@69
|
12165 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
12166 __pyx_m = Py_InitModule4("libcutils", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
|
|
jpayne@69
|
12167 if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12168 #elif CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
12169 __pyx_t_1 = PyModule_Create(&__pyx_moduledef); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12170 {
|
|
jpayne@69
|
12171 int add_module_result = PyState_AddModule(__pyx_t_1, &__pyx_moduledef);
|
|
jpayne@69
|
12172 __pyx_t_1 = 0; /* transfer ownership from __pyx_t_1 to "libcutils" pseudovariable */
|
|
jpayne@69
|
12173 if (unlikely((add_module_result < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12174 pystate_addmodule_run = 1;
|
|
jpayne@69
|
12175 }
|
|
jpayne@69
|
12176 #else
|
|
jpayne@69
|
12177 __pyx_m = PyModule_Create(&__pyx_moduledef);
|
|
jpayne@69
|
12178 if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12179 #endif
|
|
jpayne@69
|
12180 #endif
|
|
jpayne@69
|
12181 CYTHON_UNUSED_VAR(__pyx_t_1);
|
|
jpayne@69
|
12182 __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12183 Py_INCREF(__pyx_d);
|
|
jpayne@69
|
12184 __pyx_b = __Pyx_PyImport_AddModuleRef(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12185 __pyx_cython_runtime = __Pyx_PyImport_AddModuleRef((const char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12186 if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12187 #if CYTHON_REFNANNY
|
|
jpayne@69
|
12188 __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
|
|
jpayne@69
|
12189 if (!__Pyx_RefNanny) {
|
|
jpayne@69
|
12190 PyErr_Clear();
|
|
jpayne@69
|
12191 __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
|
|
jpayne@69
|
12192 if (!__Pyx_RefNanny)
|
|
jpayne@69
|
12193 Py_FatalError("failed to import 'refnanny' module");
|
|
jpayne@69
|
12194 }
|
|
jpayne@69
|
12195 #endif
|
|
jpayne@69
|
12196 __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_libcutils(void)", 0);
|
|
jpayne@69
|
12197 if (__Pyx_check_binary_version(__PYX_LIMITED_VERSION_HEX, __Pyx_get_runtime_version(), CYTHON_COMPILING_IN_LIMITED_API) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12198 #ifdef __Pxy_PyFrame_Initialize_Offsets
|
|
jpayne@69
|
12199 __Pxy_PyFrame_Initialize_Offsets();
|
|
jpayne@69
|
12200 #endif
|
|
jpayne@69
|
12201 __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12202 __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12203 __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12204 #ifdef __Pyx_CyFunction_USED
|
|
jpayne@69
|
12205 if (__pyx_CyFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12206 #endif
|
|
jpayne@69
|
12207 #ifdef __Pyx_FusedFunction_USED
|
|
jpayne@69
|
12208 if (__pyx_FusedFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12209 #endif
|
|
jpayne@69
|
12210 #ifdef __Pyx_Coroutine_USED
|
|
jpayne@69
|
12211 if (__pyx_Coroutine_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12212 #endif
|
|
jpayne@69
|
12213 #ifdef __Pyx_Generator_USED
|
|
jpayne@69
|
12214 if (__pyx_Generator_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12215 #endif
|
|
jpayne@69
|
12216 #ifdef __Pyx_AsyncGen_USED
|
|
jpayne@69
|
12217 if (__pyx_AsyncGen_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12218 #endif
|
|
jpayne@69
|
12219 #ifdef __Pyx_StopAsyncIteration_USED
|
|
jpayne@69
|
12220 if (__pyx_StopAsyncIteration_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12221 #endif
|
|
jpayne@69
|
12222 /*--- Library function declarations ---*/
|
|
jpayne@69
|
12223 /*--- Threads initialization code ---*/
|
|
jpayne@69
|
12224 #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
|
|
jpayne@69
|
12225 PyEval_InitThreads();
|
|
jpayne@69
|
12226 #endif
|
|
jpayne@69
|
12227 /*--- Initialize various global constants etc. ---*/
|
|
jpayne@69
|
12228 if (__Pyx_InitConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12229 stringtab_initialized = 1;
|
|
jpayne@69
|
12230 if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12231 #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
|
|
jpayne@69
|
12232 if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12233 #endif
|
|
jpayne@69
|
12234 if (__pyx_module_is_main_pysam__libcutils) {
|
|
jpayne@69
|
12235 if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name_2, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12236 }
|
|
jpayne@69
|
12237 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
12238 {
|
|
jpayne@69
|
12239 PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12240 if (!PyDict_GetItemString(modules, "pysam.libcutils")) {
|
|
jpayne@69
|
12241 if (unlikely((PyDict_SetItemString(modules, "pysam.libcutils", __pyx_m) < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12242 }
|
|
jpayne@69
|
12243 }
|
|
jpayne@69
|
12244 #endif
|
|
jpayne@69
|
12245 /*--- Builtin init code ---*/
|
|
jpayne@69
|
12246 if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12247 /*--- Constants init code ---*/
|
|
jpayne@69
|
12248 if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12249 /*--- Global type/function init code ---*/
|
|
jpayne@69
|
12250 (void)__Pyx_modinit_global_init_code();
|
|
jpayne@69
|
12251 (void)__Pyx_modinit_variable_export_code();
|
|
jpayne@69
|
12252 if (unlikely((__Pyx_modinit_function_export_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12253 (void)__Pyx_modinit_type_init_code();
|
|
jpayne@69
|
12254 if (unlikely((__Pyx_modinit_type_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12255 (void)__Pyx_modinit_variable_import_code();
|
|
jpayne@69
|
12256 (void)__Pyx_modinit_function_import_code();
|
|
jpayne@69
|
12257 /*--- Execution code ---*/
|
|
jpayne@69
|
12258 #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED)
|
|
jpayne@69
|
12259 if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12260 #endif
|
|
jpayne@69
|
12261
|
|
jpayne@69
|
12262 /* "pysam/libcutils.pyx":2
|
|
jpayne@69
|
12263 * # cython: language_level=3
|
|
jpayne@69
|
12264 * import types # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12265 * import sys
|
|
jpayne@69
|
12266 * import string
|
|
jpayne@69
|
12267 */
|
|
jpayne@69
|
12268 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_types, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2, __pyx_L1_error)
|
|
jpayne@69
|
12269 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12270 if (PyDict_SetItem(__pyx_d, __pyx_n_s_types, __pyx_t_2) < 0) __PYX_ERR(0, 2, __pyx_L1_error)
|
|
jpayne@69
|
12271 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12272
|
|
jpayne@69
|
12273 /* "pysam/libcutils.pyx":3
|
|
jpayne@69
|
12274 * # cython: language_level=3
|
|
jpayne@69
|
12275 * import types
|
|
jpayne@69
|
12276 * import sys # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12277 * import string
|
|
jpayne@69
|
12278 * import re
|
|
jpayne@69
|
12279 */
|
|
jpayne@69
|
12280 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_sys, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 3, __pyx_L1_error)
|
|
jpayne@69
|
12281 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12282 if (PyDict_SetItem(__pyx_d, __pyx_n_s_sys, __pyx_t_2) < 0) __PYX_ERR(0, 3, __pyx_L1_error)
|
|
jpayne@69
|
12283 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12284
|
|
jpayne@69
|
12285 /* "pysam/libcutils.pyx":4
|
|
jpayne@69
|
12286 * import types
|
|
jpayne@69
|
12287 * import sys
|
|
jpayne@69
|
12288 * import string # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12289 * import re
|
|
jpayne@69
|
12290 * import tempfile
|
|
jpayne@69
|
12291 */
|
|
jpayne@69
|
12292 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_string, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 4, __pyx_L1_error)
|
|
jpayne@69
|
12293 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12294 if (PyDict_SetItem(__pyx_d, __pyx_n_s_string, __pyx_t_2) < 0) __PYX_ERR(0, 4, __pyx_L1_error)
|
|
jpayne@69
|
12295 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12296
|
|
jpayne@69
|
12297 /* "pysam/libcutils.pyx":5
|
|
jpayne@69
|
12298 * import sys
|
|
jpayne@69
|
12299 * import string
|
|
jpayne@69
|
12300 * import re # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12301 * import tempfile
|
|
jpayne@69
|
12302 * import os
|
|
jpayne@69
|
12303 */
|
|
jpayne@69
|
12304 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_re, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 5, __pyx_L1_error)
|
|
jpayne@69
|
12305 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12306 if (PyDict_SetItem(__pyx_d, __pyx_n_s_re, __pyx_t_2) < 0) __PYX_ERR(0, 5, __pyx_L1_error)
|
|
jpayne@69
|
12307 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12308
|
|
jpayne@69
|
12309 /* "pysam/libcutils.pyx":6
|
|
jpayne@69
|
12310 * import string
|
|
jpayne@69
|
12311 * import re
|
|
jpayne@69
|
12312 * import tempfile # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12313 * import os
|
|
jpayne@69
|
12314 * import io
|
|
jpayne@69
|
12315 */
|
|
jpayne@69
|
12316 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_tempfile, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 6, __pyx_L1_error)
|
|
jpayne@69
|
12317 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12318 if (PyDict_SetItem(__pyx_d, __pyx_n_s_tempfile, __pyx_t_2) < 0) __PYX_ERR(0, 6, __pyx_L1_error)
|
|
jpayne@69
|
12319 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12320
|
|
jpayne@69
|
12321 /* "pysam/libcutils.pyx":7
|
|
jpayne@69
|
12322 * import re
|
|
jpayne@69
|
12323 * import tempfile
|
|
jpayne@69
|
12324 * import os # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12325 * import io
|
|
jpayne@69
|
12326 * from contextlib import contextmanager
|
|
jpayne@69
|
12327 */
|
|
jpayne@69
|
12328 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_os, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 7, __pyx_L1_error)
|
|
jpayne@69
|
12329 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12330 if (PyDict_SetItem(__pyx_d, __pyx_n_s_os, __pyx_t_2) < 0) __PYX_ERR(0, 7, __pyx_L1_error)
|
|
jpayne@69
|
12331 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12332
|
|
jpayne@69
|
12333 /* "pysam/libcutils.pyx":8
|
|
jpayne@69
|
12334 * import tempfile
|
|
jpayne@69
|
12335 * import os
|
|
jpayne@69
|
12336 * import io # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12337 * from contextlib import contextmanager
|
|
jpayne@69
|
12338 * from codecs import register_error
|
|
jpayne@69
|
12339 */
|
|
jpayne@69
|
12340 __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_io, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 8, __pyx_L1_error)
|
|
jpayne@69
|
12341 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12342 if (PyDict_SetItem(__pyx_d, __pyx_n_s_io, __pyx_t_2) < 0) __PYX_ERR(0, 8, __pyx_L1_error)
|
|
jpayne@69
|
12343 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12344
|
|
jpayne@69
|
12345 /* "pysam/libcutils.pyx":9
|
|
jpayne@69
|
12346 * import os
|
|
jpayne@69
|
12347 * import io
|
|
jpayne@69
|
12348 * from contextlib import contextmanager # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12349 * from codecs import register_error
|
|
jpayne@69
|
12350 *
|
|
jpayne@69
|
12351 */
|
|
jpayne@69
|
12352 __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 9, __pyx_L1_error)
|
|
jpayne@69
|
12353 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12354 __Pyx_INCREF(__pyx_n_s_contextmanager);
|
|
jpayne@69
|
12355 __Pyx_GIVEREF(__pyx_n_s_contextmanager);
|
|
jpayne@69
|
12356 if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_contextmanager)) __PYX_ERR(0, 9, __pyx_L1_error);
|
|
jpayne@69
|
12357 __pyx_t_3 = __Pyx_Import(__pyx_n_s_contextlib, __pyx_t_2, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 9, __pyx_L1_error)
|
|
jpayne@69
|
12358 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12359 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12360 __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_contextmanager); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 9, __pyx_L1_error)
|
|
jpayne@69
|
12361 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12362 if (PyDict_SetItem(__pyx_d, __pyx_n_s_contextmanager, __pyx_t_2) < 0) __PYX_ERR(0, 9, __pyx_L1_error)
|
|
jpayne@69
|
12363 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12364 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12365
|
|
jpayne@69
|
12366 /* "pysam/libcutils.pyx":10
|
|
jpayne@69
|
12367 * import io
|
|
jpayne@69
|
12368 * from contextlib import contextmanager
|
|
jpayne@69
|
12369 * from codecs import register_error # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12370 *
|
|
jpayne@69
|
12371 * from cpython.version cimport PY_MAJOR_VERSION, PY_MINOR_VERSION
|
|
jpayne@69
|
12372 */
|
|
jpayne@69
|
12373 __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 10, __pyx_L1_error)
|
|
jpayne@69
|
12374 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12375 __Pyx_INCREF(__pyx_n_s_register_error);
|
|
jpayne@69
|
12376 __Pyx_GIVEREF(__pyx_n_s_register_error);
|
|
jpayne@69
|
12377 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_s_register_error)) __PYX_ERR(0, 10, __pyx_L1_error);
|
|
jpayne@69
|
12378 __pyx_t_2 = __Pyx_Import(__pyx_n_s_codecs, __pyx_t_3, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 10, __pyx_L1_error)
|
|
jpayne@69
|
12379 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12380 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12381 __pyx_t_3 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_register_error); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 10, __pyx_L1_error)
|
|
jpayne@69
|
12382 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12383 if (PyDict_SetItem(__pyx_d, __pyx_n_s_register_error, __pyx_t_3) < 0) __PYX_ERR(0, 10, __pyx_L1_error)
|
|
jpayne@69
|
12384 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12385 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12386
|
|
jpayne@69
|
12387 /* "pysam/libcutils.pyx":32
|
|
jpayne@69
|
12388 * #####################################################################
|
|
jpayne@69
|
12389 * # hard-coded constants
|
|
jpayne@69
|
12390 * cdef int MAX_POS = (1 << 31) - 1 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12391 *
|
|
jpayne@69
|
12392 * #################################################################
|
|
jpayne@69
|
12393 */
|
|
jpayne@69
|
12394 __pyx_v_5pysam_9libcutils_MAX_POS = 0x7fffffff;
|
|
jpayne@69
|
12395
|
|
jpayne@69
|
12396 /* "pysam/libcutils.pyx":36
|
|
jpayne@69
|
12397 * #################################################################
|
|
jpayne@69
|
12398 * # Utility functions for quality string conversions
|
|
jpayne@69
|
12399 * cpdef c_array.array qualitystring_to_array(input_str, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12400 * """convert a qualitystring to an array of quality values."""
|
|
jpayne@69
|
12401 * if input_str is None:
|
|
jpayne@69
|
12402 */
|
|
jpayne@69
|
12403 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_1qualitystring_to_array, 0, __pyx_n_s_qualitystring_to_array, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__17)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 36, __pyx_L1_error)
|
|
jpayne@69
|
12404 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12405 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__18);
|
|
jpayne@69
|
12406 if (PyDict_SetItem(__pyx_d, __pyx_n_s_qualitystring_to_array, __pyx_t_2) < 0) __PYX_ERR(0, 36, __pyx_L1_error)
|
|
jpayne@69
|
12407 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12408
|
|
jpayne@69
|
12409 /* "pysam/libcutils.pyx":45
|
|
jpayne@69
|
12410 *
|
|
jpayne@69
|
12411 *
|
|
jpayne@69
|
12412 * cpdef array_to_qualitystring(c_array.array qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12413 * """convert an array of quality values to a string."""
|
|
jpayne@69
|
12414 * if qualities is None:
|
|
jpayne@69
|
12415 */
|
|
jpayne@69
|
12416 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_3array_to_qualitystring, 0, __pyx_n_s_array_to_qualitystring, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__20)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 45, __pyx_L1_error)
|
|
jpayne@69
|
12417 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12418 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__18);
|
|
jpayne@69
|
12419 if (PyDict_SetItem(__pyx_d, __pyx_n_s_array_to_qualitystring, __pyx_t_2) < 0) __PYX_ERR(0, 45, __pyx_L1_error)
|
|
jpayne@69
|
12420 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12421
|
|
jpayne@69
|
12422 /* "pysam/libcutils.pyx":59
|
|
jpayne@69
|
12423 *
|
|
jpayne@69
|
12424 *
|
|
jpayne@69
|
12425 * cpdef qualities_to_qualitystring(qualities, int offset=33): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12426 * """convert a list or array of quality scores to the string
|
|
jpayne@69
|
12427 * representation used in the SAM format.
|
|
jpayne@69
|
12428 */
|
|
jpayne@69
|
12429 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_5qualities_to_qualitystring, 0, __pyx_n_s_qualities_to_qualitystring, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__21)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 59, __pyx_L1_error)
|
|
jpayne@69
|
12430 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12431 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__18);
|
|
jpayne@69
|
12432 if (PyDict_SetItem(__pyx_d, __pyx_n_s_qualities_to_qualitystring, __pyx_t_2) < 0) __PYX_ERR(0, 59, __pyx_L1_error)
|
|
jpayne@69
|
12433 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12434
|
|
jpayne@69
|
12435 /* "pysam/libcutils.pyx":90
|
|
jpayne@69
|
12436 *
|
|
jpayne@69
|
12437 * # Codec error handler that just interprets each bad byte as ISO-8859-1.
|
|
jpayne@69
|
12438 * def latin1_replace(exception): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12439 * return (chr(exception.object[exception.start]), exception.end)
|
|
jpayne@69
|
12440 *
|
|
jpayne@69
|
12441 */
|
|
jpayne@69
|
12442 __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_7latin1_replace, 0, __pyx_n_s_latin1_replace, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__23)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 90, __pyx_L1_error)
|
|
jpayne@69
|
12443 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12444 if (PyDict_SetItem(__pyx_d, __pyx_n_s_latin1_replace, __pyx_t_2) < 0) __PYX_ERR(0, 90, __pyx_L1_error)
|
|
jpayne@69
|
12445 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12446
|
|
jpayne@69
|
12447 /* "pysam/libcutils.pyx":93
|
|
jpayne@69
|
12448 * return (chr(exception.object[exception.start]), exception.end)
|
|
jpayne@69
|
12449 *
|
|
jpayne@69
|
12450 * register_error('pysam.latin1replace', latin1_replace) # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12451 *
|
|
jpayne@69
|
12452 *
|
|
jpayne@69
|
12453 */
|
|
jpayne@69
|
12454 __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_register_error); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 93, __pyx_L1_error)
|
|
jpayne@69
|
12455 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12456 __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_latin1_replace); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 93, __pyx_L1_error)
|
|
jpayne@69
|
12457 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12458 __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 93, __pyx_L1_error)
|
|
jpayne@69
|
12459 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
12460 __Pyx_INCREF(__pyx_kp_u_pysam_latin1replace);
|
|
jpayne@69
|
12461 __Pyx_GIVEREF(__pyx_kp_u_pysam_latin1replace);
|
|
jpayne@69
|
12462 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_kp_u_pysam_latin1replace)) __PYX_ERR(0, 93, __pyx_L1_error);
|
|
jpayne@69
|
12463 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
12464 if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3)) __PYX_ERR(0, 93, __pyx_L1_error);
|
|
jpayne@69
|
12465 __pyx_t_3 = 0;
|
|
jpayne@69
|
12466 __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 93, __pyx_L1_error)
|
|
jpayne@69
|
12467 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12468 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12469 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
12470 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12471
|
|
jpayne@69
|
12472 /* "pysam/libcutils.pyx":96
|
|
jpayne@69
|
12473 *
|
|
jpayne@69
|
12474 *
|
|
jpayne@69
|
12475 * cdef str ERROR_HANDLER = 'strict' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12476 *
|
|
jpayne@69
|
12477 * cpdef get_encoding_error_handler():
|
|
jpayne@69
|
12478 */
|
|
jpayne@69
|
12479 __Pyx_INCREF(__pyx_n_u_strict);
|
|
jpayne@69
|
12480 __Pyx_XGOTREF(__pyx_v_5pysam_9libcutils_ERROR_HANDLER);
|
|
jpayne@69
|
12481 __Pyx_DECREF_SET(__pyx_v_5pysam_9libcutils_ERROR_HANDLER, __pyx_n_u_strict);
|
|
jpayne@69
|
12482 __Pyx_GIVEREF(__pyx_n_u_strict);
|
|
jpayne@69
|
12483
|
|
jpayne@69
|
12484 /* "pysam/libcutils.pyx":98
|
|
jpayne@69
|
12485 * cdef str ERROR_HANDLER = 'strict'
|
|
jpayne@69
|
12486 *
|
|
jpayne@69
|
12487 * cpdef get_encoding_error_handler(): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12488 * return ERROR_HANDLER
|
|
jpayne@69
|
12489 *
|
|
jpayne@69
|
12490 */
|
|
jpayne@69
|
12491 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_9get_encoding_error_handler, 0, __pyx_n_s_get_encoding_error_handler, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__24)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 98, __pyx_L1_error)
|
|
jpayne@69
|
12492 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12493 if (PyDict_SetItem(__pyx_d, __pyx_n_s_get_encoding_error_handler, __pyx_t_3) < 0) __PYX_ERR(0, 98, __pyx_L1_error)
|
|
jpayne@69
|
12494 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12495
|
|
jpayne@69
|
12496 /* "pysam/libcutils.pyx":101
|
|
jpayne@69
|
12497 * return ERROR_HANDLER
|
|
jpayne@69
|
12498 *
|
|
jpayne@69
|
12499 * cpdef set_encoding_error_handler(name): # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12500 * global ERROR_HANDLER
|
|
jpayne@69
|
12501 * previous = ERROR_HANDLER
|
|
jpayne@69
|
12502 */
|
|
jpayne@69
|
12503 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_11set_encoding_error_handler, 0, __pyx_n_s_set_encoding_error_handler, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__26)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 101, __pyx_L1_error)
|
|
jpayne@69
|
12504 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12505 if (PyDict_SetItem(__pyx_d, __pyx_n_s_set_encoding_error_handler, __pyx_t_3) < 0) __PYX_ERR(0, 101, __pyx_L1_error)
|
|
jpayne@69
|
12506 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12507
|
|
jpayne@69
|
12508 /* "pysam/libcutils.pyx":115
|
|
jpayne@69
|
12509 *
|
|
jpayne@69
|
12510 * # filename encoding (adapted from lxml.etree.pyx)
|
|
jpayne@69
|
12511 * cdef str FILENAME_ENCODING = sys.getfilesystemencoding() or sys.getdefaultencoding() or 'ascii' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12512 * cdef str TEXT_ENCODING = 'utf-8'
|
|
jpayne@69
|
12513 *
|
|
jpayne@69
|
12514 */
|
|
jpayne@69
|
12515 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_sys); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
12516 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
|
12517 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_getfilesystemencoding); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 115, __pyx_L1_error)
|
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jpayne@69
|
12518 __Pyx_GOTREF(__pyx_t_2);
|
|
jpayne@69
|
12519 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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jpayne@69
|
12520 __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 115, __pyx_L1_error)
|
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jpayne@69
|
12521 __Pyx_GOTREF(__pyx_t_4);
|
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jpayne@69
|
12522 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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jpayne@69
|
12523 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 115, __pyx_L1_error)
|
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jpayne@69
|
12524 if (!__pyx_t_5) {
|
|
jpayne@69
|
12525 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
12526 } else {
|
|
jpayne@69
|
12527 if (!(likely(PyUnicode_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None) || __Pyx_RaiseUnexpectedTypeError("unicode", __pyx_t_4))) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
12528 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
12529 __pyx_t_3 = __pyx_t_4;
|
|
jpayne@69
|
12530 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
12531 goto __pyx_L2_bool_binop_done;
|
|
jpayne@69
|
12532 }
|
|
jpayne@69
|
12533 __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_sys); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 115, __pyx_L1_error)
|
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jpayne@69
|
12534 __Pyx_GOTREF(__pyx_t_4);
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jpayne@69
|
12535 __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_getdefaultencoding); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 115, __pyx_L1_error)
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jpayne@69
|
12536 __Pyx_GOTREF(__pyx_t_2);
|
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jpayne@69
|
12537 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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jpayne@69
|
12538 __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 115, __pyx_L1_error)
|
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jpayne@69
|
12539 __Pyx_GOTREF(__pyx_t_4);
|
|
jpayne@69
|
12540 __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
|
|
jpayne@69
|
12541 __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 115, __pyx_L1_error)
|
|
jpayne@69
|
12542 if (!__pyx_t_5) {
|
|
jpayne@69
|
12543 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
12544 } else {
|
|
jpayne@69
|
12545 if (!(likely(PyUnicode_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None) || __Pyx_RaiseUnexpectedTypeError("unicode", __pyx_t_4))) __PYX_ERR(0, 115, __pyx_L1_error)
|
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jpayne@69
|
12546 __Pyx_INCREF(__pyx_t_4);
|
|
jpayne@69
|
12547 __pyx_t_3 = __pyx_t_4;
|
|
jpayne@69
|
12548 __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
|
|
jpayne@69
|
12549 goto __pyx_L2_bool_binop_done;
|
|
jpayne@69
|
12550 }
|
|
jpayne@69
|
12551 __Pyx_INCREF(__pyx_n_u_ascii);
|
|
jpayne@69
|
12552 __pyx_t_3 = __pyx_n_u_ascii;
|
|
jpayne@69
|
12553 __pyx_L2_bool_binop_done:;
|
|
jpayne@69
|
12554 __Pyx_XGOTREF(__pyx_v_5pysam_9libcutils_FILENAME_ENCODING);
|
|
jpayne@69
|
12555 __Pyx_DECREF_SET(__pyx_v_5pysam_9libcutils_FILENAME_ENCODING, ((PyObject*)__pyx_t_3));
|
|
jpayne@69
|
12556 __Pyx_GIVEREF(__pyx_t_3);
|
|
jpayne@69
|
12557 __pyx_t_3 = 0;
|
|
jpayne@69
|
12558
|
|
jpayne@69
|
12559 /* "pysam/libcutils.pyx":116
|
|
jpayne@69
|
12560 * # filename encoding (adapted from lxml.etree.pyx)
|
|
jpayne@69
|
12561 * cdef str FILENAME_ENCODING = sys.getfilesystemencoding() or sys.getdefaultencoding() or 'ascii'
|
|
jpayne@69
|
12562 * cdef str TEXT_ENCODING = 'utf-8' # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12563 *
|
|
jpayne@69
|
12564 * cdef bytes encode_filename(object filename):
|
|
jpayne@69
|
12565 */
|
|
jpayne@69
|
12566 __Pyx_INCREF(__pyx_kp_u_utf_8);
|
|
jpayne@69
|
12567 __Pyx_XGOTREF(__pyx_v_5pysam_9libcutils_TEXT_ENCODING);
|
|
jpayne@69
|
12568 __Pyx_DECREF_SET(__pyx_v_5pysam_9libcutils_TEXT_ENCODING, __pyx_kp_u_utf_8);
|
|
jpayne@69
|
12569 __Pyx_GIVEREF(__pyx_kp_u_utf_8);
|
|
jpayne@69
|
12570
|
|
jpayne@69
|
12571 /* "pysam/libcutils.pyx":178
|
|
jpayne@69
|
12572 *
|
|
jpayne@69
|
12573 *
|
|
jpayne@69
|
12574 * cpdef parse_region(contig=None, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12575 * start=None,
|
|
jpayne@69
|
12576 * stop=None,
|
|
jpayne@69
|
12577 */
|
|
jpayne@69
|
12578 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_13parse_region, 0, __pyx_n_s_parse_region, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__28)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 178, __pyx_L1_error)
|
|
jpayne@69
|
12579 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
12580 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__29);
|
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jpayne@69
|
12581 if (PyDict_SetItem(__pyx_d, __pyx_n_s_parse_region, __pyx_t_3) < 0) __PYX_ERR(0, 178, __pyx_L1_error)
|
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jpayne@69
|
12582 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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|
jpayne@69
|
12583
|
|
jpayne@69
|
12584 /* "pysam/libcutils.pyx":276
|
|
jpayne@69
|
12585 *
|
|
jpayne@69
|
12586 *
|
|
jpayne@69
|
12587 * def _pysam_dispatch(collection, # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12588 * method,
|
|
jpayne@69
|
12589 * args=None,
|
|
jpayne@69
|
12590 */
|
|
jpayne@69
|
12591 __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libcutils_15_pysam_dispatch, 0, __pyx_n_s_pysam_dispatch, NULL, __pyx_n_s_pysam_libcutils, __pyx_d, ((PyObject *)__pyx_codeobj__31)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 276, __pyx_L1_error)
|
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jpayne@69
|
12592 __Pyx_GOTREF(__pyx_t_3);
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jpayne@69
|
12593 __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__32);
|
|
jpayne@69
|
12594 if (PyDict_SetItem(__pyx_d, __pyx_n_s_pysam_dispatch, __pyx_t_3) < 0) __PYX_ERR(0, 276, __pyx_L1_error)
|
|
jpayne@69
|
12595 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12596
|
|
jpayne@69
|
12597 /* "pysam/libcutils.pyx":437
|
|
jpayne@69
|
12598 *
|
|
jpayne@69
|
12599 *
|
|
jpayne@69
|
12600 * __all__ = [ # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12601 * "qualitystring_to_array",
|
|
jpayne@69
|
12602 * "array_to_qualitystring",
|
|
jpayne@69
|
12603 */
|
|
jpayne@69
|
12604 __pyx_t_3 = PyList_New(5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 437, __pyx_L1_error)
|
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jpayne@69
|
12605 __Pyx_GOTREF(__pyx_t_3);
|
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jpayne@69
|
12606 __Pyx_INCREF(__pyx_n_u_qualitystring_to_array);
|
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jpayne@69
|
12607 __Pyx_GIVEREF(__pyx_n_u_qualitystring_to_array);
|
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jpayne@69
|
12608 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_u_qualitystring_to_array)) __PYX_ERR(0, 437, __pyx_L1_error);
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jpayne@69
|
12609 __Pyx_INCREF(__pyx_n_u_array_to_qualitystring);
|
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jpayne@69
|
12610 __Pyx_GIVEREF(__pyx_n_u_array_to_qualitystring);
|
|
jpayne@69
|
12611 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 1, __pyx_n_u_array_to_qualitystring)) __PYX_ERR(0, 437, __pyx_L1_error);
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jpayne@69
|
12612 __Pyx_INCREF(__pyx_n_u_qualities_to_qualitystring);
|
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jpayne@69
|
12613 __Pyx_GIVEREF(__pyx_n_u_qualities_to_qualitystring);
|
|
jpayne@69
|
12614 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 2, __pyx_n_u_qualities_to_qualitystring)) __PYX_ERR(0, 437, __pyx_L1_error);
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jpayne@69
|
12615 __Pyx_INCREF(__pyx_n_u_get_encoding_error_handler);
|
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jpayne@69
|
12616 __Pyx_GIVEREF(__pyx_n_u_get_encoding_error_handler);
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jpayne@69
|
12617 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 3, __pyx_n_u_get_encoding_error_handler)) __PYX_ERR(0, 437, __pyx_L1_error);
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jpayne@69
|
12618 __Pyx_INCREF(__pyx_n_u_set_encoding_error_handler);
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jpayne@69
|
12619 __Pyx_GIVEREF(__pyx_n_u_set_encoding_error_handler);
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jpayne@69
|
12620 if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 4, __pyx_n_u_set_encoding_error_handler)) __PYX_ERR(0, 437, __pyx_L1_error);
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jpayne@69
|
12621 if (PyDict_SetItem(__pyx_d, __pyx_n_s_all, __pyx_t_3) < 0) __PYX_ERR(0, 437, __pyx_L1_error)
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jpayne@69
|
12622 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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jpayne@69
|
12623
|
|
jpayne@69
|
12624 /* "pysam/libcutils.pyx":1
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|
jpayne@69
|
12625 * # cython: language_level=3 # <<<<<<<<<<<<<<
|
|
jpayne@69
|
12626 * import types
|
|
jpayne@69
|
12627 * import sys
|
|
jpayne@69
|
12628 */
|
|
jpayne@69
|
12629 __pyx_t_3 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error)
|
|
jpayne@69
|
12630 __Pyx_GOTREF(__pyx_t_3);
|
|
jpayne@69
|
12631 if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
|
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jpayne@69
|
12632 __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
|
|
jpayne@69
|
12633
|
|
jpayne@69
|
12634 /*--- Wrapped vars code ---*/
|
|
jpayne@69
|
12635
|
|
jpayne@69
|
12636 goto __pyx_L0;
|
|
jpayne@69
|
12637 __pyx_L1_error:;
|
|
jpayne@69
|
12638 __Pyx_XDECREF(__pyx_t_2);
|
|
jpayne@69
|
12639 __Pyx_XDECREF(__pyx_t_3);
|
|
jpayne@69
|
12640 __Pyx_XDECREF(__pyx_t_4);
|
|
jpayne@69
|
12641 if (__pyx_m) {
|
|
jpayne@69
|
12642 if (__pyx_d && stringtab_initialized) {
|
|
jpayne@69
|
12643 __Pyx_AddTraceback("init pysam.libcutils", __pyx_clineno, __pyx_lineno, __pyx_filename);
|
|
jpayne@69
|
12644 }
|
|
jpayne@69
|
12645 #if !CYTHON_USE_MODULE_STATE
|
|
jpayne@69
|
12646 Py_CLEAR(__pyx_m);
|
|
jpayne@69
|
12647 #else
|
|
jpayne@69
|
12648 Py_DECREF(__pyx_m);
|
|
jpayne@69
|
12649 if (pystate_addmodule_run) {
|
|
jpayne@69
|
12650 PyObject *tp, *value, *tb;
|
|
jpayne@69
|
12651 PyErr_Fetch(&tp, &value, &tb);
|
|
jpayne@69
|
12652 PyState_RemoveModule(&__pyx_moduledef);
|
|
jpayne@69
|
12653 PyErr_Restore(tp, value, tb);
|
|
jpayne@69
|
12654 }
|
|
jpayne@69
|
12655 #endif
|
|
jpayne@69
|
12656 } else if (!PyErr_Occurred()) {
|
|
jpayne@69
|
12657 PyErr_SetString(PyExc_ImportError, "init pysam.libcutils");
|
|
jpayne@69
|
12658 }
|
|
jpayne@69
|
12659 __pyx_L0:;
|
|
jpayne@69
|
12660 __Pyx_RefNannyFinishContext();
|
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jpayne@69
|
12661 #if CYTHON_PEP489_MULTI_PHASE_INIT
|
|
jpayne@69
|
12662 return (__pyx_m != NULL) ? 0 : -1;
|
|
jpayne@69
|
12663 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
12664 return __pyx_m;
|
|
jpayne@69
|
12665 #else
|
|
jpayne@69
|
12666 return;
|
|
jpayne@69
|
12667 #endif
|
|
jpayne@69
|
12668 }
|
|
jpayne@69
|
12669 /* #### Code section: cleanup_globals ### */
|
|
jpayne@69
|
12670 /* #### Code section: cleanup_module ### */
|
|
jpayne@69
|
12671 /* #### Code section: main_method ### */
|
|
jpayne@69
|
12672 /* #### Code section: utility_code_pragmas ### */
|
|
jpayne@69
|
12673 #ifdef _MSC_VER
|
|
jpayne@69
|
12674 #pragma warning( push )
|
|
jpayne@69
|
12675 /* Warning 4127: conditional expression is constant
|
|
jpayne@69
|
12676 * Cython uses constant conditional expressions to allow in inline functions to be optimized at
|
|
jpayne@69
|
12677 * compile-time, so this warning is not useful
|
|
jpayne@69
|
12678 */
|
|
jpayne@69
|
12679 #pragma warning( disable : 4127 )
|
|
jpayne@69
|
12680 #endif
|
|
jpayne@69
|
12681
|
|
jpayne@69
|
12682
|
|
jpayne@69
|
12683
|
|
jpayne@69
|
12684 /* #### Code section: utility_code_def ### */
|
|
jpayne@69
|
12685
|
|
jpayne@69
|
12686 /* --- Runtime support code --- */
|
|
jpayne@69
|
12687 /* Refnanny */
|
|
jpayne@69
|
12688 #if CYTHON_REFNANNY
|
|
jpayne@69
|
12689 static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
|
|
jpayne@69
|
12690 PyObject *m = NULL, *p = NULL;
|
|
jpayne@69
|
12691 void *r = NULL;
|
|
jpayne@69
|
12692 m = PyImport_ImportModule(modname);
|
|
jpayne@69
|
12693 if (!m) goto end;
|
|
jpayne@69
|
12694 p = PyObject_GetAttrString(m, "RefNannyAPI");
|
|
jpayne@69
|
12695 if (!p) goto end;
|
|
jpayne@69
|
12696 r = PyLong_AsVoidPtr(p);
|
|
jpayne@69
|
12697 end:
|
|
jpayne@69
|
12698 Py_XDECREF(p);
|
|
jpayne@69
|
12699 Py_XDECREF(m);
|
|
jpayne@69
|
12700 return (__Pyx_RefNannyAPIStruct *)r;
|
|
jpayne@69
|
12701 }
|
|
jpayne@69
|
12702 #endif
|
|
jpayne@69
|
12703
|
|
jpayne@69
|
12704 /* PyErrExceptionMatches */
|
|
jpayne@69
|
12705 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
12706 static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
|
|
jpayne@69
|
12707 Py_ssize_t i, n;
|
|
jpayne@69
|
12708 n = PyTuple_GET_SIZE(tuple);
|
|
jpayne@69
|
12709 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
12710 for (i=0; i<n; i++) {
|
|
jpayne@69
|
12711 if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
|
|
jpayne@69
|
12712 }
|
|
jpayne@69
|
12713 #endif
|
|
jpayne@69
|
12714 for (i=0; i<n; i++) {
|
|
jpayne@69
|
12715 if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1;
|
|
jpayne@69
|
12716 }
|
|
jpayne@69
|
12717 return 0;
|
|
jpayne@69
|
12718 }
|
|
jpayne@69
|
12719 static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
|
|
jpayne@69
|
12720 int result;
|
|
jpayne@69
|
12721 PyObject *exc_type;
|
|
jpayne@69
|
12722 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
12723 PyObject *current_exception = tstate->current_exception;
|
|
jpayne@69
|
12724 if (unlikely(!current_exception)) return 0;
|
|
jpayne@69
|
12725 exc_type = (PyObject*) Py_TYPE(current_exception);
|
|
jpayne@69
|
12726 if (exc_type == err) return 1;
|
|
jpayne@69
|
12727 #else
|
|
jpayne@69
|
12728 exc_type = tstate->curexc_type;
|
|
jpayne@69
|
12729 if (exc_type == err) return 1;
|
|
jpayne@69
|
12730 if (unlikely(!exc_type)) return 0;
|
|
jpayne@69
|
12731 #endif
|
|
jpayne@69
|
12732 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
12733 Py_INCREF(exc_type);
|
|
jpayne@69
|
12734 #endif
|
|
jpayne@69
|
12735 if (unlikely(PyTuple_Check(err))) {
|
|
jpayne@69
|
12736 result = __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err);
|
|
jpayne@69
|
12737 } else {
|
|
jpayne@69
|
12738 result = __Pyx_PyErr_GivenExceptionMatches(exc_type, err);
|
|
jpayne@69
|
12739 }
|
|
jpayne@69
|
12740 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
12741 Py_DECREF(exc_type);
|
|
jpayne@69
|
12742 #endif
|
|
jpayne@69
|
12743 return result;
|
|
jpayne@69
|
12744 }
|
|
jpayne@69
|
12745 #endif
|
|
jpayne@69
|
12746
|
|
jpayne@69
|
12747 /* PyErrFetchRestore */
|
|
jpayne@69
|
12748 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
12749 static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
|
|
jpayne@69
|
12750 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
12751 PyObject *tmp_value;
|
|
jpayne@69
|
12752 assert(type == NULL || (value != NULL && type == (PyObject*) Py_TYPE(value)));
|
|
jpayne@69
|
12753 if (value) {
|
|
jpayne@69
|
12754 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
12755 if (unlikely(((PyBaseExceptionObject*) value)->traceback != tb))
|
|
jpayne@69
|
12756 #endif
|
|
jpayne@69
|
12757 PyException_SetTraceback(value, tb);
|
|
jpayne@69
|
12758 }
|
|
jpayne@69
|
12759 tmp_value = tstate->current_exception;
|
|
jpayne@69
|
12760 tstate->current_exception = value;
|
|
jpayne@69
|
12761 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
12762 Py_XDECREF(type);
|
|
jpayne@69
|
12763 Py_XDECREF(tb);
|
|
jpayne@69
|
12764 #else
|
|
jpayne@69
|
12765 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
12766 tmp_type = tstate->curexc_type;
|
|
jpayne@69
|
12767 tmp_value = tstate->curexc_value;
|
|
jpayne@69
|
12768 tmp_tb = tstate->curexc_traceback;
|
|
jpayne@69
|
12769 tstate->curexc_type = type;
|
|
jpayne@69
|
12770 tstate->curexc_value = value;
|
|
jpayne@69
|
12771 tstate->curexc_traceback = tb;
|
|
jpayne@69
|
12772 Py_XDECREF(tmp_type);
|
|
jpayne@69
|
12773 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
12774 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
12775 #endif
|
|
jpayne@69
|
12776 }
|
|
jpayne@69
|
12777 static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
|
|
jpayne@69
|
12778 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
12779 PyObject* exc_value;
|
|
jpayne@69
|
12780 exc_value = tstate->current_exception;
|
|
jpayne@69
|
12781 tstate->current_exception = 0;
|
|
jpayne@69
|
12782 *value = exc_value;
|
|
jpayne@69
|
12783 *type = NULL;
|
|
jpayne@69
|
12784 *tb = NULL;
|
|
jpayne@69
|
12785 if (exc_value) {
|
|
jpayne@69
|
12786 *type = (PyObject*) Py_TYPE(exc_value);
|
|
jpayne@69
|
12787 Py_INCREF(*type);
|
|
jpayne@69
|
12788 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
12789 *tb = ((PyBaseExceptionObject*) exc_value)->traceback;
|
|
jpayne@69
|
12790 Py_XINCREF(*tb);
|
|
jpayne@69
|
12791 #else
|
|
jpayne@69
|
12792 *tb = PyException_GetTraceback(exc_value);
|
|
jpayne@69
|
12793 #endif
|
|
jpayne@69
|
12794 }
|
|
jpayne@69
|
12795 #else
|
|
jpayne@69
|
12796 *type = tstate->curexc_type;
|
|
jpayne@69
|
12797 *value = tstate->curexc_value;
|
|
jpayne@69
|
12798 *tb = tstate->curexc_traceback;
|
|
jpayne@69
|
12799 tstate->curexc_type = 0;
|
|
jpayne@69
|
12800 tstate->curexc_value = 0;
|
|
jpayne@69
|
12801 tstate->curexc_traceback = 0;
|
|
jpayne@69
|
12802 #endif
|
|
jpayne@69
|
12803 }
|
|
jpayne@69
|
12804 #endif
|
|
jpayne@69
|
12805
|
|
jpayne@69
|
12806 /* PyObjectGetAttrStr */
|
|
jpayne@69
|
12807 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
12808 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
|
|
jpayne@69
|
12809 PyTypeObject* tp = Py_TYPE(obj);
|
|
jpayne@69
|
12810 if (likely(tp->tp_getattro))
|
|
jpayne@69
|
12811 return tp->tp_getattro(obj, attr_name);
|
|
jpayne@69
|
12812 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
12813 if (likely(tp->tp_getattr))
|
|
jpayne@69
|
12814 return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
|
|
jpayne@69
|
12815 #endif
|
|
jpayne@69
|
12816 return PyObject_GetAttr(obj, attr_name);
|
|
jpayne@69
|
12817 }
|
|
jpayne@69
|
12818 #endif
|
|
jpayne@69
|
12819
|
|
jpayne@69
|
12820 /* PyObjectGetAttrStrNoError */
|
|
jpayne@69
|
12821 #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1
|
|
jpayne@69
|
12822 static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) {
|
|
jpayne@69
|
12823 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
12824 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
12825 if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError)))
|
|
jpayne@69
|
12826 __Pyx_PyErr_Clear();
|
|
jpayne@69
|
12827 }
|
|
jpayne@69
|
12828 #endif
|
|
jpayne@69
|
12829 static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) {
|
|
jpayne@69
|
12830 PyObject *result;
|
|
jpayne@69
|
12831 #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
|
|
jpayne@69
|
12832 (void) PyObject_GetOptionalAttr(obj, attr_name, &result);
|
|
jpayne@69
|
12833 return result;
|
|
jpayne@69
|
12834 #else
|
|
jpayne@69
|
12835 #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1
|
|
jpayne@69
|
12836 PyTypeObject* tp = Py_TYPE(obj);
|
|
jpayne@69
|
12837 if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) {
|
|
jpayne@69
|
12838 return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1);
|
|
jpayne@69
|
12839 }
|
|
jpayne@69
|
12840 #endif
|
|
jpayne@69
|
12841 result = __Pyx_PyObject_GetAttrStr(obj, attr_name);
|
|
jpayne@69
|
12842 if (unlikely(!result)) {
|
|
jpayne@69
|
12843 __Pyx_PyObject_GetAttrStr_ClearAttributeError();
|
|
jpayne@69
|
12844 }
|
|
jpayne@69
|
12845 return result;
|
|
jpayne@69
|
12846 #endif
|
|
jpayne@69
|
12847 }
|
|
jpayne@69
|
12848
|
|
jpayne@69
|
12849 /* GetBuiltinName */
|
|
jpayne@69
|
12850 static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
|
|
jpayne@69
|
12851 PyObject* result = __Pyx_PyObject_GetAttrStrNoError(__pyx_b, name);
|
|
jpayne@69
|
12852 if (unlikely(!result) && !PyErr_Occurred()) {
|
|
jpayne@69
|
12853 PyErr_Format(PyExc_NameError,
|
|
jpayne@69
|
12854 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
12855 "name '%U' is not defined", name);
|
|
jpayne@69
|
12856 #else
|
|
jpayne@69
|
12857 "name '%.200s' is not defined", PyString_AS_STRING(name));
|
|
jpayne@69
|
12858 #endif
|
|
jpayne@69
|
12859 }
|
|
jpayne@69
|
12860 return result;
|
|
jpayne@69
|
12861 }
|
|
jpayne@69
|
12862
|
|
jpayne@69
|
12863 /* TupleAndListFromArray */
|
|
jpayne@69
|
12864 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
12865 static CYTHON_INLINE void __Pyx_copy_object_array(PyObject *const *CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) {
|
|
jpayne@69
|
12866 PyObject *v;
|
|
jpayne@69
|
12867 Py_ssize_t i;
|
|
jpayne@69
|
12868 for (i = 0; i < length; i++) {
|
|
jpayne@69
|
12869 v = dest[i] = src[i];
|
|
jpayne@69
|
12870 Py_INCREF(v);
|
|
jpayne@69
|
12871 }
|
|
jpayne@69
|
12872 }
|
|
jpayne@69
|
12873 static CYTHON_INLINE PyObject *
|
|
jpayne@69
|
12874 __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n)
|
|
jpayne@69
|
12875 {
|
|
jpayne@69
|
12876 PyObject *res;
|
|
jpayne@69
|
12877 if (n <= 0) {
|
|
jpayne@69
|
12878 Py_INCREF(__pyx_empty_tuple);
|
|
jpayne@69
|
12879 return __pyx_empty_tuple;
|
|
jpayne@69
|
12880 }
|
|
jpayne@69
|
12881 res = PyTuple_New(n);
|
|
jpayne@69
|
12882 if (unlikely(res == NULL)) return NULL;
|
|
jpayne@69
|
12883 __Pyx_copy_object_array(src, ((PyTupleObject*)res)->ob_item, n);
|
|
jpayne@69
|
12884 return res;
|
|
jpayne@69
|
12885 }
|
|
jpayne@69
|
12886 static CYTHON_INLINE PyObject *
|
|
jpayne@69
|
12887 __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n)
|
|
jpayne@69
|
12888 {
|
|
jpayne@69
|
12889 PyObject *res;
|
|
jpayne@69
|
12890 if (n <= 0) {
|
|
jpayne@69
|
12891 return PyList_New(0);
|
|
jpayne@69
|
12892 }
|
|
jpayne@69
|
12893 res = PyList_New(n);
|
|
jpayne@69
|
12894 if (unlikely(res == NULL)) return NULL;
|
|
jpayne@69
|
12895 __Pyx_copy_object_array(src, ((PyListObject*)res)->ob_item, n);
|
|
jpayne@69
|
12896 return res;
|
|
jpayne@69
|
12897 }
|
|
jpayne@69
|
12898 #endif
|
|
jpayne@69
|
12899
|
|
jpayne@69
|
12900 /* BytesEquals */
|
|
jpayne@69
|
12901 static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
|
|
jpayne@69
|
12902 #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
12903 return PyObject_RichCompareBool(s1, s2, equals);
|
|
jpayne@69
|
12904 #else
|
|
jpayne@69
|
12905 if (s1 == s2) {
|
|
jpayne@69
|
12906 return (equals == Py_EQ);
|
|
jpayne@69
|
12907 } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
|
|
jpayne@69
|
12908 const char *ps1, *ps2;
|
|
jpayne@69
|
12909 Py_ssize_t length = PyBytes_GET_SIZE(s1);
|
|
jpayne@69
|
12910 if (length != PyBytes_GET_SIZE(s2))
|
|
jpayne@69
|
12911 return (equals == Py_NE);
|
|
jpayne@69
|
12912 ps1 = PyBytes_AS_STRING(s1);
|
|
jpayne@69
|
12913 ps2 = PyBytes_AS_STRING(s2);
|
|
jpayne@69
|
12914 if (ps1[0] != ps2[0]) {
|
|
jpayne@69
|
12915 return (equals == Py_NE);
|
|
jpayne@69
|
12916 } else if (length == 1) {
|
|
jpayne@69
|
12917 return (equals == Py_EQ);
|
|
jpayne@69
|
12918 } else {
|
|
jpayne@69
|
12919 int result;
|
|
jpayne@69
|
12920 #if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000)
|
|
jpayne@69
|
12921 Py_hash_t hash1, hash2;
|
|
jpayne@69
|
12922 hash1 = ((PyBytesObject*)s1)->ob_shash;
|
|
jpayne@69
|
12923 hash2 = ((PyBytesObject*)s2)->ob_shash;
|
|
jpayne@69
|
12924 if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
|
|
jpayne@69
|
12925 return (equals == Py_NE);
|
|
jpayne@69
|
12926 }
|
|
jpayne@69
|
12927 #endif
|
|
jpayne@69
|
12928 result = memcmp(ps1, ps2, (size_t)length);
|
|
jpayne@69
|
12929 return (equals == Py_EQ) ? (result == 0) : (result != 0);
|
|
jpayne@69
|
12930 }
|
|
jpayne@69
|
12931 } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
|
|
jpayne@69
|
12932 return (equals == Py_NE);
|
|
jpayne@69
|
12933 } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
|
|
jpayne@69
|
12934 return (equals == Py_NE);
|
|
jpayne@69
|
12935 } else {
|
|
jpayne@69
|
12936 int result;
|
|
jpayne@69
|
12937 PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
|
|
jpayne@69
|
12938 if (!py_result)
|
|
jpayne@69
|
12939 return -1;
|
|
jpayne@69
|
12940 result = __Pyx_PyObject_IsTrue(py_result);
|
|
jpayne@69
|
12941 Py_DECREF(py_result);
|
|
jpayne@69
|
12942 return result;
|
|
jpayne@69
|
12943 }
|
|
jpayne@69
|
12944 #endif
|
|
jpayne@69
|
12945 }
|
|
jpayne@69
|
12946
|
|
jpayne@69
|
12947 /* UnicodeEquals */
|
|
jpayne@69
|
12948 static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
|
|
jpayne@69
|
12949 #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
12950 return PyObject_RichCompareBool(s1, s2, equals);
|
|
jpayne@69
|
12951 #else
|
|
jpayne@69
|
12952 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
12953 PyObject* owned_ref = NULL;
|
|
jpayne@69
|
12954 #endif
|
|
jpayne@69
|
12955 int s1_is_unicode, s2_is_unicode;
|
|
jpayne@69
|
12956 if (s1 == s2) {
|
|
jpayne@69
|
12957 goto return_eq;
|
|
jpayne@69
|
12958 }
|
|
jpayne@69
|
12959 s1_is_unicode = PyUnicode_CheckExact(s1);
|
|
jpayne@69
|
12960 s2_is_unicode = PyUnicode_CheckExact(s2);
|
|
jpayne@69
|
12961 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
12962 if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
|
|
jpayne@69
|
12963 owned_ref = PyUnicode_FromObject(s2);
|
|
jpayne@69
|
12964 if (unlikely(!owned_ref))
|
|
jpayne@69
|
12965 return -1;
|
|
jpayne@69
|
12966 s2 = owned_ref;
|
|
jpayne@69
|
12967 s2_is_unicode = 1;
|
|
jpayne@69
|
12968 } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
|
|
jpayne@69
|
12969 owned_ref = PyUnicode_FromObject(s1);
|
|
jpayne@69
|
12970 if (unlikely(!owned_ref))
|
|
jpayne@69
|
12971 return -1;
|
|
jpayne@69
|
12972 s1 = owned_ref;
|
|
jpayne@69
|
12973 s1_is_unicode = 1;
|
|
jpayne@69
|
12974 } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
|
|
jpayne@69
|
12975 return __Pyx_PyBytes_Equals(s1, s2, equals);
|
|
jpayne@69
|
12976 }
|
|
jpayne@69
|
12977 #endif
|
|
jpayne@69
|
12978 if (s1_is_unicode & s2_is_unicode) {
|
|
jpayne@69
|
12979 Py_ssize_t length;
|
|
jpayne@69
|
12980 int kind;
|
|
jpayne@69
|
12981 void *data1, *data2;
|
|
jpayne@69
|
12982 if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
|
|
jpayne@69
|
12983 return -1;
|
|
jpayne@69
|
12984 length = __Pyx_PyUnicode_GET_LENGTH(s1);
|
|
jpayne@69
|
12985 if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
|
|
jpayne@69
|
12986 goto return_ne;
|
|
jpayne@69
|
12987 }
|
|
jpayne@69
|
12988 #if CYTHON_USE_UNICODE_INTERNALS
|
|
jpayne@69
|
12989 {
|
|
jpayne@69
|
12990 Py_hash_t hash1, hash2;
|
|
jpayne@69
|
12991 #if CYTHON_PEP393_ENABLED
|
|
jpayne@69
|
12992 hash1 = ((PyASCIIObject*)s1)->hash;
|
|
jpayne@69
|
12993 hash2 = ((PyASCIIObject*)s2)->hash;
|
|
jpayne@69
|
12994 #else
|
|
jpayne@69
|
12995 hash1 = ((PyUnicodeObject*)s1)->hash;
|
|
jpayne@69
|
12996 hash2 = ((PyUnicodeObject*)s2)->hash;
|
|
jpayne@69
|
12997 #endif
|
|
jpayne@69
|
12998 if (hash1 != hash2 && hash1 != -1 && hash2 != -1) {
|
|
jpayne@69
|
12999 goto return_ne;
|
|
jpayne@69
|
13000 }
|
|
jpayne@69
|
13001 }
|
|
jpayne@69
|
13002 #endif
|
|
jpayne@69
|
13003 kind = __Pyx_PyUnicode_KIND(s1);
|
|
jpayne@69
|
13004 if (kind != __Pyx_PyUnicode_KIND(s2)) {
|
|
jpayne@69
|
13005 goto return_ne;
|
|
jpayne@69
|
13006 }
|
|
jpayne@69
|
13007 data1 = __Pyx_PyUnicode_DATA(s1);
|
|
jpayne@69
|
13008 data2 = __Pyx_PyUnicode_DATA(s2);
|
|
jpayne@69
|
13009 if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
|
|
jpayne@69
|
13010 goto return_ne;
|
|
jpayne@69
|
13011 } else if (length == 1) {
|
|
jpayne@69
|
13012 goto return_eq;
|
|
jpayne@69
|
13013 } else {
|
|
jpayne@69
|
13014 int result = memcmp(data1, data2, (size_t)(length * kind));
|
|
jpayne@69
|
13015 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13016 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
13017 #endif
|
|
jpayne@69
|
13018 return (equals == Py_EQ) ? (result == 0) : (result != 0);
|
|
jpayne@69
|
13019 }
|
|
jpayne@69
|
13020 } else if ((s1 == Py_None) & s2_is_unicode) {
|
|
jpayne@69
|
13021 goto return_ne;
|
|
jpayne@69
|
13022 } else if ((s2 == Py_None) & s1_is_unicode) {
|
|
jpayne@69
|
13023 goto return_ne;
|
|
jpayne@69
|
13024 } else {
|
|
jpayne@69
|
13025 int result;
|
|
jpayne@69
|
13026 PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
|
|
jpayne@69
|
13027 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13028 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
13029 #endif
|
|
jpayne@69
|
13030 if (!py_result)
|
|
jpayne@69
|
13031 return -1;
|
|
jpayne@69
|
13032 result = __Pyx_PyObject_IsTrue(py_result);
|
|
jpayne@69
|
13033 Py_DECREF(py_result);
|
|
jpayne@69
|
13034 return result;
|
|
jpayne@69
|
13035 }
|
|
jpayne@69
|
13036 return_eq:
|
|
jpayne@69
|
13037 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13038 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
13039 #endif
|
|
jpayne@69
|
13040 return (equals == Py_EQ);
|
|
jpayne@69
|
13041 return_ne:
|
|
jpayne@69
|
13042 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13043 Py_XDECREF(owned_ref);
|
|
jpayne@69
|
13044 #endif
|
|
jpayne@69
|
13045 return (equals == Py_NE);
|
|
jpayne@69
|
13046 #endif
|
|
jpayne@69
|
13047 }
|
|
jpayne@69
|
13048
|
|
jpayne@69
|
13049 /* fastcall */
|
|
jpayne@69
|
13050 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
13051 static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s)
|
|
jpayne@69
|
13052 {
|
|
jpayne@69
|
13053 Py_ssize_t i, n = PyTuple_GET_SIZE(kwnames);
|
|
jpayne@69
|
13054 for (i = 0; i < n; i++)
|
|
jpayne@69
|
13055 {
|
|
jpayne@69
|
13056 if (s == PyTuple_GET_ITEM(kwnames, i)) return kwvalues[i];
|
|
jpayne@69
|
13057 }
|
|
jpayne@69
|
13058 for (i = 0; i < n; i++)
|
|
jpayne@69
|
13059 {
|
|
jpayne@69
|
13060 int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ);
|
|
jpayne@69
|
13061 if (unlikely(eq != 0)) {
|
|
jpayne@69
|
13062 if (unlikely(eq < 0)) return NULL;
|
|
jpayne@69
|
13063 return kwvalues[i];
|
|
jpayne@69
|
13064 }
|
|
jpayne@69
|
13065 }
|
|
jpayne@69
|
13066 return NULL;
|
|
jpayne@69
|
13067 }
|
|
jpayne@69
|
13068 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
|
|
jpayne@69
|
13069 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) {
|
|
jpayne@69
|
13070 Py_ssize_t i, nkwargs = PyTuple_GET_SIZE(kwnames);
|
|
jpayne@69
|
13071 PyObject *dict;
|
|
jpayne@69
|
13072 dict = PyDict_New();
|
|
jpayne@69
|
13073 if (unlikely(!dict))
|
|
jpayne@69
|
13074 return NULL;
|
|
jpayne@69
|
13075 for (i=0; i<nkwargs; i++) {
|
|
jpayne@69
|
13076 PyObject *key = PyTuple_GET_ITEM(kwnames, i);
|
|
jpayne@69
|
13077 if (unlikely(PyDict_SetItem(dict, key, kwvalues[i]) < 0))
|
|
jpayne@69
|
13078 goto bad;
|
|
jpayne@69
|
13079 }
|
|
jpayne@69
|
13080 return dict;
|
|
jpayne@69
|
13081 bad:
|
|
jpayne@69
|
13082 Py_DECREF(dict);
|
|
jpayne@69
|
13083 return NULL;
|
|
jpayne@69
|
13084 }
|
|
jpayne@69
|
13085 #endif
|
|
jpayne@69
|
13086 #endif
|
|
jpayne@69
|
13087
|
|
jpayne@69
|
13088 /* PyObjectCall */
|
|
jpayne@69
|
13089 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
13090 static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
|
|
jpayne@69
|
13091 PyObject *result;
|
|
jpayne@69
|
13092 ternaryfunc call = Py_TYPE(func)->tp_call;
|
|
jpayne@69
|
13093 if (unlikely(!call))
|
|
jpayne@69
|
13094 return PyObject_Call(func, arg, kw);
|
|
jpayne@69
|
13095 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13096 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
|
|
jpayne@69
|
13097 return NULL;
|
|
jpayne@69
|
13098 #else
|
|
jpayne@69
|
13099 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object")))
|
|
jpayne@69
|
13100 return NULL;
|
|
jpayne@69
|
13101 #endif
|
|
jpayne@69
|
13102 result = (*call)(func, arg, kw);
|
|
jpayne@69
|
13103 Py_LeaveRecursiveCall();
|
|
jpayne@69
|
13104 if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
|
|
jpayne@69
|
13105 PyErr_SetString(
|
|
jpayne@69
|
13106 PyExc_SystemError,
|
|
jpayne@69
|
13107 "NULL result without error in PyObject_Call");
|
|
jpayne@69
|
13108 }
|
|
jpayne@69
|
13109 return result;
|
|
jpayne@69
|
13110 }
|
|
jpayne@69
|
13111 #endif
|
|
jpayne@69
|
13112
|
|
jpayne@69
|
13113 /* RaiseDoubleKeywords */
|
|
jpayne@69
|
13114 static void __Pyx_RaiseDoubleKeywordsError(
|
|
jpayne@69
|
13115 const char* func_name,
|
|
jpayne@69
|
13116 PyObject* kw_name)
|
|
jpayne@69
|
13117 {
|
|
jpayne@69
|
13118 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13119 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13120 "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
|
|
jpayne@69
|
13121 #else
|
|
jpayne@69
|
13122 "%s() got multiple values for keyword argument '%s'", func_name,
|
|
jpayne@69
|
13123 PyString_AsString(kw_name));
|
|
jpayne@69
|
13124 #endif
|
|
jpayne@69
|
13125 }
|
|
jpayne@69
|
13126
|
|
jpayne@69
|
13127 /* ParseKeywords */
|
|
jpayne@69
|
13128 static int __Pyx_ParseOptionalKeywords(
|
|
jpayne@69
|
13129 PyObject *kwds,
|
|
jpayne@69
|
13130 PyObject *const *kwvalues,
|
|
jpayne@69
|
13131 PyObject **argnames[],
|
|
jpayne@69
|
13132 PyObject *kwds2,
|
|
jpayne@69
|
13133 PyObject *values[],
|
|
jpayne@69
|
13134 Py_ssize_t num_pos_args,
|
|
jpayne@69
|
13135 const char* function_name)
|
|
jpayne@69
|
13136 {
|
|
jpayne@69
|
13137 PyObject *key = 0, *value = 0;
|
|
jpayne@69
|
13138 Py_ssize_t pos = 0;
|
|
jpayne@69
|
13139 PyObject*** name;
|
|
jpayne@69
|
13140 PyObject*** first_kw_arg = argnames + num_pos_args;
|
|
jpayne@69
|
13141 int kwds_is_tuple = CYTHON_METH_FASTCALL && likely(PyTuple_Check(kwds));
|
|
jpayne@69
|
13142 while (1) {
|
|
jpayne@69
|
13143 Py_XDECREF(key); key = NULL;
|
|
jpayne@69
|
13144 Py_XDECREF(value); value = NULL;
|
|
jpayne@69
|
13145 if (kwds_is_tuple) {
|
|
jpayne@69
|
13146 Py_ssize_t size;
|
|
jpayne@69
|
13147 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
13148 size = PyTuple_GET_SIZE(kwds);
|
|
jpayne@69
|
13149 #else
|
|
jpayne@69
|
13150 size = PyTuple_Size(kwds);
|
|
jpayne@69
|
13151 if (size < 0) goto bad;
|
|
jpayne@69
|
13152 #endif
|
|
jpayne@69
|
13153 if (pos >= size) break;
|
|
jpayne@69
|
13154 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13155 key = __Pyx_PySequence_ITEM(kwds, pos);
|
|
jpayne@69
|
13156 if (!key) goto bad;
|
|
jpayne@69
|
13157 #elif CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
13158 key = PyTuple_GET_ITEM(kwds, pos);
|
|
jpayne@69
|
13159 #else
|
|
jpayne@69
|
13160 key = PyTuple_GetItem(kwds, pos);
|
|
jpayne@69
|
13161 if (!key) goto bad;
|
|
jpayne@69
|
13162 #endif
|
|
jpayne@69
|
13163 value = kwvalues[pos];
|
|
jpayne@69
|
13164 pos++;
|
|
jpayne@69
|
13165 }
|
|
jpayne@69
|
13166 else
|
|
jpayne@69
|
13167 {
|
|
jpayne@69
|
13168 if (!PyDict_Next(kwds, &pos, &key, &value)) break;
|
|
jpayne@69
|
13169 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13170 Py_INCREF(key);
|
|
jpayne@69
|
13171 #endif
|
|
jpayne@69
|
13172 }
|
|
jpayne@69
|
13173 name = first_kw_arg;
|
|
jpayne@69
|
13174 while (*name && (**name != key)) name++;
|
|
jpayne@69
|
13175 if (*name) {
|
|
jpayne@69
|
13176 values[name-argnames] = value;
|
|
jpayne@69
|
13177 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13178 Py_INCREF(value);
|
|
jpayne@69
|
13179 Py_DECREF(key);
|
|
jpayne@69
|
13180 #endif
|
|
jpayne@69
|
13181 key = NULL;
|
|
jpayne@69
|
13182 value = NULL;
|
|
jpayne@69
|
13183 continue;
|
|
jpayne@69
|
13184 }
|
|
jpayne@69
|
13185 #if !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13186 Py_INCREF(key);
|
|
jpayne@69
|
13187 #endif
|
|
jpayne@69
|
13188 Py_INCREF(value);
|
|
jpayne@69
|
13189 name = first_kw_arg;
|
|
jpayne@69
|
13190 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13191 if (likely(PyString_Check(key))) {
|
|
jpayne@69
|
13192 while (*name) {
|
|
jpayne@69
|
13193 if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
|
|
jpayne@69
|
13194 && _PyString_Eq(**name, key)) {
|
|
jpayne@69
|
13195 values[name-argnames] = value;
|
|
jpayne@69
|
13196 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13197 value = NULL;
|
|
jpayne@69
|
13198 #endif
|
|
jpayne@69
|
13199 break;
|
|
jpayne@69
|
13200 }
|
|
jpayne@69
|
13201 name++;
|
|
jpayne@69
|
13202 }
|
|
jpayne@69
|
13203 if (*name) continue;
|
|
jpayne@69
|
13204 else {
|
|
jpayne@69
|
13205 PyObject*** argname = argnames;
|
|
jpayne@69
|
13206 while (argname != first_kw_arg) {
|
|
jpayne@69
|
13207 if ((**argname == key) || (
|
|
jpayne@69
|
13208 (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
|
|
jpayne@69
|
13209 && _PyString_Eq(**argname, key))) {
|
|
jpayne@69
|
13210 goto arg_passed_twice;
|
|
jpayne@69
|
13211 }
|
|
jpayne@69
|
13212 argname++;
|
|
jpayne@69
|
13213 }
|
|
jpayne@69
|
13214 }
|
|
jpayne@69
|
13215 } else
|
|
jpayne@69
|
13216 #endif
|
|
jpayne@69
|
13217 if (likely(PyUnicode_Check(key))) {
|
|
jpayne@69
|
13218 while (*name) {
|
|
jpayne@69
|
13219 int cmp = (
|
|
jpayne@69
|
13220 #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13221 (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
|
|
jpayne@69
|
13222 #endif
|
|
jpayne@69
|
13223 PyUnicode_Compare(**name, key)
|
|
jpayne@69
|
13224 );
|
|
jpayne@69
|
13225 if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
|
|
jpayne@69
|
13226 if (cmp == 0) {
|
|
jpayne@69
|
13227 values[name-argnames] = value;
|
|
jpayne@69
|
13228 #if CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13229 value = NULL;
|
|
jpayne@69
|
13230 #endif
|
|
jpayne@69
|
13231 break;
|
|
jpayne@69
|
13232 }
|
|
jpayne@69
|
13233 name++;
|
|
jpayne@69
|
13234 }
|
|
jpayne@69
|
13235 if (*name) continue;
|
|
jpayne@69
|
13236 else {
|
|
jpayne@69
|
13237 PyObject*** argname = argnames;
|
|
jpayne@69
|
13238 while (argname != first_kw_arg) {
|
|
jpayne@69
|
13239 int cmp = (**argname == key) ? 0 :
|
|
jpayne@69
|
13240 #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13241 (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 :
|
|
jpayne@69
|
13242 #endif
|
|
jpayne@69
|
13243 PyUnicode_Compare(**argname, key);
|
|
jpayne@69
|
13244 if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
|
|
jpayne@69
|
13245 if (cmp == 0) goto arg_passed_twice;
|
|
jpayne@69
|
13246 argname++;
|
|
jpayne@69
|
13247 }
|
|
jpayne@69
|
13248 }
|
|
jpayne@69
|
13249 } else
|
|
jpayne@69
|
13250 goto invalid_keyword_type;
|
|
jpayne@69
|
13251 if (kwds2) {
|
|
jpayne@69
|
13252 if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
|
|
jpayne@69
|
13253 } else {
|
|
jpayne@69
|
13254 goto invalid_keyword;
|
|
jpayne@69
|
13255 }
|
|
jpayne@69
|
13256 }
|
|
jpayne@69
|
13257 Py_XDECREF(key);
|
|
jpayne@69
|
13258 Py_XDECREF(value);
|
|
jpayne@69
|
13259 return 0;
|
|
jpayne@69
|
13260 arg_passed_twice:
|
|
jpayne@69
|
13261 __Pyx_RaiseDoubleKeywordsError(function_name, key);
|
|
jpayne@69
|
13262 goto bad;
|
|
jpayne@69
|
13263 invalid_keyword_type:
|
|
jpayne@69
|
13264 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13265 "%.200s() keywords must be strings", function_name);
|
|
jpayne@69
|
13266 goto bad;
|
|
jpayne@69
|
13267 invalid_keyword:
|
|
jpayne@69
|
13268 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13269 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13270 "%.200s() got an unexpected keyword argument '%.200s'",
|
|
jpayne@69
|
13271 function_name, PyString_AsString(key));
|
|
jpayne@69
|
13272 #else
|
|
jpayne@69
|
13273 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13274 "%s() got an unexpected keyword argument '%U'",
|
|
jpayne@69
|
13275 function_name, key);
|
|
jpayne@69
|
13276 #endif
|
|
jpayne@69
|
13277 bad:
|
|
jpayne@69
|
13278 Py_XDECREF(key);
|
|
jpayne@69
|
13279 Py_XDECREF(value);
|
|
jpayne@69
|
13280 return -1;
|
|
jpayne@69
|
13281 }
|
|
jpayne@69
|
13282
|
|
jpayne@69
|
13283 /* RaiseArgTupleInvalid */
|
|
jpayne@69
|
13284 static void __Pyx_RaiseArgtupleInvalid(
|
|
jpayne@69
|
13285 const char* func_name,
|
|
jpayne@69
|
13286 int exact,
|
|
jpayne@69
|
13287 Py_ssize_t num_min,
|
|
jpayne@69
|
13288 Py_ssize_t num_max,
|
|
jpayne@69
|
13289 Py_ssize_t num_found)
|
|
jpayne@69
|
13290 {
|
|
jpayne@69
|
13291 Py_ssize_t num_expected;
|
|
jpayne@69
|
13292 const char *more_or_less;
|
|
jpayne@69
|
13293 if (num_found < num_min) {
|
|
jpayne@69
|
13294 num_expected = num_min;
|
|
jpayne@69
|
13295 more_or_less = "at least";
|
|
jpayne@69
|
13296 } else {
|
|
jpayne@69
|
13297 num_expected = num_max;
|
|
jpayne@69
|
13298 more_or_less = "at most";
|
|
jpayne@69
|
13299 }
|
|
jpayne@69
|
13300 if (exact) {
|
|
jpayne@69
|
13301 more_or_less = "exactly";
|
|
jpayne@69
|
13302 }
|
|
jpayne@69
|
13303 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13304 "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
13305 func_name, more_or_less, num_expected,
|
|
jpayne@69
|
13306 (num_expected == 1) ? "" : "s", num_found);
|
|
jpayne@69
|
13307 }
|
|
jpayne@69
|
13308
|
|
jpayne@69
|
13309 /* GetItemInt */
|
|
jpayne@69
|
13310 static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
|
|
jpayne@69
|
13311 PyObject *r;
|
|
jpayne@69
|
13312 if (unlikely(!j)) return NULL;
|
|
jpayne@69
|
13313 r = PyObject_GetItem(o, j);
|
|
jpayne@69
|
13314 Py_DECREF(j);
|
|
jpayne@69
|
13315 return r;
|
|
jpayne@69
|
13316 }
|
|
jpayne@69
|
13317 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
13318 CYTHON_NCP_UNUSED int wraparound,
|
|
jpayne@69
|
13319 CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
13320 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13321 Py_ssize_t wrapped_i = i;
|
|
jpayne@69
|
13322 if (wraparound & unlikely(i < 0)) {
|
|
jpayne@69
|
13323 wrapped_i += PyList_GET_SIZE(o);
|
|
jpayne@69
|
13324 }
|
|
jpayne@69
|
13325 if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) {
|
|
jpayne@69
|
13326 PyObject *r = PyList_GET_ITEM(o, wrapped_i);
|
|
jpayne@69
|
13327 Py_INCREF(r);
|
|
jpayne@69
|
13328 return r;
|
|
jpayne@69
|
13329 }
|
|
jpayne@69
|
13330 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
|
|
jpayne@69
|
13331 #else
|
|
jpayne@69
|
13332 return PySequence_GetItem(o, i);
|
|
jpayne@69
|
13333 #endif
|
|
jpayne@69
|
13334 }
|
|
jpayne@69
|
13335 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
|
|
jpayne@69
|
13336 CYTHON_NCP_UNUSED int wraparound,
|
|
jpayne@69
|
13337 CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
13338 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13339 Py_ssize_t wrapped_i = i;
|
|
jpayne@69
|
13340 if (wraparound & unlikely(i < 0)) {
|
|
jpayne@69
|
13341 wrapped_i += PyTuple_GET_SIZE(o);
|
|
jpayne@69
|
13342 }
|
|
jpayne@69
|
13343 if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) {
|
|
jpayne@69
|
13344 PyObject *r = PyTuple_GET_ITEM(o, wrapped_i);
|
|
jpayne@69
|
13345 Py_INCREF(r);
|
|
jpayne@69
|
13346 return r;
|
|
jpayne@69
|
13347 }
|
|
jpayne@69
|
13348 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
|
|
jpayne@69
|
13349 #else
|
|
jpayne@69
|
13350 return PySequence_GetItem(o, i);
|
|
jpayne@69
|
13351 #endif
|
|
jpayne@69
|
13352 }
|
|
jpayne@69
|
13353 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
|
|
jpayne@69
|
13354 CYTHON_NCP_UNUSED int wraparound,
|
|
jpayne@69
|
13355 CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
13356 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
13357 if (is_list || PyList_CheckExact(o)) {
|
|
jpayne@69
|
13358 Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
|
|
jpayne@69
|
13359 if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) {
|
|
jpayne@69
|
13360 PyObject *r = PyList_GET_ITEM(o, n);
|
|
jpayne@69
|
13361 Py_INCREF(r);
|
|
jpayne@69
|
13362 return r;
|
|
jpayne@69
|
13363 }
|
|
jpayne@69
|
13364 }
|
|
jpayne@69
|
13365 else if (PyTuple_CheckExact(o)) {
|
|
jpayne@69
|
13366 Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
|
|
jpayne@69
|
13367 if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) {
|
|
jpayne@69
|
13368 PyObject *r = PyTuple_GET_ITEM(o, n);
|
|
jpayne@69
|
13369 Py_INCREF(r);
|
|
jpayne@69
|
13370 return r;
|
|
jpayne@69
|
13371 }
|
|
jpayne@69
|
13372 } else {
|
|
jpayne@69
|
13373 PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping;
|
|
jpayne@69
|
13374 PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence;
|
|
jpayne@69
|
13375 if (mm && mm->mp_subscript) {
|
|
jpayne@69
|
13376 PyObject *r, *key = PyInt_FromSsize_t(i);
|
|
jpayne@69
|
13377 if (unlikely(!key)) return NULL;
|
|
jpayne@69
|
13378 r = mm->mp_subscript(o, key);
|
|
jpayne@69
|
13379 Py_DECREF(key);
|
|
jpayne@69
|
13380 return r;
|
|
jpayne@69
|
13381 }
|
|
jpayne@69
|
13382 if (likely(sm && sm->sq_item)) {
|
|
jpayne@69
|
13383 if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) {
|
|
jpayne@69
|
13384 Py_ssize_t l = sm->sq_length(o);
|
|
jpayne@69
|
13385 if (likely(l >= 0)) {
|
|
jpayne@69
|
13386 i += l;
|
|
jpayne@69
|
13387 } else {
|
|
jpayne@69
|
13388 if (!PyErr_ExceptionMatches(PyExc_OverflowError))
|
|
jpayne@69
|
13389 return NULL;
|
|
jpayne@69
|
13390 PyErr_Clear();
|
|
jpayne@69
|
13391 }
|
|
jpayne@69
|
13392 }
|
|
jpayne@69
|
13393 return sm->sq_item(o, i);
|
|
jpayne@69
|
13394 }
|
|
jpayne@69
|
13395 }
|
|
jpayne@69
|
13396 #else
|
|
jpayne@69
|
13397 if (is_list || !PyMapping_Check(o)) {
|
|
jpayne@69
|
13398 return PySequence_GetItem(o, i);
|
|
jpayne@69
|
13399 }
|
|
jpayne@69
|
13400 #endif
|
|
jpayne@69
|
13401 return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
|
|
jpayne@69
|
13402 }
|
|
jpayne@69
|
13403
|
|
jpayne@69
|
13404 /* SetItemInt */
|
|
jpayne@69
|
13405 static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
|
|
jpayne@69
|
13406 int r;
|
|
jpayne@69
|
13407 if (unlikely(!j)) return -1;
|
|
jpayne@69
|
13408 r = PyObject_SetItem(o, j, v);
|
|
jpayne@69
|
13409 Py_DECREF(j);
|
|
jpayne@69
|
13410 return r;
|
|
jpayne@69
|
13411 }
|
|
jpayne@69
|
13412 static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list,
|
|
jpayne@69
|
13413 CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) {
|
|
jpayne@69
|
13414 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
13415 if (is_list || PyList_CheckExact(o)) {
|
|
jpayne@69
|
13416 Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
|
|
jpayne@69
|
13417 if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o)))) {
|
|
jpayne@69
|
13418 PyObject* old = PyList_GET_ITEM(o, n);
|
|
jpayne@69
|
13419 Py_INCREF(v);
|
|
jpayne@69
|
13420 PyList_SET_ITEM(o, n, v);
|
|
jpayne@69
|
13421 Py_DECREF(old);
|
|
jpayne@69
|
13422 return 1;
|
|
jpayne@69
|
13423 }
|
|
jpayne@69
|
13424 } else {
|
|
jpayne@69
|
13425 PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping;
|
|
jpayne@69
|
13426 PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence;
|
|
jpayne@69
|
13427 if (mm && mm->mp_ass_subscript) {
|
|
jpayne@69
|
13428 int r;
|
|
jpayne@69
|
13429 PyObject *key = PyInt_FromSsize_t(i);
|
|
jpayne@69
|
13430 if (unlikely(!key)) return -1;
|
|
jpayne@69
|
13431 r = mm->mp_ass_subscript(o, key, v);
|
|
jpayne@69
|
13432 Py_DECREF(key);
|
|
jpayne@69
|
13433 return r;
|
|
jpayne@69
|
13434 }
|
|
jpayne@69
|
13435 if (likely(sm && sm->sq_ass_item)) {
|
|
jpayne@69
|
13436 if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) {
|
|
jpayne@69
|
13437 Py_ssize_t l = sm->sq_length(o);
|
|
jpayne@69
|
13438 if (likely(l >= 0)) {
|
|
jpayne@69
|
13439 i += l;
|
|
jpayne@69
|
13440 } else {
|
|
jpayne@69
|
13441 if (!PyErr_ExceptionMatches(PyExc_OverflowError))
|
|
jpayne@69
|
13442 return -1;
|
|
jpayne@69
|
13443 PyErr_Clear();
|
|
jpayne@69
|
13444 }
|
|
jpayne@69
|
13445 }
|
|
jpayne@69
|
13446 return sm->sq_ass_item(o, i, v);
|
|
jpayne@69
|
13447 }
|
|
jpayne@69
|
13448 }
|
|
jpayne@69
|
13449 #else
|
|
jpayne@69
|
13450 if (is_list || !PyMapping_Check(o))
|
|
jpayne@69
|
13451 {
|
|
jpayne@69
|
13452 return PySequence_SetItem(o, i, v);
|
|
jpayne@69
|
13453 }
|
|
jpayne@69
|
13454 #endif
|
|
jpayne@69
|
13455 return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
|
|
jpayne@69
|
13456 }
|
|
jpayne@69
|
13457
|
|
jpayne@69
|
13458 /* PyFunctionFastCall */
|
|
jpayne@69
|
13459 #if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL
|
|
jpayne@69
|
13460 static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na,
|
|
jpayne@69
|
13461 PyObject *globals) {
|
|
jpayne@69
|
13462 PyFrameObject *f;
|
|
jpayne@69
|
13463 PyThreadState *tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
13464 PyObject **fastlocals;
|
|
jpayne@69
|
13465 Py_ssize_t i;
|
|
jpayne@69
|
13466 PyObject *result;
|
|
jpayne@69
|
13467 assert(globals != NULL);
|
|
jpayne@69
|
13468 /* XXX Perhaps we should create a specialized
|
|
jpayne@69
|
13469 PyFrame_New() that doesn't take locals, but does
|
|
jpayne@69
|
13470 take builtins without sanity checking them.
|
|
jpayne@69
|
13471 */
|
|
jpayne@69
|
13472 assert(tstate != NULL);
|
|
jpayne@69
|
13473 f = PyFrame_New(tstate, co, globals, NULL);
|
|
jpayne@69
|
13474 if (f == NULL) {
|
|
jpayne@69
|
13475 return NULL;
|
|
jpayne@69
|
13476 }
|
|
jpayne@69
|
13477 fastlocals = __Pyx_PyFrame_GetLocalsplus(f);
|
|
jpayne@69
|
13478 for (i = 0; i < na; i++) {
|
|
jpayne@69
|
13479 Py_INCREF(*args);
|
|
jpayne@69
|
13480 fastlocals[i] = *args++;
|
|
jpayne@69
|
13481 }
|
|
jpayne@69
|
13482 result = PyEval_EvalFrameEx(f,0);
|
|
jpayne@69
|
13483 ++tstate->recursion_depth;
|
|
jpayne@69
|
13484 Py_DECREF(f);
|
|
jpayne@69
|
13485 --tstate->recursion_depth;
|
|
jpayne@69
|
13486 return result;
|
|
jpayne@69
|
13487 }
|
|
jpayne@69
|
13488 static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) {
|
|
jpayne@69
|
13489 PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func);
|
|
jpayne@69
|
13490 PyObject *globals = PyFunction_GET_GLOBALS(func);
|
|
jpayne@69
|
13491 PyObject *argdefs = PyFunction_GET_DEFAULTS(func);
|
|
jpayne@69
|
13492 PyObject *closure;
|
|
jpayne@69
|
13493 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13494 PyObject *kwdefs;
|
|
jpayne@69
|
13495 #endif
|
|
jpayne@69
|
13496 PyObject *kwtuple, **k;
|
|
jpayne@69
|
13497 PyObject **d;
|
|
jpayne@69
|
13498 Py_ssize_t nd;
|
|
jpayne@69
|
13499 Py_ssize_t nk;
|
|
jpayne@69
|
13500 PyObject *result;
|
|
jpayne@69
|
13501 assert(kwargs == NULL || PyDict_Check(kwargs));
|
|
jpayne@69
|
13502 nk = kwargs ? PyDict_Size(kwargs) : 0;
|
|
jpayne@69
|
13503 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13504 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) {
|
|
jpayne@69
|
13505 return NULL;
|
|
jpayne@69
|
13506 }
|
|
jpayne@69
|
13507 #else
|
|
jpayne@69
|
13508 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) {
|
|
jpayne@69
|
13509 return NULL;
|
|
jpayne@69
|
13510 }
|
|
jpayne@69
|
13511 #endif
|
|
jpayne@69
|
13512 if (
|
|
jpayne@69
|
13513 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13514 co->co_kwonlyargcount == 0 &&
|
|
jpayne@69
|
13515 #endif
|
|
jpayne@69
|
13516 likely(kwargs == NULL || nk == 0) &&
|
|
jpayne@69
|
13517 co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
|
|
jpayne@69
|
13518 if (argdefs == NULL && co->co_argcount == nargs) {
|
|
jpayne@69
|
13519 result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
|
|
jpayne@69
|
13520 goto done;
|
|
jpayne@69
|
13521 }
|
|
jpayne@69
|
13522 else if (nargs == 0 && argdefs != NULL
|
|
jpayne@69
|
13523 && co->co_argcount == Py_SIZE(argdefs)) {
|
|
jpayne@69
|
13524 /* function called with no arguments, but all parameters have
|
|
jpayne@69
|
13525 a default value: use default values as arguments .*/
|
|
jpayne@69
|
13526 args = &PyTuple_GET_ITEM(argdefs, 0);
|
|
jpayne@69
|
13527 result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
|
|
jpayne@69
|
13528 goto done;
|
|
jpayne@69
|
13529 }
|
|
jpayne@69
|
13530 }
|
|
jpayne@69
|
13531 if (kwargs != NULL) {
|
|
jpayne@69
|
13532 Py_ssize_t pos, i;
|
|
jpayne@69
|
13533 kwtuple = PyTuple_New(2 * nk);
|
|
jpayne@69
|
13534 if (kwtuple == NULL) {
|
|
jpayne@69
|
13535 result = NULL;
|
|
jpayne@69
|
13536 goto done;
|
|
jpayne@69
|
13537 }
|
|
jpayne@69
|
13538 k = &PyTuple_GET_ITEM(kwtuple, 0);
|
|
jpayne@69
|
13539 pos = i = 0;
|
|
jpayne@69
|
13540 while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
|
|
jpayne@69
|
13541 Py_INCREF(k[i]);
|
|
jpayne@69
|
13542 Py_INCREF(k[i+1]);
|
|
jpayne@69
|
13543 i += 2;
|
|
jpayne@69
|
13544 }
|
|
jpayne@69
|
13545 nk = i / 2;
|
|
jpayne@69
|
13546 }
|
|
jpayne@69
|
13547 else {
|
|
jpayne@69
|
13548 kwtuple = NULL;
|
|
jpayne@69
|
13549 k = NULL;
|
|
jpayne@69
|
13550 }
|
|
jpayne@69
|
13551 closure = PyFunction_GET_CLOSURE(func);
|
|
jpayne@69
|
13552 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13553 kwdefs = PyFunction_GET_KW_DEFAULTS(func);
|
|
jpayne@69
|
13554 #endif
|
|
jpayne@69
|
13555 if (argdefs != NULL) {
|
|
jpayne@69
|
13556 d = &PyTuple_GET_ITEM(argdefs, 0);
|
|
jpayne@69
|
13557 nd = Py_SIZE(argdefs);
|
|
jpayne@69
|
13558 }
|
|
jpayne@69
|
13559 else {
|
|
jpayne@69
|
13560 d = NULL;
|
|
jpayne@69
|
13561 nd = 0;
|
|
jpayne@69
|
13562 }
|
|
jpayne@69
|
13563 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
13564 result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
|
|
jpayne@69
|
13565 args, (int)nargs,
|
|
jpayne@69
|
13566 k, (int)nk,
|
|
jpayne@69
|
13567 d, (int)nd, kwdefs, closure);
|
|
jpayne@69
|
13568 #else
|
|
jpayne@69
|
13569 result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
|
|
jpayne@69
|
13570 args, (int)nargs,
|
|
jpayne@69
|
13571 k, (int)nk,
|
|
jpayne@69
|
13572 d, (int)nd, closure);
|
|
jpayne@69
|
13573 #endif
|
|
jpayne@69
|
13574 Py_XDECREF(kwtuple);
|
|
jpayne@69
|
13575 done:
|
|
jpayne@69
|
13576 Py_LeaveRecursiveCall();
|
|
jpayne@69
|
13577 return result;
|
|
jpayne@69
|
13578 }
|
|
jpayne@69
|
13579 #endif
|
|
jpayne@69
|
13580
|
|
jpayne@69
|
13581 /* PyObjectCallMethO */
|
|
jpayne@69
|
13582 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
13583 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
|
|
jpayne@69
|
13584 PyObject *self, *result;
|
|
jpayne@69
|
13585 PyCFunction cfunc;
|
|
jpayne@69
|
13586 cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func);
|
|
jpayne@69
|
13587 self = __Pyx_CyOrPyCFunction_GET_SELF(func);
|
|
jpayne@69
|
13588 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13589 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
|
|
jpayne@69
|
13590 return NULL;
|
|
jpayne@69
|
13591 #else
|
|
jpayne@69
|
13592 if (unlikely(Py_EnterRecursiveCall(" while calling a Python object")))
|
|
jpayne@69
|
13593 return NULL;
|
|
jpayne@69
|
13594 #endif
|
|
jpayne@69
|
13595 result = cfunc(self, arg);
|
|
jpayne@69
|
13596 Py_LeaveRecursiveCall();
|
|
jpayne@69
|
13597 if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
|
|
jpayne@69
|
13598 PyErr_SetString(
|
|
jpayne@69
|
13599 PyExc_SystemError,
|
|
jpayne@69
|
13600 "NULL result without error in PyObject_Call");
|
|
jpayne@69
|
13601 }
|
|
jpayne@69
|
13602 return result;
|
|
jpayne@69
|
13603 }
|
|
jpayne@69
|
13604 #endif
|
|
jpayne@69
|
13605
|
|
jpayne@69
|
13606 /* PyObjectFastCall */
|
|
jpayne@69
|
13607 #if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
13608 static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) {
|
|
jpayne@69
|
13609 PyObject *argstuple;
|
|
jpayne@69
|
13610 PyObject *result = 0;
|
|
jpayne@69
|
13611 size_t i;
|
|
jpayne@69
|
13612 argstuple = PyTuple_New((Py_ssize_t)nargs);
|
|
jpayne@69
|
13613 if (unlikely(!argstuple)) return NULL;
|
|
jpayne@69
|
13614 for (i = 0; i < nargs; i++) {
|
|
jpayne@69
|
13615 Py_INCREF(args[i]);
|
|
jpayne@69
|
13616 if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
|
|
jpayne@69
|
13617 }
|
|
jpayne@69
|
13618 result = __Pyx_PyObject_Call(func, argstuple, kwargs);
|
|
jpayne@69
|
13619 bad:
|
|
jpayne@69
|
13620 Py_DECREF(argstuple);
|
|
jpayne@69
|
13621 return result;
|
|
jpayne@69
|
13622 }
|
|
jpayne@69
|
13623 #endif
|
|
jpayne@69
|
13624 static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) {
|
|
jpayne@69
|
13625 Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs);
|
|
jpayne@69
|
13626 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
13627 if (nargs == 0 && kwargs == NULL) {
|
|
jpayne@69
|
13628 if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS))
|
|
jpayne@69
|
13629 return __Pyx_PyObject_CallMethO(func, NULL);
|
|
jpayne@69
|
13630 }
|
|
jpayne@69
|
13631 else if (nargs == 1 && kwargs == NULL) {
|
|
jpayne@69
|
13632 if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O))
|
|
jpayne@69
|
13633 return __Pyx_PyObject_CallMethO(func, args[0]);
|
|
jpayne@69
|
13634 }
|
|
jpayne@69
|
13635 #endif
|
|
jpayne@69
|
13636 #if PY_VERSION_HEX < 0x030800B1
|
|
jpayne@69
|
13637 #if CYTHON_FAST_PYCCALL
|
|
jpayne@69
|
13638 if (PyCFunction_Check(func)) {
|
|
jpayne@69
|
13639 if (kwargs) {
|
|
jpayne@69
|
13640 return _PyCFunction_FastCallDict(func, args, nargs, kwargs);
|
|
jpayne@69
|
13641 } else {
|
|
jpayne@69
|
13642 return _PyCFunction_FastCallKeywords(func, args, nargs, NULL);
|
|
jpayne@69
|
13643 }
|
|
jpayne@69
|
13644 }
|
|
jpayne@69
|
13645 #if PY_VERSION_HEX >= 0x030700A1
|
|
jpayne@69
|
13646 if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) {
|
|
jpayne@69
|
13647 return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL);
|
|
jpayne@69
|
13648 }
|
|
jpayne@69
|
13649 #endif
|
|
jpayne@69
|
13650 #endif
|
|
jpayne@69
|
13651 #if CYTHON_FAST_PYCALL
|
|
jpayne@69
|
13652 if (PyFunction_Check(func)) {
|
|
jpayne@69
|
13653 return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs);
|
|
jpayne@69
|
13654 }
|
|
jpayne@69
|
13655 #endif
|
|
jpayne@69
|
13656 #endif
|
|
jpayne@69
|
13657 if (kwargs == NULL) {
|
|
jpayne@69
|
13658 #if CYTHON_VECTORCALL
|
|
jpayne@69
|
13659 #if PY_VERSION_HEX < 0x03090000
|
|
jpayne@69
|
13660 vectorcallfunc f = _PyVectorcall_Function(func);
|
|
jpayne@69
|
13661 #else
|
|
jpayne@69
|
13662 vectorcallfunc f = PyVectorcall_Function(func);
|
|
jpayne@69
|
13663 #endif
|
|
jpayne@69
|
13664 if (f) {
|
|
jpayne@69
|
13665 return f(func, args, (size_t)nargs, NULL);
|
|
jpayne@69
|
13666 }
|
|
jpayne@69
|
13667 #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
13668 if (__Pyx_CyFunction_CheckExact(func)) {
|
|
jpayne@69
|
13669 __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func);
|
|
jpayne@69
|
13670 if (f) return f(func, args, (size_t)nargs, NULL);
|
|
jpayne@69
|
13671 }
|
|
jpayne@69
|
13672 #endif
|
|
jpayne@69
|
13673 }
|
|
jpayne@69
|
13674 if (nargs == 0) {
|
|
jpayne@69
|
13675 return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs);
|
|
jpayne@69
|
13676 }
|
|
jpayne@69
|
13677 #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
13678 return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs);
|
|
jpayne@69
|
13679 #else
|
|
jpayne@69
|
13680 return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs);
|
|
jpayne@69
|
13681 #endif
|
|
jpayne@69
|
13682 }
|
|
jpayne@69
|
13683
|
|
jpayne@69
|
13684 /* ArgTypeTest */
|
|
jpayne@69
|
13685 static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact)
|
|
jpayne@69
|
13686 {
|
|
jpayne@69
|
13687 __Pyx_TypeName type_name;
|
|
jpayne@69
|
13688 __Pyx_TypeName obj_type_name;
|
|
jpayne@69
|
13689 if (unlikely(!type)) {
|
|
jpayne@69
|
13690 PyErr_SetString(PyExc_SystemError, "Missing type object");
|
|
jpayne@69
|
13691 return 0;
|
|
jpayne@69
|
13692 }
|
|
jpayne@69
|
13693 else if (exact) {
|
|
jpayne@69
|
13694 #if PY_MAJOR_VERSION == 2
|
|
jpayne@69
|
13695 if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1;
|
|
jpayne@69
|
13696 #endif
|
|
jpayne@69
|
13697 }
|
|
jpayne@69
|
13698 else {
|
|
jpayne@69
|
13699 if (likely(__Pyx_TypeCheck(obj, type))) return 1;
|
|
jpayne@69
|
13700 }
|
|
jpayne@69
|
13701 type_name = __Pyx_PyType_GetName(type);
|
|
jpayne@69
|
13702 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
13703 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13704 "Argument '%.200s' has incorrect type (expected " __Pyx_FMT_TYPENAME
|
|
jpayne@69
|
13705 ", got " __Pyx_FMT_TYPENAME ")", name, type_name, obj_type_name);
|
|
jpayne@69
|
13706 __Pyx_DECREF_TypeName(type_name);
|
|
jpayne@69
|
13707 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
13708 return 0;
|
|
jpayne@69
|
13709 }
|
|
jpayne@69
|
13710
|
|
jpayne@69
|
13711 /* ExtTypeTest */
|
|
jpayne@69
|
13712 static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
|
|
jpayne@69
|
13713 __Pyx_TypeName obj_type_name;
|
|
jpayne@69
|
13714 __Pyx_TypeName type_name;
|
|
jpayne@69
|
13715 if (unlikely(!type)) {
|
|
jpayne@69
|
13716 PyErr_SetString(PyExc_SystemError, "Missing type object");
|
|
jpayne@69
|
13717 return 0;
|
|
jpayne@69
|
13718 }
|
|
jpayne@69
|
13719 if (likely(__Pyx_TypeCheck(obj, type)))
|
|
jpayne@69
|
13720 return 1;
|
|
jpayne@69
|
13721 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
13722 type_name = __Pyx_PyType_GetName(type);
|
|
jpayne@69
|
13723 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13724 "Cannot convert " __Pyx_FMT_TYPENAME " to " __Pyx_FMT_TYPENAME,
|
|
jpayne@69
|
13725 obj_type_name, type_name);
|
|
jpayne@69
|
13726 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
13727 __Pyx_DECREF_TypeName(type_name);
|
|
jpayne@69
|
13728 return 0;
|
|
jpayne@69
|
13729 }
|
|
jpayne@69
|
13730
|
|
jpayne@69
|
13731 /* PyObjectCallOneArg */
|
|
jpayne@69
|
13732 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
|
|
jpayne@69
|
13733 PyObject *args[2] = {NULL, arg};
|
|
jpayne@69
|
13734 return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
|
|
jpayne@69
|
13735 }
|
|
jpayne@69
|
13736
|
|
jpayne@69
|
13737 /* ObjectGetItem */
|
|
jpayne@69
|
13738 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
13739 static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject *index) {
|
|
jpayne@69
|
13740 PyObject *runerr = NULL;
|
|
jpayne@69
|
13741 Py_ssize_t key_value;
|
|
jpayne@69
|
13742 key_value = __Pyx_PyIndex_AsSsize_t(index);
|
|
jpayne@69
|
13743 if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) {
|
|
jpayne@69
|
13744 return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1);
|
|
jpayne@69
|
13745 }
|
|
jpayne@69
|
13746 if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) {
|
|
jpayne@69
|
13747 __Pyx_TypeName index_type_name = __Pyx_PyType_GetName(Py_TYPE(index));
|
|
jpayne@69
|
13748 PyErr_Clear();
|
|
jpayne@69
|
13749 PyErr_Format(PyExc_IndexError,
|
|
jpayne@69
|
13750 "cannot fit '" __Pyx_FMT_TYPENAME "' into an index-sized integer", index_type_name);
|
|
jpayne@69
|
13751 __Pyx_DECREF_TypeName(index_type_name);
|
|
jpayne@69
|
13752 }
|
|
jpayne@69
|
13753 return NULL;
|
|
jpayne@69
|
13754 }
|
|
jpayne@69
|
13755 static PyObject *__Pyx_PyObject_GetItem_Slow(PyObject *obj, PyObject *key) {
|
|
jpayne@69
|
13756 __Pyx_TypeName obj_type_name;
|
|
jpayne@69
|
13757 if (likely(PyType_Check(obj))) {
|
|
jpayne@69
|
13758 PyObject *meth = __Pyx_PyObject_GetAttrStrNoError(obj, __pyx_n_s_class_getitem);
|
|
jpayne@69
|
13759 if (!meth) {
|
|
jpayne@69
|
13760 PyErr_Clear();
|
|
jpayne@69
|
13761 } else {
|
|
jpayne@69
|
13762 PyObject *result = __Pyx_PyObject_CallOneArg(meth, key);
|
|
jpayne@69
|
13763 Py_DECREF(meth);
|
|
jpayne@69
|
13764 return result;
|
|
jpayne@69
|
13765 }
|
|
jpayne@69
|
13766 }
|
|
jpayne@69
|
13767 obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
13768 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13769 "'" __Pyx_FMT_TYPENAME "' object is not subscriptable", obj_type_name);
|
|
jpayne@69
|
13770 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
13771 return NULL;
|
|
jpayne@69
|
13772 }
|
|
jpayne@69
|
13773 static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject *key) {
|
|
jpayne@69
|
13774 PyTypeObject *tp = Py_TYPE(obj);
|
|
jpayne@69
|
13775 PyMappingMethods *mm = tp->tp_as_mapping;
|
|
jpayne@69
|
13776 PySequenceMethods *sm = tp->tp_as_sequence;
|
|
jpayne@69
|
13777 if (likely(mm && mm->mp_subscript)) {
|
|
jpayne@69
|
13778 return mm->mp_subscript(obj, key);
|
|
jpayne@69
|
13779 }
|
|
jpayne@69
|
13780 if (likely(sm && sm->sq_item)) {
|
|
jpayne@69
|
13781 return __Pyx_PyObject_GetIndex(obj, key);
|
|
jpayne@69
|
13782 }
|
|
jpayne@69
|
13783 return __Pyx_PyObject_GetItem_Slow(obj, key);
|
|
jpayne@69
|
13784 }
|
|
jpayne@69
|
13785 #endif
|
|
jpayne@69
|
13786
|
|
jpayne@69
|
13787 /* RaiseUnexpectedTypeError */
|
|
jpayne@69
|
13788 static int
|
|
jpayne@69
|
13789 __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj)
|
|
jpayne@69
|
13790 {
|
|
jpayne@69
|
13791 __Pyx_TypeName obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj));
|
|
jpayne@69
|
13792 PyErr_Format(PyExc_TypeError, "Expected %s, got " __Pyx_FMT_TYPENAME,
|
|
jpayne@69
|
13793 expected, obj_type_name);
|
|
jpayne@69
|
13794 __Pyx_DECREF_TypeName(obj_type_name);
|
|
jpayne@69
|
13795 return 0;
|
|
jpayne@69
|
13796 }
|
|
jpayne@69
|
13797
|
|
jpayne@69
|
13798 /* PyDictVersioning */
|
|
jpayne@69
|
13799 #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
13800 static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) {
|
|
jpayne@69
|
13801 PyObject *dict = Py_TYPE(obj)->tp_dict;
|
|
jpayne@69
|
13802 return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
|
|
jpayne@69
|
13803 }
|
|
jpayne@69
|
13804 static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) {
|
|
jpayne@69
|
13805 PyObject **dictptr = NULL;
|
|
jpayne@69
|
13806 Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset;
|
|
jpayne@69
|
13807 if (offset) {
|
|
jpayne@69
|
13808 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
13809 dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj);
|
|
jpayne@69
|
13810 #else
|
|
jpayne@69
|
13811 dictptr = _PyObject_GetDictPtr(obj);
|
|
jpayne@69
|
13812 #endif
|
|
jpayne@69
|
13813 }
|
|
jpayne@69
|
13814 return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
|
|
jpayne@69
|
13815 }
|
|
jpayne@69
|
13816 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
|
13817 PyObject *dict = Py_TYPE(obj)->tp_dict;
|
|
jpayne@69
|
13818 if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
|
|
jpayne@69
|
13819 return 0;
|
|
jpayne@69
|
13820 return obj_dict_version == __Pyx_get_object_dict_version(obj);
|
|
jpayne@69
|
13821 }
|
|
jpayne@69
|
13822 #endif
|
|
jpayne@69
|
13823
|
|
jpayne@69
|
13824 /* GetModuleGlobalName */
|
|
jpayne@69
|
13825 #if CYTHON_USE_DICT_VERSIONS
|
|
jpayne@69
|
13826 static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value)
|
|
jpayne@69
|
13827 #else
|
|
jpayne@69
|
13828 static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name)
|
|
jpayne@69
|
13829 #endif
|
|
jpayne@69
|
13830 {
|
|
jpayne@69
|
13831 PyObject *result;
|
|
jpayne@69
|
13832 #if !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
13833 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
13834 result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash);
|
|
jpayne@69
|
13835 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
|
|
jpayne@69
|
13836 if (likely(result)) {
|
|
jpayne@69
|
13837 return __Pyx_NewRef(result);
|
|
jpayne@69
|
13838 } else if (unlikely(PyErr_Occurred())) {
|
|
jpayne@69
|
13839 return NULL;
|
|
jpayne@69
|
13840 }
|
|
jpayne@69
|
13841 #elif CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
13842 if (unlikely(!__pyx_m)) {
|
|
jpayne@69
|
13843 return NULL;
|
|
jpayne@69
|
13844 }
|
|
jpayne@69
|
13845 result = PyObject_GetAttr(__pyx_m, name);
|
|
jpayne@69
|
13846 if (likely(result)) {
|
|
jpayne@69
|
13847 return result;
|
|
jpayne@69
|
13848 }
|
|
jpayne@69
|
13849 #else
|
|
jpayne@69
|
13850 result = PyDict_GetItem(__pyx_d, name);
|
|
jpayne@69
|
13851 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
|
|
jpayne@69
|
13852 if (likely(result)) {
|
|
jpayne@69
|
13853 return __Pyx_NewRef(result);
|
|
jpayne@69
|
13854 }
|
|
jpayne@69
|
13855 #endif
|
|
jpayne@69
|
13856 #else
|
|
jpayne@69
|
13857 result = PyObject_GetItem(__pyx_d, name);
|
|
jpayne@69
|
13858 __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
|
|
jpayne@69
|
13859 if (likely(result)) {
|
|
jpayne@69
|
13860 return __Pyx_NewRef(result);
|
|
jpayne@69
|
13861 }
|
|
jpayne@69
|
13862 PyErr_Clear();
|
|
jpayne@69
|
13863 #endif
|
|
jpayne@69
|
13864 return __Pyx_GetBuiltinName(name);
|
|
jpayne@69
|
13865 }
|
|
jpayne@69
|
13866
|
|
jpayne@69
|
13867 /* RaiseException */
|
|
jpayne@69
|
13868 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
13869 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
|
|
jpayne@69
|
13870 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
13871 CYTHON_UNUSED_VAR(cause);
|
|
jpayne@69
|
13872 Py_XINCREF(type);
|
|
jpayne@69
|
13873 if (!value || value == Py_None)
|
|
jpayne@69
|
13874 value = NULL;
|
|
jpayne@69
|
13875 else
|
|
jpayne@69
|
13876 Py_INCREF(value);
|
|
jpayne@69
|
13877 if (!tb || tb == Py_None)
|
|
jpayne@69
|
13878 tb = NULL;
|
|
jpayne@69
|
13879 else {
|
|
jpayne@69
|
13880 Py_INCREF(tb);
|
|
jpayne@69
|
13881 if (!PyTraceBack_Check(tb)) {
|
|
jpayne@69
|
13882 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13883 "raise: arg 3 must be a traceback or None");
|
|
jpayne@69
|
13884 goto raise_error;
|
|
jpayne@69
|
13885 }
|
|
jpayne@69
|
13886 }
|
|
jpayne@69
|
13887 if (PyType_Check(type)) {
|
|
jpayne@69
|
13888 #if CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
13889 if (!value) {
|
|
jpayne@69
|
13890 Py_INCREF(Py_None);
|
|
jpayne@69
|
13891 value = Py_None;
|
|
jpayne@69
|
13892 }
|
|
jpayne@69
|
13893 #endif
|
|
jpayne@69
|
13894 PyErr_NormalizeException(&type, &value, &tb);
|
|
jpayne@69
|
13895 } else {
|
|
jpayne@69
|
13896 if (value) {
|
|
jpayne@69
|
13897 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13898 "instance exception may not have a separate value");
|
|
jpayne@69
|
13899 goto raise_error;
|
|
jpayne@69
|
13900 }
|
|
jpayne@69
|
13901 value = type;
|
|
jpayne@69
|
13902 type = (PyObject*) Py_TYPE(type);
|
|
jpayne@69
|
13903 Py_INCREF(type);
|
|
jpayne@69
|
13904 if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
|
|
jpayne@69
|
13905 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13906 "raise: exception class must be a subclass of BaseException");
|
|
jpayne@69
|
13907 goto raise_error;
|
|
jpayne@69
|
13908 }
|
|
jpayne@69
|
13909 }
|
|
jpayne@69
|
13910 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
13911 __Pyx_ErrRestore(type, value, tb);
|
|
jpayne@69
|
13912 return;
|
|
jpayne@69
|
13913 raise_error:
|
|
jpayne@69
|
13914 Py_XDECREF(value);
|
|
jpayne@69
|
13915 Py_XDECREF(type);
|
|
jpayne@69
|
13916 Py_XDECREF(tb);
|
|
jpayne@69
|
13917 return;
|
|
jpayne@69
|
13918 }
|
|
jpayne@69
|
13919 #else
|
|
jpayne@69
|
13920 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
|
|
jpayne@69
|
13921 PyObject* owned_instance = NULL;
|
|
jpayne@69
|
13922 if (tb == Py_None) {
|
|
jpayne@69
|
13923 tb = 0;
|
|
jpayne@69
|
13924 } else if (tb && !PyTraceBack_Check(tb)) {
|
|
jpayne@69
|
13925 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13926 "raise: arg 3 must be a traceback or None");
|
|
jpayne@69
|
13927 goto bad;
|
|
jpayne@69
|
13928 }
|
|
jpayne@69
|
13929 if (value == Py_None)
|
|
jpayne@69
|
13930 value = 0;
|
|
jpayne@69
|
13931 if (PyExceptionInstance_Check(type)) {
|
|
jpayne@69
|
13932 if (value) {
|
|
jpayne@69
|
13933 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13934 "instance exception may not have a separate value");
|
|
jpayne@69
|
13935 goto bad;
|
|
jpayne@69
|
13936 }
|
|
jpayne@69
|
13937 value = type;
|
|
jpayne@69
|
13938 type = (PyObject*) Py_TYPE(value);
|
|
jpayne@69
|
13939 } else if (PyExceptionClass_Check(type)) {
|
|
jpayne@69
|
13940 PyObject *instance_class = NULL;
|
|
jpayne@69
|
13941 if (value && PyExceptionInstance_Check(value)) {
|
|
jpayne@69
|
13942 instance_class = (PyObject*) Py_TYPE(value);
|
|
jpayne@69
|
13943 if (instance_class != type) {
|
|
jpayne@69
|
13944 int is_subclass = PyObject_IsSubclass(instance_class, type);
|
|
jpayne@69
|
13945 if (!is_subclass) {
|
|
jpayne@69
|
13946 instance_class = NULL;
|
|
jpayne@69
|
13947 } else if (unlikely(is_subclass == -1)) {
|
|
jpayne@69
|
13948 goto bad;
|
|
jpayne@69
|
13949 } else {
|
|
jpayne@69
|
13950 type = instance_class;
|
|
jpayne@69
|
13951 }
|
|
jpayne@69
|
13952 }
|
|
jpayne@69
|
13953 }
|
|
jpayne@69
|
13954 if (!instance_class) {
|
|
jpayne@69
|
13955 PyObject *args;
|
|
jpayne@69
|
13956 if (!value)
|
|
jpayne@69
|
13957 args = PyTuple_New(0);
|
|
jpayne@69
|
13958 else if (PyTuple_Check(value)) {
|
|
jpayne@69
|
13959 Py_INCREF(value);
|
|
jpayne@69
|
13960 args = value;
|
|
jpayne@69
|
13961 } else
|
|
jpayne@69
|
13962 args = PyTuple_Pack(1, value);
|
|
jpayne@69
|
13963 if (!args)
|
|
jpayne@69
|
13964 goto bad;
|
|
jpayne@69
|
13965 owned_instance = PyObject_Call(type, args, NULL);
|
|
jpayne@69
|
13966 Py_DECREF(args);
|
|
jpayne@69
|
13967 if (!owned_instance)
|
|
jpayne@69
|
13968 goto bad;
|
|
jpayne@69
|
13969 value = owned_instance;
|
|
jpayne@69
|
13970 if (!PyExceptionInstance_Check(value)) {
|
|
jpayne@69
|
13971 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
13972 "calling %R should have returned an instance of "
|
|
jpayne@69
|
13973 "BaseException, not %R",
|
|
jpayne@69
|
13974 type, Py_TYPE(value));
|
|
jpayne@69
|
13975 goto bad;
|
|
jpayne@69
|
13976 }
|
|
jpayne@69
|
13977 }
|
|
jpayne@69
|
13978 } else {
|
|
jpayne@69
|
13979 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13980 "raise: exception class must be a subclass of BaseException");
|
|
jpayne@69
|
13981 goto bad;
|
|
jpayne@69
|
13982 }
|
|
jpayne@69
|
13983 if (cause) {
|
|
jpayne@69
|
13984 PyObject *fixed_cause;
|
|
jpayne@69
|
13985 if (cause == Py_None) {
|
|
jpayne@69
|
13986 fixed_cause = NULL;
|
|
jpayne@69
|
13987 } else if (PyExceptionClass_Check(cause)) {
|
|
jpayne@69
|
13988 fixed_cause = PyObject_CallObject(cause, NULL);
|
|
jpayne@69
|
13989 if (fixed_cause == NULL)
|
|
jpayne@69
|
13990 goto bad;
|
|
jpayne@69
|
13991 } else if (PyExceptionInstance_Check(cause)) {
|
|
jpayne@69
|
13992 fixed_cause = cause;
|
|
jpayne@69
|
13993 Py_INCREF(fixed_cause);
|
|
jpayne@69
|
13994 } else {
|
|
jpayne@69
|
13995 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
13996 "exception causes must derive from "
|
|
jpayne@69
|
13997 "BaseException");
|
|
jpayne@69
|
13998 goto bad;
|
|
jpayne@69
|
13999 }
|
|
jpayne@69
|
14000 PyException_SetCause(value, fixed_cause);
|
|
jpayne@69
|
14001 }
|
|
jpayne@69
|
14002 PyErr_SetObject(type, value);
|
|
jpayne@69
|
14003 if (tb) {
|
|
jpayne@69
|
14004 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
14005 PyException_SetTraceback(value, tb);
|
|
jpayne@69
|
14006 #elif CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14007 PyThreadState *tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
14008 PyObject* tmp_tb = tstate->curexc_traceback;
|
|
jpayne@69
|
14009 if (tb != tmp_tb) {
|
|
jpayne@69
|
14010 Py_INCREF(tb);
|
|
jpayne@69
|
14011 tstate->curexc_traceback = tb;
|
|
jpayne@69
|
14012 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
14013 }
|
|
jpayne@69
|
14014 #else
|
|
jpayne@69
|
14015 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
14016 PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb);
|
|
jpayne@69
|
14017 Py_INCREF(tb);
|
|
jpayne@69
|
14018 PyErr_Restore(tmp_type, tmp_value, tb);
|
|
jpayne@69
|
14019 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
14020 #endif
|
|
jpayne@69
|
14021 }
|
|
jpayne@69
|
14022 bad:
|
|
jpayne@69
|
14023 Py_XDECREF(owned_instance);
|
|
jpayne@69
|
14024 return;
|
|
jpayne@69
|
14025 }
|
|
jpayne@69
|
14026 #endif
|
|
jpayne@69
|
14027
|
|
jpayne@69
|
14028 /* GetTopmostException */
|
|
jpayne@69
|
14029 #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14030 static _PyErr_StackItem *
|
|
jpayne@69
|
14031 __Pyx_PyErr_GetTopmostException(PyThreadState *tstate)
|
|
jpayne@69
|
14032 {
|
|
jpayne@69
|
14033 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
14034 while ((exc_info->exc_value == NULL || exc_info->exc_value == Py_None) &&
|
|
jpayne@69
|
14035 exc_info->previous_item != NULL)
|
|
jpayne@69
|
14036 {
|
|
jpayne@69
|
14037 exc_info = exc_info->previous_item;
|
|
jpayne@69
|
14038 }
|
|
jpayne@69
|
14039 return exc_info;
|
|
jpayne@69
|
14040 }
|
|
jpayne@69
|
14041 #endif
|
|
jpayne@69
|
14042
|
|
jpayne@69
|
14043 /* SaveResetException */
|
|
jpayne@69
|
14044 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14045 static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
|
|
jpayne@69
|
14046 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
14047 _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
|
|
jpayne@69
|
14048 PyObject *exc_value = exc_info->exc_value;
|
|
jpayne@69
|
14049 if (exc_value == NULL || exc_value == Py_None) {
|
|
jpayne@69
|
14050 *value = NULL;
|
|
jpayne@69
|
14051 *type = NULL;
|
|
jpayne@69
|
14052 *tb = NULL;
|
|
jpayne@69
|
14053 } else {
|
|
jpayne@69
|
14054 *value = exc_value;
|
|
jpayne@69
|
14055 Py_INCREF(*value);
|
|
jpayne@69
|
14056 *type = (PyObject*) Py_TYPE(exc_value);
|
|
jpayne@69
|
14057 Py_INCREF(*type);
|
|
jpayne@69
|
14058 *tb = PyException_GetTraceback(exc_value);
|
|
jpayne@69
|
14059 }
|
|
jpayne@69
|
14060 #elif CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
14061 _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate);
|
|
jpayne@69
|
14062 *type = exc_info->exc_type;
|
|
jpayne@69
|
14063 *value = exc_info->exc_value;
|
|
jpayne@69
|
14064 *tb = exc_info->exc_traceback;
|
|
jpayne@69
|
14065 Py_XINCREF(*type);
|
|
jpayne@69
|
14066 Py_XINCREF(*value);
|
|
jpayne@69
|
14067 Py_XINCREF(*tb);
|
|
jpayne@69
|
14068 #else
|
|
jpayne@69
|
14069 *type = tstate->exc_type;
|
|
jpayne@69
|
14070 *value = tstate->exc_value;
|
|
jpayne@69
|
14071 *tb = tstate->exc_traceback;
|
|
jpayne@69
|
14072 Py_XINCREF(*type);
|
|
jpayne@69
|
14073 Py_XINCREF(*value);
|
|
jpayne@69
|
14074 Py_XINCREF(*tb);
|
|
jpayne@69
|
14075 #endif
|
|
jpayne@69
|
14076 }
|
|
jpayne@69
|
14077 static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
|
|
jpayne@69
|
14078 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
14079 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
14080 PyObject *tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
14081 exc_info->exc_value = value;
|
|
jpayne@69
|
14082 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
14083 Py_XDECREF(type);
|
|
jpayne@69
|
14084 Py_XDECREF(tb);
|
|
jpayne@69
|
14085 #else
|
|
jpayne@69
|
14086 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
14087 #if CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
14088 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
14089 tmp_type = exc_info->exc_type;
|
|
jpayne@69
|
14090 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
14091 tmp_tb = exc_info->exc_traceback;
|
|
jpayne@69
|
14092 exc_info->exc_type = type;
|
|
jpayne@69
|
14093 exc_info->exc_value = value;
|
|
jpayne@69
|
14094 exc_info->exc_traceback = tb;
|
|
jpayne@69
|
14095 #else
|
|
jpayne@69
|
14096 tmp_type = tstate->exc_type;
|
|
jpayne@69
|
14097 tmp_value = tstate->exc_value;
|
|
jpayne@69
|
14098 tmp_tb = tstate->exc_traceback;
|
|
jpayne@69
|
14099 tstate->exc_type = type;
|
|
jpayne@69
|
14100 tstate->exc_value = value;
|
|
jpayne@69
|
14101 tstate->exc_traceback = tb;
|
|
jpayne@69
|
14102 #endif
|
|
jpayne@69
|
14103 Py_XDECREF(tmp_type);
|
|
jpayne@69
|
14104 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
14105 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
14106 #endif
|
|
jpayne@69
|
14107 }
|
|
jpayne@69
|
14108 #endif
|
|
jpayne@69
|
14109
|
|
jpayne@69
|
14110 /* GetException */
|
|
jpayne@69
|
14111 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14112 static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb)
|
|
jpayne@69
|
14113 #else
|
|
jpayne@69
|
14114 static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
|
|
jpayne@69
|
14115 #endif
|
|
jpayne@69
|
14116 {
|
|
jpayne@69
|
14117 PyObject *local_type = NULL, *local_value, *local_tb = NULL;
|
|
jpayne@69
|
14118 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14119 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
14120 #if PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
14121 local_value = tstate->current_exception;
|
|
jpayne@69
|
14122 tstate->current_exception = 0;
|
|
jpayne@69
|
14123 if (likely(local_value)) {
|
|
jpayne@69
|
14124 local_type = (PyObject*) Py_TYPE(local_value);
|
|
jpayne@69
|
14125 Py_INCREF(local_type);
|
|
jpayne@69
|
14126 local_tb = PyException_GetTraceback(local_value);
|
|
jpayne@69
|
14127 }
|
|
jpayne@69
|
14128 #else
|
|
jpayne@69
|
14129 local_type = tstate->curexc_type;
|
|
jpayne@69
|
14130 local_value = tstate->curexc_value;
|
|
jpayne@69
|
14131 local_tb = tstate->curexc_traceback;
|
|
jpayne@69
|
14132 tstate->curexc_type = 0;
|
|
jpayne@69
|
14133 tstate->curexc_value = 0;
|
|
jpayne@69
|
14134 tstate->curexc_traceback = 0;
|
|
jpayne@69
|
14135 #endif
|
|
jpayne@69
|
14136 #else
|
|
jpayne@69
|
14137 PyErr_Fetch(&local_type, &local_value, &local_tb);
|
|
jpayne@69
|
14138 #endif
|
|
jpayne@69
|
14139 PyErr_NormalizeException(&local_type, &local_value, &local_tb);
|
|
jpayne@69
|
14140 #if CYTHON_FAST_THREAD_STATE && PY_VERSION_HEX >= 0x030C00A6
|
|
jpayne@69
|
14141 if (unlikely(tstate->current_exception))
|
|
jpayne@69
|
14142 #elif CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14143 if (unlikely(tstate->curexc_type))
|
|
jpayne@69
|
14144 #else
|
|
jpayne@69
|
14145 if (unlikely(PyErr_Occurred()))
|
|
jpayne@69
|
14146 #endif
|
|
jpayne@69
|
14147 goto bad;
|
|
jpayne@69
|
14148 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
14149 if (local_tb) {
|
|
jpayne@69
|
14150 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
|
|
jpayne@69
|
14151 goto bad;
|
|
jpayne@69
|
14152 }
|
|
jpayne@69
|
14153 #endif
|
|
jpayne@69
|
14154 Py_XINCREF(local_tb);
|
|
jpayne@69
|
14155 Py_XINCREF(local_type);
|
|
jpayne@69
|
14156 Py_XINCREF(local_value);
|
|
jpayne@69
|
14157 *type = local_type;
|
|
jpayne@69
|
14158 *value = local_value;
|
|
jpayne@69
|
14159 *tb = local_tb;
|
|
jpayne@69
|
14160 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14161 #if CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
14162 {
|
|
jpayne@69
|
14163 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
14164 #if PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
14165 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
14166 exc_info->exc_value = local_value;
|
|
jpayne@69
|
14167 tmp_type = NULL;
|
|
jpayne@69
|
14168 tmp_tb = NULL;
|
|
jpayne@69
|
14169 Py_XDECREF(local_type);
|
|
jpayne@69
|
14170 Py_XDECREF(local_tb);
|
|
jpayne@69
|
14171 #else
|
|
jpayne@69
|
14172 tmp_type = exc_info->exc_type;
|
|
jpayne@69
|
14173 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
14174 tmp_tb = exc_info->exc_traceback;
|
|
jpayne@69
|
14175 exc_info->exc_type = local_type;
|
|
jpayne@69
|
14176 exc_info->exc_value = local_value;
|
|
jpayne@69
|
14177 exc_info->exc_traceback = local_tb;
|
|
jpayne@69
|
14178 #endif
|
|
jpayne@69
|
14179 }
|
|
jpayne@69
|
14180 #else
|
|
jpayne@69
|
14181 tmp_type = tstate->exc_type;
|
|
jpayne@69
|
14182 tmp_value = tstate->exc_value;
|
|
jpayne@69
|
14183 tmp_tb = tstate->exc_traceback;
|
|
jpayne@69
|
14184 tstate->exc_type = local_type;
|
|
jpayne@69
|
14185 tstate->exc_value = local_value;
|
|
jpayne@69
|
14186 tstate->exc_traceback = local_tb;
|
|
jpayne@69
|
14187 #endif
|
|
jpayne@69
|
14188 Py_XDECREF(tmp_type);
|
|
jpayne@69
|
14189 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
14190 Py_XDECREF(tmp_tb);
|
|
jpayne@69
|
14191 #else
|
|
jpayne@69
|
14192 PyErr_SetExcInfo(local_type, local_value, local_tb);
|
|
jpayne@69
|
14193 #endif
|
|
jpayne@69
|
14194 return 0;
|
|
jpayne@69
|
14195 bad:
|
|
jpayne@69
|
14196 *type = 0;
|
|
jpayne@69
|
14197 *value = 0;
|
|
jpayne@69
|
14198 *tb = 0;
|
|
jpayne@69
|
14199 Py_XDECREF(local_type);
|
|
jpayne@69
|
14200 Py_XDECREF(local_value);
|
|
jpayne@69
|
14201 Py_XDECREF(local_tb);
|
|
jpayne@69
|
14202 return -1;
|
|
jpayne@69
|
14203 }
|
|
jpayne@69
|
14204
|
|
jpayne@69
|
14205 /* RaiseTooManyValuesToUnpack */
|
|
jpayne@69
|
14206 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
|
|
jpayne@69
|
14207 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
14208 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
|
|
jpayne@69
|
14209 }
|
|
jpayne@69
|
14210
|
|
jpayne@69
|
14211 /* RaiseNeedMoreValuesToUnpack */
|
|
jpayne@69
|
14212 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
|
|
jpayne@69
|
14213 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
14214 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
|
|
jpayne@69
|
14215 index, (index == 1) ? "" : "s");
|
|
jpayne@69
|
14216 }
|
|
jpayne@69
|
14217
|
|
jpayne@69
|
14218 /* IterFinish */
|
|
jpayne@69
|
14219 static CYTHON_INLINE int __Pyx_IterFinish(void) {
|
|
jpayne@69
|
14220 PyObject* exc_type;
|
|
jpayne@69
|
14221 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
14222 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
14223 exc_type = __Pyx_PyErr_CurrentExceptionType();
|
|
jpayne@69
|
14224 if (unlikely(exc_type)) {
|
|
jpayne@69
|
14225 if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)))
|
|
jpayne@69
|
14226 return -1;
|
|
jpayne@69
|
14227 __Pyx_PyErr_Clear();
|
|
jpayne@69
|
14228 return 0;
|
|
jpayne@69
|
14229 }
|
|
jpayne@69
|
14230 return 0;
|
|
jpayne@69
|
14231 }
|
|
jpayne@69
|
14232
|
|
jpayne@69
|
14233 /* UnpackItemEndCheck */
|
|
jpayne@69
|
14234 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
|
|
jpayne@69
|
14235 if (unlikely(retval)) {
|
|
jpayne@69
|
14236 Py_DECREF(retval);
|
|
jpayne@69
|
14237 __Pyx_RaiseTooManyValuesError(expected);
|
|
jpayne@69
|
14238 return -1;
|
|
jpayne@69
|
14239 }
|
|
jpayne@69
|
14240 return __Pyx_IterFinish();
|
|
jpayne@69
|
14241 }
|
|
jpayne@69
|
14242
|
|
jpayne@69
|
14243 /* PyIntBinop */
|
|
jpayne@69
|
14244 #if !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
14245 static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) {
|
|
jpayne@69
|
14246 CYTHON_MAYBE_UNUSED_VAR(intval);
|
|
jpayne@69
|
14247 CYTHON_MAYBE_UNUSED_VAR(inplace);
|
|
jpayne@69
|
14248 CYTHON_UNUSED_VAR(zerodivision_check);
|
|
jpayne@69
|
14249 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
14250 if (likely(PyInt_CheckExact(op1))) {
|
|
jpayne@69
|
14251 const long b = intval;
|
|
jpayne@69
|
14252 long x;
|
|
jpayne@69
|
14253 long a = PyInt_AS_LONG(op1);
|
|
jpayne@69
|
14254
|
|
jpayne@69
|
14255 x = (long)((unsigned long)a - (unsigned long)b);
|
|
jpayne@69
|
14256 if (likely((x^a) >= 0 || (x^~b) >= 0))
|
|
jpayne@69
|
14257 return PyInt_FromLong(x);
|
|
jpayne@69
|
14258 return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
|
|
jpayne@69
|
14259 }
|
|
jpayne@69
|
14260 #endif
|
|
jpayne@69
|
14261 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
14262 if (likely(PyLong_CheckExact(op1))) {
|
|
jpayne@69
|
14263 const long b = intval;
|
|
jpayne@69
|
14264 long a, x;
|
|
jpayne@69
|
14265 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14266 const PY_LONG_LONG llb = intval;
|
|
jpayne@69
|
14267 PY_LONG_LONG lla, llx;
|
|
jpayne@69
|
14268 #endif
|
|
jpayne@69
|
14269 if (unlikely(__Pyx_PyLong_IsZero(op1))) {
|
|
jpayne@69
|
14270 return PyLong_FromLong(-intval);
|
|
jpayne@69
|
14271 }
|
|
jpayne@69
|
14272 if (likely(__Pyx_PyLong_IsCompact(op1))) {
|
|
jpayne@69
|
14273 a = __Pyx_PyLong_CompactValue(op1);
|
|
jpayne@69
|
14274 } else {
|
|
jpayne@69
|
14275 const digit* digits = __Pyx_PyLong_Digits(op1);
|
|
jpayne@69
|
14276 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1);
|
|
jpayne@69
|
14277 switch (size) {
|
|
jpayne@69
|
14278 case -2:
|
|
jpayne@69
|
14279 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
14280 a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
14281 break;
|
|
jpayne@69
|
14282 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14283 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
14284 lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
14285 goto long_long;
|
|
jpayne@69
|
14286 #endif
|
|
jpayne@69
|
14287 }
|
|
jpayne@69
|
14288 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14289 case 2:
|
|
jpayne@69
|
14290 if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
14291 a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
14292 break;
|
|
jpayne@69
|
14293 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14294 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
14295 lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
|
|
jpayne@69
|
14296 goto long_long;
|
|
jpayne@69
|
14297 #endif
|
|
jpayne@69
|
14298 }
|
|
jpayne@69
|
14299 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14300 case -3:
|
|
jpayne@69
|
14301 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
14302 a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
14303 break;
|
|
jpayne@69
|
14304 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14305 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
14306 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
|
14307 goto long_long;
|
|
jpayne@69
|
14308 #endif
|
|
jpayne@69
|
14309 }
|
|
jpayne@69
|
14310 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14311 case 3:
|
|
jpayne@69
|
14312 if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
14313 a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
|
|
jpayne@69
|
14314 break;
|
|
jpayne@69
|
14315 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14316 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
14317 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
|
14318 goto long_long;
|
|
jpayne@69
|
14319 #endif
|
|
jpayne@69
|
14320 }
|
|
jpayne@69
|
14321 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14322 case -4:
|
|
jpayne@69
|
14323 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
14324 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
|
14325 break;
|
|
jpayne@69
|
14326 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14327 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
14328 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
|
14329 goto long_long;
|
|
jpayne@69
|
14330 #endif
|
|
jpayne@69
|
14331 }
|
|
jpayne@69
|
14332 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14333 case 4:
|
|
jpayne@69
|
14334 if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
14335 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
|
14336 break;
|
|
jpayne@69
|
14337 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14338 } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
14339 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
|
14340 goto long_long;
|
|
jpayne@69
|
14341 #endif
|
|
jpayne@69
|
14342 }
|
|
jpayne@69
|
14343 CYTHON_FALLTHROUGH;
|
|
jpayne@69
|
14344 default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
|
|
jpayne@69
|
14345 }
|
|
jpayne@69
|
14346 }
|
|
jpayne@69
|
14347 x = a - b;
|
|
jpayne@69
|
14348 return PyLong_FromLong(x);
|
|
jpayne@69
|
14349 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
14350 long_long:
|
|
jpayne@69
|
14351 llx = lla - llb;
|
|
jpayne@69
|
14352 return PyLong_FromLongLong(llx);
|
|
jpayne@69
|
14353 #endif
|
|
jpayne@69
|
14354
|
|
jpayne@69
|
14355
|
|
jpayne@69
|
14356 }
|
|
jpayne@69
|
14357 #endif
|
|
jpayne@69
|
14358 if (PyFloat_CheckExact(op1)) {
|
|
jpayne@69
|
14359 const long b = intval;
|
|
jpayne@69
|
14360 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14361 double a = __pyx_PyFloat_AsDouble(op1);
|
|
jpayne@69
|
14362 #else
|
|
jpayne@69
|
14363 double a = PyFloat_AS_DOUBLE(op1);
|
|
jpayne@69
|
14364 #endif
|
|
jpayne@69
|
14365 double result;
|
|
jpayne@69
|
14366
|
|
jpayne@69
|
14367 PyFPE_START_PROTECT("subtract", return NULL)
|
|
jpayne@69
|
14368 result = ((double)a) - (double)b;
|
|
jpayne@69
|
14369 PyFPE_END_PROTECT(result)
|
|
jpayne@69
|
14370 return PyFloat_FromDouble(result);
|
|
jpayne@69
|
14371 }
|
|
jpayne@69
|
14372 return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2);
|
|
jpayne@69
|
14373 }
|
|
jpayne@69
|
14374 #endif
|
|
jpayne@69
|
14375
|
|
jpayne@69
|
14376 /* PyObjectLookupSpecial */
|
|
jpayne@69
|
14377 #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
14378 static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error) {
|
|
jpayne@69
|
14379 PyObject *res;
|
|
jpayne@69
|
14380 PyTypeObject *tp = Py_TYPE(obj);
|
|
jpayne@69
|
14381 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
14382 if (unlikely(PyInstance_Check(obj)))
|
|
jpayne@69
|
14383 return with_error ? __Pyx_PyObject_GetAttrStr(obj, attr_name) : __Pyx_PyObject_GetAttrStrNoError(obj, attr_name);
|
|
jpayne@69
|
14384 #endif
|
|
jpayne@69
|
14385 res = _PyType_Lookup(tp, attr_name);
|
|
jpayne@69
|
14386 if (likely(res)) {
|
|
jpayne@69
|
14387 descrgetfunc f = Py_TYPE(res)->tp_descr_get;
|
|
jpayne@69
|
14388 if (!f) {
|
|
jpayne@69
|
14389 Py_INCREF(res);
|
|
jpayne@69
|
14390 } else {
|
|
jpayne@69
|
14391 res = f(res, obj, (PyObject *)tp);
|
|
jpayne@69
|
14392 }
|
|
jpayne@69
|
14393 } else if (with_error) {
|
|
jpayne@69
|
14394 PyErr_SetObject(PyExc_AttributeError, attr_name);
|
|
jpayne@69
|
14395 }
|
|
jpayne@69
|
14396 return res;
|
|
jpayne@69
|
14397 }
|
|
jpayne@69
|
14398 #endif
|
|
jpayne@69
|
14399
|
|
jpayne@69
|
14400 /* SwapException */
|
|
jpayne@69
|
14401 #if CYTHON_FAST_THREAD_STATE
|
|
jpayne@69
|
14402 static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
|
|
jpayne@69
|
14403 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
14404 #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4
|
|
jpayne@69
|
14405 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
14406 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
14407 exc_info->exc_value = *value;
|
|
jpayne@69
|
14408 if (tmp_value == NULL || tmp_value == Py_None) {
|
|
jpayne@69
|
14409 Py_XDECREF(tmp_value);
|
|
jpayne@69
|
14410 tmp_value = NULL;
|
|
jpayne@69
|
14411 tmp_type = NULL;
|
|
jpayne@69
|
14412 tmp_tb = NULL;
|
|
jpayne@69
|
14413 } else {
|
|
jpayne@69
|
14414 tmp_type = (PyObject*) Py_TYPE(tmp_value);
|
|
jpayne@69
|
14415 Py_INCREF(tmp_type);
|
|
jpayne@69
|
14416 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
14417 tmp_tb = ((PyBaseExceptionObject*) tmp_value)->traceback;
|
|
jpayne@69
|
14418 Py_XINCREF(tmp_tb);
|
|
jpayne@69
|
14419 #else
|
|
jpayne@69
|
14420 tmp_tb = PyException_GetTraceback(tmp_value);
|
|
jpayne@69
|
14421 #endif
|
|
jpayne@69
|
14422 }
|
|
jpayne@69
|
14423 #elif CYTHON_USE_EXC_INFO_STACK
|
|
jpayne@69
|
14424 _PyErr_StackItem *exc_info = tstate->exc_info;
|
|
jpayne@69
|
14425 tmp_type = exc_info->exc_type;
|
|
jpayne@69
|
14426 tmp_value = exc_info->exc_value;
|
|
jpayne@69
|
14427 tmp_tb = exc_info->exc_traceback;
|
|
jpayne@69
|
14428 exc_info->exc_type = *type;
|
|
jpayne@69
|
14429 exc_info->exc_value = *value;
|
|
jpayne@69
|
14430 exc_info->exc_traceback = *tb;
|
|
jpayne@69
|
14431 #else
|
|
jpayne@69
|
14432 tmp_type = tstate->exc_type;
|
|
jpayne@69
|
14433 tmp_value = tstate->exc_value;
|
|
jpayne@69
|
14434 tmp_tb = tstate->exc_traceback;
|
|
jpayne@69
|
14435 tstate->exc_type = *type;
|
|
jpayne@69
|
14436 tstate->exc_value = *value;
|
|
jpayne@69
|
14437 tstate->exc_traceback = *tb;
|
|
jpayne@69
|
14438 #endif
|
|
jpayne@69
|
14439 *type = tmp_type;
|
|
jpayne@69
|
14440 *value = tmp_value;
|
|
jpayne@69
|
14441 *tb = tmp_tb;
|
|
jpayne@69
|
14442 }
|
|
jpayne@69
|
14443 #else
|
|
jpayne@69
|
14444 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
|
|
jpayne@69
|
14445 PyObject *tmp_type, *tmp_value, *tmp_tb;
|
|
jpayne@69
|
14446 PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
|
|
jpayne@69
|
14447 PyErr_SetExcInfo(*type, *value, *tb);
|
|
jpayne@69
|
14448 *type = tmp_type;
|
|
jpayne@69
|
14449 *value = tmp_value;
|
|
jpayne@69
|
14450 *tb = tmp_tb;
|
|
jpayne@69
|
14451 }
|
|
jpayne@69
|
14452 #endif
|
|
jpayne@69
|
14453
|
|
jpayne@69
|
14454 /* PyIntCompare */
|
|
jpayne@69
|
14455 static CYTHON_INLINE int __Pyx_PyInt_BoolEqObjC(PyObject *op1, PyObject *op2, long intval, long inplace) {
|
|
jpayne@69
|
14456 CYTHON_MAYBE_UNUSED_VAR(intval);
|
|
jpayne@69
|
14457 CYTHON_UNUSED_VAR(inplace);
|
|
jpayne@69
|
14458 if (op1 == op2) {
|
|
jpayne@69
|
14459 return 1;
|
|
jpayne@69
|
14460 }
|
|
jpayne@69
|
14461 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
14462 if (likely(PyInt_CheckExact(op1))) {
|
|
jpayne@69
|
14463 const long b = intval;
|
|
jpayne@69
|
14464 long a = PyInt_AS_LONG(op1);
|
|
jpayne@69
|
14465 return (a == b);
|
|
jpayne@69
|
14466 }
|
|
jpayne@69
|
14467 #endif
|
|
jpayne@69
|
14468 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
14469 if (likely(PyLong_CheckExact(op1))) {
|
|
jpayne@69
|
14470 int unequal;
|
|
jpayne@69
|
14471 unsigned long uintval;
|
|
jpayne@69
|
14472 Py_ssize_t size = __Pyx_PyLong_DigitCount(op1);
|
|
jpayne@69
|
14473 const digit* digits = __Pyx_PyLong_Digits(op1);
|
|
jpayne@69
|
14474 if (intval == 0) {
|
|
jpayne@69
|
14475 return (__Pyx_PyLong_IsZero(op1) == 1);
|
|
jpayne@69
|
14476 } else if (intval < 0) {
|
|
jpayne@69
|
14477 if (__Pyx_PyLong_IsNonNeg(op1))
|
|
jpayne@69
|
14478 return 0;
|
|
jpayne@69
|
14479 intval = -intval;
|
|
jpayne@69
|
14480 } else {
|
|
jpayne@69
|
14481 if (__Pyx_PyLong_IsNeg(op1))
|
|
jpayne@69
|
14482 return 0;
|
|
jpayne@69
|
14483 }
|
|
jpayne@69
|
14484 uintval = (unsigned long) intval;
|
|
jpayne@69
|
14485 #if PyLong_SHIFT * 4 < SIZEOF_LONG*8
|
|
jpayne@69
|
14486 if (uintval >> (PyLong_SHIFT * 4)) {
|
|
jpayne@69
|
14487 unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
|
|
jpayne@69
|
14488 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
|
|
jpayne@69
|
14489 } else
|
|
jpayne@69
|
14490 #endif
|
|
jpayne@69
|
14491 #if PyLong_SHIFT * 3 < SIZEOF_LONG*8
|
|
jpayne@69
|
14492 if (uintval >> (PyLong_SHIFT * 3)) {
|
|
jpayne@69
|
14493 unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
|
|
jpayne@69
|
14494 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
|
|
jpayne@69
|
14495 } else
|
|
jpayne@69
|
14496 #endif
|
|
jpayne@69
|
14497 #if PyLong_SHIFT * 2 < SIZEOF_LONG*8
|
|
jpayne@69
|
14498 if (uintval >> (PyLong_SHIFT * 2)) {
|
|
jpayne@69
|
14499 unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
|
|
jpayne@69
|
14500 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
|
|
jpayne@69
|
14501 } else
|
|
jpayne@69
|
14502 #endif
|
|
jpayne@69
|
14503 #if PyLong_SHIFT * 1 < SIZEOF_LONG*8
|
|
jpayne@69
|
14504 if (uintval >> (PyLong_SHIFT * 1)) {
|
|
jpayne@69
|
14505 unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK))
|
|
jpayne@69
|
14506 | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK));
|
|
jpayne@69
|
14507 } else
|
|
jpayne@69
|
14508 #endif
|
|
jpayne@69
|
14509 unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK));
|
|
jpayne@69
|
14510 return (unequal == 0);
|
|
jpayne@69
|
14511 }
|
|
jpayne@69
|
14512 #endif
|
|
jpayne@69
|
14513 if (PyFloat_CheckExact(op1)) {
|
|
jpayne@69
|
14514 const long b = intval;
|
|
jpayne@69
|
14515 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14516 double a = __pyx_PyFloat_AsDouble(op1);
|
|
jpayne@69
|
14517 #else
|
|
jpayne@69
|
14518 double a = PyFloat_AS_DOUBLE(op1);
|
|
jpayne@69
|
14519 #endif
|
|
jpayne@69
|
14520 return ((double)a == (double)b);
|
|
jpayne@69
|
14521 }
|
|
jpayne@69
|
14522 return __Pyx_PyObject_IsTrueAndDecref(
|
|
jpayne@69
|
14523 PyObject_RichCompare(op1, op2, Py_EQ));
|
|
jpayne@69
|
14524 }
|
|
jpayne@69
|
14525
|
|
jpayne@69
|
14526 /* DictGetItem */
|
|
jpayne@69
|
14527 #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
|
|
jpayne@69
|
14528 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
|
|
jpayne@69
|
14529 PyObject *value;
|
|
jpayne@69
|
14530 value = PyDict_GetItemWithError(d, key);
|
|
jpayne@69
|
14531 if (unlikely(!value)) {
|
|
jpayne@69
|
14532 if (!PyErr_Occurred()) {
|
|
jpayne@69
|
14533 if (unlikely(PyTuple_Check(key))) {
|
|
jpayne@69
|
14534 PyObject* args = PyTuple_Pack(1, key);
|
|
jpayne@69
|
14535 if (likely(args)) {
|
|
jpayne@69
|
14536 PyErr_SetObject(PyExc_KeyError, args);
|
|
jpayne@69
|
14537 Py_DECREF(args);
|
|
jpayne@69
|
14538 }
|
|
jpayne@69
|
14539 } else {
|
|
jpayne@69
|
14540 PyErr_SetObject(PyExc_KeyError, key);
|
|
jpayne@69
|
14541 }
|
|
jpayne@69
|
14542 }
|
|
jpayne@69
|
14543 return NULL;
|
|
jpayne@69
|
14544 }
|
|
jpayne@69
|
14545 Py_INCREF(value);
|
|
jpayne@69
|
14546 return value;
|
|
jpayne@69
|
14547 }
|
|
jpayne@69
|
14548 #endif
|
|
jpayne@69
|
14549
|
|
jpayne@69
|
14550 /* FixUpExtensionType */
|
|
jpayne@69
|
14551 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
14552 static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type) {
|
|
jpayne@69
|
14553 #if PY_VERSION_HEX > 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14554 CYTHON_UNUSED_VAR(spec);
|
|
jpayne@69
|
14555 CYTHON_UNUSED_VAR(type);
|
|
jpayne@69
|
14556 #else
|
|
jpayne@69
|
14557 const PyType_Slot *slot = spec->slots;
|
|
jpayne@69
|
14558 while (slot && slot->slot && slot->slot != Py_tp_members)
|
|
jpayne@69
|
14559 slot++;
|
|
jpayne@69
|
14560 if (slot && slot->slot == Py_tp_members) {
|
|
jpayne@69
|
14561 int changed = 0;
|
|
jpayne@69
|
14562 #if !(PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON)
|
|
jpayne@69
|
14563 const
|
|
jpayne@69
|
14564 #endif
|
|
jpayne@69
|
14565 PyMemberDef *memb = (PyMemberDef*) slot->pfunc;
|
|
jpayne@69
|
14566 while (memb && memb->name) {
|
|
jpayne@69
|
14567 if (memb->name[0] == '_' && memb->name[1] == '_') {
|
|
jpayne@69
|
14568 #if PY_VERSION_HEX < 0x030900b1
|
|
jpayne@69
|
14569 if (strcmp(memb->name, "__weaklistoffset__") == 0) {
|
|
jpayne@69
|
14570 assert(memb->type == T_PYSSIZET);
|
|
jpayne@69
|
14571 assert(memb->flags == READONLY);
|
|
jpayne@69
|
14572 type->tp_weaklistoffset = memb->offset;
|
|
jpayne@69
|
14573 changed = 1;
|
|
jpayne@69
|
14574 }
|
|
jpayne@69
|
14575 else if (strcmp(memb->name, "__dictoffset__") == 0) {
|
|
jpayne@69
|
14576 assert(memb->type == T_PYSSIZET);
|
|
jpayne@69
|
14577 assert(memb->flags == READONLY);
|
|
jpayne@69
|
14578 type->tp_dictoffset = memb->offset;
|
|
jpayne@69
|
14579 changed = 1;
|
|
jpayne@69
|
14580 }
|
|
jpayne@69
|
14581 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14582 else if (strcmp(memb->name, "__vectorcalloffset__") == 0) {
|
|
jpayne@69
|
14583 assert(memb->type == T_PYSSIZET);
|
|
jpayne@69
|
14584 assert(memb->flags == READONLY);
|
|
jpayne@69
|
14585 #if PY_VERSION_HEX >= 0x030800b4
|
|
jpayne@69
|
14586 type->tp_vectorcall_offset = memb->offset;
|
|
jpayne@69
|
14587 #else
|
|
jpayne@69
|
14588 type->tp_print = (printfunc) memb->offset;
|
|
jpayne@69
|
14589 #endif
|
|
jpayne@69
|
14590 changed = 1;
|
|
jpayne@69
|
14591 }
|
|
jpayne@69
|
14592 #endif
|
|
jpayne@69
|
14593 #else
|
|
jpayne@69
|
14594 if ((0));
|
|
jpayne@69
|
14595 #endif
|
|
jpayne@69
|
14596 #if PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
14597 else if (strcmp(memb->name, "__module__") == 0) {
|
|
jpayne@69
|
14598 PyObject *descr;
|
|
jpayne@69
|
14599 assert(memb->type == T_OBJECT);
|
|
jpayne@69
|
14600 assert(memb->flags == 0 || memb->flags == READONLY);
|
|
jpayne@69
|
14601 descr = PyDescr_NewMember(type, memb);
|
|
jpayne@69
|
14602 if (unlikely(!descr))
|
|
jpayne@69
|
14603 return -1;
|
|
jpayne@69
|
14604 if (unlikely(PyDict_SetItem(type->tp_dict, PyDescr_NAME(descr), descr) < 0)) {
|
|
jpayne@69
|
14605 Py_DECREF(descr);
|
|
jpayne@69
|
14606 return -1;
|
|
jpayne@69
|
14607 }
|
|
jpayne@69
|
14608 Py_DECREF(descr);
|
|
jpayne@69
|
14609 changed = 1;
|
|
jpayne@69
|
14610 }
|
|
jpayne@69
|
14611 #endif
|
|
jpayne@69
|
14612 }
|
|
jpayne@69
|
14613 memb++;
|
|
jpayne@69
|
14614 }
|
|
jpayne@69
|
14615 if (changed)
|
|
jpayne@69
|
14616 PyType_Modified(type);
|
|
jpayne@69
|
14617 }
|
|
jpayne@69
|
14618 #endif
|
|
jpayne@69
|
14619 return 0;
|
|
jpayne@69
|
14620 }
|
|
jpayne@69
|
14621 #endif
|
|
jpayne@69
|
14622
|
|
jpayne@69
|
14623 /* FetchSharedCythonModule */
|
|
jpayne@69
|
14624 static PyObject *__Pyx_FetchSharedCythonABIModule(void) {
|
|
jpayne@69
|
14625 return __Pyx_PyImport_AddModuleRef((char*) __PYX_ABI_MODULE_NAME);
|
|
jpayne@69
|
14626 }
|
|
jpayne@69
|
14627
|
|
jpayne@69
|
14628 /* FetchCommonType */
|
|
jpayne@69
|
14629 static int __Pyx_VerifyCachedType(PyObject *cached_type,
|
|
jpayne@69
|
14630 const char *name,
|
|
jpayne@69
|
14631 Py_ssize_t basicsize,
|
|
jpayne@69
|
14632 Py_ssize_t expected_basicsize) {
|
|
jpayne@69
|
14633 if (!PyType_Check(cached_type)) {
|
|
jpayne@69
|
14634 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
14635 "Shared Cython type %.200s is not a type object", name);
|
|
jpayne@69
|
14636 return -1;
|
|
jpayne@69
|
14637 }
|
|
jpayne@69
|
14638 if (basicsize != expected_basicsize) {
|
|
jpayne@69
|
14639 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
14640 "Shared Cython type %.200s has the wrong size, try recompiling",
|
|
jpayne@69
|
14641 name);
|
|
jpayne@69
|
14642 return -1;
|
|
jpayne@69
|
14643 }
|
|
jpayne@69
|
14644 return 0;
|
|
jpayne@69
|
14645 }
|
|
jpayne@69
|
14646 #if !CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
14647 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
|
|
jpayne@69
|
14648 PyObject* abi_module;
|
|
jpayne@69
|
14649 const char* object_name;
|
|
jpayne@69
|
14650 PyTypeObject *cached_type = NULL;
|
|
jpayne@69
|
14651 abi_module = __Pyx_FetchSharedCythonABIModule();
|
|
jpayne@69
|
14652 if (!abi_module) return NULL;
|
|
jpayne@69
|
14653 object_name = strrchr(type->tp_name, '.');
|
|
jpayne@69
|
14654 object_name = object_name ? object_name+1 : type->tp_name;
|
|
jpayne@69
|
14655 cached_type = (PyTypeObject*) PyObject_GetAttrString(abi_module, object_name);
|
|
jpayne@69
|
14656 if (cached_type) {
|
|
jpayne@69
|
14657 if (__Pyx_VerifyCachedType(
|
|
jpayne@69
|
14658 (PyObject *)cached_type,
|
|
jpayne@69
|
14659 object_name,
|
|
jpayne@69
|
14660 cached_type->tp_basicsize,
|
|
jpayne@69
|
14661 type->tp_basicsize) < 0) {
|
|
jpayne@69
|
14662 goto bad;
|
|
jpayne@69
|
14663 }
|
|
jpayne@69
|
14664 goto done;
|
|
jpayne@69
|
14665 }
|
|
jpayne@69
|
14666 if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
|
|
jpayne@69
|
14667 PyErr_Clear();
|
|
jpayne@69
|
14668 if (PyType_Ready(type) < 0) goto bad;
|
|
jpayne@69
|
14669 if (PyObject_SetAttrString(abi_module, object_name, (PyObject *)type) < 0)
|
|
jpayne@69
|
14670 goto bad;
|
|
jpayne@69
|
14671 Py_INCREF(type);
|
|
jpayne@69
|
14672 cached_type = type;
|
|
jpayne@69
|
14673 done:
|
|
jpayne@69
|
14674 Py_DECREF(abi_module);
|
|
jpayne@69
|
14675 return cached_type;
|
|
jpayne@69
|
14676 bad:
|
|
jpayne@69
|
14677 Py_XDECREF(cached_type);
|
|
jpayne@69
|
14678 cached_type = NULL;
|
|
jpayne@69
|
14679 goto done;
|
|
jpayne@69
|
14680 }
|
|
jpayne@69
|
14681 #else
|
|
jpayne@69
|
14682 static PyTypeObject *__Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases) {
|
|
jpayne@69
|
14683 PyObject *abi_module, *cached_type = NULL;
|
|
jpayne@69
|
14684 const char* object_name = strrchr(spec->name, '.');
|
|
jpayne@69
|
14685 object_name = object_name ? object_name+1 : spec->name;
|
|
jpayne@69
|
14686 abi_module = __Pyx_FetchSharedCythonABIModule();
|
|
jpayne@69
|
14687 if (!abi_module) return NULL;
|
|
jpayne@69
|
14688 cached_type = PyObject_GetAttrString(abi_module, object_name);
|
|
jpayne@69
|
14689 if (cached_type) {
|
|
jpayne@69
|
14690 Py_ssize_t basicsize;
|
|
jpayne@69
|
14691 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14692 PyObject *py_basicsize;
|
|
jpayne@69
|
14693 py_basicsize = PyObject_GetAttrString(cached_type, "__basicsize__");
|
|
jpayne@69
|
14694 if (unlikely(!py_basicsize)) goto bad;
|
|
jpayne@69
|
14695 basicsize = PyLong_AsSsize_t(py_basicsize);
|
|
jpayne@69
|
14696 Py_DECREF(py_basicsize);
|
|
jpayne@69
|
14697 py_basicsize = 0;
|
|
jpayne@69
|
14698 if (unlikely(basicsize == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
|
|
jpayne@69
|
14699 #else
|
|
jpayne@69
|
14700 basicsize = likely(PyType_Check(cached_type)) ? ((PyTypeObject*) cached_type)->tp_basicsize : -1;
|
|
jpayne@69
|
14701 #endif
|
|
jpayne@69
|
14702 if (__Pyx_VerifyCachedType(
|
|
jpayne@69
|
14703 cached_type,
|
|
jpayne@69
|
14704 object_name,
|
|
jpayne@69
|
14705 basicsize,
|
|
jpayne@69
|
14706 spec->basicsize) < 0) {
|
|
jpayne@69
|
14707 goto bad;
|
|
jpayne@69
|
14708 }
|
|
jpayne@69
|
14709 goto done;
|
|
jpayne@69
|
14710 }
|
|
jpayne@69
|
14711 if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
|
|
jpayne@69
|
14712 PyErr_Clear();
|
|
jpayne@69
|
14713 CYTHON_UNUSED_VAR(module);
|
|
jpayne@69
|
14714 cached_type = __Pyx_PyType_FromModuleAndSpec(abi_module, spec, bases);
|
|
jpayne@69
|
14715 if (unlikely(!cached_type)) goto bad;
|
|
jpayne@69
|
14716 if (unlikely(__Pyx_fix_up_extension_type_from_spec(spec, (PyTypeObject *) cached_type) < 0)) goto bad;
|
|
jpayne@69
|
14717 if (PyObject_SetAttrString(abi_module, object_name, cached_type) < 0) goto bad;
|
|
jpayne@69
|
14718 done:
|
|
jpayne@69
|
14719 Py_DECREF(abi_module);
|
|
jpayne@69
|
14720 assert(cached_type == NULL || PyType_Check(cached_type));
|
|
jpayne@69
|
14721 return (PyTypeObject *) cached_type;
|
|
jpayne@69
|
14722 bad:
|
|
jpayne@69
|
14723 Py_XDECREF(cached_type);
|
|
jpayne@69
|
14724 cached_type = NULL;
|
|
jpayne@69
|
14725 goto done;
|
|
jpayne@69
|
14726 }
|
|
jpayne@69
|
14727 #endif
|
|
jpayne@69
|
14728
|
|
jpayne@69
|
14729 /* PyVectorcallFastCallDict */
|
|
jpayne@69
|
14730 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
14731 static PyObject *__Pyx_PyVectorcall_FastCallDict_kw(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw)
|
|
jpayne@69
|
14732 {
|
|
jpayne@69
|
14733 PyObject *res = NULL;
|
|
jpayne@69
|
14734 PyObject *kwnames;
|
|
jpayne@69
|
14735 PyObject **newargs;
|
|
jpayne@69
|
14736 PyObject **kwvalues;
|
|
jpayne@69
|
14737 Py_ssize_t i, pos;
|
|
jpayne@69
|
14738 size_t j;
|
|
jpayne@69
|
14739 PyObject *key, *value;
|
|
jpayne@69
|
14740 unsigned long keys_are_strings;
|
|
jpayne@69
|
14741 Py_ssize_t nkw = PyDict_GET_SIZE(kw);
|
|
jpayne@69
|
14742 newargs = (PyObject **)PyMem_Malloc((nargs + (size_t)nkw) * sizeof(args[0]));
|
|
jpayne@69
|
14743 if (unlikely(newargs == NULL)) {
|
|
jpayne@69
|
14744 PyErr_NoMemory();
|
|
jpayne@69
|
14745 return NULL;
|
|
jpayne@69
|
14746 }
|
|
jpayne@69
|
14747 for (j = 0; j < nargs; j++) newargs[j] = args[j];
|
|
jpayne@69
|
14748 kwnames = PyTuple_New(nkw);
|
|
jpayne@69
|
14749 if (unlikely(kwnames == NULL)) {
|
|
jpayne@69
|
14750 PyMem_Free(newargs);
|
|
jpayne@69
|
14751 return NULL;
|
|
jpayne@69
|
14752 }
|
|
jpayne@69
|
14753 kwvalues = newargs + nargs;
|
|
jpayne@69
|
14754 pos = i = 0;
|
|
jpayne@69
|
14755 keys_are_strings = Py_TPFLAGS_UNICODE_SUBCLASS;
|
|
jpayne@69
|
14756 while (PyDict_Next(kw, &pos, &key, &value)) {
|
|
jpayne@69
|
14757 keys_are_strings &= Py_TYPE(key)->tp_flags;
|
|
jpayne@69
|
14758 Py_INCREF(key);
|
|
jpayne@69
|
14759 Py_INCREF(value);
|
|
jpayne@69
|
14760 PyTuple_SET_ITEM(kwnames, i, key);
|
|
jpayne@69
|
14761 kwvalues[i] = value;
|
|
jpayne@69
|
14762 i++;
|
|
jpayne@69
|
14763 }
|
|
jpayne@69
|
14764 if (unlikely(!keys_are_strings)) {
|
|
jpayne@69
|
14765 PyErr_SetString(PyExc_TypeError, "keywords must be strings");
|
|
jpayne@69
|
14766 goto cleanup;
|
|
jpayne@69
|
14767 }
|
|
jpayne@69
|
14768 res = vc(func, newargs, nargs, kwnames);
|
|
jpayne@69
|
14769 cleanup:
|
|
jpayne@69
|
14770 Py_DECREF(kwnames);
|
|
jpayne@69
|
14771 for (i = 0; i < nkw; i++)
|
|
jpayne@69
|
14772 Py_DECREF(kwvalues[i]);
|
|
jpayne@69
|
14773 PyMem_Free(newargs);
|
|
jpayne@69
|
14774 return res;
|
|
jpayne@69
|
14775 }
|
|
jpayne@69
|
14776 static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw)
|
|
jpayne@69
|
14777 {
|
|
jpayne@69
|
14778 if (likely(kw == NULL) || PyDict_GET_SIZE(kw) == 0) {
|
|
jpayne@69
|
14779 return vc(func, args, nargs, NULL);
|
|
jpayne@69
|
14780 }
|
|
jpayne@69
|
14781 return __Pyx_PyVectorcall_FastCallDict_kw(func, vc, args, nargs, kw);
|
|
jpayne@69
|
14782 }
|
|
jpayne@69
|
14783 #endif
|
|
jpayne@69
|
14784
|
|
jpayne@69
|
14785 /* CythonFunctionShared */
|
|
jpayne@69
|
14786 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14787 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) {
|
|
jpayne@69
|
14788 if (__Pyx_CyFunction_Check(func)) {
|
|
jpayne@69
|
14789 return PyCFunction_GetFunction(((__pyx_CyFunctionObject*)func)->func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
14790 } else if (PyCFunction_Check(func)) {
|
|
jpayne@69
|
14791 return PyCFunction_GetFunction(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
14792 }
|
|
jpayne@69
|
14793 return 0;
|
|
jpayne@69
|
14794 }
|
|
jpayne@69
|
14795 #else
|
|
jpayne@69
|
14796 static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) {
|
|
jpayne@69
|
14797 return __Pyx_CyOrPyCFunction_Check(func) && __Pyx_CyOrPyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc;
|
|
jpayne@69
|
14798 }
|
|
jpayne@69
|
14799 #endif
|
|
jpayne@69
|
14800 static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj) {
|
|
jpayne@69
|
14801 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14802 __Pyx_Py_XDECREF_SET(
|
|
jpayne@69
|
14803 __Pyx_CyFunction_GetClassObj(f),
|
|
jpayne@69
|
14804 ((classobj) ? __Pyx_NewRef(classobj) : NULL));
|
|
jpayne@69
|
14805 #else
|
|
jpayne@69
|
14806 __Pyx_Py_XDECREF_SET(
|
|
jpayne@69
|
14807 ((PyCMethodObject *) (f))->mm_class,
|
|
jpayne@69
|
14808 (PyTypeObject*)((classobj) ? __Pyx_NewRef(classobj) : NULL));
|
|
jpayne@69
|
14809 #endif
|
|
jpayne@69
|
14810 }
|
|
jpayne@69
|
14811 static PyObject *
|
|
jpayne@69
|
14812 __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, void *closure)
|
|
jpayne@69
|
14813 {
|
|
jpayne@69
|
14814 CYTHON_UNUSED_VAR(closure);
|
|
jpayne@69
|
14815 if (unlikely(op->func_doc == NULL)) {
|
|
jpayne@69
|
14816 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14817 op->func_doc = PyObject_GetAttrString(op->func, "__doc__");
|
|
jpayne@69
|
14818 if (unlikely(!op->func_doc)) return NULL;
|
|
jpayne@69
|
14819 #else
|
|
jpayne@69
|
14820 if (((PyCFunctionObject*)op)->m_ml->ml_doc) {
|
|
jpayne@69
|
14821 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
14822 op->func_doc = PyUnicode_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc);
|
|
jpayne@69
|
14823 #else
|
|
jpayne@69
|
14824 op->func_doc = PyString_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc);
|
|
jpayne@69
|
14825 #endif
|
|
jpayne@69
|
14826 if (unlikely(op->func_doc == NULL))
|
|
jpayne@69
|
14827 return NULL;
|
|
jpayne@69
|
14828 } else {
|
|
jpayne@69
|
14829 Py_INCREF(Py_None);
|
|
jpayne@69
|
14830 return Py_None;
|
|
jpayne@69
|
14831 }
|
|
jpayne@69
|
14832 #endif
|
|
jpayne@69
|
14833 }
|
|
jpayne@69
|
14834 Py_INCREF(op->func_doc);
|
|
jpayne@69
|
14835 return op->func_doc;
|
|
jpayne@69
|
14836 }
|
|
jpayne@69
|
14837 static int
|
|
jpayne@69
|
14838 __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
14839 {
|
|
jpayne@69
|
14840 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14841 if (value == NULL) {
|
|
jpayne@69
|
14842 value = Py_None;
|
|
jpayne@69
|
14843 }
|
|
jpayne@69
|
14844 Py_INCREF(value);
|
|
jpayne@69
|
14845 __Pyx_Py_XDECREF_SET(op->func_doc, value);
|
|
jpayne@69
|
14846 return 0;
|
|
jpayne@69
|
14847 }
|
|
jpayne@69
|
14848 static PyObject *
|
|
jpayne@69
|
14849 __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
14850 {
|
|
jpayne@69
|
14851 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14852 if (unlikely(op->func_name == NULL)) {
|
|
jpayne@69
|
14853 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
14854 op->func_name = PyObject_GetAttrString(op->func, "__name__");
|
|
jpayne@69
|
14855 #elif PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
14856 op->func_name = PyUnicode_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name);
|
|
jpayne@69
|
14857 #else
|
|
jpayne@69
|
14858 op->func_name = PyString_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name);
|
|
jpayne@69
|
14859 #endif
|
|
jpayne@69
|
14860 if (unlikely(op->func_name == NULL))
|
|
jpayne@69
|
14861 return NULL;
|
|
jpayne@69
|
14862 }
|
|
jpayne@69
|
14863 Py_INCREF(op->func_name);
|
|
jpayne@69
|
14864 return op->func_name;
|
|
jpayne@69
|
14865 }
|
|
jpayne@69
|
14866 static int
|
|
jpayne@69
|
14867 __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
14868 {
|
|
jpayne@69
|
14869 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14870 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
14871 if (unlikely(value == NULL || !PyUnicode_Check(value)))
|
|
jpayne@69
|
14872 #else
|
|
jpayne@69
|
14873 if (unlikely(value == NULL || !PyString_Check(value)))
|
|
jpayne@69
|
14874 #endif
|
|
jpayne@69
|
14875 {
|
|
jpayne@69
|
14876 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
14877 "__name__ must be set to a string object");
|
|
jpayne@69
|
14878 return -1;
|
|
jpayne@69
|
14879 }
|
|
jpayne@69
|
14880 Py_INCREF(value);
|
|
jpayne@69
|
14881 __Pyx_Py_XDECREF_SET(op->func_name, value);
|
|
jpayne@69
|
14882 return 0;
|
|
jpayne@69
|
14883 }
|
|
jpayne@69
|
14884 static PyObject *
|
|
jpayne@69
|
14885 __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
14886 {
|
|
jpayne@69
|
14887 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14888 Py_INCREF(op->func_qualname);
|
|
jpayne@69
|
14889 return op->func_qualname;
|
|
jpayne@69
|
14890 }
|
|
jpayne@69
|
14891 static int
|
|
jpayne@69
|
14892 __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
14893 {
|
|
jpayne@69
|
14894 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14895 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
14896 if (unlikely(value == NULL || !PyUnicode_Check(value)))
|
|
jpayne@69
|
14897 #else
|
|
jpayne@69
|
14898 if (unlikely(value == NULL || !PyString_Check(value)))
|
|
jpayne@69
|
14899 #endif
|
|
jpayne@69
|
14900 {
|
|
jpayne@69
|
14901 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
14902 "__qualname__ must be set to a string object");
|
|
jpayne@69
|
14903 return -1;
|
|
jpayne@69
|
14904 }
|
|
jpayne@69
|
14905 Py_INCREF(value);
|
|
jpayne@69
|
14906 __Pyx_Py_XDECREF_SET(op->func_qualname, value);
|
|
jpayne@69
|
14907 return 0;
|
|
jpayne@69
|
14908 }
|
|
jpayne@69
|
14909 static PyObject *
|
|
jpayne@69
|
14910 __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
14911 {
|
|
jpayne@69
|
14912 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14913 if (unlikely(op->func_dict == NULL)) {
|
|
jpayne@69
|
14914 op->func_dict = PyDict_New();
|
|
jpayne@69
|
14915 if (unlikely(op->func_dict == NULL))
|
|
jpayne@69
|
14916 return NULL;
|
|
jpayne@69
|
14917 }
|
|
jpayne@69
|
14918 Py_INCREF(op->func_dict);
|
|
jpayne@69
|
14919 return op->func_dict;
|
|
jpayne@69
|
14920 }
|
|
jpayne@69
|
14921 static int
|
|
jpayne@69
|
14922 __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value, void *context)
|
|
jpayne@69
|
14923 {
|
|
jpayne@69
|
14924 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14925 if (unlikely(value == NULL)) {
|
|
jpayne@69
|
14926 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
14927 "function's dictionary may not be deleted");
|
|
jpayne@69
|
14928 return -1;
|
|
jpayne@69
|
14929 }
|
|
jpayne@69
|
14930 if (unlikely(!PyDict_Check(value))) {
|
|
jpayne@69
|
14931 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
14932 "setting function's dictionary to a non-dict");
|
|
jpayne@69
|
14933 return -1;
|
|
jpayne@69
|
14934 }
|
|
jpayne@69
|
14935 Py_INCREF(value);
|
|
jpayne@69
|
14936 __Pyx_Py_XDECREF_SET(op->func_dict, value);
|
|
jpayne@69
|
14937 return 0;
|
|
jpayne@69
|
14938 }
|
|
jpayne@69
|
14939 static PyObject *
|
|
jpayne@69
|
14940 __Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
14941 {
|
|
jpayne@69
|
14942 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14943 Py_INCREF(op->func_globals);
|
|
jpayne@69
|
14944 return op->func_globals;
|
|
jpayne@69
|
14945 }
|
|
jpayne@69
|
14946 static PyObject *
|
|
jpayne@69
|
14947 __Pyx_CyFunction_get_closure(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
14948 {
|
|
jpayne@69
|
14949 CYTHON_UNUSED_VAR(op);
|
|
jpayne@69
|
14950 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14951 Py_INCREF(Py_None);
|
|
jpayne@69
|
14952 return Py_None;
|
|
jpayne@69
|
14953 }
|
|
jpayne@69
|
14954 static PyObject *
|
|
jpayne@69
|
14955 __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op, void *context)
|
|
jpayne@69
|
14956 {
|
|
jpayne@69
|
14957 PyObject* result = (op->func_code) ? op->func_code : Py_None;
|
|
jpayne@69
|
14958 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14959 Py_INCREF(result);
|
|
jpayne@69
|
14960 return result;
|
|
jpayne@69
|
14961 }
|
|
jpayne@69
|
14962 static int
|
|
jpayne@69
|
14963 __Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
|
|
jpayne@69
|
14964 int result = 0;
|
|
jpayne@69
|
14965 PyObject *res = op->defaults_getter((PyObject *) op);
|
|
jpayne@69
|
14966 if (unlikely(!res))
|
|
jpayne@69
|
14967 return -1;
|
|
jpayne@69
|
14968 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
14969 op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
|
|
jpayne@69
|
14970 Py_INCREF(op->defaults_tuple);
|
|
jpayne@69
|
14971 op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
|
|
jpayne@69
|
14972 Py_INCREF(op->defaults_kwdict);
|
|
jpayne@69
|
14973 #else
|
|
jpayne@69
|
14974 op->defaults_tuple = __Pyx_PySequence_ITEM(res, 0);
|
|
jpayne@69
|
14975 if (unlikely(!op->defaults_tuple)) result = -1;
|
|
jpayne@69
|
14976 else {
|
|
jpayne@69
|
14977 op->defaults_kwdict = __Pyx_PySequence_ITEM(res, 1);
|
|
jpayne@69
|
14978 if (unlikely(!op->defaults_kwdict)) result = -1;
|
|
jpayne@69
|
14979 }
|
|
jpayne@69
|
14980 #endif
|
|
jpayne@69
|
14981 Py_DECREF(res);
|
|
jpayne@69
|
14982 return result;
|
|
jpayne@69
|
14983 }
|
|
jpayne@69
|
14984 static int
|
|
jpayne@69
|
14985 __Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
14986 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
14987 if (!value) {
|
|
jpayne@69
|
14988 value = Py_None;
|
|
jpayne@69
|
14989 } else if (unlikely(value != Py_None && !PyTuple_Check(value))) {
|
|
jpayne@69
|
14990 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
14991 "__defaults__ must be set to a tuple object");
|
|
jpayne@69
|
14992 return -1;
|
|
jpayne@69
|
14993 }
|
|
jpayne@69
|
14994 PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__defaults__ will not "
|
|
jpayne@69
|
14995 "currently affect the values used in function calls", 1);
|
|
jpayne@69
|
14996 Py_INCREF(value);
|
|
jpayne@69
|
14997 __Pyx_Py_XDECREF_SET(op->defaults_tuple, value);
|
|
jpayne@69
|
14998 return 0;
|
|
jpayne@69
|
14999 }
|
|
jpayne@69
|
15000 static PyObject *
|
|
jpayne@69
|
15001 __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
15002 PyObject* result = op->defaults_tuple;
|
|
jpayne@69
|
15003 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15004 if (unlikely(!result)) {
|
|
jpayne@69
|
15005 if (op->defaults_getter) {
|
|
jpayne@69
|
15006 if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL;
|
|
jpayne@69
|
15007 result = op->defaults_tuple;
|
|
jpayne@69
|
15008 } else {
|
|
jpayne@69
|
15009 result = Py_None;
|
|
jpayne@69
|
15010 }
|
|
jpayne@69
|
15011 }
|
|
jpayne@69
|
15012 Py_INCREF(result);
|
|
jpayne@69
|
15013 return result;
|
|
jpayne@69
|
15014 }
|
|
jpayne@69
|
15015 static int
|
|
jpayne@69
|
15016 __Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
15017 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15018 if (!value) {
|
|
jpayne@69
|
15019 value = Py_None;
|
|
jpayne@69
|
15020 } else if (unlikely(value != Py_None && !PyDict_Check(value))) {
|
|
jpayne@69
|
15021 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
15022 "__kwdefaults__ must be set to a dict object");
|
|
jpayne@69
|
15023 return -1;
|
|
jpayne@69
|
15024 }
|
|
jpayne@69
|
15025 PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__kwdefaults__ will not "
|
|
jpayne@69
|
15026 "currently affect the values used in function calls", 1);
|
|
jpayne@69
|
15027 Py_INCREF(value);
|
|
jpayne@69
|
15028 __Pyx_Py_XDECREF_SET(op->defaults_kwdict, value);
|
|
jpayne@69
|
15029 return 0;
|
|
jpayne@69
|
15030 }
|
|
jpayne@69
|
15031 static PyObject *
|
|
jpayne@69
|
15032 __Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
15033 PyObject* result = op->defaults_kwdict;
|
|
jpayne@69
|
15034 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15035 if (unlikely(!result)) {
|
|
jpayne@69
|
15036 if (op->defaults_getter) {
|
|
jpayne@69
|
15037 if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL;
|
|
jpayne@69
|
15038 result = op->defaults_kwdict;
|
|
jpayne@69
|
15039 } else {
|
|
jpayne@69
|
15040 result = Py_None;
|
|
jpayne@69
|
15041 }
|
|
jpayne@69
|
15042 }
|
|
jpayne@69
|
15043 Py_INCREF(result);
|
|
jpayne@69
|
15044 return result;
|
|
jpayne@69
|
15045 }
|
|
jpayne@69
|
15046 static int
|
|
jpayne@69
|
15047 __Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
15048 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15049 if (!value || value == Py_None) {
|
|
jpayne@69
|
15050 value = NULL;
|
|
jpayne@69
|
15051 } else if (unlikely(!PyDict_Check(value))) {
|
|
jpayne@69
|
15052 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
15053 "__annotations__ must be set to a dict object");
|
|
jpayne@69
|
15054 return -1;
|
|
jpayne@69
|
15055 }
|
|
jpayne@69
|
15056 Py_XINCREF(value);
|
|
jpayne@69
|
15057 __Pyx_Py_XDECREF_SET(op->func_annotations, value);
|
|
jpayne@69
|
15058 return 0;
|
|
jpayne@69
|
15059 }
|
|
jpayne@69
|
15060 static PyObject *
|
|
jpayne@69
|
15061 __Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
15062 PyObject* result = op->func_annotations;
|
|
jpayne@69
|
15063 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15064 if (unlikely(!result)) {
|
|
jpayne@69
|
15065 result = PyDict_New();
|
|
jpayne@69
|
15066 if (unlikely(!result)) return NULL;
|
|
jpayne@69
|
15067 op->func_annotations = result;
|
|
jpayne@69
|
15068 }
|
|
jpayne@69
|
15069 Py_INCREF(result);
|
|
jpayne@69
|
15070 return result;
|
|
jpayne@69
|
15071 }
|
|
jpayne@69
|
15072 static PyObject *
|
|
jpayne@69
|
15073 __Pyx_CyFunction_get_is_coroutine(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
15074 int is_coroutine;
|
|
jpayne@69
|
15075 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15076 if (op->func_is_coroutine) {
|
|
jpayne@69
|
15077 return __Pyx_NewRef(op->func_is_coroutine);
|
|
jpayne@69
|
15078 }
|
|
jpayne@69
|
15079 is_coroutine = op->flags & __Pyx_CYFUNCTION_COROUTINE;
|
|
jpayne@69
|
15080 #if PY_VERSION_HEX >= 0x03050000
|
|
jpayne@69
|
15081 if (is_coroutine) {
|
|
jpayne@69
|
15082 PyObject *module, *fromlist, *marker = __pyx_n_s_is_coroutine;
|
|
jpayne@69
|
15083 fromlist = PyList_New(1);
|
|
jpayne@69
|
15084 if (unlikely(!fromlist)) return NULL;
|
|
jpayne@69
|
15085 Py_INCREF(marker);
|
|
jpayne@69
|
15086 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15087 PyList_SET_ITEM(fromlist, 0, marker);
|
|
jpayne@69
|
15088 #else
|
|
jpayne@69
|
15089 if (unlikely(PyList_SetItem(fromlist, 0, marker) < 0)) {
|
|
jpayne@69
|
15090 Py_DECREF(marker);
|
|
jpayne@69
|
15091 Py_DECREF(fromlist);
|
|
jpayne@69
|
15092 return NULL;
|
|
jpayne@69
|
15093 }
|
|
jpayne@69
|
15094 #endif
|
|
jpayne@69
|
15095 module = PyImport_ImportModuleLevelObject(__pyx_n_s_asyncio_coroutines, NULL, NULL, fromlist, 0);
|
|
jpayne@69
|
15096 Py_DECREF(fromlist);
|
|
jpayne@69
|
15097 if (unlikely(!module)) goto ignore;
|
|
jpayne@69
|
15098 op->func_is_coroutine = __Pyx_PyObject_GetAttrStr(module, marker);
|
|
jpayne@69
|
15099 Py_DECREF(module);
|
|
jpayne@69
|
15100 if (likely(op->func_is_coroutine)) {
|
|
jpayne@69
|
15101 return __Pyx_NewRef(op->func_is_coroutine);
|
|
jpayne@69
|
15102 }
|
|
jpayne@69
|
15103 ignore:
|
|
jpayne@69
|
15104 PyErr_Clear();
|
|
jpayne@69
|
15105 }
|
|
jpayne@69
|
15106 #endif
|
|
jpayne@69
|
15107 op->func_is_coroutine = __Pyx_PyBool_FromLong(is_coroutine);
|
|
jpayne@69
|
15108 return __Pyx_NewRef(op->func_is_coroutine);
|
|
jpayne@69
|
15109 }
|
|
jpayne@69
|
15110 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15111 static PyObject *
|
|
jpayne@69
|
15112 __Pyx_CyFunction_get_module(__pyx_CyFunctionObject *op, void *context) {
|
|
jpayne@69
|
15113 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15114 return PyObject_GetAttrString(op->func, "__module__");
|
|
jpayne@69
|
15115 }
|
|
jpayne@69
|
15116 static int
|
|
jpayne@69
|
15117 __Pyx_CyFunction_set_module(__pyx_CyFunctionObject *op, PyObject* value, void *context) {
|
|
jpayne@69
|
15118 CYTHON_UNUSED_VAR(context);
|
|
jpayne@69
|
15119 return PyObject_SetAttrString(op->func, "__module__", value);
|
|
jpayne@69
|
15120 }
|
|
jpayne@69
|
15121 #endif
|
|
jpayne@69
|
15122 static PyGetSetDef __pyx_CyFunction_getsets[] = {
|
|
jpayne@69
|
15123 {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
|
|
jpayne@69
|
15124 {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
|
|
jpayne@69
|
15125 {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
|
|
jpayne@69
|
15126 {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
|
|
jpayne@69
|
15127 {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
|
|
jpayne@69
|
15128 {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
|
|
jpayne@69
|
15129 {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
|
|
jpayne@69
|
15130 {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
|
|
jpayne@69
|
15131 {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
|
|
jpayne@69
|
15132 {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
|
|
jpayne@69
|
15133 {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
|
|
jpayne@69
|
15134 {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
|
|
jpayne@69
|
15135 {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
|
|
jpayne@69
|
15136 {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
|
|
jpayne@69
|
15137 {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
|
|
jpayne@69
|
15138 {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0},
|
|
jpayne@69
|
15139 {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0},
|
|
jpayne@69
|
15140 {(char *) "_is_coroutine", (getter)__Pyx_CyFunction_get_is_coroutine, 0, 0, 0},
|
|
jpayne@69
|
15141 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15142 {"__module__", (getter)__Pyx_CyFunction_get_module, (setter)__Pyx_CyFunction_set_module, 0, 0},
|
|
jpayne@69
|
15143 #endif
|
|
jpayne@69
|
15144 {0, 0, 0, 0, 0}
|
|
jpayne@69
|
15145 };
|
|
jpayne@69
|
15146 static PyMemberDef __pyx_CyFunction_members[] = {
|
|
jpayne@69
|
15147 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15148 {(char *) "__module__", T_OBJECT, offsetof(PyCFunctionObject, m_module), 0, 0},
|
|
jpayne@69
|
15149 #endif
|
|
jpayne@69
|
15150 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
15151 {(char *) "__dictoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_dict), READONLY, 0},
|
|
jpayne@69
|
15152 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15153 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
15154 {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_vectorcall), READONLY, 0},
|
|
jpayne@69
|
15155 #else
|
|
jpayne@69
|
15156 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15157 {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(PyCFunctionObject, vectorcall), READONLY, 0},
|
|
jpayne@69
|
15158 #endif
|
|
jpayne@69
|
15159 #endif
|
|
jpayne@69
|
15160 #endif
|
|
jpayne@69
|
15161 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15162 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_weakreflist), READONLY, 0},
|
|
jpayne@69
|
15163 #else
|
|
jpayne@69
|
15164 {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(PyCFunctionObject, m_weakreflist), READONLY, 0},
|
|
jpayne@69
|
15165 #endif
|
|
jpayne@69
|
15166 #endif
|
|
jpayne@69
|
15167 {0, 0, 0, 0, 0}
|
|
jpayne@69
|
15168 };
|
|
jpayne@69
|
15169 static PyObject *
|
|
jpayne@69
|
15170 __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, PyObject *args)
|
|
jpayne@69
|
15171 {
|
|
jpayne@69
|
15172 CYTHON_UNUSED_VAR(args);
|
|
jpayne@69
|
15173 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
15174 Py_INCREF(m->func_qualname);
|
|
jpayne@69
|
15175 return m->func_qualname;
|
|
jpayne@69
|
15176 #else
|
|
jpayne@69
|
15177 return PyString_FromString(((PyCFunctionObject*)m)->m_ml->ml_name);
|
|
jpayne@69
|
15178 #endif
|
|
jpayne@69
|
15179 }
|
|
jpayne@69
|
15180 static PyMethodDef __pyx_CyFunction_methods[] = {
|
|
jpayne@69
|
15181 {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
|
|
jpayne@69
|
15182 {0, 0, 0, 0}
|
|
jpayne@69
|
15183 };
|
|
jpayne@69
|
15184 #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15185 #define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist)
|
|
jpayne@69
|
15186 #else
|
|
jpayne@69
|
15187 #define __Pyx_CyFunction_weakreflist(cyfunc) (((PyCFunctionObject*)cyfunc)->m_weakreflist)
|
|
jpayne@69
|
15188 #endif
|
|
jpayne@69
|
15189 static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname,
|
|
jpayne@69
|
15190 PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
|
|
jpayne@69
|
15191 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15192 PyCFunctionObject *cf = (PyCFunctionObject*) op;
|
|
jpayne@69
|
15193 #endif
|
|
jpayne@69
|
15194 if (unlikely(op == NULL))
|
|
jpayne@69
|
15195 return NULL;
|
|
jpayne@69
|
15196 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15197 op->func = PyCFunction_NewEx(ml, (PyObject*)op, module);
|
|
jpayne@69
|
15198 if (unlikely(!op->func)) return NULL;
|
|
jpayne@69
|
15199 #endif
|
|
jpayne@69
|
15200 op->flags = flags;
|
|
jpayne@69
|
15201 __Pyx_CyFunction_weakreflist(op) = NULL;
|
|
jpayne@69
|
15202 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15203 cf->m_ml = ml;
|
|
jpayne@69
|
15204 cf->m_self = (PyObject *) op;
|
|
jpayne@69
|
15205 #endif
|
|
jpayne@69
|
15206 Py_XINCREF(closure);
|
|
jpayne@69
|
15207 op->func_closure = closure;
|
|
jpayne@69
|
15208 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15209 Py_XINCREF(module);
|
|
jpayne@69
|
15210 cf->m_module = module;
|
|
jpayne@69
|
15211 #endif
|
|
jpayne@69
|
15212 op->func_dict = NULL;
|
|
jpayne@69
|
15213 op->func_name = NULL;
|
|
jpayne@69
|
15214 Py_INCREF(qualname);
|
|
jpayne@69
|
15215 op->func_qualname = qualname;
|
|
jpayne@69
|
15216 op->func_doc = NULL;
|
|
jpayne@69
|
15217 #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15218 op->func_classobj = NULL;
|
|
jpayne@69
|
15219 #else
|
|
jpayne@69
|
15220 ((PyCMethodObject*)op)->mm_class = NULL;
|
|
jpayne@69
|
15221 #endif
|
|
jpayne@69
|
15222 op->func_globals = globals;
|
|
jpayne@69
|
15223 Py_INCREF(op->func_globals);
|
|
jpayne@69
|
15224 Py_XINCREF(code);
|
|
jpayne@69
|
15225 op->func_code = code;
|
|
jpayne@69
|
15226 op->defaults_pyobjects = 0;
|
|
jpayne@69
|
15227 op->defaults_size = 0;
|
|
jpayne@69
|
15228 op->defaults = NULL;
|
|
jpayne@69
|
15229 op->defaults_tuple = NULL;
|
|
jpayne@69
|
15230 op->defaults_kwdict = NULL;
|
|
jpayne@69
|
15231 op->defaults_getter = NULL;
|
|
jpayne@69
|
15232 op->func_annotations = NULL;
|
|
jpayne@69
|
15233 op->func_is_coroutine = NULL;
|
|
jpayne@69
|
15234 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15235 switch (ml->ml_flags & (METH_VARARGS | METH_FASTCALL | METH_NOARGS | METH_O | METH_KEYWORDS | METH_METHOD)) {
|
|
jpayne@69
|
15236 case METH_NOARGS:
|
|
jpayne@69
|
15237 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_NOARGS;
|
|
jpayne@69
|
15238 break;
|
|
jpayne@69
|
15239 case METH_O:
|
|
jpayne@69
|
15240 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_O;
|
|
jpayne@69
|
15241 break;
|
|
jpayne@69
|
15242 case METH_METHOD | METH_FASTCALL | METH_KEYWORDS:
|
|
jpayne@69
|
15243 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD;
|
|
jpayne@69
|
15244 break;
|
|
jpayne@69
|
15245 case METH_FASTCALL | METH_KEYWORDS:
|
|
jpayne@69
|
15246 __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS;
|
|
jpayne@69
|
15247 break;
|
|
jpayne@69
|
15248 case METH_VARARGS | METH_KEYWORDS:
|
|
jpayne@69
|
15249 __Pyx_CyFunction_func_vectorcall(op) = NULL;
|
|
jpayne@69
|
15250 break;
|
|
jpayne@69
|
15251 default:
|
|
jpayne@69
|
15252 PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction");
|
|
jpayne@69
|
15253 Py_DECREF(op);
|
|
jpayne@69
|
15254 return NULL;
|
|
jpayne@69
|
15255 }
|
|
jpayne@69
|
15256 #endif
|
|
jpayne@69
|
15257 return (PyObject *) op;
|
|
jpayne@69
|
15258 }
|
|
jpayne@69
|
15259 static int
|
|
jpayne@69
|
15260 __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
|
|
jpayne@69
|
15261 {
|
|
jpayne@69
|
15262 Py_CLEAR(m->func_closure);
|
|
jpayne@69
|
15263 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15264 Py_CLEAR(m->func);
|
|
jpayne@69
|
15265 #else
|
|
jpayne@69
|
15266 Py_CLEAR(((PyCFunctionObject*)m)->m_module);
|
|
jpayne@69
|
15267 #endif
|
|
jpayne@69
|
15268 Py_CLEAR(m->func_dict);
|
|
jpayne@69
|
15269 Py_CLEAR(m->func_name);
|
|
jpayne@69
|
15270 Py_CLEAR(m->func_qualname);
|
|
jpayne@69
|
15271 Py_CLEAR(m->func_doc);
|
|
jpayne@69
|
15272 Py_CLEAR(m->func_globals);
|
|
jpayne@69
|
15273 Py_CLEAR(m->func_code);
|
|
jpayne@69
|
15274 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15275 #if PY_VERSION_HEX < 0x030900B1
|
|
jpayne@69
|
15276 Py_CLEAR(__Pyx_CyFunction_GetClassObj(m));
|
|
jpayne@69
|
15277 #else
|
|
jpayne@69
|
15278 {
|
|
jpayne@69
|
15279 PyObject *cls = (PyObject*) ((PyCMethodObject *) (m))->mm_class;
|
|
jpayne@69
|
15280 ((PyCMethodObject *) (m))->mm_class = NULL;
|
|
jpayne@69
|
15281 Py_XDECREF(cls);
|
|
jpayne@69
|
15282 }
|
|
jpayne@69
|
15283 #endif
|
|
jpayne@69
|
15284 #endif
|
|
jpayne@69
|
15285 Py_CLEAR(m->defaults_tuple);
|
|
jpayne@69
|
15286 Py_CLEAR(m->defaults_kwdict);
|
|
jpayne@69
|
15287 Py_CLEAR(m->func_annotations);
|
|
jpayne@69
|
15288 Py_CLEAR(m->func_is_coroutine);
|
|
jpayne@69
|
15289 if (m->defaults) {
|
|
jpayne@69
|
15290 PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
|
|
jpayne@69
|
15291 int i;
|
|
jpayne@69
|
15292 for (i = 0; i < m->defaults_pyobjects; i++)
|
|
jpayne@69
|
15293 Py_XDECREF(pydefaults[i]);
|
|
jpayne@69
|
15294 PyObject_Free(m->defaults);
|
|
jpayne@69
|
15295 m->defaults = NULL;
|
|
jpayne@69
|
15296 }
|
|
jpayne@69
|
15297 return 0;
|
|
jpayne@69
|
15298 }
|
|
jpayne@69
|
15299 static void __Pyx__CyFunction_dealloc(__pyx_CyFunctionObject *m)
|
|
jpayne@69
|
15300 {
|
|
jpayne@69
|
15301 if (__Pyx_CyFunction_weakreflist(m) != NULL)
|
|
jpayne@69
|
15302 PyObject_ClearWeakRefs((PyObject *) m);
|
|
jpayne@69
|
15303 __Pyx_CyFunction_clear(m);
|
|
jpayne@69
|
15304 __Pyx_PyHeapTypeObject_GC_Del(m);
|
|
jpayne@69
|
15305 }
|
|
jpayne@69
|
15306 static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
|
|
jpayne@69
|
15307 {
|
|
jpayne@69
|
15308 PyObject_GC_UnTrack(m);
|
|
jpayne@69
|
15309 __Pyx__CyFunction_dealloc(m);
|
|
jpayne@69
|
15310 }
|
|
jpayne@69
|
15311 static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
|
|
jpayne@69
|
15312 {
|
|
jpayne@69
|
15313 Py_VISIT(m->func_closure);
|
|
jpayne@69
|
15314 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15315 Py_VISIT(m->func);
|
|
jpayne@69
|
15316 #else
|
|
jpayne@69
|
15317 Py_VISIT(((PyCFunctionObject*)m)->m_module);
|
|
jpayne@69
|
15318 #endif
|
|
jpayne@69
|
15319 Py_VISIT(m->func_dict);
|
|
jpayne@69
|
15320 Py_VISIT(m->func_name);
|
|
jpayne@69
|
15321 Py_VISIT(m->func_qualname);
|
|
jpayne@69
|
15322 Py_VISIT(m->func_doc);
|
|
jpayne@69
|
15323 Py_VISIT(m->func_globals);
|
|
jpayne@69
|
15324 Py_VISIT(m->func_code);
|
|
jpayne@69
|
15325 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15326 Py_VISIT(__Pyx_CyFunction_GetClassObj(m));
|
|
jpayne@69
|
15327 #endif
|
|
jpayne@69
|
15328 Py_VISIT(m->defaults_tuple);
|
|
jpayne@69
|
15329 Py_VISIT(m->defaults_kwdict);
|
|
jpayne@69
|
15330 Py_VISIT(m->func_is_coroutine);
|
|
jpayne@69
|
15331 if (m->defaults) {
|
|
jpayne@69
|
15332 PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
|
|
jpayne@69
|
15333 int i;
|
|
jpayne@69
|
15334 for (i = 0; i < m->defaults_pyobjects; i++)
|
|
jpayne@69
|
15335 Py_VISIT(pydefaults[i]);
|
|
jpayne@69
|
15336 }
|
|
jpayne@69
|
15337 return 0;
|
|
jpayne@69
|
15338 }
|
|
jpayne@69
|
15339 static PyObject*
|
|
jpayne@69
|
15340 __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
|
|
jpayne@69
|
15341 {
|
|
jpayne@69
|
15342 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
15343 return PyUnicode_FromFormat("<cyfunction %U at %p>",
|
|
jpayne@69
|
15344 op->func_qualname, (void *)op);
|
|
jpayne@69
|
15345 #else
|
|
jpayne@69
|
15346 return PyString_FromFormat("<cyfunction %s at %p>",
|
|
jpayne@69
|
15347 PyString_AsString(op->func_qualname), (void *)op);
|
|
jpayne@69
|
15348 #endif
|
|
jpayne@69
|
15349 }
|
|
jpayne@69
|
15350 static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) {
|
|
jpayne@69
|
15351 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15352 PyObject *f = ((__pyx_CyFunctionObject*)func)->func;
|
|
jpayne@69
|
15353 PyObject *py_name = NULL;
|
|
jpayne@69
|
15354 PyCFunction meth;
|
|
jpayne@69
|
15355 int flags;
|
|
jpayne@69
|
15356 meth = PyCFunction_GetFunction(f);
|
|
jpayne@69
|
15357 if (unlikely(!meth)) return NULL;
|
|
jpayne@69
|
15358 flags = PyCFunction_GetFlags(f);
|
|
jpayne@69
|
15359 if (unlikely(flags < 0)) return NULL;
|
|
jpayne@69
|
15360 #else
|
|
jpayne@69
|
15361 PyCFunctionObject* f = (PyCFunctionObject*)func;
|
|
jpayne@69
|
15362 PyCFunction meth = f->m_ml->ml_meth;
|
|
jpayne@69
|
15363 int flags = f->m_ml->ml_flags;
|
|
jpayne@69
|
15364 #endif
|
|
jpayne@69
|
15365 Py_ssize_t size;
|
|
jpayne@69
|
15366 switch (flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) {
|
|
jpayne@69
|
15367 case METH_VARARGS:
|
|
jpayne@69
|
15368 if (likely(kw == NULL || PyDict_Size(kw) == 0))
|
|
jpayne@69
|
15369 return (*meth)(self, arg);
|
|
jpayne@69
|
15370 break;
|
|
jpayne@69
|
15371 case METH_VARARGS | METH_KEYWORDS:
|
|
jpayne@69
|
15372 return (*(PyCFunctionWithKeywords)(void*)meth)(self, arg, kw);
|
|
jpayne@69
|
15373 case METH_NOARGS:
|
|
jpayne@69
|
15374 if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
|
|
jpayne@69
|
15375 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15376 size = PyTuple_GET_SIZE(arg);
|
|
jpayne@69
|
15377 #else
|
|
jpayne@69
|
15378 size = PyTuple_Size(arg);
|
|
jpayne@69
|
15379 if (unlikely(size < 0)) return NULL;
|
|
jpayne@69
|
15380 #endif
|
|
jpayne@69
|
15381 if (likely(size == 0))
|
|
jpayne@69
|
15382 return (*meth)(self, NULL);
|
|
jpayne@69
|
15383 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15384 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
|
|
jpayne@69
|
15385 if (!py_name) return NULL;
|
|
jpayne@69
|
15386 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15387 "%.200S() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
15388 py_name, size);
|
|
jpayne@69
|
15389 Py_DECREF(py_name);
|
|
jpayne@69
|
15390 #else
|
|
jpayne@69
|
15391 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15392 "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
15393 f->m_ml->ml_name, size);
|
|
jpayne@69
|
15394 #endif
|
|
jpayne@69
|
15395 return NULL;
|
|
jpayne@69
|
15396 }
|
|
jpayne@69
|
15397 break;
|
|
jpayne@69
|
15398 case METH_O:
|
|
jpayne@69
|
15399 if (likely(kw == NULL || PyDict_Size(kw) == 0)) {
|
|
jpayne@69
|
15400 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15401 size = PyTuple_GET_SIZE(arg);
|
|
jpayne@69
|
15402 #else
|
|
jpayne@69
|
15403 size = PyTuple_Size(arg);
|
|
jpayne@69
|
15404 if (unlikely(size < 0)) return NULL;
|
|
jpayne@69
|
15405 #endif
|
|
jpayne@69
|
15406 if (likely(size == 1)) {
|
|
jpayne@69
|
15407 PyObject *result, *arg0;
|
|
jpayne@69
|
15408 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
15409 arg0 = PyTuple_GET_ITEM(arg, 0);
|
|
jpayne@69
|
15410 #else
|
|
jpayne@69
|
15411 arg0 = __Pyx_PySequence_ITEM(arg, 0); if (unlikely(!arg0)) return NULL;
|
|
jpayne@69
|
15412 #endif
|
|
jpayne@69
|
15413 result = (*meth)(self, arg0);
|
|
jpayne@69
|
15414 #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS)
|
|
jpayne@69
|
15415 Py_DECREF(arg0);
|
|
jpayne@69
|
15416 #endif
|
|
jpayne@69
|
15417 return result;
|
|
jpayne@69
|
15418 }
|
|
jpayne@69
|
15419 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15420 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
|
|
jpayne@69
|
15421 if (!py_name) return NULL;
|
|
jpayne@69
|
15422 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15423 "%.200S() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
15424 py_name, size);
|
|
jpayne@69
|
15425 Py_DECREF(py_name);
|
|
jpayne@69
|
15426 #else
|
|
jpayne@69
|
15427 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15428 "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
15429 f->m_ml->ml_name, size);
|
|
jpayne@69
|
15430 #endif
|
|
jpayne@69
|
15431 return NULL;
|
|
jpayne@69
|
15432 }
|
|
jpayne@69
|
15433 break;
|
|
jpayne@69
|
15434 default:
|
|
jpayne@69
|
15435 PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction");
|
|
jpayne@69
|
15436 return NULL;
|
|
jpayne@69
|
15437 }
|
|
jpayne@69
|
15438 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15439 py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL);
|
|
jpayne@69
|
15440 if (!py_name) return NULL;
|
|
jpayne@69
|
15441 PyErr_Format(PyExc_TypeError, "%.200S() takes no keyword arguments",
|
|
jpayne@69
|
15442 py_name);
|
|
jpayne@69
|
15443 Py_DECREF(py_name);
|
|
jpayne@69
|
15444 #else
|
|
jpayne@69
|
15445 PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
|
|
jpayne@69
|
15446 f->m_ml->ml_name);
|
|
jpayne@69
|
15447 #endif
|
|
jpayne@69
|
15448 return NULL;
|
|
jpayne@69
|
15449 }
|
|
jpayne@69
|
15450 static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
|
|
jpayne@69
|
15451 PyObject *self, *result;
|
|
jpayne@69
|
15452 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15453 self = PyCFunction_GetSelf(((__pyx_CyFunctionObject*)func)->func);
|
|
jpayne@69
|
15454 if (unlikely(!self) && PyErr_Occurred()) return NULL;
|
|
jpayne@69
|
15455 #else
|
|
jpayne@69
|
15456 self = ((PyCFunctionObject*)func)->m_self;
|
|
jpayne@69
|
15457 #endif
|
|
jpayne@69
|
15458 result = __Pyx_CyFunction_CallMethod(func, self, arg, kw);
|
|
jpayne@69
|
15459 return result;
|
|
jpayne@69
|
15460 }
|
|
jpayne@69
|
15461 static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) {
|
|
jpayne@69
|
15462 PyObject *result;
|
|
jpayne@69
|
15463 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
15464 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15465 __pyx_vectorcallfunc vc = __Pyx_CyFunction_func_vectorcall(cyfunc);
|
|
jpayne@69
|
15466 if (vc) {
|
|
jpayne@69
|
15467 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15468 return __Pyx_PyVectorcall_FastCallDict(func, vc, &PyTuple_GET_ITEM(args, 0), (size_t)PyTuple_GET_SIZE(args), kw);
|
|
jpayne@69
|
15469 #else
|
|
jpayne@69
|
15470 (void) &__Pyx_PyVectorcall_FastCallDict;
|
|
jpayne@69
|
15471 return PyVectorcall_Call(func, args, kw);
|
|
jpayne@69
|
15472 #endif
|
|
jpayne@69
|
15473 }
|
|
jpayne@69
|
15474 #endif
|
|
jpayne@69
|
15475 if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) {
|
|
jpayne@69
|
15476 Py_ssize_t argc;
|
|
jpayne@69
|
15477 PyObject *new_args;
|
|
jpayne@69
|
15478 PyObject *self;
|
|
jpayne@69
|
15479 #if CYTHON_ASSUME_SAFE_MACROS
|
|
jpayne@69
|
15480 argc = PyTuple_GET_SIZE(args);
|
|
jpayne@69
|
15481 #else
|
|
jpayne@69
|
15482 argc = PyTuple_Size(args);
|
|
jpayne@69
|
15483 if (unlikely(!argc) < 0) return NULL;
|
|
jpayne@69
|
15484 #endif
|
|
jpayne@69
|
15485 new_args = PyTuple_GetSlice(args, 1, argc);
|
|
jpayne@69
|
15486 if (unlikely(!new_args))
|
|
jpayne@69
|
15487 return NULL;
|
|
jpayne@69
|
15488 self = PyTuple_GetItem(args, 0);
|
|
jpayne@69
|
15489 if (unlikely(!self)) {
|
|
jpayne@69
|
15490 Py_DECREF(new_args);
|
|
jpayne@69
|
15491 #if PY_MAJOR_VERSION > 2
|
|
jpayne@69
|
15492 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15493 "unbound method %.200S() needs an argument",
|
|
jpayne@69
|
15494 cyfunc->func_qualname);
|
|
jpayne@69
|
15495 #else
|
|
jpayne@69
|
15496 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
15497 "unbound method needs an argument");
|
|
jpayne@69
|
15498 #endif
|
|
jpayne@69
|
15499 return NULL;
|
|
jpayne@69
|
15500 }
|
|
jpayne@69
|
15501 result = __Pyx_CyFunction_CallMethod(func, self, new_args, kw);
|
|
jpayne@69
|
15502 Py_DECREF(new_args);
|
|
jpayne@69
|
15503 } else {
|
|
jpayne@69
|
15504 result = __Pyx_CyFunction_Call(func, args, kw);
|
|
jpayne@69
|
15505 }
|
|
jpayne@69
|
15506 return result;
|
|
jpayne@69
|
15507 }
|
|
jpayne@69
|
15508 #if CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15509 static CYTHON_INLINE int __Pyx_CyFunction_Vectorcall_CheckArgs(__pyx_CyFunctionObject *cyfunc, Py_ssize_t nargs, PyObject *kwnames)
|
|
jpayne@69
|
15510 {
|
|
jpayne@69
|
15511 int ret = 0;
|
|
jpayne@69
|
15512 if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) {
|
|
jpayne@69
|
15513 if (unlikely(nargs < 1)) {
|
|
jpayne@69
|
15514 PyErr_Format(PyExc_TypeError, "%.200s() needs an argument",
|
|
jpayne@69
|
15515 ((PyCFunctionObject*)cyfunc)->m_ml->ml_name);
|
|
jpayne@69
|
15516 return -1;
|
|
jpayne@69
|
15517 }
|
|
jpayne@69
|
15518 ret = 1;
|
|
jpayne@69
|
15519 }
|
|
jpayne@69
|
15520 if (unlikely(kwnames) && unlikely(PyTuple_GET_SIZE(kwnames))) {
|
|
jpayne@69
|
15521 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15522 "%.200s() takes no keyword arguments", ((PyCFunctionObject*)cyfunc)->m_ml->ml_name);
|
|
jpayne@69
|
15523 return -1;
|
|
jpayne@69
|
15524 }
|
|
jpayne@69
|
15525 return ret;
|
|
jpayne@69
|
15526 }
|
|
jpayne@69
|
15527 static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
15528 {
|
|
jpayne@69
|
15529 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
15530 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
15531 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
15532 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
15533 #else
|
|
jpayne@69
|
15534 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
15535 #endif
|
|
jpayne@69
|
15536 PyObject *self;
|
|
jpayne@69
|
15537 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) {
|
|
jpayne@69
|
15538 case 1:
|
|
jpayne@69
|
15539 self = args[0];
|
|
jpayne@69
|
15540 args += 1;
|
|
jpayne@69
|
15541 nargs -= 1;
|
|
jpayne@69
|
15542 break;
|
|
jpayne@69
|
15543 case 0:
|
|
jpayne@69
|
15544 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
15545 break;
|
|
jpayne@69
|
15546 default:
|
|
jpayne@69
|
15547 return NULL;
|
|
jpayne@69
|
15548 }
|
|
jpayne@69
|
15549 if (unlikely(nargs != 0)) {
|
|
jpayne@69
|
15550 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15551 "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
15552 def->ml_name, nargs);
|
|
jpayne@69
|
15553 return NULL;
|
|
jpayne@69
|
15554 }
|
|
jpayne@69
|
15555 return def->ml_meth(self, NULL);
|
|
jpayne@69
|
15556 }
|
|
jpayne@69
|
15557 static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
15558 {
|
|
jpayne@69
|
15559 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
15560 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
15561 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
15562 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
15563 #else
|
|
jpayne@69
|
15564 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
15565 #endif
|
|
jpayne@69
|
15566 PyObject *self;
|
|
jpayne@69
|
15567 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) {
|
|
jpayne@69
|
15568 case 1:
|
|
jpayne@69
|
15569 self = args[0];
|
|
jpayne@69
|
15570 args += 1;
|
|
jpayne@69
|
15571 nargs -= 1;
|
|
jpayne@69
|
15572 break;
|
|
jpayne@69
|
15573 case 0:
|
|
jpayne@69
|
15574 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
15575 break;
|
|
jpayne@69
|
15576 default:
|
|
jpayne@69
|
15577 return NULL;
|
|
jpayne@69
|
15578 }
|
|
jpayne@69
|
15579 if (unlikely(nargs != 1)) {
|
|
jpayne@69
|
15580 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15581 "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)",
|
|
jpayne@69
|
15582 def->ml_name, nargs);
|
|
jpayne@69
|
15583 return NULL;
|
|
jpayne@69
|
15584 }
|
|
jpayne@69
|
15585 return def->ml_meth(self, args[0]);
|
|
jpayne@69
|
15586 }
|
|
jpayne@69
|
15587 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
15588 {
|
|
jpayne@69
|
15589 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
15590 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
15591 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
15592 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
15593 #else
|
|
jpayne@69
|
15594 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
15595 #endif
|
|
jpayne@69
|
15596 PyObject *self;
|
|
jpayne@69
|
15597 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) {
|
|
jpayne@69
|
15598 case 1:
|
|
jpayne@69
|
15599 self = args[0];
|
|
jpayne@69
|
15600 args += 1;
|
|
jpayne@69
|
15601 nargs -= 1;
|
|
jpayne@69
|
15602 break;
|
|
jpayne@69
|
15603 case 0:
|
|
jpayne@69
|
15604 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
15605 break;
|
|
jpayne@69
|
15606 default:
|
|
jpayne@69
|
15607 return NULL;
|
|
jpayne@69
|
15608 }
|
|
jpayne@69
|
15609 return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
|
|
jpayne@69
|
15610 }
|
|
jpayne@69
|
15611 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
|
|
jpayne@69
|
15612 {
|
|
jpayne@69
|
15613 __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func;
|
|
jpayne@69
|
15614 PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml;
|
|
jpayne@69
|
15615 PyTypeObject *cls = (PyTypeObject *) __Pyx_CyFunction_GetClassObj(cyfunc);
|
|
jpayne@69
|
15616 #if CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
15617 Py_ssize_t nargs = (Py_ssize_t)nargsf;
|
|
jpayne@69
|
15618 #else
|
|
jpayne@69
|
15619 Py_ssize_t nargs = PyVectorcall_NARGS(nargsf);
|
|
jpayne@69
|
15620 #endif
|
|
jpayne@69
|
15621 PyObject *self;
|
|
jpayne@69
|
15622 switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) {
|
|
jpayne@69
|
15623 case 1:
|
|
jpayne@69
|
15624 self = args[0];
|
|
jpayne@69
|
15625 args += 1;
|
|
jpayne@69
|
15626 nargs -= 1;
|
|
jpayne@69
|
15627 break;
|
|
jpayne@69
|
15628 case 0:
|
|
jpayne@69
|
15629 self = ((PyCFunctionObject*)cyfunc)->m_self;
|
|
jpayne@69
|
15630 break;
|
|
jpayne@69
|
15631 default:
|
|
jpayne@69
|
15632 return NULL;
|
|
jpayne@69
|
15633 }
|
|
jpayne@69
|
15634 return ((__Pyx_PyCMethod)(void(*)(void))def->ml_meth)(self, cls, args, (size_t)nargs, kwnames);
|
|
jpayne@69
|
15635 }
|
|
jpayne@69
|
15636 #endif
|
|
jpayne@69
|
15637 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
15638 static PyType_Slot __pyx_CyFunctionType_slots[] = {
|
|
jpayne@69
|
15639 {Py_tp_dealloc, (void *)__Pyx_CyFunction_dealloc},
|
|
jpayne@69
|
15640 {Py_tp_repr, (void *)__Pyx_CyFunction_repr},
|
|
jpayne@69
|
15641 {Py_tp_call, (void *)__Pyx_CyFunction_CallAsMethod},
|
|
jpayne@69
|
15642 {Py_tp_traverse, (void *)__Pyx_CyFunction_traverse},
|
|
jpayne@69
|
15643 {Py_tp_clear, (void *)__Pyx_CyFunction_clear},
|
|
jpayne@69
|
15644 {Py_tp_methods, (void *)__pyx_CyFunction_methods},
|
|
jpayne@69
|
15645 {Py_tp_members, (void *)__pyx_CyFunction_members},
|
|
jpayne@69
|
15646 {Py_tp_getset, (void *)__pyx_CyFunction_getsets},
|
|
jpayne@69
|
15647 {Py_tp_descr_get, (void *)__Pyx_PyMethod_New},
|
|
jpayne@69
|
15648 {0, 0},
|
|
jpayne@69
|
15649 };
|
|
jpayne@69
|
15650 static PyType_Spec __pyx_CyFunctionType_spec = {
|
|
jpayne@69
|
15651 __PYX_TYPE_MODULE_PREFIX "cython_function_or_method",
|
|
jpayne@69
|
15652 sizeof(__pyx_CyFunctionObject),
|
|
jpayne@69
|
15653 0,
|
|
jpayne@69
|
15654 #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR
|
|
jpayne@69
|
15655 Py_TPFLAGS_METHOD_DESCRIPTOR |
|
|
jpayne@69
|
15656 #endif
|
|
jpayne@69
|
15657 #if (defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL)
|
|
jpayne@69
|
15658 _Py_TPFLAGS_HAVE_VECTORCALL |
|
|
jpayne@69
|
15659 #endif
|
|
jpayne@69
|
15660 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE,
|
|
jpayne@69
|
15661 __pyx_CyFunctionType_slots
|
|
jpayne@69
|
15662 };
|
|
jpayne@69
|
15663 #else
|
|
jpayne@69
|
15664 static PyTypeObject __pyx_CyFunctionType_type = {
|
|
jpayne@69
|
15665 PyVarObject_HEAD_INIT(0, 0)
|
|
jpayne@69
|
15666 __PYX_TYPE_MODULE_PREFIX "cython_function_or_method",
|
|
jpayne@69
|
15667 sizeof(__pyx_CyFunctionObject),
|
|
jpayne@69
|
15668 0,
|
|
jpayne@69
|
15669 (destructor) __Pyx_CyFunction_dealloc,
|
|
jpayne@69
|
15670 #if !CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15671 0,
|
|
jpayne@69
|
15672 #elif CYTHON_BACKPORT_VECTORCALL
|
|
jpayne@69
|
15673 (printfunc)offsetof(__pyx_CyFunctionObject, func_vectorcall),
|
|
jpayne@69
|
15674 #else
|
|
jpayne@69
|
15675 offsetof(PyCFunctionObject, vectorcall),
|
|
jpayne@69
|
15676 #endif
|
|
jpayne@69
|
15677 0,
|
|
jpayne@69
|
15678 0,
|
|
jpayne@69
|
15679 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
15680 0,
|
|
jpayne@69
|
15681 #else
|
|
jpayne@69
|
15682 0,
|
|
jpayne@69
|
15683 #endif
|
|
jpayne@69
|
15684 (reprfunc) __Pyx_CyFunction_repr,
|
|
jpayne@69
|
15685 0,
|
|
jpayne@69
|
15686 0,
|
|
jpayne@69
|
15687 0,
|
|
jpayne@69
|
15688 0,
|
|
jpayne@69
|
15689 __Pyx_CyFunction_CallAsMethod,
|
|
jpayne@69
|
15690 0,
|
|
jpayne@69
|
15691 0,
|
|
jpayne@69
|
15692 0,
|
|
jpayne@69
|
15693 0,
|
|
jpayne@69
|
15694 #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR
|
|
jpayne@69
|
15695 Py_TPFLAGS_METHOD_DESCRIPTOR |
|
|
jpayne@69
|
15696 #endif
|
|
jpayne@69
|
15697 #if defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL
|
|
jpayne@69
|
15698 _Py_TPFLAGS_HAVE_VECTORCALL |
|
|
jpayne@69
|
15699 #endif
|
|
jpayne@69
|
15700 Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE,
|
|
jpayne@69
|
15701 0,
|
|
jpayne@69
|
15702 (traverseproc) __Pyx_CyFunction_traverse,
|
|
jpayne@69
|
15703 (inquiry) __Pyx_CyFunction_clear,
|
|
jpayne@69
|
15704 0,
|
|
jpayne@69
|
15705 #if PY_VERSION_HEX < 0x030500A0
|
|
jpayne@69
|
15706 offsetof(__pyx_CyFunctionObject, func_weakreflist),
|
|
jpayne@69
|
15707 #else
|
|
jpayne@69
|
15708 offsetof(PyCFunctionObject, m_weakreflist),
|
|
jpayne@69
|
15709 #endif
|
|
jpayne@69
|
15710 0,
|
|
jpayne@69
|
15711 0,
|
|
jpayne@69
|
15712 __pyx_CyFunction_methods,
|
|
jpayne@69
|
15713 __pyx_CyFunction_members,
|
|
jpayne@69
|
15714 __pyx_CyFunction_getsets,
|
|
jpayne@69
|
15715 0,
|
|
jpayne@69
|
15716 0,
|
|
jpayne@69
|
15717 __Pyx_PyMethod_New,
|
|
jpayne@69
|
15718 0,
|
|
jpayne@69
|
15719 offsetof(__pyx_CyFunctionObject, func_dict),
|
|
jpayne@69
|
15720 0,
|
|
jpayne@69
|
15721 0,
|
|
jpayne@69
|
15722 0,
|
|
jpayne@69
|
15723 0,
|
|
jpayne@69
|
15724 0,
|
|
jpayne@69
|
15725 0,
|
|
jpayne@69
|
15726 0,
|
|
jpayne@69
|
15727 0,
|
|
jpayne@69
|
15728 0,
|
|
jpayne@69
|
15729 0,
|
|
jpayne@69
|
15730 0,
|
|
jpayne@69
|
15731 0,
|
|
jpayne@69
|
15732 #if PY_VERSION_HEX >= 0x030400a1
|
|
jpayne@69
|
15733 0,
|
|
jpayne@69
|
15734 #endif
|
|
jpayne@69
|
15735 #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
|
|
jpayne@69
|
15736 0,
|
|
jpayne@69
|
15737 #endif
|
|
jpayne@69
|
15738 #if __PYX_NEED_TP_PRINT_SLOT
|
|
jpayne@69
|
15739 0,
|
|
jpayne@69
|
15740 #endif
|
|
jpayne@69
|
15741 #if PY_VERSION_HEX >= 0x030C0000
|
|
jpayne@69
|
15742 0,
|
|
jpayne@69
|
15743 #endif
|
|
jpayne@69
|
15744 #if PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
15745 0,
|
|
jpayne@69
|
15746 #endif
|
|
jpayne@69
|
15747 #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000
|
|
jpayne@69
|
15748 0,
|
|
jpayne@69
|
15749 #endif
|
|
jpayne@69
|
15750 };
|
|
jpayne@69
|
15751 #endif
|
|
jpayne@69
|
15752 static int __pyx_CyFunction_init(PyObject *module) {
|
|
jpayne@69
|
15753 #if CYTHON_USE_TYPE_SPECS
|
|
jpayne@69
|
15754 __pyx_CyFunctionType = __Pyx_FetchCommonTypeFromSpec(module, &__pyx_CyFunctionType_spec, NULL);
|
|
jpayne@69
|
15755 #else
|
|
jpayne@69
|
15756 CYTHON_UNUSED_VAR(module);
|
|
jpayne@69
|
15757 __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
|
|
jpayne@69
|
15758 #endif
|
|
jpayne@69
|
15759 if (unlikely(__pyx_CyFunctionType == NULL)) {
|
|
jpayne@69
|
15760 return -1;
|
|
jpayne@69
|
15761 }
|
|
jpayne@69
|
15762 return 0;
|
|
jpayne@69
|
15763 }
|
|
jpayne@69
|
15764 static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
|
|
jpayne@69
|
15765 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
15766 m->defaults = PyObject_Malloc(size);
|
|
jpayne@69
|
15767 if (unlikely(!m->defaults))
|
|
jpayne@69
|
15768 return PyErr_NoMemory();
|
|
jpayne@69
|
15769 memset(m->defaults, 0, size);
|
|
jpayne@69
|
15770 m->defaults_pyobjects = pyobjects;
|
|
jpayne@69
|
15771 m->defaults_size = size;
|
|
jpayne@69
|
15772 return m->defaults;
|
|
jpayne@69
|
15773 }
|
|
jpayne@69
|
15774 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
|
|
jpayne@69
|
15775 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
15776 m->defaults_tuple = tuple;
|
|
jpayne@69
|
15777 Py_INCREF(tuple);
|
|
jpayne@69
|
15778 }
|
|
jpayne@69
|
15779 static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
|
|
jpayne@69
|
15780 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
15781 m->defaults_kwdict = dict;
|
|
jpayne@69
|
15782 Py_INCREF(dict);
|
|
jpayne@69
|
15783 }
|
|
jpayne@69
|
15784 static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
|
|
jpayne@69
|
15785 __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
|
|
jpayne@69
|
15786 m->func_annotations = dict;
|
|
jpayne@69
|
15787 Py_INCREF(dict);
|
|
jpayne@69
|
15788 }
|
|
jpayne@69
|
15789
|
|
jpayne@69
|
15790 /* CythonFunction */
|
|
jpayne@69
|
15791 static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, int flags, PyObject* qualname,
|
|
jpayne@69
|
15792 PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
|
|
jpayne@69
|
15793 PyObject *op = __Pyx_CyFunction_Init(
|
|
jpayne@69
|
15794 PyObject_GC_New(__pyx_CyFunctionObject, __pyx_CyFunctionType),
|
|
jpayne@69
|
15795 ml, flags, qualname, closure, module, globals, code
|
|
jpayne@69
|
15796 );
|
|
jpayne@69
|
15797 if (likely(op)) {
|
|
jpayne@69
|
15798 PyObject_GC_Track(op);
|
|
jpayne@69
|
15799 }
|
|
jpayne@69
|
15800 return op;
|
|
jpayne@69
|
15801 }
|
|
jpayne@69
|
15802
|
|
jpayne@69
|
15803 /* RaiseUnboundLocalError */
|
|
jpayne@69
|
15804 static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
|
|
jpayne@69
|
15805 PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
|
|
jpayne@69
|
15806 }
|
|
jpayne@69
|
15807
|
|
jpayne@69
|
15808 /* TypeImport */
|
|
jpayne@69
|
15809 #ifndef __PYX_HAVE_RT_ImportType_3_0_11
|
|
jpayne@69
|
15810 #define __PYX_HAVE_RT_ImportType_3_0_11
|
|
jpayne@69
|
15811 static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject *module, const char *module_name, const char *class_name,
|
|
jpayne@69
|
15812 size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size)
|
|
jpayne@69
|
15813 {
|
|
jpayne@69
|
15814 PyObject *result = 0;
|
|
jpayne@69
|
15815 char warning[200];
|
|
jpayne@69
|
15816 Py_ssize_t basicsize;
|
|
jpayne@69
|
15817 Py_ssize_t itemsize;
|
|
jpayne@69
|
15818 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15819 PyObject *py_basicsize;
|
|
jpayne@69
|
15820 PyObject *py_itemsize;
|
|
jpayne@69
|
15821 #endif
|
|
jpayne@69
|
15822 result = PyObject_GetAttrString(module, class_name);
|
|
jpayne@69
|
15823 if (!result)
|
|
jpayne@69
|
15824 goto bad;
|
|
jpayne@69
|
15825 if (!PyType_Check(result)) {
|
|
jpayne@69
|
15826 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
15827 "%.200s.%.200s is not a type object",
|
|
jpayne@69
|
15828 module_name, class_name);
|
|
jpayne@69
|
15829 goto bad;
|
|
jpayne@69
|
15830 }
|
|
jpayne@69
|
15831 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
15832 basicsize = ((PyTypeObject *)result)->tp_basicsize;
|
|
jpayne@69
|
15833 itemsize = ((PyTypeObject *)result)->tp_itemsize;
|
|
jpayne@69
|
15834 #else
|
|
jpayne@69
|
15835 py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
|
|
jpayne@69
|
15836 if (!py_basicsize)
|
|
jpayne@69
|
15837 goto bad;
|
|
jpayne@69
|
15838 basicsize = PyLong_AsSsize_t(py_basicsize);
|
|
jpayne@69
|
15839 Py_DECREF(py_basicsize);
|
|
jpayne@69
|
15840 py_basicsize = 0;
|
|
jpayne@69
|
15841 if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
|
|
jpayne@69
|
15842 goto bad;
|
|
jpayne@69
|
15843 py_itemsize = PyObject_GetAttrString(result, "__itemsize__");
|
|
jpayne@69
|
15844 if (!py_itemsize)
|
|
jpayne@69
|
15845 goto bad;
|
|
jpayne@69
|
15846 itemsize = PyLong_AsSsize_t(py_itemsize);
|
|
jpayne@69
|
15847 Py_DECREF(py_itemsize);
|
|
jpayne@69
|
15848 py_itemsize = 0;
|
|
jpayne@69
|
15849 if (itemsize == (Py_ssize_t)-1 && PyErr_Occurred())
|
|
jpayne@69
|
15850 goto bad;
|
|
jpayne@69
|
15851 #endif
|
|
jpayne@69
|
15852 if (itemsize) {
|
|
jpayne@69
|
15853 if (size % alignment) {
|
|
jpayne@69
|
15854 alignment = size % alignment;
|
|
jpayne@69
|
15855 }
|
|
jpayne@69
|
15856 if (itemsize < (Py_ssize_t)alignment)
|
|
jpayne@69
|
15857 itemsize = (Py_ssize_t)alignment;
|
|
jpayne@69
|
15858 }
|
|
jpayne@69
|
15859 if ((size_t)(basicsize + itemsize) < size) {
|
|
jpayne@69
|
15860 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
15861 "%.200s.%.200s size changed, may indicate binary incompatibility. "
|
|
jpayne@69
|
15862 "Expected %zd from C header, got %zd from PyObject",
|
|
jpayne@69
|
15863 module_name, class_name, size, basicsize+itemsize);
|
|
jpayne@69
|
15864 goto bad;
|
|
jpayne@69
|
15865 }
|
|
jpayne@69
|
15866 if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 &&
|
|
jpayne@69
|
15867 ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) {
|
|
jpayne@69
|
15868 PyErr_Format(PyExc_ValueError,
|
|
jpayne@69
|
15869 "%.200s.%.200s size changed, may indicate binary incompatibility. "
|
|
jpayne@69
|
15870 "Expected %zd from C header, got %zd-%zd from PyObject",
|
|
jpayne@69
|
15871 module_name, class_name, size, basicsize, basicsize+itemsize);
|
|
jpayne@69
|
15872 goto bad;
|
|
jpayne@69
|
15873 }
|
|
jpayne@69
|
15874 else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_11 && (size_t)basicsize > size) {
|
|
jpayne@69
|
15875 PyOS_snprintf(warning, sizeof(warning),
|
|
jpayne@69
|
15876 "%s.%s size changed, may indicate binary incompatibility. "
|
|
jpayne@69
|
15877 "Expected %zd from C header, got %zd from PyObject",
|
|
jpayne@69
|
15878 module_name, class_name, size, basicsize);
|
|
jpayne@69
|
15879 if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
|
|
jpayne@69
|
15880 }
|
|
jpayne@69
|
15881 return (PyTypeObject *)result;
|
|
jpayne@69
|
15882 bad:
|
|
jpayne@69
|
15883 Py_XDECREF(result);
|
|
jpayne@69
|
15884 return NULL;
|
|
jpayne@69
|
15885 }
|
|
jpayne@69
|
15886 #endif
|
|
jpayne@69
|
15887
|
|
jpayne@69
|
15888 /* Import */
|
|
jpayne@69
|
15889 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
|
|
jpayne@69
|
15890 PyObject *module = 0;
|
|
jpayne@69
|
15891 PyObject *empty_dict = 0;
|
|
jpayne@69
|
15892 PyObject *empty_list = 0;
|
|
jpayne@69
|
15893 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
15894 PyObject *py_import;
|
|
jpayne@69
|
15895 py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
|
|
jpayne@69
|
15896 if (unlikely(!py_import))
|
|
jpayne@69
|
15897 goto bad;
|
|
jpayne@69
|
15898 if (!from_list) {
|
|
jpayne@69
|
15899 empty_list = PyList_New(0);
|
|
jpayne@69
|
15900 if (unlikely(!empty_list))
|
|
jpayne@69
|
15901 goto bad;
|
|
jpayne@69
|
15902 from_list = empty_list;
|
|
jpayne@69
|
15903 }
|
|
jpayne@69
|
15904 #endif
|
|
jpayne@69
|
15905 empty_dict = PyDict_New();
|
|
jpayne@69
|
15906 if (unlikely(!empty_dict))
|
|
jpayne@69
|
15907 goto bad;
|
|
jpayne@69
|
15908 {
|
|
jpayne@69
|
15909 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
15910 if (level == -1) {
|
|
jpayne@69
|
15911 if (strchr(__Pyx_MODULE_NAME, '.') != NULL) {
|
|
jpayne@69
|
15912 module = PyImport_ImportModuleLevelObject(
|
|
jpayne@69
|
15913 name, __pyx_d, empty_dict, from_list, 1);
|
|
jpayne@69
|
15914 if (unlikely(!module)) {
|
|
jpayne@69
|
15915 if (unlikely(!PyErr_ExceptionMatches(PyExc_ImportError)))
|
|
jpayne@69
|
15916 goto bad;
|
|
jpayne@69
|
15917 PyErr_Clear();
|
|
jpayne@69
|
15918 }
|
|
jpayne@69
|
15919 }
|
|
jpayne@69
|
15920 level = 0;
|
|
jpayne@69
|
15921 }
|
|
jpayne@69
|
15922 #endif
|
|
jpayne@69
|
15923 if (!module) {
|
|
jpayne@69
|
15924 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
15925 PyObject *py_level = PyInt_FromLong(level);
|
|
jpayne@69
|
15926 if (unlikely(!py_level))
|
|
jpayne@69
|
15927 goto bad;
|
|
jpayne@69
|
15928 module = PyObject_CallFunctionObjArgs(py_import,
|
|
jpayne@69
|
15929 name, __pyx_d, empty_dict, from_list, py_level, (PyObject *)NULL);
|
|
jpayne@69
|
15930 Py_DECREF(py_level);
|
|
jpayne@69
|
15931 #else
|
|
jpayne@69
|
15932 module = PyImport_ImportModuleLevelObject(
|
|
jpayne@69
|
15933 name, __pyx_d, empty_dict, from_list, level);
|
|
jpayne@69
|
15934 #endif
|
|
jpayne@69
|
15935 }
|
|
jpayne@69
|
15936 }
|
|
jpayne@69
|
15937 bad:
|
|
jpayne@69
|
15938 Py_XDECREF(empty_dict);
|
|
jpayne@69
|
15939 Py_XDECREF(empty_list);
|
|
jpayne@69
|
15940 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
15941 Py_XDECREF(py_import);
|
|
jpayne@69
|
15942 #endif
|
|
jpayne@69
|
15943 return module;
|
|
jpayne@69
|
15944 }
|
|
jpayne@69
|
15945
|
|
jpayne@69
|
15946 /* ImportDottedModule */
|
|
jpayne@69
|
15947 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
15948 static PyObject *__Pyx__ImportDottedModule_Error(PyObject *name, PyObject *parts_tuple, Py_ssize_t count) {
|
|
jpayne@69
|
15949 PyObject *partial_name = NULL, *slice = NULL, *sep = NULL;
|
|
jpayne@69
|
15950 if (unlikely(PyErr_Occurred())) {
|
|
jpayne@69
|
15951 PyErr_Clear();
|
|
jpayne@69
|
15952 }
|
|
jpayne@69
|
15953 if (likely(PyTuple_GET_SIZE(parts_tuple) == count)) {
|
|
jpayne@69
|
15954 partial_name = name;
|
|
jpayne@69
|
15955 } else {
|
|
jpayne@69
|
15956 slice = PySequence_GetSlice(parts_tuple, 0, count);
|
|
jpayne@69
|
15957 if (unlikely(!slice))
|
|
jpayne@69
|
15958 goto bad;
|
|
jpayne@69
|
15959 sep = PyUnicode_FromStringAndSize(".", 1);
|
|
jpayne@69
|
15960 if (unlikely(!sep))
|
|
jpayne@69
|
15961 goto bad;
|
|
jpayne@69
|
15962 partial_name = PyUnicode_Join(sep, slice);
|
|
jpayne@69
|
15963 }
|
|
jpayne@69
|
15964 PyErr_Format(
|
|
jpayne@69
|
15965 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
15966 PyExc_ImportError,
|
|
jpayne@69
|
15967 "No module named '%s'", PyString_AS_STRING(partial_name));
|
|
jpayne@69
|
15968 #else
|
|
jpayne@69
|
15969 #if PY_VERSION_HEX >= 0x030600B1
|
|
jpayne@69
|
15970 PyExc_ModuleNotFoundError,
|
|
jpayne@69
|
15971 #else
|
|
jpayne@69
|
15972 PyExc_ImportError,
|
|
jpayne@69
|
15973 #endif
|
|
jpayne@69
|
15974 "No module named '%U'", partial_name);
|
|
jpayne@69
|
15975 #endif
|
|
jpayne@69
|
15976 bad:
|
|
jpayne@69
|
15977 Py_XDECREF(sep);
|
|
jpayne@69
|
15978 Py_XDECREF(slice);
|
|
jpayne@69
|
15979 Py_XDECREF(partial_name);
|
|
jpayne@69
|
15980 return NULL;
|
|
jpayne@69
|
15981 }
|
|
jpayne@69
|
15982 #endif
|
|
jpayne@69
|
15983 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
15984 static PyObject *__Pyx__ImportDottedModule_Lookup(PyObject *name) {
|
|
jpayne@69
|
15985 PyObject *imported_module;
|
|
jpayne@69
|
15986 #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400)
|
|
jpayne@69
|
15987 PyObject *modules = PyImport_GetModuleDict();
|
|
jpayne@69
|
15988 if (unlikely(!modules))
|
|
jpayne@69
|
15989 return NULL;
|
|
jpayne@69
|
15990 imported_module = __Pyx_PyDict_GetItemStr(modules, name);
|
|
jpayne@69
|
15991 Py_XINCREF(imported_module);
|
|
jpayne@69
|
15992 #else
|
|
jpayne@69
|
15993 imported_module = PyImport_GetModule(name);
|
|
jpayne@69
|
15994 #endif
|
|
jpayne@69
|
15995 return imported_module;
|
|
jpayne@69
|
15996 }
|
|
jpayne@69
|
15997 #endif
|
|
jpayne@69
|
15998 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
15999 static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple) {
|
|
jpayne@69
|
16000 Py_ssize_t i, nparts;
|
|
jpayne@69
|
16001 nparts = PyTuple_GET_SIZE(parts_tuple);
|
|
jpayne@69
|
16002 for (i=1; i < nparts && module; i++) {
|
|
jpayne@69
|
16003 PyObject *part, *submodule;
|
|
jpayne@69
|
16004 #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
|
|
jpayne@69
|
16005 part = PyTuple_GET_ITEM(parts_tuple, i);
|
|
jpayne@69
|
16006 #else
|
|
jpayne@69
|
16007 part = PySequence_ITEM(parts_tuple, i);
|
|
jpayne@69
|
16008 #endif
|
|
jpayne@69
|
16009 submodule = __Pyx_PyObject_GetAttrStrNoError(module, part);
|
|
jpayne@69
|
16010 #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS)
|
|
jpayne@69
|
16011 Py_DECREF(part);
|
|
jpayne@69
|
16012 #endif
|
|
jpayne@69
|
16013 Py_DECREF(module);
|
|
jpayne@69
|
16014 module = submodule;
|
|
jpayne@69
|
16015 }
|
|
jpayne@69
|
16016 if (unlikely(!module)) {
|
|
jpayne@69
|
16017 return __Pyx__ImportDottedModule_Error(name, parts_tuple, i);
|
|
jpayne@69
|
16018 }
|
|
jpayne@69
|
16019 return module;
|
|
jpayne@69
|
16020 }
|
|
jpayne@69
|
16021 #endif
|
|
jpayne@69
|
16022 static PyObject *__Pyx__ImportDottedModule(PyObject *name, PyObject *parts_tuple) {
|
|
jpayne@69
|
16023 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16024 PyObject *module, *from_list, *star = __pyx_n_s__14;
|
|
jpayne@69
|
16025 CYTHON_UNUSED_VAR(parts_tuple);
|
|
jpayne@69
|
16026 from_list = PyList_New(1);
|
|
jpayne@69
|
16027 if (unlikely(!from_list))
|
|
jpayne@69
|
16028 return NULL;
|
|
jpayne@69
|
16029 Py_INCREF(star);
|
|
jpayne@69
|
16030 PyList_SET_ITEM(from_list, 0, star);
|
|
jpayne@69
|
16031 module = __Pyx_Import(name, from_list, 0);
|
|
jpayne@69
|
16032 Py_DECREF(from_list);
|
|
jpayne@69
|
16033 return module;
|
|
jpayne@69
|
16034 #else
|
|
jpayne@69
|
16035 PyObject *imported_module;
|
|
jpayne@69
|
16036 PyObject *module = __Pyx_Import(name, NULL, 0);
|
|
jpayne@69
|
16037 if (!parts_tuple || unlikely(!module))
|
|
jpayne@69
|
16038 return module;
|
|
jpayne@69
|
16039 imported_module = __Pyx__ImportDottedModule_Lookup(name);
|
|
jpayne@69
|
16040 if (likely(imported_module)) {
|
|
jpayne@69
|
16041 Py_DECREF(module);
|
|
jpayne@69
|
16042 return imported_module;
|
|
jpayne@69
|
16043 }
|
|
jpayne@69
|
16044 PyErr_Clear();
|
|
jpayne@69
|
16045 return __Pyx_ImportDottedModule_WalkParts(module, name, parts_tuple);
|
|
jpayne@69
|
16046 #endif
|
|
jpayne@69
|
16047 }
|
|
jpayne@69
|
16048 static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple) {
|
|
jpayne@69
|
16049 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030400B1
|
|
jpayne@69
|
16050 PyObject *module = __Pyx__ImportDottedModule_Lookup(name);
|
|
jpayne@69
|
16051 if (likely(module)) {
|
|
jpayne@69
|
16052 PyObject *spec = __Pyx_PyObject_GetAttrStrNoError(module, __pyx_n_s_spec);
|
|
jpayne@69
|
16053 if (likely(spec)) {
|
|
jpayne@69
|
16054 PyObject *unsafe = __Pyx_PyObject_GetAttrStrNoError(spec, __pyx_n_s_initializing);
|
|
jpayne@69
|
16055 if (likely(!unsafe || !__Pyx_PyObject_IsTrue(unsafe))) {
|
|
jpayne@69
|
16056 Py_DECREF(spec);
|
|
jpayne@69
|
16057 spec = NULL;
|
|
jpayne@69
|
16058 }
|
|
jpayne@69
|
16059 Py_XDECREF(unsafe);
|
|
jpayne@69
|
16060 }
|
|
jpayne@69
|
16061 if (likely(!spec)) {
|
|
jpayne@69
|
16062 PyErr_Clear();
|
|
jpayne@69
|
16063 return module;
|
|
jpayne@69
|
16064 }
|
|
jpayne@69
|
16065 Py_DECREF(spec);
|
|
jpayne@69
|
16066 Py_DECREF(module);
|
|
jpayne@69
|
16067 } else if (PyErr_Occurred()) {
|
|
jpayne@69
|
16068 PyErr_Clear();
|
|
jpayne@69
|
16069 }
|
|
jpayne@69
|
16070 #endif
|
|
jpayne@69
|
16071 return __Pyx__ImportDottedModule(name, parts_tuple);
|
|
jpayne@69
|
16072 }
|
|
jpayne@69
|
16073
|
|
jpayne@69
|
16074 /* ImportFrom */
|
|
jpayne@69
|
16075 static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
|
|
jpayne@69
|
16076 PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
|
|
jpayne@69
|
16077 if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
|
|
jpayne@69
|
16078 const char* module_name_str = 0;
|
|
jpayne@69
|
16079 PyObject* module_name = 0;
|
|
jpayne@69
|
16080 PyObject* module_dot = 0;
|
|
jpayne@69
|
16081 PyObject* full_name = 0;
|
|
jpayne@69
|
16082 PyErr_Clear();
|
|
jpayne@69
|
16083 module_name_str = PyModule_GetName(module);
|
|
jpayne@69
|
16084 if (unlikely(!module_name_str)) { goto modbad; }
|
|
jpayne@69
|
16085 module_name = PyUnicode_FromString(module_name_str);
|
|
jpayne@69
|
16086 if (unlikely(!module_name)) { goto modbad; }
|
|
jpayne@69
|
16087 module_dot = PyUnicode_Concat(module_name, __pyx_kp_u__15);
|
|
jpayne@69
|
16088 if (unlikely(!module_dot)) { goto modbad; }
|
|
jpayne@69
|
16089 full_name = PyUnicode_Concat(module_dot, name);
|
|
jpayne@69
|
16090 if (unlikely(!full_name)) { goto modbad; }
|
|
jpayne@69
|
16091 #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400)
|
|
jpayne@69
|
16092 {
|
|
jpayne@69
|
16093 PyObject *modules = PyImport_GetModuleDict();
|
|
jpayne@69
|
16094 if (unlikely(!modules))
|
|
jpayne@69
|
16095 goto modbad;
|
|
jpayne@69
|
16096 value = PyObject_GetItem(modules, full_name);
|
|
jpayne@69
|
16097 }
|
|
jpayne@69
|
16098 #else
|
|
jpayne@69
|
16099 value = PyImport_GetModule(full_name);
|
|
jpayne@69
|
16100 #endif
|
|
jpayne@69
|
16101 modbad:
|
|
jpayne@69
|
16102 Py_XDECREF(full_name);
|
|
jpayne@69
|
16103 Py_XDECREF(module_dot);
|
|
jpayne@69
|
16104 Py_XDECREF(module_name);
|
|
jpayne@69
|
16105 }
|
|
jpayne@69
|
16106 if (unlikely(!value)) {
|
|
jpayne@69
|
16107 PyErr_Format(PyExc_ImportError,
|
|
jpayne@69
|
16108 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16109 "cannot import name %.230s", PyString_AS_STRING(name));
|
|
jpayne@69
|
16110 #else
|
|
jpayne@69
|
16111 "cannot import name %S", name);
|
|
jpayne@69
|
16112 #endif
|
|
jpayne@69
|
16113 }
|
|
jpayne@69
|
16114 return value;
|
|
jpayne@69
|
16115 }
|
|
jpayne@69
|
16116
|
|
jpayne@69
|
16117 /* PyObjectCallNoArg */
|
|
jpayne@69
|
16118 static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
|
|
jpayne@69
|
16119 PyObject *arg[2] = {NULL, NULL};
|
|
jpayne@69
|
16120 return __Pyx_PyObject_FastCall(func, arg + 1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET);
|
|
jpayne@69
|
16121 }
|
|
jpayne@69
|
16122
|
|
jpayne@69
|
16123 /* CLineInTraceback */
|
|
jpayne@69
|
16124 #ifndef CYTHON_CLINE_IN_TRACEBACK
|
|
jpayne@69
|
16125 static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) {
|
|
jpayne@69
|
16126 PyObject *use_cline;
|
|
jpayne@69
|
16127 PyObject *ptype, *pvalue, *ptraceback;
|
|
jpayne@69
|
16128 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
16129 PyObject **cython_runtime_dict;
|
|
jpayne@69
|
16130 #endif
|
|
jpayne@69
|
16131 CYTHON_MAYBE_UNUSED_VAR(tstate);
|
|
jpayne@69
|
16132 if (unlikely(!__pyx_cython_runtime)) {
|
|
jpayne@69
|
16133 return c_line;
|
|
jpayne@69
|
16134 }
|
|
jpayne@69
|
16135 __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
|
|
jpayne@69
|
16136 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
16137 cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime);
|
|
jpayne@69
|
16138 if (likely(cython_runtime_dict)) {
|
|
jpayne@69
|
16139 __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
|
|
jpayne@69
|
16140 use_cline, *cython_runtime_dict,
|
|
jpayne@69
|
16141 __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback))
|
|
jpayne@69
|
16142 } else
|
|
jpayne@69
|
16143 #endif
|
|
jpayne@69
|
16144 {
|
|
jpayne@69
|
16145 PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStrNoError(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback);
|
|
jpayne@69
|
16146 if (use_cline_obj) {
|
|
jpayne@69
|
16147 use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True;
|
|
jpayne@69
|
16148 Py_DECREF(use_cline_obj);
|
|
jpayne@69
|
16149 } else {
|
|
jpayne@69
|
16150 PyErr_Clear();
|
|
jpayne@69
|
16151 use_cline = NULL;
|
|
jpayne@69
|
16152 }
|
|
jpayne@69
|
16153 }
|
|
jpayne@69
|
16154 if (!use_cline) {
|
|
jpayne@69
|
16155 c_line = 0;
|
|
jpayne@69
|
16156 (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
|
|
jpayne@69
|
16157 }
|
|
jpayne@69
|
16158 else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
|
|
jpayne@69
|
16159 c_line = 0;
|
|
jpayne@69
|
16160 }
|
|
jpayne@69
|
16161 __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
|
|
jpayne@69
|
16162 return c_line;
|
|
jpayne@69
|
16163 }
|
|
jpayne@69
|
16164 #endif
|
|
jpayne@69
|
16165
|
|
jpayne@69
|
16166 /* CodeObjectCache */
|
|
jpayne@69
|
16167 #if !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
16168 static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
|
|
jpayne@69
|
16169 int start = 0, mid = 0, end = count - 1;
|
|
jpayne@69
|
16170 if (end >= 0 && code_line > entries[end].code_line) {
|
|
jpayne@69
|
16171 return count;
|
|
jpayne@69
|
16172 }
|
|
jpayne@69
|
16173 while (start < end) {
|
|
jpayne@69
|
16174 mid = start + (end - start) / 2;
|
|
jpayne@69
|
16175 if (code_line < entries[mid].code_line) {
|
|
jpayne@69
|
16176 end = mid;
|
|
jpayne@69
|
16177 } else if (code_line > entries[mid].code_line) {
|
|
jpayne@69
|
16178 start = mid + 1;
|
|
jpayne@69
|
16179 } else {
|
|
jpayne@69
|
16180 return mid;
|
|
jpayne@69
|
16181 }
|
|
jpayne@69
|
16182 }
|
|
jpayne@69
|
16183 if (code_line <= entries[mid].code_line) {
|
|
jpayne@69
|
16184 return mid;
|
|
jpayne@69
|
16185 } else {
|
|
jpayne@69
|
16186 return mid + 1;
|
|
jpayne@69
|
16187 }
|
|
jpayne@69
|
16188 }
|
|
jpayne@69
|
16189 static PyCodeObject *__pyx_find_code_object(int code_line) {
|
|
jpayne@69
|
16190 PyCodeObject* code_object;
|
|
jpayne@69
|
16191 int pos;
|
|
jpayne@69
|
16192 if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
|
|
jpayne@69
|
16193 return NULL;
|
|
jpayne@69
|
16194 }
|
|
jpayne@69
|
16195 pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
|
|
jpayne@69
|
16196 if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
|
|
jpayne@69
|
16197 return NULL;
|
|
jpayne@69
|
16198 }
|
|
jpayne@69
|
16199 code_object = __pyx_code_cache.entries[pos].code_object;
|
|
jpayne@69
|
16200 Py_INCREF(code_object);
|
|
jpayne@69
|
16201 return code_object;
|
|
jpayne@69
|
16202 }
|
|
jpayne@69
|
16203 static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
|
|
jpayne@69
|
16204 int pos, i;
|
|
jpayne@69
|
16205 __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
|
|
jpayne@69
|
16206 if (unlikely(!code_line)) {
|
|
jpayne@69
|
16207 return;
|
|
jpayne@69
|
16208 }
|
|
jpayne@69
|
16209 if (unlikely(!entries)) {
|
|
jpayne@69
|
16210 entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
|
|
jpayne@69
|
16211 if (likely(entries)) {
|
|
jpayne@69
|
16212 __pyx_code_cache.entries = entries;
|
|
jpayne@69
|
16213 __pyx_code_cache.max_count = 64;
|
|
jpayne@69
|
16214 __pyx_code_cache.count = 1;
|
|
jpayne@69
|
16215 entries[0].code_line = code_line;
|
|
jpayne@69
|
16216 entries[0].code_object = code_object;
|
|
jpayne@69
|
16217 Py_INCREF(code_object);
|
|
jpayne@69
|
16218 }
|
|
jpayne@69
|
16219 return;
|
|
jpayne@69
|
16220 }
|
|
jpayne@69
|
16221 pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
|
|
jpayne@69
|
16222 if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
|
|
jpayne@69
|
16223 PyCodeObject* tmp = entries[pos].code_object;
|
|
jpayne@69
|
16224 entries[pos].code_object = code_object;
|
|
jpayne@69
|
16225 Py_DECREF(tmp);
|
|
jpayne@69
|
16226 return;
|
|
jpayne@69
|
16227 }
|
|
jpayne@69
|
16228 if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
|
|
jpayne@69
|
16229 int new_max = __pyx_code_cache.max_count + 64;
|
|
jpayne@69
|
16230 entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
|
|
jpayne@69
|
16231 __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry));
|
|
jpayne@69
|
16232 if (unlikely(!entries)) {
|
|
jpayne@69
|
16233 return;
|
|
jpayne@69
|
16234 }
|
|
jpayne@69
|
16235 __pyx_code_cache.entries = entries;
|
|
jpayne@69
|
16236 __pyx_code_cache.max_count = new_max;
|
|
jpayne@69
|
16237 }
|
|
jpayne@69
|
16238 for (i=__pyx_code_cache.count; i>pos; i--) {
|
|
jpayne@69
|
16239 entries[i] = entries[i-1];
|
|
jpayne@69
|
16240 }
|
|
jpayne@69
|
16241 entries[pos].code_line = code_line;
|
|
jpayne@69
|
16242 entries[pos].code_object = code_object;
|
|
jpayne@69
|
16243 __pyx_code_cache.count++;
|
|
jpayne@69
|
16244 Py_INCREF(code_object);
|
|
jpayne@69
|
16245 }
|
|
jpayne@69
|
16246 #endif
|
|
jpayne@69
|
16247
|
|
jpayne@69
|
16248 /* AddTraceback */
|
|
jpayne@69
|
16249 #include "compile.h"
|
|
jpayne@69
|
16250 #include "frameobject.h"
|
|
jpayne@69
|
16251 #include "traceback.h"
|
|
jpayne@69
|
16252 #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
16253 #ifndef Py_BUILD_CORE
|
|
jpayne@69
|
16254 #define Py_BUILD_CORE 1
|
|
jpayne@69
|
16255 #endif
|
|
jpayne@69
|
16256 #include "internal/pycore_frame.h"
|
|
jpayne@69
|
16257 #endif
|
|
jpayne@69
|
16258 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
16259 static PyObject *__Pyx_PyCode_Replace_For_AddTraceback(PyObject *code, PyObject *scratch_dict,
|
|
jpayne@69
|
16260 PyObject *firstlineno, PyObject *name) {
|
|
jpayne@69
|
16261 PyObject *replace = NULL;
|
|
jpayne@69
|
16262 if (unlikely(PyDict_SetItemString(scratch_dict, "co_firstlineno", firstlineno))) return NULL;
|
|
jpayne@69
|
16263 if (unlikely(PyDict_SetItemString(scratch_dict, "co_name", name))) return NULL;
|
|
jpayne@69
|
16264 replace = PyObject_GetAttrString(code, "replace");
|
|
jpayne@69
|
16265 if (likely(replace)) {
|
|
jpayne@69
|
16266 PyObject *result;
|
|
jpayne@69
|
16267 result = PyObject_Call(replace, __pyx_empty_tuple, scratch_dict);
|
|
jpayne@69
|
16268 Py_DECREF(replace);
|
|
jpayne@69
|
16269 return result;
|
|
jpayne@69
|
16270 }
|
|
jpayne@69
|
16271 PyErr_Clear();
|
|
jpayne@69
|
16272 #if __PYX_LIMITED_VERSION_HEX < 0x030780000
|
|
jpayne@69
|
16273 {
|
|
jpayne@69
|
16274 PyObject *compiled = NULL, *result = NULL;
|
|
jpayne@69
|
16275 if (unlikely(PyDict_SetItemString(scratch_dict, "code", code))) return NULL;
|
|
jpayne@69
|
16276 if (unlikely(PyDict_SetItemString(scratch_dict, "type", (PyObject*)(&PyType_Type)))) return NULL;
|
|
jpayne@69
|
16277 compiled = Py_CompileString(
|
|
jpayne@69
|
16278 "out = type(code)(\n"
|
|
jpayne@69
|
16279 " code.co_argcount, code.co_kwonlyargcount, code.co_nlocals, code.co_stacksize,\n"
|
|
jpayne@69
|
16280 " code.co_flags, code.co_code, code.co_consts, code.co_names,\n"
|
|
jpayne@69
|
16281 " code.co_varnames, code.co_filename, co_name, co_firstlineno,\n"
|
|
jpayne@69
|
16282 " code.co_lnotab)\n", "<dummy>", Py_file_input);
|
|
jpayne@69
|
16283 if (!compiled) return NULL;
|
|
jpayne@69
|
16284 result = PyEval_EvalCode(compiled, scratch_dict, scratch_dict);
|
|
jpayne@69
|
16285 Py_DECREF(compiled);
|
|
jpayne@69
|
16286 if (!result) PyErr_Print();
|
|
jpayne@69
|
16287 Py_DECREF(result);
|
|
jpayne@69
|
16288 result = PyDict_GetItemString(scratch_dict, "out");
|
|
jpayne@69
|
16289 if (result) Py_INCREF(result);
|
|
jpayne@69
|
16290 return result;
|
|
jpayne@69
|
16291 }
|
|
jpayne@69
|
16292 #else
|
|
jpayne@69
|
16293 return NULL;
|
|
jpayne@69
|
16294 #endif
|
|
jpayne@69
|
16295 }
|
|
jpayne@69
|
16296 static void __Pyx_AddTraceback(const char *funcname, int c_line,
|
|
jpayne@69
|
16297 int py_line, const char *filename) {
|
|
jpayne@69
|
16298 PyObject *code_object = NULL, *py_py_line = NULL, *py_funcname = NULL, *dict = NULL;
|
|
jpayne@69
|
16299 PyObject *replace = NULL, *getframe = NULL, *frame = NULL;
|
|
jpayne@69
|
16300 PyObject *exc_type, *exc_value, *exc_traceback;
|
|
jpayne@69
|
16301 int success = 0;
|
|
jpayne@69
|
16302 if (c_line) {
|
|
jpayne@69
|
16303 (void) __pyx_cfilenm;
|
|
jpayne@69
|
16304 (void) __Pyx_CLineForTraceback(__Pyx_PyThreadState_Current, c_line);
|
|
jpayne@69
|
16305 }
|
|
jpayne@69
|
16306 PyErr_Fetch(&exc_type, &exc_value, &exc_traceback);
|
|
jpayne@69
|
16307 code_object = Py_CompileString("_getframe()", filename, Py_eval_input);
|
|
jpayne@69
|
16308 if (unlikely(!code_object)) goto bad;
|
|
jpayne@69
|
16309 py_py_line = PyLong_FromLong(py_line);
|
|
jpayne@69
|
16310 if (unlikely(!py_py_line)) goto bad;
|
|
jpayne@69
|
16311 py_funcname = PyUnicode_FromString(funcname);
|
|
jpayne@69
|
16312 if (unlikely(!py_funcname)) goto bad;
|
|
jpayne@69
|
16313 dict = PyDict_New();
|
|
jpayne@69
|
16314 if (unlikely(!dict)) goto bad;
|
|
jpayne@69
|
16315 {
|
|
jpayne@69
|
16316 PyObject *old_code_object = code_object;
|
|
jpayne@69
|
16317 code_object = __Pyx_PyCode_Replace_For_AddTraceback(code_object, dict, py_py_line, py_funcname);
|
|
jpayne@69
|
16318 Py_DECREF(old_code_object);
|
|
jpayne@69
|
16319 }
|
|
jpayne@69
|
16320 if (unlikely(!code_object)) goto bad;
|
|
jpayne@69
|
16321 getframe = PySys_GetObject("_getframe");
|
|
jpayne@69
|
16322 if (unlikely(!getframe)) goto bad;
|
|
jpayne@69
|
16323 if (unlikely(PyDict_SetItemString(dict, "_getframe", getframe))) goto bad;
|
|
jpayne@69
|
16324 frame = PyEval_EvalCode(code_object, dict, dict);
|
|
jpayne@69
|
16325 if (unlikely(!frame) || frame == Py_None) goto bad;
|
|
jpayne@69
|
16326 success = 1;
|
|
jpayne@69
|
16327 bad:
|
|
jpayne@69
|
16328 PyErr_Restore(exc_type, exc_value, exc_traceback);
|
|
jpayne@69
|
16329 Py_XDECREF(code_object);
|
|
jpayne@69
|
16330 Py_XDECREF(py_py_line);
|
|
jpayne@69
|
16331 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
16332 Py_XDECREF(dict);
|
|
jpayne@69
|
16333 Py_XDECREF(replace);
|
|
jpayne@69
|
16334 if (success) {
|
|
jpayne@69
|
16335 PyTraceBack_Here(
|
|
jpayne@69
|
16336 (struct _frame*)frame);
|
|
jpayne@69
|
16337 }
|
|
jpayne@69
|
16338 Py_XDECREF(frame);
|
|
jpayne@69
|
16339 }
|
|
jpayne@69
|
16340 #else
|
|
jpayne@69
|
16341 static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
|
|
jpayne@69
|
16342 const char *funcname, int c_line,
|
|
jpayne@69
|
16343 int py_line, const char *filename) {
|
|
jpayne@69
|
16344 PyCodeObject *py_code = NULL;
|
|
jpayne@69
|
16345 PyObject *py_funcname = NULL;
|
|
jpayne@69
|
16346 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16347 PyObject *py_srcfile = NULL;
|
|
jpayne@69
|
16348 py_srcfile = PyString_FromString(filename);
|
|
jpayne@69
|
16349 if (!py_srcfile) goto bad;
|
|
jpayne@69
|
16350 #endif
|
|
jpayne@69
|
16351 if (c_line) {
|
|
jpayne@69
|
16352 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16353 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
|
|
jpayne@69
|
16354 if (!py_funcname) goto bad;
|
|
jpayne@69
|
16355 #else
|
|
jpayne@69
|
16356 py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
|
|
jpayne@69
|
16357 if (!py_funcname) goto bad;
|
|
jpayne@69
|
16358 funcname = PyUnicode_AsUTF8(py_funcname);
|
|
jpayne@69
|
16359 if (!funcname) goto bad;
|
|
jpayne@69
|
16360 #endif
|
|
jpayne@69
|
16361 }
|
|
jpayne@69
|
16362 else {
|
|
jpayne@69
|
16363 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16364 py_funcname = PyString_FromString(funcname);
|
|
jpayne@69
|
16365 if (!py_funcname) goto bad;
|
|
jpayne@69
|
16366 #endif
|
|
jpayne@69
|
16367 }
|
|
jpayne@69
|
16368 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16369 py_code = __Pyx_PyCode_New(
|
|
jpayne@69
|
16370 0,
|
|
jpayne@69
|
16371 0,
|
|
jpayne@69
|
16372 0,
|
|
jpayne@69
|
16373 0,
|
|
jpayne@69
|
16374 0,
|
|
jpayne@69
|
16375 0,
|
|
jpayne@69
|
16376 __pyx_empty_bytes, /*PyObject *code,*/
|
|
jpayne@69
|
16377 __pyx_empty_tuple, /*PyObject *consts,*/
|
|
jpayne@69
|
16378 __pyx_empty_tuple, /*PyObject *names,*/
|
|
jpayne@69
|
16379 __pyx_empty_tuple, /*PyObject *varnames,*/
|
|
jpayne@69
|
16380 __pyx_empty_tuple, /*PyObject *freevars,*/
|
|
jpayne@69
|
16381 __pyx_empty_tuple, /*PyObject *cellvars,*/
|
|
jpayne@69
|
16382 py_srcfile, /*PyObject *filename,*/
|
|
jpayne@69
|
16383 py_funcname, /*PyObject *name,*/
|
|
jpayne@69
|
16384 py_line,
|
|
jpayne@69
|
16385 __pyx_empty_bytes /*PyObject *lnotab*/
|
|
jpayne@69
|
16386 );
|
|
jpayne@69
|
16387 Py_DECREF(py_srcfile);
|
|
jpayne@69
|
16388 #else
|
|
jpayne@69
|
16389 py_code = PyCode_NewEmpty(filename, funcname, py_line);
|
|
jpayne@69
|
16390 #endif
|
|
jpayne@69
|
16391 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
16392 return py_code;
|
|
jpayne@69
|
16393 bad:
|
|
jpayne@69
|
16394 Py_XDECREF(py_funcname);
|
|
jpayne@69
|
16395 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16396 Py_XDECREF(py_srcfile);
|
|
jpayne@69
|
16397 #endif
|
|
jpayne@69
|
16398 return NULL;
|
|
jpayne@69
|
16399 }
|
|
jpayne@69
|
16400 static void __Pyx_AddTraceback(const char *funcname, int c_line,
|
|
jpayne@69
|
16401 int py_line, const char *filename) {
|
|
jpayne@69
|
16402 PyCodeObject *py_code = 0;
|
|
jpayne@69
|
16403 PyFrameObject *py_frame = 0;
|
|
jpayne@69
|
16404 PyThreadState *tstate = __Pyx_PyThreadState_Current;
|
|
jpayne@69
|
16405 PyObject *ptype, *pvalue, *ptraceback;
|
|
jpayne@69
|
16406 if (c_line) {
|
|
jpayne@69
|
16407 c_line = __Pyx_CLineForTraceback(tstate, c_line);
|
|
jpayne@69
|
16408 }
|
|
jpayne@69
|
16409 py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
|
|
jpayne@69
|
16410 if (!py_code) {
|
|
jpayne@69
|
16411 __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
|
|
jpayne@69
|
16412 py_code = __Pyx_CreateCodeObjectForTraceback(
|
|
jpayne@69
|
16413 funcname, c_line, py_line, filename);
|
|
jpayne@69
|
16414 if (!py_code) {
|
|
jpayne@69
|
16415 /* If the code object creation fails, then we should clear the
|
|
jpayne@69
|
16416 fetched exception references and propagate the new exception */
|
|
jpayne@69
|
16417 Py_XDECREF(ptype);
|
|
jpayne@69
|
16418 Py_XDECREF(pvalue);
|
|
jpayne@69
|
16419 Py_XDECREF(ptraceback);
|
|
jpayne@69
|
16420 goto bad;
|
|
jpayne@69
|
16421 }
|
|
jpayne@69
|
16422 __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
|
|
jpayne@69
|
16423 __pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
|
|
jpayne@69
|
16424 }
|
|
jpayne@69
|
16425 py_frame = PyFrame_New(
|
|
jpayne@69
|
16426 tstate, /*PyThreadState *tstate,*/
|
|
jpayne@69
|
16427 py_code, /*PyCodeObject *code,*/
|
|
jpayne@69
|
16428 __pyx_d, /*PyObject *globals,*/
|
|
jpayne@69
|
16429 0 /*PyObject *locals*/
|
|
jpayne@69
|
16430 );
|
|
jpayne@69
|
16431 if (!py_frame) goto bad;
|
|
jpayne@69
|
16432 __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
|
|
jpayne@69
|
16433 PyTraceBack_Here(py_frame);
|
|
jpayne@69
|
16434 bad:
|
|
jpayne@69
|
16435 Py_XDECREF(py_code);
|
|
jpayne@69
|
16436 Py_XDECREF(py_frame);
|
|
jpayne@69
|
16437 }
|
|
jpayne@69
|
16438 #endif
|
|
jpayne@69
|
16439
|
|
jpayne@69
|
16440 /* CIntFromPyVerify */
|
|
jpayne@69
|
16441 #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
|
|
jpayne@69
|
16442 __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
|
|
jpayne@69
|
16443 #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
|
|
jpayne@69
|
16444 __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
|
|
jpayne@69
|
16445 #define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\
|
|
jpayne@69
|
16446 {\
|
|
jpayne@69
|
16447 func_type value = func_value;\
|
|
jpayne@69
|
16448 if (sizeof(target_type) < sizeof(func_type)) {\
|
|
jpayne@69
|
16449 if (unlikely(value != (func_type) (target_type) value)) {\
|
|
jpayne@69
|
16450 func_type zero = 0;\
|
|
jpayne@69
|
16451 if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\
|
|
jpayne@69
|
16452 return (target_type) -1;\
|
|
jpayne@69
|
16453 if (is_unsigned && unlikely(value < zero))\
|
|
jpayne@69
|
16454 goto raise_neg_overflow;\
|
|
jpayne@69
|
16455 else\
|
|
jpayne@69
|
16456 goto raise_overflow;\
|
|
jpayne@69
|
16457 }\
|
|
jpayne@69
|
16458 }\
|
|
jpayne@69
|
16459 return (target_type) value;\
|
|
jpayne@69
|
16460 }
|
|
jpayne@69
|
16461
|
|
jpayne@69
|
16462 /* CIntFromPy */
|
|
jpayne@69
|
16463 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
|
|
jpayne@69
|
16464 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
16465 #pragma GCC diagnostic push
|
|
jpayne@69
|
16466 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
16467 #endif
|
|
jpayne@69
|
16468 const int neg_one = (int) -1, const_zero = (int) 0;
|
|
jpayne@69
|
16469 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
16470 #pragma GCC diagnostic pop
|
|
jpayne@69
|
16471 #endif
|
|
jpayne@69
|
16472 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
16473 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16474 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
16475 if ((sizeof(int) < sizeof(long))) {
|
|
jpayne@69
|
16476 __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
16477 } else {
|
|
jpayne@69
|
16478 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
16479 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
16480 goto raise_neg_overflow;
|
|
jpayne@69
|
16481 }
|
|
jpayne@69
|
16482 return (int) val;
|
|
jpayne@69
|
16483 }
|
|
jpayne@69
|
16484 }
|
|
jpayne@69
|
16485 #endif
|
|
jpayne@69
|
16486 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
16487 int val;
|
|
jpayne@69
|
16488 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
16489 if (!tmp) return (int) -1;
|
|
jpayne@69
|
16490 val = __Pyx_PyInt_As_int(tmp);
|
|
jpayne@69
|
16491 Py_DECREF(tmp);
|
|
jpayne@69
|
16492 return val;
|
|
jpayne@69
|
16493 }
|
|
jpayne@69
|
16494 if (is_unsigned) {
|
|
jpayne@69
|
16495 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
16496 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
16497 goto raise_neg_overflow;
|
|
jpayne@69
|
16498 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
16499 __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
16500 } else {
|
|
jpayne@69
|
16501 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
16502 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
16503 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
16504 case 2:
|
|
jpayne@69
|
16505 if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16506 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16507 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16508 } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16509 return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
|
|
jpayne@69
|
16510 }
|
|
jpayne@69
|
16511 }
|
|
jpayne@69
|
16512 break;
|
|
jpayne@69
|
16513 case 3:
|
|
jpayne@69
|
16514 if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16515 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16516 __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
|
16517 } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16518 return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
|
|
jpayne@69
|
16519 }
|
|
jpayne@69
|
16520 }
|
|
jpayne@69
|
16521 break;
|
|
jpayne@69
|
16522 case 4:
|
|
jpayne@69
|
16523 if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16524 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16525 __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
|
16526 } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16527 return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]));
|
|
jpayne@69
|
16528 }
|
|
jpayne@69
|
16529 }
|
|
jpayne@69
|
16530 break;
|
|
jpayne@69
|
16531 }
|
|
jpayne@69
|
16532 }
|
|
jpayne@69
|
16533 #endif
|
|
jpayne@69
|
16534 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
16535 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
16536 goto raise_neg_overflow;
|
|
jpayne@69
|
16537 }
|
|
jpayne@69
|
16538 #else
|
|
jpayne@69
|
16539 {
|
|
jpayne@69
|
16540 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
16541 if (unlikely(result < 0))
|
|
jpayne@69
|
16542 return (int) -1;
|
|
jpayne@69
|
16543 if (unlikely(result == 1))
|
|
jpayne@69
|
16544 goto raise_neg_overflow;
|
|
jpayne@69
|
16545 }
|
|
jpayne@69
|
16546 #endif
|
|
jpayne@69
|
16547 if ((sizeof(int) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
16548 __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
16549 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
16550 } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
16551 __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
16552 #endif
|
|
jpayne@69
|
16553 }
|
|
jpayne@69
|
16554 } else {
|
|
jpayne@69
|
16555 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
16556 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
16557 __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
16558 } else {
|
|
jpayne@69
|
16559 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
16560 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
16561 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
16562 case -2:
|
|
jpayne@69
|
16563 if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16564 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16565 __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16566 } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16567 return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
16568 }
|
|
jpayne@69
|
16569 }
|
|
jpayne@69
|
16570 break;
|
|
jpayne@69
|
16571 case 2:
|
|
jpayne@69
|
16572 if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16573 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16574 __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16575 } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16576 return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
16577 }
|
|
jpayne@69
|
16578 }
|
|
jpayne@69
|
16579 break;
|
|
jpayne@69
|
16580 case -3:
|
|
jpayne@69
|
16581 if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16582 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16583 __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
|
16584 } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16585 return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
16586 }
|
|
jpayne@69
|
16587 }
|
|
jpayne@69
|
16588 break;
|
|
jpayne@69
|
16589 case 3:
|
|
jpayne@69
|
16590 if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16591 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16592 __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
|
16593 } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16594 return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
16595 }
|
|
jpayne@69
|
16596 }
|
|
jpayne@69
|
16597 break;
|
|
jpayne@69
|
16598 case -4:
|
|
jpayne@69
|
16599 if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16600 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16601 __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
|
16602 } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16603 return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
16604 }
|
|
jpayne@69
|
16605 }
|
|
jpayne@69
|
16606 break;
|
|
jpayne@69
|
16607 case 4:
|
|
jpayne@69
|
16608 if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16609 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16610 __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
|
16611 } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16612 return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])));
|
|
jpayne@69
|
16613 }
|
|
jpayne@69
|
16614 }
|
|
jpayne@69
|
16615 break;
|
|
jpayne@69
|
16616 }
|
|
jpayne@69
|
16617 }
|
|
jpayne@69
|
16618 #endif
|
|
jpayne@69
|
16619 if ((sizeof(int) <= sizeof(long))) {
|
|
jpayne@69
|
16620 __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
|
|
jpayne@69
|
16621 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
16622 } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
16623 __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
16624 #endif
|
|
jpayne@69
|
16625 }
|
|
jpayne@69
|
16626 }
|
|
jpayne@69
|
16627 {
|
|
jpayne@69
|
16628 int val;
|
|
jpayne@69
|
16629 int ret = -1;
|
|
jpayne@69
|
16630 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
16631 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
16632 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
16633 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
16634 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
16635 goto raise_overflow;
|
|
jpayne@69
|
16636 } else {
|
|
jpayne@69
|
16637 ret = 0;
|
|
jpayne@69
|
16638 }
|
|
jpayne@69
|
16639 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
16640 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
16641 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
16642 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
16643 bytes, sizeof(val),
|
|
jpayne@69
|
16644 is_little, !is_unsigned);
|
|
jpayne@69
|
16645 #else
|
|
jpayne@69
|
16646 PyObject *v;
|
|
jpayne@69
|
16647 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
16648 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
16649 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
16650 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
16651 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
16652 } else {
|
|
jpayne@69
|
16653 v = PyNumber_Long(x);
|
|
jpayne@69
|
16654 if (unlikely(!v)) return (int) -1;
|
|
jpayne@69
|
16655 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
16656 }
|
|
jpayne@69
|
16657 {
|
|
jpayne@69
|
16658 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
16659 if (unlikely(result < 0)) {
|
|
jpayne@69
|
16660 Py_DECREF(v);
|
|
jpayne@69
|
16661 return (int) -1;
|
|
jpayne@69
|
16662 }
|
|
jpayne@69
|
16663 is_negative = result == 1;
|
|
jpayne@69
|
16664 }
|
|
jpayne@69
|
16665 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
16666 Py_DECREF(v);
|
|
jpayne@69
|
16667 goto raise_neg_overflow;
|
|
jpayne@69
|
16668 } else if (is_negative) {
|
|
jpayne@69
|
16669 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
16670 Py_DECREF(v);
|
|
jpayne@69
|
16671 if (unlikely(!stepval))
|
|
jpayne@69
|
16672 return (int) -1;
|
|
jpayne@69
|
16673 } else {
|
|
jpayne@69
|
16674 stepval = v;
|
|
jpayne@69
|
16675 }
|
|
jpayne@69
|
16676 v = NULL;
|
|
jpayne@69
|
16677 val = (int) 0;
|
|
jpayne@69
|
16678 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
16679 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
16680 for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
16681 PyObject *tmp, *digit;
|
|
jpayne@69
|
16682 long idigit;
|
|
jpayne@69
|
16683 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
16684 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
16685 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
16686 Py_DECREF(digit);
|
|
jpayne@69
|
16687 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
16688 val |= ((int) idigit) << bits;
|
|
jpayne@69
|
16689 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
16690 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
16691 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
16692 }
|
|
jpayne@69
|
16693 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
16694 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
16695 {
|
|
jpayne@69
|
16696 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
16697 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
16698 remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
16699 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
16700 goto raise_overflow;
|
|
jpayne@69
|
16701 val |= ((int) idigit) << bits;
|
|
jpayne@69
|
16702 }
|
|
jpayne@69
|
16703 if (!is_unsigned) {
|
|
jpayne@69
|
16704 if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1))))
|
|
jpayne@69
|
16705 goto raise_overflow;
|
|
jpayne@69
|
16706 if (is_negative)
|
|
jpayne@69
|
16707 val = ~val;
|
|
jpayne@69
|
16708 }
|
|
jpayne@69
|
16709 ret = 0;
|
|
jpayne@69
|
16710 done:
|
|
jpayne@69
|
16711 Py_XDECREF(shift);
|
|
jpayne@69
|
16712 Py_XDECREF(mask);
|
|
jpayne@69
|
16713 Py_XDECREF(stepval);
|
|
jpayne@69
|
16714 #endif
|
|
jpayne@69
|
16715 if (unlikely(ret))
|
|
jpayne@69
|
16716 return (int) -1;
|
|
jpayne@69
|
16717 return val;
|
|
jpayne@69
|
16718 }
|
|
jpayne@69
|
16719 raise_overflow:
|
|
jpayne@69
|
16720 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
16721 "value too large to convert to int");
|
|
jpayne@69
|
16722 return (int) -1;
|
|
jpayne@69
|
16723 raise_neg_overflow:
|
|
jpayne@69
|
16724 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
16725 "can't convert negative value to int");
|
|
jpayne@69
|
16726 return (int) -1;
|
|
jpayne@69
|
16727 }
|
|
jpayne@69
|
16728
|
|
jpayne@69
|
16729 /* CIntFromPy */
|
|
jpayne@69
|
16730 static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) {
|
|
jpayne@69
|
16731 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
16732 #pragma GCC diagnostic push
|
|
jpayne@69
|
16733 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
16734 #endif
|
|
jpayne@69
|
16735 const char neg_one = (char) -1, const_zero = (char) 0;
|
|
jpayne@69
|
16736 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
16737 #pragma GCC diagnostic pop
|
|
jpayne@69
|
16738 #endif
|
|
jpayne@69
|
16739 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
16740 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
16741 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
16742 if ((sizeof(char) < sizeof(long))) {
|
|
jpayne@69
|
16743 __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
16744 } else {
|
|
jpayne@69
|
16745 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
16746 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
16747 goto raise_neg_overflow;
|
|
jpayne@69
|
16748 }
|
|
jpayne@69
|
16749 return (char) val;
|
|
jpayne@69
|
16750 }
|
|
jpayne@69
|
16751 }
|
|
jpayne@69
|
16752 #endif
|
|
jpayne@69
|
16753 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
16754 char val;
|
|
jpayne@69
|
16755 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
16756 if (!tmp) return (char) -1;
|
|
jpayne@69
|
16757 val = __Pyx_PyInt_As_char(tmp);
|
|
jpayne@69
|
16758 Py_DECREF(tmp);
|
|
jpayne@69
|
16759 return val;
|
|
jpayne@69
|
16760 }
|
|
jpayne@69
|
16761 if (is_unsigned) {
|
|
jpayne@69
|
16762 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
16763 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
16764 goto raise_neg_overflow;
|
|
jpayne@69
|
16765 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
16766 __PYX_VERIFY_RETURN_INT(char, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
16767 } else {
|
|
jpayne@69
|
16768 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
16769 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
16770 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
16771 case 2:
|
|
jpayne@69
|
16772 if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16773 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16774 __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16775 } else if ((8 * sizeof(char) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16776 return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]));
|
|
jpayne@69
|
16777 }
|
|
jpayne@69
|
16778 }
|
|
jpayne@69
|
16779 break;
|
|
jpayne@69
|
16780 case 3:
|
|
jpayne@69
|
16781 if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16782 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16783 __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16784 } else if ((8 * sizeof(char) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16785 return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]));
|
|
jpayne@69
|
16786 }
|
|
jpayne@69
|
16787 }
|
|
jpayne@69
|
16788 break;
|
|
jpayne@69
|
16789 case 4:
|
|
jpayne@69
|
16790 if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16791 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16792 __PYX_VERIFY_RETURN_INT(char, 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
|
16793 } else if ((8 * sizeof(char) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16794 return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]));
|
|
jpayne@69
|
16795 }
|
|
jpayne@69
|
16796 }
|
|
jpayne@69
|
16797 break;
|
|
jpayne@69
|
16798 }
|
|
jpayne@69
|
16799 }
|
|
jpayne@69
|
16800 #endif
|
|
jpayne@69
|
16801 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
16802 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
16803 goto raise_neg_overflow;
|
|
jpayne@69
|
16804 }
|
|
jpayne@69
|
16805 #else
|
|
jpayne@69
|
16806 {
|
|
jpayne@69
|
16807 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
16808 if (unlikely(result < 0))
|
|
jpayne@69
|
16809 return (char) -1;
|
|
jpayne@69
|
16810 if (unlikely(result == 1))
|
|
jpayne@69
|
16811 goto raise_neg_overflow;
|
|
jpayne@69
|
16812 }
|
|
jpayne@69
|
16813 #endif
|
|
jpayne@69
|
16814 if ((sizeof(char) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
16815 __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
16816 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
16817 } else if ((sizeof(char) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
16818 __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
16819 #endif
|
|
jpayne@69
|
16820 }
|
|
jpayne@69
|
16821 } else {
|
|
jpayne@69
|
16822 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
16823 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
16824 __PYX_VERIFY_RETURN_INT(char, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
16825 } else {
|
|
jpayne@69
|
16826 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
16827 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
16828 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
16829 case -2:
|
|
jpayne@69
|
16830 if ((8 * sizeof(char) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16831 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16832 __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16833 } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16834 return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])));
|
|
jpayne@69
|
16835 }
|
|
jpayne@69
|
16836 }
|
|
jpayne@69
|
16837 break;
|
|
jpayne@69
|
16838 case 2:
|
|
jpayne@69
|
16839 if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16840 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16841 __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16842 } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16843 return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])));
|
|
jpayne@69
|
16844 }
|
|
jpayne@69
|
16845 }
|
|
jpayne@69
|
16846 break;
|
|
jpayne@69
|
16847 case -3:
|
|
jpayne@69
|
16848 if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16849 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16850 __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16851 } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16852 return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])));
|
|
jpayne@69
|
16853 }
|
|
jpayne@69
|
16854 }
|
|
jpayne@69
|
16855 break;
|
|
jpayne@69
|
16856 case 3:
|
|
jpayne@69
|
16857 if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16858 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16859 __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
16860 } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16861 return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])));
|
|
jpayne@69
|
16862 }
|
|
jpayne@69
|
16863 }
|
|
jpayne@69
|
16864 break;
|
|
jpayne@69
|
16865 case -4:
|
|
jpayne@69
|
16866 if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16867 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16868 __PYX_VERIFY_RETURN_INT(char, 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
|
16869 } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16870 return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])));
|
|
jpayne@69
|
16871 }
|
|
jpayne@69
|
16872 }
|
|
jpayne@69
|
16873 break;
|
|
jpayne@69
|
16874 case 4:
|
|
jpayne@69
|
16875 if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16876 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16877 __PYX_VERIFY_RETURN_INT(char, 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
|
16878 } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
16879 return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])));
|
|
jpayne@69
|
16880 }
|
|
jpayne@69
|
16881 }
|
|
jpayne@69
|
16882 break;
|
|
jpayne@69
|
16883 }
|
|
jpayne@69
|
16884 }
|
|
jpayne@69
|
16885 #endif
|
|
jpayne@69
|
16886 if ((sizeof(char) <= sizeof(long))) {
|
|
jpayne@69
|
16887 __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x))
|
|
jpayne@69
|
16888 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
16889 } else if ((sizeof(char) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
16890 __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
16891 #endif
|
|
jpayne@69
|
16892 }
|
|
jpayne@69
|
16893 }
|
|
jpayne@69
|
16894 {
|
|
jpayne@69
|
16895 char val;
|
|
jpayne@69
|
16896 int ret = -1;
|
|
jpayne@69
|
16897 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
16898 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
16899 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
16900 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
16901 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
16902 goto raise_overflow;
|
|
jpayne@69
|
16903 } else {
|
|
jpayne@69
|
16904 ret = 0;
|
|
jpayne@69
|
16905 }
|
|
jpayne@69
|
16906 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
16907 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
16908 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
16909 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
16910 bytes, sizeof(val),
|
|
jpayne@69
|
16911 is_little, !is_unsigned);
|
|
jpayne@69
|
16912 #else
|
|
jpayne@69
|
16913 PyObject *v;
|
|
jpayne@69
|
16914 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
16915 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
16916 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
16917 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
16918 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
16919 } else {
|
|
jpayne@69
|
16920 v = PyNumber_Long(x);
|
|
jpayne@69
|
16921 if (unlikely(!v)) return (char) -1;
|
|
jpayne@69
|
16922 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
16923 }
|
|
jpayne@69
|
16924 {
|
|
jpayne@69
|
16925 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
16926 if (unlikely(result < 0)) {
|
|
jpayne@69
|
16927 Py_DECREF(v);
|
|
jpayne@69
|
16928 return (char) -1;
|
|
jpayne@69
|
16929 }
|
|
jpayne@69
|
16930 is_negative = result == 1;
|
|
jpayne@69
|
16931 }
|
|
jpayne@69
|
16932 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
16933 Py_DECREF(v);
|
|
jpayne@69
|
16934 goto raise_neg_overflow;
|
|
jpayne@69
|
16935 } else if (is_negative) {
|
|
jpayne@69
|
16936 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
16937 Py_DECREF(v);
|
|
jpayne@69
|
16938 if (unlikely(!stepval))
|
|
jpayne@69
|
16939 return (char) -1;
|
|
jpayne@69
|
16940 } else {
|
|
jpayne@69
|
16941 stepval = v;
|
|
jpayne@69
|
16942 }
|
|
jpayne@69
|
16943 v = NULL;
|
|
jpayne@69
|
16944 val = (char) 0;
|
|
jpayne@69
|
16945 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
16946 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
16947 for (bits = 0; bits < (int) sizeof(char) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
16948 PyObject *tmp, *digit;
|
|
jpayne@69
|
16949 long idigit;
|
|
jpayne@69
|
16950 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
16951 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
16952 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
16953 Py_DECREF(digit);
|
|
jpayne@69
|
16954 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
16955 val |= ((char) idigit) << bits;
|
|
jpayne@69
|
16956 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
16957 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
16958 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
16959 }
|
|
jpayne@69
|
16960 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
16961 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
16962 {
|
|
jpayne@69
|
16963 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
16964 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
16965 remaining_bits = ((int) sizeof(char) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
16966 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
16967 goto raise_overflow;
|
|
jpayne@69
|
16968 val |= ((char) idigit) << bits;
|
|
jpayne@69
|
16969 }
|
|
jpayne@69
|
16970 if (!is_unsigned) {
|
|
jpayne@69
|
16971 if (unlikely(val & (((char) 1) << (sizeof(char) * 8 - 1))))
|
|
jpayne@69
|
16972 goto raise_overflow;
|
|
jpayne@69
|
16973 if (is_negative)
|
|
jpayne@69
|
16974 val = ~val;
|
|
jpayne@69
|
16975 }
|
|
jpayne@69
|
16976 ret = 0;
|
|
jpayne@69
|
16977 done:
|
|
jpayne@69
|
16978 Py_XDECREF(shift);
|
|
jpayne@69
|
16979 Py_XDECREF(mask);
|
|
jpayne@69
|
16980 Py_XDECREF(stepval);
|
|
jpayne@69
|
16981 #endif
|
|
jpayne@69
|
16982 if (unlikely(ret))
|
|
jpayne@69
|
16983 return (char) -1;
|
|
jpayne@69
|
16984 return val;
|
|
jpayne@69
|
16985 }
|
|
jpayne@69
|
16986 raise_overflow:
|
|
jpayne@69
|
16987 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
16988 "value too large to convert to char");
|
|
jpayne@69
|
16989 return (char) -1;
|
|
jpayne@69
|
16990 raise_neg_overflow:
|
|
jpayne@69
|
16991 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
16992 "can't convert negative value to char");
|
|
jpayne@69
|
16993 return (char) -1;
|
|
jpayne@69
|
16994 }
|
|
jpayne@69
|
16995
|
|
jpayne@69
|
16996 /* CIntToPy */
|
|
jpayne@69
|
16997 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
|
|
jpayne@69
|
16998 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
16999 #pragma GCC diagnostic push
|
|
jpayne@69
|
17000 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
17001 #endif
|
|
jpayne@69
|
17002 const int neg_one = (int) -1, const_zero = (int) 0;
|
|
jpayne@69
|
17003 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17004 #pragma GCC diagnostic pop
|
|
jpayne@69
|
17005 #endif
|
|
jpayne@69
|
17006 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
17007 if (is_unsigned) {
|
|
jpayne@69
|
17008 if (sizeof(int) < sizeof(long)) {
|
|
jpayne@69
|
17009 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
17010 } else if (sizeof(int) <= sizeof(unsigned long)) {
|
|
jpayne@69
|
17011 return PyLong_FromUnsignedLong((unsigned long) value);
|
|
jpayne@69
|
17012 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17013 } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
|
|
jpayne@69
|
17014 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
|
|
jpayne@69
|
17015 #endif
|
|
jpayne@69
|
17016 }
|
|
jpayne@69
|
17017 } else {
|
|
jpayne@69
|
17018 if (sizeof(int) <= sizeof(long)) {
|
|
jpayne@69
|
17019 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
17020 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17021 } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
|
|
jpayne@69
|
17022 return PyLong_FromLongLong((PY_LONG_LONG) value);
|
|
jpayne@69
|
17023 #endif
|
|
jpayne@69
|
17024 }
|
|
jpayne@69
|
17025 }
|
|
jpayne@69
|
17026 {
|
|
jpayne@69
|
17027 unsigned char *bytes = (unsigned char *)&value;
|
|
jpayne@69
|
17028 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
17029 if (is_unsigned) {
|
|
jpayne@69
|
17030 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
17031 } else {
|
|
jpayne@69
|
17032 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
17033 }
|
|
jpayne@69
|
17034 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
17035 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17036 return _PyLong_FromByteArray(bytes, sizeof(int),
|
|
jpayne@69
|
17037 little, !is_unsigned);
|
|
jpayne@69
|
17038 #else
|
|
jpayne@69
|
17039 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17040 PyObject *from_bytes, *result = NULL;
|
|
jpayne@69
|
17041 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
|
|
jpayne@69
|
17042 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
|
|
jpayne@69
|
17043 if (!from_bytes) return NULL;
|
|
jpayne@69
|
17044 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int));
|
|
jpayne@69
|
17045 if (!py_bytes) goto limited_bad;
|
|
jpayne@69
|
17046 order_str = PyUnicode_FromString(little ? "little" : "big");
|
|
jpayne@69
|
17047 if (!order_str) goto limited_bad;
|
|
jpayne@69
|
17048 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
|
|
jpayne@69
|
17049 if (!arg_tuple) goto limited_bad;
|
|
jpayne@69
|
17050 if (!is_unsigned) {
|
|
jpayne@69
|
17051 kwds = PyDict_New();
|
|
jpayne@69
|
17052 if (!kwds) goto limited_bad;
|
|
jpayne@69
|
17053 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
|
|
jpayne@69
|
17054 }
|
|
jpayne@69
|
17055 result = PyObject_Call(from_bytes, arg_tuple, kwds);
|
|
jpayne@69
|
17056 limited_bad:
|
|
jpayne@69
|
17057 Py_XDECREF(kwds);
|
|
jpayne@69
|
17058 Py_XDECREF(arg_tuple);
|
|
jpayne@69
|
17059 Py_XDECREF(order_str);
|
|
jpayne@69
|
17060 Py_XDECREF(py_bytes);
|
|
jpayne@69
|
17061 Py_XDECREF(from_bytes);
|
|
jpayne@69
|
17062 return result;
|
|
jpayne@69
|
17063 #endif
|
|
jpayne@69
|
17064 }
|
|
jpayne@69
|
17065 }
|
|
jpayne@69
|
17066
|
|
jpayne@69
|
17067 /* CIntFromPy */
|
|
jpayne@69
|
17068 static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) {
|
|
jpayne@69
|
17069 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17070 #pragma GCC diagnostic push
|
|
jpayne@69
|
17071 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
17072 #endif
|
|
jpayne@69
|
17073 const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0;
|
|
jpayne@69
|
17074 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17075 #pragma GCC diagnostic pop
|
|
jpayne@69
|
17076 #endif
|
|
jpayne@69
|
17077 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
17078 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
17079 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
17080 if ((sizeof(int32_t) < sizeof(long))) {
|
|
jpayne@69
|
17081 __PYX_VERIFY_RETURN_INT(int32_t, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
17082 } else {
|
|
jpayne@69
|
17083 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
17084 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
17085 goto raise_neg_overflow;
|
|
jpayne@69
|
17086 }
|
|
jpayne@69
|
17087 return (int32_t) val;
|
|
jpayne@69
|
17088 }
|
|
jpayne@69
|
17089 }
|
|
jpayne@69
|
17090 #endif
|
|
jpayne@69
|
17091 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
17092 int32_t val;
|
|
jpayne@69
|
17093 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
17094 if (!tmp) return (int32_t) -1;
|
|
jpayne@69
|
17095 val = __Pyx_PyInt_As_int32_t(tmp);
|
|
jpayne@69
|
17096 Py_DECREF(tmp);
|
|
jpayne@69
|
17097 return val;
|
|
jpayne@69
|
17098 }
|
|
jpayne@69
|
17099 if (is_unsigned) {
|
|
jpayne@69
|
17100 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
17101 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
17102 goto raise_neg_overflow;
|
|
jpayne@69
|
17103 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
17104 __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
17105 } else {
|
|
jpayne@69
|
17106 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
17107 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
17108 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
17109 case 2:
|
|
jpayne@69
|
17110 if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17111 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17112 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
17113 } else if ((8 * sizeof(int32_t) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17114 return (int32_t) (((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
|
|
jpayne@69
|
17115 }
|
|
jpayne@69
|
17116 }
|
|
jpayne@69
|
17117 break;
|
|
jpayne@69
|
17118 case 3:
|
|
jpayne@69
|
17119 if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17120 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17121 __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
|
17122 } else if ((8 * sizeof(int32_t) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17123 return (int32_t) (((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]));
|
|
jpayne@69
|
17124 }
|
|
jpayne@69
|
17125 }
|
|
jpayne@69
|
17126 break;
|
|
jpayne@69
|
17127 case 4:
|
|
jpayne@69
|
17128 if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17129 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17130 __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
|
17131 } else if ((8 * sizeof(int32_t) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17132 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
|
17133 }
|
|
jpayne@69
|
17134 }
|
|
jpayne@69
|
17135 break;
|
|
jpayne@69
|
17136 }
|
|
jpayne@69
|
17137 }
|
|
jpayne@69
|
17138 #endif
|
|
jpayne@69
|
17139 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
17140 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
17141 goto raise_neg_overflow;
|
|
jpayne@69
|
17142 }
|
|
jpayne@69
|
17143 #else
|
|
jpayne@69
|
17144 {
|
|
jpayne@69
|
17145 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
17146 if (unlikely(result < 0))
|
|
jpayne@69
|
17147 return (int32_t) -1;
|
|
jpayne@69
|
17148 if (unlikely(result == 1))
|
|
jpayne@69
|
17149 goto raise_neg_overflow;
|
|
jpayne@69
|
17150 }
|
|
jpayne@69
|
17151 #endif
|
|
jpayne@69
|
17152 if ((sizeof(int32_t) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
17153 __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
17154 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17155 } else if ((sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
17156 __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
17157 #endif
|
|
jpayne@69
|
17158 }
|
|
jpayne@69
|
17159 } else {
|
|
jpayne@69
|
17160 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
17161 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
17162 __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
17163 } else {
|
|
jpayne@69
|
17164 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
17165 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
17166 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
17167 case -2:
|
|
jpayne@69
|
17168 if ((8 * sizeof(int32_t) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17169 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17170 __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
17171 } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17172 return (int32_t) (((int32_t)-1)*(((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
17173 }
|
|
jpayne@69
|
17174 }
|
|
jpayne@69
|
17175 break;
|
|
jpayne@69
|
17176 case 2:
|
|
jpayne@69
|
17177 if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17178 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17179 __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
17180 } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17181 return (int32_t) ((((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
17182 }
|
|
jpayne@69
|
17183 }
|
|
jpayne@69
|
17184 break;
|
|
jpayne@69
|
17185 case -3:
|
|
jpayne@69
|
17186 if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17187 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17188 __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
|
17189 } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17190 return (int32_t) (((int32_t)-1)*(((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
17191 }
|
|
jpayne@69
|
17192 }
|
|
jpayne@69
|
17193 break;
|
|
jpayne@69
|
17194 case 3:
|
|
jpayne@69
|
17195 if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17196 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17197 __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
|
17198 } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17199 return (int32_t) ((((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])));
|
|
jpayne@69
|
17200 }
|
|
jpayne@69
|
17201 }
|
|
jpayne@69
|
17202 break;
|
|
jpayne@69
|
17203 case -4:
|
|
jpayne@69
|
17204 if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17205 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17206 __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
|
17207 } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17208 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
|
17209 }
|
|
jpayne@69
|
17210 }
|
|
jpayne@69
|
17211 break;
|
|
jpayne@69
|
17212 case 4:
|
|
jpayne@69
|
17213 if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17214 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17215 __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
|
17216 } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17217 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
|
17218 }
|
|
jpayne@69
|
17219 }
|
|
jpayne@69
|
17220 break;
|
|
jpayne@69
|
17221 }
|
|
jpayne@69
|
17222 }
|
|
jpayne@69
|
17223 #endif
|
|
jpayne@69
|
17224 if ((sizeof(int32_t) <= sizeof(long))) {
|
|
jpayne@69
|
17225 __PYX_VERIFY_RETURN_INT_EXC(int32_t, long, PyLong_AsLong(x))
|
|
jpayne@69
|
17226 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17227 } else if ((sizeof(int32_t) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
17228 __PYX_VERIFY_RETURN_INT_EXC(int32_t, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
17229 #endif
|
|
jpayne@69
|
17230 }
|
|
jpayne@69
|
17231 }
|
|
jpayne@69
|
17232 {
|
|
jpayne@69
|
17233 int32_t val;
|
|
jpayne@69
|
17234 int ret = -1;
|
|
jpayne@69
|
17235 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
17236 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
17237 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
17238 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
17239 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
17240 goto raise_overflow;
|
|
jpayne@69
|
17241 } else {
|
|
jpayne@69
|
17242 ret = 0;
|
|
jpayne@69
|
17243 }
|
|
jpayne@69
|
17244 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
17245 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17246 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
17247 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
17248 bytes, sizeof(val),
|
|
jpayne@69
|
17249 is_little, !is_unsigned);
|
|
jpayne@69
|
17250 #else
|
|
jpayne@69
|
17251 PyObject *v;
|
|
jpayne@69
|
17252 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
17253 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
17254 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
17255 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
17256 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
17257 } else {
|
|
jpayne@69
|
17258 v = PyNumber_Long(x);
|
|
jpayne@69
|
17259 if (unlikely(!v)) return (int32_t) -1;
|
|
jpayne@69
|
17260 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
17261 }
|
|
jpayne@69
|
17262 {
|
|
jpayne@69
|
17263 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
17264 if (unlikely(result < 0)) {
|
|
jpayne@69
|
17265 Py_DECREF(v);
|
|
jpayne@69
|
17266 return (int32_t) -1;
|
|
jpayne@69
|
17267 }
|
|
jpayne@69
|
17268 is_negative = result == 1;
|
|
jpayne@69
|
17269 }
|
|
jpayne@69
|
17270 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
17271 Py_DECREF(v);
|
|
jpayne@69
|
17272 goto raise_neg_overflow;
|
|
jpayne@69
|
17273 } else if (is_negative) {
|
|
jpayne@69
|
17274 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
17275 Py_DECREF(v);
|
|
jpayne@69
|
17276 if (unlikely(!stepval))
|
|
jpayne@69
|
17277 return (int32_t) -1;
|
|
jpayne@69
|
17278 } else {
|
|
jpayne@69
|
17279 stepval = v;
|
|
jpayne@69
|
17280 }
|
|
jpayne@69
|
17281 v = NULL;
|
|
jpayne@69
|
17282 val = (int32_t) 0;
|
|
jpayne@69
|
17283 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
17284 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
17285 for (bits = 0; bits < (int) sizeof(int32_t) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
17286 PyObject *tmp, *digit;
|
|
jpayne@69
|
17287 long idigit;
|
|
jpayne@69
|
17288 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
17289 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
17290 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
17291 Py_DECREF(digit);
|
|
jpayne@69
|
17292 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
17293 val |= ((int32_t) idigit) << bits;
|
|
jpayne@69
|
17294 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
17295 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
17296 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
17297 }
|
|
jpayne@69
|
17298 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
17299 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
17300 {
|
|
jpayne@69
|
17301 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
17302 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
17303 remaining_bits = ((int) sizeof(int32_t) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
17304 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
17305 goto raise_overflow;
|
|
jpayne@69
|
17306 val |= ((int32_t) idigit) << bits;
|
|
jpayne@69
|
17307 }
|
|
jpayne@69
|
17308 if (!is_unsigned) {
|
|
jpayne@69
|
17309 if (unlikely(val & (((int32_t) 1) << (sizeof(int32_t) * 8 - 1))))
|
|
jpayne@69
|
17310 goto raise_overflow;
|
|
jpayne@69
|
17311 if (is_negative)
|
|
jpayne@69
|
17312 val = ~val;
|
|
jpayne@69
|
17313 }
|
|
jpayne@69
|
17314 ret = 0;
|
|
jpayne@69
|
17315 done:
|
|
jpayne@69
|
17316 Py_XDECREF(shift);
|
|
jpayne@69
|
17317 Py_XDECREF(mask);
|
|
jpayne@69
|
17318 Py_XDECREF(stepval);
|
|
jpayne@69
|
17319 #endif
|
|
jpayne@69
|
17320 if (unlikely(ret))
|
|
jpayne@69
|
17321 return (int32_t) -1;
|
|
jpayne@69
|
17322 return val;
|
|
jpayne@69
|
17323 }
|
|
jpayne@69
|
17324 raise_overflow:
|
|
jpayne@69
|
17325 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
17326 "value too large to convert to int32_t");
|
|
jpayne@69
|
17327 return (int32_t) -1;
|
|
jpayne@69
|
17328 raise_neg_overflow:
|
|
jpayne@69
|
17329 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
17330 "can't convert negative value to int32_t");
|
|
jpayne@69
|
17331 return (int32_t) -1;
|
|
jpayne@69
|
17332 }
|
|
jpayne@69
|
17333
|
|
jpayne@69
|
17334 /* CIntToPy */
|
|
jpayne@69
|
17335 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
|
|
jpayne@69
|
17336 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17337 #pragma GCC diagnostic push
|
|
jpayne@69
|
17338 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
17339 #endif
|
|
jpayne@69
|
17340 const long neg_one = (long) -1, const_zero = (long) 0;
|
|
jpayne@69
|
17341 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17342 #pragma GCC diagnostic pop
|
|
jpayne@69
|
17343 #endif
|
|
jpayne@69
|
17344 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
17345 if (is_unsigned) {
|
|
jpayne@69
|
17346 if (sizeof(long) < sizeof(long)) {
|
|
jpayne@69
|
17347 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
17348 } else if (sizeof(long) <= sizeof(unsigned long)) {
|
|
jpayne@69
|
17349 return PyLong_FromUnsignedLong((unsigned long) value);
|
|
jpayne@69
|
17350 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17351 } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
|
|
jpayne@69
|
17352 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
|
|
jpayne@69
|
17353 #endif
|
|
jpayne@69
|
17354 }
|
|
jpayne@69
|
17355 } else {
|
|
jpayne@69
|
17356 if (sizeof(long) <= sizeof(long)) {
|
|
jpayne@69
|
17357 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
17358 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17359 } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
|
|
jpayne@69
|
17360 return PyLong_FromLongLong((PY_LONG_LONG) value);
|
|
jpayne@69
|
17361 #endif
|
|
jpayne@69
|
17362 }
|
|
jpayne@69
|
17363 }
|
|
jpayne@69
|
17364 {
|
|
jpayne@69
|
17365 unsigned char *bytes = (unsigned char *)&value;
|
|
jpayne@69
|
17366 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
17367 if (is_unsigned) {
|
|
jpayne@69
|
17368 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
17369 } else {
|
|
jpayne@69
|
17370 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
17371 }
|
|
jpayne@69
|
17372 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
17373 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17374 return _PyLong_FromByteArray(bytes, sizeof(long),
|
|
jpayne@69
|
17375 little, !is_unsigned);
|
|
jpayne@69
|
17376 #else
|
|
jpayne@69
|
17377 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17378 PyObject *from_bytes, *result = NULL;
|
|
jpayne@69
|
17379 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
|
|
jpayne@69
|
17380 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
|
|
jpayne@69
|
17381 if (!from_bytes) return NULL;
|
|
jpayne@69
|
17382 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(long));
|
|
jpayne@69
|
17383 if (!py_bytes) goto limited_bad;
|
|
jpayne@69
|
17384 order_str = PyUnicode_FromString(little ? "little" : "big");
|
|
jpayne@69
|
17385 if (!order_str) goto limited_bad;
|
|
jpayne@69
|
17386 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
|
|
jpayne@69
|
17387 if (!arg_tuple) goto limited_bad;
|
|
jpayne@69
|
17388 if (!is_unsigned) {
|
|
jpayne@69
|
17389 kwds = PyDict_New();
|
|
jpayne@69
|
17390 if (!kwds) goto limited_bad;
|
|
jpayne@69
|
17391 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
|
|
jpayne@69
|
17392 }
|
|
jpayne@69
|
17393 result = PyObject_Call(from_bytes, arg_tuple, kwds);
|
|
jpayne@69
|
17394 limited_bad:
|
|
jpayne@69
|
17395 Py_XDECREF(kwds);
|
|
jpayne@69
|
17396 Py_XDECREF(arg_tuple);
|
|
jpayne@69
|
17397 Py_XDECREF(order_str);
|
|
jpayne@69
|
17398 Py_XDECREF(py_bytes);
|
|
jpayne@69
|
17399 Py_XDECREF(from_bytes);
|
|
jpayne@69
|
17400 return result;
|
|
jpayne@69
|
17401 #endif
|
|
jpayne@69
|
17402 }
|
|
jpayne@69
|
17403 }
|
|
jpayne@69
|
17404
|
|
jpayne@69
|
17405 /* CIntToPy */
|
|
jpayne@69
|
17406 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) {
|
|
jpayne@69
|
17407 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17408 #pragma GCC diagnostic push
|
|
jpayne@69
|
17409 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
17410 #endif
|
|
jpayne@69
|
17411 const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0;
|
|
jpayne@69
|
17412 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17413 #pragma GCC diagnostic pop
|
|
jpayne@69
|
17414 #endif
|
|
jpayne@69
|
17415 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
17416 if (is_unsigned) {
|
|
jpayne@69
|
17417 if (sizeof(int32_t) < sizeof(long)) {
|
|
jpayne@69
|
17418 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
17419 } else if (sizeof(int32_t) <= sizeof(unsigned long)) {
|
|
jpayne@69
|
17420 return PyLong_FromUnsignedLong((unsigned long) value);
|
|
jpayne@69
|
17421 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17422 } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) {
|
|
jpayne@69
|
17423 return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
|
|
jpayne@69
|
17424 #endif
|
|
jpayne@69
|
17425 }
|
|
jpayne@69
|
17426 } else {
|
|
jpayne@69
|
17427 if (sizeof(int32_t) <= sizeof(long)) {
|
|
jpayne@69
|
17428 return PyInt_FromLong((long) value);
|
|
jpayne@69
|
17429 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17430 } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) {
|
|
jpayne@69
|
17431 return PyLong_FromLongLong((PY_LONG_LONG) value);
|
|
jpayne@69
|
17432 #endif
|
|
jpayne@69
|
17433 }
|
|
jpayne@69
|
17434 }
|
|
jpayne@69
|
17435 {
|
|
jpayne@69
|
17436 unsigned char *bytes = (unsigned char *)&value;
|
|
jpayne@69
|
17437 #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4
|
|
jpayne@69
|
17438 if (is_unsigned) {
|
|
jpayne@69
|
17439 return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
17440 } else {
|
|
jpayne@69
|
17441 return PyLong_FromNativeBytes(bytes, sizeof(value), -1);
|
|
jpayne@69
|
17442 }
|
|
jpayne@69
|
17443 #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000
|
|
jpayne@69
|
17444 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17445 return _PyLong_FromByteArray(bytes, sizeof(int32_t),
|
|
jpayne@69
|
17446 little, !is_unsigned);
|
|
jpayne@69
|
17447 #else
|
|
jpayne@69
|
17448 int one = 1; int little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17449 PyObject *from_bytes, *result = NULL;
|
|
jpayne@69
|
17450 PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL;
|
|
jpayne@69
|
17451 from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes");
|
|
jpayne@69
|
17452 if (!from_bytes) return NULL;
|
|
jpayne@69
|
17453 py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int32_t));
|
|
jpayne@69
|
17454 if (!py_bytes) goto limited_bad;
|
|
jpayne@69
|
17455 order_str = PyUnicode_FromString(little ? "little" : "big");
|
|
jpayne@69
|
17456 if (!order_str) goto limited_bad;
|
|
jpayne@69
|
17457 arg_tuple = PyTuple_Pack(2, py_bytes, order_str);
|
|
jpayne@69
|
17458 if (!arg_tuple) goto limited_bad;
|
|
jpayne@69
|
17459 if (!is_unsigned) {
|
|
jpayne@69
|
17460 kwds = PyDict_New();
|
|
jpayne@69
|
17461 if (!kwds) goto limited_bad;
|
|
jpayne@69
|
17462 if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad;
|
|
jpayne@69
|
17463 }
|
|
jpayne@69
|
17464 result = PyObject_Call(from_bytes, arg_tuple, kwds);
|
|
jpayne@69
|
17465 limited_bad:
|
|
jpayne@69
|
17466 Py_XDECREF(kwds);
|
|
jpayne@69
|
17467 Py_XDECREF(arg_tuple);
|
|
jpayne@69
|
17468 Py_XDECREF(order_str);
|
|
jpayne@69
|
17469 Py_XDECREF(py_bytes);
|
|
jpayne@69
|
17470 Py_XDECREF(from_bytes);
|
|
jpayne@69
|
17471 return result;
|
|
jpayne@69
|
17472 #endif
|
|
jpayne@69
|
17473 }
|
|
jpayne@69
|
17474 }
|
|
jpayne@69
|
17475
|
|
jpayne@69
|
17476 /* FormatTypeName */
|
|
jpayne@69
|
17477 #if CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
17478 static __Pyx_TypeName
|
|
jpayne@69
|
17479 __Pyx_PyType_GetName(PyTypeObject* tp)
|
|
jpayne@69
|
17480 {
|
|
jpayne@69
|
17481 PyObject *name = __Pyx_PyObject_GetAttrStr((PyObject *)tp,
|
|
jpayne@69
|
17482 __pyx_n_s_name_2);
|
|
jpayne@69
|
17483 if (unlikely(name == NULL) || unlikely(!PyUnicode_Check(name))) {
|
|
jpayne@69
|
17484 PyErr_Clear();
|
|
jpayne@69
|
17485 Py_XDECREF(name);
|
|
jpayne@69
|
17486 name = __Pyx_NewRef(__pyx_n_s__33);
|
|
jpayne@69
|
17487 }
|
|
jpayne@69
|
17488 return name;
|
|
jpayne@69
|
17489 }
|
|
jpayne@69
|
17490 #endif
|
|
jpayne@69
|
17491
|
|
jpayne@69
|
17492 /* CIntFromPy */
|
|
jpayne@69
|
17493 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
|
|
jpayne@69
|
17494 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17495 #pragma GCC diagnostic push
|
|
jpayne@69
|
17496 #pragma GCC diagnostic ignored "-Wconversion"
|
|
jpayne@69
|
17497 #endif
|
|
jpayne@69
|
17498 const long neg_one = (long) -1, const_zero = (long) 0;
|
|
jpayne@69
|
17499 #ifdef __Pyx_HAS_GCC_DIAGNOSTIC
|
|
jpayne@69
|
17500 #pragma GCC diagnostic pop
|
|
jpayne@69
|
17501 #endif
|
|
jpayne@69
|
17502 const int is_unsigned = neg_one > const_zero;
|
|
jpayne@69
|
17503 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
17504 if (likely(PyInt_Check(x))) {
|
|
jpayne@69
|
17505 if ((sizeof(long) < sizeof(long))) {
|
|
jpayne@69
|
17506 __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
|
|
jpayne@69
|
17507 } else {
|
|
jpayne@69
|
17508 long val = PyInt_AS_LONG(x);
|
|
jpayne@69
|
17509 if (is_unsigned && unlikely(val < 0)) {
|
|
jpayne@69
|
17510 goto raise_neg_overflow;
|
|
jpayne@69
|
17511 }
|
|
jpayne@69
|
17512 return (long) val;
|
|
jpayne@69
|
17513 }
|
|
jpayne@69
|
17514 }
|
|
jpayne@69
|
17515 #endif
|
|
jpayne@69
|
17516 if (unlikely(!PyLong_Check(x))) {
|
|
jpayne@69
|
17517 long val;
|
|
jpayne@69
|
17518 PyObject *tmp = __Pyx_PyNumber_IntOrLong(x);
|
|
jpayne@69
|
17519 if (!tmp) return (long) -1;
|
|
jpayne@69
|
17520 val = __Pyx_PyInt_As_long(tmp);
|
|
jpayne@69
|
17521 Py_DECREF(tmp);
|
|
jpayne@69
|
17522 return val;
|
|
jpayne@69
|
17523 }
|
|
jpayne@69
|
17524 if (is_unsigned) {
|
|
jpayne@69
|
17525 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
17526 if (unlikely(__Pyx_PyLong_IsNeg(x))) {
|
|
jpayne@69
|
17527 goto raise_neg_overflow;
|
|
jpayne@69
|
17528 } else if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
17529 __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x))
|
|
jpayne@69
|
17530 } else {
|
|
jpayne@69
|
17531 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
17532 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
17533 switch (__Pyx_PyLong_DigitCount(x)) {
|
|
jpayne@69
|
17534 case 2:
|
|
jpayne@69
|
17535 if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17536 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17537 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
17538 } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17539 return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
|
|
jpayne@69
|
17540 }
|
|
jpayne@69
|
17541 }
|
|
jpayne@69
|
17542 break;
|
|
jpayne@69
|
17543 case 3:
|
|
jpayne@69
|
17544 if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17545 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17546 __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
|
17547 } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17548 return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
|
|
jpayne@69
|
17549 }
|
|
jpayne@69
|
17550 }
|
|
jpayne@69
|
17551 break;
|
|
jpayne@69
|
17552 case 4:
|
|
jpayne@69
|
17553 if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17554 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17555 __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
|
17556 } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17557 return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]));
|
|
jpayne@69
|
17558 }
|
|
jpayne@69
|
17559 }
|
|
jpayne@69
|
17560 break;
|
|
jpayne@69
|
17561 }
|
|
jpayne@69
|
17562 }
|
|
jpayne@69
|
17563 #endif
|
|
jpayne@69
|
17564 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7
|
|
jpayne@69
|
17565 if (unlikely(Py_SIZE(x) < 0)) {
|
|
jpayne@69
|
17566 goto raise_neg_overflow;
|
|
jpayne@69
|
17567 }
|
|
jpayne@69
|
17568 #else
|
|
jpayne@69
|
17569 {
|
|
jpayne@69
|
17570 int result = PyObject_RichCompareBool(x, Py_False, Py_LT);
|
|
jpayne@69
|
17571 if (unlikely(result < 0))
|
|
jpayne@69
|
17572 return (long) -1;
|
|
jpayne@69
|
17573 if (unlikely(result == 1))
|
|
jpayne@69
|
17574 goto raise_neg_overflow;
|
|
jpayne@69
|
17575 }
|
|
jpayne@69
|
17576 #endif
|
|
jpayne@69
|
17577 if ((sizeof(long) <= sizeof(unsigned long))) {
|
|
jpayne@69
|
17578 __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
|
|
jpayne@69
|
17579 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17580 } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) {
|
|
jpayne@69
|
17581 __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
|
|
jpayne@69
|
17582 #endif
|
|
jpayne@69
|
17583 }
|
|
jpayne@69
|
17584 } else {
|
|
jpayne@69
|
17585 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
17586 if (__Pyx_PyLong_IsCompact(x)) {
|
|
jpayne@69
|
17587 __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x))
|
|
jpayne@69
|
17588 } else {
|
|
jpayne@69
|
17589 const digit* digits = __Pyx_PyLong_Digits(x);
|
|
jpayne@69
|
17590 assert(__Pyx_PyLong_DigitCount(x) > 1);
|
|
jpayne@69
|
17591 switch (__Pyx_PyLong_SignedDigitCount(x)) {
|
|
jpayne@69
|
17592 case -2:
|
|
jpayne@69
|
17593 if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17594 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17595 __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
17596 } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17597 return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
17598 }
|
|
jpayne@69
|
17599 }
|
|
jpayne@69
|
17600 break;
|
|
jpayne@69
|
17601 case 2:
|
|
jpayne@69
|
17602 if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17603 if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17604 __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])))
|
|
jpayne@69
|
17605 } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17606 return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
17607 }
|
|
jpayne@69
|
17608 }
|
|
jpayne@69
|
17609 break;
|
|
jpayne@69
|
17610 case -3:
|
|
jpayne@69
|
17611 if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17612 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17613 __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
|
17614 } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17615 return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
17616 }
|
|
jpayne@69
|
17617 }
|
|
jpayne@69
|
17618 break;
|
|
jpayne@69
|
17619 case 3:
|
|
jpayne@69
|
17620 if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17621 if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17622 __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
|
17623 } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17624 return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
17625 }
|
|
jpayne@69
|
17626 }
|
|
jpayne@69
|
17627 break;
|
|
jpayne@69
|
17628 case -4:
|
|
jpayne@69
|
17629 if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17630 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17631 __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
|
17632 } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17633 return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
17634 }
|
|
jpayne@69
|
17635 }
|
|
jpayne@69
|
17636 break;
|
|
jpayne@69
|
17637 case 4:
|
|
jpayne@69
|
17638 if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17639 if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17640 __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
|
17641 } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) {
|
|
jpayne@69
|
17642 return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])));
|
|
jpayne@69
|
17643 }
|
|
jpayne@69
|
17644 }
|
|
jpayne@69
|
17645 break;
|
|
jpayne@69
|
17646 }
|
|
jpayne@69
|
17647 }
|
|
jpayne@69
|
17648 #endif
|
|
jpayne@69
|
17649 if ((sizeof(long) <= sizeof(long))) {
|
|
jpayne@69
|
17650 __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
|
|
jpayne@69
|
17651 #ifdef HAVE_LONG_LONG
|
|
jpayne@69
|
17652 } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) {
|
|
jpayne@69
|
17653 __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
|
|
jpayne@69
|
17654 #endif
|
|
jpayne@69
|
17655 }
|
|
jpayne@69
|
17656 }
|
|
jpayne@69
|
17657 {
|
|
jpayne@69
|
17658 long val;
|
|
jpayne@69
|
17659 int ret = -1;
|
|
jpayne@69
|
17660 #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API
|
|
jpayne@69
|
17661 Py_ssize_t bytes_copied = PyLong_AsNativeBytes(
|
|
jpayne@69
|
17662 x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0));
|
|
jpayne@69
|
17663 if (unlikely(bytes_copied == -1)) {
|
|
jpayne@69
|
17664 } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) {
|
|
jpayne@69
|
17665 goto raise_overflow;
|
|
jpayne@69
|
17666 } else {
|
|
jpayne@69
|
17667 ret = 0;
|
|
jpayne@69
|
17668 }
|
|
jpayne@69
|
17669 #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray)
|
|
jpayne@69
|
17670 int one = 1; int is_little = (int)*(unsigned char *)&one;
|
|
jpayne@69
|
17671 unsigned char *bytes = (unsigned char *)&val;
|
|
jpayne@69
|
17672 ret = _PyLong_AsByteArray((PyLongObject *)x,
|
|
jpayne@69
|
17673 bytes, sizeof(val),
|
|
jpayne@69
|
17674 is_little, !is_unsigned);
|
|
jpayne@69
|
17675 #else
|
|
jpayne@69
|
17676 PyObject *v;
|
|
jpayne@69
|
17677 PyObject *stepval = NULL, *mask = NULL, *shift = NULL;
|
|
jpayne@69
|
17678 int bits, remaining_bits, is_negative = 0;
|
|
jpayne@69
|
17679 int chunk_size = (sizeof(long) < 8) ? 30 : 62;
|
|
jpayne@69
|
17680 if (likely(PyLong_CheckExact(x))) {
|
|
jpayne@69
|
17681 v = __Pyx_NewRef(x);
|
|
jpayne@69
|
17682 } else {
|
|
jpayne@69
|
17683 v = PyNumber_Long(x);
|
|
jpayne@69
|
17684 if (unlikely(!v)) return (long) -1;
|
|
jpayne@69
|
17685 assert(PyLong_CheckExact(v));
|
|
jpayne@69
|
17686 }
|
|
jpayne@69
|
17687 {
|
|
jpayne@69
|
17688 int result = PyObject_RichCompareBool(v, Py_False, Py_LT);
|
|
jpayne@69
|
17689 if (unlikely(result < 0)) {
|
|
jpayne@69
|
17690 Py_DECREF(v);
|
|
jpayne@69
|
17691 return (long) -1;
|
|
jpayne@69
|
17692 }
|
|
jpayne@69
|
17693 is_negative = result == 1;
|
|
jpayne@69
|
17694 }
|
|
jpayne@69
|
17695 if (is_unsigned && unlikely(is_negative)) {
|
|
jpayne@69
|
17696 Py_DECREF(v);
|
|
jpayne@69
|
17697 goto raise_neg_overflow;
|
|
jpayne@69
|
17698 } else if (is_negative) {
|
|
jpayne@69
|
17699 stepval = PyNumber_Invert(v);
|
|
jpayne@69
|
17700 Py_DECREF(v);
|
|
jpayne@69
|
17701 if (unlikely(!stepval))
|
|
jpayne@69
|
17702 return (long) -1;
|
|
jpayne@69
|
17703 } else {
|
|
jpayne@69
|
17704 stepval = v;
|
|
jpayne@69
|
17705 }
|
|
jpayne@69
|
17706 v = NULL;
|
|
jpayne@69
|
17707 val = (long) 0;
|
|
jpayne@69
|
17708 mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done;
|
|
jpayne@69
|
17709 shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done;
|
|
jpayne@69
|
17710 for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) {
|
|
jpayne@69
|
17711 PyObject *tmp, *digit;
|
|
jpayne@69
|
17712 long idigit;
|
|
jpayne@69
|
17713 digit = PyNumber_And(stepval, mask);
|
|
jpayne@69
|
17714 if (unlikely(!digit)) goto done;
|
|
jpayne@69
|
17715 idigit = PyLong_AsLong(digit);
|
|
jpayne@69
|
17716 Py_DECREF(digit);
|
|
jpayne@69
|
17717 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
17718 val |= ((long) idigit) << bits;
|
|
jpayne@69
|
17719 tmp = PyNumber_Rshift(stepval, shift);
|
|
jpayne@69
|
17720 if (unlikely(!tmp)) goto done;
|
|
jpayne@69
|
17721 Py_DECREF(stepval); stepval = tmp;
|
|
jpayne@69
|
17722 }
|
|
jpayne@69
|
17723 Py_DECREF(shift); shift = NULL;
|
|
jpayne@69
|
17724 Py_DECREF(mask); mask = NULL;
|
|
jpayne@69
|
17725 {
|
|
jpayne@69
|
17726 long idigit = PyLong_AsLong(stepval);
|
|
jpayne@69
|
17727 if (unlikely(idigit < 0)) goto done;
|
|
jpayne@69
|
17728 remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1);
|
|
jpayne@69
|
17729 if (unlikely(idigit >= (1L << remaining_bits)))
|
|
jpayne@69
|
17730 goto raise_overflow;
|
|
jpayne@69
|
17731 val |= ((long) idigit) << bits;
|
|
jpayne@69
|
17732 }
|
|
jpayne@69
|
17733 if (!is_unsigned) {
|
|
jpayne@69
|
17734 if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1))))
|
|
jpayne@69
|
17735 goto raise_overflow;
|
|
jpayne@69
|
17736 if (is_negative)
|
|
jpayne@69
|
17737 val = ~val;
|
|
jpayne@69
|
17738 }
|
|
jpayne@69
|
17739 ret = 0;
|
|
jpayne@69
|
17740 done:
|
|
jpayne@69
|
17741 Py_XDECREF(shift);
|
|
jpayne@69
|
17742 Py_XDECREF(mask);
|
|
jpayne@69
|
17743 Py_XDECREF(stepval);
|
|
jpayne@69
|
17744 #endif
|
|
jpayne@69
|
17745 if (unlikely(ret))
|
|
jpayne@69
|
17746 return (long) -1;
|
|
jpayne@69
|
17747 return val;
|
|
jpayne@69
|
17748 }
|
|
jpayne@69
|
17749 raise_overflow:
|
|
jpayne@69
|
17750 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
17751 "value too large to convert to long");
|
|
jpayne@69
|
17752 return (long) -1;
|
|
jpayne@69
|
17753 raise_neg_overflow:
|
|
jpayne@69
|
17754 PyErr_SetString(PyExc_OverflowError,
|
|
jpayne@69
|
17755 "can't convert negative value to long");
|
|
jpayne@69
|
17756 return (long) -1;
|
|
jpayne@69
|
17757 }
|
|
jpayne@69
|
17758
|
|
jpayne@69
|
17759 /* FastTypeChecks */
|
|
jpayne@69
|
17760 #if CYTHON_COMPILING_IN_CPYTHON
|
|
jpayne@69
|
17761 static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) {
|
|
jpayne@69
|
17762 while (a) {
|
|
jpayne@69
|
17763 a = __Pyx_PyType_GetSlot(a, tp_base, PyTypeObject*);
|
|
jpayne@69
|
17764 if (a == b)
|
|
jpayne@69
|
17765 return 1;
|
|
jpayne@69
|
17766 }
|
|
jpayne@69
|
17767 return b == &PyBaseObject_Type;
|
|
jpayne@69
|
17768 }
|
|
jpayne@69
|
17769 static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) {
|
|
jpayne@69
|
17770 PyObject *mro;
|
|
jpayne@69
|
17771 if (a == b) return 1;
|
|
jpayne@69
|
17772 mro = a->tp_mro;
|
|
jpayne@69
|
17773 if (likely(mro)) {
|
|
jpayne@69
|
17774 Py_ssize_t i, n;
|
|
jpayne@69
|
17775 n = PyTuple_GET_SIZE(mro);
|
|
jpayne@69
|
17776 for (i = 0; i < n; i++) {
|
|
jpayne@69
|
17777 if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b)
|
|
jpayne@69
|
17778 return 1;
|
|
jpayne@69
|
17779 }
|
|
jpayne@69
|
17780 return 0;
|
|
jpayne@69
|
17781 }
|
|
jpayne@69
|
17782 return __Pyx_InBases(a, b);
|
|
jpayne@69
|
17783 }
|
|
jpayne@69
|
17784 static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b) {
|
|
jpayne@69
|
17785 PyObject *mro;
|
|
jpayne@69
|
17786 if (cls == a || cls == b) return 1;
|
|
jpayne@69
|
17787 mro = cls->tp_mro;
|
|
jpayne@69
|
17788 if (likely(mro)) {
|
|
jpayne@69
|
17789 Py_ssize_t i, n;
|
|
jpayne@69
|
17790 n = PyTuple_GET_SIZE(mro);
|
|
jpayne@69
|
17791 for (i = 0; i < n; i++) {
|
|
jpayne@69
|
17792 PyObject *base = PyTuple_GET_ITEM(mro, i);
|
|
jpayne@69
|
17793 if (base == (PyObject *)a || base == (PyObject *)b)
|
|
jpayne@69
|
17794 return 1;
|
|
jpayne@69
|
17795 }
|
|
jpayne@69
|
17796 return 0;
|
|
jpayne@69
|
17797 }
|
|
jpayne@69
|
17798 return __Pyx_InBases(cls, a) || __Pyx_InBases(cls, b);
|
|
jpayne@69
|
17799 }
|
|
jpayne@69
|
17800 #if PY_MAJOR_VERSION == 2
|
|
jpayne@69
|
17801 static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) {
|
|
jpayne@69
|
17802 PyObject *exception, *value, *tb;
|
|
jpayne@69
|
17803 int res;
|
|
jpayne@69
|
17804 __Pyx_PyThreadState_declare
|
|
jpayne@69
|
17805 __Pyx_PyThreadState_assign
|
|
jpayne@69
|
17806 __Pyx_ErrFetch(&exception, &value, &tb);
|
|
jpayne@69
|
17807 res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0;
|
|
jpayne@69
|
17808 if (unlikely(res == -1)) {
|
|
jpayne@69
|
17809 PyErr_WriteUnraisable(err);
|
|
jpayne@69
|
17810 res = 0;
|
|
jpayne@69
|
17811 }
|
|
jpayne@69
|
17812 if (!res) {
|
|
jpayne@69
|
17813 res = PyObject_IsSubclass(err, exc_type2);
|
|
jpayne@69
|
17814 if (unlikely(res == -1)) {
|
|
jpayne@69
|
17815 PyErr_WriteUnraisable(err);
|
|
jpayne@69
|
17816 res = 0;
|
|
jpayne@69
|
17817 }
|
|
jpayne@69
|
17818 }
|
|
jpayne@69
|
17819 __Pyx_ErrRestore(exception, value, tb);
|
|
jpayne@69
|
17820 return res;
|
|
jpayne@69
|
17821 }
|
|
jpayne@69
|
17822 #else
|
|
jpayne@69
|
17823 static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) {
|
|
jpayne@69
|
17824 if (exc_type1) {
|
|
jpayne@69
|
17825 return __Pyx_IsAnySubtype2((PyTypeObject*)err, (PyTypeObject*)exc_type1, (PyTypeObject*)exc_type2);
|
|
jpayne@69
|
17826 } else {
|
|
jpayne@69
|
17827 return __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2);
|
|
jpayne@69
|
17828 }
|
|
jpayne@69
|
17829 }
|
|
jpayne@69
|
17830 #endif
|
|
jpayne@69
|
17831 static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) {
|
|
jpayne@69
|
17832 Py_ssize_t i, n;
|
|
jpayne@69
|
17833 assert(PyExceptionClass_Check(exc_type));
|
|
jpayne@69
|
17834 n = PyTuple_GET_SIZE(tuple);
|
|
jpayne@69
|
17835 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
17836 for (i=0; i<n; i++) {
|
|
jpayne@69
|
17837 if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1;
|
|
jpayne@69
|
17838 }
|
|
jpayne@69
|
17839 #endif
|
|
jpayne@69
|
17840 for (i=0; i<n; i++) {
|
|
jpayne@69
|
17841 PyObject *t = PyTuple_GET_ITEM(tuple, i);
|
|
jpayne@69
|
17842 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
17843 if (likely(exc_type == t)) return 1;
|
|
jpayne@69
|
17844 #endif
|
|
jpayne@69
|
17845 if (likely(PyExceptionClass_Check(t))) {
|
|
jpayne@69
|
17846 if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1;
|
|
jpayne@69
|
17847 } else {
|
|
jpayne@69
|
17848 }
|
|
jpayne@69
|
17849 }
|
|
jpayne@69
|
17850 return 0;
|
|
jpayne@69
|
17851 }
|
|
jpayne@69
|
17852 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) {
|
|
jpayne@69
|
17853 if (likely(err == exc_type)) return 1;
|
|
jpayne@69
|
17854 if (likely(PyExceptionClass_Check(err))) {
|
|
jpayne@69
|
17855 if (likely(PyExceptionClass_Check(exc_type))) {
|
|
jpayne@69
|
17856 return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type);
|
|
jpayne@69
|
17857 } else if (likely(PyTuple_Check(exc_type))) {
|
|
jpayne@69
|
17858 return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type);
|
|
jpayne@69
|
17859 } else {
|
|
jpayne@69
|
17860 }
|
|
jpayne@69
|
17861 }
|
|
jpayne@69
|
17862 return PyErr_GivenExceptionMatches(err, exc_type);
|
|
jpayne@69
|
17863 }
|
|
jpayne@69
|
17864 static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) {
|
|
jpayne@69
|
17865 assert(PyExceptionClass_Check(exc_type1));
|
|
jpayne@69
|
17866 assert(PyExceptionClass_Check(exc_type2));
|
|
jpayne@69
|
17867 if (likely(err == exc_type1 || err == exc_type2)) return 1;
|
|
jpayne@69
|
17868 if (likely(PyExceptionClass_Check(err))) {
|
|
jpayne@69
|
17869 return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2);
|
|
jpayne@69
|
17870 }
|
|
jpayne@69
|
17871 return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2));
|
|
jpayne@69
|
17872 }
|
|
jpayne@69
|
17873 #endif
|
|
jpayne@69
|
17874
|
|
jpayne@69
|
17875 /* CheckBinaryVersion */
|
|
jpayne@69
|
17876 static unsigned long __Pyx_get_runtime_version(void) {
|
|
jpayne@69
|
17877 #if __PYX_LIMITED_VERSION_HEX >= 0x030B00A4
|
|
jpayne@69
|
17878 return Py_Version & ~0xFFUL;
|
|
jpayne@69
|
17879 #else
|
|
jpayne@69
|
17880 const char* rt_version = Py_GetVersion();
|
|
jpayne@69
|
17881 unsigned long version = 0;
|
|
jpayne@69
|
17882 unsigned long factor = 0x01000000UL;
|
|
jpayne@69
|
17883 unsigned int digit = 0;
|
|
jpayne@69
|
17884 int i = 0;
|
|
jpayne@69
|
17885 while (factor) {
|
|
jpayne@69
|
17886 while ('0' <= rt_version[i] && rt_version[i] <= '9') {
|
|
jpayne@69
|
17887 digit = digit * 10 + (unsigned int) (rt_version[i] - '0');
|
|
jpayne@69
|
17888 ++i;
|
|
jpayne@69
|
17889 }
|
|
jpayne@69
|
17890 version += factor * digit;
|
|
jpayne@69
|
17891 if (rt_version[i] != '.')
|
|
jpayne@69
|
17892 break;
|
|
jpayne@69
|
17893 digit = 0;
|
|
jpayne@69
|
17894 factor >>= 8;
|
|
jpayne@69
|
17895 ++i;
|
|
jpayne@69
|
17896 }
|
|
jpayne@69
|
17897 return version;
|
|
jpayne@69
|
17898 #endif
|
|
jpayne@69
|
17899 }
|
|
jpayne@69
|
17900 static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer) {
|
|
jpayne@69
|
17901 const unsigned long MAJOR_MINOR = 0xFFFF0000UL;
|
|
jpayne@69
|
17902 if ((rt_version & MAJOR_MINOR) == (ct_version & MAJOR_MINOR))
|
|
jpayne@69
|
17903 return 0;
|
|
jpayne@69
|
17904 if (likely(allow_newer && (rt_version & MAJOR_MINOR) > (ct_version & MAJOR_MINOR)))
|
|
jpayne@69
|
17905 return 1;
|
|
jpayne@69
|
17906 {
|
|
jpayne@69
|
17907 char message[200];
|
|
jpayne@69
|
17908 PyOS_snprintf(message, sizeof(message),
|
|
jpayne@69
|
17909 "compile time Python version %d.%d "
|
|
jpayne@69
|
17910 "of module '%.100s' "
|
|
jpayne@69
|
17911 "%s "
|
|
jpayne@69
|
17912 "runtime version %d.%d",
|
|
jpayne@69
|
17913 (int) (ct_version >> 24), (int) ((ct_version >> 16) & 0xFF),
|
|
jpayne@69
|
17914 __Pyx_MODULE_NAME,
|
|
jpayne@69
|
17915 (allow_newer) ? "was newer than" : "does not match",
|
|
jpayne@69
|
17916 (int) (rt_version >> 24), (int) ((rt_version >> 16) & 0xFF)
|
|
jpayne@69
|
17917 );
|
|
jpayne@69
|
17918 return PyErr_WarnEx(NULL, message, 1);
|
|
jpayne@69
|
17919 }
|
|
jpayne@69
|
17920 }
|
|
jpayne@69
|
17921
|
|
jpayne@69
|
17922 /* FunctionExport */
|
|
jpayne@69
|
17923 static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) {
|
|
jpayne@69
|
17924 PyObject *d = 0;
|
|
jpayne@69
|
17925 PyObject *cobj = 0;
|
|
jpayne@69
|
17926 union {
|
|
jpayne@69
|
17927 void (*fp)(void);
|
|
jpayne@69
|
17928 void *p;
|
|
jpayne@69
|
17929 } tmp;
|
|
jpayne@69
|
17930 d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__");
|
|
jpayne@69
|
17931 if (!d) {
|
|
jpayne@69
|
17932 PyErr_Clear();
|
|
jpayne@69
|
17933 d = PyDict_New();
|
|
jpayne@69
|
17934 if (!d)
|
|
jpayne@69
|
17935 goto bad;
|
|
jpayne@69
|
17936 Py_INCREF(d);
|
|
jpayne@69
|
17937 if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0)
|
|
jpayne@69
|
17938 goto bad;
|
|
jpayne@69
|
17939 }
|
|
jpayne@69
|
17940 tmp.fp = f;
|
|
jpayne@69
|
17941 cobj = PyCapsule_New(tmp.p, sig, 0);
|
|
jpayne@69
|
17942 if (!cobj)
|
|
jpayne@69
|
17943 goto bad;
|
|
jpayne@69
|
17944 if (PyDict_SetItemString(d, name, cobj) < 0)
|
|
jpayne@69
|
17945 goto bad;
|
|
jpayne@69
|
17946 Py_DECREF(cobj);
|
|
jpayne@69
|
17947 Py_DECREF(d);
|
|
jpayne@69
|
17948 return 0;
|
|
jpayne@69
|
17949 bad:
|
|
jpayne@69
|
17950 Py_XDECREF(cobj);
|
|
jpayne@69
|
17951 Py_XDECREF(d);
|
|
jpayne@69
|
17952 return -1;
|
|
jpayne@69
|
17953 }
|
|
jpayne@69
|
17954
|
|
jpayne@69
|
17955 /* InitStrings */
|
|
jpayne@69
|
17956 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
17957 static int __Pyx_InitString(__Pyx_StringTabEntry t, PyObject **str) {
|
|
jpayne@69
|
17958 if (t.is_unicode | t.is_str) {
|
|
jpayne@69
|
17959 if (t.intern) {
|
|
jpayne@69
|
17960 *str = PyUnicode_InternFromString(t.s);
|
|
jpayne@69
|
17961 } else if (t.encoding) {
|
|
jpayne@69
|
17962 *str = PyUnicode_Decode(t.s, t.n - 1, t.encoding, NULL);
|
|
jpayne@69
|
17963 } else {
|
|
jpayne@69
|
17964 *str = PyUnicode_FromStringAndSize(t.s, t.n - 1);
|
|
jpayne@69
|
17965 }
|
|
jpayne@69
|
17966 } else {
|
|
jpayne@69
|
17967 *str = PyBytes_FromStringAndSize(t.s, t.n - 1);
|
|
jpayne@69
|
17968 }
|
|
jpayne@69
|
17969 if (!*str)
|
|
jpayne@69
|
17970 return -1;
|
|
jpayne@69
|
17971 if (PyObject_Hash(*str) == -1)
|
|
jpayne@69
|
17972 return -1;
|
|
jpayne@69
|
17973 return 0;
|
|
jpayne@69
|
17974 }
|
|
jpayne@69
|
17975 #endif
|
|
jpayne@69
|
17976 static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
|
|
jpayne@69
|
17977 while (t->p) {
|
|
jpayne@69
|
17978 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
17979 __Pyx_InitString(*t, t->p);
|
|
jpayne@69
|
17980 #else
|
|
jpayne@69
|
17981 if (t->is_unicode) {
|
|
jpayne@69
|
17982 *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
|
|
jpayne@69
|
17983 } else if (t->intern) {
|
|
jpayne@69
|
17984 *t->p = PyString_InternFromString(t->s);
|
|
jpayne@69
|
17985 } else {
|
|
jpayne@69
|
17986 *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
|
|
jpayne@69
|
17987 }
|
|
jpayne@69
|
17988 if (!*t->p)
|
|
jpayne@69
|
17989 return -1;
|
|
jpayne@69
|
17990 if (PyObject_Hash(*t->p) == -1)
|
|
jpayne@69
|
17991 return -1;
|
|
jpayne@69
|
17992 #endif
|
|
jpayne@69
|
17993 ++t;
|
|
jpayne@69
|
17994 }
|
|
jpayne@69
|
17995 return 0;
|
|
jpayne@69
|
17996 }
|
|
jpayne@69
|
17997
|
|
jpayne@69
|
17998 #include <string.h>
|
|
jpayne@69
|
17999 static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s) {
|
|
jpayne@69
|
18000 size_t len = strlen(s);
|
|
jpayne@69
|
18001 if (unlikely(len > (size_t) PY_SSIZE_T_MAX)) {
|
|
jpayne@69
|
18002 PyErr_SetString(PyExc_OverflowError, "byte string is too long");
|
|
jpayne@69
|
18003 return -1;
|
|
jpayne@69
|
18004 }
|
|
jpayne@69
|
18005 return (Py_ssize_t) len;
|
|
jpayne@69
|
18006 }
|
|
jpayne@69
|
18007 static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
|
|
jpayne@69
|
18008 Py_ssize_t len = __Pyx_ssize_strlen(c_str);
|
|
jpayne@69
|
18009 if (unlikely(len < 0)) return NULL;
|
|
jpayne@69
|
18010 return __Pyx_PyUnicode_FromStringAndSize(c_str, len);
|
|
jpayne@69
|
18011 }
|
|
jpayne@69
|
18012 static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char* c_str) {
|
|
jpayne@69
|
18013 Py_ssize_t len = __Pyx_ssize_strlen(c_str);
|
|
jpayne@69
|
18014 if (unlikely(len < 0)) return NULL;
|
|
jpayne@69
|
18015 return PyByteArray_FromStringAndSize(c_str, len);
|
|
jpayne@69
|
18016 }
|
|
jpayne@69
|
18017 static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) {
|
|
jpayne@69
|
18018 Py_ssize_t ignore;
|
|
jpayne@69
|
18019 return __Pyx_PyObject_AsStringAndSize(o, &ignore);
|
|
jpayne@69
|
18020 }
|
|
jpayne@69
|
18021 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
|
|
jpayne@69
|
18022 #if !CYTHON_PEP393_ENABLED
|
|
jpayne@69
|
18023 static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
|
|
jpayne@69
|
18024 char* defenc_c;
|
|
jpayne@69
|
18025 PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
|
|
jpayne@69
|
18026 if (!defenc) return NULL;
|
|
jpayne@69
|
18027 defenc_c = PyBytes_AS_STRING(defenc);
|
|
jpayne@69
|
18028 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
18029 {
|
|
jpayne@69
|
18030 char* end = defenc_c + PyBytes_GET_SIZE(defenc);
|
|
jpayne@69
|
18031 char* c;
|
|
jpayne@69
|
18032 for (c = defenc_c; c < end; c++) {
|
|
jpayne@69
|
18033 if ((unsigned char) (*c) >= 128) {
|
|
jpayne@69
|
18034 PyUnicode_AsASCIIString(o);
|
|
jpayne@69
|
18035 return NULL;
|
|
jpayne@69
|
18036 }
|
|
jpayne@69
|
18037 }
|
|
jpayne@69
|
18038 }
|
|
jpayne@69
|
18039 #endif
|
|
jpayne@69
|
18040 *length = PyBytes_GET_SIZE(defenc);
|
|
jpayne@69
|
18041 return defenc_c;
|
|
jpayne@69
|
18042 }
|
|
jpayne@69
|
18043 #else
|
|
jpayne@69
|
18044 static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
|
|
jpayne@69
|
18045 if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL;
|
|
jpayne@69
|
18046 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
18047 if (likely(PyUnicode_IS_ASCII(o))) {
|
|
jpayne@69
|
18048 *length = PyUnicode_GET_LENGTH(o);
|
|
jpayne@69
|
18049 return PyUnicode_AsUTF8(o);
|
|
jpayne@69
|
18050 } else {
|
|
jpayne@69
|
18051 PyUnicode_AsASCIIString(o);
|
|
jpayne@69
|
18052 return NULL;
|
|
jpayne@69
|
18053 }
|
|
jpayne@69
|
18054 #else
|
|
jpayne@69
|
18055 return PyUnicode_AsUTF8AndSize(o, length);
|
|
jpayne@69
|
18056 #endif
|
|
jpayne@69
|
18057 }
|
|
jpayne@69
|
18058 #endif
|
|
jpayne@69
|
18059 #endif
|
|
jpayne@69
|
18060 static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
|
|
jpayne@69
|
18061 #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
|
|
jpayne@69
|
18062 if (
|
|
jpayne@69
|
18063 #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
|
|
jpayne@69
|
18064 __Pyx_sys_getdefaultencoding_not_ascii &&
|
|
jpayne@69
|
18065 #endif
|
|
jpayne@69
|
18066 PyUnicode_Check(o)) {
|
|
jpayne@69
|
18067 return __Pyx_PyUnicode_AsStringAndSize(o, length);
|
|
jpayne@69
|
18068 } else
|
|
jpayne@69
|
18069 #endif
|
|
jpayne@69
|
18070 #if (!CYTHON_COMPILING_IN_PYPY && !CYTHON_COMPILING_IN_LIMITED_API) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE))
|
|
jpayne@69
|
18071 if (PyByteArray_Check(o)) {
|
|
jpayne@69
|
18072 *length = PyByteArray_GET_SIZE(o);
|
|
jpayne@69
|
18073 return PyByteArray_AS_STRING(o);
|
|
jpayne@69
|
18074 } else
|
|
jpayne@69
|
18075 #endif
|
|
jpayne@69
|
18076 {
|
|
jpayne@69
|
18077 char* result;
|
|
jpayne@69
|
18078 int r = PyBytes_AsStringAndSize(o, &result, length);
|
|
jpayne@69
|
18079 if (unlikely(r < 0)) {
|
|
jpayne@69
|
18080 return NULL;
|
|
jpayne@69
|
18081 } else {
|
|
jpayne@69
|
18082 return result;
|
|
jpayne@69
|
18083 }
|
|
jpayne@69
|
18084 }
|
|
jpayne@69
|
18085 }
|
|
jpayne@69
|
18086 static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
|
|
jpayne@69
|
18087 int is_true = x == Py_True;
|
|
jpayne@69
|
18088 if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
|
|
jpayne@69
|
18089 else return PyObject_IsTrue(x);
|
|
jpayne@69
|
18090 }
|
|
jpayne@69
|
18091 static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) {
|
|
jpayne@69
|
18092 int retval;
|
|
jpayne@69
|
18093 if (unlikely(!x)) return -1;
|
|
jpayne@69
|
18094 retval = __Pyx_PyObject_IsTrue(x);
|
|
jpayne@69
|
18095 Py_DECREF(x);
|
|
jpayne@69
|
18096 return retval;
|
|
jpayne@69
|
18097 }
|
|
jpayne@69
|
18098 static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) {
|
|
jpayne@69
|
18099 __Pyx_TypeName result_type_name = __Pyx_PyType_GetName(Py_TYPE(result));
|
|
jpayne@69
|
18100 #if PY_MAJOR_VERSION >= 3
|
|
jpayne@69
|
18101 if (PyLong_Check(result)) {
|
|
jpayne@69
|
18102 if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1,
|
|
jpayne@69
|
18103 "__int__ returned non-int (type " __Pyx_FMT_TYPENAME "). "
|
|
jpayne@69
|
18104 "The ability to return an instance of a strict subclass of int is deprecated, "
|
|
jpayne@69
|
18105 "and may be removed in a future version of Python.",
|
|
jpayne@69
|
18106 result_type_name)) {
|
|
jpayne@69
|
18107 __Pyx_DECREF_TypeName(result_type_name);
|
|
jpayne@69
|
18108 Py_DECREF(result);
|
|
jpayne@69
|
18109 return NULL;
|
|
jpayne@69
|
18110 }
|
|
jpayne@69
|
18111 __Pyx_DECREF_TypeName(result_type_name);
|
|
jpayne@69
|
18112 return result;
|
|
jpayne@69
|
18113 }
|
|
jpayne@69
|
18114 #endif
|
|
jpayne@69
|
18115 PyErr_Format(PyExc_TypeError,
|
|
jpayne@69
|
18116 "__%.4s__ returned non-%.4s (type " __Pyx_FMT_TYPENAME ")",
|
|
jpayne@69
|
18117 type_name, type_name, result_type_name);
|
|
jpayne@69
|
18118 __Pyx_DECREF_TypeName(result_type_name);
|
|
jpayne@69
|
18119 Py_DECREF(result);
|
|
jpayne@69
|
18120 return NULL;
|
|
jpayne@69
|
18121 }
|
|
jpayne@69
|
18122 static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
|
|
jpayne@69
|
18123 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
18124 PyNumberMethods *m;
|
|
jpayne@69
|
18125 #endif
|
|
jpayne@69
|
18126 const char *name = NULL;
|
|
jpayne@69
|
18127 PyObject *res = NULL;
|
|
jpayne@69
|
18128 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
18129 if (likely(PyInt_Check(x) || PyLong_Check(x)))
|
|
jpayne@69
|
18130 #else
|
|
jpayne@69
|
18131 if (likely(PyLong_Check(x)))
|
|
jpayne@69
|
18132 #endif
|
|
jpayne@69
|
18133 return __Pyx_NewRef(x);
|
|
jpayne@69
|
18134 #if CYTHON_USE_TYPE_SLOTS
|
|
jpayne@69
|
18135 m = Py_TYPE(x)->tp_as_number;
|
|
jpayne@69
|
18136 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
18137 if (m && m->nb_int) {
|
|
jpayne@69
|
18138 name = "int";
|
|
jpayne@69
|
18139 res = m->nb_int(x);
|
|
jpayne@69
|
18140 }
|
|
jpayne@69
|
18141 else if (m && m->nb_long) {
|
|
jpayne@69
|
18142 name = "long";
|
|
jpayne@69
|
18143 res = m->nb_long(x);
|
|
jpayne@69
|
18144 }
|
|
jpayne@69
|
18145 #else
|
|
jpayne@69
|
18146 if (likely(m && m->nb_int)) {
|
|
jpayne@69
|
18147 name = "int";
|
|
jpayne@69
|
18148 res = m->nb_int(x);
|
|
jpayne@69
|
18149 }
|
|
jpayne@69
|
18150 #endif
|
|
jpayne@69
|
18151 #else
|
|
jpayne@69
|
18152 if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) {
|
|
jpayne@69
|
18153 res = PyNumber_Int(x);
|
|
jpayne@69
|
18154 }
|
|
jpayne@69
|
18155 #endif
|
|
jpayne@69
|
18156 if (likely(res)) {
|
|
jpayne@69
|
18157 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
18158 if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) {
|
|
jpayne@69
|
18159 #else
|
|
jpayne@69
|
18160 if (unlikely(!PyLong_CheckExact(res))) {
|
|
jpayne@69
|
18161 #endif
|
|
jpayne@69
|
18162 return __Pyx_PyNumber_IntOrLongWrongResultType(res, name);
|
|
jpayne@69
|
18163 }
|
|
jpayne@69
|
18164 }
|
|
jpayne@69
|
18165 else if (!PyErr_Occurred()) {
|
|
jpayne@69
|
18166 PyErr_SetString(PyExc_TypeError,
|
|
jpayne@69
|
18167 "an integer is required");
|
|
jpayne@69
|
18168 }
|
|
jpayne@69
|
18169 return res;
|
|
jpayne@69
|
18170 }
|
|
jpayne@69
|
18171 static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
|
|
jpayne@69
|
18172 Py_ssize_t ival;
|
|
jpayne@69
|
18173 PyObject *x;
|
|
jpayne@69
|
18174 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
18175 if (likely(PyInt_CheckExact(b))) {
|
|
jpayne@69
|
18176 if (sizeof(Py_ssize_t) >= sizeof(long))
|
|
jpayne@69
|
18177 return PyInt_AS_LONG(b);
|
|
jpayne@69
|
18178 else
|
|
jpayne@69
|
18179 return PyInt_AsSsize_t(b);
|
|
jpayne@69
|
18180 }
|
|
jpayne@69
|
18181 #endif
|
|
jpayne@69
|
18182 if (likely(PyLong_CheckExact(b))) {
|
|
jpayne@69
|
18183 #if CYTHON_USE_PYLONG_INTERNALS
|
|
jpayne@69
|
18184 if (likely(__Pyx_PyLong_IsCompact(b))) {
|
|
jpayne@69
|
18185 return __Pyx_PyLong_CompactValue(b);
|
|
jpayne@69
|
18186 } else {
|
|
jpayne@69
|
18187 const digit* digits = __Pyx_PyLong_Digits(b);
|
|
jpayne@69
|
18188 const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(b);
|
|
jpayne@69
|
18189 switch (size) {
|
|
jpayne@69
|
18190 case 2:
|
|
jpayne@69
|
18191 if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
18192 return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
18193 }
|
|
jpayne@69
|
18194 break;
|
|
jpayne@69
|
18195 case -2:
|
|
jpayne@69
|
18196 if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) {
|
|
jpayne@69
|
18197 return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
18198 }
|
|
jpayne@69
|
18199 break;
|
|
jpayne@69
|
18200 case 3:
|
|
jpayne@69
|
18201 if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
18202 return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
18203 }
|
|
jpayne@69
|
18204 break;
|
|
jpayne@69
|
18205 case -3:
|
|
jpayne@69
|
18206 if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) {
|
|
jpayne@69
|
18207 return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]));
|
|
jpayne@69
|
18208 }
|
|
jpayne@69
|
18209 break;
|
|
jpayne@69
|
18210 case 4:
|
|
jpayne@69
|
18211 if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
18212 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
|
18213 }
|
|
jpayne@69
|
18214 break;
|
|
jpayne@69
|
18215 case -4:
|
|
jpayne@69
|
18216 if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) {
|
|
jpayne@69
|
18217 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
|
18218 }
|
|
jpayne@69
|
18219 break;
|
|
jpayne@69
|
18220 }
|
|
jpayne@69
|
18221 }
|
|
jpayne@69
|
18222 #endif
|
|
jpayne@69
|
18223 return PyLong_AsSsize_t(b);
|
|
jpayne@69
|
18224 }
|
|
jpayne@69
|
18225 x = PyNumber_Index(b);
|
|
jpayne@69
|
18226 if (!x) return -1;
|
|
jpayne@69
|
18227 ival = PyInt_AsSsize_t(x);
|
|
jpayne@69
|
18228 Py_DECREF(x);
|
|
jpayne@69
|
18229 return ival;
|
|
jpayne@69
|
18230 }
|
|
jpayne@69
|
18231 static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
|
|
jpayne@69
|
18232 if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
|
|
jpayne@69
|
18233 return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
|
|
jpayne@69
|
18234 #if PY_MAJOR_VERSION < 3
|
|
jpayne@69
|
18235 } else if (likely(PyInt_CheckExact(o))) {
|
|
jpayne@69
|
18236 return PyInt_AS_LONG(o);
|
|
jpayne@69
|
18237 #endif
|
|
jpayne@69
|
18238 } else {
|
|
jpayne@69
|
18239 Py_ssize_t ival;
|
|
jpayne@69
|
18240 PyObject *x;
|
|
jpayne@69
|
18241 x = PyNumber_Index(o);
|
|
jpayne@69
|
18242 if (!x) return -1;
|
|
jpayne@69
|
18243 ival = PyInt_AsLong(x);
|
|
jpayne@69
|
18244 Py_DECREF(x);
|
|
jpayne@69
|
18245 return ival;
|
|
jpayne@69
|
18246 }
|
|
jpayne@69
|
18247 }
|
|
jpayne@69
|
18248 static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
|
|
jpayne@69
|
18249 return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
|
|
jpayne@69
|
18250 }
|
|
jpayne@69
|
18251 static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
|
|
jpayne@69
|
18252 return PyInt_FromSize_t(ival);
|
|
jpayne@69
|
18253 }
|
|
jpayne@69
|
18254
|
|
jpayne@69
|
18255
|
|
jpayne@69
|
18256 /* #### Code section: utility_code_pragmas_end ### */
|
|
jpayne@69
|
18257 #ifdef _MSC_VER
|
|
jpayne@69
|
18258 #pragma warning( pop )
|
|
jpayne@69
|
18259 #endif
|
|
jpayne@69
|
18260
|
|
jpayne@69
|
18261
|
|
jpayne@69
|
18262
|
|
jpayne@69
|
18263 /* #### Code section: end ### */
|
|
jpayne@69
|
18264 #endif /* Py_PYTHON_H */
|
