jpayne@68: /* Generated by Cython 3.0.11 */ jpayne@68: jpayne@68: /* BEGIN: Cython Metadata jpayne@68: { jpayne@68: "distutils": { jpayne@68: "define_macros": [ jpayne@68: [ jpayne@68: "BUILDING_WHEEL", jpayne@68: null jpayne@68: ] jpayne@68: ], jpayne@68: "depends": [ jpayne@68: "/project/htslib/htslib/bgzf.h", jpayne@68: "/project/htslib/htslib/cram.h", jpayne@68: "/project/htslib/htslib/faidx.h", jpayne@68: "/project/htslib/htslib/hfile.h", jpayne@68: "/project/htslib/htslib/hts.h", jpayne@68: "/project/htslib/htslib/kstring.h", jpayne@68: "/project/htslib/htslib/sam.h", jpayne@68: "/project/htslib/htslib/tbx.h", jpayne@68: "/project/htslib/htslib/vcf.h", jpayne@68: "/project/htslib/htslib/vcfutils.h", jpayne@68: "/project/pysam/htslib_util.h", jpayne@68: "/project/pysam/pysam_stream.h" jpayne@68: ], jpayne@68: "extra_compile_args": [ jpayne@68: "-Wno-unused", jpayne@68: "-Wno-strict-prototypes", jpayne@68: "-Wno-sign-compare", jpayne@68: "-Wno-error=declaration-after-statement" jpayne@68: ], jpayne@68: "extra_link_args": [ jpayne@68: "-Wl,-rpath,$ORIGIN" jpayne@68: ], jpayne@68: "include_dirs": [ jpayne@68: "pysam", jpayne@68: "/project/pysam", jpayne@68: "/project/htslib", jpayne@68: "/project/samtools", jpayne@68: "/project/samtools/lz4", jpayne@68: "/project/bcftools", jpayne@68: "/project" jpayne@68: ], jpayne@68: "language": "c", jpayne@68: "libraries": [ jpayne@68: "z", jpayne@68: "lzma", jpayne@68: "bz2", jpayne@68: "z", jpayne@68: "m", jpayne@68: "curl", jpayne@68: "crypto", jpayne@68: "chtslib.cpython-37m-x86_64-linux-gnu", jpayne@68: "cutils.cpython-37m-x86_64-linux-gnu" jpayne@68: ], jpayne@68: "library_dirs": [ jpayne@68: "/project/pysam", jpayne@68: "/project", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam", jpayne@68: "build/lib.linux-x86_64-cpython-37/pysam" jpayne@68: ], jpayne@68: "name": "pysam.libctabix", jpayne@68: "sources": [ jpayne@68: "pysam/libctabix.pyx" jpayne@68: ] jpayne@68: }, jpayne@68: "module_name": "pysam.libctabix" jpayne@68: } jpayne@68: END: Cython Metadata */ jpayne@68: jpayne@68: #ifndef PY_SSIZE_T_CLEAN jpayne@68: #define PY_SSIZE_T_CLEAN jpayne@68: #endif /* PY_SSIZE_T_CLEAN */ jpayne@68: #if defined(CYTHON_LIMITED_API) && 0 jpayne@68: #ifndef Py_LIMITED_API jpayne@68: #if CYTHON_LIMITED_API+0 > 0x03030000 jpayne@68: #define Py_LIMITED_API CYTHON_LIMITED_API jpayne@68: #else jpayne@68: #define Py_LIMITED_API 0x03030000 jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: #include "Python.h" jpayne@68: jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj) jpayne@68: #else jpayne@68: #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj, NULL) jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: #if PY_MAJOR_VERSION <= 2 jpayne@68: #define PyDict_GetItemWithError _PyDict_GetItemWithError jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: #if (PY_VERSION_HEX < 0x030700b1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030600)) && !defined(PyContextVar_Get) jpayne@68: #define PyContextVar_Get(var, d, v) ((d) ? ((void)(var), Py_INCREF(d), (v)[0] = (d), 0) : ((v)[0] = NULL, 0) ) jpayne@68: #endif jpayne@68: jpayne@68: #ifndef Py_PYTHON_H jpayne@68: #error Python headers needed to compile C extensions, please install development version of Python. jpayne@68: #elif PY_VERSION_HEX < 0x02070000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) jpayne@68: #error Cython requires Python 2.7+ or Python 3.3+. jpayne@68: #else jpayne@68: #if defined(CYTHON_LIMITED_API) && CYTHON_LIMITED_API jpayne@68: #define __PYX_EXTRA_ABI_MODULE_NAME "limited" jpayne@68: #else jpayne@68: #define __PYX_EXTRA_ABI_MODULE_NAME "" jpayne@68: #endif jpayne@68: #define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME jpayne@68: #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI jpayne@68: #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "." jpayne@68: #define CYTHON_HEX_VERSION 0x03000BF0 jpayne@68: #define CYTHON_FUTURE_DIVISION 1 jpayne@68: #include jpayne@68: #ifndef offsetof jpayne@68: #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) jpayne@68: #endif jpayne@68: #if !defined(_WIN32) && !defined(WIN32) && !defined(MS_WINDOWS) jpayne@68: #ifndef __stdcall jpayne@68: #define __stdcall jpayne@68: #endif jpayne@68: #ifndef __cdecl jpayne@68: #define __cdecl jpayne@68: #endif jpayne@68: #ifndef __fastcall jpayne@68: #define __fastcall jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef DL_IMPORT jpayne@68: #define DL_IMPORT(t) t jpayne@68: #endif jpayne@68: #ifndef DL_EXPORT jpayne@68: #define DL_EXPORT(t) t jpayne@68: #endif jpayne@68: #define __PYX_COMMA , jpayne@68: #ifndef HAVE_LONG_LONG jpayne@68: #define HAVE_LONG_LONG jpayne@68: #endif jpayne@68: #ifndef PY_LONG_LONG jpayne@68: #define PY_LONG_LONG LONG_LONG jpayne@68: #endif jpayne@68: #ifndef Py_HUGE_VAL jpayne@68: #define Py_HUGE_VAL HUGE_VAL jpayne@68: #endif jpayne@68: #define __PYX_LIMITED_VERSION_HEX PY_VERSION_HEX jpayne@68: #if defined(GRAALVM_PYTHON) jpayne@68: /* For very preliminary testing purposes. Most variables are set the same as PyPy. jpayne@68: The existence of this section does not imply that anything works or is even tested */ jpayne@68: #define CYTHON_COMPILING_IN_PYPY 0 jpayne@68: #define CYTHON_COMPILING_IN_CPYTHON 0 jpayne@68: #define CYTHON_COMPILING_IN_LIMITED_API 0 jpayne@68: #define CYTHON_COMPILING_IN_GRAAL 1 jpayne@68: #define CYTHON_COMPILING_IN_NOGIL 0 jpayne@68: #undef CYTHON_USE_TYPE_SLOTS jpayne@68: #define CYTHON_USE_TYPE_SLOTS 0 jpayne@68: #undef CYTHON_USE_TYPE_SPECS jpayne@68: #define CYTHON_USE_TYPE_SPECS 0 jpayne@68: #undef CYTHON_USE_PYTYPE_LOOKUP jpayne@68: #define CYTHON_USE_PYTYPE_LOOKUP 0 jpayne@68: #if PY_VERSION_HEX < 0x03050000 jpayne@68: #undef CYTHON_USE_ASYNC_SLOTS jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 0 jpayne@68: #elif !defined(CYTHON_USE_ASYNC_SLOTS) jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 1 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_PYLIST_INTERNALS jpayne@68: #define CYTHON_USE_PYLIST_INTERNALS 0 jpayne@68: #undef CYTHON_USE_UNICODE_INTERNALS jpayne@68: #define CYTHON_USE_UNICODE_INTERNALS 0 jpayne@68: #undef CYTHON_USE_UNICODE_WRITER jpayne@68: #define CYTHON_USE_UNICODE_WRITER 0 jpayne@68: #undef CYTHON_USE_PYLONG_INTERNALS jpayne@68: #define CYTHON_USE_PYLONG_INTERNALS 0 jpayne@68: #undef CYTHON_AVOID_BORROWED_REFS jpayne@68: #define CYTHON_AVOID_BORROWED_REFS 1 jpayne@68: #undef CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define CYTHON_ASSUME_SAFE_MACROS 0 jpayne@68: #undef CYTHON_UNPACK_METHODS jpayne@68: #define CYTHON_UNPACK_METHODS 0 jpayne@68: #undef CYTHON_FAST_THREAD_STATE jpayne@68: #define CYTHON_FAST_THREAD_STATE 0 jpayne@68: #undef CYTHON_FAST_GIL jpayne@68: #define CYTHON_FAST_GIL 0 jpayne@68: #undef CYTHON_METH_FASTCALL jpayne@68: #define CYTHON_METH_FASTCALL 0 jpayne@68: #undef CYTHON_FAST_PYCALL jpayne@68: #define CYTHON_FAST_PYCALL 0 jpayne@68: #ifndef CYTHON_PEP487_INIT_SUBCLASS jpayne@68: #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3) jpayne@68: #endif jpayne@68: #undef CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 1 jpayne@68: #undef CYTHON_USE_MODULE_STATE jpayne@68: #define CYTHON_USE_MODULE_STATE 0 jpayne@68: #undef CYTHON_USE_TP_FINALIZE jpayne@68: #define CYTHON_USE_TP_FINALIZE 0 jpayne@68: #undef CYTHON_USE_DICT_VERSIONS jpayne@68: #define CYTHON_USE_DICT_VERSIONS 0 jpayne@68: #undef CYTHON_USE_EXC_INFO_STACK jpayne@68: #define CYTHON_USE_EXC_INFO_STACK 0 jpayne@68: #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_FREELISTS jpayne@68: #define CYTHON_USE_FREELISTS 0 jpayne@68: #elif defined(PYPY_VERSION) jpayne@68: #define CYTHON_COMPILING_IN_PYPY 1 jpayne@68: #define CYTHON_COMPILING_IN_CPYTHON 0 jpayne@68: #define CYTHON_COMPILING_IN_LIMITED_API 0 jpayne@68: #define CYTHON_COMPILING_IN_GRAAL 0 jpayne@68: #define CYTHON_COMPILING_IN_NOGIL 0 jpayne@68: #undef CYTHON_USE_TYPE_SLOTS jpayne@68: #define CYTHON_USE_TYPE_SLOTS 0 jpayne@68: #ifndef CYTHON_USE_TYPE_SPECS jpayne@68: #define CYTHON_USE_TYPE_SPECS 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_PYTYPE_LOOKUP jpayne@68: #define CYTHON_USE_PYTYPE_LOOKUP 0 jpayne@68: #if PY_VERSION_HEX < 0x03050000 jpayne@68: #undef CYTHON_USE_ASYNC_SLOTS jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 0 jpayne@68: #elif !defined(CYTHON_USE_ASYNC_SLOTS) jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 1 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_PYLIST_INTERNALS jpayne@68: #define CYTHON_USE_PYLIST_INTERNALS 0 jpayne@68: #undef CYTHON_USE_UNICODE_INTERNALS jpayne@68: #define CYTHON_USE_UNICODE_INTERNALS 0 jpayne@68: #undef CYTHON_USE_UNICODE_WRITER jpayne@68: #define CYTHON_USE_UNICODE_WRITER 0 jpayne@68: #undef CYTHON_USE_PYLONG_INTERNALS jpayne@68: #define CYTHON_USE_PYLONG_INTERNALS 0 jpayne@68: #undef CYTHON_AVOID_BORROWED_REFS jpayne@68: #define CYTHON_AVOID_BORROWED_REFS 1 jpayne@68: #undef CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define CYTHON_ASSUME_SAFE_MACROS 0 jpayne@68: #undef CYTHON_UNPACK_METHODS jpayne@68: #define CYTHON_UNPACK_METHODS 0 jpayne@68: #undef CYTHON_FAST_THREAD_STATE jpayne@68: #define CYTHON_FAST_THREAD_STATE 0 jpayne@68: #undef CYTHON_FAST_GIL jpayne@68: #define CYTHON_FAST_GIL 0 jpayne@68: #undef CYTHON_METH_FASTCALL jpayne@68: #define CYTHON_METH_FASTCALL 0 jpayne@68: #undef CYTHON_FAST_PYCALL jpayne@68: #define CYTHON_FAST_PYCALL 0 jpayne@68: #ifndef CYTHON_PEP487_INIT_SUBCLASS jpayne@68: #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x03090000 jpayne@68: #undef CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 0 jpayne@68: #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT) jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 1 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_MODULE_STATE jpayne@68: #define CYTHON_USE_MODULE_STATE 0 jpayne@68: #undef CYTHON_USE_TP_FINALIZE jpayne@68: #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1 && PYPY_VERSION_NUM >= 0x07030C00) jpayne@68: #undef CYTHON_USE_DICT_VERSIONS jpayne@68: #define CYTHON_USE_DICT_VERSIONS 0 jpayne@68: #undef CYTHON_USE_EXC_INFO_STACK jpayne@68: #define CYTHON_USE_EXC_INFO_STACK 0 jpayne@68: #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_FREELISTS jpayne@68: #define CYTHON_USE_FREELISTS 0 jpayne@68: #elif defined(CYTHON_LIMITED_API) jpayne@68: #ifdef Py_LIMITED_API jpayne@68: #undef __PYX_LIMITED_VERSION_HEX jpayne@68: #define __PYX_LIMITED_VERSION_HEX Py_LIMITED_API jpayne@68: #endif jpayne@68: #define CYTHON_COMPILING_IN_PYPY 0 jpayne@68: #define CYTHON_COMPILING_IN_CPYTHON 0 jpayne@68: #define CYTHON_COMPILING_IN_LIMITED_API 1 jpayne@68: #define CYTHON_COMPILING_IN_GRAAL 0 jpayne@68: #define CYTHON_COMPILING_IN_NOGIL 0 jpayne@68: #undef CYTHON_CLINE_IN_TRACEBACK jpayne@68: #define CYTHON_CLINE_IN_TRACEBACK 0 jpayne@68: #undef CYTHON_USE_TYPE_SLOTS jpayne@68: #define CYTHON_USE_TYPE_SLOTS 0 jpayne@68: #undef CYTHON_USE_TYPE_SPECS jpayne@68: #define CYTHON_USE_TYPE_SPECS 1 jpayne@68: #undef CYTHON_USE_PYTYPE_LOOKUP jpayne@68: #define CYTHON_USE_PYTYPE_LOOKUP 0 jpayne@68: #undef CYTHON_USE_ASYNC_SLOTS jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 0 jpayne@68: #undef CYTHON_USE_PYLIST_INTERNALS jpayne@68: #define CYTHON_USE_PYLIST_INTERNALS 0 jpayne@68: #undef CYTHON_USE_UNICODE_INTERNALS jpayne@68: #define CYTHON_USE_UNICODE_INTERNALS 0 jpayne@68: #ifndef CYTHON_USE_UNICODE_WRITER jpayne@68: #define CYTHON_USE_UNICODE_WRITER 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_PYLONG_INTERNALS jpayne@68: #define CYTHON_USE_PYLONG_INTERNALS 0 jpayne@68: #ifndef CYTHON_AVOID_BORROWED_REFS jpayne@68: #define CYTHON_AVOID_BORROWED_REFS 0 jpayne@68: #endif jpayne@68: #undef CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define CYTHON_ASSUME_SAFE_MACROS 0 jpayne@68: #undef CYTHON_UNPACK_METHODS jpayne@68: #define CYTHON_UNPACK_METHODS 0 jpayne@68: #undef CYTHON_FAST_THREAD_STATE jpayne@68: #define CYTHON_FAST_THREAD_STATE 0 jpayne@68: #undef CYTHON_FAST_GIL jpayne@68: #define CYTHON_FAST_GIL 0 jpayne@68: #undef CYTHON_METH_FASTCALL jpayne@68: #define CYTHON_METH_FASTCALL 0 jpayne@68: #undef CYTHON_FAST_PYCALL jpayne@68: #define CYTHON_FAST_PYCALL 0 jpayne@68: #ifndef CYTHON_PEP487_INIT_SUBCLASS jpayne@68: #define CYTHON_PEP487_INIT_SUBCLASS 1 jpayne@68: #endif jpayne@68: #undef CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 0 jpayne@68: #undef CYTHON_USE_MODULE_STATE jpayne@68: #define CYTHON_USE_MODULE_STATE 1 jpayne@68: #ifndef CYTHON_USE_TP_FINALIZE jpayne@68: #define CYTHON_USE_TP_FINALIZE 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_DICT_VERSIONS jpayne@68: #define CYTHON_USE_DICT_VERSIONS 0 jpayne@68: #undef CYTHON_USE_EXC_INFO_STACK jpayne@68: #define CYTHON_USE_EXC_INFO_STACK 0 jpayne@68: #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_FREELISTS jpayne@68: #define CYTHON_USE_FREELISTS 0 jpayne@68: #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL) jpayne@68: #define CYTHON_COMPILING_IN_PYPY 0 jpayne@68: #define CYTHON_COMPILING_IN_CPYTHON 0 jpayne@68: #define CYTHON_COMPILING_IN_LIMITED_API 0 jpayne@68: #define CYTHON_COMPILING_IN_GRAAL 0 jpayne@68: #define CYTHON_COMPILING_IN_NOGIL 1 jpayne@68: #ifndef CYTHON_USE_TYPE_SLOTS jpayne@68: #define CYTHON_USE_TYPE_SLOTS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_TYPE_SPECS jpayne@68: #define CYTHON_USE_TYPE_SPECS 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_PYTYPE_LOOKUP jpayne@68: #define CYTHON_USE_PYTYPE_LOOKUP 0 jpayne@68: #ifndef CYTHON_USE_ASYNC_SLOTS jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_PYLONG_INTERNALS jpayne@68: #define CYTHON_USE_PYLONG_INTERNALS 0 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_PYLIST_INTERNALS jpayne@68: #define CYTHON_USE_PYLIST_INTERNALS 0 jpayne@68: #ifndef CYTHON_USE_UNICODE_INTERNALS jpayne@68: #define CYTHON_USE_UNICODE_INTERNALS 1 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_UNICODE_WRITER jpayne@68: #define CYTHON_USE_UNICODE_WRITER 0 jpayne@68: #ifndef CYTHON_AVOID_BORROWED_REFS jpayne@68: #define CYTHON_AVOID_BORROWED_REFS 0 jpayne@68: #endif jpayne@68: #ifndef CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define CYTHON_ASSUME_SAFE_MACROS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_UNPACK_METHODS jpayne@68: #define CYTHON_UNPACK_METHODS 1 jpayne@68: #endif jpayne@68: #undef CYTHON_FAST_THREAD_STATE jpayne@68: #define CYTHON_FAST_THREAD_STATE 0 jpayne@68: #undef CYTHON_FAST_GIL jpayne@68: #define CYTHON_FAST_GIL 0 jpayne@68: #ifndef CYTHON_METH_FASTCALL jpayne@68: #define CYTHON_METH_FASTCALL 1 jpayne@68: #endif jpayne@68: #undef CYTHON_FAST_PYCALL jpayne@68: #define CYTHON_FAST_PYCALL 0 jpayne@68: #ifndef CYTHON_PEP487_INIT_SUBCLASS jpayne@68: #define CYTHON_PEP487_INIT_SUBCLASS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_MODULE_STATE jpayne@68: #define CYTHON_USE_MODULE_STATE 0 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_TP_FINALIZE jpayne@68: #define CYTHON_USE_TP_FINALIZE 1 jpayne@68: #endif jpayne@68: #undef CYTHON_USE_DICT_VERSIONS jpayne@68: #define CYTHON_USE_DICT_VERSIONS 0 jpayne@68: #undef CYTHON_USE_EXC_INFO_STACK jpayne@68: #define CYTHON_USE_EXC_INFO_STACK 0 jpayne@68: #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_FREELISTS jpayne@68: #define CYTHON_USE_FREELISTS 0 jpayne@68: #endif jpayne@68: #else jpayne@68: #define CYTHON_COMPILING_IN_PYPY 0 jpayne@68: #define CYTHON_COMPILING_IN_CPYTHON 1 jpayne@68: #define CYTHON_COMPILING_IN_LIMITED_API 0 jpayne@68: #define CYTHON_COMPILING_IN_GRAAL 0 jpayne@68: #define CYTHON_COMPILING_IN_NOGIL 0 jpayne@68: #ifndef CYTHON_USE_TYPE_SLOTS jpayne@68: #define CYTHON_USE_TYPE_SLOTS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_TYPE_SPECS jpayne@68: #define CYTHON_USE_TYPE_SPECS 0 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_PYTYPE_LOOKUP jpayne@68: #define CYTHON_USE_PYTYPE_LOOKUP 1 jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: #undef CYTHON_USE_ASYNC_SLOTS jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 0 jpayne@68: #elif !defined(CYTHON_USE_ASYNC_SLOTS) jpayne@68: #define CYTHON_USE_ASYNC_SLOTS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_PYLONG_INTERNALS jpayne@68: #define CYTHON_USE_PYLONG_INTERNALS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_PYLIST_INTERNALS jpayne@68: #define CYTHON_USE_PYLIST_INTERNALS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_UNICODE_INTERNALS jpayne@68: #define CYTHON_USE_UNICODE_INTERNALS 1 jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 jpayne@68: #undef CYTHON_USE_UNICODE_WRITER jpayne@68: #define CYTHON_USE_UNICODE_WRITER 0 jpayne@68: #elif !defined(CYTHON_USE_UNICODE_WRITER) jpayne@68: #define CYTHON_USE_UNICODE_WRITER 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_AVOID_BORROWED_REFS jpayne@68: #define CYTHON_AVOID_BORROWED_REFS 0 jpayne@68: #endif jpayne@68: #ifndef CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define CYTHON_ASSUME_SAFE_MACROS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_UNPACK_METHODS jpayne@68: #define CYTHON_UNPACK_METHODS 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_FAST_THREAD_STATE jpayne@68: #define CYTHON_FAST_THREAD_STATE 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_FAST_GIL jpayne@68: #define CYTHON_FAST_GIL (PY_MAJOR_VERSION < 3 || PY_VERSION_HEX >= 0x03060000 && PY_VERSION_HEX < 0x030C00A6) jpayne@68: #endif jpayne@68: #ifndef CYTHON_METH_FASTCALL jpayne@68: #define CYTHON_METH_FASTCALL (PY_VERSION_HEX >= 0x030700A1) jpayne@68: #endif jpayne@68: #ifndef CYTHON_FAST_PYCALL jpayne@68: #define CYTHON_FAST_PYCALL 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_PEP487_INIT_SUBCLASS jpayne@68: #define CYTHON_PEP487_INIT_SUBCLASS 1 jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x03050000 jpayne@68: #undef CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 0 jpayne@68: #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT) jpayne@68: #define CYTHON_PEP489_MULTI_PHASE_INIT 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_MODULE_STATE jpayne@68: #define CYTHON_USE_MODULE_STATE 0 jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030400a1 jpayne@68: #undef CYTHON_USE_TP_FINALIZE jpayne@68: #define CYTHON_USE_TP_FINALIZE 0 jpayne@68: #elif !defined(CYTHON_USE_TP_FINALIZE) jpayne@68: #define CYTHON_USE_TP_FINALIZE 1 jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030600B1 jpayne@68: #undef CYTHON_USE_DICT_VERSIONS jpayne@68: #define CYTHON_USE_DICT_VERSIONS 0 jpayne@68: #elif !defined(CYTHON_USE_DICT_VERSIONS) jpayne@68: #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX < 0x030C00A5) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030700A3 jpayne@68: #undef CYTHON_USE_EXC_INFO_STACK jpayne@68: #define CYTHON_USE_EXC_INFO_STACK 0 jpayne@68: #elif !defined(CYTHON_USE_EXC_INFO_STACK) jpayne@68: #define CYTHON_USE_EXC_INFO_STACK 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_FREELISTS jpayne@68: #define CYTHON_USE_FREELISTS 1 jpayne@68: #endif jpayne@68: #endif jpayne@68: #if !defined(CYTHON_FAST_PYCCALL) jpayne@68: #define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) jpayne@68: #endif jpayne@68: #if !defined(CYTHON_VECTORCALL) jpayne@68: #define CYTHON_VECTORCALL (CYTHON_FAST_PYCCALL && PY_VERSION_HEX >= 0x030800B1) jpayne@68: #endif jpayne@68: #define CYTHON_BACKPORT_VECTORCALL (CYTHON_METH_FASTCALL && PY_VERSION_HEX < 0x030800B1) jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: #include "longintrepr.h" jpayne@68: #endif jpayne@68: #undef SHIFT jpayne@68: #undef BASE jpayne@68: #undef MASK jpayne@68: #ifdef SIZEOF_VOID_P jpayne@68: enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef __has_attribute jpayne@68: #define __has_attribute(x) 0 jpayne@68: #endif jpayne@68: #ifndef __has_cpp_attribute jpayne@68: #define __has_cpp_attribute(x) 0 jpayne@68: #endif jpayne@68: #ifndef CYTHON_RESTRICT jpayne@68: #if defined(__GNUC__) jpayne@68: #define CYTHON_RESTRICT __restrict__ jpayne@68: #elif defined(_MSC_VER) && _MSC_VER >= 1400 jpayne@68: #define CYTHON_RESTRICT __restrict jpayne@68: #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L jpayne@68: #define CYTHON_RESTRICT restrict jpayne@68: #else jpayne@68: #define CYTHON_RESTRICT jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_UNUSED jpayne@68: #if defined(__cplusplus) jpayne@68: /* for clang __has_cpp_attribute(maybe_unused) is true even before C++17 jpayne@68: * but leads to warnings with -pedantic, since it is a C++17 feature */ jpayne@68: #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L) jpayne@68: #if __has_cpp_attribute(maybe_unused) jpayne@68: #define CYTHON_UNUSED [[maybe_unused]] jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_UNUSED jpayne@68: # if defined(__GNUC__) jpayne@68: # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) jpayne@68: # define CYTHON_UNUSED __attribute__ ((__unused__)) jpayne@68: # else jpayne@68: # define CYTHON_UNUSED jpayne@68: # endif jpayne@68: # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) jpayne@68: # define CYTHON_UNUSED __attribute__ ((__unused__)) jpayne@68: # else jpayne@68: # define CYTHON_UNUSED jpayne@68: # endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_UNUSED_VAR jpayne@68: # if defined(__cplusplus) jpayne@68: template void CYTHON_UNUSED_VAR( const T& ) { } jpayne@68: # else jpayne@68: # define CYTHON_UNUSED_VAR(x) (void)(x) jpayne@68: # endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_MAYBE_UNUSED_VAR jpayne@68: #define CYTHON_MAYBE_UNUSED_VAR(x) CYTHON_UNUSED_VAR(x) jpayne@68: #endif jpayne@68: #ifndef CYTHON_NCP_UNUSED jpayne@68: # if CYTHON_COMPILING_IN_CPYTHON jpayne@68: # define CYTHON_NCP_UNUSED jpayne@68: # else jpayne@68: # define CYTHON_NCP_UNUSED CYTHON_UNUSED jpayne@68: # endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_USE_CPP_STD_MOVE jpayne@68: #if defined(__cplusplus) && (\ jpayne@68: __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600)) jpayne@68: #define CYTHON_USE_CPP_STD_MOVE 1 jpayne@68: #else jpayne@68: #define CYTHON_USE_CPP_STD_MOVE 0 jpayne@68: #endif jpayne@68: #endif jpayne@68: #define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) jpayne@68: #ifdef _MSC_VER jpayne@68: #ifndef _MSC_STDINT_H_ jpayne@68: #if _MSC_VER < 1300 jpayne@68: typedef unsigned char uint8_t; jpayne@68: typedef unsigned short uint16_t; jpayne@68: typedef unsigned int uint32_t; jpayne@68: #else jpayne@68: typedef unsigned __int8 uint8_t; jpayne@68: typedef unsigned __int16 uint16_t; jpayne@68: typedef unsigned __int32 uint32_t; jpayne@68: #endif jpayne@68: #endif jpayne@68: #if _MSC_VER < 1300 jpayne@68: #ifdef _WIN64 jpayne@68: typedef unsigned long long __pyx_uintptr_t; jpayne@68: #else jpayne@68: typedef unsigned int __pyx_uintptr_t; jpayne@68: #endif jpayne@68: #else jpayne@68: #ifdef _WIN64 jpayne@68: typedef unsigned __int64 __pyx_uintptr_t; jpayne@68: #else jpayne@68: typedef unsigned __int32 __pyx_uintptr_t; jpayne@68: #endif jpayne@68: #endif jpayne@68: #else jpayne@68: #include jpayne@68: typedef uintptr_t __pyx_uintptr_t; jpayne@68: #endif jpayne@68: #ifndef CYTHON_FALLTHROUGH jpayne@68: #if defined(__cplusplus) jpayne@68: /* for clang __has_cpp_attribute(fallthrough) is true even before C++17 jpayne@68: * but leads to warnings with -pedantic, since it is a C++17 feature */ jpayne@68: #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L) jpayne@68: #if __has_cpp_attribute(fallthrough) jpayne@68: #define CYTHON_FALLTHROUGH [[fallthrough]] jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_FALLTHROUGH jpayne@68: #if __has_cpp_attribute(clang::fallthrough) jpayne@68: #define CYTHON_FALLTHROUGH [[clang::fallthrough]] jpayne@68: #elif __has_cpp_attribute(gnu::fallthrough) jpayne@68: #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_FALLTHROUGH jpayne@68: #if __has_attribute(fallthrough) jpayne@68: #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) jpayne@68: #else jpayne@68: #define CYTHON_FALLTHROUGH jpayne@68: #endif jpayne@68: #endif jpayne@68: #if defined(__clang__) && defined(__apple_build_version__) jpayne@68: #if __apple_build_version__ < 7000000 jpayne@68: #undef CYTHON_FALLTHROUGH jpayne@68: #define CYTHON_FALLTHROUGH jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifdef __cplusplus jpayne@68: template jpayne@68: struct __PYX_IS_UNSIGNED_IMPL {static const bool value = T(0) < T(-1);}; jpayne@68: #define __PYX_IS_UNSIGNED(type) (__PYX_IS_UNSIGNED_IMPL::value) jpayne@68: #else jpayne@68: #define __PYX_IS_UNSIGNED(type) (((type)-1) > 0) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY == 1 jpayne@68: #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x030A0000) jpayne@68: #else jpayne@68: #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000) jpayne@68: #endif jpayne@68: #define __PYX_REINTERPRET_FUNCION(func_pointer, other_pointer) ((func_pointer)(void(*)(void))(other_pointer)) jpayne@68: jpayne@68: #ifndef CYTHON_INLINE jpayne@68: #if defined(__clang__) jpayne@68: #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) jpayne@68: #elif defined(__GNUC__) jpayne@68: #define CYTHON_INLINE __inline__ jpayne@68: #elif defined(_MSC_VER) jpayne@68: #define CYTHON_INLINE __inline jpayne@68: #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L jpayne@68: #define CYTHON_INLINE inline jpayne@68: #else jpayne@68: #define CYTHON_INLINE jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: #define __PYX_BUILD_PY_SSIZE_T "n" jpayne@68: #define CYTHON_FORMAT_SSIZE_T "z" jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" jpayne@68: #define __Pyx_DefaultClassType PyClass_Type jpayne@68: #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ jpayne@68: PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) jpayne@68: #else jpayne@68: #define __Pyx_BUILTIN_MODULE_NAME "builtins" jpayne@68: #define __Pyx_DefaultClassType PyType_Type jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f, jpayne@68: PyObject *code, PyObject *c, PyObject* n, PyObject *v, jpayne@68: PyObject *fv, PyObject *cell, PyObject* fn, jpayne@68: PyObject *name, int fline, PyObject *lnos) { jpayne@68: PyObject *exception_table = NULL; jpayne@68: PyObject *types_module=NULL, *code_type=NULL, *result=NULL; jpayne@68: #if __PYX_LIMITED_VERSION_HEX < 0x030B0000 jpayne@68: PyObject *version_info; jpayne@68: PyObject *py_minor_version = NULL; jpayne@68: #endif jpayne@68: long minor_version = 0; jpayne@68: PyObject *type, *value, *traceback; jpayne@68: PyErr_Fetch(&type, &value, &traceback); jpayne@68: #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000 jpayne@68: minor_version = 11; jpayne@68: #else jpayne@68: if (!(version_info = PySys_GetObject("version_info"))) goto end; jpayne@68: if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end; jpayne@68: minor_version = PyLong_AsLong(py_minor_version); jpayne@68: Py_DECREF(py_minor_version); jpayne@68: if (minor_version == -1 && PyErr_Occurred()) goto end; jpayne@68: #endif jpayne@68: if (!(types_module = PyImport_ImportModule("types"))) goto end; jpayne@68: if (!(code_type = PyObject_GetAttrString(types_module, "CodeType"))) goto end; jpayne@68: if (minor_version <= 7) { jpayne@68: (void)p; jpayne@68: result = PyObject_CallFunction(code_type, "iiiiiOOOOOOiOO", a, k, l, s, f, code, jpayne@68: c, n, v, fn, name, fline, lnos, fv, cell); jpayne@68: } else if (minor_version <= 10) { jpayne@68: result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOiOO", a,p, k, l, s, f, code, jpayne@68: c, n, v, fn, name, fline, lnos, fv, cell); jpayne@68: } else { jpayne@68: if (!(exception_table = PyBytes_FromStringAndSize(NULL, 0))) goto end; jpayne@68: result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOOiOO", a,p, k, l, s, f, code, jpayne@68: c, n, v, fn, name, name, fline, lnos, exception_table, fv, cell); jpayne@68: } jpayne@68: end: jpayne@68: Py_XDECREF(code_type); jpayne@68: Py_XDECREF(exception_table); jpayne@68: Py_XDECREF(types_module); jpayne@68: if (type) { jpayne@68: PyErr_Restore(type, value, traceback); jpayne@68: } jpayne@68: return result; jpayne@68: } jpayne@68: #ifndef CO_OPTIMIZED jpayne@68: #define CO_OPTIMIZED 0x0001 jpayne@68: #endif jpayne@68: #ifndef CO_NEWLOCALS jpayne@68: #define CO_NEWLOCALS 0x0002 jpayne@68: #endif jpayne@68: #ifndef CO_VARARGS jpayne@68: #define CO_VARARGS 0x0004 jpayne@68: #endif jpayne@68: #ifndef CO_VARKEYWORDS jpayne@68: #define CO_VARKEYWORDS 0x0008 jpayne@68: #endif jpayne@68: #ifndef CO_ASYNC_GENERATOR jpayne@68: #define CO_ASYNC_GENERATOR 0x0200 jpayne@68: #endif jpayne@68: #ifndef CO_GENERATOR jpayne@68: #define CO_GENERATOR 0x0020 jpayne@68: #endif jpayne@68: #ifndef CO_COROUTINE jpayne@68: #define CO_COROUTINE 0x0080 jpayne@68: #endif jpayne@68: #elif PY_VERSION_HEX >= 0x030B0000 jpayne@68: static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f, jpayne@68: PyObject *code, PyObject *c, PyObject* n, PyObject *v, jpayne@68: PyObject *fv, PyObject *cell, PyObject* fn, jpayne@68: PyObject *name, int fline, PyObject *lnos) { jpayne@68: PyCodeObject *result; jpayne@68: PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0); jpayne@68: if (!empty_bytes) return NULL; jpayne@68: result = jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: PyUnstable_Code_NewWithPosOnlyArgs jpayne@68: #else jpayne@68: PyCode_NewWithPosOnlyArgs jpayne@68: #endif jpayne@68: (a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, name, fline, lnos, empty_bytes); jpayne@68: Py_DECREF(empty_bytes); jpayne@68: return result; jpayne@68: } jpayne@68: #elif PY_VERSION_HEX >= 0x030800B2 && !CYTHON_COMPILING_IN_PYPY jpayne@68: #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ jpayne@68: PyCode_NewWithPosOnlyArgs(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) jpayne@68: #else jpayne@68: #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ jpayne@68: PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030900A4 || defined(Py_IS_TYPE) jpayne@68: #define __Pyx_IS_TYPE(ob, type) Py_IS_TYPE(ob, type) jpayne@68: #else jpayne@68: #define __Pyx_IS_TYPE(ob, type) (((const PyObject*)ob)->ob_type == (type)) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_Is) jpayne@68: #define __Pyx_Py_Is(x, y) Py_Is(x, y) jpayne@68: #else jpayne@68: #define __Pyx_Py_Is(x, y) ((x) == (y)) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsNone) jpayne@68: #define __Pyx_Py_IsNone(ob) Py_IsNone(ob) jpayne@68: #else jpayne@68: #define __Pyx_Py_IsNone(ob) __Pyx_Py_Is((ob), Py_None) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsTrue) jpayne@68: #define __Pyx_Py_IsTrue(ob) Py_IsTrue(ob) jpayne@68: #else jpayne@68: #define __Pyx_Py_IsTrue(ob) __Pyx_Py_Is((ob), Py_True) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsFalse) jpayne@68: #define __Pyx_Py_IsFalse(ob) Py_IsFalse(ob) jpayne@68: #else jpayne@68: #define __Pyx_Py_IsFalse(ob) __Pyx_Py_Is((ob), Py_False) jpayne@68: #endif jpayne@68: #define __Pyx_NoneAsNull(obj) (__Pyx_Py_IsNone(obj) ? NULL : (obj)) jpayne@68: #if PY_VERSION_HEX >= 0x030900F0 && !CYTHON_COMPILING_IN_PYPY jpayne@68: #define __Pyx_PyObject_GC_IsFinalized(o) PyObject_GC_IsFinalized(o) jpayne@68: #else jpayne@68: #define __Pyx_PyObject_GC_IsFinalized(o) _PyGC_FINALIZED(o) jpayne@68: #endif jpayne@68: #ifndef CO_COROUTINE jpayne@68: #define CO_COROUTINE 0x80 jpayne@68: #endif jpayne@68: #ifndef CO_ASYNC_GENERATOR jpayne@68: #define CO_ASYNC_GENERATOR 0x200 jpayne@68: #endif jpayne@68: #ifndef Py_TPFLAGS_CHECKTYPES jpayne@68: #define Py_TPFLAGS_CHECKTYPES 0 jpayne@68: #endif jpayne@68: #ifndef Py_TPFLAGS_HAVE_INDEX jpayne@68: #define Py_TPFLAGS_HAVE_INDEX 0 jpayne@68: #endif jpayne@68: #ifndef Py_TPFLAGS_HAVE_NEWBUFFER jpayne@68: #define Py_TPFLAGS_HAVE_NEWBUFFER 0 jpayne@68: #endif jpayne@68: #ifndef Py_TPFLAGS_HAVE_FINALIZE jpayne@68: #define Py_TPFLAGS_HAVE_FINALIZE 0 jpayne@68: #endif jpayne@68: #ifndef Py_TPFLAGS_SEQUENCE jpayne@68: #define Py_TPFLAGS_SEQUENCE 0 jpayne@68: #endif jpayne@68: #ifndef Py_TPFLAGS_MAPPING jpayne@68: #define Py_TPFLAGS_MAPPING 0 jpayne@68: #endif jpayne@68: #ifndef METH_STACKLESS jpayne@68: #define METH_STACKLESS 0 jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) jpayne@68: #ifndef METH_FASTCALL jpayne@68: #define METH_FASTCALL 0x80 jpayne@68: #endif jpayne@68: typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); jpayne@68: typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, jpayne@68: Py_ssize_t nargs, PyObject *kwnames); jpayne@68: #else jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: # define __Pyx_PyCFunctionFast PyCFunctionFast jpayne@68: # define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords jpayne@68: #else jpayne@68: # define __Pyx_PyCFunctionFast _PyCFunctionFast jpayne@68: # define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords jpayne@68: #endif jpayne@68: #endif jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: #define __Pyx_METH_FASTCALL METH_FASTCALL jpayne@68: #define __Pyx_PyCFunction_FastCall __Pyx_PyCFunctionFast jpayne@68: #define __Pyx_PyCFunction_FastCallWithKeywords __Pyx_PyCFunctionFastWithKeywords jpayne@68: #else jpayne@68: #define __Pyx_METH_FASTCALL METH_VARARGS jpayne@68: #define __Pyx_PyCFunction_FastCall PyCFunction jpayne@68: #define __Pyx_PyCFunction_FastCallWithKeywords PyCFunctionWithKeywords jpayne@68: #endif jpayne@68: #if CYTHON_VECTORCALL jpayne@68: #define __pyx_vectorcallfunc vectorcallfunc jpayne@68: #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET PY_VECTORCALL_ARGUMENTS_OFFSET jpayne@68: #define __Pyx_PyVectorcall_NARGS(n) PyVectorcall_NARGS((size_t)(n)) jpayne@68: #elif CYTHON_BACKPORT_VECTORCALL jpayne@68: typedef PyObject *(*__pyx_vectorcallfunc)(PyObject *callable, PyObject *const *args, jpayne@68: size_t nargsf, PyObject *kwnames); jpayne@68: #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET ((size_t)1 << (8 * sizeof(size_t) - 1)) jpayne@68: #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(((size_t)(n)) & ~__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET)) jpayne@68: #else jpayne@68: #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET 0 jpayne@68: #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(n)) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 0x030900B1 jpayne@68: #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_CheckExact(func) jpayne@68: #else jpayne@68: #define __Pyx_PyCFunction_CheckExact(func) PyCFunction_Check(func) jpayne@68: #endif jpayne@68: #define __Pyx_CyOrPyCFunction_Check(func) PyCFunction_Check(func) jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) (((PyCFunctionObject*)(func))->m_ml->ml_meth) jpayne@68: #elif !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) PyCFunction_GET_FUNCTION(func) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: #define __Pyx_CyOrPyCFunction_GET_FLAGS(func) (((PyCFunctionObject*)(func))->m_ml->ml_flags) jpayne@68: static CYTHON_INLINE PyObject* __Pyx_CyOrPyCFunction_GET_SELF(PyObject *func) { jpayne@68: return (__Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_STATIC) ? NULL : ((PyCFunctionObject*)func)->m_self; jpayne@68: } jpayne@68: #endif jpayne@68: static CYTHON_INLINE int __Pyx__IsSameCFunction(PyObject *func, void *cfunc) { jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: return PyCFunction_Check(func) && PyCFunction_GetFunction(func) == (PyCFunction) cfunc; jpayne@68: #else jpayne@68: return PyCFunction_Check(func) && PyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc; jpayne@68: #endif jpayne@68: } jpayne@68: #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCFunction(func, cfunc) jpayne@68: #if __PYX_LIMITED_VERSION_HEX < 0x030900B1 jpayne@68: #define __Pyx_PyType_FromModuleAndSpec(m, s, b) ((void)m, PyType_FromSpecWithBases(s, b)) jpayne@68: typedef PyObject *(*__Pyx_PyCMethod)(PyObject *, PyTypeObject *, PyObject *const *, size_t, PyObject *); jpayne@68: #else jpayne@68: #define __Pyx_PyType_FromModuleAndSpec(m, s, b) PyType_FromModuleAndSpec(m, s, b) jpayne@68: #define __Pyx_PyCMethod PyCMethod jpayne@68: #endif jpayne@68: #ifndef METH_METHOD jpayne@68: #define METH_METHOD 0x200 jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) jpayne@68: #define PyObject_Malloc(s) PyMem_Malloc(s) jpayne@68: #define PyObject_Free(p) PyMem_Free(p) jpayne@68: #define PyObject_Realloc(p) PyMem_Realloc(p) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) jpayne@68: #define __Pyx_PyFrame_SetLineNumber(frame, lineno) jpayne@68: #else jpayne@68: #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) jpayne@68: #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_PyThreadState_Current PyThreadState_Get() jpayne@68: #elif !CYTHON_FAST_THREAD_STATE jpayne@68: #define __Pyx_PyThreadState_Current PyThreadState_GET() jpayne@68: #elif PY_VERSION_HEX >= 0x030d00A1 jpayne@68: #define __Pyx_PyThreadState_Current PyThreadState_GetUnchecked() jpayne@68: #elif PY_VERSION_HEX >= 0x03060000 jpayne@68: #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() jpayne@68: #elif PY_VERSION_HEX >= 0x03000000 jpayne@68: #define __Pyx_PyThreadState_Current PyThreadState_GET() jpayne@68: #else jpayne@68: #define __Pyx_PyThreadState_Current _PyThreadState_Current jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static CYTHON_INLINE void *__Pyx_PyModule_GetState(PyObject *op) jpayne@68: { jpayne@68: void *result; jpayne@68: result = PyModule_GetState(op); jpayne@68: if (!result) jpayne@68: Py_FatalError("Couldn't find the module state"); jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: #define __Pyx_PyObject_GetSlot(obj, name, func_ctype) __Pyx_PyType_GetSlot(Py_TYPE(obj), name, func_ctype) jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((func_ctype) PyType_GetSlot((type), Py_##name)) jpayne@68: #else jpayne@68: #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((type)->name) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) jpayne@68: #include "pythread.h" jpayne@68: #define Py_tss_NEEDS_INIT 0 jpayne@68: typedef int Py_tss_t; jpayne@68: static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { jpayne@68: *key = PyThread_create_key(); jpayne@68: return 0; jpayne@68: } jpayne@68: static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { jpayne@68: Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); jpayne@68: *key = Py_tss_NEEDS_INIT; jpayne@68: return key; jpayne@68: } jpayne@68: static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { jpayne@68: PyObject_Free(key); jpayne@68: } jpayne@68: static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { jpayne@68: return *key != Py_tss_NEEDS_INIT; jpayne@68: } jpayne@68: static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { jpayne@68: PyThread_delete_key(*key); jpayne@68: *key = Py_tss_NEEDS_INIT; jpayne@68: } jpayne@68: static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { jpayne@68: return PyThread_set_key_value(*key, value); jpayne@68: } jpayne@68: static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { jpayne@68: return PyThread_get_key_value(*key); jpayne@68: } jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: #if PYPY_VERSION_NUM < 0x07030600 jpayne@68: #if defined(__cplusplus) && __cplusplus >= 201402L jpayne@68: [[deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")]] jpayne@68: #elif defined(__GNUC__) || defined(__clang__) jpayne@68: __attribute__ ((__deprecated__("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6"))) jpayne@68: #elif defined(_MSC_VER) jpayne@68: __declspec(deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")) jpayne@68: #endif jpayne@68: static CYTHON_INLINE int PyGILState_Check(void) { jpayne@68: return 0; jpayne@68: } jpayne@68: #else // PYPY_VERSION_NUM < 0x07030600 jpayne@68: #endif // PYPY_VERSION_NUM < 0x07030600 jpayne@68: #else jpayne@68: static CYTHON_INLINE int PyGILState_Check(void) { jpayne@68: PyThreadState * tstate = _PyThreadState_Current; jpayne@68: return tstate && (tstate == PyGILState_GetThisThreadState()); jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030d0000 || defined(_PyDict_NewPresized) jpayne@68: #define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) jpayne@68: #else jpayne@68: #define __Pyx_PyDict_NewPresized(n) PyDict_New() jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION jpayne@68: #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) jpayne@68: #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) jpayne@68: #else jpayne@68: #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) jpayne@68: #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX > 0x030600B4 && PY_VERSION_HEX < 0x030d0000 && CYTHON_USE_UNICODE_INTERNALS jpayne@68: #define __Pyx_PyDict_GetItemStrWithError(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) jpayne@68: static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStr(PyObject *dict, PyObject *name) { jpayne@68: PyObject *res = __Pyx_PyDict_GetItemStrWithError(dict, name); jpayne@68: if (res == NULL) PyErr_Clear(); jpayne@68: return res; jpayne@68: } jpayne@68: #elif PY_MAJOR_VERSION >= 3 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07020000) jpayne@68: #define __Pyx_PyDict_GetItemStrWithError PyDict_GetItemWithError jpayne@68: #define __Pyx_PyDict_GetItemStr PyDict_GetItem jpayne@68: #else jpayne@68: static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict, PyObject *name) { jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: return PyDict_GetItem(dict, name); jpayne@68: #else jpayne@68: PyDictEntry *ep; jpayne@68: PyDictObject *mp = (PyDictObject*) dict; jpayne@68: long hash = ((PyStringObject *) name)->ob_shash; jpayne@68: assert(hash != -1); jpayne@68: ep = (mp->ma_lookup)(mp, name, hash); jpayne@68: if (ep == NULL) { jpayne@68: return NULL; jpayne@68: } jpayne@68: return ep->me_value; jpayne@68: #endif jpayne@68: } jpayne@68: #define __Pyx_PyDict_GetItemStr PyDict_GetItem jpayne@68: #endif jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: #define __Pyx_PyType_GetFlags(tp) (((PyTypeObject *)tp)->tp_flags) jpayne@68: #define __Pyx_PyType_HasFeature(type, feature) ((__Pyx_PyType_GetFlags(type) & (feature)) != 0) jpayne@68: #define __Pyx_PyObject_GetIterNextFunc(obj) (Py_TYPE(obj)->tp_iternext) jpayne@68: #else jpayne@68: #define __Pyx_PyType_GetFlags(tp) (PyType_GetFlags((PyTypeObject *)tp)) jpayne@68: #define __Pyx_PyType_HasFeature(type, feature) PyType_HasFeature(type, feature) jpayne@68: #define __Pyx_PyObject_GetIterNextFunc(obj) PyIter_Next jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_SetItemOnTypeDict(tp, k, v) PyObject_GenericSetAttr((PyObject*)tp, k, v) jpayne@68: #else jpayne@68: #define __Pyx_SetItemOnTypeDict(tp, k, v) PyDict_SetItem(tp->tp_dict, k, v) jpayne@68: #endif jpayne@68: #if CYTHON_USE_TYPE_SPECS && PY_VERSION_HEX >= 0x03080000 jpayne@68: #define __Pyx_PyHeapTypeObject_GC_Del(obj) {\ jpayne@68: PyTypeObject *type = Py_TYPE((PyObject*)obj);\ jpayne@68: assert(__Pyx_PyType_HasFeature(type, Py_TPFLAGS_HEAPTYPE));\ jpayne@68: PyObject_GC_Del(obj);\ jpayne@68: Py_DECREF(type);\ jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_PyHeapTypeObject_GC_Del(obj) PyObject_GC_Del(obj) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define CYTHON_PEP393_ENABLED 1 jpayne@68: #define __Pyx_PyUnicode_READY(op) (0) jpayne@68: #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GetLength(u) jpayne@68: #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_ReadChar(u, i) jpayne@68: #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((void)u, 1114111U) jpayne@68: #define __Pyx_PyUnicode_KIND(u) ((void)u, (0)) jpayne@68: #define __Pyx_PyUnicode_DATA(u) ((void*)u) jpayne@68: #define __Pyx_PyUnicode_READ(k, d, i) ((void)k, PyUnicode_ReadChar((PyObject*)(d), i)) jpayne@68: #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GetLength(u)) jpayne@68: #elif PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) jpayne@68: #define CYTHON_PEP393_ENABLED 1 jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: #define __Pyx_PyUnicode_READY(op) (0) jpayne@68: #else jpayne@68: #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ jpayne@68: 0 : _PyUnicode_Ready((PyObject *)(op))) jpayne@68: #endif jpayne@68: #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) jpayne@68: #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) jpayne@68: #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) jpayne@68: #define __Pyx_PyUnicode_KIND(u) ((int)PyUnicode_KIND(u)) jpayne@68: #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) jpayne@68: #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) jpayne@68: #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, (Py_UCS4) ch) jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) jpayne@68: #else jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 jpayne@68: #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) jpayne@68: #else jpayne@68: #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) jpayne@68: #endif jpayne@68: #endif jpayne@68: #else jpayne@68: #define CYTHON_PEP393_ENABLED 0 jpayne@68: #define PyUnicode_1BYTE_KIND 1 jpayne@68: #define PyUnicode_2BYTE_KIND 2 jpayne@68: #define PyUnicode_4BYTE_KIND 4 jpayne@68: #define __Pyx_PyUnicode_READY(op) (0) jpayne@68: #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) jpayne@68: #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) jpayne@68: #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535U : 1114111U) jpayne@68: #define __Pyx_PyUnicode_KIND(u) ((int)sizeof(Py_UNICODE)) jpayne@68: #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) jpayne@68: #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) jpayne@68: #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = (Py_UNICODE) ch) jpayne@68: #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) jpayne@68: #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) jpayne@68: #else jpayne@68: #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) jpayne@68: #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ jpayne@68: PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: #if !defined(PyUnicode_DecodeUnicodeEscape) jpayne@68: #define PyUnicode_DecodeUnicodeEscape(s, size, errors) PyUnicode_Decode(s, size, "unicode_escape", errors) jpayne@68: #endif jpayne@68: #if !defined(PyUnicode_Contains) || (PY_MAJOR_VERSION == 2 && PYPY_VERSION_NUM < 0x07030500) jpayne@68: #undef PyUnicode_Contains jpayne@68: #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) jpayne@68: #endif jpayne@68: #if !defined(PyByteArray_Check) jpayne@68: #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) jpayne@68: #endif jpayne@68: #if !defined(PyObject_Format) jpayne@68: #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) jpayne@68: #endif jpayne@68: #endif jpayne@68: #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@68: #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@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) jpayne@68: #else jpayne@68: #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) jpayne@68: #define PyObject_ASCII(o) PyObject_Repr(o) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define PyBaseString_Type PyUnicode_Type jpayne@68: #define PyStringObject PyUnicodeObject jpayne@68: #define PyString_Type PyUnicode_Type jpayne@68: #define PyString_Check PyUnicode_Check jpayne@68: #define PyString_CheckExact PyUnicode_CheckExact jpayne@68: #ifndef PyObject_Unicode jpayne@68: #define PyObject_Unicode PyObject_Str jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) jpayne@68: #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) jpayne@68: #else jpayne@68: #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) jpayne@68: #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: #define __Pyx_PySequence_ListKeepNew(obj)\ jpayne@68: (likely(PyList_CheckExact(obj) && Py_REFCNT(obj) == 1) ? __Pyx_NewRef(obj) : PySequence_List(obj)) jpayne@68: #else jpayne@68: #define __Pyx_PySequence_ListKeepNew(obj) PySequence_List(obj) jpayne@68: #endif jpayne@68: #ifndef PySet_CheckExact jpayne@68: #define PySet_CheckExact(obj) __Pyx_IS_TYPE(obj, &PySet_Type) jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030900A4 jpayne@68: #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) jpayne@68: #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) jpayne@68: #else jpayne@68: #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) jpayne@68: #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) jpayne@68: #endif jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define __Pyx_PySequence_ITEM(o, i) PySequence_ITEM(o, i) jpayne@68: #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) jpayne@68: #define __Pyx_PyTuple_SET_ITEM(o, i, v) (PyTuple_SET_ITEM(o, i, v), (0)) jpayne@68: #define __Pyx_PyList_SET_ITEM(o, i, v) (PyList_SET_ITEM(o, i, v), (0)) jpayne@68: #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_GET_SIZE(o) jpayne@68: #define __Pyx_PyList_GET_SIZE(o) PyList_GET_SIZE(o) jpayne@68: #define __Pyx_PySet_GET_SIZE(o) PySet_GET_SIZE(o) jpayne@68: #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_GET_SIZE(o) jpayne@68: #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_GET_SIZE(o) jpayne@68: #else jpayne@68: #define __Pyx_PySequence_ITEM(o, i) PySequence_GetItem(o, i) jpayne@68: #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) jpayne@68: #define __Pyx_PyTuple_SET_ITEM(o, i, v) PyTuple_SetItem(o, i, v) jpayne@68: #define __Pyx_PyList_SET_ITEM(o, i, v) PyList_SetItem(o, i, v) jpayne@68: #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_Size(o) jpayne@68: #define __Pyx_PyList_GET_SIZE(o) PyList_Size(o) jpayne@68: #define __Pyx_PySet_GET_SIZE(o) PySet_Size(o) jpayne@68: #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o) jpayne@68: #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o) jpayne@68: #endif jpayne@68: #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 jpayne@68: #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name) jpayne@68: #else jpayne@68: static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) { jpayne@68: PyObject *module = PyImport_AddModule(name); jpayne@68: Py_XINCREF(module); jpayne@68: return module; jpayne@68: } jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define PyIntObject PyLongObject jpayne@68: #define PyInt_Type PyLong_Type jpayne@68: #define PyInt_Check(op) PyLong_Check(op) jpayne@68: #define PyInt_CheckExact(op) PyLong_CheckExact(op) jpayne@68: #define __Pyx_Py3Int_Check(op) PyLong_Check(op) jpayne@68: #define __Pyx_Py3Int_CheckExact(op) PyLong_CheckExact(op) jpayne@68: #define PyInt_FromString PyLong_FromString jpayne@68: #define PyInt_FromUnicode PyLong_FromUnicode jpayne@68: #define PyInt_FromLong PyLong_FromLong jpayne@68: #define PyInt_FromSize_t PyLong_FromSize_t jpayne@68: #define PyInt_FromSsize_t PyLong_FromSsize_t jpayne@68: #define PyInt_AsLong PyLong_AsLong jpayne@68: #define PyInt_AS_LONG PyLong_AS_LONG jpayne@68: #define PyInt_AsSsize_t PyLong_AsSsize_t jpayne@68: #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask jpayne@68: #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask jpayne@68: #define PyNumber_Int PyNumber_Long jpayne@68: #else jpayne@68: #define __Pyx_Py3Int_Check(op) (PyLong_Check(op) || PyInt_Check(op)) jpayne@68: #define __Pyx_Py3Int_CheckExact(op) (PyLong_CheckExact(op) || PyInt_CheckExact(op)) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define PyBoolObject PyLongObject jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY jpayne@68: #ifndef PyUnicode_InternFromString jpayne@68: #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030200A4 jpayne@68: typedef long Py_hash_t; jpayne@68: #define __Pyx_PyInt_FromHash_t PyInt_FromLong jpayne@68: #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t jpayne@68: #else jpayne@68: #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t jpayne@68: #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t jpayne@68: #endif jpayne@68: #if CYTHON_USE_ASYNC_SLOTS jpayne@68: #if PY_VERSION_HEX >= 0x030500B1 jpayne@68: #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods jpayne@68: #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) jpayne@68: #else jpayne@68: #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) jpayne@68: #endif jpayne@68: #else jpayne@68: #define __Pyx_PyType_AsAsync(obj) NULL jpayne@68: #endif jpayne@68: #ifndef __Pyx_PyAsyncMethodsStruct jpayne@68: typedef struct { jpayne@68: unaryfunc am_await; jpayne@68: unaryfunc am_aiter; jpayne@68: unaryfunc am_anext; jpayne@68: } __Pyx_PyAsyncMethodsStruct; jpayne@68: #endif jpayne@68: jpayne@68: #if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS) jpayne@68: #if !defined(_USE_MATH_DEFINES) jpayne@68: #define _USE_MATH_DEFINES jpayne@68: #endif jpayne@68: #endif jpayne@68: #include jpayne@68: #ifdef NAN jpayne@68: #define __PYX_NAN() ((float) NAN) jpayne@68: #else jpayne@68: static CYTHON_INLINE float __PYX_NAN() { jpayne@68: float value; jpayne@68: memset(&value, 0xFF, sizeof(value)); jpayne@68: return value; jpayne@68: } jpayne@68: #endif jpayne@68: #if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) jpayne@68: #define __Pyx_truncl trunc jpayne@68: #else jpayne@68: #define __Pyx_truncl truncl jpayne@68: #endif jpayne@68: jpayne@68: #define __PYX_MARK_ERR_POS(f_index, lineno) \ jpayne@68: { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } jpayne@68: #define __PYX_ERR(f_index, lineno, Ln_error) \ jpayne@68: { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } jpayne@68: jpayne@68: #ifdef CYTHON_EXTERN_C jpayne@68: #undef __PYX_EXTERN_C jpayne@68: #define __PYX_EXTERN_C CYTHON_EXTERN_C jpayne@68: #elif defined(__PYX_EXTERN_C) jpayne@68: #ifdef _MSC_VER jpayne@68: #pragma message ("Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.") jpayne@68: #else jpayne@68: #warning Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead. jpayne@68: #endif jpayne@68: #else jpayne@68: #ifdef __cplusplus jpayne@68: #define __PYX_EXTERN_C extern "C" jpayne@68: #else jpayne@68: #define __PYX_EXTERN_C extern jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: #define __PYX_HAVE__pysam__libctabix jpayne@68: #define __PYX_HAVE_API__pysam__libctabix jpayne@68: /* Early includes */ jpayne@68: #include jpayne@68: #include jpayne@68: #include jpayne@68: #include jpayne@68: #include "fcntl.h" jpayne@68: #include "unistd.h" jpayne@68: #include jpayne@68: #include "stdarg.h" jpayne@68: #include "htslib/kstring.h" jpayne@68: #include "htslib_util.h" jpayne@68: #include "htslib/hfile.h" jpayne@68: #include "htslib/bgzf.h" jpayne@68: #include "htslib/hts.h" jpayne@68: #include "htslib/sam.h" jpayne@68: #include "htslib/faidx.h" jpayne@68: #include "htslib/tbx.h" jpayne@68: #include "htslib/vcf.h" jpayne@68: #include "htslib/vcfutils.h" jpayne@68: #include "htslib/cram.h" jpayne@68: #include "pysam_stream.h" jpayne@68: #include jpayne@68: #include jpayne@68: #include jpayne@68: #include "pythread.h" jpayne@68: jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: #ifdef _MSC_VER jpayne@68: #pragma message ("This module uses CPython specific internals of 'array.array', which are not available in PyPy.") jpayne@68: #else jpayne@68: #warning This module uses CPython specific internals of 'array.array', which are not available in PyPy. jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: #ifdef _OPENMP jpayne@68: #include jpayne@68: #endif /* _OPENMP */ jpayne@68: jpayne@68: #if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) jpayne@68: #define CYTHON_WITHOUT_ASSERTIONS jpayne@68: #endif jpayne@68: jpayne@68: typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; jpayne@68: const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; jpayne@68: jpayne@68: #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 jpayne@68: #define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0 jpayne@68: #define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8) jpayne@68: #define __PYX_DEFAULT_STRING_ENCODING "" jpayne@68: #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString jpayne@68: #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize jpayne@68: #define __Pyx_uchar_cast(c) ((unsigned char)c) jpayne@68: #define __Pyx_long_cast(x) ((long)x) jpayne@68: #define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ jpayne@68: (sizeof(type) < sizeof(Py_ssize_t)) ||\ jpayne@68: (sizeof(type) > sizeof(Py_ssize_t) &&\ jpayne@68: likely(v < (type)PY_SSIZE_T_MAX ||\ jpayne@68: v == (type)PY_SSIZE_T_MAX) &&\ jpayne@68: (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ jpayne@68: v == (type)PY_SSIZE_T_MIN))) ||\ jpayne@68: (sizeof(type) == sizeof(Py_ssize_t) &&\ jpayne@68: (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ jpayne@68: v == (type)PY_SSIZE_T_MAX))) ) jpayne@68: static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) { jpayne@68: return (size_t) i < (size_t) limit; jpayne@68: } jpayne@68: #if defined (__cplusplus) && __cplusplus >= 201103L jpayne@68: #include jpayne@68: #define __Pyx_sst_abs(value) std::abs(value) jpayne@68: #elif SIZEOF_INT >= SIZEOF_SIZE_T jpayne@68: #define __Pyx_sst_abs(value) abs(value) jpayne@68: #elif SIZEOF_LONG >= SIZEOF_SIZE_T jpayne@68: #define __Pyx_sst_abs(value) labs(value) jpayne@68: #elif defined (_MSC_VER) jpayne@68: #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) jpayne@68: #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L jpayne@68: #define __Pyx_sst_abs(value) llabs(value) jpayne@68: #elif defined (__GNUC__) jpayne@68: #define __Pyx_sst_abs(value) __builtin_llabs(value) jpayne@68: #else jpayne@68: #define __Pyx_sst_abs(value) ((value<0) ? -value : value) jpayne@68: #endif jpayne@68: static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s); jpayne@68: static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); jpayne@68: static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char*); jpayne@68: #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) jpayne@68: #define __Pyx_PyBytes_FromString PyBytes_FromString jpayne@68: #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString jpayne@68: #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize jpayne@68: #else jpayne@68: #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString jpayne@68: #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize jpayne@68: #endif jpayne@68: #define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) jpayne@68: #define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) jpayne@68: #define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) jpayne@68: #define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) jpayne@68: #define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) jpayne@68: #define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) jpayne@68: #define __Pyx_PyObject_AsWritableString(s) ((char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s)) jpayne@68: #define __Pyx_PyObject_AsWritableSString(s) ((signed char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s)) jpayne@68: #define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s)) jpayne@68: #define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) jpayne@68: #define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) jpayne@68: #define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) jpayne@68: #define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) jpayne@68: #define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) jpayne@68: #define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) jpayne@68: #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) jpayne@68: #define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o) jpayne@68: #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode jpayne@68: #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) jpayne@68: #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) jpayne@68: static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); jpayne@68: static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); jpayne@68: static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); jpayne@68: #define __Pyx_PySequence_Tuple(obj)\ jpayne@68: (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) jpayne@68: static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); jpayne@68: static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); jpayne@68: static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) jpayne@68: #else jpayne@68: #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) jpayne@68: #endif jpayne@68: #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) jpayne@68: #else jpayne@68: #define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) jpayne@68: #endif jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: #if PY_VERSION_HEX >= 0x030C00A7 jpayne@68: #ifndef _PyLong_SIGN_MASK jpayne@68: #define _PyLong_SIGN_MASK 3 jpayne@68: #endif jpayne@68: #ifndef _PyLong_NON_SIZE_BITS jpayne@68: #define _PyLong_NON_SIZE_BITS 3 jpayne@68: #endif jpayne@68: #define __Pyx_PyLong_Sign(x) (((PyLongObject*)x)->long_value.lv_tag & _PyLong_SIGN_MASK) jpayne@68: #define __Pyx_PyLong_IsNeg(x) ((__Pyx_PyLong_Sign(x) & 2) != 0) jpayne@68: #define __Pyx_PyLong_IsNonNeg(x) (!__Pyx_PyLong_IsNeg(x)) jpayne@68: #define __Pyx_PyLong_IsZero(x) (__Pyx_PyLong_Sign(x) & 1) jpayne@68: #define __Pyx_PyLong_IsPos(x) (__Pyx_PyLong_Sign(x) == 0) jpayne@68: #define __Pyx_PyLong_CompactValueUnsigned(x) (__Pyx_PyLong_Digits(x)[0]) jpayne@68: #define __Pyx_PyLong_DigitCount(x) ((Py_ssize_t) (((PyLongObject*)x)->long_value.lv_tag >> _PyLong_NON_SIZE_BITS)) jpayne@68: #define __Pyx_PyLong_SignedDigitCount(x)\ jpayne@68: ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * __Pyx_PyLong_DigitCount(x)) jpayne@68: #if defined(PyUnstable_Long_IsCompact) && defined(PyUnstable_Long_CompactValue) jpayne@68: #define __Pyx_PyLong_IsCompact(x) PyUnstable_Long_IsCompact((PyLongObject*) x) jpayne@68: #define __Pyx_PyLong_CompactValue(x) PyUnstable_Long_CompactValue((PyLongObject*) x) jpayne@68: #else jpayne@68: #define __Pyx_PyLong_IsCompact(x) (((PyLongObject*)x)->long_value.lv_tag < (2 << _PyLong_NON_SIZE_BITS)) jpayne@68: #define __Pyx_PyLong_CompactValue(x) ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * (Py_ssize_t) __Pyx_PyLong_Digits(x)[0]) jpayne@68: #endif jpayne@68: typedef Py_ssize_t __Pyx_compact_pylong; jpayne@68: typedef size_t __Pyx_compact_upylong; jpayne@68: #else jpayne@68: #define __Pyx_PyLong_IsNeg(x) (Py_SIZE(x) < 0) jpayne@68: #define __Pyx_PyLong_IsNonNeg(x) (Py_SIZE(x) >= 0) jpayne@68: #define __Pyx_PyLong_IsZero(x) (Py_SIZE(x) == 0) jpayne@68: #define __Pyx_PyLong_IsPos(x) (Py_SIZE(x) > 0) jpayne@68: #define __Pyx_PyLong_CompactValueUnsigned(x) ((Py_SIZE(x) == 0) ? 0 : __Pyx_PyLong_Digits(x)[0]) jpayne@68: #define __Pyx_PyLong_DigitCount(x) __Pyx_sst_abs(Py_SIZE(x)) jpayne@68: #define __Pyx_PyLong_SignedDigitCount(x) Py_SIZE(x) jpayne@68: #define __Pyx_PyLong_IsCompact(x) (Py_SIZE(x) == 0 || Py_SIZE(x) == 1 || Py_SIZE(x) == -1) jpayne@68: #define __Pyx_PyLong_CompactValue(x)\ jpayne@68: ((Py_SIZE(x) == 0) ? (sdigit) 0 : ((Py_SIZE(x) < 0) ? -(sdigit)__Pyx_PyLong_Digits(x)[0] : (sdigit)__Pyx_PyLong_Digits(x)[0])) jpayne@68: typedef sdigit __Pyx_compact_pylong; jpayne@68: typedef digit __Pyx_compact_upylong; jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C00A5 jpayne@68: #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->long_value.ob_digit) jpayne@68: #else jpayne@68: #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->ob_digit) jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII jpayne@68: #include jpayne@68: static int __Pyx_sys_getdefaultencoding_not_ascii; jpayne@68: static int __Pyx_init_sys_getdefaultencoding_params(void) { jpayne@68: PyObject* sys; jpayne@68: PyObject* default_encoding = NULL; jpayne@68: PyObject* ascii_chars_u = NULL; jpayne@68: PyObject* ascii_chars_b = NULL; jpayne@68: const char* default_encoding_c; jpayne@68: sys = PyImport_ImportModule("sys"); jpayne@68: if (!sys) goto bad; jpayne@68: default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); jpayne@68: Py_DECREF(sys); jpayne@68: if (!default_encoding) goto bad; jpayne@68: default_encoding_c = PyBytes_AsString(default_encoding); jpayne@68: if (!default_encoding_c) goto bad; jpayne@68: if (strcmp(default_encoding_c, "ascii") == 0) { jpayne@68: __Pyx_sys_getdefaultencoding_not_ascii = 0; jpayne@68: } else { jpayne@68: char ascii_chars[128]; jpayne@68: int c; jpayne@68: for (c = 0; c < 128; c++) { jpayne@68: ascii_chars[c] = (char) c; jpayne@68: } jpayne@68: __Pyx_sys_getdefaultencoding_not_ascii = 1; jpayne@68: ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); jpayne@68: if (!ascii_chars_u) goto bad; jpayne@68: ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); jpayne@68: if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { jpayne@68: PyErr_Format( jpayne@68: PyExc_ValueError, jpayne@68: "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", jpayne@68: default_encoding_c); jpayne@68: goto bad; jpayne@68: } jpayne@68: Py_DECREF(ascii_chars_u); jpayne@68: Py_DECREF(ascii_chars_b); jpayne@68: } jpayne@68: Py_DECREF(default_encoding); jpayne@68: return 0; jpayne@68: bad: jpayne@68: Py_XDECREF(default_encoding); jpayne@68: Py_XDECREF(ascii_chars_u); jpayne@68: Py_XDECREF(ascii_chars_b); jpayne@68: return -1; jpayne@68: } jpayne@68: #endif jpayne@68: #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) jpayne@68: #else jpayne@68: #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) jpayne@68: #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT jpayne@68: #include jpayne@68: static char* __PYX_DEFAULT_STRING_ENCODING; jpayne@68: static int __Pyx_init_sys_getdefaultencoding_params(void) { jpayne@68: PyObject* sys; jpayne@68: PyObject* default_encoding = NULL; jpayne@68: char* default_encoding_c; jpayne@68: sys = PyImport_ImportModule("sys"); jpayne@68: if (!sys) goto bad; jpayne@68: default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); jpayne@68: Py_DECREF(sys); jpayne@68: if (!default_encoding) goto bad; jpayne@68: default_encoding_c = PyBytes_AsString(default_encoding); jpayne@68: if (!default_encoding_c) goto bad; jpayne@68: __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1); jpayne@68: if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; jpayne@68: strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); jpayne@68: Py_DECREF(default_encoding); jpayne@68: return 0; jpayne@68: bad: jpayne@68: Py_XDECREF(default_encoding); jpayne@68: return -1; jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: /* Test for GCC > 2.95 */ jpayne@68: #if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) jpayne@68: #define likely(x) __builtin_expect(!!(x), 1) jpayne@68: #define unlikely(x) __builtin_expect(!!(x), 0) jpayne@68: #else /* !__GNUC__ or GCC < 2.95 */ jpayne@68: #define likely(x) (x) jpayne@68: #define unlikely(x) (x) jpayne@68: #endif /* __GNUC__ */ jpayne@68: static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } jpayne@68: jpayne@68: #if !CYTHON_USE_MODULE_STATE jpayne@68: static PyObject *__pyx_m = NULL; jpayne@68: #endif jpayne@68: static int __pyx_lineno; jpayne@68: static int __pyx_clineno = 0; jpayne@68: static const char * __pyx_cfilenm = __FILE__; jpayne@68: static const char *__pyx_filename; jpayne@68: jpayne@68: /* #### Code section: filename_table ### */ jpayne@68: jpayne@68: static const char *__pyx_f[] = { jpayne@68: "pysam/libctabix.pyx", jpayne@68: "", jpayne@68: "contextvars.pxd", jpayne@68: "array.pxd", jpayne@68: "pysam/libctabix.pxd", jpayne@68: "type.pxd", jpayne@68: "bool.pxd", jpayne@68: "complex.pxd", jpayne@68: "pysam/libctabixproxies.pxd", jpayne@68: }; jpayne@68: /* #### Code section: utility_code_proto_before_types ### */ jpayne@68: /* ForceInitThreads.proto */ jpayne@68: #ifndef __PYX_FORCE_INIT_THREADS jpayne@68: #define __PYX_FORCE_INIT_THREADS 0 jpayne@68: #endif jpayne@68: jpayne@68: /* NoFastGil.proto */ jpayne@68: #define __Pyx_PyGILState_Ensure PyGILState_Ensure jpayne@68: #define __Pyx_PyGILState_Release PyGILState_Release jpayne@68: #define __Pyx_FastGIL_Remember() jpayne@68: #define __Pyx_FastGIL_Forget() jpayne@68: #define __Pyx_FastGilFuncInit() jpayne@68: jpayne@68: /* #### Code section: numeric_typedefs ### */ jpayne@68: /* #### Code section: complex_type_declarations ### */ jpayne@68: /* #### Code section: type_declarations ### */ jpayne@68: jpayne@68: /*--- Type declarations ---*/ jpayne@68: #ifndef _ARRAYARRAY_H jpayne@68: struct arrayobject; jpayne@68: typedef struct arrayobject arrayobject; jpayne@68: #endif jpayne@68: struct __pyx_obj_5pysam_10libchtslib_HTSFile; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_BedProxy; jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy; jpayne@68: struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser; jpayne@68: struct __pyx_obj_5pysam_9libctabix_asTuple; jpayne@68: struct __pyx_obj_5pysam_9libctabix_asGTF; jpayne@68: struct __pyx_obj_5pysam_9libctabix_asGFF3; jpayne@68: struct __pyx_obj_5pysam_9libctabix_asBed; jpayne@68: struct __pyx_obj_5pysam_9libctabix_asVCF; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorHead; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Tabixfile; jpayne@68: struct __pyx_opt_args_7cpython_11contextvars_get_value; jpayne@68: struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":112 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<< jpayne@68: * """Return a new reference to the value of the context variable, jpayne@68: * or the default value of the context variable, jpayne@68: */ jpayne@68: struct __pyx_opt_args_7cpython_11contextvars_get_value { jpayne@68: int __pyx_n; jpayne@68: PyObject *default_value; jpayne@68: }; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":129 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<< jpayne@68: * """Return a new reference to the value of the context variable, jpayne@68: * or the provided default value if no such value was found. jpayne@68: */ jpayne@68: struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default { jpayne@68: int __pyx_n; jpayne@68: PyObject *default_value; jpayne@68: }; jpayne@68: struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy; jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":23 jpayne@68: * cdef take(self, char * buffer, size_t nbytes) jpayne@68: * cdef present(self, char * buffer, size_t nbytes) jpayne@68: * cdef copy(self, char * buffer, size_t nbytes, bint reset=*) # <<<<<<<<<<<<<< jpayne@68: * cdef update(self, char * buffer, size_t nbytes) jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy { jpayne@68: int __pyx_n; jpayne@68: int reset; jpayne@68: }; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_parse_region; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_str; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_bytes; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_decode_bytes; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":8 jpayne@68: * from cpython cimport array as c_array jpayne@68: * jpayne@68: * cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef int libc_whence_from_io(int whence) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_parse_region { jpayne@68: int __pyx_n; jpayne@68: PyObject *contig; jpayne@68: PyObject *start; jpayne@68: PyObject *stop; jpayne@68: PyObject *region; jpayne@68: PyObject *reference; jpayne@68: PyObject *end; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":15 jpayne@68: * # Utility functions for quality string conversions jpayne@68: * jpayne@68: * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) # <<<<<<<<<<<<<< jpayne@68: * cpdef array_to_qualitystring(c_array.array arr, int offset=*) jpayne@68: * cpdef qualities_to_qualitystring(qualities, int offset=*) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array { jpayne@68: int __pyx_n; jpayne@68: int offset; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":16 jpayne@68: * jpayne@68: * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) jpayne@68: * cpdef array_to_qualitystring(c_array.array arr, int offset=*) # <<<<<<<<<<<<<< jpayne@68: * cpdef qualities_to_qualitystring(qualities, int offset=*) jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring { jpayne@68: int __pyx_n; jpayne@68: int offset; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":17 jpayne@68: * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) jpayne@68: * cpdef array_to_qualitystring(c_array.array arr, int offset=*) jpayne@68: * cpdef qualities_to_qualitystring(qualities, int offset=*) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * ######################################################################## jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring { jpayne@68: int __pyx_n; jpayne@68: int offset; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":29 jpayne@68: * ## Python 3 compatibility functions jpayne@68: * ######################################################################## jpayne@68: * cdef charptr_to_str(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<< jpayne@68: * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) jpayne@68: * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str { jpayne@68: int __pyx_n; jpayne@68: PyObject *encoding; jpayne@68: PyObject *errors; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":30 jpayne@68: * ######################################################################## jpayne@68: * cdef charptr_to_str(const char *s, encoding=*, errors=*) jpayne@68: * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<< jpayne@68: * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) jpayne@68: * cdef force_str(object s, encoding=*, errors=*) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes { jpayne@68: int __pyx_n; jpayne@68: PyObject *encoding; jpayne@68: PyObject *errors; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":31 jpayne@68: * cdef charptr_to_str(const char *s, encoding=*, errors=*) jpayne@68: * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) jpayne@68: * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) # <<<<<<<<<<<<<< jpayne@68: * cdef force_str(object s, encoding=*, errors=*) jpayne@68: * cdef bytes force_bytes(object s, encoding=*, errors=*) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len { jpayne@68: int __pyx_n; jpayne@68: PyObject *encoding; jpayne@68: PyObject *errors; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":32 jpayne@68: * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) jpayne@68: * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) jpayne@68: * cdef force_str(object s, encoding=*, errors=*) # <<<<<<<<<<<<<< jpayne@68: * cdef bytes force_bytes(object s, encoding=*, errors=*) jpayne@68: * cdef decode_bytes(bytes s, encoding=*, errors=*) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_str { jpayne@68: int __pyx_n; jpayne@68: PyObject *encoding; jpayne@68: PyObject *errors; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":33 jpayne@68: * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) jpayne@68: * cdef force_str(object s, encoding=*, errors=*) jpayne@68: * cdef bytes force_bytes(object s, encoding=*, errors=*) # <<<<<<<<<<<<<< jpayne@68: * cdef decode_bytes(bytes s, encoding=*, errors=*) jpayne@68: * cdef bytes encode_filename(object filename) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_bytes { jpayne@68: int __pyx_n; jpayne@68: PyObject *encoding; jpayne@68: PyObject *errors; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libcutils.pxd":34 jpayne@68: * cdef force_str(object s, encoding=*, errors=*) jpayne@68: * cdef bytes force_bytes(object s, encoding=*, errors=*) jpayne@68: * cdef decode_bytes(bytes s, encoding=*, errors=*) # <<<<<<<<<<<<<< jpayne@68: * cdef bytes encode_filename(object filename) jpayne@68: * cdef from_string_and_size(const char *s, size_t length) jpayne@68: */ jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_decode_bytes { jpayne@68: int __pyx_n; jpayne@68: PyObject *encoding; jpayne@68: PyObject *errors; jpayne@68: }; jpayne@68: jpayne@68: /* "pysam/libchtslib.pxd":2706 jpayne@68: * jpayne@68: * jpayne@68: * cdef class HTSFile(object): # <<<<<<<<<<<<<< jpayne@68: * cdef htsFile *htsfile # pointer to htsFile structure jpayne@68: * cdef int64_t start_offset # BGZF offset of first record jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_10libchtslib_HTSFile { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtab; jpayne@68: htsFile *htsfile; jpayne@68: int64_t start_offset; jpayne@68: PyObject *filename; jpayne@68: PyObject *mode; jpayne@68: PyObject *threads; jpayne@68: PyObject *index_filename; jpayne@68: int is_stream; jpayne@68: int is_remote; jpayne@68: int duplicate_filehandle; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":5 jpayne@68: * from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t jpayne@68: * jpayne@68: * cdef class TupleProxy: # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef: jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *__pyx_vtab; jpayne@68: char *data; jpayne@68: char **fields; jpayne@68: int nfields; jpayne@68: int nbytes; jpayne@68: int offset; jpayne@68: int is_modified; jpayne@68: PyObject *encoding; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":27 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TupleProxyIterator: # <<<<<<<<<<<<<< jpayne@68: * cdef TupleProxy proxy jpayne@68: * cdef int index jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *proxy; jpayne@68: int index; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":32 jpayne@68: * jpayne@68: * jpayne@68: * cdef class NamedTupleProxy(TupleProxy): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":36 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GTFProxy(NamedTupleProxy): # <<<<<<<<<<<<<< jpayne@68: * cdef object attribute_dict jpayne@68: * cpdef int getMaxFields(self) jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base; jpayne@68: PyObject *attribute_dict; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":42 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GFF3Proxy(GTFProxy): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":46 jpayne@68: * jpayne@68: * jpayne@68: * cdef class BedProxy(NamedTupleProxy): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef: jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_BedProxy { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base; jpayne@68: char *contig; jpayne@68: uint32_t start; jpayne@68: uint32_t end; jpayne@68: int bedfields; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":58 jpayne@68: * cdef update(self, char * buffer, size_t nbytes) jpayne@68: * jpayne@68: * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef: jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base; jpayne@68: char *contig; jpayne@68: uint32_t pos; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":48 jpayne@68: * jpayne@68: * jpayne@68: * cdef class tabix_file_iterator: # <<<<<<<<<<<<<< jpayne@68: * cdef BGZF * fh jpayne@68: * cdef kstream_t * kstream jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *__pyx_vtab; jpayne@68: BGZF *fh; jpayne@68: kstream_t *kstream; jpayne@68: kstring_t buffer; jpayne@68: size_t size; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *parser; jpayne@68: int fd; jpayne@68: int duplicated_fd; jpayne@68: PyObject *infile; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":61 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TabixFile(HTSFile): # <<<<<<<<<<<<<< jpayne@68: * # pointer to index structure jpayne@68: * cdef tbx_t * index jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile { jpayne@68: struct __pyx_obj_5pysam_10libchtslib_HTSFile __pyx_base; jpayne@68: tbx_t *index; jpayne@68: PyObject *filename_index; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *parser; jpayne@68: PyObject *encoding; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":72 jpayne@68: * jpayne@68: * jpayne@68: * cdef class Parser: # <<<<<<<<<<<<<< jpayne@68: * cdef encoding jpayne@68: * cdef parse(self, char * buffer, int len) jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser *__pyx_vtab; jpayne@68: PyObject *encoding; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":77 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asTuple(Parser): # <<<<<<<<<<<<<< jpayne@68: * cdef parse(self, char * buffer, int len) jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_asTuple { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":81 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asGTF(Parser): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_asGTF { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":85 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asGFF3(Parser): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_asGFF3 { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":89 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asBed(Parser): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_asBed { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":93 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asVCF(Parser): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_asVCF { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":97 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TabixIterator: # <<<<<<<<<<<<<< jpayne@68: * cdef hts_itr_t * iterator jpayne@68: * cdef TabixFile tabixfile jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *__pyx_vtab; jpayne@68: hts_itr_t *iterator; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile *tabixfile; jpayne@68: kstring_t buffer; jpayne@68: PyObject *encoding; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":105 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TabixIteratorParsed(TabixIterator): # <<<<<<<<<<<<<< jpayne@68: * cdef Parser parser jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator __pyx_base; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *parser; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":109 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GZIterator: # <<<<<<<<<<<<<< jpayne@68: * cdef object _filename jpayne@68: * cdef BGZF * gzipfile jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator { jpayne@68: PyObject_HEAD jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *__pyx_vtab; jpayne@68: PyObject *_filename; jpayne@68: BGZF *gzipfile; jpayne@68: kstream_t *kstream; jpayne@68: kstring_t buffer; jpayne@68: PyObject *encoding; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":118 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GZIteratorHead(GZIterator): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorHead { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":122 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GZIteratorParsed(GZIterator): # <<<<<<<<<<<<<< jpayne@68: * cdef Parser parser jpayne@68: * jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator __pyx_base; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *parser; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":127 jpayne@68: * jpayne@68: * # Compatibility Layer for pysam < 0.8 jpayne@68: * cdef class Tabixfile(TabixFile): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: */ jpayne@68: struct __pyx_obj_5pysam_9libctabix_Tabixfile { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile __pyx_base; jpayne@68: }; jpayne@68: jpayne@68: jpayne@68: jpayne@68: /* "pysam/libchtslib.pxd":2706 jpayne@68: * jpayne@68: * jpayne@68: * cdef class HTSFile(object): # <<<<<<<<<<<<<< jpayne@68: * cdef htsFile *htsfile # pointer to htsFile structure jpayne@68: * cdef int64_t start_offset # BGZF offset of first record jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile { jpayne@68: htsFile *(*_open_htsfile)(struct __pyx_obj_5pysam_10libchtslib_HTSFile *); jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtabptr_5pysam_10libchtslib_HTSFile; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":5 jpayne@68: * from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t jpayne@68: * jpayne@68: * cdef class TupleProxy: # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy { jpayne@68: int (*getMaxFields)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, int __pyx_skip_dispatch); jpayne@68: int (*getMinFields)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, int __pyx_skip_dispatch); jpayne@68: PyObject *(*take)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t); jpayne@68: PyObject *(*present)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t); jpayne@68: PyObject *(*copy)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t, struct __pyx_opt_args_5pysam_16libctabixproxies_10TupleProxy_copy *__pyx_optional_args); jpayne@68: PyObject *(*update)(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *, char *, size_t); jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":32 jpayne@68: * jpayne@68: * jpayne@68: * cdef class NamedTupleProxy(TupleProxy): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy { jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy *__pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":36 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GTFProxy(NamedTupleProxy): # <<<<<<<<<<<<<< jpayne@68: * cdef object attribute_dict jpayne@68: * cpdef int getMaxFields(self) jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy { jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy *__pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":42 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GFF3Proxy(GTFProxy): # <<<<<<<<<<<<<< jpayne@68: * pass jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy { jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy *__pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":46 jpayne@68: * jpayne@68: * jpayne@68: * cdef class BedProxy(NamedTupleProxy): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy { jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy *__pyx_vtabptr_5pysam_16libctabixproxies_BedProxy; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabixproxies.pxd":58 jpayne@68: * cdef update(self, char * buffer, size_t nbytes) jpayne@68: * jpayne@68: * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy { jpayne@68: struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy *__pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1098 jpayne@68: * jpayne@68: * jpayne@68: * cdef class tabix_file_iterator: # <<<<<<<<<<<<<< jpayne@68: * '''iterate over a compressed or uncompressed ``infile``. jpayne@68: * ''' jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator { jpayne@68: PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *); jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *__pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":287 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TabixFile: # <<<<<<<<<<<<<< jpayne@68: * """Random access to bgzf formatted files that jpayne@68: * have been indexed by :term:`tabix`. jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile { jpayne@68: struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile *__pyx_vtabptr_5pysam_9libctabix_TabixFile; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":82 jpayne@68: * from pysam.libcutils cimport encode_filename, from_string_and_size jpayne@68: * jpayne@68: * cdef class Parser: # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser { jpayne@68: PyObject *(*parse)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int); jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_Parser *__pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":101 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asTuple(Parser): # <<<<<<<<<<<<<< jpayne@68: * '''converts a :term:`tabix row` into a python tuple. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_asTuple { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asTuple *__pyx_vtabptr_5pysam_9libctabix_asTuple; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":151 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asGTF(Parser): # <<<<<<<<<<<<<< jpayne@68: * '''converts a :term:`tabix row` into a GTF record with the following jpayne@68: * fields: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_asGTF { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asGTF *__pyx_vtabptr_5pysam_9libctabix_asGTF; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":115 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asGFF3(Parser): # <<<<<<<<<<<<<< jpayne@68: * '''converts a :term:`tabix row` into a GFF record with the following jpayne@68: * fields: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 *__pyx_vtabptr_5pysam_9libctabix_asGFF3; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":198 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asBed(Parser): # <<<<<<<<<<<<<< jpayne@68: * '''converts a :term:`tabix row` into a bed record jpayne@68: * with the following fields: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_asBed { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asBed *__pyx_vtabptr_5pysam_9libctabix_asBed; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":246 jpayne@68: * jpayne@68: * jpayne@68: * cdef class asVCF(Parser): # <<<<<<<<<<<<<< jpayne@68: * '''converts a :term:`tabix row` into a VCF record with jpayne@68: * the following fields: jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_asVCF { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asVCF *__pyx_vtabptr_5pysam_9libctabix_asVCF; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":619 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TabixIterator: # <<<<<<<<<<<<<< jpayne@68: * """iterates over rows in *tabixfile* in region jpayne@68: * given by *tid*, *start* and *end*. jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator { jpayne@68: int (*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_TabixIterator *); jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *__pyx_vtabptr_5pysam_9libctabix_TabixIterator; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":692 jpayne@68: * jpayne@68: * jpayne@68: * cdef class TabixIteratorParsed(TabixIterator): # <<<<<<<<<<<<<< jpayne@68: * """iterates over mapped reads in a region. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed *__pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":720 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GZIterator: # <<<<<<<<<<<<<< jpayne@68: * def __init__(self, filename, int buffer_size=65536, encoding="ascii"): jpayne@68: * '''iterate line-by-line through gzip (or bgzip) jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator { jpayne@68: int (*__pyx___cnext__)(struct __pyx_obj_5pysam_9libctabix_GZIterator *); jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *__pyx_vtabptr_5pysam_9libctabix_GZIterator; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":775 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GZIteratorHead(GZIterator): # <<<<<<<<<<<<<< jpayne@68: * '''iterate line-by-line through gzip (or bgzip) jpayne@68: * compressed file returning comments at top of file. jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead *__pyx_vtabptr_5pysam_9libctabix_GZIteratorHead; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":792 jpayne@68: * jpayne@68: * jpayne@68: * cdef class GZIteratorParsed(GZIterator): # <<<<<<<<<<<<<< jpayne@68: * '''iterate line-by-line through gzip (or bgzip) jpayne@68: * compressed file returning comments at top of file. jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed *__pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed; jpayne@68: jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1251 jpayne@68: * jpayne@68: * jpayne@68: * cdef class Tabixfile(TabixFile): # <<<<<<<<<<<<<< jpayne@68: * """Tabixfile is deprecated: use TabixFile instead""" jpayne@68: * pass jpayne@68: */ jpayne@68: jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile { jpayne@68: struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile __pyx_base; jpayne@68: }; jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile *__pyx_vtabptr_5pysam_9libctabix_Tabixfile; jpayne@68: /* #### Code section: utility_code_proto ### */ jpayne@68: jpayne@68: /* --- Runtime support code (head) --- */ jpayne@68: /* Refnanny.proto */ jpayne@68: #ifndef CYTHON_REFNANNY jpayne@68: #define CYTHON_REFNANNY 0 jpayne@68: #endif jpayne@68: #if CYTHON_REFNANNY jpayne@68: typedef struct { jpayne@68: void (*INCREF)(void*, PyObject*, Py_ssize_t); jpayne@68: void (*DECREF)(void*, PyObject*, Py_ssize_t); jpayne@68: void (*GOTREF)(void*, PyObject*, Py_ssize_t); jpayne@68: void (*GIVEREF)(void*, PyObject*, Py_ssize_t); jpayne@68: void* (*SetupContext)(const char*, Py_ssize_t, const char*); jpayne@68: void (*FinishContext)(void**); jpayne@68: } __Pyx_RefNannyAPIStruct; jpayne@68: static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; jpayne@68: static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); jpayne@68: #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; jpayne@68: #ifdef WITH_THREAD jpayne@68: #define __Pyx_RefNannySetupContext(name, acquire_gil)\ jpayne@68: if (acquire_gil) {\ jpayne@68: PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ jpayne@68: __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\ jpayne@68: PyGILState_Release(__pyx_gilstate_save);\ jpayne@68: } else {\ jpayne@68: __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\ jpayne@68: } jpayne@68: #define __Pyx_RefNannyFinishContextNogil() {\ jpayne@68: PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ jpayne@68: __Pyx_RefNannyFinishContext();\ jpayne@68: PyGILState_Release(__pyx_gilstate_save);\ jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_RefNannySetupContext(name, acquire_gil)\ jpayne@68: __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__)) jpayne@68: #define __Pyx_RefNannyFinishContextNogil() __Pyx_RefNannyFinishContext() jpayne@68: #endif jpayne@68: #define __Pyx_RefNannyFinishContextNogil() {\ jpayne@68: PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ jpayne@68: __Pyx_RefNannyFinishContext();\ jpayne@68: PyGILState_Release(__pyx_gilstate_save);\ jpayne@68: } jpayne@68: #define __Pyx_RefNannyFinishContext()\ jpayne@68: __Pyx_RefNanny->FinishContext(&__pyx_refnanny) jpayne@68: #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) jpayne@68: #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) jpayne@68: #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) jpayne@68: #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) jpayne@68: #define __Pyx_XINCREF(r) do { if((r) == NULL); else {__Pyx_INCREF(r); }} while(0) jpayne@68: #define __Pyx_XDECREF(r) do { if((r) == NULL); else {__Pyx_DECREF(r); }} while(0) jpayne@68: #define __Pyx_XGOTREF(r) do { if((r) == NULL); else {__Pyx_GOTREF(r); }} while(0) jpayne@68: #define __Pyx_XGIVEREF(r) do { if((r) == NULL); else {__Pyx_GIVEREF(r);}} while(0) jpayne@68: #else jpayne@68: #define __Pyx_RefNannyDeclarations jpayne@68: #define __Pyx_RefNannySetupContext(name, acquire_gil) jpayne@68: #define __Pyx_RefNannyFinishContextNogil() jpayne@68: #define __Pyx_RefNannyFinishContext() jpayne@68: #define __Pyx_INCREF(r) Py_INCREF(r) jpayne@68: #define __Pyx_DECREF(r) Py_DECREF(r) jpayne@68: #define __Pyx_GOTREF(r) jpayne@68: #define __Pyx_GIVEREF(r) jpayne@68: #define __Pyx_XINCREF(r) Py_XINCREF(r) jpayne@68: #define __Pyx_XDECREF(r) Py_XDECREF(r) jpayne@68: #define __Pyx_XGOTREF(r) jpayne@68: #define __Pyx_XGIVEREF(r) jpayne@68: #endif jpayne@68: #define __Pyx_Py_XDECREF_SET(r, v) do {\ jpayne@68: PyObject *tmp = (PyObject *) r;\ jpayne@68: r = v; Py_XDECREF(tmp);\ jpayne@68: } while (0) jpayne@68: #define __Pyx_XDECREF_SET(r, v) do {\ jpayne@68: PyObject *tmp = (PyObject *) r;\ jpayne@68: r = v; __Pyx_XDECREF(tmp);\ jpayne@68: } while (0) jpayne@68: #define __Pyx_DECREF_SET(r, v) do {\ jpayne@68: PyObject *tmp = (PyObject *) r;\ jpayne@68: r = v; __Pyx_DECREF(tmp);\ jpayne@68: } while (0) jpayne@68: #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) jpayne@68: #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) jpayne@68: jpayne@68: /* PyErrExceptionMatches.proto */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: #define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) jpayne@68: static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); jpayne@68: #else jpayne@68: #define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) jpayne@68: #endif jpayne@68: jpayne@68: /* PyThreadStateGet.proto */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: #define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; jpayne@68: #define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; jpayne@68: #if PY_VERSION_HEX >= 0x030C00A6 jpayne@68: #define __Pyx_PyErr_Occurred() (__pyx_tstate->current_exception != NULL) jpayne@68: #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->current_exception ? (PyObject*) Py_TYPE(__pyx_tstate->current_exception) : (PyObject*) NULL) jpayne@68: #else jpayne@68: #define __Pyx_PyErr_Occurred() (__pyx_tstate->curexc_type != NULL) jpayne@68: #define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->curexc_type) jpayne@68: #endif jpayne@68: #else jpayne@68: #define __Pyx_PyThreadState_declare jpayne@68: #define __Pyx_PyThreadState_assign jpayne@68: #define __Pyx_PyErr_Occurred() (PyErr_Occurred() != NULL) jpayne@68: #define __Pyx_PyErr_CurrentExceptionType() PyErr_Occurred() jpayne@68: #endif jpayne@68: jpayne@68: /* PyErrFetchRestore.proto */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: #define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) jpayne@68: #define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) jpayne@68: #define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) jpayne@68: #define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) jpayne@68: #define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) jpayne@68: static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); jpayne@68: static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A6 jpayne@68: #define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) jpayne@68: #else jpayne@68: #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) jpayne@68: #endif jpayne@68: #else jpayne@68: #define __Pyx_PyErr_Clear() PyErr_Clear() jpayne@68: #define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) jpayne@68: #define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) jpayne@68: #define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) jpayne@68: #define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) jpayne@68: #define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) jpayne@68: #define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) jpayne@68: #define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectGetAttrStr.proto */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name); jpayne@68: #else jpayne@68: #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectGetAttrStrNoError.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); jpayne@68: jpayne@68: /* GetBuiltinName.proto */ jpayne@68: static PyObject *__Pyx_GetBuiltinName(PyObject *name); jpayne@68: jpayne@68: /* TupleAndListFromArray.proto */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n); jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n); jpayne@68: #endif jpayne@68: jpayne@68: /* IncludeStringH.proto */ jpayne@68: #include jpayne@68: jpayne@68: /* BytesEquals.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); jpayne@68: jpayne@68: /* UnicodeEquals.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); jpayne@68: jpayne@68: /* fastcall.proto */ jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: #define __Pyx_Arg_VARARGS(args, i) PySequence_GetItem(args, i) jpayne@68: #elif CYTHON_ASSUME_SAFE_MACROS jpayne@68: #define __Pyx_Arg_VARARGS(args, i) PyTuple_GET_ITEM(args, i) jpayne@68: #else jpayne@68: #define __Pyx_Arg_VARARGS(args, i) PyTuple_GetItem(args, i) jpayne@68: #endif jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg) jpayne@68: #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg) jpayne@68: #else jpayne@68: #define __Pyx_Arg_NewRef_VARARGS(arg) arg jpayne@68: #define __Pyx_Arg_XDECREF_VARARGS(arg) jpayne@68: #endif jpayne@68: #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds) jpayne@68: #define __Pyx_KwValues_VARARGS(args, nargs) NULL jpayne@68: #define __Pyx_GetKwValue_VARARGS(kw, kwvalues, s) __Pyx_PyDict_GetItemStrWithError(kw, s) jpayne@68: #define __Pyx_KwargsAsDict_VARARGS(kw, kwvalues) PyDict_Copy(kw) jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: #define __Pyx_Arg_FASTCALL(args, i) args[i] jpayne@68: #define __Pyx_NumKwargs_FASTCALL(kwds) PyTuple_GET_SIZE(kwds) jpayne@68: #define __Pyx_KwValues_FASTCALL(args, nargs) ((args) + (nargs)) jpayne@68: static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000 jpayne@68: CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues); jpayne@68: #else jpayne@68: #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw) jpayne@68: #endif jpayne@68: #define __Pyx_Arg_NewRef_FASTCALL(arg) arg /* no-op, __Pyx_Arg_FASTCALL is direct and this needs jpayne@68: to have the same reference counting */ jpayne@68: #define __Pyx_Arg_XDECREF_FASTCALL(arg) jpayne@68: #else jpayne@68: #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS jpayne@68: #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS jpayne@68: #define __Pyx_KwValues_FASTCALL __Pyx_KwValues_VARARGS jpayne@68: #define __Pyx_GetKwValue_FASTCALL __Pyx_GetKwValue_VARARGS jpayne@68: #define __Pyx_KwargsAsDict_FASTCALL __Pyx_KwargsAsDict_VARARGS jpayne@68: #define __Pyx_Arg_NewRef_FASTCALL(arg) __Pyx_Arg_NewRef_VARARGS(arg) jpayne@68: #define __Pyx_Arg_XDECREF_FASTCALL(arg) __Pyx_Arg_XDECREF_VARARGS(arg) jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: #define __Pyx_ArgsSlice_VARARGS(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_VARARGS(args, start), stop - start) jpayne@68: #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_FASTCALL(args, start), stop - start) jpayne@68: #else jpayne@68: #define __Pyx_ArgsSlice_VARARGS(args, start, stop) PyTuple_GetSlice(args, start, stop) jpayne@68: #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) PyTuple_GetSlice(args, start, stop) jpayne@68: #endif jpayne@68: jpayne@68: /* RaiseDoubleKeywords.proto */ jpayne@68: static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); jpayne@68: jpayne@68: /* ParseKeywords.proto */ jpayne@68: static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject *const *kwvalues, jpayne@68: PyObject **argnames[], jpayne@68: PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, jpayne@68: const char* function_name); jpayne@68: jpayne@68: /* RaiseArgTupleInvalid.proto */ jpayne@68: static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, jpayne@68: Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); jpayne@68: jpayne@68: /* Profile.proto */ jpayne@68: #ifndef CYTHON_PROFILE jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY jpayne@68: #define CYTHON_PROFILE 0 jpayne@68: #else jpayne@68: #define CYTHON_PROFILE 1 jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_TRACE_NOGIL jpayne@68: #define CYTHON_TRACE_NOGIL 0 jpayne@68: #else jpayne@68: #if CYTHON_TRACE_NOGIL && !defined(CYTHON_TRACE) jpayne@68: #define CYTHON_TRACE 1 jpayne@68: #endif jpayne@68: #endif jpayne@68: #ifndef CYTHON_TRACE jpayne@68: #define CYTHON_TRACE 0 jpayne@68: #endif jpayne@68: #if CYTHON_TRACE jpayne@68: #undef CYTHON_PROFILE_REUSE_FRAME jpayne@68: #endif jpayne@68: #ifndef CYTHON_PROFILE_REUSE_FRAME jpayne@68: #define CYTHON_PROFILE_REUSE_FRAME 0 jpayne@68: #endif jpayne@68: #if CYTHON_PROFILE || CYTHON_TRACE jpayne@68: #include "compile.h" jpayne@68: #include "frameobject.h" jpayne@68: #include "traceback.h" jpayne@68: #if PY_VERSION_HEX >= 0x030b00a6 jpayne@68: #ifndef Py_BUILD_CORE jpayne@68: #define Py_BUILD_CORE 1 jpayne@68: #endif jpayne@68: #include "internal/pycore_frame.h" jpayne@68: #endif jpayne@68: #if CYTHON_PROFILE_REUSE_FRAME jpayne@68: #define CYTHON_FRAME_MODIFIER static jpayne@68: #define CYTHON_FRAME_DEL(frame) jpayne@68: #else jpayne@68: #define CYTHON_FRAME_MODIFIER jpayne@68: #define CYTHON_FRAME_DEL(frame) Py_CLEAR(frame) jpayne@68: #endif jpayne@68: #define __Pyx_TraceDeclarations\ jpayne@68: static PyCodeObject *__pyx_frame_code = NULL;\ jpayne@68: CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL;\ jpayne@68: int __Pyx_use_tracing = 0; jpayne@68: #define __Pyx_TraceFrameInit(codeobj)\ jpayne@68: if (codeobj) __pyx_frame_code = (PyCodeObject*) codeobj; jpayne@68: #if PY_VERSION_HEX >= 0x030b00a2 jpayne@68: #if PY_VERSION_HEX >= 0x030C00b1 jpayne@68: #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ jpayne@68: ((!(check_tracing) || !(tstate)->tracing) &&\ jpayne@68: (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) jpayne@68: #else jpayne@68: #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ jpayne@68: (unlikely((tstate)->cframe->use_tracing) &&\ jpayne@68: (!(check_tracing) || !(tstate)->tracing) &&\ jpayne@68: (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) jpayne@68: #endif jpayne@68: #define __Pyx_EnterTracing(tstate) PyThreadState_EnterTracing(tstate) jpayne@68: #define __Pyx_LeaveTracing(tstate) PyThreadState_LeaveTracing(tstate) jpayne@68: #elif PY_VERSION_HEX >= 0x030a00b1 jpayne@68: #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ jpayne@68: (unlikely((tstate)->cframe->use_tracing) &&\ jpayne@68: (!(check_tracing) || !(tstate)->tracing) &&\ jpayne@68: (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) jpayne@68: #define __Pyx_EnterTracing(tstate)\ jpayne@68: do { tstate->tracing++; tstate->cframe->use_tracing = 0; } while (0) jpayne@68: #define __Pyx_LeaveTracing(tstate)\ jpayne@68: do {\ jpayne@68: tstate->tracing--;\ jpayne@68: tstate->cframe->use_tracing = ((CYTHON_TRACE && tstate->c_tracefunc != NULL)\ jpayne@68: || tstate->c_profilefunc != NULL);\ jpayne@68: } while (0) jpayne@68: #else jpayne@68: #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ jpayne@68: (unlikely((tstate)->use_tracing) &&\ jpayne@68: (!(check_tracing) || !(tstate)->tracing) &&\ jpayne@68: (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) jpayne@68: #define __Pyx_EnterTracing(tstate)\ jpayne@68: do { tstate->tracing++; tstate->use_tracing = 0; } while (0) jpayne@68: #define __Pyx_LeaveTracing(tstate)\ jpayne@68: do {\ jpayne@68: tstate->tracing--;\ jpayne@68: tstate->use_tracing = ((CYTHON_TRACE && tstate->c_tracefunc != NULL)\ jpayne@68: || tstate->c_profilefunc != NULL);\ jpayne@68: } while (0) jpayne@68: #endif jpayne@68: #ifdef WITH_THREAD jpayne@68: #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\ jpayne@68: if (nogil) {\ jpayne@68: if (CYTHON_TRACE_NOGIL) {\ jpayne@68: PyThreadState *tstate;\ jpayne@68: PyGILState_STATE state = PyGILState_Ensure();\ jpayne@68: tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 1, 1)) {\ jpayne@68: __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\ jpayne@68: }\ jpayne@68: PyGILState_Release(state);\ jpayne@68: if (unlikely(__Pyx_use_tracing < 0)) goto_error;\ jpayne@68: }\ jpayne@68: } else {\ jpayne@68: PyThreadState* tstate = PyThreadState_GET();\ jpayne@68: if (__Pyx_IsTracing(tstate, 1, 1)) {\ jpayne@68: __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\ jpayne@68: if (unlikely(__Pyx_use_tracing < 0)) goto_error;\ jpayne@68: }\ jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\ jpayne@68: { PyThreadState* tstate = PyThreadState_GET();\ jpayne@68: if (__Pyx_IsTracing(tstate, 1, 1)) {\ jpayne@68: __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\ jpayne@68: if (unlikely(__Pyx_use_tracing < 0)) goto_error;\ jpayne@68: }\ jpayne@68: } jpayne@68: #endif jpayne@68: #define __Pyx_TraceException()\ jpayne@68: if (likely(!__Pyx_use_tracing)); else {\ jpayne@68: PyThreadState* tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 1)) {\ jpayne@68: __Pyx_EnterTracing(tstate);\ jpayne@68: PyObject *exc_info = __Pyx_GetExceptionTuple(tstate);\ jpayne@68: if (exc_info) {\ jpayne@68: if (CYTHON_TRACE && tstate->c_tracefunc)\ jpayne@68: tstate->c_tracefunc(\ jpayne@68: tstate->c_traceobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\ jpayne@68: tstate->c_profilefunc(\ jpayne@68: tstate->c_profileobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\ jpayne@68: Py_DECREF(exc_info);\ jpayne@68: }\ jpayne@68: __Pyx_LeaveTracing(tstate);\ jpayne@68: }\ jpayne@68: } jpayne@68: static void __Pyx_call_return_trace_func(PyThreadState *tstate, PyFrameObject *frame, PyObject *result) { jpayne@68: PyObject *type, *value, *traceback; jpayne@68: __Pyx_ErrFetchInState(tstate, &type, &value, &traceback); jpayne@68: __Pyx_EnterTracing(tstate); jpayne@68: if (CYTHON_TRACE && tstate->c_tracefunc) jpayne@68: tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_RETURN, result); jpayne@68: if (tstate->c_profilefunc) jpayne@68: tstate->c_profilefunc(tstate->c_profileobj, frame, PyTrace_RETURN, result); jpayne@68: CYTHON_FRAME_DEL(frame); jpayne@68: __Pyx_LeaveTracing(tstate); jpayne@68: __Pyx_ErrRestoreInState(tstate, type, value, traceback); jpayne@68: } jpayne@68: #ifdef WITH_THREAD jpayne@68: #define __Pyx_TraceReturn(result, nogil)\ jpayne@68: if (likely(!__Pyx_use_tracing)); else {\ jpayne@68: if (nogil) {\ jpayne@68: if (CYTHON_TRACE_NOGIL) {\ jpayne@68: PyThreadState *tstate;\ jpayne@68: PyGILState_STATE state = PyGILState_Ensure();\ jpayne@68: tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 0)) {\ jpayne@68: __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\ jpayne@68: }\ jpayne@68: PyGILState_Release(state);\ jpayne@68: }\ jpayne@68: } else {\ jpayne@68: PyThreadState* tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 0)) {\ jpayne@68: __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\ jpayne@68: }\ jpayne@68: }\ jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_TraceReturn(result, nogil)\ jpayne@68: if (likely(!__Pyx_use_tracing)); else {\ jpayne@68: PyThreadState* tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 0)) {\ jpayne@68: __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\ jpayne@68: }\ jpayne@68: } jpayne@68: #endif jpayne@68: static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); jpayne@68: static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, PyThreadState* tstate, const char *funcname, const char *srcfile, int firstlineno); jpayne@68: #else jpayne@68: #define __Pyx_TraceDeclarations jpayne@68: #define __Pyx_TraceFrameInit(codeobj) jpayne@68: #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error) if ((1)); else goto_error; jpayne@68: #define __Pyx_TraceException() jpayne@68: #define __Pyx_TraceReturn(result, nogil) jpayne@68: #endif jpayne@68: #if CYTHON_TRACE jpayne@68: static int __Pyx_call_line_trace_func(PyThreadState *tstate, PyFrameObject *frame, int lineno) { jpayne@68: int ret; jpayne@68: PyObject *type, *value, *traceback; jpayne@68: __Pyx_ErrFetchInState(tstate, &type, &value, &traceback); jpayne@68: __Pyx_PyFrame_SetLineNumber(frame, lineno); jpayne@68: __Pyx_EnterTracing(tstate); jpayne@68: ret = tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_LINE, NULL); jpayne@68: __Pyx_LeaveTracing(tstate); jpayne@68: if (likely(!ret)) { jpayne@68: __Pyx_ErrRestoreInState(tstate, type, value, traceback); jpayne@68: } else { jpayne@68: Py_XDECREF(type); jpayne@68: Py_XDECREF(value); jpayne@68: Py_XDECREF(traceback); jpayne@68: } jpayne@68: return ret; jpayne@68: } jpayne@68: #ifdef WITH_THREAD jpayne@68: #define __Pyx_TraceLine(lineno, nogil, goto_error)\ jpayne@68: if (likely(!__Pyx_use_tracing)); else {\ jpayne@68: if (nogil) {\ jpayne@68: if (CYTHON_TRACE_NOGIL) {\ jpayne@68: int ret = 0;\ jpayne@68: PyThreadState *tstate;\ jpayne@68: PyGILState_STATE state = __Pyx_PyGILState_Ensure();\ jpayne@68: tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\ jpayne@68: ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\ jpayne@68: }\ jpayne@68: __Pyx_PyGILState_Release(state);\ jpayne@68: if (unlikely(ret)) goto_error;\ jpayne@68: }\ jpayne@68: } else {\ jpayne@68: PyThreadState* tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\ jpayne@68: int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\ jpayne@68: if (unlikely(ret)) goto_error;\ jpayne@68: }\ jpayne@68: }\ jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_TraceLine(lineno, nogil, goto_error)\ jpayne@68: if (likely(!__Pyx_use_tracing)); else {\ jpayne@68: PyThreadState* tstate = __Pyx_PyThreadState_Current;\ jpayne@68: if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\ jpayne@68: int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\ jpayne@68: if (unlikely(ret)) goto_error;\ jpayne@68: }\ jpayne@68: } jpayne@68: #endif jpayne@68: #else jpayne@68: #define __Pyx_TraceLine(lineno, nogil, goto_error) if ((1)); else goto_error; jpayne@68: #endif jpayne@68: jpayne@68: /* KeywordStringCheck.proto */ jpayne@68: static int __Pyx_CheckKeywordStrings(PyObject *kw, const char* function_name, int kw_allowed); jpayne@68: jpayne@68: /* PyObject_Unicode.proto */ jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyObject_Unicode(obj)\ jpayne@68: (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj)) jpayne@68: #else jpayne@68: #define __Pyx_PyObject_Unicode(obj)\ jpayne@68: (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Unicode(obj)) jpayne@68: #endif jpayne@68: jpayne@68: /* PyFunctionFastCall.proto */ jpayne@68: #if CYTHON_FAST_PYCALL jpayne@68: #if !CYTHON_VECTORCALL jpayne@68: #define __Pyx_PyFunction_FastCall(func, args, nargs)\ jpayne@68: __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) jpayne@68: static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); jpayne@68: #endif jpayne@68: #define __Pyx_BUILD_ASSERT_EXPR(cond)\ jpayne@68: (sizeof(char [1 - 2*!(cond)]) - 1) jpayne@68: #ifndef Py_MEMBER_SIZE jpayne@68: #define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) jpayne@68: #endif jpayne@68: #if !CYTHON_VECTORCALL jpayne@68: #if PY_VERSION_HEX >= 0x03080000 jpayne@68: #include "frameobject.h" jpayne@68: #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #ifndef Py_BUILD_CORE jpayne@68: #define Py_BUILD_CORE 1 jpayne@68: #endif jpayne@68: #include "internal/pycore_frame.h" jpayne@68: #endif jpayne@68: #define __Pxy_PyFrame_Initialize_Offsets() jpayne@68: #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus) jpayne@68: #else jpayne@68: static size_t __pyx_pyframe_localsplus_offset = 0; jpayne@68: #include "frameobject.h" jpayne@68: #define __Pxy_PyFrame_Initialize_Offsets()\ jpayne@68: ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ jpayne@68: (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) jpayne@68: #define __Pyx_PyFrame_GetLocalsplus(frame)\ jpayne@68: (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectCall.proto */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); jpayne@68: #else jpayne@68: #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectCallMethO.proto */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectFastCall.proto */ jpayne@68: #define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL) jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs); jpayne@68: jpayne@68: /* PyObjectCallOneArg.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); jpayne@68: jpayne@68: /* RaiseException.proto */ jpayne@68: static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); jpayne@68: jpayne@68: /* GetAttr3.proto */ jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); jpayne@68: jpayne@68: /* PyDictVersioning.proto */ jpayne@68: #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS jpayne@68: #define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1) jpayne@68: #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) jpayne@68: #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\ jpayne@68: (version_var) = __PYX_GET_DICT_VERSION(dict);\ jpayne@68: (cache_var) = (value); jpayne@68: #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\ jpayne@68: static PY_UINT64_T __pyx_dict_version = 0;\ jpayne@68: static PyObject *__pyx_dict_cached_value = NULL;\ jpayne@68: if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ jpayne@68: (VAR) = __pyx_dict_cached_value;\ jpayne@68: } else {\ jpayne@68: (VAR) = __pyx_dict_cached_value = (LOOKUP);\ jpayne@68: __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ jpayne@68: }\ jpayne@68: } jpayne@68: static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj); jpayne@68: static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj); jpayne@68: static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version); jpayne@68: #else jpayne@68: #define __PYX_GET_DICT_VERSION(dict) (0) jpayne@68: #define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var) jpayne@68: #define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP); jpayne@68: #endif jpayne@68: jpayne@68: /* GetModuleGlobalName.proto */ jpayne@68: #if CYTHON_USE_DICT_VERSIONS jpayne@68: #define __Pyx_GetModuleGlobalName(var, name) do {\ jpayne@68: static PY_UINT64_T __pyx_dict_version = 0;\ jpayne@68: static PyObject *__pyx_dict_cached_value = NULL;\ jpayne@68: (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ jpayne@68: (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\ jpayne@68: __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ jpayne@68: } while(0) jpayne@68: #define __Pyx_GetModuleGlobalNameUncached(var, name) do {\ jpayne@68: PY_UINT64_T __pyx_dict_version;\ jpayne@68: PyObject *__pyx_dict_cached_value;\ jpayne@68: (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ jpayne@68: } while(0) jpayne@68: static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value); jpayne@68: #else jpayne@68: #define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name) jpayne@68: #define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name) jpayne@68: static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); jpayne@68: #endif jpayne@68: jpayne@68: /* RaiseUnexpectedTypeError.proto */ jpayne@68: static int __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj); jpayne@68: jpayne@68: /* ExtTypeTest.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); jpayne@68: jpayne@68: /* PyIntBinop.proto */ jpayne@68: #if !CYTHON_COMPILING_IN_PYPY jpayne@68: static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); jpayne@68: #else jpayne@68: #define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ jpayne@68: (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) jpayne@68: #endif jpayne@68: jpayne@68: /* ListAppend.proto */ jpayne@68: #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS jpayne@68: static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { jpayne@68: PyListObject* L = (PyListObject*) list; jpayne@68: Py_ssize_t len = Py_SIZE(list); jpayne@68: if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { jpayne@68: Py_INCREF(x); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000 jpayne@68: L->ob_item[len] = x; jpayne@68: #else jpayne@68: PyList_SET_ITEM(list, len, x); jpayne@68: #endif jpayne@68: __Pyx_SET_SIZE(list, len + 1); jpayne@68: return 0; jpayne@68: } jpayne@68: return PyList_Append(list, x); jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_PyList_Append(L,x) PyList_Append(L,x) jpayne@68: #endif jpayne@68: jpayne@68: /* WriteUnraisableException.proto */ jpayne@68: static void __Pyx_WriteUnraisable(const char *name, int clineno, jpayne@68: int lineno, const char *filename, jpayne@68: int full_traceback, int nogil); jpayne@68: jpayne@68: /* PyObjectCallNoArg.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); jpayne@68: jpayne@68: /* ArgTypeTest.proto */ jpayne@68: #define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ jpayne@68: ((likely(__Pyx_IS_TYPE(obj, type) | (none_allowed && (obj == Py_None)))) ? 1 :\ jpayne@68: __Pyx__ArgTypeTest(obj, type, name, exact)) jpayne@68: static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); jpayne@68: jpayne@68: /* PyObjectFormatAndDecref.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f); jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f); jpayne@68: jpayne@68: /* JoinPyUnicode.proto */ jpayne@68: static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength, jpayne@68: Py_UCS4 max_char); jpayne@68: jpayne@68: /* DictGetItem.proto */ jpayne@68: #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY jpayne@68: static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key); jpayne@68: #define __Pyx_PyObject_Dict_GetItem(obj, name)\ jpayne@68: (likely(PyDict_CheckExact(obj)) ?\ jpayne@68: __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name)) jpayne@68: #else jpayne@68: #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) jpayne@68: #define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name) jpayne@68: #endif jpayne@68: jpayne@68: /* GetTopmostException.proto */ jpayne@68: #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE jpayne@68: static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); jpayne@68: #endif jpayne@68: jpayne@68: /* SaveResetException.proto */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: #define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) jpayne@68: static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); jpayne@68: #define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) jpayne@68: static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); jpayne@68: #else jpayne@68: #define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) jpayne@68: #define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) jpayne@68: #endif jpayne@68: jpayne@68: /* GetException.proto */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: #define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) jpayne@68: static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); jpayne@68: #else jpayne@68: static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); jpayne@68: #endif jpayne@68: jpayne@68: /* py_dict_keys.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d); jpayne@68: jpayne@68: /* UnpackUnboundCMethod.proto */ jpayne@68: typedef struct { jpayne@68: PyObject *type; jpayne@68: PyObject **method_name; jpayne@68: PyCFunction func; jpayne@68: PyObject *method; jpayne@68: int flag; jpayne@68: } __Pyx_CachedCFunction; jpayne@68: jpayne@68: /* CallUnboundCMethod0.proto */ jpayne@68: static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: #define __Pyx_CallUnboundCMethod0(cfunc, self)\ jpayne@68: (likely((cfunc)->func) ?\ jpayne@68: (likely((cfunc)->flag == METH_NOARGS) ? (*((cfunc)->func))(self, NULL) :\ jpayne@68: (PY_VERSION_HEX >= 0x030600B1 && likely((cfunc)->flag == METH_FASTCALL) ?\ jpayne@68: (PY_VERSION_HEX >= 0x030700A0 ?\ jpayne@68: (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0) :\ jpayne@68: (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0, NULL)) :\ jpayne@68: (PY_VERSION_HEX >= 0x030700A0 && (cfunc)->flag == (METH_FASTCALL | METH_KEYWORDS) ?\ jpayne@68: (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0, NULL) :\ jpayne@68: (likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ? ((*(PyCFunctionWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\ jpayne@68: ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) :\ jpayne@68: __Pyx__CallUnboundCMethod0(cfunc, self)))))) :\ jpayne@68: __Pyx__CallUnboundCMethod0(cfunc, self)) jpayne@68: #else jpayne@68: #define __Pyx_CallUnboundCMethod0(cfunc, self) __Pyx__CallUnboundCMethod0(cfunc, self) jpayne@68: #endif jpayne@68: jpayne@68: /* UnicodeAsUCS4.proto */ jpayne@68: static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject*); jpayne@68: jpayne@68: /* object_ord.proto */ jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #define __Pyx_PyObject_Ord(c)\ jpayne@68: (likely(PyUnicode_Check(c)) ? (long)__Pyx_PyUnicode_AsPy_UCS4(c) : __Pyx__PyObject_Ord(c)) jpayne@68: #else jpayne@68: #define __Pyx_PyObject_Ord(c) __Pyx__PyObject_Ord(c) jpayne@68: #endif jpayne@68: static long __Pyx__PyObject_Ord(PyObject* c); jpayne@68: jpayne@68: /* RaiseTooManyValuesToUnpack.proto */ jpayne@68: static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); jpayne@68: jpayne@68: /* RaiseNeedMoreValuesToUnpack.proto */ jpayne@68: static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); jpayne@68: jpayne@68: /* IterFinish.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_IterFinish(void); jpayne@68: jpayne@68: /* UnpackItemEndCheck.proto */ jpayne@68: static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); jpayne@68: jpayne@68: /* PyObjectSetAttrStr.proto */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: #define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL) jpayne@68: static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value); jpayne@68: #else jpayne@68: #define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) jpayne@68: #define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) jpayne@68: #endif jpayne@68: jpayne@68: /* AssertionsEnabled.proto */ jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) jpayne@68: #define __Pyx_init_assertions_enabled() (0) jpayne@68: #define __pyx_assertions_enabled() (1) jpayne@68: #elif CYTHON_COMPILING_IN_LIMITED_API || (CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030C0000) jpayne@68: static int __pyx_assertions_enabled_flag; jpayne@68: #define __pyx_assertions_enabled() (__pyx_assertions_enabled_flag) jpayne@68: static int __Pyx_init_assertions_enabled(void) { jpayne@68: PyObject *builtins, *debug, *debug_str; jpayne@68: int flag; jpayne@68: builtins = PyEval_GetBuiltins(); jpayne@68: if (!builtins) goto bad; jpayne@68: debug_str = PyUnicode_FromStringAndSize("__debug__", 9); jpayne@68: if (!debug_str) goto bad; jpayne@68: debug = PyObject_GetItem(builtins, debug_str); jpayne@68: Py_DECREF(debug_str); jpayne@68: if (!debug) goto bad; jpayne@68: flag = PyObject_IsTrue(debug); jpayne@68: Py_DECREF(debug); jpayne@68: if (flag == -1) goto bad; jpayne@68: __pyx_assertions_enabled_flag = flag; jpayne@68: return 0; jpayne@68: bad: jpayne@68: __pyx_assertions_enabled_flag = 1; jpayne@68: return -1; jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_init_assertions_enabled() (0) jpayne@68: #define __pyx_assertions_enabled() (!Py_OptimizeFlag) jpayne@68: #endif jpayne@68: jpayne@68: /* PySequenceContains.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { jpayne@68: int result = PySequence_Contains(seq, item); jpayne@68: return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); jpayne@68: } jpayne@68: jpayne@68: /* Import.proto */ jpayne@68: static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); jpayne@68: jpayne@68: /* ImportFrom.proto */ jpayne@68: static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); jpayne@68: jpayne@68: /* GetItemInt.proto */ jpayne@68: #define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ jpayne@68: (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ jpayne@68: __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ jpayne@68: (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ jpayne@68: __Pyx_GetItemInt_Generic(o, to_py_func(i)))) jpayne@68: #define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ jpayne@68: (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ jpayne@68: __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ jpayne@68: (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, jpayne@68: int wraparound, int boundscheck); jpayne@68: #define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ jpayne@68: (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ jpayne@68: __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ jpayne@68: (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, jpayne@68: int wraparound, int boundscheck); jpayne@68: static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, jpayne@68: int is_list, int wraparound, int boundscheck); jpayne@68: jpayne@68: /* GetAttr.proto */ jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); jpayne@68: jpayne@68: /* HasAttr.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); jpayne@68: jpayne@68: /* CallNextTpDealloc.proto */ jpayne@68: static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc); jpayne@68: jpayne@68: /* CallNextTpTraverse.proto */ jpayne@68: static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); jpayne@68: jpayne@68: /* CallNextTpClear.proto */ jpayne@68: static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear); jpayne@68: jpayne@68: /* IncludeStructmemberH.proto */ jpayne@68: #include jpayne@68: jpayne@68: /* FixUpExtensionType.proto */ jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type); jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectGetMethod.proto */ jpayne@68: static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method); jpayne@68: jpayne@68: /* PyObjectCallMethod0.proto */ jpayne@68: static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); jpayne@68: jpayne@68: /* ValidateBasesTuple.proto */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS jpayne@68: static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases); jpayne@68: #endif jpayne@68: jpayne@68: /* PyType_Ready.proto */ jpayne@68: CYTHON_UNUSED static int __Pyx_PyType_Ready(PyTypeObject *t); jpayne@68: jpayne@68: /* PyObject_GenericGetAttrNoDict.proto */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); jpayne@68: #else jpayne@68: #define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr jpayne@68: #endif jpayne@68: jpayne@68: /* PyObject_GenericGetAttr.proto */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 jpayne@68: static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); jpayne@68: #else jpayne@68: #define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr jpayne@68: #endif jpayne@68: jpayne@68: /* SetVTable.proto */ jpayne@68: static int __Pyx_SetVtable(PyTypeObject* typeptr , void* vtable); jpayne@68: jpayne@68: /* GetVTable.proto */ jpayne@68: static void* __Pyx_GetVtable(PyTypeObject *type); jpayne@68: jpayne@68: /* MergeVTables.proto */ jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static int __Pyx_MergeVtables(PyTypeObject *type); jpayne@68: #endif jpayne@68: jpayne@68: /* SetupReduce.proto */ jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static int __Pyx_setup_reduce(PyObject* type_obj); jpayne@68: #endif jpayne@68: jpayne@68: /* TypeImport.proto */ jpayne@68: #ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11 jpayne@68: #define __PYX_HAVE_RT_ImportType_proto_3_0_11 jpayne@68: #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L jpayne@68: #include jpayne@68: #endif jpayne@68: #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L jpayne@68: #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s) jpayne@68: #else jpayne@68: #define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*) jpayne@68: #endif jpayne@68: enum __Pyx_ImportType_CheckSize_3_0_11 { jpayne@68: __Pyx_ImportType_CheckSize_Error_3_0_11 = 0, jpayne@68: __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1, jpayne@68: __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2 jpayne@68: }; jpayne@68: 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@68: #endif jpayne@68: jpayne@68: /* ImportDottedModule.proto */ jpayne@68: static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple); jpayne@68: #endif jpayne@68: jpayne@68: /* FetchSharedCythonModule.proto */ jpayne@68: static PyObject *__Pyx_FetchSharedCythonABIModule(void); jpayne@68: jpayne@68: /* FetchCommonType.proto */ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); jpayne@68: #else jpayne@68: static PyTypeObject* __Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases); jpayne@68: #endif jpayne@68: jpayne@68: /* PyMethodNew.proto */ jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) { jpayne@68: PyObject *typesModule=NULL, *methodType=NULL, *result=NULL; jpayne@68: CYTHON_UNUSED_VAR(typ); jpayne@68: if (!self) jpayne@68: return __Pyx_NewRef(func); jpayne@68: typesModule = PyImport_ImportModule("types"); jpayne@68: if (!typesModule) return NULL; jpayne@68: methodType = PyObject_GetAttrString(typesModule, "MethodType"); jpayne@68: Py_DECREF(typesModule); jpayne@68: if (!methodType) return NULL; jpayne@68: result = PyObject_CallFunctionObjArgs(methodType, func, self, NULL); jpayne@68: Py_DECREF(methodType); jpayne@68: return result; jpayne@68: } jpayne@68: #elif PY_MAJOR_VERSION >= 3 jpayne@68: static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) { jpayne@68: CYTHON_UNUSED_VAR(typ); jpayne@68: if (!self) jpayne@68: return __Pyx_NewRef(func); jpayne@68: return PyMethod_New(func, self); jpayne@68: } jpayne@68: #else jpayne@68: #define __Pyx_PyMethod_New PyMethod_New jpayne@68: #endif jpayne@68: jpayne@68: /* PyVectorcallFastCallDict.proto */ jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw); jpayne@68: #endif jpayne@68: jpayne@68: /* CythonFunctionShared.proto */ jpayne@68: #define __Pyx_CyFunction_USED jpayne@68: #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 jpayne@68: #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 jpayne@68: #define __Pyx_CYFUNCTION_CCLASS 0x04 jpayne@68: #define __Pyx_CYFUNCTION_COROUTINE 0x08 jpayne@68: #define __Pyx_CyFunction_GetClosure(f)\ jpayne@68: (((__pyx_CyFunctionObject *) (f))->func_closure) jpayne@68: #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_CyFunction_GetClassObj(f)\ jpayne@68: (((__pyx_CyFunctionObject *) (f))->func_classobj) jpayne@68: #else jpayne@68: #define __Pyx_CyFunction_GetClassObj(f)\ jpayne@68: ((PyObject*) ((PyCMethodObject *) (f))->mm_class) jpayne@68: #endif jpayne@68: #define __Pyx_CyFunction_SetClassObj(f, classobj)\ jpayne@68: __Pyx__CyFunction_SetClassObj((__pyx_CyFunctionObject *) (f), (classobj)) jpayne@68: #define __Pyx_CyFunction_Defaults(type, f)\ jpayne@68: ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) jpayne@68: #define __Pyx_CyFunction_SetDefaultsGetter(f, g)\ jpayne@68: ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) jpayne@68: typedef struct { jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject_HEAD jpayne@68: PyObject *func; jpayne@68: #elif PY_VERSION_HEX < 0x030900B1 jpayne@68: PyCFunctionObject func; jpayne@68: #else jpayne@68: PyCMethodObject func; jpayne@68: #endif jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: __pyx_vectorcallfunc func_vectorcall; jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject *func_weakreflist; jpayne@68: #endif jpayne@68: PyObject *func_dict; jpayne@68: PyObject *func_name; jpayne@68: PyObject *func_qualname; jpayne@68: PyObject *func_doc; jpayne@68: PyObject *func_globals; jpayne@68: PyObject *func_code; jpayne@68: PyObject *func_closure; jpayne@68: #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject *func_classobj; jpayne@68: #endif jpayne@68: void *defaults; jpayne@68: int defaults_pyobjects; jpayne@68: size_t defaults_size; jpayne@68: int flags; jpayne@68: PyObject *defaults_tuple; jpayne@68: PyObject *defaults_kwdict; jpayne@68: PyObject *(*defaults_getter)(PyObject *); jpayne@68: PyObject *func_annotations; jpayne@68: PyObject *func_is_coroutine; jpayne@68: } __pyx_CyFunctionObject; jpayne@68: #undef __Pyx_CyOrPyCFunction_Check jpayne@68: #define __Pyx_CyFunction_Check(obj) __Pyx_TypeCheck(obj, __pyx_CyFunctionType) jpayne@68: #define __Pyx_CyOrPyCFunction_Check(obj) __Pyx_TypeCheck2(obj, __pyx_CyFunctionType, &PyCFunction_Type) jpayne@68: #define __Pyx_CyFunction_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_CyFunctionType) jpayne@68: static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc); jpayne@68: #undef __Pyx_IsSameCFunction jpayne@68: #define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCyOrCFunction(func, cfunc) jpayne@68: static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml, jpayne@68: int flags, PyObject* qualname, jpayne@68: PyObject *closure, jpayne@68: PyObject *module, PyObject *globals, jpayne@68: PyObject* code); jpayne@68: static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj); jpayne@68: static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, jpayne@68: size_t size, jpayne@68: int pyobjects); jpayne@68: static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, jpayne@68: PyObject *tuple); jpayne@68: static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, jpayne@68: PyObject *dict); jpayne@68: static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, jpayne@68: PyObject *dict); jpayne@68: static int __pyx_CyFunction_init(PyObject *module); jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: #define __Pyx_CyFunction_func_vectorcall(f) (((__pyx_CyFunctionObject*)f)->func_vectorcall) jpayne@68: #else jpayne@68: #define __Pyx_CyFunction_func_vectorcall(f) (((PyCFunctionObject*)f)->vectorcall) jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: /* CythonFunction.proto */ jpayne@68: static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, jpayne@68: int flags, PyObject* qualname, jpayne@68: PyObject *closure, jpayne@68: PyObject *module, PyObject *globals, jpayne@68: PyObject* code); jpayne@68: jpayne@68: /* SetNameInClass.proto */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000 jpayne@68: #define __Pyx_SetNameInClass(ns, name, value)\ jpayne@68: (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value)) jpayne@68: #elif CYTHON_COMPILING_IN_CPYTHON jpayne@68: #define __Pyx_SetNameInClass(ns, name, value)\ jpayne@68: (likely(PyDict_CheckExact(ns)) ? PyDict_SetItem(ns, name, value) : PyObject_SetItem(ns, name, value)) jpayne@68: #else jpayne@68: #define __Pyx_SetNameInClass(ns, name, value) PyObject_SetItem(ns, name, value) jpayne@68: #endif jpayne@68: jpayne@68: /* CalculateMetaclass.proto */ jpayne@68: static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); jpayne@68: jpayne@68: /* PyObjectCall2Args.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); jpayne@68: jpayne@68: /* PyObjectLookupSpecial.proto */ jpayne@68: #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS jpayne@68: #define __Pyx_PyObject_LookupSpecialNoError(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 0) jpayne@68: #define __Pyx_PyObject_LookupSpecial(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 1) jpayne@68: static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error); jpayne@68: #else jpayne@68: #define __Pyx_PyObject_LookupSpecialNoError(o,n) __Pyx_PyObject_GetAttrStrNoError(o,n) jpayne@68: #define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) jpayne@68: #endif jpayne@68: jpayne@68: /* Py3ClassCreate.proto */ jpayne@68: static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, jpayne@68: PyObject *mkw, PyObject *modname, PyObject *doc); jpayne@68: static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, jpayne@68: PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); jpayne@68: jpayne@68: /* CLineInTraceback.proto */ jpayne@68: #ifdef CYTHON_CLINE_IN_TRACEBACK jpayne@68: #define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) jpayne@68: #else jpayne@68: static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); jpayne@68: #endif jpayne@68: jpayne@68: /* CodeObjectCache.proto */ jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: typedef struct { jpayne@68: PyCodeObject* code_object; jpayne@68: int code_line; jpayne@68: } __Pyx_CodeObjectCacheEntry; jpayne@68: struct __Pyx_CodeObjectCache { jpayne@68: int count; jpayne@68: int max_count; jpayne@68: __Pyx_CodeObjectCacheEntry* entries; jpayne@68: }; jpayne@68: static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; jpayne@68: static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); jpayne@68: static PyCodeObject *__pyx_find_code_object(int code_line); jpayne@68: static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); jpayne@68: #endif jpayne@68: jpayne@68: /* AddTraceback.proto */ jpayne@68: static void __Pyx_AddTraceback(const char *funcname, int c_line, jpayne@68: int py_line, const char *filename); jpayne@68: jpayne@68: /* GCCDiagnostics.proto */ jpayne@68: #if !defined(__INTEL_COMPILER) && defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) jpayne@68: #define __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #endif jpayne@68: jpayne@68: /* ArrayAPI.proto */ jpayne@68: #ifndef _ARRAYARRAY_H jpayne@68: #define _ARRAYARRAY_H jpayne@68: typedef struct arraydescr { jpayne@68: int typecode; jpayne@68: int itemsize; jpayne@68: PyObject * (*getitem)(struct arrayobject *, Py_ssize_t); jpayne@68: int (*setitem)(struct arrayobject *, Py_ssize_t, PyObject *); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: char *formats; jpayne@68: #endif jpayne@68: } arraydescr; jpayne@68: struct arrayobject { jpayne@68: PyObject_HEAD jpayne@68: Py_ssize_t ob_size; jpayne@68: union { jpayne@68: char *ob_item; jpayne@68: float *as_floats; jpayne@68: double *as_doubles; jpayne@68: int *as_ints; jpayne@68: unsigned int *as_uints; jpayne@68: unsigned char *as_uchars; jpayne@68: signed char *as_schars; jpayne@68: char *as_chars; jpayne@68: unsigned long *as_ulongs; jpayne@68: long *as_longs; jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: unsigned long long *as_ulonglongs; jpayne@68: long long *as_longlongs; jpayne@68: #endif jpayne@68: short *as_shorts; jpayne@68: unsigned short *as_ushorts; jpayne@68: Py_UNICODE *as_pyunicodes; jpayne@68: void *as_voidptr; jpayne@68: } data; jpayne@68: Py_ssize_t allocated; jpayne@68: struct arraydescr *ob_descr; jpayne@68: PyObject *weakreflist; jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: int ob_exports; jpayne@68: #endif jpayne@68: }; jpayne@68: #ifndef NO_NEWARRAY_INLINE jpayne@68: static CYTHON_INLINE PyObject * newarrayobject(PyTypeObject *type, Py_ssize_t size, jpayne@68: struct arraydescr *descr) { jpayne@68: arrayobject *op; jpayne@68: size_t nbytes; jpayne@68: if (size < 0) { jpayne@68: PyErr_BadInternalCall(); jpayne@68: return NULL; jpayne@68: } jpayne@68: nbytes = size * descr->itemsize; jpayne@68: if (nbytes / descr->itemsize != (size_t)size) { jpayne@68: return PyErr_NoMemory(); jpayne@68: } jpayne@68: op = (arrayobject *) type->tp_alloc(type, 0); jpayne@68: if (op == NULL) { jpayne@68: return NULL; jpayne@68: } jpayne@68: op->ob_descr = descr; jpayne@68: op->allocated = size; jpayne@68: op->weakreflist = NULL; jpayne@68: __Pyx_SET_SIZE(op, size); jpayne@68: if (size <= 0) { jpayne@68: op->data.ob_item = NULL; jpayne@68: } jpayne@68: else { jpayne@68: op->data.ob_item = PyMem_NEW(char, nbytes); jpayne@68: if (op->data.ob_item == NULL) { jpayne@68: Py_DECREF(op); jpayne@68: return PyErr_NoMemory(); jpayne@68: } jpayne@68: } jpayne@68: return (PyObject *) op; jpayne@68: } jpayne@68: #else jpayne@68: PyObject* newarrayobject(PyTypeObject *type, Py_ssize_t size, jpayne@68: struct arraydescr *descr); jpayne@68: #endif jpayne@68: static CYTHON_INLINE int resize(arrayobject *self, Py_ssize_t n) { jpayne@68: void *items = (void*) self->data.ob_item; jpayne@68: PyMem_Resize(items, char, (size_t)(n * self->ob_descr->itemsize)); jpayne@68: if (items == NULL) { jpayne@68: PyErr_NoMemory(); jpayne@68: return -1; jpayne@68: } jpayne@68: self->data.ob_item = (char*) items; jpayne@68: __Pyx_SET_SIZE(self, n); jpayne@68: self->allocated = n; jpayne@68: return 0; jpayne@68: } jpayne@68: static CYTHON_INLINE int resize_smart(arrayobject *self, Py_ssize_t n) { jpayne@68: void *items = (void*) self->data.ob_item; jpayne@68: Py_ssize_t newsize; jpayne@68: if (n < self->allocated && n*4 > self->allocated) { jpayne@68: __Pyx_SET_SIZE(self, n); jpayne@68: return 0; jpayne@68: } jpayne@68: newsize = n + (n / 2) + 1; jpayne@68: if (newsize <= n) { jpayne@68: PyErr_NoMemory(); jpayne@68: return -1; jpayne@68: } jpayne@68: PyMem_Resize(items, char, (size_t)(newsize * self->ob_descr->itemsize)); jpayne@68: if (items == NULL) { jpayne@68: PyErr_NoMemory(); jpayne@68: return -1; jpayne@68: } jpayne@68: self->data.ob_item = (char*) items; jpayne@68: __Pyx_SET_SIZE(self, n); jpayne@68: self->allocated = newsize; jpayne@68: return 0; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* CIntFromPy.proto */ jpayne@68: static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); jpayne@68: jpayne@68: /* CIntToPy.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); jpayne@68: jpayne@68: /* CIntFromPy.proto */ jpayne@68: static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); jpayne@68: jpayne@68: /* CIntFromPy.proto */ jpayne@68: static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *); jpayne@68: jpayne@68: /* CIntToPy.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value); jpayne@68: jpayne@68: /* CIntToPy.proto */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); jpayne@68: jpayne@68: /* CIntFromPy.proto */ jpayne@68: static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *); jpayne@68: jpayne@68: /* FormatTypeName.proto */ jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: typedef PyObject *__Pyx_TypeName; jpayne@68: #define __Pyx_FMT_TYPENAME "%U" jpayne@68: static __Pyx_TypeName __Pyx_PyType_GetName(PyTypeObject* tp); jpayne@68: #define __Pyx_DECREF_TypeName(obj) Py_XDECREF(obj) jpayne@68: #else jpayne@68: typedef const char *__Pyx_TypeName; jpayne@68: #define __Pyx_FMT_TYPENAME "%.200s" jpayne@68: #define __Pyx_PyType_GetName(tp) ((tp)->tp_name) jpayne@68: #define __Pyx_DECREF_TypeName(obj) jpayne@68: #endif jpayne@68: jpayne@68: /* FastTypeChecks.proto */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: #define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) jpayne@68: #define __Pyx_TypeCheck2(obj, type1, type2) __Pyx_IsAnySubtype2(Py_TYPE(obj), (PyTypeObject *)type1, (PyTypeObject *)type2) jpayne@68: static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); jpayne@68: static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b); jpayne@68: static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); jpayne@68: static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); jpayne@68: #else jpayne@68: #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) jpayne@68: #define __Pyx_TypeCheck2(obj, type1, type2) (PyObject_TypeCheck(obj, (PyTypeObject *)type1) || PyObject_TypeCheck(obj, (PyTypeObject *)type2)) jpayne@68: #define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) jpayne@68: #define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) jpayne@68: #endif jpayne@68: #define __Pyx_PyErr_ExceptionMatches2(err1, err2) __Pyx_PyErr_GivenExceptionMatches2(__Pyx_PyErr_CurrentExceptionType(), err1, err2) jpayne@68: #define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) jpayne@68: jpayne@68: /* CheckBinaryVersion.proto */ jpayne@68: static unsigned long __Pyx_get_runtime_version(void); jpayne@68: static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer); jpayne@68: jpayne@68: /* FunctionImport.proto */ jpayne@68: static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig); jpayne@68: jpayne@68: /* InitStrings.proto */ jpayne@68: static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); jpayne@68: jpayne@68: /* #### Code section: module_declarations ### */ jpayne@68: static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self); /* proto*/ jpayne@68: static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_6Parser_parse(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, CYTHON_UNUSED char *__pyx_v_buffer, CYTHON_UNUSED int __pyx_v_length); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_7asTuple_parse(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_6asGFF3_parse(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_5asGTF_parse(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_5asBed_parse(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_5asVCF_parse(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto*/ jpayne@68: static int __pyx_f_5pysam_9libctabix_13TabixIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto*/ jpayne@68: static int __pyx_f_5pysam_9libctabix_10GZIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_19tabix_file_iterator___cnext__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto*/ jpayne@68: jpayne@68: /* Module declarations from "libc.stdint" */ jpayne@68: jpayne@68: /* Module declarations from "libc.string" */ jpayne@68: jpayne@68: /* Module declarations from "libc.stdlib" */ jpayne@68: jpayne@68: /* Module declarations from "libc.stdio" */ jpayne@68: jpayne@68: /* Module declarations from "posix.types" */ jpayne@68: jpayne@68: /* Module declarations from "pysam.libchtslib" */ jpayne@68: jpayne@68: /* Module declarations from "libc.errno" */ jpayne@68: jpayne@68: /* Module declarations from "posix.unistd" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.version" */ jpayne@68: jpayne@68: /* Module declarations from "__builtin__" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.type" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.object" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.ref" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.exc" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.module" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.mem" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.tuple" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.list" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.sequence" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.mapping" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.iterator" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.number" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.int" */ jpayne@68: jpayne@68: /* Module declarations from "__builtin__" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.bool" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.long" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.float" */ jpayne@68: jpayne@68: /* Module declarations from "__builtin__" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.complex" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.string" */ jpayne@68: jpayne@68: /* Module declarations from "libc.stddef" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.unicode" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.pyport" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.dict" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.instance" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.function" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.method" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.weakref" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.getargs" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.pythread" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.pystate" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.cobject" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.oldbuffer" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.set" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.buffer" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.bytes" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.pycapsule" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.contextvars" */ jpayne@68: jpayne@68: /* Module declarations from "cpython" */ jpayne@68: jpayne@68: /* Module declarations from "pysam.libctabixproxies" */ jpayne@68: jpayne@68: /* Module declarations from "cython" */ jpayne@68: jpayne@68: /* Module declarations from "array" */ jpayne@68: jpayne@68: /* Module declarations from "cpython.array" */ jpayne@68: static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *, char *, Py_ssize_t); /*proto*/ jpayne@68: jpayne@68: /* Module declarations from "pysam.libcutils" */ jpayne@68: static PyObject *(*__pyx_f_5pysam_9libcutils_charptr_to_str)(char const *, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str *__pyx_optional_args); /*proto*/ jpayne@68: static PyObject *(*__pyx_f_5pysam_9libcutils_force_str)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args); /*proto*/ jpayne@68: static PyObject *(*__pyx_f_5pysam_9libcutils_force_bytes)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_bytes *__pyx_optional_args); /*proto*/ jpayne@68: static PyObject *(*__pyx_f_5pysam_9libcutils_encode_filename)(PyObject *); /*proto*/ jpayne@68: static PyObject *(*__pyx_f_5pysam_9libcutils_from_string_and_size)(char const *, size_t); /*proto*/ jpayne@68: jpayne@68: /* Module declarations from "pysam.libctabix" */ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(struct __pyx_obj_5pysam_9libctabix_Parser *, PyObject *); /*proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(struct __pyx_obj_5pysam_9libctabix_asTuple *, PyObject *); /*proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(struct __pyx_obj_5pysam_9libctabix_asGFF3 *, PyObject *); /*proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(struct __pyx_obj_5pysam_9libctabix_asGTF *, PyObject *); /*proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(struct __pyx_obj_5pysam_9libctabix_asBed *, PyObject *); /*proto*/ jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(struct __pyx_obj_5pysam_9libctabix_asVCF *, PyObject *); /*proto*/ jpayne@68: /* #### Code section: typeinfo ### */ jpayne@68: /* #### Code section: before_global_var ### */ jpayne@68: #define __Pyx_MODULE_NAME "pysam.libctabix" jpayne@68: extern int __pyx_module_is_main_pysam__libctabix; jpayne@68: int __pyx_module_is_main_pysam__libctabix = 0; jpayne@68: jpayne@68: /* Implementation of "pysam.libctabix" */ jpayne@68: /* #### Code section: global_var ### */ jpayne@68: static PyObject *__pyx_builtin_NotImplementedError; jpayne@68: static PyObject *__pyx_builtin_ValueError; jpayne@68: static PyObject *__pyx_builtin_IOError; jpayne@68: static PyObject *__pyx_builtin_OSError; jpayne@68: static PyObject *__pyx_builtin_TypeError; jpayne@68: static PyObject *__pyx_builtin_StopIteration; jpayne@68: static PyObject *__pyx_builtin_super; jpayne@68: static PyObject *__pyx_builtin_KeyError; jpayne@68: static PyObject *__pyx_builtin_AssertionError; jpayne@68: static PyObject *__pyx_builtin_MemoryError; jpayne@68: /* #### Code section: string_decls ### */ jpayne@68: static const char __pyx_k_a[] = "a"; jpayne@68: static const char __pyx_k_b[] = "b"; jpayne@68: static const char __pyx_k_c[] = "c"; jpayne@68: static const char __pyx_k_r[] = "r"; jpayne@68: static const char __pyx_k_s[] = "%s"; jpayne@68: static const char __pyx_k_fn[] = "fn"; jpayne@68: static const char __pyx_k_fp[] = "fp"; jpayne@68: static const char __pyx_k_gc[] = "gc"; jpayne@68: static const char __pyx_k_gz[] = ".gz"; jpayne@68: static const char __pyx_k_os[] = "os"; jpayne@68: static const char __pyx_k__16[] = "-"; jpayne@68: static const char __pyx_k__39[] = "#"; jpayne@68: static const char __pyx_k__42[] = "': "; jpayne@68: static const char __pyx_k__43[] = ","; jpayne@68: static const char __pyx_k__44[] = "'"; jpayne@68: static const char __pyx_k__56[] = "."; jpayne@68: static const char __pyx_k__62[] = "*"; jpayne@68: static const char __pyx_k__78[] = "?"; jpayne@68: static const char __pyx_k_all[] = "__all__"; jpayne@68: static const char __pyx_k_bcf[] = "bcf"; jpayne@68: static const char __pyx_k_bed[] = "bed"; jpayne@68: static const char __pyx_k_cfn[] = "cfn"; jpayne@68: static const char __pyx_k_cpy[] = "cpy"; jpayne@68: static const char __pyx_k_csi[] = "csi"; jpayne@68: static const char __pyx_k_doc[] = "__doc__"; jpayne@68: static const char __pyx_k_dup[] = "_dup"; jpayne@68: static const char __pyx_k_end[] = "end"; jpayne@68: static const char __pyx_k_fmt[] = "fmt"; jpayne@68: static const char __pyx_k_gff[] = "gff"; jpayne@68: static const char __pyx_k_itr[] = "itr"; jpayne@68: static const char __pyx_k_new[] = "__new__"; jpayne@68: static const char __pyx_k_s_2[] = "s"; jpayne@68: static const char __pyx_k_s_i[] = "%s:%i"; jpayne@68: static const char __pyx_k_sam[] = "sam"; jpayne@68: static const char __pyx_k_sys[] = "sys"; jpayne@68: static const char __pyx_k_tbi[] = ".tbi"; jpayne@68: static const char __pyx_k_vcf[] = "vcf"; jpayne@68: static const char __pyx_k_conf[] = "conf"; jpayne@68: static const char __pyx_k_cstr[] = "cstr"; jpayne@68: static const char __pyx_k_dict[] = "__dict__"; jpayne@68: static const char __pyx_k_init[] = "__init__"; jpayne@68: static const char __pyx_k_iter[] = "__iter__"; jpayne@68: static const char __pyx_k_keys[] = "keys"; jpayne@68: static const char __pyx_k_line[] = "line"; jpayne@68: static const char __pyx_k_main[] = "__main__"; jpayne@68: static const char __pyx_k_mode[] = "mode"; jpayne@68: static const char __pyx_k_name[] = "__name__"; jpayne@68: static const char __pyx_k_next[] = "__next__"; jpayne@68: static const char __pyx_k_open[] = "_open"; jpayne@68: static const char __pyx_k_path[] = "path"; jpayne@68: static const char __pyx_k_self[] = "self"; jpayne@68: static const char __pyx_k_spec[] = "__spec__"; jpayne@68: static const char __pyx_k_tell[] = "tell"; jpayne@68: static const char __pyx_k_test[] = "__test__"; jpayne@68: static const char __pyx_k_asBed[] = "asBed"; jpayne@68: static const char __pyx_k_asGTF[] = "asGTF"; jpayne@68: static const char __pyx_k_asVCF[] = "asVCF"; jpayne@68: static const char __pyx_k_ascii[] = "ascii"; jpayne@68: static const char __pyx_k_close[] = "close"; jpayne@68: static const char __pyx_k_csi_2[] = ".csi"; jpayne@68: static const char __pyx_k_fetch[] = "fetch"; jpayne@68: static const char __pyx_k_fnidx[] = "fnidx"; jpayne@68: static const char __pyx_k_force[] = "force"; jpayne@68: static const char __pyx_k_index[] = "index"; jpayne@68: static const char __pyx_k_s_i_i[] = "%s:%i-%i"; jpayne@68: static const char __pyx_k_start[] = "start"; jpayne@68: static const char __pyx_k_state[] = "state"; jpayne@68: static const char __pyx_k_super[] = "super"; jpayne@68: static const char __pyx_k_Parser[] = "Parser"; jpayne@68: static const char __pyx_k_asGFF3[] = "asGFF3"; jpayne@68: static const char __pyx_k_buffer[] = "buffer"; jpayne@68: static const char __pyx_k_closed[] = "closed"; jpayne@68: static const char __pyx_k_dict_2[] = "_dict"; jpayne@68: static const char __pyx_k_enable[] = "enable"; jpayne@68: static const char __pyx_k_exists[] = "exists"; jpayne@68: static const char __pyx_k_fd_src[] = "fd_src"; jpayne@68: static const char __pyx_k_format[] = "format"; jpayne@68: static const char __pyx_k_import[] = "__import__"; jpayne@68: static const char __pyx_k_infile[] = "infile"; jpayne@68: static const char __pyx_k_length[] = "length"; jpayne@68: static const char __pyx_k_module[] = "__module__"; jpayne@68: static const char __pyx_k_nbytes[] = "nbytes"; jpayne@68: static const char __pyx_k_parser[] = "parser"; jpayne@68: static const char __pyx_k_pickle[] = "pickle"; jpayne@68: static const char __pyx_k_preset[] = "preset"; jpayne@68: static const char __pyx_k_psltbl[] = "psltbl"; jpayne@68: static const char __pyx_k_reduce[] = "__reduce__"; jpayne@68: static const char __pyx_k_region[] = "region"; jpayne@68: static const char __pyx_k_retval[] = "retval"; jpayne@68: static const char __pyx_k_suffix[] = "suffix"; jpayne@68: static const char __pyx_k_unlink[] = "unlink"; jpayne@68: static const char __pyx_k_update[] = "update"; jpayne@68: static const char __pyx_k_IOError[] = "IOError"; jpayne@68: static const char __pyx_k_OSError[] = "OSError"; jpayne@68: static const char __pyx_k_asTuple[] = "asTuple"; jpayne@68: static const char __pyx_k_contigs[] = "contigs"; jpayne@68: static const char __pyx_k_disable[] = "disable"; jpayne@68: static const char __pyx_k_end_col[] = "end_col"; jpayne@68: static const char __pyx_k_fileobj[] = "fileobj"; jpayne@68: static const char __pyx_k_is_open[] = "is_open"; jpayne@68: static const char __pyx_k_prepare[] = "__prepare__"; jpayne@68: static const char __pyx_k_seq_col[] = "seq_col"; jpayne@68: static const char __pyx_k_threads[] = "threads"; jpayne@68: static const char __pyx_k_KeyError[] = "KeyError"; jpayne@68: static const char __pyx_k_O_RDONLY[] = "O_RDONLY"; jpayne@68: static const char __pyx_k_encoding[] = "encoding"; jpayne@68: static const char __pyx_k_filename[] = "filename"; jpayne@68: static const char __pyx_k_fn_index[] = "fn_index"; jpayne@68: static const char __pyx_k_getstate[] = "__getstate__"; jpayne@68: static const char __pyx_k_is_empty[] = "is_empty"; jpayne@68: static const char __pyx_k_pyx_type[] = "__pyx_type"; jpayne@68: static const char __pyx_k_qualname[] = "__qualname__"; jpayne@68: static const char __pyx_k_readline[] = "readline"; jpayne@68: static const char __pyx_k_set_name[] = "__set_name__"; jpayne@68: static const char __pyx_k_setstate[] = "__setstate__"; jpayne@68: static const char __pyx_k_TabixFile[] = "TabixFile"; jpayne@68: static const char __pyx_k_Tabixfile[] = "Tabixfile"; jpayne@68: static const char __pyx_k_TypeError[] = "TypeError"; jpayne@68: static const char __pyx_k_bytes_cpy[] = "bytes_cpy"; jpayne@68: static const char __pyx_k_cfilename[] = "cfilename"; jpayne@68: static const char __pyx_k_conf_data[] = "conf_data"; jpayne@68: static const char __pyx_k_isenabled[] = "isenabled"; jpayne@68: static const char __pyx_k_line_skip[] = "line_skip"; jpayne@68: static const char __pyx_k_meta_char[] = "meta_char"; jpayne@68: static const char __pyx_k_metaclass[] = "__metaclass__"; jpayne@68: static const char __pyx_k_min_shift[] = "min_shift"; jpayne@68: static const char __pyx_k_pyx_state[] = "__pyx_state"; jpayne@68: static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; jpayne@68: static const char __pyx_k_reference[] = "reference"; jpayne@68: static const char __pyx_k_start_col[] = "start_col"; jpayne@68: static const char __pyx_k_zerobased[] = "zerobased"; jpayne@68: static const char __pyx_k_GZIterator[] = "GZIterator"; jpayne@68: static const char __pyx_k_ValueError[] = "ValueError"; jpayne@68: static const char __pyx_k_pyx_result[] = "__pyx_result"; jpayne@68: static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; jpayne@68: static const char __pyx_k_MemoryError[] = "MemoryError"; jpayne@68: static const char __pyx_k_PickleError[] = "PickleError"; jpayne@68: static const char __pyx_k_WINDOW_SIZE[] = "WINDOW_SIZE"; jpayne@68: static const char __pyx_k_buffer_size[] = "buffer_size"; jpayne@68: static const char __pyx_k_filename_in[] = "filename_in"; jpayne@68: static const char __pyx_k_preset2conf[] = "preset2conf"; jpayne@68: static const char __pyx_k_tabix_index[] = "tabix_index"; jpayne@68: static const char __pyx_k_filename_out[] = "filename_out"; jpayne@68: static const char __pyx_k_get_encoding[] = "get_encoding"; jpayne@68: static const char __pyx_k_initializing[] = "_initializing"; jpayne@68: static const char __pyx_k_is_coroutine[] = "_is_coroutine"; jpayne@68: static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; jpayne@68: static const char __pyx_k_set_encoding[] = "set_encoding"; jpayne@68: static const char __pyx_k_stringsource[] = ""; jpayne@68: static const char __pyx_k_use_setstate[] = "use_setstate"; jpayne@68: static const char __pyx_k_EmptyIterator[] = "EmptyIterator"; jpayne@68: static const char __pyx_k_StopIteration[] = "StopIteration"; jpayne@68: static const char __pyx_k_TabixIterator[] = "TabixIterator"; jpayne@68: static const char __pyx_k_init_subclass[] = "__init_subclass__"; jpayne@68: static const char __pyx_k_keep_original[] = "keep_original"; jpayne@68: static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; jpayne@68: static const char __pyx_k_start_i_end_i[] = "start (%i) >= end (%i)"; jpayne@68: static const char __pyx_k_AssertionError[] = "AssertionError"; jpayne@68: static const char __pyx_k_GZIteratorHead[] = "GZIteratorHead"; jpayne@68: static const char __pyx_k_TabixFile__dup[] = "TabixFile._dup"; jpayne@68: static const char __pyx_k_empty_iterator[] = "empty iterator"; jpayne@68: static const char __pyx_k_filename_index[] = "filename_index"; jpayne@68: static const char __pyx_k_tabix_compress[] = "tabix_compress"; jpayne@68: static const char __pyx_k_tabix_iterator[] = "tabix_iterator"; jpayne@68: static const char __pyx_k_unknown_preset[] = "unknown preset '"; jpayne@68: static const char __pyx_k_writing_failed[] = "writing failed"; jpayne@68: static const char __pyx_k_TabixFile__open[] = "TabixFile._open"; jpayne@68: static const char __pyx_k_TabixFile_close[] = "TabixFile.close"; jpayne@68: static const char __pyx_k_TabixFile_fetch[] = "TabixFile.fetch"; jpayne@68: static const char __pyx_k_cfilename_index[] = "cfilename_index"; jpayne@68: static const char __pyx_k_pysam_libctabix[] = "pysam.libctabix"; jpayne@68: static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; jpayne@68: static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; jpayne@68: static const char __pyx_k_GZIteratorParsed[] = "GZIteratorParsed"; jpayne@68: static const char __pyx_k_file_s_not_found[] = "file `%s` not found"; jpayne@68: static const char __pyx_k_index_s_not_found[] = "index `%s` not found"; jpayne@68: static const char __pyx_k_valid_presets_are[] = "', valid presets are '"; jpayne@68: static const char __pyx_k_asyncio_coroutines[] = "asyncio.coroutines"; jpayne@68: static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; jpayne@68: static const char __pyx_k_end_out_of_range_i[] = "end out of range (%i)"; jpayne@68: static const char __pyx_k_multiple_iterators[] = "multiple_iterators"; jpayne@68: static const char __pyx_k_pyx_unpickle_asBed[] = "__pyx_unpickle_asBed"; jpayne@68: static const char __pyx_k_pyx_unpickle_asGTF[] = "__pyx_unpickle_asGTF"; jpayne@68: static const char __pyx_k_pyx_unpickle_asVCF[] = "__pyx_unpickle_asVCF"; jpayne@68: static const char __pyx_k_Could_not_open_file[] = "Could not open file '"; jpayne@68: static const char __pyx_k_NotImplementedError[] = "NotImplementedError"; jpayne@68: static const char __pyx_k_Parser_get_encoding[] = "Parser.get_encoding"; jpayne@68: static const char __pyx_k_Parser_set_encoding[] = "Parser.set_encoding"; jpayne@68: static const char __pyx_k_TabixIteratorParsed[] = "TabixIteratorParsed"; jpayne@68: static const char __pyx_k_pysam_libctabix_pyx[] = "pysam/libctabix.pyx"; jpayne@68: static const char __pyx_k_pyx_unpickle_Parser[] = "__pyx_unpickle_Parser"; jpayne@68: static const char __pyx_k_pyx_unpickle_asGFF3[] = "__pyx_unpickle_asGFF3"; jpayne@68: static const char __pyx_k_tabix_file_iterator[] = "tabix_file_iterator"; jpayne@68: static const char __pyx_k_EmptyIterator___iter[] = "EmptyIterator.__iter__"; jpayne@68: static const char __pyx_k_EmptyIterator___next[] = "EmptyIterator.__next__"; jpayne@68: static const char __pyx_k_incomplete_line_at_s[] = "incomplete line at %s"; jpayne@68: static const char __pyx_k_pyx_unpickle_asTuple[] = "__pyx_unpickle_asTuple"; jpayne@68: static const char __pyx_k_start_out_of_range_i[] = "start out of range (%i)"; jpayne@68: static const char __pyx_k_asBed___reduce_cython[] = "asBed.__reduce_cython__"; jpayne@68: static const char __pyx_k_asGTF___reduce_cython[] = "asGTF.__reduce_cython__"; jpayne@68: static const char __pyx_k_asVCF___reduce_cython[] = "asVCF.__reduce_cython__"; jpayne@68: static const char __pyx_k_could_not_open_file_s[] = "could not open file `%s`"; jpayne@68: static const char __pyx_k_Parser___reduce_cython[] = "Parser.__reduce_cython__"; jpayne@68: static const char __pyx_k_asGFF3___reduce_cython[] = "asGFF3.__reduce_cython__"; jpayne@68: static const char __pyx_k_tabix_generic_iterator[] = "tabix_generic_iterator"; jpayne@68: static const char __pyx_k_asBed___setstate_cython[] = "asBed.__setstate_cython__"; jpayne@68: static const char __pyx_k_asGTF___setstate_cython[] = "asGTF.__setstate_cython__"; jpayne@68: static const char __pyx_k_asTuple___reduce_cython[] = "asTuple.__reduce_cython__"; jpayne@68: static const char __pyx_k_asVCF___setstate_cython[] = "asVCF.__setstate_cython__"; jpayne@68: static const char __pyx_k_Parser___setstate_cython[] = "Parser.__setstate_cython__"; jpayne@68: static const char __pyx_k_asGFF3___setstate_cython[] = "asGFF3.__setstate_cython__"; jpayne@68: static const char __pyx_k_iteration_on_closed_file[] = "iteration on closed file"; jpayne@68: static const char __pyx_k_TabixFile___reduce_cython[] = "TabixFile.__reduce_cython__"; jpayne@68: static const char __pyx_k_Tabixfile___reduce_cython[] = "Tabixfile.__reduce_cython__"; jpayne@68: static const char __pyx_k_asTuple___setstate_cython[] = "asTuple.__setstate_cython__"; jpayne@68: static const char __pyx_k_GZIterator___reduce_cython[] = "GZIterator.__reduce_cython__"; jpayne@68: static const char __pyx_k_could_not_open_index_for_s[] = "could not open index for `%s`"; jpayne@68: static const char __pyx_k_No_such_file_or_directory_s[] = "No such file or directory: %s"; jpayne@68: static const char __pyx_k_TabixFile___setstate_cython[] = "TabixFile.__setstate_cython__"; jpayne@68: static const char __pyx_k_Tabixfile___setstate_cython[] = "Tabixfile.__setstate_cython__"; jpayne@68: static const char __pyx_k_error_i_when_closing_file_s[] = "error %i when closing file %s"; jpayne@68: static const char __pyx_k_invalid_file_opening_mode_s[] = "invalid file opening mode `%s`"; jpayne@68: static const char __pyx_k_GZIterator___setstate_cython[] = "GZIterator.__setstate_cython__"; jpayne@68: static const char __pyx_k_I_O_operation_on_closed_file[] = "I/O operation on closed file"; jpayne@68: static const char __pyx_k_building_of_index_for_failed[] = "building of index for {} failed"; jpayne@68: static const char __pyx_k_could_not_open_s_for_reading[] = "could not open '%s' for reading"; jpayne@68: static const char __pyx_k_could_not_open_s_for_writing[] = "could not open '%s' for writing"; jpayne@68: static const char __pyx_k_TabixIterator___reduce_cython[] = "TabixIterator.__reduce_cython__"; jpayne@68: static const char __pyx_k_tabix_generic_iterator___init[] = "tabix_generic_iterator.__init__"; jpayne@68: static const char __pyx_k_tabix_generic_iterator___iter[] = "tabix_generic_iterator.__iter__"; jpayne@68: static const char __pyx_k_tabix_generic_iterator___next[] = "tabix_generic_iterator.__next__"; jpayne@68: static const char __pyx_k_GZIteratorHead___reduce_cython[] = "GZIteratorHead.__reduce_cython__"; jpayne@68: static const char __pyx_k_I_O_operation_on_closed_file_2[] = "I/O operation on closed file."; jpayne@68: static const char __pyx_k_error_i_when_writing_to_file_s[] = "error %i when writing to file %s"; jpayne@68: static const char __pyx_k_TabixIterator___setstate_cython[] = "TabixIterator.__setstate_cython__"; jpayne@68: static const char __pyx_k_could_not_load_tbi_csi_index_of[] = "could not load .tbi/.csi index of {}"; jpayne@68: static const char __pyx_k_iterate_over_infile_Permits_the[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; jpayne@68: static const char __pyx_k_Filename_s_already_exists_use_fo[] = "Filename '%s' already exists, use *force* to overwrite"; jpayne@68: static const char __pyx_k_GZIteratorHead___setstate_cython[] = "GZIteratorHead.__setstate_cython__"; jpayne@68: static const char __pyx_k_GZIteratorParsed___reduce_cython[] = "GZIteratorParsed.__reduce_cython__"; jpayne@68: static const char __pyx_k_GZIteratorParsed___setstate_cyth[] = "GZIteratorParsed.__setstate_cython__"; jpayne@68: static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))"; jpayne@68: static const char __pyx_k_TabixIteratorParsed___reduce_cyt[] = "TabixIteratorParsed.__reduce_cython__"; jpayne@68: static const char __pyx_k_TabixIteratorParsed___setstate_c[] = "TabixIteratorParsed.__setstate_cython__"; jpayne@68: static const char __pyx_k_could_not_create_iterator_for_re[] = "could not create iterator for region '%s'"; jpayne@68: static const char __pyx_k_could_not_create_iterator_possib[] = "could not create iterator, possible tabix version mismatch"; jpayne@68: static const char __pyx_k_could_not_open_for_reading_heade[] = "could not open {} for reading header"; jpayne@68: static const char __pyx_k_filename_s_already_exists_use_fo[] = "filename '%s' already exists, use *force* to overwrite"; jpayne@68: static const char __pyx_k_neither_preset_nor_seq_col_start[] = "neither preset nor seq_col,start_col and end_col given"; jpayne@68: static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; jpayne@68: static const char __pyx_k_parse_method_of_s_not_implemente[] = "parse method of %s not implemented"; jpayne@68: static const char __pyx_k_self_gzipfile_self_kstream_canno[] = "self.gzipfile,self.kstream cannot be converted to a Python object for pickling"; jpayne@68: static const char __pyx_k_self_iterator_cannot_be_converte[] = "self.iterator cannot be converted to a Python object for pickling"; jpayne@68: static const char __pyx_k_tabix_file_iterator___reduce_cyt[] = "tabix_file_iterator.__reduce_cython__"; jpayne@68: static const char __pyx_k_tabix_file_iterator___setstate_c[] = "tabix_file_iterator.__setstate_cython__"; jpayne@68: /* #### Code section: decls ### */ jpayne@68: 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@68: static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_6Parser___init__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_2set_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_4get_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_6__call__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_8__reduce_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_10__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asBed___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asBed_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_9TabixFile___cinit__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_parser, PyObject *__pyx_v_index, PyObject *__pyx_v_encoding, PyObject *__pyx_v_threads, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_2_open(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_index, PyObject *__pyx_v_threads); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_4_dup(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6fetch(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser, PyObject *__pyx_v_multiple_iterators); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6header___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_8close(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static void __pyx_pf_5pysam_9libctabix_9TabixFile_10__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14filename_index___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_12__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_13TabixIterator___init__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */ jpayne@68: static void __pyx_pf_5pysam_9libctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator___iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator_2__next__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_10GZIterator___init__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, PyObject *__pyx_v_filename, int __pyx_v_buffer_size, PyObject *__pyx_v_encoding); /* proto */ jpayne@68: static void __pyx_pf_5pysam_9libctabix_10GZIterator_2__dealloc__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_4__iter__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_6__next__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead___next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_16GZIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, PyObject *__pyx_v_parser); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, int __pyx_v_line_skip, PyObject *__pyx_v_zerobased, int __pyx_v_min_shift, PyObject *__pyx_v_index, PyObject *__pyx_v_keep_original, PyObject *__pyx_v_csi); /* proto */ jpayne@68: static int __pyx_pf_5pysam_9libctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */ jpayne@68: static void __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile___reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile_2__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6__pyx_unpickle_Parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_8__pyx_unpickle_asTuple(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10__pyx_unpickle_asGFF3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_12__pyx_unpickle_asGTF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14__pyx_unpickle_asBed(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16__pyx_unpickle_asVCF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asGFF3(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorHead(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ jpayne@68: static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_keys = {0, 0, 0, 0, 0}; jpayne@68: /* #### Code section: late_includes ### */ jpayne@68: /* #### Code section: module_state ### */ jpayne@68: typedef struct { jpayne@68: PyObject *__pyx_d; jpayne@68: PyObject *__pyx_b; jpayne@68: PyObject *__pyx_cython_runtime; jpayne@68: PyObject *__pyx_empty_tuple; jpayne@68: PyObject *__pyx_empty_bytes; jpayne@68: PyObject *__pyx_empty_unicode; jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: PyTypeObject *__pyx_CyFunctionType; jpayne@68: #endif jpayne@68: #ifdef __Pyx_FusedFunction_USED jpayne@68: PyTypeObject *__pyx_FusedFunctionType; jpayne@68: #endif jpayne@68: #ifdef __Pyx_Generator_USED jpayne@68: PyTypeObject *__pyx_GeneratorType; jpayne@68: #endif jpayne@68: #ifdef __Pyx_IterableCoroutine_USED jpayne@68: PyTypeObject *__pyx_IterableCoroutineType; jpayne@68: #endif jpayne@68: #ifdef __Pyx_Coroutine_USED jpayne@68: PyTypeObject *__pyx_CoroutineAwaitType; jpayne@68: #endif jpayne@68: #ifdef __Pyx_Coroutine_USED jpayne@68: PyTypeObject *__pyx_CoroutineType; jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_5pysam_10libchtslib_HTSFile; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_7cpython_4type_type; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_7cpython_4bool_bool; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_7cpython_7complex_complex; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_TupleProxy; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_GTFProxy; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_BedProxy; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_16libctabixproxies_VCFProxy; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_7cpython_5array_array; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_tabix_file_iterator; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_TabixFile; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_Parser; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_asTuple; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_asGTF; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_asGFF3; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_asBed; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_asVCF; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_TabixIterator; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_GZIterator; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_GZIteratorHead; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_GZIteratorParsed; jpayne@68: PyObject *__pyx_type_5pysam_9libctabix_Tabixfile; jpayne@68: #endif jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_tabix_file_iterator; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixFile; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_Parser; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_asTuple; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_asGTF; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_asGFF3; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_asBed; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_asVCF; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixIterator; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIterator; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIteratorHead; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_GZIteratorParsed; jpayne@68: PyTypeObject *__pyx_ptype_5pysam_9libctabix_Tabixfile; jpayne@68: PyObject *__pyx_n_s_AssertionError; jpayne@68: PyObject *__pyx_kp_u_Could_not_open_file; jpayne@68: PyObject *__pyx_n_s_EmptyIterator; jpayne@68: PyObject *__pyx_n_s_EmptyIterator___iter; jpayne@68: PyObject *__pyx_n_s_EmptyIterator___next; jpayne@68: PyObject *__pyx_kp_u_Filename_s_already_exists_use_fo; jpayne@68: PyObject *__pyx_n_s_GZIterator; jpayne@68: PyObject *__pyx_n_u_GZIterator; jpayne@68: PyObject *__pyx_n_s_GZIteratorHead; jpayne@68: PyObject *__pyx_n_u_GZIteratorHead; jpayne@68: PyObject *__pyx_n_s_GZIteratorHead___reduce_cython; jpayne@68: PyObject *__pyx_n_s_GZIteratorHead___setstate_cython; jpayne@68: PyObject *__pyx_n_s_GZIteratorParsed; jpayne@68: PyObject *__pyx_n_s_GZIteratorParsed___reduce_cython; jpayne@68: PyObject *__pyx_n_s_GZIteratorParsed___setstate_cyth; jpayne@68: PyObject *__pyx_n_s_GZIterator___reduce_cython; jpayne@68: PyObject *__pyx_n_s_GZIterator___setstate_cython; jpayne@68: PyObject *__pyx_n_s_IOError; jpayne@68: PyObject *__pyx_kp_u_I_O_operation_on_closed_file; jpayne@68: PyObject *__pyx_kp_u_I_O_operation_on_closed_file_2; jpayne@68: PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; jpayne@68: PyObject *__pyx_n_s_KeyError; jpayne@68: PyObject *__pyx_n_s_MemoryError; jpayne@68: PyObject *__pyx_kp_u_No_such_file_or_directory_s; jpayne@68: PyObject *__pyx_n_s_NotImplementedError; jpayne@68: PyObject *__pyx_n_s_OSError; jpayne@68: PyObject *__pyx_n_s_O_RDONLY; jpayne@68: PyObject *__pyx_n_s_Parser; jpayne@68: PyObject *__pyx_n_s_Parser___reduce_cython; jpayne@68: PyObject *__pyx_n_s_Parser___setstate_cython; jpayne@68: PyObject *__pyx_n_s_Parser_get_encoding; jpayne@68: PyObject *__pyx_n_s_Parser_set_encoding; jpayne@68: PyObject *__pyx_n_s_PickleError; jpayne@68: PyObject *__pyx_n_s_StopIteration; jpayne@68: PyObject *__pyx_n_s_TabixFile; jpayne@68: PyObject *__pyx_n_u_TabixFile; jpayne@68: PyObject *__pyx_n_s_TabixFile___reduce_cython; jpayne@68: PyObject *__pyx_n_s_TabixFile___setstate_cython; jpayne@68: PyObject *__pyx_n_s_TabixFile__dup; jpayne@68: PyObject *__pyx_n_s_TabixFile__open; jpayne@68: PyObject *__pyx_n_s_TabixFile_close; jpayne@68: PyObject *__pyx_n_s_TabixFile_fetch; jpayne@68: PyObject *__pyx_n_s_TabixIterator; jpayne@68: PyObject *__pyx_n_s_TabixIteratorParsed; jpayne@68: PyObject *__pyx_n_s_TabixIteratorParsed___reduce_cyt; jpayne@68: PyObject *__pyx_n_s_TabixIteratorParsed___setstate_c; jpayne@68: PyObject *__pyx_n_s_TabixIterator___reduce_cython; jpayne@68: PyObject *__pyx_n_s_TabixIterator___setstate_cython; jpayne@68: PyObject *__pyx_n_s_Tabixfile; jpayne@68: PyObject *__pyx_n_u_Tabixfile; jpayne@68: PyObject *__pyx_n_s_Tabixfile___reduce_cython; jpayne@68: PyObject *__pyx_n_s_Tabixfile___setstate_cython; jpayne@68: PyObject *__pyx_n_s_TypeError; jpayne@68: PyObject *__pyx_n_s_ValueError; jpayne@68: PyObject *__pyx_n_s_WINDOW_SIZE; jpayne@68: PyObject *__pyx_kp_b__16; jpayne@68: PyObject *__pyx_kp_u__39; jpayne@68: PyObject *__pyx_kp_u__42; jpayne@68: PyObject *__pyx_kp_u__43; jpayne@68: PyObject *__pyx_kp_u__44; jpayne@68: PyObject *__pyx_kp_u__56; jpayne@68: PyObject *__pyx_n_s__62; jpayne@68: PyObject *__pyx_n_s__78; jpayne@68: PyObject *__pyx_n_s_a; jpayne@68: PyObject *__pyx_n_s_all; jpayne@68: PyObject *__pyx_n_s_asBed; jpayne@68: PyObject *__pyx_n_u_asBed; jpayne@68: PyObject *__pyx_n_s_asBed___reduce_cython; jpayne@68: PyObject *__pyx_n_s_asBed___setstate_cython; jpayne@68: PyObject *__pyx_n_s_asGFF3; jpayne@68: PyObject *__pyx_n_u_asGFF3; jpayne@68: PyObject *__pyx_n_s_asGFF3___reduce_cython; jpayne@68: PyObject *__pyx_n_s_asGFF3___setstate_cython; jpayne@68: PyObject *__pyx_n_s_asGTF; jpayne@68: PyObject *__pyx_n_u_asGTF; jpayne@68: PyObject *__pyx_n_s_asGTF___reduce_cython; jpayne@68: PyObject *__pyx_n_s_asGTF___setstate_cython; jpayne@68: PyObject *__pyx_n_s_asTuple; jpayne@68: PyObject *__pyx_n_u_asTuple; jpayne@68: PyObject *__pyx_n_s_asTuple___reduce_cython; jpayne@68: PyObject *__pyx_n_s_asTuple___setstate_cython; jpayne@68: PyObject *__pyx_n_s_asVCF; jpayne@68: PyObject *__pyx_n_u_asVCF; jpayne@68: PyObject *__pyx_n_s_asVCF___reduce_cython; jpayne@68: PyObject *__pyx_n_s_asVCF___setstate_cython; jpayne@68: PyObject *__pyx_n_u_ascii; jpayne@68: PyObject *__pyx_n_s_asyncio_coroutines; jpayne@68: PyObject *__pyx_n_s_b; jpayne@68: PyObject *__pyx_n_u_bcf; jpayne@68: PyObject *__pyx_n_u_bed; jpayne@68: PyObject *__pyx_n_s_buffer; jpayne@68: PyObject *__pyx_n_s_buffer_size; jpayne@68: PyObject *__pyx_kp_u_building_of_index_for_failed; jpayne@68: PyObject *__pyx_n_s_bytes_cpy; jpayne@68: PyObject *__pyx_n_s_c; jpayne@68: PyObject *__pyx_n_s_cfilename; jpayne@68: PyObject *__pyx_n_s_cfilename_index; jpayne@68: PyObject *__pyx_n_s_cfn; jpayne@68: PyObject *__pyx_n_s_cline_in_traceback; jpayne@68: PyObject *__pyx_n_s_close; jpayne@68: PyObject *__pyx_n_s_closed; jpayne@68: PyObject *__pyx_n_s_conf; jpayne@68: PyObject *__pyx_n_s_conf_data; jpayne@68: PyObject *__pyx_n_s_contigs; jpayne@68: PyObject *__pyx_kp_u_could_not_create_iterator_for_re; jpayne@68: PyObject *__pyx_kp_u_could_not_create_iterator_possib; jpayne@68: PyObject *__pyx_kp_u_could_not_load_tbi_csi_index_of; jpayne@68: PyObject *__pyx_kp_u_could_not_open_file_s; jpayne@68: PyObject *__pyx_kp_u_could_not_open_for_reading_heade; jpayne@68: PyObject *__pyx_kp_u_could_not_open_index_for_s; jpayne@68: PyObject *__pyx_kp_u_could_not_open_s_for_reading; jpayne@68: PyObject *__pyx_kp_u_could_not_open_s_for_writing; jpayne@68: PyObject *__pyx_n_s_cpy; jpayne@68: PyObject *__pyx_n_s_csi; jpayne@68: PyObject *__pyx_kp_u_csi_2; jpayne@68: PyObject *__pyx_n_s_cstr; jpayne@68: PyObject *__pyx_n_s_dict; jpayne@68: PyObject *__pyx_n_s_dict_2; jpayne@68: PyObject *__pyx_kp_u_disable; jpayne@68: PyObject *__pyx_n_s_doc; jpayne@68: PyObject *__pyx_n_s_dup; jpayne@68: PyObject *__pyx_kp_s_empty_iterator; jpayne@68: PyObject *__pyx_kp_u_enable; jpayne@68: PyObject *__pyx_n_s_encoding; jpayne@68: PyObject *__pyx_n_s_end; jpayne@68: PyObject *__pyx_n_s_end_col; jpayne@68: PyObject *__pyx_kp_u_end_out_of_range_i; jpayne@68: PyObject *__pyx_kp_u_error_i_when_closing_file_s; jpayne@68: PyObject *__pyx_kp_u_error_i_when_writing_to_file_s; jpayne@68: PyObject *__pyx_n_s_exists; jpayne@68: PyObject *__pyx_n_s_fd_src; jpayne@68: PyObject *__pyx_n_s_fetch; jpayne@68: PyObject *__pyx_kp_u_file_s_not_found; jpayne@68: PyObject *__pyx_n_s_filename; jpayne@68: PyObject *__pyx_n_s_filename_in; jpayne@68: PyObject *__pyx_n_s_filename_index; jpayne@68: PyObject *__pyx_n_s_filename_out; jpayne@68: PyObject *__pyx_kp_u_filename_s_already_exists_use_fo; jpayne@68: PyObject *__pyx_n_s_fileobj; jpayne@68: PyObject *__pyx_n_s_fmt; jpayne@68: PyObject *__pyx_n_s_fn; jpayne@68: PyObject *__pyx_n_s_fn_index; jpayne@68: PyObject *__pyx_n_s_fnidx; jpayne@68: PyObject *__pyx_n_s_force; jpayne@68: PyObject *__pyx_n_s_format; jpayne@68: PyObject *__pyx_n_s_fp; jpayne@68: PyObject *__pyx_kp_u_gc; jpayne@68: PyObject *__pyx_n_s_get_encoding; jpayne@68: PyObject *__pyx_n_s_getstate; jpayne@68: PyObject *__pyx_n_u_gff; jpayne@68: PyObject *__pyx_kp_u_gz; jpayne@68: PyObject *__pyx_n_s_import; jpayne@68: PyObject *__pyx_kp_u_incomplete_line_at_s; jpayne@68: PyObject *__pyx_n_s_index; jpayne@68: PyObject *__pyx_kp_u_index_s_not_found; jpayne@68: PyObject *__pyx_n_s_infile; jpayne@68: PyObject *__pyx_n_s_init; jpayne@68: PyObject *__pyx_n_s_init_subclass; jpayne@68: PyObject *__pyx_n_s_initializing; jpayne@68: PyObject *__pyx_kp_u_invalid_file_opening_mode_s; jpayne@68: PyObject *__pyx_n_s_is_coroutine; jpayne@68: PyObject *__pyx_n_s_is_empty; jpayne@68: PyObject *__pyx_n_s_is_open; jpayne@68: PyObject *__pyx_kp_u_isenabled; jpayne@68: PyObject *__pyx_n_s_iter; jpayne@68: PyObject *__pyx_kp_s_iterate_over_infile_Permits_the; jpayne@68: PyObject *__pyx_kp_u_iteration_on_closed_file; jpayne@68: PyObject *__pyx_n_s_itr; jpayne@68: PyObject *__pyx_n_s_keep_original; jpayne@68: PyObject *__pyx_n_s_keys; jpayne@68: PyObject *__pyx_n_s_length; jpayne@68: PyObject *__pyx_n_s_line; jpayne@68: PyObject *__pyx_n_s_line_skip; jpayne@68: PyObject *__pyx_n_s_main; jpayne@68: PyObject *__pyx_n_s_meta_char; jpayne@68: PyObject *__pyx_n_s_metaclass; jpayne@68: PyObject *__pyx_n_s_min_shift; jpayne@68: PyObject *__pyx_n_s_mode; jpayne@68: PyObject *__pyx_n_s_module; jpayne@68: PyObject *__pyx_n_s_multiple_iterators; jpayne@68: PyObject *__pyx_n_s_name; jpayne@68: PyObject *__pyx_n_s_nbytes; jpayne@68: PyObject *__pyx_kp_u_neither_preset_nor_seq_col_start; jpayne@68: PyObject *__pyx_n_s_new; jpayne@68: PyObject *__pyx_n_s_next; jpayne@68: PyObject *__pyx_kp_s_no_default___reduce___due_to_non; jpayne@68: PyObject *__pyx_n_s_open; jpayne@68: PyObject *__pyx_n_s_os; jpayne@68: PyObject *__pyx_kp_u_parse_method_of_s_not_implemente; jpayne@68: PyObject *__pyx_n_s_parser; jpayne@68: PyObject *__pyx_n_s_path; jpayne@68: PyObject *__pyx_n_s_pickle; jpayne@68: PyObject *__pyx_n_s_prepare; jpayne@68: PyObject *__pyx_n_s_preset; jpayne@68: PyObject *__pyx_n_s_preset2conf; jpayne@68: PyObject *__pyx_n_u_psltbl; jpayne@68: PyObject *__pyx_n_s_pysam_libctabix; jpayne@68: PyObject *__pyx_kp_s_pysam_libctabix_pyx; jpayne@68: PyObject *__pyx_n_s_pyx_PickleError; jpayne@68: PyObject *__pyx_n_s_pyx_checksum; jpayne@68: PyObject *__pyx_n_s_pyx_result; jpayne@68: PyObject *__pyx_n_s_pyx_state; jpayne@68: PyObject *__pyx_n_s_pyx_type; jpayne@68: PyObject *__pyx_n_s_pyx_unpickle_Parser; jpayne@68: PyObject *__pyx_n_s_pyx_unpickle_asBed; jpayne@68: PyObject *__pyx_n_s_pyx_unpickle_asGFF3; jpayne@68: PyObject *__pyx_n_s_pyx_unpickle_asGTF; jpayne@68: PyObject *__pyx_n_s_pyx_unpickle_asTuple; jpayne@68: PyObject *__pyx_n_s_pyx_unpickle_asVCF; jpayne@68: PyObject *__pyx_n_s_pyx_vtable; jpayne@68: PyObject *__pyx_n_s_qualname; jpayne@68: PyObject *__pyx_n_s_r; jpayne@68: PyObject *__pyx_n_u_r; jpayne@68: PyObject *__pyx_n_s_readline; jpayne@68: PyObject *__pyx_n_s_reduce; jpayne@68: PyObject *__pyx_n_s_reduce_cython; jpayne@68: PyObject *__pyx_n_s_reduce_ex; jpayne@68: PyObject *__pyx_n_s_reference; jpayne@68: PyObject *__pyx_n_s_region; jpayne@68: PyObject *__pyx_n_s_retval; jpayne@68: PyObject *__pyx_kp_u_s; jpayne@68: PyObject *__pyx_n_s_s_2; jpayne@68: PyObject *__pyx_kp_u_s_i; jpayne@68: PyObject *__pyx_kp_u_s_i_i; jpayne@68: PyObject *__pyx_n_u_sam; jpayne@68: PyObject *__pyx_n_s_self; jpayne@68: PyObject *__pyx_kp_s_self_gzipfile_self_kstream_canno; jpayne@68: PyObject *__pyx_kp_s_self_iterator_cannot_be_converte; jpayne@68: PyObject *__pyx_n_s_seq_col; jpayne@68: PyObject *__pyx_n_s_set_encoding; jpayne@68: PyObject *__pyx_n_s_set_name; jpayne@68: PyObject *__pyx_n_s_setstate; jpayne@68: PyObject *__pyx_n_s_setstate_cython; jpayne@68: PyObject *__pyx_n_s_spec; jpayne@68: PyObject *__pyx_n_s_start; jpayne@68: PyObject *__pyx_n_s_start_col; jpayne@68: PyObject *__pyx_kp_u_start_i_end_i; jpayne@68: PyObject *__pyx_kp_u_start_out_of_range_i; jpayne@68: PyObject *__pyx_n_s_state; jpayne@68: PyObject *__pyx_kp_s_stringsource; jpayne@68: PyObject *__pyx_n_s_suffix; jpayne@68: PyObject *__pyx_n_s_super; jpayne@68: PyObject *__pyx_n_s_sys; jpayne@68: PyObject *__pyx_n_s_tabix_compress; jpayne@68: PyObject *__pyx_n_u_tabix_compress; jpayne@68: PyObject *__pyx_n_s_tabix_file_iterator; jpayne@68: PyObject *__pyx_n_u_tabix_file_iterator; jpayne@68: PyObject *__pyx_n_s_tabix_file_iterator___reduce_cyt; jpayne@68: PyObject *__pyx_n_s_tabix_file_iterator___setstate_c; jpayne@68: PyObject *__pyx_n_s_tabix_generic_iterator; jpayne@68: PyObject *__pyx_n_u_tabix_generic_iterator; jpayne@68: PyObject *__pyx_n_s_tabix_generic_iterator___init; jpayne@68: PyObject *__pyx_n_s_tabix_generic_iterator___iter; jpayne@68: PyObject *__pyx_n_s_tabix_generic_iterator___next; jpayne@68: PyObject *__pyx_n_s_tabix_index; jpayne@68: PyObject *__pyx_n_u_tabix_index; jpayne@68: PyObject *__pyx_n_s_tabix_iterator; jpayne@68: PyObject *__pyx_n_u_tabix_iterator; jpayne@68: PyObject *__pyx_kp_u_tbi; jpayne@68: PyObject *__pyx_n_s_tell; jpayne@68: PyObject *__pyx_n_s_test; jpayne@68: PyObject *__pyx_n_s_threads; jpayne@68: PyObject *__pyx_kp_u_unknown_preset; jpayne@68: PyObject *__pyx_n_s_unlink; jpayne@68: PyObject *__pyx_n_s_update; jpayne@68: PyObject *__pyx_n_s_use_setstate; jpayne@68: PyObject *__pyx_kp_u_valid_presets_are; jpayne@68: PyObject *__pyx_n_u_vcf; jpayne@68: PyObject *__pyx_kp_u_writing_failed; jpayne@68: PyObject *__pyx_n_s_zerobased; jpayne@68: PyObject *__pyx_int_0; jpayne@68: PyObject *__pyx_int_1; jpayne@68: PyObject *__pyx_int_2; jpayne@68: PyObject *__pyx_int_3; jpayne@68: PyObject *__pyx_int_4; jpayne@68: PyObject *__pyx_int_5; jpayne@68: PyObject *__pyx_int_15; jpayne@68: PyObject *__pyx_int_17; jpayne@68: PyObject *__pyx_int_18; jpayne@68: PyObject *__pyx_int_35; jpayne@68: PyObject *__pyx_int_64; jpayne@68: PyObject *__pyx_int_21667264; jpayne@68: PyObject *__pyx_int_139192863; jpayne@68: PyObject *__pyx_int_243541226; jpayne@68: PyObject *__pyx_int_neg_1; jpayne@68: PyObject *__pyx_codeobj_; jpayne@68: PyObject *__pyx_tuple__19; jpayne@68: PyObject *__pyx_tuple__20; jpayne@68: PyObject *__pyx_tuple__24; jpayne@68: PyObject *__pyx_tuple__38; jpayne@68: PyObject *__pyx_tuple__41; jpayne@68: PyObject *__pyx_tuple__45; jpayne@68: PyObject *__pyx_tuple__55; jpayne@68: PyObject *__pyx_tuple__63; jpayne@68: PyObject *__pyx_tuple__64; jpayne@68: PyObject *__pyx_tuple__65; jpayne@68: PyObject *__pyx_tuple__66; jpayne@68: PyObject *__pyx_tuple__67; jpayne@68: PyObject *__pyx_tuple__68; jpayne@68: PyObject *__pyx_tuple__69; jpayne@68: PyObject *__pyx_tuple__70; jpayne@68: PyObject *__pyx_tuple__71; jpayne@68: PyObject *__pyx_tuple__72; jpayne@68: PyObject *__pyx_tuple__73; jpayne@68: PyObject *__pyx_tuple__74; jpayne@68: PyObject *__pyx_tuple__75; jpayne@68: PyObject *__pyx_tuple__76; jpayne@68: PyObject *__pyx_tuple__77; jpayne@68: PyObject *__pyx_codeobj__2; jpayne@68: PyObject *__pyx_codeobj__3; jpayne@68: PyObject *__pyx_codeobj__4; jpayne@68: PyObject *__pyx_codeobj__5; jpayne@68: PyObject *__pyx_codeobj__6; jpayne@68: PyObject *__pyx_codeobj__7; jpayne@68: PyObject *__pyx_codeobj__8; jpayne@68: PyObject *__pyx_codeobj__9; jpayne@68: PyObject *__pyx_codeobj__10; jpayne@68: PyObject *__pyx_codeobj__11; jpayne@68: PyObject *__pyx_codeobj__12; jpayne@68: PyObject *__pyx_codeobj__13; jpayne@68: PyObject *__pyx_codeobj__14; jpayne@68: PyObject *__pyx_codeobj__15; jpayne@68: PyObject *__pyx_codeobj__17; jpayne@68: PyObject *__pyx_codeobj__18; jpayne@68: PyObject *__pyx_codeobj__21; jpayne@68: PyObject *__pyx_codeobj__22; jpayne@68: PyObject *__pyx_codeobj__23; jpayne@68: PyObject *__pyx_codeobj__25; jpayne@68: PyObject *__pyx_codeobj__26; jpayne@68: PyObject *__pyx_codeobj__27; jpayne@68: PyObject *__pyx_codeobj__28; jpayne@68: PyObject *__pyx_codeobj__29; jpayne@68: PyObject *__pyx_codeobj__30; jpayne@68: PyObject *__pyx_codeobj__31; jpayne@68: PyObject *__pyx_codeobj__32; jpayne@68: PyObject *__pyx_codeobj__33; jpayne@68: PyObject *__pyx_codeobj__34; jpayne@68: PyObject *__pyx_codeobj__35; jpayne@68: PyObject *__pyx_codeobj__36; jpayne@68: PyObject *__pyx_codeobj__37; jpayne@68: PyObject *__pyx_codeobj__40; jpayne@68: PyObject *__pyx_codeobj__46; jpayne@68: PyObject *__pyx_codeobj__47; jpayne@68: PyObject *__pyx_codeobj__48; jpayne@68: PyObject *__pyx_codeobj__49; jpayne@68: PyObject *__pyx_codeobj__50; jpayne@68: PyObject *__pyx_codeobj__51; jpayne@68: PyObject *__pyx_codeobj__52; jpayne@68: PyObject *__pyx_codeobj__53; jpayne@68: PyObject *__pyx_codeobj__54; jpayne@68: PyObject *__pyx_codeobj__57; jpayne@68: PyObject *__pyx_codeobj__58; jpayne@68: PyObject *__pyx_codeobj__59; jpayne@68: PyObject *__pyx_codeobj__60; jpayne@68: PyObject *__pyx_codeobj__61; jpayne@68: } __pyx_mstate; jpayne@68: jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #ifdef __cplusplus jpayne@68: namespace { jpayne@68: extern struct PyModuleDef __pyx_moduledef; jpayne@68: } /* anonymous namespace */ jpayne@68: #else jpayne@68: static struct PyModuleDef __pyx_moduledef; jpayne@68: #endif jpayne@68: jpayne@68: #define __pyx_mstate(o) ((__pyx_mstate *)__Pyx_PyModule_GetState(o)) jpayne@68: jpayne@68: #define __pyx_mstate_global (__pyx_mstate(PyState_FindModule(&__pyx_moduledef))) jpayne@68: jpayne@68: #define __pyx_m (PyState_FindModule(&__pyx_moduledef)) jpayne@68: #else jpayne@68: static __pyx_mstate __pyx_mstate_global_static = jpayne@68: #ifdef __cplusplus jpayne@68: {}; jpayne@68: #else jpayne@68: {0}; jpayne@68: #endif jpayne@68: static __pyx_mstate *__pyx_mstate_global = &__pyx_mstate_global_static; jpayne@68: #endif jpayne@68: /* #### Code section: module_state_clear ### */ jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: static int __pyx_m_clear(PyObject *m) { jpayne@68: __pyx_mstate *clear_module_state = __pyx_mstate(m); jpayne@68: if (!clear_module_state) return 0; jpayne@68: Py_CLEAR(clear_module_state->__pyx_d); jpayne@68: Py_CLEAR(clear_module_state->__pyx_b); jpayne@68: Py_CLEAR(clear_module_state->__pyx_cython_runtime); jpayne@68: Py_CLEAR(clear_module_state->__pyx_empty_tuple); jpayne@68: Py_CLEAR(clear_module_state->__pyx_empty_bytes); jpayne@68: Py_CLEAR(clear_module_state->__pyx_empty_unicode); jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: Py_CLEAR(clear_module_state->__pyx_CyFunctionType); jpayne@68: #endif jpayne@68: #ifdef __Pyx_FusedFunction_USED jpayne@68: Py_CLEAR(clear_module_state->__pyx_FusedFunctionType); jpayne@68: #endif jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4type_type); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4bool_bool); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_7complex_complex); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_BedProxy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_5array_array); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_tabix_file_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixFile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_TabixFile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_Parser); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_Parser); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asTuple); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asTuple); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asGTF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asGTF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asGFF3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asGFF3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asBed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asBed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_asVCF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_asVCF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_TabixIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_TabixIteratorParsed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_GZIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorHead); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_GZIteratorHead); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_GZIteratorParsed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_9libctabix_Tabixfile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_type_5pysam_9libctabix_Tabixfile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_AssertionError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_Could_not_open_file); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_EmptyIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_EmptyIterator___iter); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_EmptyIterator___next); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_Filename_s_already_exists_use_fo); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_GZIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorHead); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_GZIteratorHead); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorHead___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorHead___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorParsed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorParsed___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIteratorParsed___setstate_cyth); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIterator___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_GZIterator___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_IOError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_I_O_operation_on_closed_file); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_I_O_operation_on_closed_file_2); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_KeyError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_MemoryError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_No_such_file_or_directory_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_NotImplementedError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_OSError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_O_RDONLY); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Parser); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Parser___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Parser___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Parser_get_encoding); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Parser_set_encoding); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_PickleError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_StopIteration); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_TabixFile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile__dup); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile__open); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile_close); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixFile_fetch); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixIterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixIteratorParsed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixIteratorParsed___reduce_cyt); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixIteratorParsed___setstate_c); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixIterator___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TabixIterator___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_Tabixfile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_Tabixfile___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_TypeError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_ValueError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_WINDOW_SIZE); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_b__16); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u__39); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u__42); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u__43); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u__44); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u__56); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s__62); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s__78); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_a); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_all); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asBed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_asBed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asBed___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asBed___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asGFF3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_asGFF3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asGFF3___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asGFF3___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asGTF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_asGTF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asGTF___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asGTF___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asTuple); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_asTuple); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asTuple___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asTuple___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asVCF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_asVCF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asVCF___reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asVCF___setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_ascii); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_asyncio_coroutines); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_b); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_bcf); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_bed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_buffer); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_buffer_size); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_building_of_index_for_failed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_bytes_cpy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_c); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_cfilename); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_cfilename_index); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_cfn); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_cline_in_traceback); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_close); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_closed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_conf); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_conf_data); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_contigs); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_create_iterator_for_re); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_create_iterator_possib); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_load_tbi_csi_index_of); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_file_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_for_reading_heade); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_index_for_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_s_for_reading); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_could_not_open_s_for_writing); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_cpy); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_csi); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_csi_2); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_cstr); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_dict); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_dict_2); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_disable); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_doc); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_dup); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_empty_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_enable); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_encoding); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_end); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_end_col); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_end_out_of_range_i); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_error_i_when_closing_file_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_error_i_when_writing_to_file_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_exists); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fd_src); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fetch); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_file_s_not_found); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_filename); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_filename_in); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_filename_index); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_filename_out); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_filename_s_already_exists_use_fo); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fileobj); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fmt); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fn); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fn_index); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fnidx); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_force); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_format); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_fp); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_gc); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_get_encoding); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_getstate); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_gff); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_gz); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_import); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_incomplete_line_at_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_index); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_index_s_not_found); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_infile); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_init); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_init_subclass); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_initializing); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_invalid_file_opening_mode_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_is_coroutine); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_is_empty); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_is_open); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_isenabled); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_iter); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_iterate_over_infile_Permits_the); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_iteration_on_closed_file); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_itr); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_keep_original); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_keys); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_length); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_line); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_line_skip); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_main); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_meta_char); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_metaclass); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_min_shift); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_mode); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_module); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_multiple_iterators); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_name); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_nbytes); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_neither_preset_nor_seq_col_start); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_new); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_next); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_no_default___reduce___due_to_non); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_open); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_os); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_parse_method_of_s_not_implemente); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_parser); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_path); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pickle); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_prepare); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_preset); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_preset2conf); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_psltbl); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pysam_libctabix); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_pysam_libctabix_pyx); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_PickleError); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_checksum); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_result); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_state); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_type); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_Parser); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asBed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asGFF3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asGTF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asTuple); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_unpickle_asVCF); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_pyx_vtable); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_qualname); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_r); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_r); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_readline); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_reduce); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_reduce_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_reduce_ex); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_reference); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_region); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_retval); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_s); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_s_2); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_s_i); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_s_i_i); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_sam); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_self); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_self_gzipfile_self_kstream_canno); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_self_iterator_cannot_be_converte); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_seq_col); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_set_encoding); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_set_name); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_setstate); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_setstate_cython); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_spec); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_start); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_start_col); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_start_i_end_i); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_start_out_of_range_i); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_state); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_s_stringsource); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_suffix); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_super); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_sys); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_compress); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_tabix_compress); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_file_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_tabix_file_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_file_iterator___reduce_cyt); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_file_iterator___setstate_c); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_tabix_generic_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator___init); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator___iter); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_generic_iterator___next); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_index); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_tabix_index); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tabix_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_tabix_iterator); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_tbi); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_tell); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_test); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_threads); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_unknown_preset); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_unlink); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_update); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_use_setstate); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_valid_presets_are); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_u_vcf); jpayne@68: Py_CLEAR(clear_module_state->__pyx_kp_u_writing_failed); jpayne@68: Py_CLEAR(clear_module_state->__pyx_n_s_zerobased); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_0); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_1); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_2); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_4); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_5); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_15); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_17); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_18); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_35); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_64); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_21667264); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_139192863); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_243541226); jpayne@68: Py_CLEAR(clear_module_state->__pyx_int_neg_1); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj_); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__19); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__20); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__24); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__38); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__41); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__45); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__55); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__63); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__64); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__65); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__66); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__67); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__68); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__69); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__70); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__71); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__72); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__73); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__74); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__75); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__76); jpayne@68: Py_CLEAR(clear_module_state->__pyx_tuple__77); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__2); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__3); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__4); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__5); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__6); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__7); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__8); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__9); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__10); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__11); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__12); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__13); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__14); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__15); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__17); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__18); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__21); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__22); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__23); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__25); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__26); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__27); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__28); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__29); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__30); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__31); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__32); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__33); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__34); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__35); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__36); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__37); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__40); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__46); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__47); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__48); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__49); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__50); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__51); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__52); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__53); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__54); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__57); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__58); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__59); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__60); jpayne@68: Py_CLEAR(clear_module_state->__pyx_codeobj__61); jpayne@68: return 0; jpayne@68: } jpayne@68: #endif jpayne@68: /* #### Code section: module_state_traverse ### */ jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { jpayne@68: __pyx_mstate *traverse_module_state = __pyx_mstate(m); jpayne@68: if (!traverse_module_state) return 0; jpayne@68: Py_VISIT(traverse_module_state->__pyx_d); jpayne@68: Py_VISIT(traverse_module_state->__pyx_b); jpayne@68: Py_VISIT(traverse_module_state->__pyx_cython_runtime); jpayne@68: Py_VISIT(traverse_module_state->__pyx_empty_tuple); jpayne@68: Py_VISIT(traverse_module_state->__pyx_empty_bytes); jpayne@68: Py_VISIT(traverse_module_state->__pyx_empty_unicode); jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: Py_VISIT(traverse_module_state->__pyx_CyFunctionType); jpayne@68: #endif jpayne@68: #ifdef __Pyx_FusedFunction_USED jpayne@68: Py_VISIT(traverse_module_state->__pyx_FusedFunctionType); jpayne@68: #endif jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4type_type); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4bool_bool); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_7complex_complex); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_BedProxy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_5array_array); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_tabix_file_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixFile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_TabixFile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_Parser); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_Parser); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asTuple); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asTuple); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asGTF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asGTF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asGFF3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asGFF3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asBed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asBed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_asVCF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_asVCF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_TabixIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_TabixIteratorParsed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_GZIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorHead); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_GZIteratorHead); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_GZIteratorParsed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_9libctabix_Tabixfile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_type_5pysam_9libctabix_Tabixfile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_AssertionError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_Could_not_open_file); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_EmptyIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_EmptyIterator___iter); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_EmptyIterator___next); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_Filename_s_already_exists_use_fo); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_GZIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorHead); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_GZIteratorHead); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorHead___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorHead___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorParsed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorParsed___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIteratorParsed___setstate_cyth); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIterator___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_GZIterator___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_IOError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_I_O_operation_on_closed_file); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_I_O_operation_on_closed_file_2); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_KeyError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_MemoryError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_No_such_file_or_directory_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_NotImplementedError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_OSError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_O_RDONLY); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Parser); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Parser___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Parser___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Parser_get_encoding); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Parser_set_encoding); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_PickleError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_StopIteration); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_TabixFile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile__dup); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile__open); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile_close); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixFile_fetch); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixIterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixIteratorParsed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixIteratorParsed___reduce_cyt); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixIteratorParsed___setstate_c); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixIterator___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TabixIterator___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_Tabixfile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_Tabixfile___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_TypeError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_ValueError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_WINDOW_SIZE); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_b__16); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u__39); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u__42); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u__43); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u__44); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u__56); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s__62); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s__78); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_a); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_all); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asBed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_asBed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asBed___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asBed___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asGFF3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_asGFF3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asGFF3___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asGFF3___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asGTF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_asGTF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asGTF___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asGTF___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asTuple); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_asTuple); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asTuple___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asTuple___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asVCF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_asVCF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asVCF___reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asVCF___setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_ascii); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_asyncio_coroutines); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_b); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_bcf); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_bed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_buffer); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_buffer_size); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_building_of_index_for_failed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_bytes_cpy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_c); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_cfilename); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_cfilename_index); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_cfn); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_cline_in_traceback); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_close); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_closed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_conf); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_conf_data); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_contigs); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_create_iterator_for_re); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_create_iterator_possib); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_load_tbi_csi_index_of); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_file_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_for_reading_heade); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_index_for_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_s_for_reading); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_could_not_open_s_for_writing); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_cpy); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_csi); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_csi_2); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_cstr); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_dict); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_dict_2); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_disable); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_doc); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_dup); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_empty_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_enable); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_encoding); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_end); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_end_col); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_end_out_of_range_i); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_error_i_when_closing_file_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_error_i_when_writing_to_file_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_exists); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fd_src); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fetch); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_file_s_not_found); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_filename); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_filename_in); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_filename_index); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_filename_out); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_filename_s_already_exists_use_fo); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fileobj); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fmt); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fn); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fn_index); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fnidx); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_force); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_format); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_fp); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_gc); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_get_encoding); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_getstate); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_gff); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_gz); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_import); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_incomplete_line_at_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_index); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_index_s_not_found); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_infile); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_init); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_init_subclass); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_initializing); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_invalid_file_opening_mode_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_is_coroutine); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_is_empty); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_is_open); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_isenabled); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_iter); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_iterate_over_infile_Permits_the); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_iteration_on_closed_file); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_itr); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_keep_original); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_keys); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_length); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_line); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_line_skip); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_main); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_meta_char); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_metaclass); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_min_shift); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_mode); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_module); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_multiple_iterators); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_name); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_nbytes); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_neither_preset_nor_seq_col_start); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_new); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_next); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_no_default___reduce___due_to_non); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_open); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_os); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_parse_method_of_s_not_implemente); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_parser); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_path); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pickle); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_prepare); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_preset); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_preset2conf); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_psltbl); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pysam_libctabix); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_pysam_libctabix_pyx); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_PickleError); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_checksum); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_result); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_state); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_type); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_Parser); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asBed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asGFF3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asGTF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asTuple); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_unpickle_asVCF); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_pyx_vtable); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_qualname); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_r); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_r); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_readline); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_reduce); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_reduce_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_reduce_ex); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_reference); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_region); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_retval); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_s); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_s_2); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_s_i); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_s_i_i); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_sam); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_self); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_self_gzipfile_self_kstream_canno); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_self_iterator_cannot_be_converte); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_seq_col); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_set_encoding); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_set_name); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_setstate); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_setstate_cython); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_spec); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_start); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_start_col); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_start_i_end_i); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_start_out_of_range_i); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_state); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_s_stringsource); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_suffix); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_super); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_sys); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_compress); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_tabix_compress); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_file_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_tabix_file_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_file_iterator___reduce_cyt); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_file_iterator___setstate_c); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_tabix_generic_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator___init); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator___iter); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_generic_iterator___next); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_index); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_tabix_index); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tabix_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_tabix_iterator); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_tbi); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_tell); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_test); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_threads); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_unknown_preset); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_unlink); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_update); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_use_setstate); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_valid_presets_are); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_u_vcf); jpayne@68: Py_VISIT(traverse_module_state->__pyx_kp_u_writing_failed); jpayne@68: Py_VISIT(traverse_module_state->__pyx_n_s_zerobased); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_0); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_1); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_2); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_4); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_5); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_15); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_17); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_18); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_35); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_64); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_21667264); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_139192863); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_243541226); jpayne@68: Py_VISIT(traverse_module_state->__pyx_int_neg_1); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj_); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__19); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__20); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__24); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__38); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__41); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__45); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__55); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__63); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__64); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__65); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__66); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__67); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__68); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__69); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__70); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__71); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__72); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__73); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__74); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__75); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__76); jpayne@68: Py_VISIT(traverse_module_state->__pyx_tuple__77); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__2); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__3); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__4); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__5); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__6); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__7); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__8); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__9); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__10); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__11); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__12); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__13); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__14); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__15); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__17); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__18); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__21); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__22); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__23); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__25); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__26); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__27); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__28); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__29); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__30); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__31); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__32); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__33); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__34); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__35); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__36); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__37); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__40); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__46); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__47); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__48); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__49); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__50); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__51); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__52); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__53); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__54); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__57); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__58); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__59); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__60); jpayne@68: Py_VISIT(traverse_module_state->__pyx_codeobj__61); jpayne@68: return 0; jpayne@68: } jpayne@68: #endif jpayne@68: /* #### Code section: module_state_defines ### */ jpayne@68: #define __pyx_d __pyx_mstate_global->__pyx_d jpayne@68: #define __pyx_b __pyx_mstate_global->__pyx_b jpayne@68: #define __pyx_cython_runtime __pyx_mstate_global->__pyx_cython_runtime jpayne@68: #define __pyx_empty_tuple __pyx_mstate_global->__pyx_empty_tuple jpayne@68: #define __pyx_empty_bytes __pyx_mstate_global->__pyx_empty_bytes jpayne@68: #define __pyx_empty_unicode __pyx_mstate_global->__pyx_empty_unicode jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: #define __pyx_CyFunctionType __pyx_mstate_global->__pyx_CyFunctionType jpayne@68: #endif jpayne@68: #ifdef __Pyx_FusedFunction_USED jpayne@68: #define __pyx_FusedFunctionType __pyx_mstate_global->__pyx_FusedFunctionType jpayne@68: #endif jpayne@68: #ifdef __Pyx_Generator_USED jpayne@68: #define __pyx_GeneratorType __pyx_mstate_global->__pyx_GeneratorType jpayne@68: #endif jpayne@68: #ifdef __Pyx_IterableCoroutine_USED jpayne@68: #define __pyx_IterableCoroutineType __pyx_mstate_global->__pyx_IterableCoroutineType jpayne@68: #endif jpayne@68: #ifdef __Pyx_Coroutine_USED jpayne@68: #define __pyx_CoroutineAwaitType __pyx_mstate_global->__pyx_CoroutineAwaitType jpayne@68: #endif jpayne@68: #ifdef __Pyx_Coroutine_USED jpayne@68: #define __pyx_CoroutineType __pyx_mstate_global->__pyx_CoroutineType jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #define __pyx_ptype_5pysam_10libchtslib_HTSFile __pyx_mstate_global->__pyx_ptype_5pysam_10libchtslib_HTSFile jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #define __pyx_ptype_7cpython_4type_type __pyx_mstate_global->__pyx_ptype_7cpython_4type_type jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #define __pyx_ptype_7cpython_4bool_bool __pyx_mstate_global->__pyx_ptype_7cpython_4bool_bool jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #define __pyx_ptype_7cpython_7complex_complex __pyx_mstate_global->__pyx_ptype_7cpython_7complex_complex jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_TupleProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_TupleProxy jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_GTFProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_GTFProxy jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_BedProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_BedProxy jpayne@68: #define __pyx_ptype_5pysam_16libctabixproxies_VCFProxy __pyx_mstate_global->__pyx_ptype_5pysam_16libctabixproxies_VCFProxy jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #define __pyx_ptype_7cpython_5array_array __pyx_mstate_global->__pyx_ptype_7cpython_5array_array jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: #define __pyx_type_5pysam_9libctabix_tabix_file_iterator __pyx_mstate_global->__pyx_type_5pysam_9libctabix_tabix_file_iterator jpayne@68: #define __pyx_type_5pysam_9libctabix_TabixFile __pyx_mstate_global->__pyx_type_5pysam_9libctabix_TabixFile jpayne@68: #define __pyx_type_5pysam_9libctabix_Parser __pyx_mstate_global->__pyx_type_5pysam_9libctabix_Parser jpayne@68: #define __pyx_type_5pysam_9libctabix_asTuple __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asTuple jpayne@68: #define __pyx_type_5pysam_9libctabix_asGTF __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asGTF jpayne@68: #define __pyx_type_5pysam_9libctabix_asGFF3 __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asGFF3 jpayne@68: #define __pyx_type_5pysam_9libctabix_asBed __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asBed jpayne@68: #define __pyx_type_5pysam_9libctabix_asVCF __pyx_mstate_global->__pyx_type_5pysam_9libctabix_asVCF jpayne@68: #define __pyx_type_5pysam_9libctabix_TabixIterator __pyx_mstate_global->__pyx_type_5pysam_9libctabix_TabixIterator jpayne@68: #define __pyx_type_5pysam_9libctabix_TabixIteratorParsed __pyx_mstate_global->__pyx_type_5pysam_9libctabix_TabixIteratorParsed jpayne@68: #define __pyx_type_5pysam_9libctabix_GZIterator __pyx_mstate_global->__pyx_type_5pysam_9libctabix_GZIterator jpayne@68: #define __pyx_type_5pysam_9libctabix_GZIteratorHead __pyx_mstate_global->__pyx_type_5pysam_9libctabix_GZIteratorHead jpayne@68: #define __pyx_type_5pysam_9libctabix_GZIteratorParsed __pyx_mstate_global->__pyx_type_5pysam_9libctabix_GZIteratorParsed jpayne@68: #define __pyx_type_5pysam_9libctabix_Tabixfile __pyx_mstate_global->__pyx_type_5pysam_9libctabix_Tabixfile jpayne@68: #endif jpayne@68: #define __pyx_ptype_5pysam_9libctabix_tabix_file_iterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_tabix_file_iterator jpayne@68: #define __pyx_ptype_5pysam_9libctabix_TabixFile __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixFile jpayne@68: #define __pyx_ptype_5pysam_9libctabix_Parser __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_Parser jpayne@68: #define __pyx_ptype_5pysam_9libctabix_asTuple __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asTuple jpayne@68: #define __pyx_ptype_5pysam_9libctabix_asGTF __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asGTF jpayne@68: #define __pyx_ptype_5pysam_9libctabix_asGFF3 __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asGFF3 jpayne@68: #define __pyx_ptype_5pysam_9libctabix_asBed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asBed jpayne@68: #define __pyx_ptype_5pysam_9libctabix_asVCF __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_asVCF jpayne@68: #define __pyx_ptype_5pysam_9libctabix_TabixIterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixIterator jpayne@68: #define __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed jpayne@68: #define __pyx_ptype_5pysam_9libctabix_GZIterator __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIterator jpayne@68: #define __pyx_ptype_5pysam_9libctabix_GZIteratorHead __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIteratorHead jpayne@68: #define __pyx_ptype_5pysam_9libctabix_GZIteratorParsed __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_GZIteratorParsed jpayne@68: #define __pyx_ptype_5pysam_9libctabix_Tabixfile __pyx_mstate_global->__pyx_ptype_5pysam_9libctabix_Tabixfile jpayne@68: #define __pyx_n_s_AssertionError __pyx_mstate_global->__pyx_n_s_AssertionError jpayne@68: #define __pyx_kp_u_Could_not_open_file __pyx_mstate_global->__pyx_kp_u_Could_not_open_file jpayne@68: #define __pyx_n_s_EmptyIterator __pyx_mstate_global->__pyx_n_s_EmptyIterator jpayne@68: #define __pyx_n_s_EmptyIterator___iter __pyx_mstate_global->__pyx_n_s_EmptyIterator___iter jpayne@68: #define __pyx_n_s_EmptyIterator___next __pyx_mstate_global->__pyx_n_s_EmptyIterator___next jpayne@68: #define __pyx_kp_u_Filename_s_already_exists_use_fo __pyx_mstate_global->__pyx_kp_u_Filename_s_already_exists_use_fo jpayne@68: #define __pyx_n_s_GZIterator __pyx_mstate_global->__pyx_n_s_GZIterator jpayne@68: #define __pyx_n_u_GZIterator __pyx_mstate_global->__pyx_n_u_GZIterator jpayne@68: #define __pyx_n_s_GZIteratorHead __pyx_mstate_global->__pyx_n_s_GZIteratorHead jpayne@68: #define __pyx_n_u_GZIteratorHead __pyx_mstate_global->__pyx_n_u_GZIteratorHead jpayne@68: #define __pyx_n_s_GZIteratorHead___reduce_cython __pyx_mstate_global->__pyx_n_s_GZIteratorHead___reduce_cython jpayne@68: #define __pyx_n_s_GZIteratorHead___setstate_cython __pyx_mstate_global->__pyx_n_s_GZIteratorHead___setstate_cython jpayne@68: #define __pyx_n_s_GZIteratorParsed __pyx_mstate_global->__pyx_n_s_GZIteratorParsed jpayne@68: #define __pyx_n_s_GZIteratorParsed___reduce_cython __pyx_mstate_global->__pyx_n_s_GZIteratorParsed___reduce_cython jpayne@68: #define __pyx_n_s_GZIteratorParsed___setstate_cyth __pyx_mstate_global->__pyx_n_s_GZIteratorParsed___setstate_cyth jpayne@68: #define __pyx_n_s_GZIterator___reduce_cython __pyx_mstate_global->__pyx_n_s_GZIterator___reduce_cython jpayne@68: #define __pyx_n_s_GZIterator___setstate_cython __pyx_mstate_global->__pyx_n_s_GZIterator___setstate_cython jpayne@68: #define __pyx_n_s_IOError __pyx_mstate_global->__pyx_n_s_IOError jpayne@68: #define __pyx_kp_u_I_O_operation_on_closed_file __pyx_mstate_global->__pyx_kp_u_I_O_operation_on_closed_file jpayne@68: #define __pyx_kp_u_I_O_operation_on_closed_file_2 __pyx_mstate_global->__pyx_kp_u_I_O_operation_on_closed_file_2 jpayne@68: #define __pyx_kp_s_Incompatible_checksums_0x_x_vs_0 __pyx_mstate_global->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0 jpayne@68: #define __pyx_n_s_KeyError __pyx_mstate_global->__pyx_n_s_KeyError jpayne@68: #define __pyx_n_s_MemoryError __pyx_mstate_global->__pyx_n_s_MemoryError jpayne@68: #define __pyx_kp_u_No_such_file_or_directory_s __pyx_mstate_global->__pyx_kp_u_No_such_file_or_directory_s jpayne@68: #define __pyx_n_s_NotImplementedError __pyx_mstate_global->__pyx_n_s_NotImplementedError jpayne@68: #define __pyx_n_s_OSError __pyx_mstate_global->__pyx_n_s_OSError jpayne@68: #define __pyx_n_s_O_RDONLY __pyx_mstate_global->__pyx_n_s_O_RDONLY jpayne@68: #define __pyx_n_s_Parser __pyx_mstate_global->__pyx_n_s_Parser jpayne@68: #define __pyx_n_s_Parser___reduce_cython __pyx_mstate_global->__pyx_n_s_Parser___reduce_cython jpayne@68: #define __pyx_n_s_Parser___setstate_cython __pyx_mstate_global->__pyx_n_s_Parser___setstate_cython jpayne@68: #define __pyx_n_s_Parser_get_encoding __pyx_mstate_global->__pyx_n_s_Parser_get_encoding jpayne@68: #define __pyx_n_s_Parser_set_encoding __pyx_mstate_global->__pyx_n_s_Parser_set_encoding jpayne@68: #define __pyx_n_s_PickleError __pyx_mstate_global->__pyx_n_s_PickleError jpayne@68: #define __pyx_n_s_StopIteration __pyx_mstate_global->__pyx_n_s_StopIteration jpayne@68: #define __pyx_n_s_TabixFile __pyx_mstate_global->__pyx_n_s_TabixFile jpayne@68: #define __pyx_n_u_TabixFile __pyx_mstate_global->__pyx_n_u_TabixFile jpayne@68: #define __pyx_n_s_TabixFile___reduce_cython __pyx_mstate_global->__pyx_n_s_TabixFile___reduce_cython jpayne@68: #define __pyx_n_s_TabixFile___setstate_cython __pyx_mstate_global->__pyx_n_s_TabixFile___setstate_cython jpayne@68: #define __pyx_n_s_TabixFile__dup __pyx_mstate_global->__pyx_n_s_TabixFile__dup jpayne@68: #define __pyx_n_s_TabixFile__open __pyx_mstate_global->__pyx_n_s_TabixFile__open jpayne@68: #define __pyx_n_s_TabixFile_close __pyx_mstate_global->__pyx_n_s_TabixFile_close jpayne@68: #define __pyx_n_s_TabixFile_fetch __pyx_mstate_global->__pyx_n_s_TabixFile_fetch jpayne@68: #define __pyx_n_s_TabixIterator __pyx_mstate_global->__pyx_n_s_TabixIterator jpayne@68: #define __pyx_n_s_TabixIteratorParsed __pyx_mstate_global->__pyx_n_s_TabixIteratorParsed jpayne@68: #define __pyx_n_s_TabixIteratorParsed___reduce_cyt __pyx_mstate_global->__pyx_n_s_TabixIteratorParsed___reduce_cyt jpayne@68: #define __pyx_n_s_TabixIteratorParsed___setstate_c __pyx_mstate_global->__pyx_n_s_TabixIteratorParsed___setstate_c jpayne@68: #define __pyx_n_s_TabixIterator___reduce_cython __pyx_mstate_global->__pyx_n_s_TabixIterator___reduce_cython jpayne@68: #define __pyx_n_s_TabixIterator___setstate_cython __pyx_mstate_global->__pyx_n_s_TabixIterator___setstate_cython jpayne@68: #define __pyx_n_s_Tabixfile __pyx_mstate_global->__pyx_n_s_Tabixfile jpayne@68: #define __pyx_n_u_Tabixfile __pyx_mstate_global->__pyx_n_u_Tabixfile jpayne@68: #define __pyx_n_s_Tabixfile___reduce_cython __pyx_mstate_global->__pyx_n_s_Tabixfile___reduce_cython jpayne@68: #define __pyx_n_s_Tabixfile___setstate_cython __pyx_mstate_global->__pyx_n_s_Tabixfile___setstate_cython jpayne@68: #define __pyx_n_s_TypeError __pyx_mstate_global->__pyx_n_s_TypeError jpayne@68: #define __pyx_n_s_ValueError __pyx_mstate_global->__pyx_n_s_ValueError jpayne@68: #define __pyx_n_s_WINDOW_SIZE __pyx_mstate_global->__pyx_n_s_WINDOW_SIZE jpayne@68: #define __pyx_kp_b__16 __pyx_mstate_global->__pyx_kp_b__16 jpayne@68: #define __pyx_kp_u__39 __pyx_mstate_global->__pyx_kp_u__39 jpayne@68: #define __pyx_kp_u__42 __pyx_mstate_global->__pyx_kp_u__42 jpayne@68: #define __pyx_kp_u__43 __pyx_mstate_global->__pyx_kp_u__43 jpayne@68: #define __pyx_kp_u__44 __pyx_mstate_global->__pyx_kp_u__44 jpayne@68: #define __pyx_kp_u__56 __pyx_mstate_global->__pyx_kp_u__56 jpayne@68: #define __pyx_n_s__62 __pyx_mstate_global->__pyx_n_s__62 jpayne@68: #define __pyx_n_s__78 __pyx_mstate_global->__pyx_n_s__78 jpayne@68: #define __pyx_n_s_a __pyx_mstate_global->__pyx_n_s_a jpayne@68: #define __pyx_n_s_all __pyx_mstate_global->__pyx_n_s_all jpayne@68: #define __pyx_n_s_asBed __pyx_mstate_global->__pyx_n_s_asBed jpayne@68: #define __pyx_n_u_asBed __pyx_mstate_global->__pyx_n_u_asBed jpayne@68: #define __pyx_n_s_asBed___reduce_cython __pyx_mstate_global->__pyx_n_s_asBed___reduce_cython jpayne@68: #define __pyx_n_s_asBed___setstate_cython __pyx_mstate_global->__pyx_n_s_asBed___setstate_cython jpayne@68: #define __pyx_n_s_asGFF3 __pyx_mstate_global->__pyx_n_s_asGFF3 jpayne@68: #define __pyx_n_u_asGFF3 __pyx_mstate_global->__pyx_n_u_asGFF3 jpayne@68: #define __pyx_n_s_asGFF3___reduce_cython __pyx_mstate_global->__pyx_n_s_asGFF3___reduce_cython jpayne@68: #define __pyx_n_s_asGFF3___setstate_cython __pyx_mstate_global->__pyx_n_s_asGFF3___setstate_cython jpayne@68: #define __pyx_n_s_asGTF __pyx_mstate_global->__pyx_n_s_asGTF jpayne@68: #define __pyx_n_u_asGTF __pyx_mstate_global->__pyx_n_u_asGTF jpayne@68: #define __pyx_n_s_asGTF___reduce_cython __pyx_mstate_global->__pyx_n_s_asGTF___reduce_cython jpayne@68: #define __pyx_n_s_asGTF___setstate_cython __pyx_mstate_global->__pyx_n_s_asGTF___setstate_cython jpayne@68: #define __pyx_n_s_asTuple __pyx_mstate_global->__pyx_n_s_asTuple jpayne@68: #define __pyx_n_u_asTuple __pyx_mstate_global->__pyx_n_u_asTuple jpayne@68: #define __pyx_n_s_asTuple___reduce_cython __pyx_mstate_global->__pyx_n_s_asTuple___reduce_cython jpayne@68: #define __pyx_n_s_asTuple___setstate_cython __pyx_mstate_global->__pyx_n_s_asTuple___setstate_cython jpayne@68: #define __pyx_n_s_asVCF __pyx_mstate_global->__pyx_n_s_asVCF jpayne@68: #define __pyx_n_u_asVCF __pyx_mstate_global->__pyx_n_u_asVCF jpayne@68: #define __pyx_n_s_asVCF___reduce_cython __pyx_mstate_global->__pyx_n_s_asVCF___reduce_cython jpayne@68: #define __pyx_n_s_asVCF___setstate_cython __pyx_mstate_global->__pyx_n_s_asVCF___setstate_cython jpayne@68: #define __pyx_n_u_ascii __pyx_mstate_global->__pyx_n_u_ascii jpayne@68: #define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines jpayne@68: #define __pyx_n_s_b __pyx_mstate_global->__pyx_n_s_b jpayne@68: #define __pyx_n_u_bcf __pyx_mstate_global->__pyx_n_u_bcf jpayne@68: #define __pyx_n_u_bed __pyx_mstate_global->__pyx_n_u_bed jpayne@68: #define __pyx_n_s_buffer __pyx_mstate_global->__pyx_n_s_buffer jpayne@68: #define __pyx_n_s_buffer_size __pyx_mstate_global->__pyx_n_s_buffer_size jpayne@68: #define __pyx_kp_u_building_of_index_for_failed __pyx_mstate_global->__pyx_kp_u_building_of_index_for_failed jpayne@68: #define __pyx_n_s_bytes_cpy __pyx_mstate_global->__pyx_n_s_bytes_cpy jpayne@68: #define __pyx_n_s_c __pyx_mstate_global->__pyx_n_s_c jpayne@68: #define __pyx_n_s_cfilename __pyx_mstate_global->__pyx_n_s_cfilename jpayne@68: #define __pyx_n_s_cfilename_index __pyx_mstate_global->__pyx_n_s_cfilename_index jpayne@68: #define __pyx_n_s_cfn __pyx_mstate_global->__pyx_n_s_cfn jpayne@68: #define __pyx_n_s_cline_in_traceback __pyx_mstate_global->__pyx_n_s_cline_in_traceback jpayne@68: #define __pyx_n_s_close __pyx_mstate_global->__pyx_n_s_close jpayne@68: #define __pyx_n_s_closed __pyx_mstate_global->__pyx_n_s_closed jpayne@68: #define __pyx_n_s_conf __pyx_mstate_global->__pyx_n_s_conf jpayne@68: #define __pyx_n_s_conf_data __pyx_mstate_global->__pyx_n_s_conf_data jpayne@68: #define __pyx_n_s_contigs __pyx_mstate_global->__pyx_n_s_contigs jpayne@68: #define __pyx_kp_u_could_not_create_iterator_for_re __pyx_mstate_global->__pyx_kp_u_could_not_create_iterator_for_re jpayne@68: #define __pyx_kp_u_could_not_create_iterator_possib __pyx_mstate_global->__pyx_kp_u_could_not_create_iterator_possib jpayne@68: #define __pyx_kp_u_could_not_load_tbi_csi_index_of __pyx_mstate_global->__pyx_kp_u_could_not_load_tbi_csi_index_of jpayne@68: #define __pyx_kp_u_could_not_open_file_s __pyx_mstate_global->__pyx_kp_u_could_not_open_file_s jpayne@68: #define __pyx_kp_u_could_not_open_for_reading_heade __pyx_mstate_global->__pyx_kp_u_could_not_open_for_reading_heade jpayne@68: #define __pyx_kp_u_could_not_open_index_for_s __pyx_mstate_global->__pyx_kp_u_could_not_open_index_for_s jpayne@68: #define __pyx_kp_u_could_not_open_s_for_reading __pyx_mstate_global->__pyx_kp_u_could_not_open_s_for_reading jpayne@68: #define __pyx_kp_u_could_not_open_s_for_writing __pyx_mstate_global->__pyx_kp_u_could_not_open_s_for_writing jpayne@68: #define __pyx_n_s_cpy __pyx_mstate_global->__pyx_n_s_cpy jpayne@68: #define __pyx_n_s_csi __pyx_mstate_global->__pyx_n_s_csi jpayne@68: #define __pyx_kp_u_csi_2 __pyx_mstate_global->__pyx_kp_u_csi_2 jpayne@68: #define __pyx_n_s_cstr __pyx_mstate_global->__pyx_n_s_cstr jpayne@68: #define __pyx_n_s_dict __pyx_mstate_global->__pyx_n_s_dict jpayne@68: #define __pyx_n_s_dict_2 __pyx_mstate_global->__pyx_n_s_dict_2 jpayne@68: #define __pyx_kp_u_disable __pyx_mstate_global->__pyx_kp_u_disable jpayne@68: #define __pyx_n_s_doc __pyx_mstate_global->__pyx_n_s_doc jpayne@68: #define __pyx_n_s_dup __pyx_mstate_global->__pyx_n_s_dup jpayne@68: #define __pyx_kp_s_empty_iterator __pyx_mstate_global->__pyx_kp_s_empty_iterator jpayne@68: #define __pyx_kp_u_enable __pyx_mstate_global->__pyx_kp_u_enable jpayne@68: #define __pyx_n_s_encoding __pyx_mstate_global->__pyx_n_s_encoding jpayne@68: #define __pyx_n_s_end __pyx_mstate_global->__pyx_n_s_end jpayne@68: #define __pyx_n_s_end_col __pyx_mstate_global->__pyx_n_s_end_col jpayne@68: #define __pyx_kp_u_end_out_of_range_i __pyx_mstate_global->__pyx_kp_u_end_out_of_range_i jpayne@68: #define __pyx_kp_u_error_i_when_closing_file_s __pyx_mstate_global->__pyx_kp_u_error_i_when_closing_file_s jpayne@68: #define __pyx_kp_u_error_i_when_writing_to_file_s __pyx_mstate_global->__pyx_kp_u_error_i_when_writing_to_file_s jpayne@68: #define __pyx_n_s_exists __pyx_mstate_global->__pyx_n_s_exists jpayne@68: #define __pyx_n_s_fd_src __pyx_mstate_global->__pyx_n_s_fd_src jpayne@68: #define __pyx_n_s_fetch __pyx_mstate_global->__pyx_n_s_fetch jpayne@68: #define __pyx_kp_u_file_s_not_found __pyx_mstate_global->__pyx_kp_u_file_s_not_found jpayne@68: #define __pyx_n_s_filename __pyx_mstate_global->__pyx_n_s_filename jpayne@68: #define __pyx_n_s_filename_in __pyx_mstate_global->__pyx_n_s_filename_in jpayne@68: #define __pyx_n_s_filename_index __pyx_mstate_global->__pyx_n_s_filename_index jpayne@68: #define __pyx_n_s_filename_out __pyx_mstate_global->__pyx_n_s_filename_out jpayne@68: #define __pyx_kp_u_filename_s_already_exists_use_fo __pyx_mstate_global->__pyx_kp_u_filename_s_already_exists_use_fo jpayne@68: #define __pyx_n_s_fileobj __pyx_mstate_global->__pyx_n_s_fileobj jpayne@68: #define __pyx_n_s_fmt __pyx_mstate_global->__pyx_n_s_fmt jpayne@68: #define __pyx_n_s_fn __pyx_mstate_global->__pyx_n_s_fn jpayne@68: #define __pyx_n_s_fn_index __pyx_mstate_global->__pyx_n_s_fn_index jpayne@68: #define __pyx_n_s_fnidx __pyx_mstate_global->__pyx_n_s_fnidx jpayne@68: #define __pyx_n_s_force __pyx_mstate_global->__pyx_n_s_force jpayne@68: #define __pyx_n_s_format __pyx_mstate_global->__pyx_n_s_format jpayne@68: #define __pyx_n_s_fp __pyx_mstate_global->__pyx_n_s_fp jpayne@68: #define __pyx_kp_u_gc __pyx_mstate_global->__pyx_kp_u_gc jpayne@68: #define __pyx_n_s_get_encoding __pyx_mstate_global->__pyx_n_s_get_encoding jpayne@68: #define __pyx_n_s_getstate __pyx_mstate_global->__pyx_n_s_getstate jpayne@68: #define __pyx_n_u_gff __pyx_mstate_global->__pyx_n_u_gff jpayne@68: #define __pyx_kp_u_gz __pyx_mstate_global->__pyx_kp_u_gz jpayne@68: #define __pyx_n_s_import __pyx_mstate_global->__pyx_n_s_import jpayne@68: #define __pyx_kp_u_incomplete_line_at_s __pyx_mstate_global->__pyx_kp_u_incomplete_line_at_s jpayne@68: #define __pyx_n_s_index __pyx_mstate_global->__pyx_n_s_index jpayne@68: #define __pyx_kp_u_index_s_not_found __pyx_mstate_global->__pyx_kp_u_index_s_not_found jpayne@68: #define __pyx_n_s_infile __pyx_mstate_global->__pyx_n_s_infile jpayne@68: #define __pyx_n_s_init __pyx_mstate_global->__pyx_n_s_init jpayne@68: #define __pyx_n_s_init_subclass __pyx_mstate_global->__pyx_n_s_init_subclass jpayne@68: #define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing jpayne@68: #define __pyx_kp_u_invalid_file_opening_mode_s __pyx_mstate_global->__pyx_kp_u_invalid_file_opening_mode_s jpayne@68: #define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine jpayne@68: #define __pyx_n_s_is_empty __pyx_mstate_global->__pyx_n_s_is_empty jpayne@68: #define __pyx_n_s_is_open __pyx_mstate_global->__pyx_n_s_is_open jpayne@68: #define __pyx_kp_u_isenabled __pyx_mstate_global->__pyx_kp_u_isenabled jpayne@68: #define __pyx_n_s_iter __pyx_mstate_global->__pyx_n_s_iter jpayne@68: #define __pyx_kp_s_iterate_over_infile_Permits_the __pyx_mstate_global->__pyx_kp_s_iterate_over_infile_Permits_the jpayne@68: #define __pyx_kp_u_iteration_on_closed_file __pyx_mstate_global->__pyx_kp_u_iteration_on_closed_file jpayne@68: #define __pyx_n_s_itr __pyx_mstate_global->__pyx_n_s_itr jpayne@68: #define __pyx_n_s_keep_original __pyx_mstate_global->__pyx_n_s_keep_original jpayne@68: #define __pyx_n_s_keys __pyx_mstate_global->__pyx_n_s_keys jpayne@68: #define __pyx_n_s_length __pyx_mstate_global->__pyx_n_s_length jpayne@68: #define __pyx_n_s_line __pyx_mstate_global->__pyx_n_s_line jpayne@68: #define __pyx_n_s_line_skip __pyx_mstate_global->__pyx_n_s_line_skip jpayne@68: #define __pyx_n_s_main __pyx_mstate_global->__pyx_n_s_main jpayne@68: #define __pyx_n_s_meta_char __pyx_mstate_global->__pyx_n_s_meta_char jpayne@68: #define __pyx_n_s_metaclass __pyx_mstate_global->__pyx_n_s_metaclass jpayne@68: #define __pyx_n_s_min_shift __pyx_mstate_global->__pyx_n_s_min_shift jpayne@68: #define __pyx_n_s_mode __pyx_mstate_global->__pyx_n_s_mode jpayne@68: #define __pyx_n_s_module __pyx_mstate_global->__pyx_n_s_module jpayne@68: #define __pyx_n_s_multiple_iterators __pyx_mstate_global->__pyx_n_s_multiple_iterators jpayne@68: #define __pyx_n_s_name __pyx_mstate_global->__pyx_n_s_name jpayne@68: #define __pyx_n_s_nbytes __pyx_mstate_global->__pyx_n_s_nbytes jpayne@68: #define __pyx_kp_u_neither_preset_nor_seq_col_start __pyx_mstate_global->__pyx_kp_u_neither_preset_nor_seq_col_start jpayne@68: #define __pyx_n_s_new __pyx_mstate_global->__pyx_n_s_new jpayne@68: #define __pyx_n_s_next __pyx_mstate_global->__pyx_n_s_next jpayne@68: #define __pyx_kp_s_no_default___reduce___due_to_non __pyx_mstate_global->__pyx_kp_s_no_default___reduce___due_to_non jpayne@68: #define __pyx_n_s_open __pyx_mstate_global->__pyx_n_s_open jpayne@68: #define __pyx_n_s_os __pyx_mstate_global->__pyx_n_s_os jpayne@68: #define __pyx_kp_u_parse_method_of_s_not_implemente __pyx_mstate_global->__pyx_kp_u_parse_method_of_s_not_implemente jpayne@68: #define __pyx_n_s_parser __pyx_mstate_global->__pyx_n_s_parser jpayne@68: #define __pyx_n_s_path __pyx_mstate_global->__pyx_n_s_path jpayne@68: #define __pyx_n_s_pickle __pyx_mstate_global->__pyx_n_s_pickle jpayne@68: #define __pyx_n_s_prepare __pyx_mstate_global->__pyx_n_s_prepare jpayne@68: #define __pyx_n_s_preset __pyx_mstate_global->__pyx_n_s_preset jpayne@68: #define __pyx_n_s_preset2conf __pyx_mstate_global->__pyx_n_s_preset2conf jpayne@68: #define __pyx_n_u_psltbl __pyx_mstate_global->__pyx_n_u_psltbl jpayne@68: #define __pyx_n_s_pysam_libctabix __pyx_mstate_global->__pyx_n_s_pysam_libctabix jpayne@68: #define __pyx_kp_s_pysam_libctabix_pyx __pyx_mstate_global->__pyx_kp_s_pysam_libctabix_pyx jpayne@68: #define __pyx_n_s_pyx_PickleError __pyx_mstate_global->__pyx_n_s_pyx_PickleError jpayne@68: #define __pyx_n_s_pyx_checksum __pyx_mstate_global->__pyx_n_s_pyx_checksum jpayne@68: #define __pyx_n_s_pyx_result __pyx_mstate_global->__pyx_n_s_pyx_result jpayne@68: #define __pyx_n_s_pyx_state __pyx_mstate_global->__pyx_n_s_pyx_state jpayne@68: #define __pyx_n_s_pyx_type __pyx_mstate_global->__pyx_n_s_pyx_type jpayne@68: #define __pyx_n_s_pyx_unpickle_Parser __pyx_mstate_global->__pyx_n_s_pyx_unpickle_Parser jpayne@68: #define __pyx_n_s_pyx_unpickle_asBed __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asBed jpayne@68: #define __pyx_n_s_pyx_unpickle_asGFF3 __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asGFF3 jpayne@68: #define __pyx_n_s_pyx_unpickle_asGTF __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asGTF jpayne@68: #define __pyx_n_s_pyx_unpickle_asTuple __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asTuple jpayne@68: #define __pyx_n_s_pyx_unpickle_asVCF __pyx_mstate_global->__pyx_n_s_pyx_unpickle_asVCF jpayne@68: #define __pyx_n_s_pyx_vtable __pyx_mstate_global->__pyx_n_s_pyx_vtable jpayne@68: #define __pyx_n_s_qualname __pyx_mstate_global->__pyx_n_s_qualname jpayne@68: #define __pyx_n_s_r __pyx_mstate_global->__pyx_n_s_r jpayne@68: #define __pyx_n_u_r __pyx_mstate_global->__pyx_n_u_r jpayne@68: #define __pyx_n_s_readline __pyx_mstate_global->__pyx_n_s_readline jpayne@68: #define __pyx_n_s_reduce __pyx_mstate_global->__pyx_n_s_reduce jpayne@68: #define __pyx_n_s_reduce_cython __pyx_mstate_global->__pyx_n_s_reduce_cython jpayne@68: #define __pyx_n_s_reduce_ex __pyx_mstate_global->__pyx_n_s_reduce_ex jpayne@68: #define __pyx_n_s_reference __pyx_mstate_global->__pyx_n_s_reference jpayne@68: #define __pyx_n_s_region __pyx_mstate_global->__pyx_n_s_region jpayne@68: #define __pyx_n_s_retval __pyx_mstate_global->__pyx_n_s_retval jpayne@68: #define __pyx_kp_u_s __pyx_mstate_global->__pyx_kp_u_s jpayne@68: #define __pyx_n_s_s_2 __pyx_mstate_global->__pyx_n_s_s_2 jpayne@68: #define __pyx_kp_u_s_i __pyx_mstate_global->__pyx_kp_u_s_i jpayne@68: #define __pyx_kp_u_s_i_i __pyx_mstate_global->__pyx_kp_u_s_i_i jpayne@68: #define __pyx_n_u_sam __pyx_mstate_global->__pyx_n_u_sam jpayne@68: #define __pyx_n_s_self __pyx_mstate_global->__pyx_n_s_self jpayne@68: #define __pyx_kp_s_self_gzipfile_self_kstream_canno __pyx_mstate_global->__pyx_kp_s_self_gzipfile_self_kstream_canno jpayne@68: #define __pyx_kp_s_self_iterator_cannot_be_converte __pyx_mstate_global->__pyx_kp_s_self_iterator_cannot_be_converte jpayne@68: #define __pyx_n_s_seq_col __pyx_mstate_global->__pyx_n_s_seq_col jpayne@68: #define __pyx_n_s_set_encoding __pyx_mstate_global->__pyx_n_s_set_encoding jpayne@68: #define __pyx_n_s_set_name __pyx_mstate_global->__pyx_n_s_set_name jpayne@68: #define __pyx_n_s_setstate __pyx_mstate_global->__pyx_n_s_setstate jpayne@68: #define __pyx_n_s_setstate_cython __pyx_mstate_global->__pyx_n_s_setstate_cython jpayne@68: #define __pyx_n_s_spec __pyx_mstate_global->__pyx_n_s_spec jpayne@68: #define __pyx_n_s_start __pyx_mstate_global->__pyx_n_s_start jpayne@68: #define __pyx_n_s_start_col __pyx_mstate_global->__pyx_n_s_start_col jpayne@68: #define __pyx_kp_u_start_i_end_i __pyx_mstate_global->__pyx_kp_u_start_i_end_i jpayne@68: #define __pyx_kp_u_start_out_of_range_i __pyx_mstate_global->__pyx_kp_u_start_out_of_range_i jpayne@68: #define __pyx_n_s_state __pyx_mstate_global->__pyx_n_s_state jpayne@68: #define __pyx_kp_s_stringsource __pyx_mstate_global->__pyx_kp_s_stringsource jpayne@68: #define __pyx_n_s_suffix __pyx_mstate_global->__pyx_n_s_suffix jpayne@68: #define __pyx_n_s_super __pyx_mstate_global->__pyx_n_s_super jpayne@68: #define __pyx_n_s_sys __pyx_mstate_global->__pyx_n_s_sys jpayne@68: #define __pyx_n_s_tabix_compress __pyx_mstate_global->__pyx_n_s_tabix_compress jpayne@68: #define __pyx_n_u_tabix_compress __pyx_mstate_global->__pyx_n_u_tabix_compress jpayne@68: #define __pyx_n_s_tabix_file_iterator __pyx_mstate_global->__pyx_n_s_tabix_file_iterator jpayne@68: #define __pyx_n_u_tabix_file_iterator __pyx_mstate_global->__pyx_n_u_tabix_file_iterator jpayne@68: #define __pyx_n_s_tabix_file_iterator___reduce_cyt __pyx_mstate_global->__pyx_n_s_tabix_file_iterator___reduce_cyt jpayne@68: #define __pyx_n_s_tabix_file_iterator___setstate_c __pyx_mstate_global->__pyx_n_s_tabix_file_iterator___setstate_c jpayne@68: #define __pyx_n_s_tabix_generic_iterator __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator jpayne@68: #define __pyx_n_u_tabix_generic_iterator __pyx_mstate_global->__pyx_n_u_tabix_generic_iterator jpayne@68: #define __pyx_n_s_tabix_generic_iterator___init __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator___init jpayne@68: #define __pyx_n_s_tabix_generic_iterator___iter __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator___iter jpayne@68: #define __pyx_n_s_tabix_generic_iterator___next __pyx_mstate_global->__pyx_n_s_tabix_generic_iterator___next jpayne@68: #define __pyx_n_s_tabix_index __pyx_mstate_global->__pyx_n_s_tabix_index jpayne@68: #define __pyx_n_u_tabix_index __pyx_mstate_global->__pyx_n_u_tabix_index jpayne@68: #define __pyx_n_s_tabix_iterator __pyx_mstate_global->__pyx_n_s_tabix_iterator jpayne@68: #define __pyx_n_u_tabix_iterator __pyx_mstate_global->__pyx_n_u_tabix_iterator jpayne@68: #define __pyx_kp_u_tbi __pyx_mstate_global->__pyx_kp_u_tbi jpayne@68: #define __pyx_n_s_tell __pyx_mstate_global->__pyx_n_s_tell jpayne@68: #define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test jpayne@68: #define __pyx_n_s_threads __pyx_mstate_global->__pyx_n_s_threads jpayne@68: #define __pyx_kp_u_unknown_preset __pyx_mstate_global->__pyx_kp_u_unknown_preset jpayne@68: #define __pyx_n_s_unlink __pyx_mstate_global->__pyx_n_s_unlink jpayne@68: #define __pyx_n_s_update __pyx_mstate_global->__pyx_n_s_update jpayne@68: #define __pyx_n_s_use_setstate __pyx_mstate_global->__pyx_n_s_use_setstate jpayne@68: #define __pyx_kp_u_valid_presets_are __pyx_mstate_global->__pyx_kp_u_valid_presets_are jpayne@68: #define __pyx_n_u_vcf __pyx_mstate_global->__pyx_n_u_vcf jpayne@68: #define __pyx_kp_u_writing_failed __pyx_mstate_global->__pyx_kp_u_writing_failed jpayne@68: #define __pyx_n_s_zerobased __pyx_mstate_global->__pyx_n_s_zerobased jpayne@68: #define __pyx_int_0 __pyx_mstate_global->__pyx_int_0 jpayne@68: #define __pyx_int_1 __pyx_mstate_global->__pyx_int_1 jpayne@68: #define __pyx_int_2 __pyx_mstate_global->__pyx_int_2 jpayne@68: #define __pyx_int_3 __pyx_mstate_global->__pyx_int_3 jpayne@68: #define __pyx_int_4 __pyx_mstate_global->__pyx_int_4 jpayne@68: #define __pyx_int_5 __pyx_mstate_global->__pyx_int_5 jpayne@68: #define __pyx_int_15 __pyx_mstate_global->__pyx_int_15 jpayne@68: #define __pyx_int_17 __pyx_mstate_global->__pyx_int_17 jpayne@68: #define __pyx_int_18 __pyx_mstate_global->__pyx_int_18 jpayne@68: #define __pyx_int_35 __pyx_mstate_global->__pyx_int_35 jpayne@68: #define __pyx_int_64 __pyx_mstate_global->__pyx_int_64 jpayne@68: #define __pyx_int_21667264 __pyx_mstate_global->__pyx_int_21667264 jpayne@68: #define __pyx_int_139192863 __pyx_mstate_global->__pyx_int_139192863 jpayne@68: #define __pyx_int_243541226 __pyx_mstate_global->__pyx_int_243541226 jpayne@68: #define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1 jpayne@68: #define __pyx_codeobj_ __pyx_mstate_global->__pyx_codeobj_ jpayne@68: #define __pyx_tuple__19 __pyx_mstate_global->__pyx_tuple__19 jpayne@68: #define __pyx_tuple__20 __pyx_mstate_global->__pyx_tuple__20 jpayne@68: #define __pyx_tuple__24 __pyx_mstate_global->__pyx_tuple__24 jpayne@68: #define __pyx_tuple__38 __pyx_mstate_global->__pyx_tuple__38 jpayne@68: #define __pyx_tuple__41 __pyx_mstate_global->__pyx_tuple__41 jpayne@68: #define __pyx_tuple__45 __pyx_mstate_global->__pyx_tuple__45 jpayne@68: #define __pyx_tuple__55 __pyx_mstate_global->__pyx_tuple__55 jpayne@68: #define __pyx_tuple__63 __pyx_mstate_global->__pyx_tuple__63 jpayne@68: #define __pyx_tuple__64 __pyx_mstate_global->__pyx_tuple__64 jpayne@68: #define __pyx_tuple__65 __pyx_mstate_global->__pyx_tuple__65 jpayne@68: #define __pyx_tuple__66 __pyx_mstate_global->__pyx_tuple__66 jpayne@68: #define __pyx_tuple__67 __pyx_mstate_global->__pyx_tuple__67 jpayne@68: #define __pyx_tuple__68 __pyx_mstate_global->__pyx_tuple__68 jpayne@68: #define __pyx_tuple__69 __pyx_mstate_global->__pyx_tuple__69 jpayne@68: #define __pyx_tuple__70 __pyx_mstate_global->__pyx_tuple__70 jpayne@68: #define __pyx_tuple__71 __pyx_mstate_global->__pyx_tuple__71 jpayne@68: #define __pyx_tuple__72 __pyx_mstate_global->__pyx_tuple__72 jpayne@68: #define __pyx_tuple__73 __pyx_mstate_global->__pyx_tuple__73 jpayne@68: #define __pyx_tuple__74 __pyx_mstate_global->__pyx_tuple__74 jpayne@68: #define __pyx_tuple__75 __pyx_mstate_global->__pyx_tuple__75 jpayne@68: #define __pyx_tuple__76 __pyx_mstate_global->__pyx_tuple__76 jpayne@68: #define __pyx_tuple__77 __pyx_mstate_global->__pyx_tuple__77 jpayne@68: #define __pyx_codeobj__2 __pyx_mstate_global->__pyx_codeobj__2 jpayne@68: #define __pyx_codeobj__3 __pyx_mstate_global->__pyx_codeobj__3 jpayne@68: #define __pyx_codeobj__4 __pyx_mstate_global->__pyx_codeobj__4 jpayne@68: #define __pyx_codeobj__5 __pyx_mstate_global->__pyx_codeobj__5 jpayne@68: #define __pyx_codeobj__6 __pyx_mstate_global->__pyx_codeobj__6 jpayne@68: #define __pyx_codeobj__7 __pyx_mstate_global->__pyx_codeobj__7 jpayne@68: #define __pyx_codeobj__8 __pyx_mstate_global->__pyx_codeobj__8 jpayne@68: #define __pyx_codeobj__9 __pyx_mstate_global->__pyx_codeobj__9 jpayne@68: #define __pyx_codeobj__10 __pyx_mstate_global->__pyx_codeobj__10 jpayne@68: #define __pyx_codeobj__11 __pyx_mstate_global->__pyx_codeobj__11 jpayne@68: #define __pyx_codeobj__12 __pyx_mstate_global->__pyx_codeobj__12 jpayne@68: #define __pyx_codeobj__13 __pyx_mstate_global->__pyx_codeobj__13 jpayne@68: #define __pyx_codeobj__14 __pyx_mstate_global->__pyx_codeobj__14 jpayne@68: #define __pyx_codeobj__15 __pyx_mstate_global->__pyx_codeobj__15 jpayne@68: #define __pyx_codeobj__17 __pyx_mstate_global->__pyx_codeobj__17 jpayne@68: #define __pyx_codeobj__18 __pyx_mstate_global->__pyx_codeobj__18 jpayne@68: #define __pyx_codeobj__21 __pyx_mstate_global->__pyx_codeobj__21 jpayne@68: #define __pyx_codeobj__22 __pyx_mstate_global->__pyx_codeobj__22 jpayne@68: #define __pyx_codeobj__23 __pyx_mstate_global->__pyx_codeobj__23 jpayne@68: #define __pyx_codeobj__25 __pyx_mstate_global->__pyx_codeobj__25 jpayne@68: #define __pyx_codeobj__26 __pyx_mstate_global->__pyx_codeobj__26 jpayne@68: #define __pyx_codeobj__27 __pyx_mstate_global->__pyx_codeobj__27 jpayne@68: #define __pyx_codeobj__28 __pyx_mstate_global->__pyx_codeobj__28 jpayne@68: #define __pyx_codeobj__29 __pyx_mstate_global->__pyx_codeobj__29 jpayne@68: #define __pyx_codeobj__30 __pyx_mstate_global->__pyx_codeobj__30 jpayne@68: #define __pyx_codeobj__31 __pyx_mstate_global->__pyx_codeobj__31 jpayne@68: #define __pyx_codeobj__32 __pyx_mstate_global->__pyx_codeobj__32 jpayne@68: #define __pyx_codeobj__33 __pyx_mstate_global->__pyx_codeobj__33 jpayne@68: #define __pyx_codeobj__34 __pyx_mstate_global->__pyx_codeobj__34 jpayne@68: #define __pyx_codeobj__35 __pyx_mstate_global->__pyx_codeobj__35 jpayne@68: #define __pyx_codeobj__36 __pyx_mstate_global->__pyx_codeobj__36 jpayne@68: #define __pyx_codeobj__37 __pyx_mstate_global->__pyx_codeobj__37 jpayne@68: #define __pyx_codeobj__40 __pyx_mstate_global->__pyx_codeobj__40 jpayne@68: #define __pyx_codeobj__46 __pyx_mstate_global->__pyx_codeobj__46 jpayne@68: #define __pyx_codeobj__47 __pyx_mstate_global->__pyx_codeobj__47 jpayne@68: #define __pyx_codeobj__48 __pyx_mstate_global->__pyx_codeobj__48 jpayne@68: #define __pyx_codeobj__49 __pyx_mstate_global->__pyx_codeobj__49 jpayne@68: #define __pyx_codeobj__50 __pyx_mstate_global->__pyx_codeobj__50 jpayne@68: #define __pyx_codeobj__51 __pyx_mstate_global->__pyx_codeobj__51 jpayne@68: #define __pyx_codeobj__52 __pyx_mstate_global->__pyx_codeobj__52 jpayne@68: #define __pyx_codeobj__53 __pyx_mstate_global->__pyx_codeobj__53 jpayne@68: #define __pyx_codeobj__54 __pyx_mstate_global->__pyx_codeobj__54 jpayne@68: #define __pyx_codeobj__57 __pyx_mstate_global->__pyx_codeobj__57 jpayne@68: #define __pyx_codeobj__58 __pyx_mstate_global->__pyx_codeobj__58 jpayne@68: #define __pyx_codeobj__59 __pyx_mstate_global->__pyx_codeobj__59 jpayne@68: #define __pyx_codeobj__60 __pyx_mstate_global->__pyx_codeobj__60 jpayne@68: #define __pyx_codeobj__61 __pyx_mstate_global->__pyx_codeobj__61 jpayne@68: /* #### Code section: module_code ### */ jpayne@68: jpayne@68: /* "cpython/complex.pxd":19 jpayne@68: * jpayne@68: * @property jpayne@68: * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<< jpayne@68: * return self.cval.real jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self) { jpayne@68: double __pyx_r; jpayne@68: jpayne@68: /* "cpython/complex.pxd":20 jpayne@68: * @property jpayne@68: * cdef inline double real(self) noexcept: jpayne@68: * return self.cval.real # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * @property jpayne@68: */ jpayne@68: __pyx_r = __pyx_v_self->cval.real; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "cpython/complex.pxd":19 jpayne@68: * jpayne@68: * @property jpayne@68: * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<< jpayne@68: * return self.cval.real jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L0:; jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "cpython/complex.pxd":23 jpayne@68: * jpayne@68: * @property jpayne@68: * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<< jpayne@68: * return self.cval.imag jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self) { jpayne@68: double __pyx_r; jpayne@68: jpayne@68: /* "cpython/complex.pxd":24 jpayne@68: * @property jpayne@68: * cdef inline double imag(self) noexcept: jpayne@68: * return self.cval.imag # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # PyTypeObject PyComplex_Type jpayne@68: */ jpayne@68: __pyx_r = __pyx_v_self->cval.imag; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "cpython/complex.pxd":23 jpayne@68: * jpayne@68: * @property jpayne@68: * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<< jpayne@68: * return self.cval.imag jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L0:; jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":112 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<< jpayne@68: * """Return a new reference to the value of the context variable, jpayne@68: * or the default value of the context variable, jpayne@68: */ jpayne@68: jpayne@68: 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@68: PyObject *__pyx_v_default_value = ((PyObject *)Py_None); jpayne@68: PyObject *__pyx_v_value; jpayne@68: PyObject *__pyx_v_pyvalue = NULL; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("get_value", 1); jpayne@68: if (__pyx_optional_args) { jpayne@68: if (__pyx_optional_args->__pyx_n > 0) { jpayne@68: __pyx_v_default_value = __pyx_optional_args->default_value; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":117 jpayne@68: * or None if no such value or default was found. jpayne@68: * """ jpayne@68: * cdef PyObject *value = NULL # <<<<<<<<<<<<<< jpayne@68: * PyContextVar_Get(var, NULL, &value) jpayne@68: * if value is NULL: jpayne@68: */ jpayne@68: __pyx_v_value = NULL; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":118 jpayne@68: * """ jpayne@68: * cdef PyObject *value = NULL jpayne@68: * PyContextVar_Get(var, NULL, &value) # <<<<<<<<<<<<<< jpayne@68: * if value is NULL: jpayne@68: * # context variable does not have a default jpayne@68: */ jpayne@68: __pyx_t_1 = PyContextVar_Get(__pyx_v_var, NULL, (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 118, __pyx_L1_error) jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":119 jpayne@68: * cdef PyObject *value = NULL jpayne@68: * PyContextVar_Get(var, NULL, &value) jpayne@68: * if value is NULL: # <<<<<<<<<<<<<< jpayne@68: * # context variable does not have a default jpayne@68: * pyvalue = default_value jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_value == NULL); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":121 jpayne@68: * if value is NULL: jpayne@68: * # context variable does not have a default jpayne@68: * pyvalue = default_value # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * # value or default value of context variable jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_default_value); jpayne@68: __pyx_v_pyvalue = __pyx_v_default_value; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":119 jpayne@68: * cdef PyObject *value = NULL jpayne@68: * PyContextVar_Get(var, NULL, &value) jpayne@68: * if value is NULL: # <<<<<<<<<<<<<< jpayne@68: * # context variable does not have a default jpayne@68: * pyvalue = default_value jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":124 jpayne@68: * else: jpayne@68: * # value or default value of context variable jpayne@68: * pyvalue = value # <<<<<<<<<<<<<< jpayne@68: * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' jpayne@68: * return pyvalue jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_3 = ((PyObject *)__pyx_v_value); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __pyx_v_pyvalue = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":125 jpayne@68: * # value or default value of context variable jpayne@68: * pyvalue = value jpayne@68: * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<< jpayne@68: * return pyvalue jpayne@68: * jpayne@68: */ jpayne@68: Py_XDECREF(__pyx_v_value); jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":126 jpayne@68: * pyvalue = value jpayne@68: * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' jpayne@68: * return pyvalue # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_pyvalue); jpayne@68: __pyx_r = __pyx_v_pyvalue; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":112 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<< jpayne@68: * """Return a new reference to the value of the context variable, jpayne@68: * or the default value of the context variable, jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("cpython.contextvars.get_value", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_pyvalue); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":129 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<< jpayne@68: * """Return a new reference to the value of the context variable, jpayne@68: * or the provided default value if no such value was found. jpayne@68: */ jpayne@68: jpayne@68: 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@68: PyObject *__pyx_v_default_value = ((PyObject *)Py_None); jpayne@68: PyObject *__pyx_v_value; jpayne@68: PyObject *__pyx_v_pyvalue = NULL; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("get_value_no_default", 1); jpayne@68: if (__pyx_optional_args) { jpayne@68: if (__pyx_optional_args->__pyx_n > 0) { jpayne@68: __pyx_v_default_value = __pyx_optional_args->default_value; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":135 jpayne@68: * Ignores the default value of the context variable, if any. jpayne@68: * """ jpayne@68: * cdef PyObject *value = NULL # <<<<<<<<<<<<<< jpayne@68: * PyContextVar_Get(var, default_value, &value) jpayne@68: * # value of context variable or 'default_value' jpayne@68: */ jpayne@68: __pyx_v_value = NULL; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":136 jpayne@68: * """ jpayne@68: * cdef PyObject *value = NULL jpayne@68: * PyContextVar_Get(var, default_value, &value) # <<<<<<<<<<<<<< jpayne@68: * # value of context variable or 'default_value' jpayne@68: * pyvalue = value jpayne@68: */ jpayne@68: __pyx_t_1 = PyContextVar_Get(__pyx_v_var, ((PyObject *)__pyx_v_default_value), (&__pyx_v_value)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 136, __pyx_L1_error) jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":138 jpayne@68: * PyContextVar_Get(var, default_value, &value) jpayne@68: * # value of context variable or 'default_value' jpayne@68: * pyvalue = value # <<<<<<<<<<<<<< jpayne@68: * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' jpayne@68: * return pyvalue jpayne@68: */ jpayne@68: __pyx_t_2 = ((PyObject *)__pyx_v_value); jpayne@68: __Pyx_INCREF(__pyx_t_2); jpayne@68: __pyx_v_pyvalue = __pyx_t_2; jpayne@68: __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":139 jpayne@68: * # value of context variable or 'default_value' jpayne@68: * pyvalue = value jpayne@68: * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<< jpayne@68: * return pyvalue jpayne@68: */ jpayne@68: Py_XDECREF(__pyx_v_value); jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":140 jpayne@68: * pyvalue = value jpayne@68: * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' jpayne@68: * return pyvalue # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_pyvalue); jpayne@68: __pyx_r = __pyx_v_pyvalue; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "cpython/contextvars.pxd":129 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<< jpayne@68: * """Return a new reference to the value of the context variable, jpayne@68: * or the provided default value if no such value was found. jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_AddTraceback("cpython.contextvars.get_value_no_default", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_pyvalue); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":104 jpayne@68: * __data_union data jpayne@68: * jpayne@68: * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< jpayne@68: * # This implementation of getbuffer is geared towards Cython jpayne@68: * # requirements, and does not yet fulfill the PEP. jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: CYTHON_UNUSED static int __pyx_pw_7cpython_5array_5array_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ jpayne@68: 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@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_7cpython_5array_5array___getbuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags) { jpayne@68: PyObject *__pyx_v_item_count = NULL; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: char *__pyx_t_2; jpayne@68: int __pyx_t_3; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: Py_ssize_t __pyx_t_5; jpayne@68: int __pyx_t_6; jpayne@68: char __pyx_t_7; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: if (unlikely(__pyx_v_info == NULL)) { jpayne@68: PyErr_SetString(PyExc_BufferError, "PyObject_GetBuffer: view==NULL argument is obsolete"); jpayne@68: return -1; jpayne@68: } jpayne@68: __Pyx_RefNannySetupContext("__getbuffer__", 0); jpayne@68: __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(__pyx_v_info->obj); jpayne@68: jpayne@68: /* "array.pxd":109 jpayne@68: * # In particular strided access is always provided regardless jpayne@68: * # of flags jpayne@68: * item_count = Py_SIZE(self) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * info.suboffsets = NULL jpayne@68: */ jpayne@68: __pyx_t_1 = PyInt_FromSsize_t(Py_SIZE(((PyObject *)__pyx_v_self))); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 109, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_item_count = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "array.pxd":111 jpayne@68: * item_count = Py_SIZE(self) jpayne@68: * jpayne@68: * info.suboffsets = NULL # <<<<<<<<<<<<<< jpayne@68: * info.buf = self.data.as_chars jpayne@68: * info.readonly = 0 jpayne@68: */ jpayne@68: __pyx_v_info->suboffsets = NULL; jpayne@68: jpayne@68: /* "array.pxd":112 jpayne@68: * jpayne@68: * info.suboffsets = NULL jpayne@68: * info.buf = self.data.as_chars # <<<<<<<<<<<<<< jpayne@68: * info.readonly = 0 jpayne@68: * info.ndim = 1 jpayne@68: */ jpayne@68: __pyx_t_2 = __pyx_v_self->data.as_chars; jpayne@68: __pyx_v_info->buf = __pyx_t_2; jpayne@68: jpayne@68: /* "array.pxd":113 jpayne@68: * info.suboffsets = NULL jpayne@68: * info.buf = self.data.as_chars jpayne@68: * info.readonly = 0 # <<<<<<<<<<<<<< jpayne@68: * info.ndim = 1 jpayne@68: * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) jpayne@68: */ jpayne@68: __pyx_v_info->readonly = 0; jpayne@68: jpayne@68: /* "array.pxd":114 jpayne@68: * info.buf = self.data.as_chars jpayne@68: * info.readonly = 0 jpayne@68: * info.ndim = 1 # <<<<<<<<<<<<<< jpayne@68: * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) jpayne@68: * info.len = info.itemsize * item_count jpayne@68: */ jpayne@68: __pyx_v_info->ndim = 1; jpayne@68: jpayne@68: /* "array.pxd":115 jpayne@68: * info.readonly = 0 jpayne@68: * info.ndim = 1 jpayne@68: * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) # <<<<<<<<<<<<<< jpayne@68: * info.len = info.itemsize * item_count jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __pyx_v_self->ob_descr->itemsize; jpayne@68: __pyx_v_info->itemsize = __pyx_t_3; jpayne@68: jpayne@68: /* "array.pxd":116 jpayne@68: * info.ndim = 1 jpayne@68: * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) jpayne@68: * info.len = info.itemsize * item_count # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * info.shape = PyObject_Malloc(sizeof(Py_ssize_t) + 2) jpayne@68: */ jpayne@68: __pyx_t_1 = PyInt_FromSsize_t(__pyx_v_info->itemsize); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 116, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_4 = PyNumber_Multiply(__pyx_t_1, __pyx_v_item_count); if (unlikely(!__pyx_t_4)) __PYX_ERR(3, 116, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(3, 116, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_v_info->len = __pyx_t_5; jpayne@68: jpayne@68: /* "array.pxd":118 jpayne@68: * info.len = info.itemsize * item_count jpayne@68: * jpayne@68: * info.shape = PyObject_Malloc(sizeof(Py_ssize_t) + 2) # <<<<<<<<<<<<<< jpayne@68: * if not info.shape: jpayne@68: * raise MemoryError() jpayne@68: */ jpayne@68: __pyx_v_info->shape = ((Py_ssize_t *)PyObject_Malloc(((sizeof(Py_ssize_t)) + 2))); jpayne@68: jpayne@68: /* "array.pxd":119 jpayne@68: * jpayne@68: * info.shape = PyObject_Malloc(sizeof(Py_ssize_t) + 2) jpayne@68: * if not info.shape: # <<<<<<<<<<<<<< jpayne@68: * raise MemoryError() jpayne@68: * info.shape[0] = item_count # constant regardless of resizing jpayne@68: */ jpayne@68: __pyx_t_6 = (!(__pyx_v_info->shape != 0)); jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "array.pxd":120 jpayne@68: * info.shape = PyObject_Malloc(sizeof(Py_ssize_t) + 2) jpayne@68: * if not info.shape: jpayne@68: * raise MemoryError() # <<<<<<<<<<<<<< jpayne@68: * info.shape[0] = item_count # constant regardless of resizing jpayne@68: * info.strides = &info.itemsize jpayne@68: */ jpayne@68: PyErr_NoMemory(); __PYX_ERR(3, 120, __pyx_L1_error) jpayne@68: jpayne@68: /* "array.pxd":119 jpayne@68: * jpayne@68: * info.shape = PyObject_Malloc(sizeof(Py_ssize_t) + 2) jpayne@68: * if not info.shape: # <<<<<<<<<<<<<< jpayne@68: * raise MemoryError() jpayne@68: * info.shape[0] = item_count # constant regardless of resizing jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":121 jpayne@68: * if not info.shape: jpayne@68: * raise MemoryError() jpayne@68: * info.shape[0] = item_count # constant regardless of resizing # <<<<<<<<<<<<<< jpayne@68: * info.strides = &info.itemsize jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_item_count); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(3, 121, __pyx_L1_error) jpayne@68: (__pyx_v_info->shape[0]) = __pyx_t_5; jpayne@68: jpayne@68: /* "array.pxd":122 jpayne@68: * raise MemoryError() jpayne@68: * info.shape[0] = item_count # constant regardless of resizing jpayne@68: * info.strides = &info.itemsize # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * info.format = (info.shape + 1) jpayne@68: */ jpayne@68: __pyx_v_info->strides = (&__pyx_v_info->itemsize); jpayne@68: jpayne@68: /* "array.pxd":124 jpayne@68: * info.strides = &info.itemsize jpayne@68: * jpayne@68: * info.format = (info.shape + 1) # <<<<<<<<<<<<<< jpayne@68: * info.format[0] = self.ob_descr.typecode jpayne@68: * info.format[1] = 0 jpayne@68: */ jpayne@68: __pyx_v_info->format = ((char *)(__pyx_v_info->shape + 1)); jpayne@68: jpayne@68: /* "array.pxd":125 jpayne@68: * jpayne@68: * info.format = (info.shape + 1) jpayne@68: * info.format[0] = self.ob_descr.typecode # <<<<<<<<<<<<<< jpayne@68: * info.format[1] = 0 jpayne@68: * info.obj = self jpayne@68: */ jpayne@68: __pyx_t_7 = __pyx_v_self->ob_descr->typecode; jpayne@68: (__pyx_v_info->format[0]) = __pyx_t_7; jpayne@68: jpayne@68: /* "array.pxd":126 jpayne@68: * info.format = (info.shape + 1) jpayne@68: * info.format[0] = self.ob_descr.typecode jpayne@68: * info.format[1] = 0 # <<<<<<<<<<<<<< jpayne@68: * info.obj = self jpayne@68: * jpayne@68: */ jpayne@68: (__pyx_v_info->format[1]) = 0; jpayne@68: jpayne@68: /* "array.pxd":127 jpayne@68: * info.format[0] = self.ob_descr.typecode jpayne@68: * info.format[1] = 0 jpayne@68: * info.obj = self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __releasebuffer__(self, Py_buffer* info): jpayne@68: */ jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_self); jpayne@68: __Pyx_GIVEREF((PyObject *)__pyx_v_self); jpayne@68: __Pyx_GOTREF(__pyx_v_info->obj); jpayne@68: __Pyx_DECREF(__pyx_v_info->obj); jpayne@68: __pyx_v_info->obj = ((PyObject *)__pyx_v_self); jpayne@68: jpayne@68: /* "array.pxd":104 jpayne@68: * __data_union data jpayne@68: * jpayne@68: * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< jpayne@68: * # This implementation of getbuffer is geared towards Cython jpayne@68: * # requirements, and does not yet fulfill the PEP. jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("cpython.array.array.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: if (__pyx_v_info->obj != NULL) { jpayne@68: __Pyx_GOTREF(__pyx_v_info->obj); jpayne@68: __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0; jpayne@68: } jpayne@68: goto __pyx_L2; jpayne@68: __pyx_L0:; jpayne@68: if (__pyx_v_info->obj == Py_None) { jpayne@68: __Pyx_GOTREF(__pyx_v_info->obj); jpayne@68: __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0; jpayne@68: } jpayne@68: __pyx_L2:; jpayne@68: __Pyx_XDECREF(__pyx_v_item_count); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":129 jpayne@68: * info.obj = self jpayne@68: * jpayne@68: * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<< jpayne@68: * PyObject_Free(info.shape) jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/ jpayne@68: CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_pf_7cpython_5array_5array_2__releasebuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: } jpayne@68: jpayne@68: static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info) { jpayne@68: jpayne@68: /* "array.pxd":130 jpayne@68: * jpayne@68: * def __releasebuffer__(self, Py_buffer* info): jpayne@68: * PyObject_Free(info.shape) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * array newarrayobject(PyTypeObject* type, Py_ssize_t size, arraydescr *descr) jpayne@68: */ jpayne@68: PyObject_Free(__pyx_v_info->shape); jpayne@68: jpayne@68: /* "array.pxd":129 jpayne@68: * info.obj = self jpayne@68: * jpayne@68: * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<< jpayne@68: * PyObject_Free(info.shape) jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":141 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<< jpayne@68: * """ fast creation of a new array, given a template array. jpayne@68: * type will be same as template. jpayne@68: */ jpayne@68: jpayne@68: static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_clone(arrayobject *__pyx_v_template, Py_ssize_t __pyx_v_length, int __pyx_v_zero) { jpayne@68: arrayobject *__pyx_v_op = 0; jpayne@68: arrayobject *__pyx_r = NULL; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: int __pyx_t_3; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("clone", 1); jpayne@68: jpayne@68: /* "array.pxd":145 jpayne@68: * type will be same as template. jpayne@68: * if zero is true, new array will be initialized with zeroes.""" jpayne@68: * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) # <<<<<<<<<<<<<< jpayne@68: * if zero and op is not None: jpayne@68: * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) jpayne@68: */ jpayne@68: __pyx_t_1 = ((PyObject *)newarrayobject(Py_TYPE(((PyObject *)__pyx_v_template)), __pyx_v_length, __pyx_v_template->ob_descr)); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 145, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_op = ((arrayobject *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "array.pxd":146 jpayne@68: * if zero is true, new array will be initialized with zeroes.""" jpayne@68: * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) jpayne@68: * if zero and op is not None: # <<<<<<<<<<<<<< jpayne@68: * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) jpayne@68: * return op jpayne@68: */ jpayne@68: if (__pyx_v_zero) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_v_zero; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_3 = (((PyObject *)__pyx_v_op) != Py_None); jpayne@68: __pyx_t_2 = __pyx_t_3; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "array.pxd":147 jpayne@68: * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) jpayne@68: * if zero and op is not None: jpayne@68: * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) # <<<<<<<<<<<<<< jpayne@68: * return op jpayne@68: * jpayne@68: */ jpayne@68: (void)(memset(__pyx_v_op->data.as_chars, 0, (__pyx_v_length * __pyx_v_op->ob_descr->itemsize))); jpayne@68: jpayne@68: /* "array.pxd":146 jpayne@68: * if zero is true, new array will be initialized with zeroes.""" jpayne@68: * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) jpayne@68: * if zero and op is not None: # <<<<<<<<<<<<<< jpayne@68: * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) jpayne@68: * return op jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":148 jpayne@68: * if zero and op is not None: jpayne@68: * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) jpayne@68: * return op # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef inline array copy(array self): jpayne@68: */ jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_op); jpayne@68: __pyx_r = __pyx_v_op; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "array.pxd":141 jpayne@68: * jpayne@68: * jpayne@68: * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<< jpayne@68: * """ fast creation of a new array, given a template array. jpayne@68: * type will be same as template. jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("cpython.array.clone", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_op); jpayne@68: __Pyx_XGIVEREF((PyObject *)__pyx_r); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":150 jpayne@68: * return op jpayne@68: * jpayne@68: * cdef inline array copy(array self): # <<<<<<<<<<<<<< jpayne@68: * """ make a copy of an array. """ jpayne@68: * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) jpayne@68: */ jpayne@68: jpayne@68: static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_copy(arrayobject *__pyx_v_self) { jpayne@68: arrayobject *__pyx_v_op = 0; jpayne@68: arrayobject *__pyx_r = NULL; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("copy", 1); jpayne@68: jpayne@68: /* "array.pxd":152 jpayne@68: * cdef inline array copy(array self): jpayne@68: * """ make a copy of an array. """ jpayne@68: * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) # <<<<<<<<<<<<<< jpayne@68: * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) jpayne@68: * return op jpayne@68: */ jpayne@68: __pyx_t_1 = ((PyObject *)newarrayobject(Py_TYPE(((PyObject *)__pyx_v_self)), Py_SIZE(((PyObject *)__pyx_v_self)), __pyx_v_self->ob_descr)); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 152, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_op = ((arrayobject *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "array.pxd":153 jpayne@68: * """ make a copy of an array. """ jpayne@68: * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) jpayne@68: * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) # <<<<<<<<<<<<<< jpayne@68: * return op jpayne@68: * jpayne@68: */ jpayne@68: (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@68: jpayne@68: /* "array.pxd":154 jpayne@68: * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) jpayne@68: * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) jpayne@68: * return op # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: jpayne@68: */ jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_op); jpayne@68: __pyx_r = __pyx_v_op; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "array.pxd":150 jpayne@68: * return op jpayne@68: * jpayne@68: * cdef inline array copy(array self): # <<<<<<<<<<<<<< jpayne@68: * """ make a copy of an array. """ jpayne@68: * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("cpython.array.copy", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_op); jpayne@68: __Pyx_XGIVEREF((PyObject *)__pyx_r); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":156 jpayne@68: * return op jpayne@68: * jpayne@68: * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<< jpayne@68: * """ efficient appending of new stuff of same type jpayne@68: * (e.g. of same array type) jpayne@68: */ jpayne@68: jpayne@68: 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@68: Py_ssize_t __pyx_v_itemsize; jpayne@68: Py_ssize_t __pyx_v_origsize; jpayne@68: int __pyx_r; jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: jpayne@68: /* "array.pxd":160 jpayne@68: * (e.g. of same array type) jpayne@68: * n: number of elements (not number of bytes!) """ jpayne@68: * cdef Py_ssize_t itemsize = self.ob_descr.itemsize # <<<<<<<<<<<<<< jpayne@68: * cdef Py_ssize_t origsize = Py_SIZE(self) jpayne@68: * resize_smart(self, origsize + n) jpayne@68: */ jpayne@68: __pyx_t_1 = __pyx_v_self->ob_descr->itemsize; jpayne@68: __pyx_v_itemsize = __pyx_t_1; jpayne@68: jpayne@68: /* "array.pxd":161 jpayne@68: * n: number of elements (not number of bytes!) """ jpayne@68: * cdef Py_ssize_t itemsize = self.ob_descr.itemsize jpayne@68: * cdef Py_ssize_t origsize = Py_SIZE(self) # <<<<<<<<<<<<<< jpayne@68: * resize_smart(self, origsize + n) jpayne@68: * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) jpayne@68: */ jpayne@68: __pyx_v_origsize = Py_SIZE(((PyObject *)__pyx_v_self)); jpayne@68: jpayne@68: /* "array.pxd":162 jpayne@68: * cdef Py_ssize_t itemsize = self.ob_descr.itemsize jpayne@68: * cdef Py_ssize_t origsize = Py_SIZE(self) jpayne@68: * resize_smart(self, origsize + n) # <<<<<<<<<<<<<< jpayne@68: * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) jpayne@68: * return 0 jpayne@68: */ jpayne@68: __pyx_t_1 = resize_smart(__pyx_v_self, (__pyx_v_origsize + __pyx_v_n)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(3, 162, __pyx_L1_error) jpayne@68: jpayne@68: /* "array.pxd":163 jpayne@68: * cdef Py_ssize_t origsize = Py_SIZE(self) jpayne@68: * resize_smart(self, origsize + n) jpayne@68: * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) # <<<<<<<<<<<<<< jpayne@68: * return 0 jpayne@68: * jpayne@68: */ jpayne@68: (void)(memcpy((__pyx_v_self->data.as_chars + (__pyx_v_origsize * __pyx_v_itemsize)), __pyx_v_stuff, (__pyx_v_n * __pyx_v_itemsize))); jpayne@68: jpayne@68: /* "array.pxd":164 jpayne@68: * resize_smart(self, origsize + n) jpayne@68: * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) jpayne@68: * return 0 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef inline int extend(array self, array other) except -1: jpayne@68: */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "array.pxd":156 jpayne@68: * return op jpayne@68: * jpayne@68: * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<< jpayne@68: * """ efficient appending of new stuff of same type jpayne@68: * (e.g. of same array type) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("cpython.array.extend_buffer", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":166 jpayne@68: * return 0 jpayne@68: * jpayne@68: * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<< jpayne@68: * """ extend array with data from another array; types must match. """ jpayne@68: * if self.ob_descr.typecode != other.ob_descr.typecode: jpayne@68: */ jpayne@68: jpayne@68: static CYTHON_INLINE int __pyx_f_7cpython_5array_extend(arrayobject *__pyx_v_self, arrayobject *__pyx_v_other) { jpayne@68: int __pyx_r; jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: jpayne@68: /* "array.pxd":168 jpayne@68: * cdef inline int extend(array self, array other) except -1: jpayne@68: * """ extend array with data from another array; types must match. """ jpayne@68: * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<< jpayne@68: * PyErr_BadArgument() jpayne@68: * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->ob_descr->typecode != __pyx_v_other->ob_descr->typecode); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "array.pxd":169 jpayne@68: * """ extend array with data from another array; types must match. """ jpayne@68: * if self.ob_descr.typecode != other.ob_descr.typecode: jpayne@68: * PyErr_BadArgument() # <<<<<<<<<<<<<< jpayne@68: * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = PyErr_BadArgument(); if (unlikely(__pyx_t_2 == ((int)0))) __PYX_ERR(3, 169, __pyx_L1_error) jpayne@68: jpayne@68: /* "array.pxd":168 jpayne@68: * cdef inline int extend(array self, array other) except -1: jpayne@68: * """ extend array with data from another array; types must match. """ jpayne@68: * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<< jpayne@68: * PyErr_BadArgument() jpayne@68: * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":170 jpayne@68: * if self.ob_descr.typecode != other.ob_descr.typecode: jpayne@68: * PyErr_BadArgument() jpayne@68: * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef inline void zero(array self) noexcept: jpayne@68: */ jpayne@68: __pyx_t_2 = __pyx_f_7cpython_5array_extend_buffer(__pyx_v_self, __pyx_v_other->data.as_chars, Py_SIZE(((PyObject *)__pyx_v_other))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(3, 170, __pyx_L1_error) jpayne@68: __pyx_r = __pyx_t_2; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "array.pxd":166 jpayne@68: * return 0 jpayne@68: * jpayne@68: * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<< jpayne@68: * """ extend array with data from another array; types must match. """ jpayne@68: * if self.ob_descr.typecode != other.ob_descr.typecode: jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("cpython.array.extend", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "array.pxd":172 jpayne@68: * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) jpayne@68: * jpayne@68: * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<< jpayne@68: * """ set all elements of array to zero. """ jpayne@68: * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) jpayne@68: */ jpayne@68: jpayne@68: static CYTHON_INLINE void __pyx_f_7cpython_5array_zero(arrayobject *__pyx_v_self) { jpayne@68: jpayne@68: /* "array.pxd":174 jpayne@68: * cdef inline void zero(array self) noexcept: jpayne@68: * """ set all elements of array to zero. """ jpayne@68: * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: (void)(memset(__pyx_v_self->data.as_chars, 0, (Py_SIZE(((PyObject *)__pyx_v_self)) * __pyx_v_self->ob_descr->itemsize))); jpayne@68: jpayne@68: /* "array.pxd":172 jpayne@68: * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) jpayne@68: * jpayne@68: * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<< jpayne@68: * """ set all elements of array to zero. """ jpayne@68: * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":84 jpayne@68: * cdef class Parser: jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_6Parser_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static int __pyx_pw_5pysam_9libctabix_6Parser_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: PyObject *__pyx_v_encoding = 0; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_encoding,0}; jpayne@68: values[0] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii)); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding); jpayne@68: if (value) { values[0] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 84, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 84, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_encoding = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 84, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser___init__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v_encoding); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_6Parser___init__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding) { jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__init__", 1); jpayne@68: __Pyx_TraceCall("__init__", __pyx_f[0], 84, 0, __PYX_ERR(0, 84, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":85 jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): jpayne@68: * self.encoding = encoding # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def set_encoding(self, encoding): jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_encoding); jpayne@68: __Pyx_GOTREF(__pyx_v_self->encoding); jpayne@68: __Pyx_DECREF(__pyx_v_self->encoding); jpayne@68: __pyx_v_self->encoding = __pyx_v_encoding; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":84 jpayne@68: * cdef class Parser: jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":87 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def set_encoding(self, encoding): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_2set_encoding, "Parser.set_encoding(self, encoding)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_3set_encoding = {"set_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_2set_encoding}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_encoding = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("set_encoding (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_encoding,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 87, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "set_encoding") < 0)) __PYX_ERR(0, 87, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_encoding = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("set_encoding", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 87, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.set_encoding", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_2set_encoding(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v_encoding); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_2set_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj_) jpayne@68: __Pyx_RefNannySetupContext("set_encoding", 1); jpayne@68: __Pyx_TraceCall("set_encoding", __pyx_f[0], 87, 0, __PYX_ERR(0, 87, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":88 jpayne@68: * jpayne@68: * def set_encoding(self, encoding): jpayne@68: * self.encoding = encoding # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def get_encoding(self): jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_encoding); jpayne@68: __Pyx_GOTREF(__pyx_v_self->encoding); jpayne@68: __Pyx_DECREF(__pyx_v_self->encoding); jpayne@68: __pyx_v_self->encoding = __pyx_v_encoding; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":87 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def set_encoding(self, encoding): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.set_encoding", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":90 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def get_encoding(self): # <<<<<<<<<<<<<< jpayne@68: * return self.encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_4get_encoding, "Parser.get_encoding(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_5get_encoding = {"get_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_4get_encoding}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("get_encoding (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("get_encoding", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "get_encoding", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_4get_encoding(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_4get_encoding(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__2) jpayne@68: __Pyx_RefNannySetupContext("get_encoding", 1); jpayne@68: __Pyx_TraceCall("get_encoding", __pyx_f[0], 90, 0, __PYX_ERR(0, 90, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":91 jpayne@68: * jpayne@68: * def get_encoding(self): jpayne@68: * return self.encoding # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef parse(self, char * buffer, int length): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_self->encoding); jpayne@68: __pyx_r = __pyx_v_self->encoding; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":90 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def get_encoding(self): # <<<<<<<<<<<<<< jpayne@68: * return self.encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.get_encoding", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":93 jpayne@68: * return self.encoding jpayne@68: * jpayne@68: * cdef parse(self, char * buffer, int length): # <<<<<<<<<<<<<< jpayne@68: * raise NotImplementedError( jpayne@68: * 'parse method of %s not implemented' % str(self)) jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_6Parser_parse(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, CYTHON_UNUSED char *__pyx_v_buffer, CYTHON_UNUSED int __pyx_v_length) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("parse", 1); jpayne@68: __Pyx_TraceCall("parse", __pyx_f[0], 93, 0, __PYX_ERR(0, 93, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":95 jpayne@68: * cdef parse(self, char * buffer, int length): jpayne@68: * raise NotImplementedError( jpayne@68: * 'parse method of %s not implemented' % str(self)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __call__(self, char * buffer, int length): jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_Unicode(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 95, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_parse_method_of_s_not_implemente, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 95, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":94 jpayne@68: * jpayne@68: * cdef parse(self, char * buffer, int length): jpayne@68: * raise NotImplementedError( # <<<<<<<<<<<<<< jpayne@68: * 'parse method of %s not implemented' % str(self)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_NotImplementedError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 94, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 94, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":93 jpayne@68: * return self.encoding jpayne@68: * jpayne@68: * cdef parse(self, char * buffer, int length): # <<<<<<<<<<<<<< jpayne@68: * raise NotImplementedError( jpayne@68: * 'parse method of %s not implemented' % str(self)) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":97 jpayne@68: * 'parse method of %s not implemented' % str(self)) jpayne@68: * jpayne@68: * def __call__(self, char * buffer, int length): # <<<<<<<<<<<<<< jpayne@68: * return self.parse(buffer, length) jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_7__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_7__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: char *__pyx_v_buffer; jpayne@68: int __pyx_v_length; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[2] = {0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_buffer,&__pyx_n_s_length,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buffer)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_length)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__call__") < 0)) __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 2)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: } jpayne@68: __pyx_v_buffer = __Pyx_PyObject_AsWritableString(values[0]); if (unlikely((!__pyx_v_buffer) && PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: __pyx_v_length = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_length == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 97, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_6__call__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v_buffer, __pyx_v_length); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_6__call__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__call__", 1); jpayne@68: __Pyx_TraceCall("__call__", __pyx_f[0], 97, 0, __PYX_ERR(0, 97, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":98 jpayne@68: * jpayne@68: * def __call__(self, char * buffer, int length): jpayne@68: * return self.parse(buffer, length) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->__pyx_vtab)->parse(__pyx_v_self, __pyx_v_buffer, __pyx_v_length); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 98, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_r = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":97 jpayne@68: * 'parse method of %s not implemented' % str(self)) jpayne@68: * jpayne@68: * def __call__(self, char * buffer, int length): # <<<<<<<<<<<<<< jpayne@68: * return self.parse(buffer, length) jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_8__reduce_cython__, "Parser.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_8__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_8__reduce_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self) { jpayne@68: PyObject *__pyx_v_state = 0; jpayne@68: PyObject *__pyx_v__dict = 0; jpayne@68: int __pyx_v_use_setstate; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__3) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object _dict jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) # <<<<<<<<<<<<<< jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->encoding); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->encoding)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_v_state = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v__dict = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v__dict != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) # <<<<<<<<<<<<<< jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v__dict); jpayne@68: __Pyx_GIVEREF(__pyx_v__dict); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: */ jpayne@68: __pyx_v_use_setstate = 1; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None # <<<<<<<<<<<<<< jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_self->encoding != Py_None); jpayne@68: __pyx_v_use_setstate = __pyx_t_2; jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: if (__pyx_v_use_setstate) { jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_Parser); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":15 jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_Parser__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_Parser); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_state); jpayne@68: __Pyx_XDECREF(__pyx_v__dict); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_Parser__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6Parser_10__setstate_cython__, "Parser.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_6Parser_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_10__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6Parser_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6Parser_10__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_self, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__4) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":17 jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_Parser__set_state(self, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_Parser__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Parser.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":106 jpayne@68: * A field in a row is accessed by numeric index. jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.TupleProxy r jpayne@68: * r = ctabixproxies.TupleProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_7asTuple_parse(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *__pyx_v_r = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("parse", 1); jpayne@68: __Pyx_TraceCall("parse", __pyx_f[0], 106, 0, __PYX_ERR(0, 106, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":108 jpayne@68: * cdef parse(self, char * buffer, int len): jpayne@68: * cdef ctabixproxies.TupleProxy r jpayne@68: * r = ctabixproxies.TupleProxy(self.encoding) # <<<<<<<<<<<<<< jpayne@68: * # need to copy - there were some jpayne@68: * # persistence issues with "present" jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_TupleProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 108, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":111 jpayne@68: * # need to copy - there were some jpayne@68: * # persistence issues with "present" jpayne@68: * r.copy(buffer, len) # <<<<<<<<<<<<<< jpayne@68: * return r jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r->__pyx_vtab)->copy(__pyx_v_r, __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 111, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":112 jpayne@68: * # persistence issues with "present" jpayne@68: * r.copy(buffer, len) jpayne@68: * return r # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_r); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_r); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":106 jpayne@68: * A field in a row is accessed by numeric index. jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.TupleProxy r jpayne@68: * r = ctabixproxies.TupleProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asTuple.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_r); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_7asTuple___reduce_cython__, "asTuple.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_7asTuple_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple___reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_7asTuple___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asTuple *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self) { jpayne@68: PyObject *__pyx_v_state = 0; jpayne@68: PyObject *__pyx_v__dict = 0; jpayne@68: int __pyx_v_use_setstate; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__5) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object _dict jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) # <<<<<<<<<<<<<< jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_v_state = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v__dict = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v__dict != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) # <<<<<<<<<<<<<< jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v__dict); jpayne@68: __Pyx_GIVEREF(__pyx_v__dict); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: */ jpayne@68: __pyx_v_use_setstate = 1; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None # <<<<<<<<<<<<<< jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None); jpayne@68: __pyx_v_use_setstate = __pyx_t_2; jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: if (__pyx_v_use_setstate) { jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asTuple); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":15 jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asTuple__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asTuple); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asTuple.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_state); jpayne@68: __Pyx_XDECREF(__pyx_v__dict); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asTuple__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_7asTuple_2__setstate_cython__, "asTuple.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_7asTuple_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple_2__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asTuple.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_7asTuple_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asTuple *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_7asTuple_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v_self, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__6) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":17 jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asTuple__set_state(self, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asTuple__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asTuple.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":144 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.GFF3Proxy r jpayne@68: * r = ctabixproxies.GFF3Proxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_6asGFF3_parse(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy *__pyx_v_r = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("parse", 1); jpayne@68: __Pyx_TraceCall("parse", __pyx_f[0], 144, 0, __PYX_ERR(0, 144, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":146 jpayne@68: * cdef parse(self, char * buffer, int len): jpayne@68: * cdef ctabixproxies.GFF3Proxy r jpayne@68: * r = ctabixproxies.GFF3Proxy(self.encoding) # <<<<<<<<<<<<<< jpayne@68: * r.copy(buffer, len) jpayne@68: * return r jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 146, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":147 jpayne@68: * cdef ctabixproxies.GFF3Proxy r jpayne@68: * r = ctabixproxies.GFF3Proxy(self.encoding) jpayne@68: * r.copy(buffer, len) # <<<<<<<<<<<<<< jpayne@68: * return r jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 147, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":148 jpayne@68: * r = ctabixproxies.GFF3Proxy(self.encoding) jpayne@68: * r.copy(buffer, len) jpayne@68: * return r # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_r); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_r); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":144 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.GFF3Proxy r jpayne@68: * r = ctabixproxies.GFF3Proxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGFF3.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_r); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6asGFF3___reduce_cython__, "asGFF3.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_6asGFF3_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3___reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6asGFF3___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self) { jpayne@68: PyObject *__pyx_v_state = 0; jpayne@68: PyObject *__pyx_v__dict = 0; jpayne@68: int __pyx_v_use_setstate; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__7) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object _dict jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) # <<<<<<<<<<<<<< jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_v_state = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v__dict = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v__dict != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) # <<<<<<<<<<<<<< jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v__dict); jpayne@68: __Pyx_GIVEREF(__pyx_v__dict); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: */ jpayne@68: __pyx_v_use_setstate = 1; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None # <<<<<<<<<<<<<< jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None); jpayne@68: __pyx_v_use_setstate = __pyx_t_2; jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: if (__pyx_v_use_setstate) { jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asGFF3); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":15 jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asGFF3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGFF3.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_state); jpayne@68: __Pyx_XDECREF(__pyx_v__dict); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6asGFF3_2__setstate_cython__, "asGFF3.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_6asGFF3_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3_2__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGFF3.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6asGFF3_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6asGFF3_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v_self, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__8) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":17 jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGFF3.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":191 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.GTFProxy r jpayne@68: * r = ctabixproxies.GTFProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_5asGTF_parse(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy *__pyx_v_r = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("parse", 1); jpayne@68: __Pyx_TraceCall("parse", __pyx_f[0], 191, 0, __PYX_ERR(0, 191, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":193 jpayne@68: * cdef parse(self, char * buffer, int len): jpayne@68: * cdef ctabixproxies.GTFProxy r jpayne@68: * r = ctabixproxies.GTFProxy(self.encoding) # <<<<<<<<<<<<<< jpayne@68: * r.copy(buffer, len) jpayne@68: * return r jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_GTFProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 193, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":194 jpayne@68: * cdef ctabixproxies.GTFProxy r jpayne@68: * r = ctabixproxies.GTFProxy(self.encoding) jpayne@68: * r.copy(buffer, len) # <<<<<<<<<<<<<< jpayne@68: * return r jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 194, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":195 jpayne@68: * r = ctabixproxies.GTFProxy(self.encoding) jpayne@68: * r.copy(buffer, len) jpayne@68: * return r # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_r); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_r); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":191 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.GTFProxy r jpayne@68: * r = ctabixproxies.GTFProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGTF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_r); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asGTF___reduce_cython__, "asGTF.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asGTF_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF___reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_5asGTF___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asGTF *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self) { jpayne@68: PyObject *__pyx_v_state = 0; jpayne@68: PyObject *__pyx_v__dict = 0; jpayne@68: int __pyx_v_use_setstate; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__9) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object _dict jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) # <<<<<<<<<<<<<< jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_v_state = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v__dict = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v__dict != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) # <<<<<<<<<<<<<< jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v__dict); jpayne@68: __Pyx_GIVEREF(__pyx_v__dict); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: */ jpayne@68: __pyx_v_use_setstate = 1; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None # <<<<<<<<<<<<<< jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None); jpayne@68: __pyx_v_use_setstate = __pyx_t_2; jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: if (__pyx_v_use_setstate) { jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asGTF); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":15 jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asGTF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asGTF); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGTF.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_state); jpayne@68: __Pyx_XDECREF(__pyx_v__dict); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGTF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asGTF_2__setstate_cython__, "asGTF.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asGTF_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF_2__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGTF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_5asGTF_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asGTF *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asGTF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v_self, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__10) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":17 jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asGTF__set_state(self, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGTF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asGTF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":239 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.BedProxy r jpayne@68: * r = ctabixproxies.BedProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_5asBed_parse(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_BedProxy *__pyx_v_r = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("parse", 1); jpayne@68: __Pyx_TraceCall("parse", __pyx_f[0], 239, 0, __PYX_ERR(0, 239, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":241 jpayne@68: * cdef parse(self, char * buffer, int len): jpayne@68: * cdef ctabixproxies.BedProxy r jpayne@68: * r = ctabixproxies.BedProxy(self.encoding) # <<<<<<<<<<<<<< jpayne@68: * r.copy(buffer, len) jpayne@68: * return r jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_BedProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 241, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_BedProxy *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":242 jpayne@68: * cdef ctabixproxies.BedProxy r jpayne@68: * r = ctabixproxies.BedProxy(self.encoding) jpayne@68: * r.copy(buffer, len) # <<<<<<<<<<<<<< jpayne@68: * return r jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 242, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":243 jpayne@68: * r = ctabixproxies.BedProxy(self.encoding) jpayne@68: * r.copy(buffer, len) jpayne@68: * return r # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_r); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_r); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":239 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.BedProxy r jpayne@68: * r = ctabixproxies.BedProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asBed.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_r); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asBed___reduce_cython__, "asBed.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asBed_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed___reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_5asBed___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asBed *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asBed___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self) { jpayne@68: PyObject *__pyx_v_state = 0; jpayne@68: PyObject *__pyx_v__dict = 0; jpayne@68: int __pyx_v_use_setstate; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__11) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object _dict jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) # <<<<<<<<<<<<<< jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_v_state = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v__dict = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v__dict != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) # <<<<<<<<<<<<<< jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v__dict); jpayne@68: __Pyx_GIVEREF(__pyx_v__dict); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: */ jpayne@68: __pyx_v_use_setstate = 1; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None # <<<<<<<<<<<<<< jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None); jpayne@68: __pyx_v_use_setstate = __pyx_t_2; jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: if (__pyx_v_use_setstate) { jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asBed); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":15 jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asBed__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asBed); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asBed.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_state); jpayne@68: __Pyx_XDECREF(__pyx_v__dict); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asBed__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asBed_2__setstate_cython__, "asBed.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asBed_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed_2__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asBed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_5asBed_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asBed *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asBed_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v_self, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__12) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":17 jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asBed__set_state(self, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asBed__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asBed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":280 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.VCFProxy r jpayne@68: * r = ctabixproxies.VCFProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_5asVCF_parse(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { jpayne@68: struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy *__pyx_v_r = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("parse", 1); jpayne@68: __Pyx_TraceCall("parse", __pyx_f[0], 280, 0, __PYX_ERR(0, 280, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":282 jpayne@68: * cdef parse(self, char * buffer, int len): jpayne@68: * cdef ctabixproxies.VCFProxy r jpayne@68: * r = ctabixproxies.VCFProxy(self.encoding) # <<<<<<<<<<<<<< jpayne@68: * r.copy(buffer, len) jpayne@68: * return r jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_16libctabixproxies_VCFProxy), __pyx_v_self->__pyx_base.encoding); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 282, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_r = ((struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":283 jpayne@68: * cdef ctabixproxies.VCFProxy r jpayne@68: * r = ctabixproxies.VCFProxy(self.encoding) jpayne@68: * r.copy(buffer, len) # <<<<<<<<<<<<<< jpayne@68: * return r jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 283, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":284 jpayne@68: * r = ctabixproxies.VCFProxy(self.encoding) jpayne@68: * r.copy(buffer, len) jpayne@68: * return r # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_r); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_r); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":280 jpayne@68: * jpayne@68: * ''' jpayne@68: * cdef parse(self, char * buffer, int len): # <<<<<<<<<<<<<< jpayne@68: * cdef ctabixproxies.VCFProxy r jpayne@68: * r = ctabixproxies.VCFProxy(self.encoding) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asVCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_r); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asVCF___reduce_cython__, "asVCF.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asVCF_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF___reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_5asVCF___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_asVCF *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF___reduce_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self) { jpayne@68: PyObject *__pyx_v_state = 0; jpayne@68: PyObject *__pyx_v__dict = 0; jpayne@68: int __pyx_v_use_setstate; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__13) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object _dict jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) # <<<<<<<<<<<<<< jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->__pyx_base.encoding); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.encoding)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_v_state = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * cdef bint use_setstate jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v__dict = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v__dict != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) # <<<<<<<<<<<<<< jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v__dict); jpayne@68: __Pyx_GIVEREF(__pyx_v__dict); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v__dict)) __PYX_ERR(1, 8, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * if _dict is not None: jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: */ jpayne@68: __pyx_v_use_setstate = 1; jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * state = (self.encoding,) jpayne@68: * _dict = getattr(self, '__dict__', None) jpayne@68: * if _dict is not None: # <<<<<<<<<<<<<< jpayne@68: * state += (_dict,) jpayne@68: * use_setstate = True jpayne@68: */ jpayne@68: goto __pyx_L3; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * use_setstate = True jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None # <<<<<<<<<<<<<< jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_self->__pyx_base.encoding != Py_None); jpayne@68: __pyx_v_use_setstate = __pyx_t_2; jpayne@68: } jpayne@68: __pyx_L3:; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: if (__pyx_v_use_setstate) { jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_pyx_unpickle_asVCF); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, Py_None)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_state)) __PYX_ERR(1, 13, __pyx_L1_error); jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * else: jpayne@68: * use_setstate = self.encoding is not None jpayne@68: * if use_setstate: # <<<<<<<<<<<<<< jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":15 jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, None), state jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asVCF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_asVCF); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))))) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_243541226); jpayne@68: __Pyx_GIVEREF(__pyx_int_243541226); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_243541226)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_state); jpayne@68: __Pyx_GIVEREF(__pyx_v_state); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_state)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asVCF.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_state); jpayne@68: __Pyx_XDECREF(__pyx_v__dict); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asVCF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_5asVCF_2__setstate_cython__, "asVCF.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5asVCF_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF_2__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 16, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asVCF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_5asVCF_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_asVCF *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_5asVCF_2__setstate_cython__(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v_self, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__14) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 16, 0, __PYX_ERR(1, 16, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":17 jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * __pyx_unpickle_asVCF__set_state(self, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asVCF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.asVCF.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":334 jpayne@68: * if file could not be opened jpayne@68: * """ jpayne@68: * def __cinit__(self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_9TabixFile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static int __pyx_pw_5pysam_9libctabix_9TabixFile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: PyObject *__pyx_v_filename = 0; jpayne@68: PyObject *__pyx_v_mode = 0; jpayne@68: PyObject *__pyx_v_parser = 0; jpayne@68: PyObject *__pyx_v_index = 0; jpayne@68: PyObject *__pyx_v_encoding = 0; jpayne@68: PyObject *__pyx_v_threads = 0; jpayne@68: PyObject *__pyx_v_args = 0; jpayne@68: PyObject *__pyx_v_kwargs = 0; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[6] = {0,0,0,0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1; jpayne@68: __Pyx_GOTREF(__pyx_v_kwargs); jpayne@68: __pyx_v_args = __Pyx_ArgsSlice_VARARGS(__pyx_args, 6, __pyx_nargs); jpayne@68: if (unlikely(!__pyx_v_args)) { jpayne@68: __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0; jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: } jpayne@68: __Pyx_GOTREF(__pyx_v_args); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_mode,&__pyx_n_s_parser,&__pyx_n_s_index,&__pyx_n_s_encoding,&__pyx_n_s_threads,0}; jpayne@68: values[1] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_r)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":337 jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: * parser=None, # <<<<<<<<<<<<<< jpayne@68: * index=None, jpayne@68: * encoding="ascii", jpayne@68: */ jpayne@68: values[2] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":338 jpayne@68: * mode='r', jpayne@68: * parser=None, jpayne@68: * index=None, # <<<<<<<<<<<<<< jpayne@68: * encoding="ascii", jpayne@68: * threads=1, jpayne@68: */ jpayne@68: values[3] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)Py_None)); jpayne@68: values[4] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii)); jpayne@68: values[5] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_int_1)); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: default: jpayne@68: case 6: values[5] = __Pyx_Arg_VARARGS(__pyx_args, 5); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: values[4] = __Pyx_Arg_VARARGS(__pyx_args, 4); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: values[3] = __Pyx_Arg_VARARGS(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_mode); jpayne@68: if (value) { values[1] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_index); jpayne@68: if (value) { values[3] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding); jpayne@68: if (value) { values[4] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_threads); jpayne@68: if (value) { values[5] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: const Py_ssize_t used_pos_args = (kwd_pos_args < 6) ? kwd_pos_args : 6; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, __pyx_v_kwargs, values + 0, used_pos_args, "__cinit__") < 0)) __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: default: jpayne@68: case 6: values[5] = __Pyx_Arg_VARARGS(__pyx_args, 5); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: values[4] = __Pyx_Arg_VARARGS(__pyx_args, 4); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: values[3] = __Pyx_Arg_VARARGS(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: break; jpayne@68: case 0: jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_filename = values[0]; jpayne@68: __pyx_v_mode = values[1]; jpayne@68: __pyx_v_parser = values[2]; jpayne@68: __pyx_v_index = values[3]; jpayne@68: __pyx_v_encoding = values[4]; jpayne@68: __pyx_v_threads = values[5]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 6, __pyx_nargs); __PYX_ERR(0, 334, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_v_args); __pyx_v_args = 0; jpayne@68: __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile___cinit__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_parser, __pyx_v_index, __pyx_v_encoding, __pyx_v_threads, __pyx_v_args, __pyx_v_kwargs); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":334 jpayne@68: * if file could not be opened jpayne@68: * """ jpayne@68: * def __cinit__(self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_DECREF(__pyx_v_args); jpayne@68: __Pyx_DECREF(__pyx_v_kwargs); jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_9TabixFile___cinit__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_parser, PyObject *__pyx_v_index, PyObject *__pyx_v_encoding, PyObject *__pyx_v_threads, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) { jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__cinit__", 1); jpayne@68: __Pyx_TraceCall("__cinit__", __pyx_f[0], 334, 0, __PYX_ERR(0, 334, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":344 jpayne@68: * **kwargs ): jpayne@68: * jpayne@68: * self.htsfile = NULL # <<<<<<<<<<<<<< jpayne@68: * self.is_remote = False jpayne@68: * self.is_stream = False jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.htsfile = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":345 jpayne@68: * jpayne@68: * self.htsfile = NULL jpayne@68: * self.is_remote = False # <<<<<<<<<<<<<< jpayne@68: * self.is_stream = False jpayne@68: * self.parser = parser jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.is_remote = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":346 jpayne@68: * self.htsfile = NULL jpayne@68: * self.is_remote = False jpayne@68: * self.is_stream = False # <<<<<<<<<<<<<< jpayne@68: * self.parser = parser jpayne@68: * self.threads = threads jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.is_stream = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":347 jpayne@68: * self.is_remote = False jpayne@68: * self.is_stream = False jpayne@68: * self.parser = parser # <<<<<<<<<<<<<< jpayne@68: * self.threads = threads jpayne@68: * self._open(filename, mode, index, *args, **kwargs) jpayne@68: */ jpayne@68: if (!(likely(((__pyx_v_parser) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_parser, __pyx_ptype_5pysam_9libctabix_Parser))))) __PYX_ERR(0, 347, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_v_parser; jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF((PyObject *)__pyx_v_self->parser); jpayne@68: __Pyx_DECREF((PyObject *)__pyx_v_self->parser); jpayne@68: __pyx_v_self->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":348 jpayne@68: * self.is_stream = False jpayne@68: * self.parser = parser jpayne@68: * self.threads = threads # <<<<<<<<<<<<<< jpayne@68: * self._open(filename, mode, index, *args, **kwargs) jpayne@68: * self.encoding = encoding jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_threads); jpayne@68: __Pyx_GIVEREF(__pyx_v_threads); jpayne@68: __Pyx_GOTREF(__pyx_v_self->__pyx_base.threads); jpayne@68: __Pyx_DECREF(__pyx_v_self->__pyx_base.threads); jpayne@68: __pyx_v_self->__pyx_base.threads = __pyx_v_threads; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":349 jpayne@68: * self.parser = parser jpayne@68: * self.threads = threads jpayne@68: * self._open(filename, mode, index, *args, **kwargs) # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 349, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 349, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_v_filename); jpayne@68: __Pyx_GIVEREF(__pyx_v_filename); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_filename)) __PYX_ERR(0, 349, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_mode); jpayne@68: __Pyx_GIVEREF(__pyx_v_mode); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_mode)) __PYX_ERR(0, 349, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_index); jpayne@68: __Pyx_GIVEREF(__pyx_v_index); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_index)) __PYX_ERR(0, 349, __pyx_L1_error); jpayne@68: __pyx_t_3 = PyNumber_Add(__pyx_t_2, __pyx_v_args); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 349, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_t_2 = PyDict_Copy(__pyx_v_kwargs); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 349, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 349, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":350 jpayne@68: * self.threads = threads jpayne@68: * self._open(filename, mode, index, *args, **kwargs) jpayne@68: * self.encoding = encoding # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def _open( self, jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_encoding); jpayne@68: __Pyx_GOTREF(__pyx_v_self->encoding); jpayne@68: __Pyx_DECREF(__pyx_v_self->encoding); jpayne@68: __pyx_v_self->encoding = __pyx_v_encoding; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":334 jpayne@68: * if file could not be opened jpayne@68: * """ jpayne@68: * def __cinit__(self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":352 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def _open( self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_3_open(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_2_open, "TabixFile._open(self, filename, mode=u'r', index=None, threads=1)\nopen a :term:`tabix file` for reading."); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_3_open = {"_open", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_3_open, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_2_open}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_3_open(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_filename = 0; jpayne@68: PyObject *__pyx_v_mode = 0; jpayne@68: PyObject *__pyx_v_index = 0; jpayne@68: PyObject *__pyx_v_threads = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[4] = {0,0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("_open (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_mode,&__pyx_n_s_index,&__pyx_n_s_threads,0}; jpayne@68: values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)__pyx_n_u_r)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":355 jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: * index=None, # <<<<<<<<<<<<<< jpayne@68: * threads=1, jpayne@68: * ): jpayne@68: */ jpayne@68: values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)__pyx_int_1)); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_mode); jpayne@68: if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_index); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_threads); jpayne@68: if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 352, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "_open") < 0)) __PYX_ERR(0, 352, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_filename = values[0]; jpayne@68: __pyx_v_mode = values[1]; jpayne@68: __pyx_v_index = values[2]; jpayne@68: __pyx_v_threads = values[3]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 4, __pyx_nargs); __PYX_ERR(0, 352, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_2_open(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_index, __pyx_v_threads); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":352 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def _open( self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_2_open(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_index, PyObject *__pyx_v_threads) { jpayne@68: PyObject *__pyx_v_filename_index = NULL; jpayne@68: char *__pyx_v_cfilename; jpayne@68: char *__pyx_v_cfilename_index; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: char const *__pyx_t_6; jpayne@68: int __pyx_t_7; jpayne@68: char *__pyx_t_8; jpayne@68: int64_t __pyx_t_9; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__15) jpayne@68: __Pyx_RefNannySetupContext("_open", 1); jpayne@68: __Pyx_TraceCall("_open", __pyx_f[0], 352, 0, __PYX_ERR(0, 352, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":360 jpayne@68: * '''open a :term:`tabix file` for reading.''' jpayne@68: * jpayne@68: * if mode != 'r': # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("invalid file opening mode `%s`" % mode) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_mode, __pyx_n_u_r, Py_NE)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 360, __pyx_L1_error) jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":361 jpayne@68: * jpayne@68: * if mode != 'r': jpayne@68: * raise ValueError("invalid file opening mode `%s`" % mode) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if self.htsfile != NULL: jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_invalid_file_opening_mode_s, __pyx_v_mode); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 361, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 361, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 361, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":360 jpayne@68: * '''open a :term:`tabix file` for reading.''' jpayne@68: * jpayne@68: * if mode != 'r': # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("invalid file opening mode `%s`" % mode) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":363 jpayne@68: * raise ValueError("invalid file opening mode `%s`" % mode) jpayne@68: * jpayne@68: * if self.htsfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * self.close() jpayne@68: * self.htsfile = NULL jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":364 jpayne@68: * jpayne@68: * if self.htsfile != NULL: jpayne@68: * self.close() # <<<<<<<<<<<<<< jpayne@68: * self.htsfile = NULL jpayne@68: * self.threads=threads jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 364, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, NULL}; jpayne@68: __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 364, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":363 jpayne@68: * raise ValueError("invalid file opening mode `%s`" % mode) jpayne@68: * jpayne@68: * if self.htsfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * self.close() jpayne@68: * self.htsfile = NULL jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":365 jpayne@68: * if self.htsfile != NULL: jpayne@68: * self.close() jpayne@68: * self.htsfile = NULL # <<<<<<<<<<<<<< jpayne@68: * self.threads=threads jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.htsfile = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":366 jpayne@68: * self.close() jpayne@68: * self.htsfile = NULL jpayne@68: * self.threads=threads # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * filename_index = index or (filename + ".tbi") jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_threads); jpayne@68: __Pyx_GIVEREF(__pyx_v_threads); jpayne@68: __Pyx_GOTREF(__pyx_v_self->__pyx_base.threads); jpayne@68: __Pyx_DECREF(__pyx_v_self->__pyx_base.threads); jpayne@68: __pyx_v_self->__pyx_base.threads = __pyx_v_threads; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":368 jpayne@68: * self.threads=threads jpayne@68: * jpayne@68: * filename_index = index or (filename + ".tbi") # <<<<<<<<<<<<<< jpayne@68: * # encode all the strings to pass to tabix jpayne@68: * self.filename = encode_filename(filename) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_index); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 368, __pyx_L1_error) jpayne@68: if (!__pyx_t_1) { jpayne@68: } else { jpayne@68: __Pyx_INCREF(__pyx_v_index); jpayne@68: __pyx_t_3 = __pyx_v_index; jpayne@68: goto __pyx_L5_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_2 = PyNumber_Add(__pyx_v_filename, __pyx_kp_u_tbi); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 368, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __pyx_t_2; jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_L5_bool_binop_done:; jpayne@68: __pyx_v_filename_index = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":370 jpayne@68: * filename_index = index or (filename + ".tbi") jpayne@68: * # encode all the strings to pass to tabix jpayne@68: * self.filename = encode_filename(filename) # <<<<<<<<<<<<<< jpayne@68: * self.filename_index = encode_filename(filename_index) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 370, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: __Pyx_GOTREF(__pyx_v_self->__pyx_base.filename); jpayne@68: __Pyx_DECREF(__pyx_v_self->__pyx_base.filename); jpayne@68: __pyx_v_self->__pyx_base.filename = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":371 jpayne@68: * # encode all the strings to pass to tabix jpayne@68: * self.filename = encode_filename(filename) jpayne@68: * self.filename_index = encode_filename(filename_index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.is_stream = self.filename == b'-' jpayne@68: */ jpayne@68: __pyx_t_3 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename_index); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 371, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: __Pyx_GOTREF(__pyx_v_self->filename_index); jpayne@68: __Pyx_DECREF(__pyx_v_self->filename_index); jpayne@68: __pyx_v_self->filename_index = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":373 jpayne@68: * self.filename_index = encode_filename(filename_index) jpayne@68: * jpayne@68: * self.is_stream = self.filename == b'-' # <<<<<<<<<<<<<< jpayne@68: * self.is_remote = hisremote(self.filename) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = PyObject_RichCompare(__pyx_v_self->__pyx_base.filename, __pyx_kp_b__16, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 373, __pyx_L1_error) jpayne@68: __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 373, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_v_self->__pyx_base.is_stream = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":374 jpayne@68: * jpayne@68: * self.is_stream = self.filename == b'-' jpayne@68: * self.is_remote = hisremote(self.filename) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if not self.is_remote: jpayne@68: */ jpayne@68: __pyx_t_6 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.filename); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) __PYX_ERR(0, 374, __pyx_L1_error) jpayne@68: __pyx_v_self->__pyx_base.is_remote = hisremote(__pyx_t_6); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":376 jpayne@68: * self.is_remote = hisremote(self.filename) jpayne@68: * jpayne@68: * if not self.is_remote: # <<<<<<<<<<<<<< jpayne@68: * if not os.path.exists(filename): jpayne@68: * raise IOError("file `%s` not found" % filename) jpayne@68: */ jpayne@68: __pyx_t_1 = (!__pyx_v_self->__pyx_base.is_remote); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":377 jpayne@68: * jpayne@68: * if not self.is_remote: jpayne@68: * if not os.path.exists(filename): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("file `%s` not found" % filename) jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_os); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 377, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_path); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 377, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 377, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v_filename}; jpayne@68: __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 377, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 377, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_t_7 = (!__pyx_t_1); jpayne@68: if (unlikely(__pyx_t_7)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":378 jpayne@68: * if not self.is_remote: jpayne@68: * if not os.path.exists(filename): jpayne@68: * raise IOError("file `%s` not found" % filename) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if not os.path.exists(filename_index): jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_file_s_not_found, __pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 378, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 378, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 378, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":377 jpayne@68: * jpayne@68: * if not self.is_remote: jpayne@68: * if not os.path.exists(filename): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("file `%s` not found" % filename) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":380 jpayne@68: * raise IOError("file `%s` not found" % filename) jpayne@68: * jpayne@68: * if not os.path.exists(filename_index): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("index `%s` not found" % filename_index) jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_os); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 380, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_path); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 380, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_exists); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 380, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v_filename_index}; jpayne@68: __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 380, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_7 < 0))) __PYX_ERR(0, 380, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_t_1 = (!__pyx_t_7); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":381 jpayne@68: * jpayne@68: * if not os.path.exists(filename_index): jpayne@68: * raise IOError("index `%s` not found" % filename_index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # open file jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_index_s_not_found, __pyx_v_filename_index); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 381, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 381, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 381, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":380 jpayne@68: * raise IOError("file `%s` not found" % filename) jpayne@68: * jpayne@68: * if not os.path.exists(filename_index): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("index `%s` not found" % filename_index) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":376 jpayne@68: * self.is_remote = hisremote(self.filename) jpayne@68: * jpayne@68: * if not self.is_remote: # <<<<<<<<<<<<<< jpayne@68: * if not os.path.exists(filename): jpayne@68: * raise IOError("file `%s` not found" % filename) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":384 jpayne@68: * jpayne@68: * # open file jpayne@68: * cdef char *cfilename = self.filename # <<<<<<<<<<<<<< jpayne@68: * cdef char *cfilename_index = self.filename_index jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_t_8 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.filename); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 384, __pyx_L1_error) jpayne@68: __pyx_v_cfilename = __pyx_t_8; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":385 jpayne@68: * # open file jpayne@68: * cdef char *cfilename = self.filename jpayne@68: * cdef char *cfilename_index = self.filename_index # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * self.htsfile = hts_open(cfilename, 'r') jpayne@68: */ jpayne@68: __pyx_t_8 = __Pyx_PyObject_AsWritableString(__pyx_v_self->filename_index); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 385, __pyx_L1_error) jpayne@68: __pyx_v_cfilename_index = __pyx_t_8; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":386 jpayne@68: * cdef char *cfilename = self.filename jpayne@68: * cdef char *cfilename_index = self.filename_index jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * self.htsfile = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":387 jpayne@68: * cdef char *cfilename_index = self.filename_index jpayne@68: * with nogil: jpayne@68: * self.htsfile = hts_open(cfilename, 'r') # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if self.htsfile == NULL: jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.htsfile = hts_open(__pyx_v_cfilename, ((char const *)"r")); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":386 jpayne@68: * cdef char *cfilename = self.filename jpayne@68: * cdef char *cfilename_index = self.filename_index jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * self.htsfile = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L12; jpayne@68: } jpayne@68: __pyx_L12:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":389 jpayne@68: * self.htsfile = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: * if self.htsfile == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open file `%s`" % filename) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile == NULL); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":390 jpayne@68: * jpayne@68: * if self.htsfile == NULL: jpayne@68: * raise IOError("could not open file `%s`" % filename) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * #if self.htsfile.format.category != region_list: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_file_s, __pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 390, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 390, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 390, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":389 jpayne@68: * self.htsfile = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: * if self.htsfile == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open file `%s`" % filename) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":395 jpayne@68: * # raise ValueError("file does not contain region data") jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * self.index = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":396 jpayne@68: * jpayne@68: * with nogil: jpayne@68: * self.index = tbx_index_load2(cfilename, cfilename_index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if self.index == NULL: jpayne@68: */ jpayne@68: __pyx_v_self->index = tbx_index_load2(__pyx_v_cfilename, __pyx_v_cfilename_index); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":395 jpayne@68: * # raise ValueError("file does not contain region data") jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * self.index = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L16; jpayne@68: } jpayne@68: __pyx_L16:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":398 jpayne@68: * self.index = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: * if self.index == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open index for `%s`" % filename) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->index == NULL); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":399 jpayne@68: * jpayne@68: * if self.index == NULL: jpayne@68: * raise IOError("could not open index for `%s`" % filename) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if not self.is_stream: jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_index_for_s, __pyx_v_filename); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 399, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 399, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 399, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":398 jpayne@68: * self.index = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: * if self.index == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open index for `%s`" % filename) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":401 jpayne@68: * raise IOError("could not open index for `%s`" % filename) jpayne@68: * jpayne@68: * if not self.is_stream: # <<<<<<<<<<<<<< jpayne@68: * self.start_offset = self.tell() jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (!__pyx_v_self->__pyx_base.is_stream); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":402 jpayne@68: * jpayne@68: * if not self.is_stream: jpayne@68: * self.start_offset = self.tell() # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def _dup(self): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_tell); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 402, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, NULL}; jpayne@68: __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 0+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 402, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_t_9 = __Pyx_PyInt_As_int64_t(__pyx_t_3); if (unlikely((__pyx_t_9 == ((int64_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 402, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_v_self->__pyx_base.start_offset = __pyx_t_9; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":401 jpayne@68: * raise IOError("could not open index for `%s`" % filename) jpayne@68: * jpayne@68: * if not self.is_stream: # <<<<<<<<<<<<<< jpayne@68: * self.start_offset = self.tell() jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":352 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def _open( self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_filename_index); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":404 jpayne@68: * self.start_offset = self.tell() jpayne@68: * jpayne@68: * def _dup(self): # <<<<<<<<<<<<<< jpayne@68: * '''return a copy of this tabix file. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_4_dup, "TabixFile._dup(self)\nreturn a copy of this tabix file.\n \n The file is being re-opened.\n "); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_5_dup = {"_dup", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_4_dup}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("_dup (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("_dup", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "_dup", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_4_dup(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_4_dup(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__17) jpayne@68: __Pyx_RefNannySetupContext("_dup", 1); jpayne@68: __Pyx_TraceCall("_dup", __pyx_f[0], 404, 0, __PYX_ERR(0, 404, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":409 jpayne@68: * The file is being re-opened. jpayne@68: * ''' jpayne@68: * return TabixFile(self.filename, # <<<<<<<<<<<<<< jpayne@68: * mode="r", jpayne@68: * threads=self.threads, jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 409, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_self->__pyx_base.filename); jpayne@68: __Pyx_GIVEREF(__pyx_v_self->__pyx_base.filename); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->__pyx_base.filename)) __PYX_ERR(0, 409, __pyx_L1_error); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":410 jpayne@68: * ''' jpayne@68: * return TabixFile(self.filename, jpayne@68: * mode="r", # <<<<<<<<<<<<<< jpayne@68: * threads=self.threads, jpayne@68: * parser=self.parser, jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyDict_NewPresized(5); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 410, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_mode, __pyx_n_u_r) < 0) __PYX_ERR(0, 410, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":411 jpayne@68: * return TabixFile(self.filename, jpayne@68: * mode="r", jpayne@68: * threads=self.threads, # <<<<<<<<<<<<<< jpayne@68: * parser=self.parser, jpayne@68: * index=self.filename_index, jpayne@68: */ jpayne@68: if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_threads, __pyx_v_self->__pyx_base.threads) < 0) __PYX_ERR(0, 410, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":412 jpayne@68: * mode="r", jpayne@68: * threads=self.threads, jpayne@68: * parser=self.parser, # <<<<<<<<<<<<<< jpayne@68: * index=self.filename_index, jpayne@68: * encoding=self.encoding) jpayne@68: */ jpayne@68: if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_parser, ((PyObject *)__pyx_v_self->parser)) < 0) __PYX_ERR(0, 410, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":413 jpayne@68: * threads=self.threads, jpayne@68: * parser=self.parser, jpayne@68: * index=self.filename_index, # <<<<<<<<<<<<<< jpayne@68: * encoding=self.encoding) jpayne@68: * jpayne@68: */ jpayne@68: if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_index, __pyx_v_self->filename_index) < 0) __PYX_ERR(0, 410, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":414 jpayne@68: * parser=self.parser, jpayne@68: * index=self.filename_index, jpayne@68: * encoding=self.encoding) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def fetch(self, jpayne@68: */ jpayne@68: if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_encoding, __pyx_v_self->encoding) < 0) __PYX_ERR(0, 410, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":409 jpayne@68: * The file is being re-opened. jpayne@68: * ''' jpayne@68: * return TabixFile(self.filename, # <<<<<<<<<<<<<< jpayne@68: * mode="r", jpayne@68: * threads=self.threads, jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile), __pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 409, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":404 jpayne@68: * self.start_offset = self.tell() jpayne@68: * jpayne@68: * def _dup(self): # <<<<<<<<<<<<<< jpayne@68: * '''return a copy of this tabix file. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile._dup", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":416 jpayne@68: * encoding=self.encoding) jpayne@68: * jpayne@68: * def fetch(self, # <<<<<<<<<<<<<< jpayne@68: * reference=None, jpayne@68: * start=None, jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_6fetch, "TabixFile.fetch(self, reference=None, start=None, end=None, region=None, parser=None, multiple_iterators=False)\nfetch one or more rows in a :term:`region` using 0-based\n indexing. The region is specified by :term:`reference`,\n *start* and *end*. Alternatively, a samtools :term:`region`\n string can be supplied.\n\n Without *reference* or *region* all entries will be fetched. \n \n If only *reference* is set, all reads matching on *reference*\n will be fetched.\n\n If *parser* is None, the default parser will be used for\n parsing.\n \n Set *multiple_iterators* to true if you will be using multiple\n iterators on the same file at the same time. The iterator\n returned will receive its own copy of a filehandle to the file\n effectively re-opening the file. Re-opening a file creates\n some overhead, so beware.\n\n "); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_7fetch = {"fetch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_6fetch}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_reference = 0; jpayne@68: PyObject *__pyx_v_start = 0; jpayne@68: PyObject *__pyx_v_end = 0; jpayne@68: PyObject *__pyx_v_region = 0; jpayne@68: PyObject *__pyx_v_parser = 0; jpayne@68: PyObject *__pyx_v_multiple_iterators = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[6] = {0,0,0,0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("fetch (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_reference,&__pyx_n_s_start,&__pyx_n_s_end,&__pyx_n_s_region,&__pyx_n_s_parser,&__pyx_n_s_multiple_iterators,0}; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":417 jpayne@68: * jpayne@68: * def fetch(self, jpayne@68: * reference=None, # <<<<<<<<<<<<<< jpayne@68: * start=None, jpayne@68: * end=None, jpayne@68: */ jpayne@68: values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":418 jpayne@68: * def fetch(self, jpayne@68: * reference=None, jpayne@68: * start=None, # <<<<<<<<<<<<<< jpayne@68: * end=None, jpayne@68: * region=None, jpayne@68: */ jpayne@68: values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":419 jpayne@68: * reference=None, jpayne@68: * start=None, jpayne@68: * end=None, # <<<<<<<<<<<<<< jpayne@68: * region=None, jpayne@68: * parser=None, jpayne@68: */ jpayne@68: values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":420 jpayne@68: * start=None, jpayne@68: * end=None, jpayne@68: * region=None, # <<<<<<<<<<<<<< jpayne@68: * parser=None, jpayne@68: * multiple_iterators=False): jpayne@68: */ jpayne@68: values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":421 jpayne@68: * end=None, jpayne@68: * region=None, jpayne@68: * parser=None, # <<<<<<<<<<<<<< jpayne@68: * multiple_iterators=False): jpayne@68: * '''fetch one or more rows in a :term:`region` using 0-based jpayne@68: */ jpayne@68: values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":422 jpayne@68: * region=None, jpayne@68: * parser=None, jpayne@68: * multiple_iterators=False): # <<<<<<<<<<<<<< jpayne@68: * '''fetch one or more rows in a :term:`region` using 0-based jpayne@68: * indexing. The region is specified by :term:`reference`, jpayne@68: */ jpayne@68: values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_False)); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_reference); jpayne@68: if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start); jpayne@68: if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_region); jpayne@68: if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser); jpayne@68: if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_multiple_iterators); jpayne@68: if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "fetch") < 0)) __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_reference = values[0]; jpayne@68: __pyx_v_start = values[1]; jpayne@68: __pyx_v_end = values[2]; jpayne@68: __pyx_v_region = values[3]; jpayne@68: __pyx_v_parser = values[4]; jpayne@68: __pyx_v_multiple_iterators = values[5]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, __pyx_nargs); __PYX_ERR(0, 416, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_6fetch(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_parser, __pyx_v_multiple_iterators); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":416 jpayne@68: * encoding=self.encoding) jpayne@68: * jpayne@68: * def fetch(self, # <<<<<<<<<<<<<< jpayne@68: * reference=None, jpayne@68: * start=None, jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6fetch(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser, PyObject *__pyx_v_multiple_iterators) { jpayne@68: hts_itr_t *__pyx_v_itr; jpayne@68: char *__pyx_v_cstr; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_fileobj = 0; jpayne@68: PyObject *__pyx_v_s = NULL; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_a = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: unsigned int __pyx_t_4; jpayne@68: int __pyx_t_5; jpayne@68: int __pyx_t_6; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_bytes __pyx_t_7; jpayne@68: char *__pyx_t_8; jpayne@68: Py_ssize_t __pyx_t_9; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__18) jpayne@68: __Pyx_RefNannySetupContext("fetch", 0); jpayne@68: __Pyx_TraceCall("fetch", __pyx_f[0], 416, 0, __PYX_ERR(0, 416, __pyx_L1_error)); jpayne@68: __Pyx_INCREF(__pyx_v_start); jpayne@68: __Pyx_INCREF(__pyx_v_region); jpayne@68: __Pyx_INCREF(__pyx_v_parser); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":443 jpayne@68: * jpayne@68: * ''' jpayne@68: * if not self.is_open(): # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file") jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_is_open); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 443, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 443, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 443, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_6 = (!__pyx_t_5); jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":444 jpayne@68: * ''' jpayne@68: * if not self.is_open(): jpayne@68: * raise ValueError("I/O operation on closed file") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # convert coordinates to region string, which is one-based jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 444, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 444, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":443 jpayne@68: * jpayne@68: * ''' jpayne@68: * if not self.is_open(): # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file") jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":447 jpayne@68: * jpayne@68: * # convert coordinates to region string, which is one-based jpayne@68: * if reference: # <<<<<<<<<<<<<< jpayne@68: * if end is not None: jpayne@68: * if end < 0: jpayne@68: */ jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 447, __pyx_L1_error) jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":448 jpayne@68: * # convert coordinates to region string, which is one-based jpayne@68: * if reference: jpayne@68: * if end is not None: # <<<<<<<<<<<<<< jpayne@68: * if end < 0: jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_end != Py_None); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":449 jpayne@68: * if reference: jpayne@68: * if end is not None: jpayne@68: * if end < 0: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: * if start is None: jpayne@68: */ jpayne@68: __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 449, __pyx_L1_error) jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 449, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":450 jpayne@68: * if end is not None: jpayne@68: * if end < 0: jpayne@68: * raise ValueError("end out of range (%i)" % end) # <<<<<<<<<<<<<< jpayne@68: * if start is None: jpayne@68: * start = 0 jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_end_out_of_range_i, __pyx_v_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 450, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 450, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 450, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":449 jpayne@68: * if reference: jpayne@68: * if end is not None: jpayne@68: * if end < 0: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: * if start is None: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":451 jpayne@68: * if end < 0: jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: * if start is None: # <<<<<<<<<<<<<< jpayne@68: * start = 0 jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_start == Py_None); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":452 jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: * if start is None: jpayne@68: * start = 0 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if start < 0: jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_DECREF_SET(__pyx_v_start, __pyx_int_0); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":451 jpayne@68: * if end < 0: jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: * if start is None: # <<<<<<<<<<<<<< jpayne@68: * start = 0 jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":454 jpayne@68: * start = 0 jpayne@68: * jpayne@68: * if start < 0: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * elif start > end: jpayne@68: */ jpayne@68: __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 454, __pyx_L1_error) jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 454, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":455 jpayne@68: * jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) # <<<<<<<<<<<<<< jpayne@68: * elif start > end: jpayne@68: * raise ValueError( jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_start_out_of_range_i, __pyx_v_end); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 455, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 455, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 455, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":454 jpayne@68: * start = 0 jpayne@68: * jpayne@68: * if start < 0: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * elif start > end: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":456 jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * elif start > end: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError( jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) jpayne@68: */ jpayne@68: __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 456, __pyx_L1_error) jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 456, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":458 jpayne@68: * elif start > end: jpayne@68: * raise ValueError( jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) # <<<<<<<<<<<<<< jpayne@68: * elif start == end: jpayne@68: * return EmptyIterator() jpayne@68: */ jpayne@68: __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 458, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_start); jpayne@68: __Pyx_GIVEREF(__pyx_v_start); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_start)) __PYX_ERR(0, 458, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_end); jpayne@68: __Pyx_GIVEREF(__pyx_v_end); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_end)) __PYX_ERR(0, 458, __pyx_L1_error); jpayne@68: __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_start_i_end_i, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 458, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":457 jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * elif start > end: jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) jpayne@68: * elif start == end: jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 457, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 457, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":456 jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * elif start > end: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError( jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":459 jpayne@68: * raise ValueError( jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) jpayne@68: * elif start == end: # <<<<<<<<<<<<<< jpayne@68: * return EmptyIterator() jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 459, __pyx_L1_error) jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 459, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":460 jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) jpayne@68: * elif start == end: jpayne@68: * return EmptyIterator() # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * region = '%s:%i-%i' % (reference, start + 1, end) jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_EmptyIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 460, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (unlikely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 460, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_r = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":459 jpayne@68: * raise ValueError( jpayne@68: * 'start (%i) >= end (%i)' % (start, end)) jpayne@68: * elif start == end: # <<<<<<<<<<<<<< jpayne@68: * return EmptyIterator() jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":462 jpayne@68: * return EmptyIterator() jpayne@68: * else: jpayne@68: * region = '%s:%i-%i' % (reference, start + 1, end) # <<<<<<<<<<<<<< jpayne@68: * elif start is not None: jpayne@68: * if start < 0: jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_start, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 462, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_v_reference); jpayne@68: __Pyx_GIVEREF(__pyx_v_reference); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference)) __PYX_ERR(0, 462, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_end); jpayne@68: __Pyx_GIVEREF(__pyx_v_end); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end)) __PYX_ERR(0, 462, __pyx_L1_error); jpayne@68: __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = PyUnicode_Format(__pyx_kp_u_s_i_i, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 462, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_region, __pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":448 jpayne@68: * # convert coordinates to region string, which is one-based jpayne@68: * if reference: jpayne@68: * if end is not None: # <<<<<<<<<<<<<< jpayne@68: * if end < 0: jpayne@68: * raise ValueError("end out of range (%i)" % end) jpayne@68: */ jpayne@68: goto __pyx_L5; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":463 jpayne@68: * else: jpayne@68: * region = '%s:%i-%i' % (reference, start + 1, end) jpayne@68: * elif start is not None: # <<<<<<<<<<<<<< jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_start != Py_None); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":464 jpayne@68: * region = '%s:%i-%i' % (reference, start + 1, end) jpayne@68: * elif start is not None: jpayne@68: * if start < 0: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * region = '%s:%i' % (reference, start + 1) jpayne@68: */ jpayne@68: __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 464, __pyx_L1_error) jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 464, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":465 jpayne@68: * elif start is not None: jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) # <<<<<<<<<<<<<< jpayne@68: * region = '%s:%i' % (reference, start + 1) jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_start_out_of_range_i, __pyx_v_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 465, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 465, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 465, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":464 jpayne@68: * region = '%s:%i-%i' % (reference, start + 1, end) jpayne@68: * elif start is not None: jpayne@68: * if start < 0: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * region = '%s:%i' % (reference, start + 1) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":466 jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: * region = '%s:%i' % (reference, start + 1) # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * region = reference jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyInt_AddObjC(__pyx_v_start, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 466, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 466, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_v_reference); jpayne@68: __Pyx_GIVEREF(__pyx_v_reference); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference)) __PYX_ERR(0, 466, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_2); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2)) __PYX_ERR(0, 466, __pyx_L1_error); jpayne@68: __pyx_t_2 = 0; jpayne@68: __pyx_t_2 = PyUnicode_Format(__pyx_kp_u_s_i, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 466, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_region, __pyx_t_2); jpayne@68: __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":463 jpayne@68: * else: jpayne@68: * region = '%s:%i-%i' % (reference, start + 1, end) jpayne@68: * elif start is not None: # <<<<<<<<<<<<<< jpayne@68: * if start < 0: jpayne@68: * raise ValueError("start out of range (%i)" % end) jpayne@68: */ jpayne@68: goto __pyx_L5; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":468 jpayne@68: * region = '%s:%i' % (reference, start + 1) jpayne@68: * else: jpayne@68: * region = reference # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # get iterator jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_INCREF(__pyx_v_reference); jpayne@68: __Pyx_DECREF_SET(__pyx_v_region, __pyx_v_reference); jpayne@68: } jpayne@68: __pyx_L5:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":447 jpayne@68: * jpayne@68: * # convert coordinates to region string, which is one-based jpayne@68: * if reference: # <<<<<<<<<<<<<< jpayne@68: * if end is not None: jpayne@68: * if end < 0: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":476 jpayne@68: * jpayne@68: * # reopen the same file if necessary jpayne@68: * if multiple_iterators: # <<<<<<<<<<<<<< jpayne@68: * fileobj = self._dup() jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_multiple_iterators); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 476, __pyx_L1_error) jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":477 jpayne@68: * # reopen the same file if necessary jpayne@68: * if multiple_iterators: jpayne@68: * fileobj = self._dup() # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * fileobj = self jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_dup); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 477, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_1))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_1); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_1, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; jpayne@68: __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 477, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: } jpayne@68: if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5pysam_9libctabix_TabixFile))))) __PYX_ERR(0, 477, __pyx_L1_error) jpayne@68: __pyx_v_fileobj = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_t_2); jpayne@68: __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":476 jpayne@68: * jpayne@68: * # reopen the same file if necessary jpayne@68: * if multiple_iterators: # <<<<<<<<<<<<<< jpayne@68: * fileobj = self._dup() jpayne@68: * else: jpayne@68: */ jpayne@68: goto __pyx_L10; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":479 jpayne@68: * fileobj = self._dup() jpayne@68: * else: jpayne@68: * fileobj = self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if region is None: jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_self); jpayne@68: __pyx_v_fileobj = __pyx_v_self; jpayne@68: } jpayne@68: __pyx_L10:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":481 jpayne@68: * fileobj = self jpayne@68: * jpayne@68: * if region is None: # <<<<<<<<<<<<<< jpayne@68: * # without region or reference - iterate from start jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_region == Py_None); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":483 jpayne@68: * if region is None: jpayne@68: * # without region or reference - iterate from start jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * itr = tbx_itr_queryi(fileobj.index, jpayne@68: * HTS_IDX_START, jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":484 jpayne@68: * # without region or reference - iterate from start jpayne@68: * with nogil: jpayne@68: * itr = tbx_itr_queryi(fileobj.index, # <<<<<<<<<<<<<< jpayne@68: * HTS_IDX_START, jpayne@68: * 0, jpayne@68: */ jpayne@68: __pyx_v_itr = tbx_itr_queryi(__pyx_v_fileobj->index, HTS_IDX_START, 0, 0); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":483 jpayne@68: * if region is None: jpayne@68: * # without region or reference - iterate from start jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * itr = tbx_itr_queryi(fileobj.index, jpayne@68: * HTS_IDX_START, jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L14; jpayne@68: } jpayne@68: __pyx_L14:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":481 jpayne@68: * fileobj = self jpayne@68: * jpayne@68: * if region is None: # <<<<<<<<<<<<<< jpayne@68: * # without region or reference - iterate from start jpayne@68: * with nogil: jpayne@68: */ jpayne@68: goto __pyx_L11; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":489 jpayne@68: * 0) jpayne@68: * else: jpayne@68: * s = force_bytes(region, encoding=fileobj.encoding) # <<<<<<<<<<<<<< jpayne@68: * cstr = s jpayne@68: * with nogil: jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = __pyx_v_fileobj->encoding; jpayne@68: __Pyx_INCREF(__pyx_t_2); jpayne@68: __pyx_t_7.__pyx_n = 1; jpayne@68: __pyx_t_7.encoding = __pyx_t_2; jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_region, &__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 489, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_v_s = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":490 jpayne@68: * else: jpayne@68: * s = force_bytes(region, encoding=fileobj.encoding) jpayne@68: * cstr = s # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * itr = tbx_itr_querys(fileobj.index, cstr) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_s == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 490, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_8 = __Pyx_PyBytes_AsWritableString(__pyx_v_s); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 490, __pyx_L1_error) jpayne@68: __pyx_v_cstr = __pyx_t_8; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":491 jpayne@68: * s = force_bytes(region, encoding=fileobj.encoding) jpayne@68: * cstr = s jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * itr = tbx_itr_querys(fileobj.index, cstr) jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":492 jpayne@68: * cstr = s jpayne@68: * with nogil: jpayne@68: * itr = tbx_itr_querys(fileobj.index, cstr) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if itr == NULL: jpayne@68: */ jpayne@68: __pyx_v_itr = tbx_itr_querys(__pyx_v_fileobj->index, __pyx_v_cstr); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":491 jpayne@68: * s = force_bytes(region, encoding=fileobj.encoding) jpayne@68: * cstr = s jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * itr = tbx_itr_querys(fileobj.index, cstr) jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L17; jpayne@68: } jpayne@68: __pyx_L17:; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: __pyx_L11:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":494 jpayne@68: * itr = tbx_itr_querys(fileobj.index, cstr) jpayne@68: * jpayne@68: * if itr == NULL: # <<<<<<<<<<<<<< jpayne@68: * if region is None: jpayne@68: * if len(self.contigs) > 0: jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_itr == NULL); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":495 jpayne@68: * jpayne@68: * if itr == NULL: jpayne@68: * if region is None: # <<<<<<<<<<<<<< jpayne@68: * if len(self.contigs) > 0: jpayne@68: * # when accessing a tabix file created prior tabix 1.0 jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_region == Py_None); jpayne@68: if (likely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":496 jpayne@68: * if itr == NULL: jpayne@68: * if region is None: jpayne@68: * if len(self.contigs) > 0: # <<<<<<<<<<<<<< jpayne@68: * # when accessing a tabix file created prior tabix 1.0 jpayne@68: * # the full-file iterator is empty. jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_contigs); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 496, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_9 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 496, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_6 = (__pyx_t_9 > 0); jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":499 jpayne@68: * # when accessing a tabix file created prior tabix 1.0 jpayne@68: * # the full-file iterator is empty. jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * "could not create iterator, possible " jpayne@68: * "tabix version mismatch") jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 499, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 499, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":496 jpayne@68: * if itr == NULL: jpayne@68: * if region is None: jpayne@68: * if len(self.contigs) > 0: # <<<<<<<<<<<<<< jpayne@68: * # when accessing a tabix file created prior tabix 1.0 jpayne@68: * # the full-file iterator is empty. jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":505 jpayne@68: * # possible reason is that the file is empty - jpayne@68: * # return an empty iterator jpayne@68: * return EmptyIterator() # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * raise ValueError( jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_EmptyIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 505, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (unlikely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 505, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_r = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":495 jpayne@68: * jpayne@68: * if itr == NULL: jpayne@68: * if region is None: # <<<<<<<<<<<<<< jpayne@68: * if len(self.contigs) > 0: jpayne@68: * # when accessing a tabix file created prior tabix 1.0 jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":507 jpayne@68: * return EmptyIterator() jpayne@68: * else: jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * "could not create iterator for region '%s'" % jpayne@68: * region) jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":508 jpayne@68: * else: jpayne@68: * raise ValueError( jpayne@68: * "could not create iterator for region '%s'" % # <<<<<<<<<<<<<< jpayne@68: * region) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_create_iterator_for_re, __pyx_v_region); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 508, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":507 jpayne@68: * return EmptyIterator() jpayne@68: * else: jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * "could not create iterator for region '%s'" % jpayne@68: * region) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 507, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 507, __pyx_L1_error) jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":494 jpayne@68: * itr = tbx_itr_querys(fileobj.index, cstr) jpayne@68: * jpayne@68: * if itr == NULL: # <<<<<<<<<<<<<< jpayne@68: * if region is None: jpayne@68: * if len(self.contigs) > 0: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":512 jpayne@68: * jpayne@68: * # use default parser if no parser is specified jpayne@68: * if parser is None: # <<<<<<<<<<<<<< jpayne@68: * parser = fileobj.parser jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_parser == Py_None); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":513 jpayne@68: * # use default parser if no parser is specified jpayne@68: * if parser is None: jpayne@68: * parser = fileobj.parser # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef TabixIterator a jpayne@68: */ jpayne@68: __pyx_t_2 = ((PyObject *)__pyx_v_fileobj->parser); jpayne@68: __Pyx_INCREF(__pyx_t_2); jpayne@68: __Pyx_DECREF_SET(__pyx_v_parser, __pyx_t_2); jpayne@68: __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":512 jpayne@68: * jpayne@68: * # use default parser if no parser is specified jpayne@68: * if parser is None: # <<<<<<<<<<<<<< jpayne@68: * parser = fileobj.parser jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":516 jpayne@68: * jpayne@68: * cdef TabixIterator a jpayne@68: * if parser is None: # <<<<<<<<<<<<<< jpayne@68: * a = TabixIterator(encoding=fileobj.encoding) jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_6 = (__pyx_v_parser == Py_None); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":517 jpayne@68: * cdef TabixIterator a jpayne@68: * if parser is None: jpayne@68: * a = TabixIterator(encoding=fileobj.encoding) # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * parser.set_encoding(fileobj.encoding) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 517, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_encoding, __pyx_v_fileobj->encoding) < 0) __PYX_ERR(0, 517, __pyx_L1_error) jpayne@68: __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIterator), __pyx_empty_tuple, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 517, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_v_a = ((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":516 jpayne@68: * jpayne@68: * cdef TabixIterator a jpayne@68: * if parser is None: # <<<<<<<<<<<<<< jpayne@68: * a = TabixIterator(encoding=fileobj.encoding) jpayne@68: * else: jpayne@68: */ jpayne@68: goto __pyx_L22; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":519 jpayne@68: * a = TabixIterator(encoding=fileobj.encoding) jpayne@68: * else: jpayne@68: * parser.set_encoding(fileobj.encoding) # <<<<<<<<<<<<<< jpayne@68: * a = TabixIteratorParsed(parser) jpayne@68: * jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_parser, __pyx_n_s_set_encoding); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 519, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_fileobj->encoding}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 519, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":520 jpayne@68: * else: jpayne@68: * parser.set_encoding(fileobj.encoding) jpayne@68: * a = TabixIteratorParsed(parser) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * a.tabixfile = fileobj jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed), __pyx_v_parser); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 520, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_a = ((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: } jpayne@68: __pyx_L22:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":522 jpayne@68: * a = TabixIteratorParsed(parser) jpayne@68: * jpayne@68: * a.tabixfile = fileobj # <<<<<<<<<<<<<< jpayne@68: * a.iterator = itr jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_fileobj); jpayne@68: __Pyx_GIVEREF((PyObject *)__pyx_v_fileobj); jpayne@68: __Pyx_GOTREF((PyObject *)__pyx_v_a->tabixfile); jpayne@68: __Pyx_DECREF((PyObject *)__pyx_v_a->tabixfile); jpayne@68: __pyx_v_a->tabixfile = __pyx_v_fileobj; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":523 jpayne@68: * jpayne@68: * a.tabixfile = fileobj jpayne@68: * a.iterator = itr # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return a jpayne@68: */ jpayne@68: __pyx_v_a->iterator = __pyx_v_itr; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":525 jpayne@68: * a.iterator = itr jpayne@68: * jpayne@68: * return a # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * ############################################################### jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_a); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_a); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":416 jpayne@68: * encoding=self.encoding) jpayne@68: * jpayne@68: * def fetch(self, # <<<<<<<<<<<<<< jpayne@68: * reference=None, jpayne@68: * start=None, jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_fileobj); jpayne@68: __Pyx_XDECREF(__pyx_v_s); jpayne@68: __Pyx_XDECREF((PyObject *)__pyx_v_a); jpayne@68: __Pyx_XDECREF(__pyx_v_start); jpayne@68: __Pyx_XDECREF(__pyx_v_region); jpayne@68: __Pyx_XDECREF(__pyx_v_parser); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":543 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __get__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char *cfilename = self.filename jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_6header_1__get__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_6header___get__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_6header___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: char *__pyx_v_cfilename; jpayne@68: char *__pyx_v_cfilename_index; jpayne@68: kstring_t __pyx_v_buffer; jpayne@68: htsFile *__pyx_v_fp; jpayne@68: int __pyx_v_KS_SEP_LINE; jpayne@68: tbx_t *__pyx_v_tbx; jpayne@68: PyObject *__pyx_v_lines = NULL; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: char *__pyx_t_1; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: int __pyx_t_3; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: unsigned int __pyx_t_6; jpayne@68: int __pyx_t_7; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_str __pyx_t_8; jpayne@68: int __pyx_t_9; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__get__", 1); jpayne@68: __Pyx_TraceCall("__get__", __pyx_f[0], 543, 0, __PYX_ERR(0, 543, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":545 jpayne@68: * def __get__(self): jpayne@68: * jpayne@68: * cdef char *cfilename = self.filename # <<<<<<<<<<<<<< jpayne@68: * cdef char *cfilename_index = self.filename_index jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->__pyx_base.filename); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 545, __pyx_L1_error) jpayne@68: __pyx_v_cfilename = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":546 jpayne@68: * jpayne@68: * cdef char *cfilename = self.filename jpayne@68: * cdef char *cfilename_index = self.filename_index # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef kstring_t buffer jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->filename_index); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 546, __pyx_L1_error) jpayne@68: __pyx_v_cfilename_index = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":549 jpayne@68: * jpayne@68: * cdef kstring_t buffer jpayne@68: * buffer.l = buffer.m = 0 # <<<<<<<<<<<<<< jpayne@68: * buffer.s = NULL jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_buffer.l = 0; jpayne@68: __pyx_v_buffer.m = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":550 jpayne@68: * cdef kstring_t buffer jpayne@68: * buffer.l = buffer.m = 0 jpayne@68: * buffer.s = NULL # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef htsFile * fp = NULL jpayne@68: */ jpayne@68: __pyx_v_buffer.s = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":552 jpayne@68: * buffer.s = NULL jpayne@68: * jpayne@68: * cdef htsFile * fp = NULL # <<<<<<<<<<<<<< jpayne@68: * cdef int KS_SEP_LINE = 2 jpayne@68: * cdef tbx_t * tbx = NULL jpayne@68: */ jpayne@68: __pyx_v_fp = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":553 jpayne@68: * jpayne@68: * cdef htsFile * fp = NULL jpayne@68: * cdef int KS_SEP_LINE = 2 # <<<<<<<<<<<<<< jpayne@68: * cdef tbx_t * tbx = NULL jpayne@68: * lines = [] jpayne@68: */ jpayne@68: __pyx_v_KS_SEP_LINE = 2; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":554 jpayne@68: * cdef htsFile * fp = NULL jpayne@68: * cdef int KS_SEP_LINE = 2 jpayne@68: * cdef tbx_t * tbx = NULL # <<<<<<<<<<<<<< jpayne@68: * lines = [] jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_v_tbx = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":555 jpayne@68: * cdef int KS_SEP_LINE = 2 jpayne@68: * cdef tbx_t * tbx = NULL jpayne@68: * lines = [] # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * fp = hts_open(cfilename, 'r') jpayne@68: */ jpayne@68: __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 555, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_v_lines = ((PyObject*)__pyx_t_2); jpayne@68: __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":556 jpayne@68: * cdef tbx_t * tbx = NULL jpayne@68: * lines = [] jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * fp = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":557 jpayne@68: * lines = [] jpayne@68: * with nogil: jpayne@68: * fp = hts_open(cfilename, 'r') # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if fp == NULL: jpayne@68: */ jpayne@68: __pyx_v_fp = hts_open(__pyx_v_cfilename, ((char const *)"r")); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":556 jpayne@68: * cdef tbx_t * tbx = NULL jpayne@68: * lines = [] jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * fp = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L5; jpayne@68: } jpayne@68: __pyx_L5:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":559 jpayne@68: * fp = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: * if fp == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise OSError("could not open {} for reading header".format(self.filename)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = (__pyx_v_fp == NULL); jpayne@68: if (unlikely(__pyx_t_3)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":560 jpayne@68: * jpayne@68: * if fp == NULL: jpayne@68: * raise OSError("could not open {} for reading header".format(self.filename)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_could_not_open_for_reading_heade, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 560, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_5 = NULL; jpayne@68: __pyx_t_6 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_4))) { jpayne@68: __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); jpayne@68: if (likely(__pyx_t_5)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); jpayne@68: __Pyx_INCREF(__pyx_t_5); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_4, function); jpayne@68: __pyx_t_6 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_self->__pyx_base.filename}; jpayne@68: __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 560, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_OSError, __pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 560, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_Raise(__pyx_t_4, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __PYX_ERR(0, 560, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":559 jpayne@68: * fp = hts_open(cfilename, 'r') jpayne@68: * jpayne@68: * if fp == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise OSError("could not open {} for reading header".format(self.filename)) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":562 jpayne@68: * raise OSError("could not open {} for reading header".format(self.filename)) jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * tbx = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":563 jpayne@68: * jpayne@68: * with nogil: jpayne@68: * tbx = tbx_index_load2(cfilename, cfilename_index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if tbx == NULL: jpayne@68: */ jpayne@68: __pyx_v_tbx = tbx_index_load2(__pyx_v_cfilename, __pyx_v_cfilename_index); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":562 jpayne@68: * raise OSError("could not open {} for reading header".format(self.filename)) jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * tbx = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L9; jpayne@68: } jpayne@68: __pyx_L9:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":565 jpayne@68: * tbx = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: * if tbx == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise OSError("could not load .tbi/.csi index of {}".format(self.filename)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = (__pyx_v_tbx == NULL); jpayne@68: if (unlikely(__pyx_t_3)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":566 jpayne@68: * jpayne@68: * if tbx == NULL: jpayne@68: * raise OSError("could not load .tbi/.csi index of {}".format(self.filename)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_could_not_load_tbi_csi_index_of, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 566, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_5 = NULL; jpayne@68: __pyx_t_6 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_5)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_5); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_6 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_self->__pyx_base.filename}; jpayne@68: __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_6, 1+__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 566, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_OSError, __pyx_t_4); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 566, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 566, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":565 jpayne@68: * tbx = tbx_index_load2(cfilename, cfilename_index) jpayne@68: * jpayne@68: * if tbx == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise OSError("could not load .tbi/.csi index of {}".format(self.filename)) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":568 jpayne@68: * raise OSError("could not load .tbi/.csi index of {}".format(self.filename)) jpayne@68: * jpayne@68: * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: # <<<<<<<<<<<<<< jpayne@68: * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: jpayne@68: * break jpayne@68: */ jpayne@68: while (1) { jpayne@68: __pyx_t_3 = (hts_getline(__pyx_v_fp, __pyx_v_KS_SEP_LINE, (&__pyx_v_buffer)) >= 0); jpayne@68: if (!__pyx_t_3) break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":569 jpayne@68: * jpayne@68: * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: jpayne@68: * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * lines.append(force_str(buffer.s, self.encoding)) jpayne@68: */ jpayne@68: __pyx_t_7 = (!(__pyx_v_buffer.l != 0)); jpayne@68: if (!__pyx_t_7) { jpayne@68: } else { jpayne@68: __pyx_t_3 = __pyx_t_7; jpayne@68: goto __pyx_L14_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_7 = ((__pyx_v_buffer.s[0]) != __pyx_v_tbx->conf.meta_char); jpayne@68: __pyx_t_3 = __pyx_t_7; jpayne@68: __pyx_L14_bool_binop_done:; jpayne@68: if (__pyx_t_3) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":570 jpayne@68: * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: jpayne@68: * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: jpayne@68: * break # <<<<<<<<<<<<<< jpayne@68: * lines.append(force_str(buffer.s, self.encoding)) jpayne@68: * jpayne@68: */ jpayne@68: goto __pyx_L12_break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":569 jpayne@68: * jpayne@68: * while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0: jpayne@68: * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * lines.append(force_str(buffer.s, self.encoding)) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":571 jpayne@68: * if not buffer.l or buffer.s[0] != tbx.conf.meta_char: jpayne@68: * break jpayne@68: * lines.append(force_str(buffer.s, self.encoding)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_buffer.s); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 571, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_4 = __pyx_v_self->encoding; jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __pyx_t_8.__pyx_n = 1; jpayne@68: __pyx_t_8.encoding = __pyx_t_4; jpayne@68: __pyx_t_5 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_2, &__pyx_t_8); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 571, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_lines, __pyx_t_5); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 571, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: } jpayne@68: __pyx_L12_break:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":573 jpayne@68: * lines.append(force_str(buffer.s, self.encoding)) jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * hts_close(fp) jpayne@68: * free(buffer.s) jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":574 jpayne@68: * jpayne@68: * with nogil: jpayne@68: * hts_close(fp) # <<<<<<<<<<<<<< jpayne@68: * free(buffer.s) jpayne@68: * jpayne@68: */ jpayne@68: (void)(hts_close(__pyx_v_fp)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":575 jpayne@68: * with nogil: jpayne@68: * hts_close(fp) jpayne@68: * free(buffer.s) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return lines jpayne@68: */ jpayne@68: free(__pyx_v_buffer.s); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":573 jpayne@68: * lines.append(force_str(buffer.s, self.encoding)) jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * hts_close(fp) jpayne@68: * free(buffer.s) jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L18; jpayne@68: } jpayne@68: __pyx_L18:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":577 jpayne@68: * free(buffer.s) jpayne@68: * jpayne@68: * return lines # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * property contigs: jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_lines); jpayne@68: __pyx_r = __pyx_v_lines; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":543 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __get__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char *cfilename = self.filename jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_lines); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":581 jpayne@68: * property contigs: jpayne@68: * '''list of chromosome names''' jpayne@68: * def __get__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef const char ** sequences jpayne@68: * cdef int nsequences jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7contigs_1__get__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_7contigs_1__get__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: char const **__pyx_v_sequences; jpayne@68: int __pyx_v_nsequences; jpayne@68: int __pyx_v_x; jpayne@68: PyObject *__pyx_v_result = NULL; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: int __pyx_t_4; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__get__", 1); jpayne@68: __Pyx_TraceCall("__get__", __pyx_f[0], 581, 0, __PYX_ERR(0, 581, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":585 jpayne@68: * cdef int nsequences jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * sequences = tbx_seqnames(self.index, &nsequences) jpayne@68: * cdef int x jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":586 jpayne@68: * jpayne@68: * with nogil: jpayne@68: * sequences = tbx_seqnames(self.index, &nsequences) # <<<<<<<<<<<<<< jpayne@68: * cdef int x jpayne@68: * result = [] jpayne@68: */ jpayne@68: __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":585 jpayne@68: * cdef int nsequences jpayne@68: * jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * sequences = tbx_seqnames(self.index, &nsequences) jpayne@68: * cdef int x jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L5; jpayne@68: } jpayne@68: __pyx_L5:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":588 jpayne@68: * sequences = tbx_seqnames(self.index, &nsequences) jpayne@68: * cdef int x jpayne@68: * result = [] # <<<<<<<<<<<<<< jpayne@68: * for x from 0 <= x < nsequences: jpayne@68: * result.append(force_str(sequences[x])) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 588, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_v_result = ((PyObject*)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":589 jpayne@68: * cdef int x jpayne@68: * result = [] jpayne@68: * for x from 0 <= x < nsequences: # <<<<<<<<<<<<<< jpayne@68: * result.append(force_str(sequences[x])) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __pyx_v_nsequences; jpayne@68: for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":590 jpayne@68: * result = [] jpayne@68: * for x from 0 <= x < nsequences: jpayne@68: * result.append(force_str(sequences[x])) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # htslib instructions: jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyBytes_FromString((__pyx_v_sequences[__pyx_v_x])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 590, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 590, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_4 = __Pyx_PyList_Append(__pyx_v_result, __pyx_t_3); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 590, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":594 jpayne@68: * # htslib instructions: jpayne@68: * # only free container, not the sequences themselves jpayne@68: * free(sequences) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return result jpayne@68: */ jpayne@68: free(__pyx_v_sequences); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":596 jpayne@68: * free(sequences) jpayne@68: * jpayne@68: * return result # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def close(self): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_result); jpayne@68: __pyx_r = __pyx_v_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":581 jpayne@68: * property contigs: jpayne@68: * '''list of chromosome names''' jpayne@68: * def __get__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef const char ** sequences jpayne@68: * cdef int nsequences jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.contigs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":598 jpayne@68: * return result jpayne@68: * jpayne@68: * def close(self): # <<<<<<<<<<<<<< jpayne@68: * ''' jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_9close(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_8close, "TabixFile.close(self)\n\n closes the :class:`pysam.TabixFile`."); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_9close = {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_9close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_8close}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_9close(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("close (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("close", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "close", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_8close(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_8close(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__21) jpayne@68: __Pyx_RefNannySetupContext("close", 1); jpayne@68: __Pyx_TraceCall("close", __pyx_f[0], 598, 0, __PYX_ERR(0, 598, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":601 jpayne@68: * ''' jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: * if self.htsfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":602 jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: * if self.htsfile != NULL: jpayne@68: * hts_close(self.htsfile) # <<<<<<<<<<<<<< jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: jpayne@68: */ jpayne@68: (void)(hts_close(__pyx_v_self->__pyx_base.htsfile)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":603 jpayne@68: * if self.htsfile != NULL: jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL # <<<<<<<<<<<<<< jpayne@68: * if self.index != NULL: jpayne@68: * tbx_destroy(self.index) jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.htsfile = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":601 jpayne@68: * ''' jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: * if self.htsfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":604 jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: # <<<<<<<<<<<<<< jpayne@68: * tbx_destroy(self.index) jpayne@68: * self.index = NULL jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->index != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":605 jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: jpayne@68: * tbx_destroy(self.index) # <<<<<<<<<<<<<< jpayne@68: * self.index = NULL jpayne@68: * jpayne@68: */ jpayne@68: tbx_destroy(__pyx_v_self->index); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":606 jpayne@68: * if self.index != NULL: jpayne@68: * tbx_destroy(self.index) jpayne@68: * self.index = NULL # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __dealloc__( self ): jpayne@68: */ jpayne@68: __pyx_v_self->index = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":604 jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: # <<<<<<<<<<<<<< jpayne@68: * tbx_destroy(self.index) jpayne@68: * self.index = NULL jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":598 jpayne@68: * return result jpayne@68: * jpayne@68: * def close(self): # <<<<<<<<<<<<<< jpayne@68: * ''' jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.close", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":608 jpayne@68: * self.index = NULL jpayne@68: * jpayne@68: * def __dealloc__( self ): # <<<<<<<<<<<<<< jpayne@68: * # remember: dealloc cannot call other python methods jpayne@68: * # note: no doc string jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static void __pyx_pw_5pysam_9libctabix_9TabixFile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static void __pyx_pw_5pysam_9libctabix_9TabixFile_11__dealloc__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_pf_5pysam_9libctabix_9TabixFile_10__dealloc__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: } jpayne@68: jpayne@68: static void __pyx_pf_5pysam_9libctabix_9TabixFile_10__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: __Pyx_TraceDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceCall("__dealloc__", __pyx_f[0], 608, 0, __PYX_ERR(0, 608, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":612 jpayne@68: * # note: no doc string jpayne@68: * # note: __del__ is not called. jpayne@68: * if self.htsfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->__pyx_base.htsfile != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":613 jpayne@68: * # note: __del__ is not called. jpayne@68: * if self.htsfile != NULL: jpayne@68: * hts_close(self.htsfile) # <<<<<<<<<<<<<< jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: jpayne@68: */ jpayne@68: (void)(hts_close(__pyx_v_self->__pyx_base.htsfile)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":614 jpayne@68: * if self.htsfile != NULL: jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL # <<<<<<<<<<<<<< jpayne@68: * if self.index != NULL: jpayne@68: * tbx_destroy(self.index) jpayne@68: */ jpayne@68: __pyx_v_self->__pyx_base.htsfile = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":612 jpayne@68: * # note: no doc string jpayne@68: * # note: __del__ is not called. jpayne@68: * if self.htsfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":615 jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: # <<<<<<<<<<<<<< jpayne@68: * tbx_destroy(self.index) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->index != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":616 jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: jpayne@68: * tbx_destroy(self.index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: tbx_destroy(__pyx_v_self->index); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":615 jpayne@68: * hts_close(self.htsfile) jpayne@68: * self.htsfile = NULL jpayne@68: * if self.index != NULL: # <<<<<<<<<<<<<< jpayne@68: * tbx_destroy(self.index) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":608 jpayne@68: * self.index = NULL jpayne@68: * jpayne@68: * def __dealloc__( self ): # <<<<<<<<<<<<<< jpayne@68: * # remember: dealloc cannot call other python methods jpayne@68: * # note: no doc string jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_WriteUnraisable("pysam.libctabix.TabixFile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pxd":65 jpayne@68: * cdef tbx_t * index jpayne@68: * jpayne@68: * cdef readonly object filename_index # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef Parser parser jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_14filename_index_1__get__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_14filename_index_1__get__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_14filename_index___get__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14filename_index___get__(struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__get__", 1); jpayne@68: __Pyx_TraceCall("__get__", __pyx_f[4], 65, 0, __PYX_ERR(4, 65, __pyx_L1_error)); jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_self->filename_index); jpayne@68: __pyx_r = __pyx_v_self->filename_index; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.filename_index.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_12__reduce_cython__, "TabixFile.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_13__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_12__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_12__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_12__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__22) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9TabixFile_14__setstate_cython__, "TabixFile.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9TabixFile_15__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_14__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9TabixFile_14__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixFile *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9TabixFile_14__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__23) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":624 jpayne@68: * """ jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static int __pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: PyObject *__pyx_v_encoding = 0; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_encoding,0}; jpayne@68: values[0] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii)); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding); jpayne@68: if (value) { values[0] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 624, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 624, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_encoding = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 624, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator___init__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self), __pyx_v_encoding); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_13TabixIterator___init__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, PyObject *__pyx_v_encoding) { jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__init__", 1); jpayne@68: __Pyx_TraceCall("__init__", __pyx_f[0], 624, 0, __PYX_ERR(0, 624, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":625 jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): jpayne@68: * self.encoding = encoding # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_encoding); jpayne@68: __Pyx_GOTREF(__pyx_v_self->encoding); jpayne@68: __Pyx_DECREF(__pyx_v_self->encoding); jpayne@68: __pyx_v_self->encoding = __pyx_v_encoding; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":624 jpayne@68: * """ jpayne@68: * jpayne@68: * def __init__(self, encoding="ascii"): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":627 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * self.buffer.s = NULL jpayne@68: * self.buffer.l = 0 jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_2__iter__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__iter__", 1); jpayne@68: __Pyx_TraceCall("__iter__", __pyx_f[0], 627, 0, __PYX_ERR(0, 627, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":628 jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: * self.buffer.s = NULL # <<<<<<<<<<<<<< jpayne@68: * self.buffer.l = 0 jpayne@68: * self.buffer.m = 0 jpayne@68: */ jpayne@68: __pyx_v_self->buffer.s = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":629 jpayne@68: * def __iter__(self): jpayne@68: * self.buffer.s = NULL jpayne@68: * self.buffer.l = 0 # <<<<<<<<<<<<<< jpayne@68: * self.buffer.m = 0 jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_self->buffer.l = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":630 jpayne@68: * self.buffer.s = NULL jpayne@68: * self.buffer.l = 0 jpayne@68: * self.buffer.m = 0 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return self jpayne@68: */ jpayne@68: __pyx_v_self->buffer.m = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":632 jpayne@68: * self.buffer.m = 0 jpayne@68: * jpayne@68: * return self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef int __cnext__(self): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_self); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_self); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":627 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * self.buffer.s = NULL jpayne@68: * self.buffer.l = 0 jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":634 jpayne@68: * return self jpayne@68: * jpayne@68: * cdef int __cnext__(self): # <<<<<<<<<<<<<< jpayne@68: * '''iterate to next element. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: static int __pyx_f_5pysam_9libctabix_13TabixIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) { jpayne@68: int __pyx_v_retval; jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceCall("__cnext__", __pyx_f[0], 634, 0, __PYX_ERR(0, 634, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":640 jpayne@68: * was called. jpayne@68: * ''' jpayne@68: * if self.tabixfile.htsfile == NULL: # <<<<<<<<<<<<<< jpayne@68: * return -5 jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->tabixfile->__pyx_base.htsfile == NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":641 jpayne@68: * ''' jpayne@68: * if self.tabixfile.htsfile == NULL: jpayne@68: * return -5 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef int retval jpayne@68: */ jpayne@68: __pyx_r = -5; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":640 jpayne@68: * was called. jpayne@68: * ''' jpayne@68: * if self.tabixfile.htsfile == NULL: # <<<<<<<<<<<<<< jpayne@68: * return -5 jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":645 jpayne@68: * cdef int retval jpayne@68: * jpayne@68: * while 1: # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * retval = tbx_itr_next( jpayne@68: */ jpayne@68: while (1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":646 jpayne@68: * jpayne@68: * while 1: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = tbx_itr_next( jpayne@68: * self.tabixfile.htsfile, jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":647 jpayne@68: * while 1: jpayne@68: * with nogil: jpayne@68: * retval = tbx_itr_next( # <<<<<<<<<<<<<< jpayne@68: * self.tabixfile.htsfile, jpayne@68: * self.tabixfile.index, jpayne@68: */ jpayne@68: __pyx_v_retval = tbx_itr_next(__pyx_v_self->tabixfile->__pyx_base.htsfile, __pyx_v_self->tabixfile->index, __pyx_v_self->iterator, (&__pyx_v_self->buffer)); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":646 jpayne@68: * jpayne@68: * while 1: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = tbx_itr_next( jpayne@68: * self.tabixfile.htsfile, jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L10; jpayne@68: } jpayne@68: __pyx_L10:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":653 jpayne@68: * &self.buffer) jpayne@68: * jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_retval < 0); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":654 jpayne@68: * jpayne@68: * if retval < 0: jpayne@68: * break # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if self.buffer.s[0] != b'#': jpayne@68: */ jpayne@68: goto __pyx_L5_break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":653 jpayne@68: * &self.buffer) jpayne@68: * jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":656 jpayne@68: * break jpayne@68: * jpayne@68: * if self.buffer.s[0] != b'#': # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((__pyx_v_self->buffer.s[0]) != '#'); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":657 jpayne@68: * jpayne@68: * if self.buffer.s[0] != b'#': jpayne@68: * break # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return retval jpayne@68: */ jpayne@68: goto __pyx_L5_break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":656 jpayne@68: * break jpayne@68: * jpayne@68: * if self.buffer.s[0] != b'#': # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: } jpayne@68: __pyx_L5_break:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":659 jpayne@68: * break jpayne@68: * jpayne@68: * return retval # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: */ jpayne@68: __pyx_r = __pyx_v_retval; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":634 jpayne@68: * return self jpayne@68: * jpayne@68: * cdef int __cnext__(self): # <<<<<<<<<<<<<< jpayne@68: * '''iterate to next element. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":661 jpayne@68: * return retval jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13TabixIterator_4__next__, "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "); jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__; jpayne@68: #endif jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_4__next__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) { jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_error_without_exception = 0; /* StopIteration */ jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 661, 0, __PYX_ERR(0, 661, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":667 jpayne@68: * """ jpayne@68: * jpayne@68: * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<< jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 667, __pyx_L1_error) jpayne@68: __pyx_v_retval = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":668 jpayne@68: * jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval == -5L); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":669 jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") # <<<<<<<<<<<<<< jpayne@68: * elif retval < 0: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 669, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 669, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":668 jpayne@68: * jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":670 jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval < 0); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":671 jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return charptr_to_str(self.buffer.s, self.encoding) jpayne@68: */ jpayne@68: __pyx_error_without_exception = 1; jpayne@68: goto __pyx_L1_error;; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":670 jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":673 jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: * return charptr_to_str(self.buffer.s, self.encoding) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __dealloc__(self): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_3 = __pyx_v_self->encoding; jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __pyx_t_5.__pyx_n = 1; jpayne@68: __pyx_t_5.encoding = __pyx_t_3; jpayne@68: __pyx_t_4 = __pyx_f_5pysam_9libcutils_charptr_to_str(__pyx_v_self->buffer.s, &__pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 673, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":661 jpayne@68: * return retval jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: if (!__pyx_error_without_exception) { jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: } jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":675 jpayne@68: * return charptr_to_str(self.buffer.s, self.encoding) jpayne@68: * jpayne@68: * def __dealloc__(self): # <<<<<<<<<<<<<< jpayne@68: * if self.iterator != NULL: jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static void __pyx_pw_5pysam_9libctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static void __pyx_pw_5pysam_9libctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_pf_5pysam_9libctabix_13TabixIterator_6__dealloc__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: } jpayne@68: jpayne@68: static void __pyx_pf_5pysam_9libctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) { jpayne@68: __Pyx_TraceDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceCall("__dealloc__", __pyx_f[0], 675, 0, __PYX_ERR(0, 675, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":676 jpayne@68: * jpayne@68: * def __dealloc__(self): jpayne@68: * if self.iterator != NULL: # <<<<<<<<<<<<<< jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: * if self.buffer.s != NULL: jpayne@68: */ jpayne@68: __pyx_t_1 = (((void *)__pyx_v_self->iterator) != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":677 jpayne@68: * def __dealloc__(self): jpayne@68: * if self.iterator != NULL: jpayne@68: * tbx_itr_destroy(self.iterator) # <<<<<<<<<<<<<< jpayne@68: * if self.buffer.s != NULL: jpayne@68: * free(self.buffer.s) jpayne@68: */ jpayne@68: tbx_itr_destroy(__pyx_v_self->iterator); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":676 jpayne@68: * jpayne@68: * def __dealloc__(self): jpayne@68: * if self.iterator != NULL: # <<<<<<<<<<<<<< jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: * if self.buffer.s != NULL: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":678 jpayne@68: * if self.iterator != NULL: jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: * if self.buffer.s != NULL: # <<<<<<<<<<<<<< jpayne@68: * free(self.buffer.s) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->buffer.s != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":679 jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: * if self.buffer.s != NULL: jpayne@68: * free(self.buffer.s) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: free(__pyx_v_self->buffer.s); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":678 jpayne@68: * if self.iterator != NULL: jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: * if self.buffer.s != NULL: # <<<<<<<<<<<<<< jpayne@68: * free(self.buffer.s) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":675 jpayne@68: * return charptr_to_str(self.buffer.s, self.encoding) jpayne@68: * jpayne@68: * def __dealloc__(self): # <<<<<<<<<<<<<< jpayne@68: * if self.iterator != NULL: jpayne@68: * tbx_itr_destroy(self.iterator) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_WriteUnraisable("pysam.libctabix.TabixIterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13TabixIterator_8__reduce_cython__, "TabixIterator.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_13TabixIterator_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_8__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__25) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13TabixIterator_10__setstate_cython__, "TabixIterator.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_13TabixIterator_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_10__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13TabixIterator_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13TabixIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__26) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":685 jpayne@68: * '''empty iterator''' jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_1__iter__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13EmptyIterator___iter__, "EmptyIterator.__iter__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_13EmptyIterator_1__iter__ = {"__iter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13EmptyIterator_1__iter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13EmptyIterator___iter__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_1__iter__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_self = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 685, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__iter__") < 0)) __PYX_ERR(0, 685, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_self = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__iter__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 685, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13EmptyIterator___iter__(__pyx_self, __pyx_v_self); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator___iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__27) jpayne@68: __Pyx_RefNannySetupContext("__iter__", 1); jpayne@68: __Pyx_TraceCall("__iter__", __pyx_f[0], 685, 0, __PYX_ERR(0, 685, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":686 jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: * return self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_self); jpayne@68: __pyx_r = __pyx_v_self; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":685 jpayne@68: * '''empty iterator''' jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":688 jpayne@68: * return self jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration() jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_3__next__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_13EmptyIterator_2__next__, "EmptyIterator.__next__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_13EmptyIterator_3__next__ = {"__next__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13EmptyIterator_3__next__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13EmptyIterator_2__next__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13EmptyIterator_3__next__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v_self = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 688, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__next__") < 0)) __PYX_ERR(0, 688, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_self = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__next__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 688, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_13EmptyIterator_2__next__(__pyx_self, __pyx_v_self); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_13EmptyIterator_2__next__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__28) jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 688, 0, __PYX_ERR(0, 688, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":689 jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: * raise StopIteration() # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_builtin_StopIteration); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 689, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 689, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":688 jpayne@68: * return self jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration() jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.EmptyIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":700 jpayne@68: * """ jpayne@68: * jpayne@68: * def __init__(self, Parser parser): # <<<<<<<<<<<<<< jpayne@68: * super().__init__() jpayne@68: * self.parser = parser jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static int __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser = 0; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_parser,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 700, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 700, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)values[0]); jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 700, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_5pysam_9libctabix_Parser, 1, "parser", 0))) __PYX_ERR(0, 700, __pyx_L1_error) jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed___init__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self), __pyx_v_parser); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser) { jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: unsigned int __pyx_t_4; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__init__", 1); jpayne@68: __Pyx_TraceCall("__init__", __pyx_f[0], 700, 0, __PYX_ERR(0, 700, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":701 jpayne@68: * jpayne@68: * def __init__(self, Parser parser): jpayne@68: * super().__init__() # <<<<<<<<<<<<<< jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 701, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed); jpayne@68: __Pyx_GIVEREF((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed))) __PYX_ERR(0, 701, __pyx_L1_error); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_self); jpayne@68: __Pyx_GIVEREF((PyObject *)__pyx_v_self); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_self))) __PYX_ERR(0, 701, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_super, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 701, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_init); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 701, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 701, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":702 jpayne@68: * def __init__(self, Parser parser): jpayne@68: * super().__init__() jpayne@68: * self.parser = parser # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: */ jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_parser); jpayne@68: __Pyx_GIVEREF((PyObject *)__pyx_v_parser); jpayne@68: __Pyx_GOTREF((PyObject *)__pyx_v_self->parser); jpayne@68: __Pyx_DECREF((PyObject *)__pyx_v_self->parser); jpayne@68: __pyx_v_self->parser = __pyx_v_parser; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":700 jpayne@68: * """ jpayne@68: * jpayne@68: * def __init__(self, Parser parser): # <<<<<<<<<<<<<< jpayne@68: * super().__init__() jpayne@68: * self.parser = parser jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":704 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_2__next__, "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "); jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__; jpayne@68: #endif jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_2__next__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self) { jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_error_without_exception = 0; /* StopIteration */ jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 704, 0, __PYX_ERR(0, 704, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":710 jpayne@68: * """ jpayne@68: * jpayne@68: * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<< jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.__pyx___cnext__(((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)__pyx_v_self)); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 710, __pyx_L1_error) jpayne@68: __pyx_v_retval = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":711 jpayne@68: * jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval == -5L); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":712 jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") # <<<<<<<<<<<<<< jpayne@68: * elif retval < 0: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 712, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 712, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":711 jpayne@68: * jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":713 jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval < 0); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":714 jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return self.parser.parse(self.buffer.s, jpayne@68: */ jpayne@68: __pyx_error_without_exception = 1; jpayne@68: goto __pyx_L1_error;; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":713 jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") jpayne@68: * elif retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":716 jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: * return self.parser.parse(self.buffer.s, # <<<<<<<<<<<<<< jpayne@68: * self.buffer.l) jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":717 jpayne@68: * jpayne@68: * return self.parser.parse(self.buffer.s, jpayne@68: * self.buffer.l) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->parser->__pyx_vtab)->parse(__pyx_v_self->parser, __pyx_v_self->__pyx_base.buffer.s, __pyx_v_self->__pyx_base.buffer.l); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 716, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":704 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: if (!__pyx_error_without_exception) { jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: } jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__, "TabixIteratorParsed.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__29) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__, "TabixIteratorParsed.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__30) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_iterator_cannot_be_converte, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.TabixIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":721 jpayne@68: * jpayne@68: * cdef class GZIterator: jpayne@68: * def __init__(self, filename, int buffer_size=65536, encoding="ascii"): # <<<<<<<<<<<<<< jpayne@68: * '''iterate line-by-line through gzip (or bgzip) jpayne@68: * compressed file. jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator___init__, "iterate line-by-line through gzip (or bgzip)\n compressed file.\n "); jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__; jpayne@68: #endif jpayne@68: static int __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: PyObject *__pyx_v_filename = 0; jpayne@68: int __pyx_v_buffer_size; jpayne@68: PyObject *__pyx_v_encoding = 0; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_buffer_size,&__pyx_n_s_encoding,0}; jpayne@68: values[2] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_ascii)); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buffer_size); jpayne@68: if (value) { values[1] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_encoding); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 721, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_filename = values[0]; jpayne@68: if (values[1]) { jpayne@68: __pyx_v_buffer_size = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_buffer_size == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 721, __pyx_L3_error) jpayne@68: } else { jpayne@68: __pyx_v_buffer_size = ((int)0x10000); jpayne@68: } jpayne@68: __pyx_v_encoding = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 3, __pyx_nargs); __PYX_ERR(0, 721, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator___init__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self), __pyx_v_filename, __pyx_v_buffer_size, __pyx_v_encoding); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_10GZIterator___init__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, PyObject *__pyx_v_filename, int __pyx_v_buffer_size, PyObject *__pyx_v_encoding) { jpayne@68: char *__pyx_v_cfilename; jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: unsigned int __pyx_t_4; jpayne@68: int __pyx_t_5; jpayne@68: int __pyx_t_6; jpayne@68: char *__pyx_t_7; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__init__", 0); jpayne@68: __Pyx_TraceCall("__init__", __pyx_f[0], 721, 0, __PYX_ERR(0, 721, __pyx_L1_error)); jpayne@68: __Pyx_INCREF(__pyx_v_filename); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":725 jpayne@68: * compressed file. jpayne@68: * ''' jpayne@68: * if not os.path.exists(filename): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("No such file or directory: %s" % filename) jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_os); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 725, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_path); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 725, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 725, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_filename}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 725, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 725, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_6 = (!__pyx_t_5); jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":726 jpayne@68: * ''' jpayne@68: * if not os.path.exists(filename): jpayne@68: * raise IOError("No such file or directory: %s" % filename) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * filename = encode_filename(filename) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_No_such_file_or_directory_s, __pyx_v_filename); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 726, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 726, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 726, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":725 jpayne@68: * compressed file. jpayne@68: * ''' jpayne@68: * if not os.path.exists(filename): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("No such file or directory: %s" % filename) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":728 jpayne@68: * raise IOError("No such file or directory: %s" % filename) jpayne@68: * jpayne@68: * filename = encode_filename(filename) # <<<<<<<<<<<<<< jpayne@68: * cdef char *cfilename = filename jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_t_2 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 728, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_2); jpayne@68: __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":729 jpayne@68: * jpayne@68: * filename = encode_filename(filename) jpayne@68: * cdef char *cfilename = filename # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * self.gzipfile = bgzf_open(cfilename, "r") jpayne@68: */ jpayne@68: __pyx_t_7 = __Pyx_PyObject_AsWritableString(__pyx_v_filename); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) __PYX_ERR(0, 729, __pyx_L1_error) jpayne@68: __pyx_v_cfilename = __pyx_t_7; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":730 jpayne@68: * filename = encode_filename(filename) jpayne@68: * cdef char *cfilename = filename jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * self.gzipfile = bgzf_open(cfilename, "r") jpayne@68: * self._filename = filename jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":731 jpayne@68: * cdef char *cfilename = filename jpayne@68: * with nogil: jpayne@68: * self.gzipfile = bgzf_open(cfilename, "r") # <<<<<<<<<<<<<< jpayne@68: * self._filename = filename jpayne@68: * self.kstream = ks_init(self.gzipfile) jpayne@68: */ jpayne@68: __pyx_v_self->gzipfile = bgzf_open(__pyx_v_cfilename, ((char const *)"r")); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":730 jpayne@68: * filename = encode_filename(filename) jpayne@68: * cdef char *cfilename = filename jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * self.gzipfile = bgzf_open(cfilename, "r") jpayne@68: * self._filename = filename jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L6; jpayne@68: } jpayne@68: __pyx_L6:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":732 jpayne@68: * with nogil: jpayne@68: * self.gzipfile = bgzf_open(cfilename, "r") jpayne@68: * self._filename = filename # <<<<<<<<<<<<<< jpayne@68: * self.kstream = ks_init(self.gzipfile) jpayne@68: * self.encoding = encoding jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_filename); jpayne@68: __Pyx_GIVEREF(__pyx_v_filename); jpayne@68: __Pyx_GOTREF(__pyx_v_self->_filename); jpayne@68: __Pyx_DECREF(__pyx_v_self->_filename); jpayne@68: __pyx_v_self->_filename = __pyx_v_filename; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":733 jpayne@68: * self.gzipfile = bgzf_open(cfilename, "r") jpayne@68: * self._filename = filename jpayne@68: * self.kstream = ks_init(self.gzipfile) # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_self->kstream = ks_init(__pyx_v_self->gzipfile); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":734 jpayne@68: * self._filename = filename jpayne@68: * self.kstream = ks_init(self.gzipfile) jpayne@68: * self.encoding = encoding # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.buffer.l = 0 jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_encoding); jpayne@68: __Pyx_GIVEREF(__pyx_v_encoding); jpayne@68: __Pyx_GOTREF(__pyx_v_self->encoding); jpayne@68: __Pyx_DECREF(__pyx_v_self->encoding); jpayne@68: __pyx_v_self->encoding = __pyx_v_encoding; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":736 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * self.buffer.l = 0 # <<<<<<<<<<<<<< jpayne@68: * self.buffer.m = 0 jpayne@68: * self.buffer.s = malloc(buffer_size) jpayne@68: */ jpayne@68: __pyx_v_self->buffer.l = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":737 jpayne@68: * jpayne@68: * self.buffer.l = 0 jpayne@68: * self.buffer.m = 0 # <<<<<<<<<<<<<< jpayne@68: * self.buffer.s = malloc(buffer_size) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_self->buffer.m = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":738 jpayne@68: * self.buffer.l = 0 jpayne@68: * self.buffer.m = 0 jpayne@68: * self.buffer.s = malloc(buffer_size) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __dealloc__(self): jpayne@68: */ jpayne@68: __pyx_v_self->buffer.s = ((char *)malloc(__pyx_v_buffer_size)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":721 jpayne@68: * jpayne@68: * cdef class GZIterator: jpayne@68: * def __init__(self, filename, int buffer_size=65536, encoding="ascii"): # <<<<<<<<<<<<<< jpayne@68: * '''iterate line-by-line through gzip (or bgzip) jpayne@68: * compressed file. jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_filename); jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":740 jpayne@68: * self.buffer.s = malloc(buffer_size) jpayne@68: * jpayne@68: * def __dealloc__(self): # <<<<<<<<<<<<<< jpayne@68: * '''close file.''' jpayne@68: * if self.gzipfile != NULL: jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static void __pyx_pw_5pysam_9libctabix_10GZIterator_3__dealloc__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static void __pyx_pw_5pysam_9libctabix_10GZIterator_3__dealloc__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_pf_5pysam_9libctabix_10GZIterator_2__dealloc__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: } jpayne@68: jpayne@68: static void __pyx_pf_5pysam_9libctabix_10GZIterator_2__dealloc__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) { jpayne@68: __Pyx_TraceDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceCall("__dealloc__", __pyx_f[0], 740, 0, __PYX_ERR(0, 740, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":742 jpayne@68: * def __dealloc__(self): jpayne@68: * '''close file.''' jpayne@68: * if self.gzipfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * bgzf_close(self.gzipfile) jpayne@68: * self.gzipfile = NULL jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->gzipfile != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":743 jpayne@68: * '''close file.''' jpayne@68: * if self.gzipfile != NULL: jpayne@68: * bgzf_close(self.gzipfile) # <<<<<<<<<<<<<< jpayne@68: * self.gzipfile = NULL jpayne@68: * if self.buffer.s != NULL: jpayne@68: */ jpayne@68: (void)(bgzf_close(__pyx_v_self->gzipfile)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":744 jpayne@68: * if self.gzipfile != NULL: jpayne@68: * bgzf_close(self.gzipfile) jpayne@68: * self.gzipfile = NULL # <<<<<<<<<<<<<< jpayne@68: * if self.buffer.s != NULL: jpayne@68: * free(self.buffer.s) jpayne@68: */ jpayne@68: __pyx_v_self->gzipfile = NULL; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":742 jpayne@68: * def __dealloc__(self): jpayne@68: * '''close file.''' jpayne@68: * if self.gzipfile != NULL: # <<<<<<<<<<<<<< jpayne@68: * bgzf_close(self.gzipfile) jpayne@68: * self.gzipfile = NULL jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":745 jpayne@68: * bgzf_close(self.gzipfile) jpayne@68: * self.gzipfile = NULL jpayne@68: * if self.buffer.s != NULL: # <<<<<<<<<<<<<< jpayne@68: * free(self.buffer.s) jpayne@68: * if self.kstream != NULL: jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->buffer.s != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":746 jpayne@68: * self.gzipfile = NULL jpayne@68: * if self.buffer.s != NULL: jpayne@68: * free(self.buffer.s) # <<<<<<<<<<<<<< jpayne@68: * if self.kstream != NULL: jpayne@68: * ks_destroy(self.kstream) jpayne@68: */ jpayne@68: free(__pyx_v_self->buffer.s); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":745 jpayne@68: * bgzf_close(self.gzipfile) jpayne@68: * self.gzipfile = NULL jpayne@68: * if self.buffer.s != NULL: # <<<<<<<<<<<<<< jpayne@68: * free(self.buffer.s) jpayne@68: * if self.kstream != NULL: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":747 jpayne@68: * if self.buffer.s != NULL: jpayne@68: * free(self.buffer.s) jpayne@68: * if self.kstream != NULL: # <<<<<<<<<<<<<< jpayne@68: * ks_destroy(self.kstream) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_self->kstream != NULL); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":748 jpayne@68: * free(self.buffer.s) jpayne@68: * if self.kstream != NULL: jpayne@68: * ks_destroy(self.kstream) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: */ jpayne@68: ks_destroy(__pyx_v_self->kstream); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":747 jpayne@68: * if self.buffer.s != NULL: jpayne@68: * free(self.buffer.s) jpayne@68: * if self.kstream != NULL: # <<<<<<<<<<<<<< jpayne@68: * ks_destroy(self.kstream) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":740 jpayne@68: * self.buffer.s = malloc(buffer_size) jpayne@68: * jpayne@68: * def __dealloc__(self): # <<<<<<<<<<<<<< jpayne@68: * '''close file.''' jpayne@68: * if self.gzipfile != NULL: jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_WriteUnraisable("pysam.libctabix.GZIterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":750 jpayne@68: * ks_destroy(self.kstream) jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_4__iter__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_4__iter__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__iter__", 1); jpayne@68: __Pyx_TraceCall("__iter__", __pyx_f[0], 750, 0, __PYX_ERR(0, 750, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":751 jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: * return self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef int __cnext__(self): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_self); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_self); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":750 jpayne@68: * ks_destroy(self.kstream) jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":753 jpayne@68: * return self jpayne@68: * jpayne@68: * cdef int __cnext__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef int dret = 0 jpayne@68: * cdef int retval = 0 jpayne@68: */ jpayne@68: jpayne@68: static int __pyx_f_5pysam_9libctabix_10GZIterator___cnext__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) { jpayne@68: int __pyx_v_dret; jpayne@68: int __pyx_v_retval; jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceCall("__cnext__", __pyx_f[0], 753, 0, __PYX_ERR(0, 753, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":754 jpayne@68: * jpayne@68: * cdef int __cnext__(self): jpayne@68: * cdef int dret = 0 # <<<<<<<<<<<<<< jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: jpayne@68: */ jpayne@68: __pyx_v_dret = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":755 jpayne@68: * cdef int __cnext__(self): jpayne@68: * cdef int dret = 0 jpayne@68: * cdef int retval = 0 # <<<<<<<<<<<<<< jpayne@68: * while 1: jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_v_retval = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":756 jpayne@68: * cdef int dret = 0 jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: */ jpayne@68: while (1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":757 jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":758 jpayne@68: * while 1: jpayne@68: * with nogil: jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if retval < 0: jpayne@68: */ jpayne@68: __pyx_v_retval = ks_getuntil(__pyx_v_self->kstream, '\n', (&__pyx_v_self->buffer), (&__pyx_v_dret)); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":757 jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L9; jpayne@68: } jpayne@68: __pyx_L9:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":760 jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_retval < 0); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":761 jpayne@68: * jpayne@68: * if retval < 0: jpayne@68: * break # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return dret jpayne@68: */ jpayne@68: goto __pyx_L4_break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":760 jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":763 jpayne@68: * break jpayne@68: * jpayne@68: * return dret # <<<<<<<<<<<<<< jpayne@68: * return -1 jpayne@68: * jpayne@68: */ jpayne@68: __pyx_r = __pyx_v_dret; jpayne@68: goto __pyx_L0; jpayne@68: } jpayne@68: __pyx_L4_break:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":764 jpayne@68: * jpayne@68: * return dret jpayne@68: * return -1 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: */ jpayne@68: __pyx_r = -1; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":753 jpayne@68: * return self jpayne@68: * jpayne@68: * cdef int __cnext__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef int dret = 0 jpayne@68: * cdef int retval = 0 jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":766 jpayne@68: * return -1 jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator_6__next__, "python version of next().\n "); jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__; jpayne@68: #endif jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_6__next__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_6__next__(struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) { jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_error_without_exception = 0; /* StopIteration */ jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_str __pyx_t_6; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 766, 0, __PYX_ERR(0, 766, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":769 jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<< jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 769, __pyx_L1_error) jpayne@68: __pyx_v_retval = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":770 jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * return force_str(self.buffer.s, self.encoding) jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval < 0); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":771 jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * return force_str(self.buffer.s, self.encoding) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_error_without_exception = 1; jpayne@68: goto __pyx_L1_error;; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":770 jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * return force_str(self.buffer.s, self.encoding) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":772 jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration jpayne@68: * return force_str(self.buffer.s, self.encoding) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_self->buffer.s); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 772, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = __pyx_v_self->encoding; jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __pyx_t_6.__pyx_n = 1; jpayne@68: __pyx_t_6.encoding = __pyx_t_4; jpayne@68: __pyx_t_5 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_3, &__pyx_t_6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 772, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_r = __pyx_t_5; jpayne@68: __pyx_t_5 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":766 jpayne@68: * return -1 jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: if (!__pyx_error_without_exception) { jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: } jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator_8__reduce_cython__, "GZIterator.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_10GZIterator_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_8__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__31) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10GZIterator_10__setstate_cython__, "GZIterator.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_10GZIterator_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_10__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_10GZIterator_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10GZIterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__32) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":780 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14GZIteratorHead___next__, "python version of next().\n "); jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__; jpayne@68: #endif jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_14GZIteratorHead___next__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead___next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self) { jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_error_without_exception = 0; /* StopIteration */ jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 780, 0, __PYX_ERR(0, 780, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":783 jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<< jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.__pyx___cnext__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 783, __pyx_L1_error) jpayne@68: __pyx_v_retval = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":784 jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * if self.buffer.s[0] == b'#': jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval < 0); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":785 jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * if self.buffer.s[0] == b'#': jpayne@68: * return self.buffer.s jpayne@68: */ jpayne@68: __pyx_error_without_exception = 1; jpayne@68: goto __pyx_L1_error;; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":784 jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * if self.buffer.s[0] == b'#': jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":786 jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration jpayne@68: * if self.buffer.s[0] == b'#': # <<<<<<<<<<<<<< jpayne@68: * return self.buffer.s jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_2 = ((__pyx_v_self->__pyx_base.buffer.s[0]) == '#'); jpayne@68: if (likely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":787 jpayne@68: * raise StopIteration jpayne@68: * if self.buffer.s[0] == b'#': jpayne@68: * return self.buffer.s # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_3 = __Pyx_PyBytes_FromString(__pyx_v_self->__pyx_base.buffer.s); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 787, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":786 jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration jpayne@68: * if self.buffer.s[0] == b'#': # <<<<<<<<<<<<<< jpayne@68: * return self.buffer.s jpayne@68: * else: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":789 jpayne@68: * return self.buffer.s jpayne@68: * else: jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_error_without_exception = 1; jpayne@68: goto __pyx_L1_error;; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":780 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: if (!__pyx_error_without_exception) { jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: } jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__, "GZIteratorHead.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__33) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__, "GZIteratorHead.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__34) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorHead.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":797 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __init__(self, parser): # <<<<<<<<<<<<<< jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static int __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: PyObject *__pyx_v_parser = 0; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_parser,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 797, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 797, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_parser = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 797, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed___init__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self), __pyx_v_parser); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_16GZIteratorParsed___init__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, PyObject *__pyx_v_parser) { jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__init__", 1); jpayne@68: __Pyx_TraceCall("__init__", __pyx_f[0], 797, 0, __PYX_ERR(0, 797, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":798 jpayne@68: * jpayne@68: * def __init__(self, parser): jpayne@68: * self.parser = parser # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: */ jpayne@68: if (!(likely(((__pyx_v_parser) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_parser, __pyx_ptype_5pysam_9libctabix_Parser))))) __PYX_ERR(0, 798, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_v_parser; jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF((PyObject *)__pyx_v_self->parser); jpayne@68: __Pyx_DECREF((PyObject *)__pyx_v_self->parser); jpayne@68: __pyx_v_self->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_t_1); jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":797 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __init__(self, parser): # <<<<<<<<<<<<<< jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":800 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16GZIteratorParsed_2__next__, "python version of next().\n "); jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: struct wrapperbase __pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__; jpayne@68: #endif jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed_2__next__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_2__next__(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self) { jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_error_without_exception = 0; /* StopIteration */ jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 800, 0, __PYX_ERR(0, 800, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":803 jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() # <<<<<<<<<<<<<< jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.__pyx___cnext__(((struct __pyx_obj_5pysam_9libctabix_GZIterator *)__pyx_v_self)); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 803, __pyx_L1_error) jpayne@68: __pyx_v_retval = __pyx_t_1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":804 jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval < 0); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":805 jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return self.parser.parse(self.buffer.s, jpayne@68: */ jpayne@68: __pyx_error_without_exception = 1; jpayne@68: goto __pyx_L1_error;; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":804 jpayne@68: * """ jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":807 jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: * return self.parser.parse(self.buffer.s, # <<<<<<<<<<<<<< jpayne@68: * self.buffer.l) jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":808 jpayne@68: * jpayne@68: * return self.parser.parse(self.buffer.s, jpayne@68: * self.buffer.l) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->parser->__pyx_vtab)->parse(__pyx_v_self->parser, __pyx_v_self->__pyx_base.buffer.s, __pyx_v_self->__pyx_base.buffer.l); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 807, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":800 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * """python version of next(). jpayne@68: * """ jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: if (!__pyx_error_without_exception) { jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: } jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__, "GZIteratorParsed.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__35) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__, "GZIteratorParsed.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__36) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_gzipfile_self_kstream_canno, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.GZIteratorParsed.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":811 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_compress(filename_in, # <<<<<<<<<<<<<< jpayne@68: * filename_out, jpayne@68: * force=False): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_1tabix_compress(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_tabix_compress, "tabix_compress(filename_in, filename_out, force=False)\ncompress *filename_in* writing the output to *filename_out*.\n \n Raise an IOError if *filename_out* already exists, unless *force*\n is set.\n "); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_1tabix_compress = {"tabix_compress", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_1tabix_compress, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_tabix_compress}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_1tabix_compress(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_filename_in = 0; jpayne@68: PyObject *__pyx_v_filename_out = 0; jpayne@68: PyObject *__pyx_v_force = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("tabix_compress (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename_in,&__pyx_n_s_filename_out,&__pyx_n_s_force,0}; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":813 jpayne@68: * def tabix_compress(filename_in, jpayne@68: * filename_out, jpayne@68: * force=False): # <<<<<<<<<<<<<< jpayne@68: * '''compress *filename_in* writing the output to *filename_out*. jpayne@68: * jpayne@68: */ jpayne@68: values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False))); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename_in)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 811, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename_out)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 811, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, 1); __PYX_ERR(0, 811, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_force); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 811, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "tabix_compress") < 0)) __PYX_ERR(0, 811, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_filename_in = values[0]; jpayne@68: __pyx_v_filename_out = values[1]; jpayne@68: __pyx_v_force = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 811, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_tabix_compress(__pyx_self, __pyx_v_filename_in, __pyx_v_filename_out, __pyx_v_force); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":811 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_compress(filename_in, # <<<<<<<<<<<<<< jpayne@68: * filename_out, jpayne@68: * force=False): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force) { jpayne@68: int __pyx_v_WINDOW_SIZE; jpayne@68: int __pyx_v_c; jpayne@68: int __pyx_v_r; jpayne@68: void *__pyx_v_buffer; jpayne@68: BGZF *__pyx_v_fp; jpayne@68: int __pyx_v_fd_src; jpayne@68: int __pyx_v_is_empty; jpayne@68: int __pyx_v_O_RDONLY; jpayne@68: PyObject *__pyx_v_fn = NULL; jpayne@68: char *__pyx_v_cfn; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: int __pyx_t_3; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: unsigned int __pyx_t_7; jpayne@68: int __pyx_t_8; jpayne@68: char *__pyx_t_9; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__37) jpayne@68: __Pyx_RefNannySetupContext("tabix_compress", 1); jpayne@68: __Pyx_TraceCall("tabix_compress", __pyx_f[0], 811, 0, __PYX_ERR(0, 811, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":820 jpayne@68: * ''' jpayne@68: * jpayne@68: * if not force and os.path.exists(filename_out): # <<<<<<<<<<<<<< jpayne@68: * raise IOError( jpayne@68: * "Filename '%s' already exists, use *force* to " jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_force); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 820, __pyx_L1_error) jpayne@68: __pyx_t_3 = (!__pyx_t_2); jpayne@68: if (__pyx_t_3) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_3; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_os); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 820, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_path); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 820, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_exists); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 820, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: __pyx_t_6 = NULL; jpayne@68: __pyx_t_7 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_5))) { jpayne@68: __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5); jpayne@68: if (likely(__pyx_t_6)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); jpayne@68: __Pyx_INCREF(__pyx_t_6); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_5, function); jpayne@68: __pyx_t_7 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_v_filename_out}; jpayne@68: __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_7, 1+__pyx_t_7); jpayne@68: __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 820, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 820, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_t_1 = __pyx_t_3; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":823 jpayne@68: * raise IOError( jpayne@68: * "Filename '%s' already exists, use *force* to " jpayne@68: * "overwrite" % filename_out) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef int WINDOW_SIZE jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_Filename_s_already_exists_use_fo, __pyx_v_filename_out); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 823, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":821 jpayne@68: * jpayne@68: * if not force and os.path.exists(filename_out): jpayne@68: * raise IOError( # <<<<<<<<<<<<<< jpayne@68: * "Filename '%s' already exists, use *force* to " jpayne@68: * "overwrite" % filename_out) jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 821, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __Pyx_Raise(__pyx_t_5, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __PYX_ERR(0, 821, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":820 jpayne@68: * ''' jpayne@68: * jpayne@68: * if not force and os.path.exists(filename_out): # <<<<<<<<<<<<<< jpayne@68: * raise IOError( jpayne@68: * "Filename '%s' already exists, use *force* to " jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":830 jpayne@68: * cdef BGZF * fp jpayne@68: * cdef int fd_src jpayne@68: * cdef bint is_empty = True # <<<<<<<<<<<<<< jpayne@68: * cdef int O_RDONLY jpayne@68: * O_RDONLY = os.O_RDONLY jpayne@68: */ jpayne@68: __pyx_v_is_empty = 1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":832 jpayne@68: * cdef bint is_empty = True jpayne@68: * cdef int O_RDONLY jpayne@68: * O_RDONLY = os.O_RDONLY # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * WINDOW_SIZE = 64 * 1024 jpayne@68: */ jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_os); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 832, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_O_RDONLY); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 832, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 832, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_v_O_RDONLY = __pyx_t_8; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":834 jpayne@68: * O_RDONLY = os.O_RDONLY jpayne@68: * jpayne@68: * WINDOW_SIZE = 64 * 1024 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * fn = encode_filename(filename_out) jpayne@68: */ jpayne@68: __pyx_v_WINDOW_SIZE = 0x10000; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":836 jpayne@68: * WINDOW_SIZE = 64 * 1024 jpayne@68: * jpayne@68: * fn = encode_filename(filename_out) # <<<<<<<<<<<<<< jpayne@68: * cdef char *cfn = fn jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_t_4 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename_out); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 836, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_v_fn = ((PyObject*)__pyx_t_4); jpayne@68: __pyx_t_4 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":837 jpayne@68: * jpayne@68: * fn = encode_filename(filename_out) jpayne@68: * cdef char *cfn = fn # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * fp = bgzf_open(cfn, "w") jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_fn == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 837, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_9 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_9) && PyErr_Occurred())) __PYX_ERR(0, 837, __pyx_L1_error) jpayne@68: __pyx_v_cfn = __pyx_t_9; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":838 jpayne@68: * fn = encode_filename(filename_out) jpayne@68: * cdef char *cfn = fn jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * fp = bgzf_open(cfn, "w") jpayne@68: * if fp == NULL: jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":839 jpayne@68: * cdef char *cfn = fn jpayne@68: * with nogil: jpayne@68: * fp = bgzf_open(cfn, "w") # <<<<<<<<<<<<<< jpayne@68: * if fp == NULL: jpayne@68: * raise IOError("could not open '%s' for writing" % filename_out) jpayne@68: */ jpayne@68: __pyx_v_fp = bgzf_open(__pyx_v_cfn, ((char const *)"w")); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":838 jpayne@68: * fn = encode_filename(filename_out) jpayne@68: * cdef char *cfn = fn jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * fp = bgzf_open(cfn, "w") jpayne@68: * if fp == NULL: jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L8; jpayne@68: } jpayne@68: __pyx_L8:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":840 jpayne@68: * with nogil: jpayne@68: * fp = bgzf_open(cfn, "w") jpayne@68: * if fp == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open '%s' for writing" % filename_out) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_fp == NULL); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":841 jpayne@68: * fp = bgzf_open(cfn, "w") jpayne@68: * if fp == NULL: jpayne@68: * raise IOError("could not open '%s' for writing" % filename_out) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * fn = encode_filename(filename_in) jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_s_for_writing, __pyx_v_filename_out); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 841, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 841, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __Pyx_Raise(__pyx_t_5, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __PYX_ERR(0, 841, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":840 jpayne@68: * with nogil: jpayne@68: * fp = bgzf_open(cfn, "w") jpayne@68: * if fp == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open '%s' for writing" % filename_out) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":843 jpayne@68: * raise IOError("could not open '%s' for writing" % filename_out) jpayne@68: * jpayne@68: * fn = encode_filename(filename_in) # <<<<<<<<<<<<<< jpayne@68: * fd_src = open(fn, O_RDONLY) jpayne@68: * if fd_src == 0: jpayne@68: */ jpayne@68: __pyx_t_5 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename_in); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 843, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF_SET(__pyx_v_fn, ((PyObject*)__pyx_t_5)); jpayne@68: __pyx_t_5 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":844 jpayne@68: * jpayne@68: * fn = encode_filename(filename_in) jpayne@68: * fd_src = open(fn, O_RDONLY) # <<<<<<<<<<<<<< jpayne@68: * if fd_src == 0: jpayne@68: * raise IOError("could not open '%s' for reading" % filename_in) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_fn == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 844, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_9 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_9) && PyErr_Occurred())) __PYX_ERR(0, 844, __pyx_L1_error) jpayne@68: __pyx_v_fd_src = open(__pyx_t_9, __pyx_v_O_RDONLY); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":845 jpayne@68: * fn = encode_filename(filename_in) jpayne@68: * fd_src = open(fn, O_RDONLY) jpayne@68: * if fd_src == 0: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open '%s' for reading" % filename_in) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_fd_src == 0); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":846 jpayne@68: * fd_src = open(fn, O_RDONLY) jpayne@68: * if fd_src == 0: jpayne@68: * raise IOError("could not open '%s' for reading" % filename_in) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * buffer = malloc(WINDOW_SIZE) jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_could_not_open_s_for_reading, __pyx_v_filename_in); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 846, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 846, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __Pyx_Raise(__pyx_t_4, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __PYX_ERR(0, 846, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":845 jpayne@68: * fn = encode_filename(filename_in) jpayne@68: * fd_src = open(fn, O_RDONLY) jpayne@68: * if fd_src == 0: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("could not open '%s' for reading" % filename_in) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":848 jpayne@68: * raise IOError("could not open '%s' for reading" % filename_in) jpayne@68: * jpayne@68: * buffer = malloc(WINDOW_SIZE) # <<<<<<<<<<<<<< jpayne@68: * c = 1 jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_buffer = malloc(__pyx_v_WINDOW_SIZE); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":849 jpayne@68: * jpayne@68: * buffer = malloc(WINDOW_SIZE) jpayne@68: * c = 1 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * while c > 0: jpayne@68: */ jpayne@68: __pyx_v_c = 1; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":851 jpayne@68: * c = 1 jpayne@68: * jpayne@68: * while c > 0: # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) jpayne@68: */ jpayne@68: while (1) { jpayne@68: __pyx_t_1 = (__pyx_v_c > 0); jpayne@68: if (!__pyx_t_1) break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":852 jpayne@68: * jpayne@68: * while c > 0: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) jpayne@68: * if c > 0: jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":853 jpayne@68: * while c > 0: jpayne@68: * with nogil: jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) # <<<<<<<<<<<<<< jpayne@68: * if c > 0: jpayne@68: * is_empty = False jpayne@68: */ jpayne@68: __pyx_v_c = read(__pyx_v_fd_src, __pyx_v_buffer, __pyx_v_WINDOW_SIZE); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":854 jpayne@68: * with nogil: jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) jpayne@68: * if c > 0: # <<<<<<<<<<<<<< jpayne@68: * is_empty = False jpayne@68: * r = bgzf_write(fp, buffer, c) jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_c > 0); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":855 jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) jpayne@68: * if c > 0: jpayne@68: * is_empty = False # <<<<<<<<<<<<<< jpayne@68: * r = bgzf_write(fp, buffer, c) jpayne@68: * if r < 0: jpayne@68: */ jpayne@68: __pyx_v_is_empty = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":854 jpayne@68: * with nogil: jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) jpayne@68: * if c > 0: # <<<<<<<<<<<<<< jpayne@68: * is_empty = False jpayne@68: * r = bgzf_write(fp, buffer, c) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":856 jpayne@68: * if c > 0: jpayne@68: * is_empty = False jpayne@68: * r = bgzf_write(fp, buffer, c) # <<<<<<<<<<<<<< jpayne@68: * if r < 0: jpayne@68: * free(buffer) jpayne@68: */ jpayne@68: __pyx_v_r = bgzf_write(__pyx_v_fp, __pyx_v_buffer, __pyx_v_c); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":852 jpayne@68: * jpayne@68: * while c > 0: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * c = read(fd_src, buffer, WINDOW_SIZE) jpayne@68: * if c > 0: jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L17; jpayne@68: } jpayne@68: __pyx_L17:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":857 jpayne@68: * is_empty = False jpayne@68: * r = bgzf_write(fp, buffer, c) jpayne@68: * if r < 0: # <<<<<<<<<<<<<< jpayne@68: * free(buffer) jpayne@68: * raise IOError("writing failed") jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_r < 0); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":858 jpayne@68: * r = bgzf_write(fp, buffer, c) jpayne@68: * if r < 0: jpayne@68: * free(buffer) # <<<<<<<<<<<<<< jpayne@68: * raise IOError("writing failed") jpayne@68: * jpayne@68: */ jpayne@68: free(__pyx_v_buffer); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":859 jpayne@68: * if r < 0: jpayne@68: * free(buffer) jpayne@68: * raise IOError("writing failed") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * free(buffer) jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__38, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 859, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_Raise(__pyx_t_4, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __PYX_ERR(0, 859, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":857 jpayne@68: * is_empty = False jpayne@68: * r = bgzf_write(fp, buffer, c) jpayne@68: * if r < 0: # <<<<<<<<<<<<<< jpayne@68: * free(buffer) jpayne@68: * raise IOError("writing failed") jpayne@68: */ jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":861 jpayne@68: * raise IOError("writing failed") jpayne@68: * jpayne@68: * free(buffer) # <<<<<<<<<<<<<< jpayne@68: * r = bgzf_close(fp) jpayne@68: * if r < 0: jpayne@68: */ jpayne@68: free(__pyx_v_buffer); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":862 jpayne@68: * jpayne@68: * free(buffer) jpayne@68: * r = bgzf_close(fp) # <<<<<<<<<<<<<< jpayne@68: * if r < 0: jpayne@68: * raise IOError("error %i when writing to file %s" % (r, filename_out)) jpayne@68: */ jpayne@68: __pyx_v_r = bgzf_close(__pyx_v_fp); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":863 jpayne@68: * free(buffer) jpayne@68: * r = bgzf_close(fp) jpayne@68: * if r < 0: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("error %i when writing to file %s" % (r, filename_out)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_r < 0); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":864 jpayne@68: * r = bgzf_close(fp) jpayne@68: * if r < 0: jpayne@68: * raise IOError("error %i when writing to file %s" % (r, filename_out)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * r = close(fd_src) jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_r); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 864, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 864, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_GIVEREF(__pyx_t_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4)) __PYX_ERR(0, 864, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_filename_out); jpayne@68: __Pyx_GIVEREF(__pyx_v_filename_out); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_filename_out)) __PYX_ERR(0, 864, __pyx_L1_error); jpayne@68: __pyx_t_4 = 0; jpayne@68: __pyx_t_4 = PyUnicode_Format(__pyx_kp_u_error_i_when_writing_to_file_s, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 864, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 864, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __Pyx_Raise(__pyx_t_5, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __PYX_ERR(0, 864, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":863 jpayne@68: * free(buffer) jpayne@68: * r = bgzf_close(fp) jpayne@68: * if r < 0: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("error %i when writing to file %s" % (r, filename_out)) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":866 jpayne@68: * raise IOError("error %i when writing to file %s" % (r, filename_out)) jpayne@68: * jpayne@68: * r = close(fd_src) # <<<<<<<<<<<<<< jpayne@68: * # an empty file will return with -1, thus ignore this. jpayne@68: * if r < 0: jpayne@68: */ jpayne@68: __pyx_v_r = close(__pyx_v_fd_src); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":868 jpayne@68: * r = close(fd_src) jpayne@68: * # an empty file will return with -1, thus ignore this. jpayne@68: * if r < 0: # <<<<<<<<<<<<<< jpayne@68: * if not (r == -1 and is_empty): jpayne@68: * raise IOError("error %i when closing file %s" % (r, filename_in)) jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_r < 0); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":869 jpayne@68: * # an empty file will return with -1, thus ignore this. jpayne@68: * if r < 0: jpayne@68: * if not (r == -1 and is_empty): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("error %i when closing file %s" % (r, filename_in)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = (__pyx_v_r == -1L); jpayne@68: if (__pyx_t_3) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_3; jpayne@68: goto __pyx_L23_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_1 = __pyx_v_is_empty; jpayne@68: __pyx_L23_bool_binop_done:; jpayne@68: __pyx_t_3 = (!__pyx_t_1); jpayne@68: if (unlikely(__pyx_t_3)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":870 jpayne@68: * if r < 0: jpayne@68: * if not (r == -1 and is_empty): jpayne@68: * raise IOError("error %i when closing file %s" % (r, filename_in)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_r); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 870, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_GIVEREF(__pyx_t_5); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_v_filename_in); jpayne@68: __Pyx_GIVEREF(__pyx_v_filename_in); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_filename_in)) __PYX_ERR(0, 870, __pyx_L1_error); jpayne@68: __pyx_t_5 = 0; jpayne@68: __pyx_t_5 = PyUnicode_Format(__pyx_kp_u_error_i_when_closing_file_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_5); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 870, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: __Pyx_Raise(__pyx_t_4, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __PYX_ERR(0, 870, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":869 jpayne@68: * # an empty file will return with -1, thus ignore this. jpayne@68: * if r < 0: jpayne@68: * if not (r == -1 and is_empty): # <<<<<<<<<<<<<< jpayne@68: * raise IOError("error %i when closing file %s" % (r, filename_in)) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":868 jpayne@68: * r = close(fd_src) jpayne@68: * # an empty file will return with -1, thus ignore this. jpayne@68: * if r < 0: # <<<<<<<<<<<<<< jpayne@68: * if not (r == -1 and is_empty): jpayne@68: * raise IOError("error %i when closing file %s" % (r, filename_in)) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":811 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_compress(filename_in, # <<<<<<<<<<<<<< jpayne@68: * filename_out, jpayne@68: * force=False): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_fn); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":873 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_index(filename, # <<<<<<<<<<<<<< jpayne@68: * force=False, jpayne@68: * seq_col=None, jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_3tabix_index(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_2tabix_index, "tabix_index(filename, force=False, seq_col=None, start_col=None, end_col=None, preset=None, meta_char=u'#', int line_skip=0, zerobased=False, int min_shift=-1, index=None, keep_original=False, csi=False)\nindex tab-separated *filename* using tabix.\n\n An existing index will not be overwritten unless *force* is set.\n\n The index will be built from coordinates in columns *seq_col*,\n *start_col* and *end_col*.\n\n The contents of *filename* have to be sorted by contig and\n position - the method does not check if the file is sorted.\n\n Column indices are 0-based. Note that this is different from the\n tabix command line utility where column indices start at 1.\n \n Coordinates in the file are assumed to be 1-based unless\n *zerobased* is set.\n\n If *preset* is provided, the column coordinates are taken from a\n preset. Valid values for preset are \"gff\", \"bed\", \"sam\", \"vcf\",\n psltbl\", \"pileup\".\n \n Lines beginning with *meta_char* and the first *line_skip* lines\n will be skipped.\n\n If *filename* is not detected as a gzip file it will be automatically\n compressed. The original file will be removed and only the compressed\n file will be retained.\n\n By default or when *min_shift* is 0, creates a TBI index. If *min_shift*\n is greater than zero and/or *csi* is True, creates a CSI index with a\n minimal interval size of 1<<*min_shift* (1<<14 if only *csi* is set).\n\n *index* controls the filename which should be used for creating the index.\n If not set, the default is to append ``.tbi`` to *filename*.\n\n When automatically compressing files, if *keep_original* is set the\n uncompressed file will not be deleted.\n\n returns the filename of the compressed data\n\n "); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_3tabix_index = {"tabix_index", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_3tabix_index, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_2tabix_index}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_3tabix_index(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_filename = 0; jpayne@68: PyObject *__pyx_v_force = 0; jpayne@68: PyObject *__pyx_v_seq_col = 0; jpayne@68: PyObject *__pyx_v_start_col = 0; jpayne@68: PyObject *__pyx_v_end_col = 0; jpayne@68: PyObject *__pyx_v_preset = 0; jpayne@68: PyObject *__pyx_v_meta_char = 0; jpayne@68: int __pyx_v_line_skip; jpayne@68: PyObject *__pyx_v_zerobased = 0; jpayne@68: int __pyx_v_min_shift; jpayne@68: PyObject *__pyx_v_index = 0; jpayne@68: PyObject *__pyx_v_keep_original = 0; jpayne@68: PyObject *__pyx_v_csi = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[13] = {0,0,0,0,0,0,0,0,0,0,0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("tabix_index (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_filename,&__pyx_n_s_force,&__pyx_n_s_seq_col,&__pyx_n_s_start_col,&__pyx_n_s_end_col,&__pyx_n_s_preset,&__pyx_n_s_meta_char,&__pyx_n_s_line_skip,&__pyx_n_s_zerobased,&__pyx_n_s_min_shift,&__pyx_n_s_index,&__pyx_n_s_keep_original,&__pyx_n_s_csi,0}; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":874 jpayne@68: * jpayne@68: * def tabix_index(filename, jpayne@68: * force=False, # <<<<<<<<<<<<<< jpayne@68: * seq_col=None, jpayne@68: * start_col=None, jpayne@68: */ jpayne@68: values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False))); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":875 jpayne@68: * def tabix_index(filename, jpayne@68: * force=False, jpayne@68: * seq_col=None, # <<<<<<<<<<<<<< jpayne@68: * start_col=None, jpayne@68: * end_col=None, jpayne@68: */ jpayne@68: values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":876 jpayne@68: * force=False, jpayne@68: * seq_col=None, jpayne@68: * start_col=None, # <<<<<<<<<<<<<< jpayne@68: * end_col=None, jpayne@68: * preset=None, jpayne@68: */ jpayne@68: values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":877 jpayne@68: * seq_col=None, jpayne@68: * start_col=None, jpayne@68: * end_col=None, # <<<<<<<<<<<<<< jpayne@68: * preset=None, jpayne@68: * meta_char="#", jpayne@68: */ jpayne@68: values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":878 jpayne@68: * start_col=None, jpayne@68: * end_col=None, jpayne@68: * preset=None, # <<<<<<<<<<<<<< jpayne@68: * meta_char="#", jpayne@68: * int line_skip=0, jpayne@68: */ jpayne@68: values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: values[6] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject*)__pyx_kp_u__39))); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":881 jpayne@68: * meta_char="#", jpayne@68: * int line_skip=0, jpayne@68: * zerobased=False, # <<<<<<<<<<<<<< jpayne@68: * int min_shift=-1, jpayne@68: * index=None, jpayne@68: */ jpayne@68: values[8] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False))); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":883 jpayne@68: * zerobased=False, jpayne@68: * int min_shift=-1, jpayne@68: * index=None, # <<<<<<<<<<<<<< jpayne@68: * keep_original=False, jpayne@68: * csi=False, jpayne@68: */ jpayne@68: values[10] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":884 jpayne@68: * int min_shift=-1, jpayne@68: * index=None, jpayne@68: * keep_original=False, # <<<<<<<<<<<<<< jpayne@68: * csi=False, jpayne@68: * ): jpayne@68: */ jpayne@68: values[11] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False))); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":885 jpayne@68: * index=None, jpayne@68: * keep_original=False, jpayne@68: * csi=False, # <<<<<<<<<<<<<< jpayne@68: * ): jpayne@68: * '''index tab-separated *filename* using tabix. jpayne@68: */ jpayne@68: values[12] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)((PyObject *)Py_False))); jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 13: values[12] = __Pyx_Arg_FASTCALL(__pyx_args, 12); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 12: values[11] = __Pyx_Arg_FASTCALL(__pyx_args, 11); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 11: values[10] = __Pyx_Arg_FASTCALL(__pyx_args, 10); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 10: values[9] = __Pyx_Arg_FASTCALL(__pyx_args, 9); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 9: values[8] = __Pyx_Arg_FASTCALL(__pyx_args, 8); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 8: values[7] = __Pyx_Arg_FASTCALL(__pyx_args, 7); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_filename)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_force); jpayne@68: if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_seq_col); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start_col); jpayne@68: if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end_col); jpayne@68: if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_preset); jpayne@68: if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 6: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_meta_char); jpayne@68: if (value) { values[6] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 7: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_line_skip); jpayne@68: if (value) { values[7] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 8: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_zerobased); jpayne@68: if (value) { values[8] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 9: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_min_shift); jpayne@68: if (value) { values[9] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 10: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_index); jpayne@68: if (value) { values[10] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 11: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_keep_original); jpayne@68: if (value) { values[11] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 12: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_csi); jpayne@68: if (value) { values[12] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "tabix_index") < 0)) __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 13: values[12] = __Pyx_Arg_FASTCALL(__pyx_args, 12); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 12: values[11] = __Pyx_Arg_FASTCALL(__pyx_args, 11); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 11: values[10] = __Pyx_Arg_FASTCALL(__pyx_args, 10); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 10: values[9] = __Pyx_Arg_FASTCALL(__pyx_args, 9); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 9: values[8] = __Pyx_Arg_FASTCALL(__pyx_args, 8); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 8: values[7] = __Pyx_Arg_FASTCALL(__pyx_args, 7); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_filename = values[0]; jpayne@68: __pyx_v_force = values[1]; jpayne@68: __pyx_v_seq_col = values[2]; jpayne@68: __pyx_v_start_col = values[3]; jpayne@68: __pyx_v_end_col = values[4]; jpayne@68: __pyx_v_preset = values[5]; jpayne@68: __pyx_v_meta_char = values[6]; jpayne@68: if (values[7]) { jpayne@68: __pyx_v_line_skip = __Pyx_PyInt_As_int(values[7]); if (unlikely((__pyx_v_line_skip == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 880, __pyx_L3_error) jpayne@68: } else { jpayne@68: __pyx_v_line_skip = ((int)((int)0)); jpayne@68: } jpayne@68: __pyx_v_zerobased = values[8]; jpayne@68: if (values[9]) { jpayne@68: __pyx_v_min_shift = __Pyx_PyInt_As_int(values[9]); if (unlikely((__pyx_v_min_shift == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 882, __pyx_L3_error) jpayne@68: } else { jpayne@68: __pyx_v_min_shift = ((int)((int)-1)); jpayne@68: } jpayne@68: __pyx_v_index = values[10]; jpayne@68: __pyx_v_keep_original = values[11]; jpayne@68: __pyx_v_csi = values[12]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("tabix_index", 0, 1, 13, __pyx_nargs); __PYX_ERR(0, 873, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_2tabix_index(__pyx_self, __pyx_v_filename, __pyx_v_force, __pyx_v_seq_col, __pyx_v_start_col, __pyx_v_end_col, __pyx_v_preset, __pyx_v_meta_char, __pyx_v_line_skip, __pyx_v_zerobased, __pyx_v_min_shift, __pyx_v_index, __pyx_v_keep_original, __pyx_v_csi); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":873 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_index(filename, # <<<<<<<<<<<<<< jpayne@68: * force=False, jpayne@68: * seq_col=None, jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, int __pyx_v_line_skip, PyObject *__pyx_v_zerobased, int __pyx_v_min_shift, PyObject *__pyx_v_index, PyObject *__pyx_v_keep_original, PyObject *__pyx_v_csi) { jpayne@68: PyObject *__pyx_v_fn = NULL; jpayne@68: char *__pyx_v_cfn; jpayne@68: htsFile *__pyx_v_fp; jpayne@68: htsFormat __pyx_v_fmt; jpayne@68: PyObject *__pyx_v_preset2conf = NULL; jpayne@68: PyObject *__pyx_v_conf_data = NULL; jpayne@68: tbx_conf_t __pyx_v_conf; jpayne@68: PyObject *__pyx_v_suffix = NULL; jpayne@68: PyObject *__pyx_v_fn_index = NULL; jpayne@68: char *__pyx_v_fnidx; jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: char *__pyx_t_4; jpayne@68: Py_ssize_t __pyx_t_5; jpayne@68: Py_UCS4 __pyx_t_6; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: PyObject *__pyx_t_8 = NULL; jpayne@68: PyObject *__pyx_t_9 = NULL; jpayne@68: unsigned int __pyx_t_10; jpayne@68: PyObject *__pyx_t_11 = NULL; jpayne@68: PyObject *__pyx_t_12 = NULL; jpayne@68: PyObject *__pyx_t_13 = NULL; jpayne@68: int __pyx_t_14; jpayne@68: PyObject *__pyx_t_15 = NULL; jpayne@68: PyObject *__pyx_t_16 = NULL; jpayne@68: long __pyx_t_17; jpayne@68: PyObject *__pyx_t_18 = NULL; jpayne@68: PyObject *(*__pyx_t_19)(PyObject *); jpayne@68: int32_t __pyx_t_20; jpayne@68: int32_t __pyx_t_21; jpayne@68: int32_t __pyx_t_22; jpayne@68: int32_t __pyx_t_23; jpayne@68: int32_t __pyx_t_24; jpayne@68: int32_t __pyx_t_25; jpayne@68: int __pyx_t_26; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__40) jpayne@68: __Pyx_RefNannySetupContext("tabix_index", 0); jpayne@68: __Pyx_TraceCall("tabix_index", __pyx_f[0], 873, 0, __PYX_ERR(0, 873, __pyx_L1_error)); jpayne@68: __Pyx_INCREF(__pyx_v_filename); jpayne@68: __Pyx_INCREF(__pyx_v_end_col); jpayne@68: __Pyx_INCREF(__pyx_v_preset); jpayne@68: __Pyx_INCREF(__pyx_v_index); jpayne@68: __Pyx_INCREF(__pyx_v_csi); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":928 jpayne@68: * ''' jpayne@68: * jpayne@68: * if preset is None and \ # <<<<<<<<<<<<<< jpayne@68: * (seq_col is None or start_col is None or end_col is None): jpayne@68: * raise ValueError( jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_preset == Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_2; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":929 jpayne@68: * jpayne@68: * if preset is None and \ jpayne@68: * (seq_col is None or start_col is None or end_col is None): # <<<<<<<<<<<<<< jpayne@68: * raise ValueError( jpayne@68: * "neither preset nor seq_col,start_col and end_col given") jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_seq_col == Py_None); jpayne@68: if (!__pyx_t_2) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_2; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_2 = (__pyx_v_start_col == Py_None); jpayne@68: if (!__pyx_t_2) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_2; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_2 = (__pyx_v_end_col == Py_None); jpayne@68: __pyx_t_1 = __pyx_t_2; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":928 jpayne@68: * ''' jpayne@68: * jpayne@68: * if preset is None and \ # <<<<<<<<<<<<<< jpayne@68: * (seq_col is None or start_col is None or end_col is None): jpayne@68: * raise ValueError( jpayne@68: */ jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":930 jpayne@68: * if preset is None and \ jpayne@68: * (seq_col is None or start_col is None or end_col is None): jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * "neither preset nor seq_col,start_col and end_col given") jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__41, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 930, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 930, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":928 jpayne@68: * ''' jpayne@68: * jpayne@68: * if preset is None and \ # <<<<<<<<<<<<<< jpayne@68: * (seq_col is None or start_col is None or end_col is None): jpayne@68: * raise ValueError( jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":933 jpayne@68: * "neither preset nor seq_col,start_col and end_col given") jpayne@68: * jpayne@68: * fn = encode_filename(filename) # <<<<<<<<<<<<<< jpayne@68: * cdef char *cfn = fn jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 933, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_v_fn = ((PyObject*)__pyx_t_3); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":934 jpayne@68: * jpayne@68: * fn = encode_filename(filename) jpayne@68: * cdef char *cfn = fn # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef htsFile *fp = hts_open(cfn, "r") jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_fn == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 934, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 934, __pyx_L1_error) jpayne@68: __pyx_v_cfn = __pyx_t_4; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":936 jpayne@68: * cdef char *cfn = fn jpayne@68: * jpayne@68: * cdef htsFile *fp = hts_open(cfn, "r") # <<<<<<<<<<<<<< jpayne@68: * if fp == NULL: jpayne@68: * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) jpayne@68: */ jpayne@68: __pyx_v_fp = hts_open(__pyx_v_cfn, ((char const *)"r")); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":937 jpayne@68: * jpayne@68: * cdef htsFile *fp = hts_open(cfn, "r") jpayne@68: * if fp == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_fp == NULL); jpayne@68: if (unlikely(__pyx_t_1)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":938 jpayne@68: * cdef htsFile *fp = hts_open(cfn, "r") jpayne@68: * if fp == NULL: jpayne@68: * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef htsFormat fmt = hts_get_format(fp)[0] jpayne@68: */ jpayne@68: __pyx_t_3 = PyTuple_New(4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_5 = 0; jpayne@68: __pyx_t_6 = 127; jpayne@68: __Pyx_INCREF(__pyx_kp_u_Could_not_open_file); jpayne@68: __pyx_t_5 += 21; jpayne@68: __Pyx_GIVEREF(__pyx_kp_u_Could_not_open_file); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_Could_not_open_file); jpayne@68: __pyx_t_7 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_filename), __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_6; jpayne@68: __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7); jpayne@68: __Pyx_GIVEREF(__pyx_t_7); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_7); jpayne@68: __pyx_t_7 = 0; jpayne@68: __Pyx_INCREF(__pyx_kp_u__42); jpayne@68: __pyx_t_5 += 3; jpayne@68: __Pyx_GIVEREF(__pyx_kp_u__42); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u__42); jpayne@68: __pyx_t_7 = __Pyx_PyBytes_FromString(strerror(errno)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_8 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_7, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __pyx_t_7 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_t_8), __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_6; jpayne@68: __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7); jpayne@68: __Pyx_GIVEREF(__pyx_t_7); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_7); jpayne@68: __pyx_t_7 = 0; jpayne@68: __pyx_t_7 = __Pyx_PyUnicode_Join(__pyx_t_3, 4, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 938, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":937 jpayne@68: * jpayne@68: * cdef htsFile *fp = hts_open(cfn, "r") jpayne@68: * if fp == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":940 jpayne@68: * raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno)))) jpayne@68: * jpayne@68: * cdef htsFormat fmt = hts_get_format(fp)[0] # <<<<<<<<<<<<<< jpayne@68: * hts_close(fp) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_v_fmt = (hts_get_format(__pyx_v_fp)[0]); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":941 jpayne@68: * jpayne@68: * cdef htsFormat fmt = hts_get_format(fp)[0] jpayne@68: * hts_close(fp) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if fmt.compression == no_compression: jpayne@68: */ jpayne@68: (void)(hts_close(__pyx_v_fp)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":943 jpayne@68: * hts_close(fp) jpayne@68: * jpayne@68: * if fmt.compression == no_compression: # <<<<<<<<<<<<<< jpayne@68: * tabix_compress(filename, filename + ".gz", force=force) jpayne@68: * if not keep_original: jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_fmt.compression == no_compression); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":944 jpayne@68: * jpayne@68: * if fmt.compression == no_compression: jpayne@68: * tabix_compress(filename, filename + ".gz", force=force) # <<<<<<<<<<<<<< jpayne@68: * if not keep_original: jpayne@68: * os.unlink(filename) jpayne@68: */ jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_tabix_compress); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 944, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_7 = PyNumber_Add(__pyx_v_filename, __pyx_kp_u_gz); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 944, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 944, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_INCREF(__pyx_v_filename); jpayne@68: __Pyx_GIVEREF(__pyx_v_filename); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_filename)) __PYX_ERR(0, 944, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_7); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7)) __PYX_ERR(0, 944, __pyx_L1_error); jpayne@68: __pyx_t_7 = 0; jpayne@68: __pyx_t_7 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 944, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_force, __pyx_v_force) < 0) __PYX_ERR(0, 944, __pyx_L1_error) jpayne@68: __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_8, __pyx_t_7); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 944, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":945 jpayne@68: * if fmt.compression == no_compression: jpayne@68: * tabix_compress(filename, filename + ".gz", force=force) jpayne@68: * if not keep_original: # <<<<<<<<<<<<<< jpayne@68: * os.unlink(filename) jpayne@68: * filename += ".gz" jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_keep_original); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 945, __pyx_L1_error) jpayne@68: __pyx_t_2 = (!__pyx_t_1); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":946 jpayne@68: * tabix_compress(filename, filename + ".gz", force=force) jpayne@68: * if not keep_original: jpayne@68: * os.unlink(filename) # <<<<<<<<<<<<<< jpayne@68: * filename += ".gz" jpayne@68: * fn = encode_filename(filename) jpayne@68: */ jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_os); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 946, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_unlink); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 946, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_10 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (unlikely(PyMethod_Check(__pyx_t_8))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_8); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_8, function); jpayne@68: __pyx_t_10 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_v_filename}; jpayne@68: __pyx_t_9 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 946, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":945 jpayne@68: * if fmt.compression == no_compression: jpayne@68: * tabix_compress(filename, filename + ".gz", force=force) jpayne@68: * if not keep_original: # <<<<<<<<<<<<<< jpayne@68: * os.unlink(filename) jpayne@68: * filename += ".gz" jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":947 jpayne@68: * if not keep_original: jpayne@68: * os.unlink(filename) jpayne@68: * filename += ".gz" # <<<<<<<<<<<<<< jpayne@68: * fn = encode_filename(filename) jpayne@68: * cfn = fn jpayne@68: */ jpayne@68: __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_v_filename, __pyx_kp_u_gz); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 947, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_9); jpayne@68: __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":948 jpayne@68: * os.unlink(filename) jpayne@68: * filename += ".gz" jpayne@68: * fn = encode_filename(filename) # <<<<<<<<<<<<<< jpayne@68: * cfn = fn jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_9 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 948, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __Pyx_DECREF_SET(__pyx_v_fn, ((PyObject*)__pyx_t_9)); jpayne@68: __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":949 jpayne@68: * filename += ".gz" jpayne@68: * fn = encode_filename(filename) jpayne@68: * cfn = fn # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # columns (1-based): jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_fn == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 949, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 949, __pyx_L1_error) jpayne@68: __pyx_v_cfn = __pyx_t_4; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":943 jpayne@68: * hts_close(fp) jpayne@68: * jpayne@68: * if fmt.compression == no_compression: # <<<<<<<<<<<<<< jpayne@68: * tabix_compress(filename, filename + ".gz", force=force) jpayne@68: * if not keep_original: jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":956 jpayne@68: * # 0 is a missing column jpayne@68: * preset2conf = { jpayne@68: * 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0), # <<<<<<<<<<<<<< jpayne@68: * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0), jpayne@68: * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), jpayne@68: */ jpayne@68: __pyx_t_9 = __Pyx_PyDict_NewPresized(5); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_GENERIC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_GIVEREF(__pyx_t_8); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8)) __PYX_ERR(0, 956, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_1); jpayne@68: __Pyx_GIVEREF(__pyx_int_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_1)) __PYX_ERR(0, 956, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_4); jpayne@68: __Pyx_GIVEREF(__pyx_int_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_4)) __PYX_ERR(0, 956, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_5); jpayne@68: __Pyx_GIVEREF(__pyx_int_5); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_5)) __PYX_ERR(0, 956, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_35); jpayne@68: __Pyx_GIVEREF(__pyx_int_35); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_35)) __PYX_ERR(0, 956, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_0)) __PYX_ERR(0, 956, __pyx_L1_error); jpayne@68: __pyx_t_8 = 0; jpayne@68: if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_gff, __pyx_t_7) < 0) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":957 jpayne@68: * preset2conf = { jpayne@68: * 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0), jpayne@68: * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0), # <<<<<<<<<<<<<< jpayne@68: * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), jpayne@68: * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0), jpayne@68: */ jpayne@68: __pyx_t_7 = __Pyx_PyInt_From_int32_t(TBX_UCSC); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 957, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_8 = PyTuple_New(6); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 957, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_GIVEREF(__pyx_t_7); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_7)) __PYX_ERR(0, 957, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_1); jpayne@68: __Pyx_GIVEREF(__pyx_int_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_int_1)) __PYX_ERR(0, 957, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_2); jpayne@68: __Pyx_GIVEREF(__pyx_int_2); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_int_2)) __PYX_ERR(0, 957, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_3); jpayne@68: __Pyx_GIVEREF(__pyx_int_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 3, __pyx_int_3)) __PYX_ERR(0, 957, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_35); jpayne@68: __Pyx_GIVEREF(__pyx_int_35); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 4, __pyx_int_35)) __PYX_ERR(0, 957, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 5, __pyx_int_0)) __PYX_ERR(0, 957, __pyx_L1_error); jpayne@68: __pyx_t_7 = 0; jpayne@68: if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_bed, __pyx_t_8) < 0) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":958 jpayne@68: * 'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0), jpayne@68: * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0), jpayne@68: * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), # <<<<<<<<<<<<<< jpayne@68: * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0), jpayne@68: * 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0), jpayne@68: */ jpayne@68: __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 958, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 958, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_GIVEREF(__pyx_t_8); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8)) __PYX_ERR(0, 958, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_15); jpayne@68: __Pyx_GIVEREF(__pyx_int_15); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_15)) __PYX_ERR(0, 958, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_17); jpayne@68: __Pyx_GIVEREF(__pyx_int_17); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_17)) __PYX_ERR(0, 958, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_18); jpayne@68: __Pyx_GIVEREF(__pyx_int_18); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_18)) __PYX_ERR(0, 958, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_35); jpayne@68: __Pyx_GIVEREF(__pyx_int_35); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_35)) __PYX_ERR(0, 958, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_0)) __PYX_ERR(0, 958, __pyx_L1_error); jpayne@68: __pyx_t_8 = 0; jpayne@68: if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_psltbl, __pyx_t_7) < 0) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":959 jpayne@68: * 'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0), jpayne@68: * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), jpayne@68: * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0), # <<<<<<<<<<<<<< jpayne@68: * 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0), jpayne@68: * } jpayne@68: */ jpayne@68: __pyx_t_7 = __Pyx_PyInt_From_int32_t(TBX_SAM); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 959, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_8 = PyTuple_New(6); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 959, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_GIVEREF(__pyx_t_7); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_7)) __PYX_ERR(0, 959, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_3); jpayne@68: __Pyx_GIVEREF(__pyx_int_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_int_3)) __PYX_ERR(0, 959, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_4); jpayne@68: __Pyx_GIVEREF(__pyx_int_4); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_int_4)) __PYX_ERR(0, 959, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 3, __pyx_int_0)) __PYX_ERR(0, 959, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_64); jpayne@68: __Pyx_GIVEREF(__pyx_int_64); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 4, __pyx_int_64)) __PYX_ERR(0, 959, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 5, __pyx_int_0)) __PYX_ERR(0, 959, __pyx_L1_error); jpayne@68: __pyx_t_7 = 0; jpayne@68: if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_sam, __pyx_t_8) < 0) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":960 jpayne@68: * 'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0), jpayne@68: * 'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0), jpayne@68: * 'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0), # <<<<<<<<<<<<<< jpayne@68: * } jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_VCF); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 960, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 960, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_GIVEREF(__pyx_t_8); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8)) __PYX_ERR(0, 960, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_1); jpayne@68: __Pyx_GIVEREF(__pyx_int_1); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_1)) __PYX_ERR(0, 960, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_2); jpayne@68: __Pyx_GIVEREF(__pyx_int_2); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_2)) __PYX_ERR(0, 960, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_0)) __PYX_ERR(0, 960, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_35); jpayne@68: __Pyx_GIVEREF(__pyx_int_35); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_int_35)) __PYX_ERR(0, 960, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_GIVEREF(__pyx_int_0); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_int_0)) __PYX_ERR(0, 960, __pyx_L1_error); jpayne@68: __pyx_t_8 = 0; jpayne@68: if (PyDict_SetItem(__pyx_t_9, __pyx_n_u_vcf, __pyx_t_7) < 0) __PYX_ERR(0, 956, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __pyx_v_preset2conf = ((PyObject*)__pyx_t_9); jpayne@68: __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":963 jpayne@68: * } jpayne@68: * jpayne@68: * conf_data = None # <<<<<<<<<<<<<< jpayne@68: * if preset == "bcf" or fmt.format == bcf: jpayne@68: * csi = True jpayne@68: */ jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __pyx_v_conf_data = Py_None; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":964 jpayne@68: * jpayne@68: * conf_data = None jpayne@68: * if preset == "bcf" or fmt.format == bcf: # <<<<<<<<<<<<<< jpayne@68: * csi = True jpayne@68: * elif preset: jpayne@68: */ jpayne@68: __pyx_t_1 = (__Pyx_PyUnicode_Equals(__pyx_v_preset, __pyx_n_u_bcf, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 964, __pyx_L1_error) jpayne@68: if (!__pyx_t_1) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_1; jpayne@68: goto __pyx_L12_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_1 = (__pyx_v_fmt.format == bcf); jpayne@68: __pyx_t_2 = __pyx_t_1; jpayne@68: __pyx_L12_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":965 jpayne@68: * conf_data = None jpayne@68: * if preset == "bcf" or fmt.format == bcf: jpayne@68: * csi = True # <<<<<<<<<<<<<< jpayne@68: * elif preset: jpayne@68: * try: jpayne@68: */ jpayne@68: __Pyx_INCREF(Py_True); jpayne@68: __Pyx_DECREF_SET(__pyx_v_csi, Py_True); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":964 jpayne@68: * jpayne@68: * conf_data = None jpayne@68: * if preset == "bcf" or fmt.format == bcf: # <<<<<<<<<<<<<< jpayne@68: * csi = True jpayne@68: * elif preset: jpayne@68: */ jpayne@68: goto __pyx_L11; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":966 jpayne@68: * if preset == "bcf" or fmt.format == bcf: jpayne@68: * csi = True jpayne@68: * elif preset: # <<<<<<<<<<<<<< jpayne@68: * try: jpayne@68: * conf_data = preset2conf[preset] jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_preset); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 966, __pyx_L1_error) jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":967 jpayne@68: * csi = True jpayne@68: * elif preset: jpayne@68: * try: # <<<<<<<<<<<<<< jpayne@68: * conf_data = preset2conf[preset] jpayne@68: * except KeyError: jpayne@68: */ jpayne@68: { jpayne@68: __Pyx_PyThreadState_declare jpayne@68: __Pyx_PyThreadState_assign jpayne@68: __Pyx_ExceptionSave(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13); jpayne@68: __Pyx_XGOTREF(__pyx_t_11); jpayne@68: __Pyx_XGOTREF(__pyx_t_12); jpayne@68: __Pyx_XGOTREF(__pyx_t_13); jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":968 jpayne@68: * elif preset: jpayne@68: * try: jpayne@68: * conf_data = preset2conf[preset] # <<<<<<<<<<<<<< jpayne@68: * except KeyError: jpayne@68: * raise KeyError( jpayne@68: */ jpayne@68: __pyx_t_9 = __Pyx_PyDict_GetItem(__pyx_v_preset2conf, __pyx_v_preset); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 968, __pyx_L14_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __Pyx_DECREF_SET(__pyx_v_conf_data, __pyx_t_9); jpayne@68: __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":967 jpayne@68: * csi = True jpayne@68: * elif preset: jpayne@68: * try: # <<<<<<<<<<<<<< jpayne@68: * conf_data = preset2conf[preset] jpayne@68: * except KeyError: jpayne@68: */ jpayne@68: } jpayne@68: __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0; jpayne@68: __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0; jpayne@68: __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; jpayne@68: goto __pyx_L19_try_end; jpayne@68: __pyx_L14_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":969 jpayne@68: * try: jpayne@68: * conf_data = preset2conf[preset] jpayne@68: * except KeyError: # <<<<<<<<<<<<<< jpayne@68: * raise KeyError( jpayne@68: * "unknown preset '%s', valid presets are '%s'" % jpayne@68: */ jpayne@68: __pyx_t_14 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError); jpayne@68: if (__pyx_t_14) { jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_7, &__pyx_t_8) < 0) __PYX_ERR(0, 969, __pyx_L16_except_error) jpayne@68: __Pyx_XGOTREF(__pyx_t_9); jpayne@68: __Pyx_XGOTREF(__pyx_t_7); jpayne@68: __Pyx_XGOTREF(__pyx_t_8); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":971 jpayne@68: * except KeyError: jpayne@68: * raise KeyError( jpayne@68: * "unknown preset '%s', valid presets are '%s'" % # <<<<<<<<<<<<<< jpayne@68: * (preset, ",".join(preset2conf.keys()))) jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 971, __pyx_L16_except_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_5 = 0; jpayne@68: __pyx_t_6 = 127; jpayne@68: __Pyx_INCREF(__pyx_kp_u_unknown_preset); jpayne@68: __pyx_t_5 += 16; jpayne@68: __Pyx_GIVEREF(__pyx_kp_u_unknown_preset); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_unknown_preset); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":972 jpayne@68: * raise KeyError( jpayne@68: * "unknown preset '%s', valid presets are '%s'" % jpayne@68: * (preset, ",".join(preset2conf.keys()))) # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * if end_col is None: jpayne@68: */ jpayne@68: __pyx_t_15 = __Pyx_PyObject_FormatSimpleAndDecref(PyObject_Unicode(__pyx_v_preset), __pyx_empty_unicode); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 972, __pyx_L16_except_error) jpayne@68: __Pyx_GOTREF(__pyx_t_15); jpayne@68: __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_15) : __pyx_t_6; jpayne@68: __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_15); jpayne@68: __Pyx_GIVEREF(__pyx_t_15); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_15); jpayne@68: __pyx_t_15 = 0; jpayne@68: __Pyx_INCREF(__pyx_kp_u_valid_presets_are); jpayne@68: __pyx_t_5 += 22; jpayne@68: __Pyx_GIVEREF(__pyx_kp_u_valid_presets_are); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_valid_presets_are); jpayne@68: __pyx_t_15 = __Pyx_PyDict_Keys(__pyx_v_preset2conf); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 972, __pyx_L16_except_error) jpayne@68: __Pyx_GOTREF(__pyx_t_15); jpayne@68: __pyx_t_16 = PyUnicode_Join(__pyx_kp_u__43, __pyx_t_15); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 972, __pyx_L16_except_error) jpayne@68: __Pyx_GOTREF(__pyx_t_16); jpayne@68: __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; jpayne@68: __pyx_t_6 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_16) > __pyx_t_6) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_16) : __pyx_t_6; jpayne@68: __pyx_t_5 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_16); jpayne@68: __Pyx_GIVEREF(__pyx_t_16); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_t_16); jpayne@68: __pyx_t_16 = 0; jpayne@68: __Pyx_INCREF(__pyx_kp_u__44); jpayne@68: __pyx_t_5 += 1; jpayne@68: __Pyx_GIVEREF(__pyx_kp_u__44); jpayne@68: PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_kp_u__44); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":971 jpayne@68: * except KeyError: jpayne@68: * raise KeyError( jpayne@68: * "unknown preset '%s', valid presets are '%s'" % # <<<<<<<<<<<<<< jpayne@68: * (preset, ",".join(preset2conf.keys()))) jpayne@68: * else: jpayne@68: */ jpayne@68: __pyx_t_16 = __Pyx_PyUnicode_Join(__pyx_t_3, 5, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 971, __pyx_L16_except_error) jpayne@68: __Pyx_GOTREF(__pyx_t_16); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":970 jpayne@68: * conf_data = preset2conf[preset] jpayne@68: * except KeyError: jpayne@68: * raise KeyError( # <<<<<<<<<<<<<< jpayne@68: * "unknown preset '%s', valid presets are '%s'" % jpayne@68: * (preset, ",".join(preset2conf.keys()))) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_builtin_KeyError, __pyx_t_16); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 970, __pyx_L16_except_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 970, __pyx_L16_except_error) jpayne@68: } jpayne@68: goto __pyx_L16_except_error; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":967 jpayne@68: * csi = True jpayne@68: * elif preset: jpayne@68: * try: # <<<<<<<<<<<<<< jpayne@68: * conf_data = preset2conf[preset] jpayne@68: * except KeyError: jpayne@68: */ jpayne@68: __pyx_L16_except_error:; jpayne@68: __Pyx_XGIVEREF(__pyx_t_11); jpayne@68: __Pyx_XGIVEREF(__pyx_t_12); jpayne@68: __Pyx_XGIVEREF(__pyx_t_13); jpayne@68: __Pyx_ExceptionReset(__pyx_t_11, __pyx_t_12, __pyx_t_13); jpayne@68: goto __pyx_L1_error; jpayne@68: __pyx_L19_try_end:; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":966 jpayne@68: * if preset == "bcf" or fmt.format == bcf: jpayne@68: * csi = True jpayne@68: * elif preset: # <<<<<<<<<<<<<< jpayne@68: * try: jpayne@68: * conf_data = preset2conf[preset] jpayne@68: */ jpayne@68: goto __pyx_L11; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":974 jpayne@68: * (preset, ",".join(preset2conf.keys()))) jpayne@68: * else: jpayne@68: * if end_col is None: # <<<<<<<<<<<<<< jpayne@68: * end_col = -1 jpayne@68: * jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __pyx_t_2 = (__pyx_v_end_col == Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":975 jpayne@68: * else: jpayne@68: * if end_col is None: jpayne@68: * end_col = -1 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * preset = 0 jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_int_neg_1); jpayne@68: __Pyx_DECREF_SET(__pyx_v_end_col, __pyx_int_neg_1); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":974 jpayne@68: * (preset, ",".join(preset2conf.keys()))) jpayne@68: * else: jpayne@68: * if end_col is None: # <<<<<<<<<<<<<< jpayne@68: * end_col = -1 jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":977 jpayne@68: * end_col = -1 jpayne@68: * jpayne@68: * preset = 0 # <<<<<<<<<<<<<< jpayne@68: * # tabix internally works with 0-based coordinates and jpayne@68: * # open/closed intervals. When using a preset, conversion is jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_int_0); jpayne@68: __Pyx_DECREF_SET(__pyx_v_preset, __pyx_int_0); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":984 jpayne@68: * # from the start coordinate. To avoid doing this, set the jpayne@68: * # TI_FLAG_UCSC=0x10000 flag: jpayne@68: * if zerobased: # <<<<<<<<<<<<<< jpayne@68: * preset = preset | TBX_UCSC jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_zerobased); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 984, __pyx_L1_error) jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":985 jpayne@68: * # TI_FLAG_UCSC=0x10000 flag: jpayne@68: * if zerobased: jpayne@68: * preset = preset | TBX_UCSC # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * conf_data = (preset, seq_col + 1, start_col + 1, end_col + 1, ord(meta_char), line_skip) jpayne@68: */ jpayne@68: __pyx_t_8 = __Pyx_PyInt_From_int32_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 985, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __pyx_t_7 = PyNumber_Or(__pyx_v_preset, __pyx_t_8); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 985, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_preset, __pyx_t_7); jpayne@68: __pyx_t_7 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":984 jpayne@68: * # from the start coordinate. To avoid doing this, set the jpayne@68: * # TI_FLAG_UCSC=0x10000 flag: jpayne@68: * if zerobased: # <<<<<<<<<<<<<< jpayne@68: * preset = preset | TBX_UCSC jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":987 jpayne@68: * preset = preset | TBX_UCSC jpayne@68: * jpayne@68: * conf_data = (preset, seq_col + 1, start_col + 1, end_col + 1, ord(meta_char), line_skip) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef tbx_conf_t conf jpayne@68: */ jpayne@68: __pyx_t_7 = __Pyx_PyInt_AddObjC(__pyx_v_seq_col, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_8 = __Pyx_PyInt_AddObjC(__pyx_v_start_col, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __pyx_t_9 = __Pyx_PyInt_AddObjC(__pyx_v_end_col, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __pyx_t_17 = __Pyx_PyObject_Ord(__pyx_v_meta_char); if (unlikely(__pyx_t_17 == ((long)(long)(Py_UCS4)-1))) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_t_17); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_16 = __Pyx_PyInt_From_int(__pyx_v_line_skip); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_16); jpayne@68: __pyx_t_15 = PyTuple_New(6); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 987, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_15); jpayne@68: __Pyx_INCREF(__pyx_v_preset); jpayne@68: __Pyx_GIVEREF(__pyx_v_preset); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_preset)) __PYX_ERR(0, 987, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_7); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 1, __pyx_t_7)) __PYX_ERR(0, 987, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_8); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 2, __pyx_t_8)) __PYX_ERR(0, 987, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_9); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 3, __pyx_t_9)) __PYX_ERR(0, 987, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 4, __pyx_t_3)) __PYX_ERR(0, 987, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_16); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_15, 5, __pyx_t_16)) __PYX_ERR(0, 987, __pyx_L1_error); jpayne@68: __pyx_t_7 = 0; jpayne@68: __pyx_t_8 = 0; jpayne@68: __pyx_t_9 = 0; jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_16 = 0; jpayne@68: __Pyx_DECREF_SET(__pyx_v_conf_data, __pyx_t_15); jpayne@68: __pyx_t_15 = 0; jpayne@68: } jpayne@68: __pyx_L11:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":990 jpayne@68: * jpayne@68: * cdef tbx_conf_t conf jpayne@68: * if conf_data: # <<<<<<<<<<<<<< jpayne@68: * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_conf_data); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 990, __pyx_L1_error) jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":991 jpayne@68: * cdef tbx_conf_t conf jpayne@68: * if conf_data: jpayne@68: * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if csi or min_shift > 0: jpayne@68: */ jpayne@68: if ((likely(PyTuple_CheckExact(__pyx_v_conf_data))) || (PyList_CheckExact(__pyx_v_conf_data))) { jpayne@68: PyObject* sequence = __pyx_v_conf_data; jpayne@68: Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); jpayne@68: if (unlikely(size != 6)) { jpayne@68: if (size > 6) __Pyx_RaiseTooManyValuesError(6); jpayne@68: else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); jpayne@68: __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: } jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: if (likely(PyTuple_CheckExact(sequence))) { jpayne@68: __pyx_t_15 = PyTuple_GET_ITEM(sequence, 0); jpayne@68: __pyx_t_16 = PyTuple_GET_ITEM(sequence, 1); jpayne@68: __pyx_t_3 = PyTuple_GET_ITEM(sequence, 2); jpayne@68: __pyx_t_9 = PyTuple_GET_ITEM(sequence, 3); jpayne@68: __pyx_t_8 = PyTuple_GET_ITEM(sequence, 4); jpayne@68: __pyx_t_7 = PyTuple_GET_ITEM(sequence, 5); jpayne@68: } else { jpayne@68: __pyx_t_15 = PyList_GET_ITEM(sequence, 0); jpayne@68: __pyx_t_16 = PyList_GET_ITEM(sequence, 1); jpayne@68: __pyx_t_3 = PyList_GET_ITEM(sequence, 2); jpayne@68: __pyx_t_9 = PyList_GET_ITEM(sequence, 3); jpayne@68: __pyx_t_8 = PyList_GET_ITEM(sequence, 4); jpayne@68: __pyx_t_7 = PyList_GET_ITEM(sequence, 5); jpayne@68: } jpayne@68: __Pyx_INCREF(__pyx_t_15); jpayne@68: __Pyx_INCREF(__pyx_t_16); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_9); jpayne@68: __Pyx_INCREF(__pyx_t_8); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: #else jpayne@68: { jpayne@68: Py_ssize_t i; jpayne@68: PyObject** temps[6] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_3,&__pyx_t_9,&__pyx_t_8,&__pyx_t_7}; jpayne@68: for (i=0; i < 6; i++) { jpayne@68: PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(item); jpayne@68: *(temps[i]) = item; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: } else { jpayne@68: Py_ssize_t index = -1; jpayne@68: PyObject** temps[6] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_3,&__pyx_t_9,&__pyx_t_8,&__pyx_t_7}; jpayne@68: __pyx_t_18 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_18); jpayne@68: __pyx_t_19 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_18); jpayne@68: for (index=0; index < 6; index++) { jpayne@68: PyObject* item = __pyx_t_19(__pyx_t_18); if (unlikely(!item)) goto __pyx_L25_unpacking_failed; jpayne@68: __Pyx_GOTREF(item); jpayne@68: *(temps[index]) = item; jpayne@68: } jpayne@68: if (__Pyx_IternextUnpackEndCheck(__pyx_t_19(__pyx_t_18), 6) < 0) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __pyx_t_19 = NULL; jpayne@68: __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; jpayne@68: goto __pyx_L26_unpacking_done; jpayne@68: __pyx_L25_unpacking_failed:; jpayne@68: __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; jpayne@68: __pyx_t_19 = NULL; jpayne@68: if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); jpayne@68: __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __pyx_L26_unpacking_done:; jpayne@68: } jpayne@68: __pyx_t_20 = __Pyx_PyInt_As_int32_t(__pyx_t_15); if (unlikely((__pyx_t_20 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; jpayne@68: __pyx_t_21 = __Pyx_PyInt_As_int32_t(__pyx_t_16); if (unlikely((__pyx_t_21 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; jpayne@68: __pyx_t_22 = __Pyx_PyInt_As_int32_t(__pyx_t_3); if (unlikely((__pyx_t_22 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __pyx_t_23 = __Pyx_PyInt_As_int32_t(__pyx_t_9); if (unlikely((__pyx_t_23 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: __pyx_t_24 = __Pyx_PyInt_As_int32_t(__pyx_t_8); if (unlikely((__pyx_t_24 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __pyx_t_25 = __Pyx_PyInt_As_int32_t(__pyx_t_7); if (unlikely((__pyx_t_25 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 991, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __pyx_v_conf.preset = __pyx_t_20; jpayne@68: __pyx_v_conf.sc = __pyx_t_21; jpayne@68: __pyx_v_conf.bc = __pyx_t_22; jpayne@68: __pyx_v_conf.ec = __pyx_t_23; jpayne@68: __pyx_v_conf.meta_char = __pyx_t_24; jpayne@68: __pyx_v_conf.line_skip = __pyx_t_25; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":990 jpayne@68: * jpayne@68: * cdef tbx_conf_t conf jpayne@68: * if conf_data: # <<<<<<<<<<<<<< jpayne@68: * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":993 jpayne@68: * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data jpayne@68: * jpayne@68: * if csi or min_shift > 0: # <<<<<<<<<<<<<< jpayne@68: * suffix = ".csi" jpayne@68: * if min_shift <= 0: min_shift = 14 jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_csi); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 993, __pyx_L1_error) jpayne@68: if (!__pyx_t_1) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_1; jpayne@68: goto __pyx_L28_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_1 = (__pyx_v_min_shift > 0); jpayne@68: __pyx_t_2 = __pyx_t_1; jpayne@68: __pyx_L28_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":994 jpayne@68: * jpayne@68: * if csi or min_shift > 0: jpayne@68: * suffix = ".csi" # <<<<<<<<<<<<<< jpayne@68: * if min_shift <= 0: min_shift = 14 jpayne@68: * else: jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_kp_u_csi_2); jpayne@68: __pyx_v_suffix = __pyx_kp_u_csi_2; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":995 jpayne@68: * if csi or min_shift > 0: jpayne@68: * suffix = ".csi" jpayne@68: * if min_shift <= 0: min_shift = 14 # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * suffix = ".tbi" jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_min_shift <= 0); jpayne@68: if (__pyx_t_2) { jpayne@68: __pyx_v_min_shift = 14; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":993 jpayne@68: * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data jpayne@68: * jpayne@68: * if csi or min_shift > 0: # <<<<<<<<<<<<<< jpayne@68: * suffix = ".csi" jpayne@68: * if min_shift <= 0: min_shift = 14 jpayne@68: */ jpayne@68: goto __pyx_L27; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":997 jpayne@68: * if min_shift <= 0: min_shift = 14 jpayne@68: * else: jpayne@68: * suffix = ".tbi" # <<<<<<<<<<<<<< jpayne@68: * min_shift = 0 jpayne@68: * jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: __Pyx_INCREF(__pyx_kp_u_tbi); jpayne@68: __pyx_v_suffix = __pyx_kp_u_tbi; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":998 jpayne@68: * else: jpayne@68: * suffix = ".tbi" jpayne@68: * min_shift = 0 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * index = index or filename + suffix jpayne@68: */ jpayne@68: __pyx_v_min_shift = 0; jpayne@68: } jpayne@68: __pyx_L27:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1000 jpayne@68: * min_shift = 0 jpayne@68: * jpayne@68: * index = index or filename + suffix # <<<<<<<<<<<<<< jpayne@68: * fn_index = encode_filename(index) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_index); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 1000, __pyx_L1_error) jpayne@68: if (!__pyx_t_2) { jpayne@68: } else { jpayne@68: __Pyx_INCREF(__pyx_v_index); jpayne@68: __pyx_t_7 = __pyx_v_index; jpayne@68: goto __pyx_L31_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_8 = PyNumber_Add(__pyx_v_filename, __pyx_v_suffix); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1000, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_INCREF(__pyx_t_8); jpayne@68: __pyx_t_7 = __pyx_t_8; jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __pyx_L31_bool_binop_done:; jpayne@68: __Pyx_DECREF_SET(__pyx_v_index, __pyx_t_7); jpayne@68: __pyx_t_7 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1001 jpayne@68: * jpayne@68: * index = index or filename + suffix jpayne@68: * fn_index = encode_filename(index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if not force and os.path.exists(index): jpayne@68: */ jpayne@68: __pyx_t_7 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1001, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_v_fn_index = ((PyObject*)__pyx_t_7); jpayne@68: __pyx_t_7 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1003 jpayne@68: * fn_index = encode_filename(index) jpayne@68: * jpayne@68: * if not force and os.path.exists(index): # <<<<<<<<<<<<<< jpayne@68: * raise IOError( jpayne@68: * "filename '%s' already exists, use *force* to overwrite" % index) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_force); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 1003, __pyx_L1_error) jpayne@68: __pyx_t_26 = (!__pyx_t_1); jpayne@68: if (__pyx_t_26) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_26; jpayne@68: goto __pyx_L34_bool_binop_done; jpayne@68: } jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_os); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1003, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_path); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 1003, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_9); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_exists); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1003, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: __pyx_t_9 = NULL; jpayne@68: __pyx_t_10 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_8))) { jpayne@68: __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_8); jpayne@68: if (likely(__pyx_t_9)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8); jpayne@68: __Pyx_INCREF(__pyx_t_9); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_8, function); jpayne@68: __pyx_t_10 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_index}; jpayne@68: __pyx_t_7 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10); jpayne@68: __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1003, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: } jpayne@68: __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 1003, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __pyx_t_2 = __pyx_t_26; jpayne@68: __pyx_L34_bool_binop_done:; jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1005 jpayne@68: * if not force and os.path.exists(index): jpayne@68: * raise IOError( jpayne@68: * "filename '%s' already exists, use *force* to overwrite" % index) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char *fnidx = fn_index jpayne@68: */ jpayne@68: __pyx_t_7 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_filename_s_already_exists_use_fo, __pyx_v_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1005, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1004 jpayne@68: * jpayne@68: * if not force and os.path.exists(index): jpayne@68: * raise IOError( # <<<<<<<<<<<<<< jpayne@68: * "filename '%s' already exists, use *force* to overwrite" % index) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_8 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_7); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1004, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_Raise(__pyx_t_8, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __PYX_ERR(0, 1004, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1003 jpayne@68: * fn_index = encode_filename(index) jpayne@68: * jpayne@68: * if not force and os.path.exists(index): # <<<<<<<<<<<<<< jpayne@68: * raise IOError( jpayne@68: * "filename '%s' already exists, use *force* to overwrite" % index) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1007 jpayne@68: * "filename '%s' already exists, use *force* to overwrite" % index) jpayne@68: * jpayne@68: * cdef char *fnidx = fn_index # <<<<<<<<<<<<<< jpayne@68: * cdef int retval = 0 jpayne@68: * jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_fn_index == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 1007, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_PyBytes_AsWritableString(__pyx_v_fn_index); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 1007, __pyx_L1_error) jpayne@68: __pyx_v_fnidx = __pyx_t_4; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1008 jpayne@68: * jpayne@68: * cdef char *fnidx = fn_index jpayne@68: * cdef int retval = 0 # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if csi and fmt.format == bcf: jpayne@68: */ jpayne@68: __pyx_v_retval = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1010 jpayne@68: * cdef int retval = 0 jpayne@68: * jpayne@68: * if csi and fmt.format == bcf: # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) jpayne@68: */ jpayne@68: __pyx_t_26 = __Pyx_PyObject_IsTrue(__pyx_v_csi); if (unlikely((__pyx_t_26 < 0))) __PYX_ERR(0, 1010, __pyx_L1_error) jpayne@68: if (__pyx_t_26) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_26; jpayne@68: goto __pyx_L37_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_26 = (__pyx_v_fmt.format == bcf); jpayne@68: __pyx_t_2 = __pyx_t_26; jpayne@68: __pyx_L37_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1011 jpayne@68: * jpayne@68: * if csi and fmt.format == bcf: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) jpayne@68: * else: jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1012 jpayne@68: * if csi and fmt.format == bcf: jpayne@68: * with nogil: jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) # <<<<<<<<<<<<<< jpayne@68: * else: jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_v_retval = bcf_index_build2(__pyx_v_cfn, __pyx_v_fnidx, __pyx_v_min_shift); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1011 jpayne@68: * jpayne@68: * if csi and fmt.format == bcf: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) jpayne@68: * else: jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L41; jpayne@68: } jpayne@68: __pyx_L41:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1010 jpayne@68: * cdef int retval = 0 jpayne@68: * jpayne@68: * if csi and fmt.format == bcf: # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) jpayne@68: */ jpayne@68: goto __pyx_L36; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1014 jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) jpayne@68: * else: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) jpayne@68: * jpayne@68: */ jpayne@68: /*else*/ { jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1015 jpayne@68: * else: jpayne@68: * with nogil: jpayne@68: * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if retval != 0: jpayne@68: */ jpayne@68: __pyx_v_retval = tbx_index_build2(__pyx_v_cfn, __pyx_v_fnidx, __pyx_v_min_shift, (&__pyx_v_conf)); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1014 jpayne@68: * retval = bcf_index_build2(cfn, fnidx, min_shift) jpayne@68: * else: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L44; jpayne@68: } jpayne@68: __pyx_L44:; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: __pyx_L36:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1017 jpayne@68: * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) jpayne@68: * jpayne@68: * if retval != 0: # <<<<<<<<<<<<<< jpayne@68: * raise OSError("building of index for {} failed".format(filename)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_retval != 0); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1018 jpayne@68: * jpayne@68: * if retval != 0: jpayne@68: * raise OSError("building of index for {} failed".format(filename)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return filename jpayne@68: */ jpayne@68: __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_building_of_index_for_failed, __pyx_n_s_format); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1018, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __pyx_t_9 = NULL; jpayne@68: __pyx_t_10 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_7))) { jpayne@68: __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_7); jpayne@68: if (likely(__pyx_t_9)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7); jpayne@68: __Pyx_INCREF(__pyx_t_9); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_7, function); jpayne@68: __pyx_t_10 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_filename}; jpayne@68: __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_10, 1+__pyx_t_10); jpayne@68: __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; jpayne@68: if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1018, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_8); jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: } jpayne@68: __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_builtin_OSError, __pyx_t_8); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1018, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_7); jpayne@68: __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; jpayne@68: __Pyx_Raise(__pyx_t_7, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __PYX_ERR(0, 1018, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1017 jpayne@68: * retval = tbx_index_build2(cfn, fnidx, min_shift, &conf) jpayne@68: * jpayne@68: * if retval != 0: # <<<<<<<<<<<<<< jpayne@68: * raise OSError("building of index for {} failed".format(filename)) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1020 jpayne@68: * raise OSError("building of index for {} failed".format(filename)) jpayne@68: * jpayne@68: * return filename # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # ######################################################### jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_filename); jpayne@68: __pyx_r = __pyx_v_filename; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":873 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_index(filename, # <<<<<<<<<<<<<< jpayne@68: * force=False, jpayne@68: * seq_col=None, jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_XDECREF(__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_9); jpayne@68: __Pyx_XDECREF(__pyx_t_15); jpayne@68: __Pyx_XDECREF(__pyx_t_16); jpayne@68: __Pyx_XDECREF(__pyx_t_18); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_fn); jpayne@68: __Pyx_XDECREF(__pyx_v_preset2conf); jpayne@68: __Pyx_XDECREF(__pyx_v_conf_data); jpayne@68: __Pyx_XDECREF(__pyx_v_suffix); jpayne@68: __Pyx_XDECREF(__pyx_v_fn_index); jpayne@68: __Pyx_XDECREF(__pyx_v_filename); jpayne@68: __Pyx_XDECREF(__pyx_v_end_col); jpayne@68: __Pyx_XDECREF(__pyx_v_preset); jpayne@68: __Pyx_XDECREF(__pyx_v_index); jpayne@68: __Pyx_XDECREF(__pyx_v_csi); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1102 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __cinit__(self, # <<<<<<<<<<<<<< jpayne@68: * infile, jpayne@68: * Parser parser, jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static int __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ jpayne@68: static int __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { jpayne@68: PyObject *__pyx_v_infile = 0; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser = 0; jpayne@68: int __pyx_v_buffer_size; jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: int __pyx_r; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_infile,&__pyx_n_s_parser,&__pyx_n_s_buffer_size,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_infile)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1102, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_VARARGS(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1102, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); __PYX_ERR(0, 1102, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (kw_args > 0) { jpayne@68: PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buffer_size); jpayne@68: if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1102, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__cinit__") < 0)) __PYX_ERR(0, 1102, __pyx_L3_error) jpayne@68: } jpayne@68: } else { jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); jpayne@68: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); jpayne@68: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: } jpayne@68: __pyx_v_infile = values[0]; jpayne@68: __pyx_v_parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)values[1]); jpayne@68: if (values[2]) { jpayne@68: __pyx_v_buffer_size = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_buffer_size == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1105, __pyx_L3_error) jpayne@68: } else { jpayne@68: __pyx_v_buffer_size = ((int)0x10000); jpayne@68: } jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, __pyx_nargs); __PYX_ERR(0, 1102, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_5pysam_9libctabix_Parser, 1, "parser", 0))) __PYX_ERR(0, 1104, __pyx_L1_error) jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator___cinit__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_parser, __pyx_v_buffer_size); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_pf_5pysam_9libctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size) { jpayne@68: int __pyx_v_fd; jpayne@68: int __pyx_r; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: int __pyx_t_3; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__cinit__", 1); jpayne@68: __Pyx_TraceCall("__cinit__", __pyx_f[0], 1102, 0, __PYX_ERR(0, 1102, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1107 jpayne@68: * int buffer_size=65536): jpayne@68: * jpayne@68: * if infile.closed: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_infile, __pyx_n_s_closed); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1107, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 1107, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1108 jpayne@68: * jpayne@68: * if infile.closed: jpayne@68: * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1108, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 1108, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1107 jpayne@68: * int buffer_size=65536): jpayne@68: * jpayne@68: * if infile.closed: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1110 jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: * self.infile = infile # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef int fd = PyObject_AsFileDescriptor(infile) jpayne@68: */ jpayne@68: __Pyx_INCREF(__pyx_v_infile); jpayne@68: __Pyx_GIVEREF(__pyx_v_infile); jpayne@68: __Pyx_GOTREF(__pyx_v_self->infile); jpayne@68: __Pyx_DECREF(__pyx_v_self->infile); jpayne@68: __pyx_v_self->infile = __pyx_v_infile; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1112 jpayne@68: * self.infile = infile jpayne@68: * jpayne@68: * cdef int fd = PyObject_AsFileDescriptor(infile) # <<<<<<<<<<<<<< jpayne@68: * if fd == -1: jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: */ jpayne@68: __pyx_t_3 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 1112, __pyx_L1_error) jpayne@68: __pyx_v_fd = __pyx_t_3; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1113 jpayne@68: * jpayne@68: * cdef int fd = PyObject_AsFileDescriptor(infile) jpayne@68: * if fd == -1: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_fd == -1L); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1114 jpayne@68: * cdef int fd = PyObject_AsFileDescriptor(infile) jpayne@68: * if fd == -1: jpayne@68: * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.duplicated_fd = dup(fd) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1114, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 1114, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1113 jpayne@68: * jpayne@68: * cdef int fd = PyObject_AsFileDescriptor(infile) jpayne@68: * if fd == -1: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1116 jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: * self.duplicated_fd = dup(fd) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # From the manual: jpayne@68: */ jpayne@68: __pyx_v_self->duplicated_fd = dup(__pyx_v_fd); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1123 jpayne@68: * # When reading, this will be detected automatically by looking jpayne@68: * # for the magic two-byte gzip header. jpayne@68: * self.fh = bgzf_dopen(self.duplicated_fd, 'r') # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if self.fh == NULL: jpayne@68: */ jpayne@68: __pyx_v_self->fh = bgzf_dopen(__pyx_v_self->duplicated_fd, ((char const *)"r")); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1125 jpayne@68: * self.fh = bgzf_dopen(self.duplicated_fd, 'r') jpayne@68: * jpayne@68: * if self.fh == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError('%s' % strerror(errno)) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v_self->fh == NULL); jpayne@68: if (unlikely(__pyx_t_2)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1126 jpayne@68: * jpayne@68: * if self.fh == NULL: jpayne@68: * raise IOError('%s' % strerror(errno)) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.kstream = ks_init(self.fh) jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyBytes_FromString(strerror(errno)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1126, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_4 = PyUnicode_Format(__pyx_kp_u_s, __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1126, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_t_4); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1126, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __Pyx_Raise(__pyx_t_1, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(0, 1126, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1125 jpayne@68: * self.fh = bgzf_dopen(self.duplicated_fd, 'r') jpayne@68: * jpayne@68: * if self.fh == NULL: # <<<<<<<<<<<<<< jpayne@68: * raise IOError('%s' % strerror(errno)) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1128 jpayne@68: * raise IOError('%s' % strerror(errno)) jpayne@68: * jpayne@68: * self.kstream = ks_init(self.fh) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.buffer.s = malloc(buffer_size) jpayne@68: */ jpayne@68: __pyx_v_self->kstream = ks_init(__pyx_v_self->fh); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1130 jpayne@68: * self.kstream = ks_init(self.fh) jpayne@68: * jpayne@68: * self.buffer.s = malloc(buffer_size) # <<<<<<<<<<<<<< jpayne@68: * #if self.buffer == NULL: jpayne@68: * # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size) jpayne@68: */ jpayne@68: __pyx_v_self->buffer.s = ((char *)malloc(__pyx_v_buffer_size)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1134 jpayne@68: * # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size) jpayne@68: * #self.size = buffer_size jpayne@68: * self.parser = parser # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: */ jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_parser); jpayne@68: __Pyx_GIVEREF((PyObject *)__pyx_v_parser); jpayne@68: __Pyx_GOTREF((PyObject *)__pyx_v_self->parser); jpayne@68: __Pyx_DECREF((PyObject *)__pyx_v_self->parser); jpayne@68: __pyx_v_self->parser = __pyx_v_parser; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1102 jpayne@68: * ''' jpayne@68: * jpayne@68: * def __cinit__(self, # <<<<<<<<<<<<<< jpayne@68: * infile, jpayne@68: * Parser parser, jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = -1; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1136 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_2__iter__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__iter__", 1); jpayne@68: __Pyx_TraceCall("__iter__", __pyx_f[0], 1136, 0, __PYX_ERR(0, 1136, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1137 jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: * return self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef __cnext__(self): jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF((PyObject *)__pyx_v_self); jpayne@68: __pyx_r = ((PyObject *)__pyx_v_self); jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1136 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1139 jpayne@68: * return self jpayne@68: * jpayne@68: * cdef __cnext__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char * b jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix_19tabix_file_iterator___cnext__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) { jpayne@68: char *__pyx_v_b; jpayne@68: int __pyx_v_dret; jpayne@68: int __pyx_v_retval; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_t_1; jpayne@68: char *__pyx_t_2; jpayne@68: int __pyx_t_3; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__cnext__", 1); jpayne@68: __Pyx_TraceCall("__cnext__", __pyx_f[0], 1139, 0, __PYX_ERR(0, 1139, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1142 jpayne@68: * jpayne@68: * cdef char * b jpayne@68: * cdef int dret = 0 # <<<<<<<<<<<<<< jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: jpayne@68: */ jpayne@68: __pyx_v_dret = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1143 jpayne@68: * cdef char * b jpayne@68: * cdef int dret = 0 jpayne@68: * cdef int retval = 0 # <<<<<<<<<<<<<< jpayne@68: * while 1: jpayne@68: * with nogil: jpayne@68: */ jpayne@68: __pyx_v_retval = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1144 jpayne@68: * cdef int dret = 0 jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: # <<<<<<<<<<<<<< jpayne@68: * with nogil: jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: */ jpayne@68: while (1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1145 jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: */ jpayne@68: { jpayne@68: #ifdef WITH_THREAD jpayne@68: PyThreadState *_save; jpayne@68: _save = NULL; jpayne@68: Py_UNBLOCK_THREADS jpayne@68: __Pyx_FastGIL_Remember(); jpayne@68: #endif jpayne@68: /*try:*/ { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1146 jpayne@68: * while 1: jpayne@68: * with nogil: jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * if retval < 0: jpayne@68: */ jpayne@68: __pyx_v_retval = ks_getuntil(__pyx_v_self->kstream, '\n', (&__pyx_v_self->buffer), (&__pyx_v_dret)); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1145 jpayne@68: * cdef int retval = 0 jpayne@68: * while 1: jpayne@68: * with nogil: # <<<<<<<<<<<<<< jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: */ jpayne@68: /*finally:*/ { jpayne@68: /*normal exit:*/{ jpayne@68: #ifdef WITH_THREAD jpayne@68: __Pyx_FastGIL_Forget(); jpayne@68: Py_BLOCK_THREADS jpayne@68: #endif jpayne@68: goto __pyx_L9; jpayne@68: } jpayne@68: __pyx_L9:; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1148 jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * #raise IOError('gzip error: %s' % buildGzipError( self.fh )) jpayne@68: */ jpayne@68: __pyx_t_1 = (__pyx_v_retval < 0); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1149 jpayne@68: * jpayne@68: * if retval < 0: jpayne@68: * break # <<<<<<<<<<<<<< jpayne@68: * #raise IOError('gzip error: %s' % buildGzipError( self.fh )) jpayne@68: * jpayne@68: */ jpayne@68: goto __pyx_L4_break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1148 jpayne@68: * retval = ks_getuntil(self.kstream, b'\n', &self.buffer, &dret) jpayne@68: * jpayne@68: * if retval < 0: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * #raise IOError('gzip error: %s' % buildGzipError( self.fh )) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1152 jpayne@68: * #raise IOError('gzip error: %s' % buildGzipError( self.fh )) jpayne@68: * jpayne@68: * b = self.buffer.s # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # skip comments jpayne@68: */ jpayne@68: __pyx_t_2 = __pyx_v_self->buffer.s; jpayne@68: __pyx_v_b = __pyx_t_2; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1155 jpayne@68: * jpayne@68: * # skip comments jpayne@68: * if (b[0] == b'#'): # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = ((__pyx_v_b[0]) == '#'); jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1156 jpayne@68: * # skip comments jpayne@68: * if (b[0] == b'#'): jpayne@68: * continue # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # skip empty lines jpayne@68: */ jpayne@68: goto __pyx_L3_continue; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1155 jpayne@68: * jpayne@68: * # skip comments jpayne@68: * if (b[0] == b'#'): # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1159 jpayne@68: * jpayne@68: * # skip empty lines jpayne@68: * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = ((__pyx_v_b[0]) == '\x00'); jpayne@68: if (!__pyx_t_3) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_3; jpayne@68: goto __pyx_L13_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_3 = ((__pyx_v_b[0]) == '\n'); jpayne@68: if (!__pyx_t_3) { jpayne@68: } else { jpayne@68: __pyx_t_1 = __pyx_t_3; jpayne@68: goto __pyx_L13_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_3 = ((__pyx_v_b[0]) == '\r'); jpayne@68: __pyx_t_1 = __pyx_t_3; jpayne@68: __pyx_L13_bool_binop_done:; jpayne@68: if (__pyx_t_1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1160 jpayne@68: * # skip empty lines jpayne@68: * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': jpayne@68: * continue # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # gzgets terminates at \n, no need to test jpayne@68: */ jpayne@68: goto __pyx_L3_continue; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1159 jpayne@68: * jpayne@68: * # skip empty lines jpayne@68: * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1165 jpayne@68: * jpayne@68: * # parser creates a copy jpayne@68: * return self.parser.parse(b, self.buffer.l) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_4 = ((struct __pyx_vtabstruct_5pysam_9libctabix_Parser *)__pyx_v_self->parser->__pyx_vtab)->parse(__pyx_v_self->parser, __pyx_v_b, __pyx_v_self->buffer.l); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1165, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __pyx_r = __pyx_t_4; jpayne@68: __pyx_t_4 = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L3_continue:; jpayne@68: } jpayne@68: __pyx_L4_break:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1167 jpayne@68: * return self.parser.parse(b, self.buffer.l) jpayne@68: * jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __dealloc__(self): jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); jpayne@68: __PYX_ERR(0, 1167, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1139 jpayne@68: * return self jpayne@68: * jpayne@68: * cdef __cnext__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char * b jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1169 jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: * def __dealloc__(self): # <<<<<<<<<<<<<< jpayne@68: * free(self.buffer.s) jpayne@68: * ks_destroy(self.kstream) jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static void __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static void __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_5__dealloc__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_4__dealloc__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: } jpayne@68: jpayne@68: static void __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) { jpayne@68: __Pyx_TraceDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1169, 0, __PYX_ERR(0, 1169, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1170 jpayne@68: * jpayne@68: * def __dealloc__(self): jpayne@68: * free(self.buffer.s) # <<<<<<<<<<<<<< jpayne@68: * ks_destroy(self.kstream) jpayne@68: * bgzf_close(self.fh) jpayne@68: */ jpayne@68: free(__pyx_v_self->buffer.s); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1171 jpayne@68: * def __dealloc__(self): jpayne@68: * free(self.buffer.s) jpayne@68: * ks_destroy(self.kstream) # <<<<<<<<<<<<<< jpayne@68: * bgzf_close(self.fh) jpayne@68: * jpayne@68: */ jpayne@68: ks_destroy(__pyx_v_self->kstream); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1172 jpayne@68: * free(self.buffer.s) jpayne@68: * ks_destroy(self.kstream) jpayne@68: * bgzf_close(self.fh) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: */ jpayne@68: (void)(bgzf_close(__pyx_v_self->fh)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1169 jpayne@68: * raise StopIteration jpayne@68: * jpayne@68: * def __dealloc__(self): # <<<<<<<<<<<<<< jpayne@68: * free(self.buffer.s) jpayne@68: * ks_destroy(self.kstream) jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_WriteUnraisable("pysam.libctabix.tabix_file_iterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); jpayne@68: __pyx_L0:; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1174 jpayne@68: * bgzf_close(self.fh) jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * return self.__cnext__() jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(PyObject *__pyx_v_self); /*proto*/ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(PyObject *__pyx_v_self) { jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_6__next__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 1174, 0, __PYX_ERR(0, 1174, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1175 jpayne@68: * jpayne@68: * def __next__(self): jpayne@68: * return self.__cnext__() # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1175, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_r = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1174 jpayne@68: * bgzf_close(self.fh) jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * return self.__cnext__() jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__, "tabix_file_iterator.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__46) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__, "tabix_file_iterator.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__47) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_file_iterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1183 jpayne@68: * Permits the use of file-like objects for example from the gzip module. jpayne@68: * ''' jpayne@68: * def __init__(self, infile, parser): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_22tabix_generic_iterator___init__, "tabix_generic_iterator.__init__(self, infile, parser)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_1__init__ = {"__init__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_22tabix_generic_iterator___init__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_self = 0; jpayne@68: PyObject *__pyx_v_infile = 0; jpayne@68: PyObject *__pyx_v_parser = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_infile,&__pyx_n_s_parser,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_infile)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v_self = values[0]; jpayne@68: __pyx_v_infile = values[1]; jpayne@68: __pyx_v_parser = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 1183, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_22tabix_generic_iterator___init__(__pyx_self, __pyx_v_self, __pyx_v_infile, __pyx_v_parser); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: int __pyx_t_3; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__48) jpayne@68: __Pyx_RefNannySetupContext("__init__", 1); jpayne@68: __Pyx_TraceCall("__init__", __pyx_f[0], 1183, 0, __PYX_ERR(0, 1183, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1185 jpayne@68: * def __init__(self, infile, parser): jpayne@68: * jpayne@68: * self.infile = infile # <<<<<<<<<<<<<< jpayne@68: * if self.infile.closed: jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: */ jpayne@68: if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_infile, __pyx_v_infile) < 0) __PYX_ERR(0, 1185, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1186 jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: * if self.infile.closed: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * self.parser = parser jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_infile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1186, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_closed); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1186, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 1186, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(__pyx_t_3)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1187 jpayne@68: * self.infile = infile jpayne@68: * if self.infile.closed: jpayne@68: * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<< jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1187, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 1187, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1186 jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: * if self.infile.closed: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * self.parser = parser jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1188 jpayne@68: * if self.infile.closed: jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * self.parser = parser # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: */ jpayne@68: if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_parser, __pyx_v_parser) < 0) __PYX_ERR(0, 1188, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1183 jpayne@68: * Permits the use of file-like objects for example from the gzip module. jpayne@68: * ''' jpayne@68: * def __init__(self, infile, parser): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1190 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_2__iter__, "tabix_generic_iterator.__iter__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_3__iter__ = {"__iter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_3__iter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_2__iter__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_self = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1190, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__iter__") < 0)) __PYX_ERR(0, 1190, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_self = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__iter__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 1190, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_2__iter__(__pyx_self, __pyx_v_self); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__49) jpayne@68: __Pyx_RefNannySetupContext("__iter__", 1); jpayne@68: __Pyx_TraceCall("__iter__", __pyx_f[0], 1190, 0, __PYX_ERR(0, 1190, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1191 jpayne@68: * jpayne@68: * def __iter__(self): jpayne@68: * return self # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # cython version - required for python 3 jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v_self); jpayne@68: __pyx_r = __pyx_v_self; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1190 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1194 jpayne@68: * jpayne@68: * # cython version - required for python 3 jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char * b jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_4__next__, "tabix_generic_iterator.__next__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_5__next__ = {"__next__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_5__next__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_22tabix_generic_iterator_4__next__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_self = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1194, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__next__") < 0)) __PYX_ERR(0, 1194, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v_self = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__next__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 1194, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_4__next__(__pyx_self, __pyx_v_self); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { jpayne@68: char *__pyx_v_b; jpayne@68: char *__pyx_v_cpy; jpayne@68: size_t __pyx_v_nbytes; jpayne@68: PyObject *__pyx_v_encoding = NULL; jpayne@68: PyObject *__pyx_v_line = NULL; jpayne@68: PyObject *__pyx_v_s = NULL; jpayne@68: PyObject *__pyx_v_bytes_cpy = NULL; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: unsigned int __pyx_t_4; jpayne@68: int __pyx_t_5; jpayne@68: int __pyx_t_6; jpayne@68: struct __pyx_opt_args_5pysam_9libcutils_force_bytes __pyx_t_7; jpayne@68: char *__pyx_t_8; jpayne@68: Py_ssize_t __pyx_t_9; jpayne@68: PyObject *__pyx_t_10 = NULL; jpayne@68: PyObject *__pyx_t_11 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__50) jpayne@68: __Pyx_RefNannySetupContext("__next__", 1); jpayne@68: __Pyx_TraceCall("__next__", __pyx_f[0], 1194, 0, __PYX_ERR(0, 1194, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1200 jpayne@68: * cdef size_t nbytes jpayne@68: * jpayne@68: * encoding = self.parser.get_encoding() # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # note that GzipFile.close() does not close the file jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1200, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_get_encoding); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1200, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_t_2 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_2)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_2); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_2, NULL}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1200, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v_encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1204 jpayne@68: * # note that GzipFile.close() does not close the file jpayne@68: * # reading is still possible. jpayne@68: * if self.infile.closed: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_infile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1204, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_closed); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1204, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 1204, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(__pyx_t_5)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1205 jpayne@68: * # reading is still possible. jpayne@68: * if self.infile.closed: jpayne@68: * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * while 1: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__45, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1205, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_Raise(__pyx_t_3, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __PYX_ERR(0, 1205, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1204 jpayne@68: * # note that GzipFile.close() does not close the file jpayne@68: * # reading is still possible. jpayne@68: * if self.infile.closed: # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1207 jpayne@68: * raise ValueError("I/O operation on closed file.") jpayne@68: * jpayne@68: * while 1: # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * line = self.infile.readline() jpayne@68: */ jpayne@68: while (1) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1209 jpayne@68: * while 1: jpayne@68: * jpayne@68: * line = self.infile.readline() # <<<<<<<<<<<<<< jpayne@68: * if not line: jpayne@68: * break jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_infile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1209, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_readline); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1209, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_1)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_1, NULL}; jpayne@68: __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1209, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __Pyx_XDECREF_SET(__pyx_v_line, __pyx_t_3); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1210 jpayne@68: * jpayne@68: * line = self.infile.readline() jpayne@68: * if not line: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_line); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 1210, __pyx_L1_error) jpayne@68: __pyx_t_6 = (!__pyx_t_5); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1211 jpayne@68: * line = self.infile.readline() jpayne@68: * if not line: jpayne@68: * break # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * s = force_bytes(line, encoding) jpayne@68: */ jpayne@68: goto __pyx_L5_break; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1210 jpayne@68: * jpayne@68: * line = self.infile.readline() jpayne@68: * if not line: # <<<<<<<<<<<<<< jpayne@68: * break jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1213 jpayne@68: * break jpayne@68: * jpayne@68: * s = force_bytes(line, encoding) # <<<<<<<<<<<<<< jpayne@68: * b = s jpayne@68: * nbytes = len(line) jpayne@68: */ jpayne@68: __pyx_t_7.__pyx_n = 1; jpayne@68: __pyx_t_7.encoding = __pyx_v_encoding; jpayne@68: __pyx_t_3 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_line, &__pyx_t_7); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1213, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF_SET(__pyx_v_s, ((PyObject*)__pyx_t_3)); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1214 jpayne@68: * jpayne@68: * s = force_bytes(line, encoding) jpayne@68: * b = s # <<<<<<<<<<<<<< jpayne@68: * nbytes = len(line) jpayne@68: * assert b[nbytes] == b'\0' jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_s == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 1214, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_8 = __Pyx_PyBytes_AsWritableString(__pyx_v_s); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 1214, __pyx_L1_error) jpayne@68: __pyx_v_b = __pyx_t_8; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1215 jpayne@68: * s = force_bytes(line, encoding) jpayne@68: * b = s jpayne@68: * nbytes = len(line) # <<<<<<<<<<<<<< jpayne@68: * assert b[nbytes] == b'\0' jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_9 = PyObject_Length(__pyx_v_line); if (unlikely(__pyx_t_9 == ((Py_ssize_t)-1))) __PYX_ERR(0, 1215, __pyx_L1_error) jpayne@68: __pyx_v_nbytes = __pyx_t_9; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1216 jpayne@68: * b = s jpayne@68: * nbytes = len(line) jpayne@68: * assert b[nbytes] == b'\0' # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # skip comments jpayne@68: */ jpayne@68: #ifndef CYTHON_WITHOUT_ASSERTIONS jpayne@68: if (unlikely(__pyx_assertions_enabled())) { jpayne@68: __pyx_t_6 = ((__pyx_v_b[__pyx_v_nbytes]) == '\x00'); jpayne@68: if (unlikely(!__pyx_t_6)) { jpayne@68: __Pyx_Raise(__pyx_builtin_AssertionError, 0, 0, 0); jpayne@68: __PYX_ERR(0, 1216, __pyx_L1_error) jpayne@68: } jpayne@68: } jpayne@68: #else jpayne@68: if ((1)); else __PYX_ERR(0, 1216, __pyx_L1_error) jpayne@68: #endif jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1219 jpayne@68: * jpayne@68: * # skip comments jpayne@68: * if b[0] == b'#': # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_6 = ((__pyx_v_b[0]) == '#'); jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1220 jpayne@68: * # skip comments jpayne@68: * if b[0] == b'#': jpayne@68: * continue # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # skip empty lines jpayne@68: */ jpayne@68: goto __pyx_L4_continue; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1219 jpayne@68: * jpayne@68: * # skip comments jpayne@68: * if b[0] == b'#': # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1223 jpayne@68: * jpayne@68: * # skip empty lines jpayne@68: * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_5 = ((__pyx_v_b[0]) == '\x00'); jpayne@68: if (!__pyx_t_5) { jpayne@68: } else { jpayne@68: __pyx_t_6 = __pyx_t_5; jpayne@68: goto __pyx_L9_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_5 = ((__pyx_v_b[0]) == '\n'); jpayne@68: if (!__pyx_t_5) { jpayne@68: } else { jpayne@68: __pyx_t_6 = __pyx_t_5; jpayne@68: goto __pyx_L9_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_5 = ((__pyx_v_b[0]) == '\r'); jpayne@68: __pyx_t_6 = __pyx_t_5; jpayne@68: __pyx_L9_bool_binop_done:; jpayne@68: if (__pyx_t_6) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1224 jpayne@68: * # skip empty lines jpayne@68: * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': jpayne@68: * continue # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # make sure that entry is complete jpayne@68: */ jpayne@68: goto __pyx_L4_continue; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1223 jpayne@68: * jpayne@68: * # skip empty lines jpayne@68: * if b[0] == b'\0' or b[0] == b'\n' or b[0] == b'\r': # <<<<<<<<<<<<<< jpayne@68: * continue jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1227 jpayne@68: * jpayne@68: * # make sure that entry is complete jpayne@68: * if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r': # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("incomplete line at %s" % line) jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n'); jpayne@68: if (__pyx_t_5) { jpayne@68: } else { jpayne@68: __pyx_t_6 = __pyx_t_5; jpayne@68: goto __pyx_L13_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r'); jpayne@68: __pyx_t_6 = __pyx_t_5; jpayne@68: __pyx_L13_bool_binop_done:; jpayne@68: if (unlikely(__pyx_t_6)) { jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1228 jpayne@68: * # make sure that entry is complete jpayne@68: * if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r': jpayne@68: * raise ValueError("incomplete line at %s" % line) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * bytes_cpy = b jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_incomplete_line_at_s, __pyx_v_line); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1228, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1228, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_t_2, 0, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __PYX_ERR(0, 1228, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1227 jpayne@68: * jpayne@68: * # make sure that entry is complete jpayne@68: * if b[nbytes-1] != b'\n' and b[nbytes-1] != b'\r': # <<<<<<<<<<<<<< jpayne@68: * raise ValueError("incomplete line at %s" % line) jpayne@68: * jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1230 jpayne@68: * raise ValueError("incomplete line at %s" % line) jpayne@68: * jpayne@68: * bytes_cpy = b # <<<<<<<<<<<<<< jpayne@68: * cpy = bytes_cpy jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1230, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = __pyx_t_2; jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: __pyx_v_bytes_cpy = ((PyObject*)__pyx_t_3); jpayne@68: __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1231 jpayne@68: * jpayne@68: * bytes_cpy = b jpayne@68: * cpy = bytes_cpy # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * return self.parser(cpy, nbytes) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v_bytes_cpy == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); jpayne@68: __PYX_ERR(0, 1231, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_8 = __Pyx_PyBytes_AsWritableString(__pyx_v_bytes_cpy); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 1231, __pyx_L1_error) jpayne@68: __pyx_v_cpy = ((char *)__pyx_t_8); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1233 jpayne@68: * cpy = bytes_cpy jpayne@68: * jpayne@68: * return self.parser(cpy, nbytes) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1233, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_cpy); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1233, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_10 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 1233, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_10); jpayne@68: __pyx_t_11 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_11)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_11); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[3] = {__pyx_t_11, __pyx_t_1, __pyx_t_10}; jpayne@68: __pyx_t_3 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; jpayne@68: if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1233, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_r = __pyx_t_3; jpayne@68: __pyx_t_3 = 0; jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L4_continue:; jpayne@68: } jpayne@68: __pyx_L5_break:; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1235 jpayne@68: * return self.parser(cpy, nbytes) jpayne@68: * jpayne@68: * raise StopIteration # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); jpayne@68: __PYX_ERR(0, 1235, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1194 jpayne@68: * jpayne@68: * # cython version - required for python 3 jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char * b jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_10); jpayne@68: __Pyx_XDECREF(__pyx_t_11); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_generic_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v_encoding); jpayne@68: __Pyx_XDECREF(__pyx_v_line); jpayne@68: __Pyx_XDECREF(__pyx_v_s); jpayne@68: __Pyx_XDECREF(__pyx_v_bytes_cpy); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1238 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<< jpayne@68: * """return an iterator over all entries in a file. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5tabix_iterator(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_4tabix_iterator, "tabix_iterator(infile, parser)\nreturn an iterator over all entries in a file.\n \n Results are returned parsed as specified by the *parser*. If\n *parser* is None, the results are returned as an unparsed string.\n Otherwise, *parser* is assumed to be a functor that will return\n parsed data (see for example :class:`~pysam.asTuple` and\n :class:`~pysam.asGTF`).\n\n "); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_5tabix_iterator = {"tabix_iterator", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5tabix_iterator, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_4tabix_iterator}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_5tabix_iterator(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v_infile = 0; jpayne@68: PyObject *__pyx_v_parser = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[2] = {0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("tabix_iterator (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_infile,&__pyx_n_s_parser,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_infile)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1238, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_parser)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1238, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); __PYX_ERR(0, 1238, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "tabix_iterator") < 0)) __PYX_ERR(0, 1238, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 2)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: } jpayne@68: __pyx_v_infile = values[0]; jpayne@68: __pyx_v_parser = values[1]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 1238, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_4tabix_iterator(__pyx_self, __pyx_v_infile, __pyx_v_parser); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: unsigned int __pyx_t_4; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__51) jpayne@68: __Pyx_RefNannySetupContext("tabix_iterator", 1); jpayne@68: __Pyx_TraceCall("tabix_iterator", __pyx_f[0], 1238, 0, __PYX_ERR(0, 1238, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1248 jpayne@68: * jpayne@68: * """ jpayne@68: * return tabix_generic_iterator(infile, parser) # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_tabix_generic_iterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1248, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_t_3 = NULL; jpayne@68: __pyx_t_4 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (unlikely(PyMethod_Check(__pyx_t_2))) { jpayne@68: __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); jpayne@68: if (likely(__pyx_t_3)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); jpayne@68: __Pyx_INCREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_2, function); jpayne@68: __pyx_t_4 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[3] = {__pyx_t_3, __pyx_v_infile, __pyx_v_parser}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 2+__pyx_t_4); jpayne@68: __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1248, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: } jpayne@68: __pyx_r = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1238 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<< jpayne@68: * """return an iterator over all entries in a file. jpayne@68: * jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9Tabixfile___reduce_cython__, "Tabixfile.__reduce_cython__(self)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9Tabixfile_1__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile___reduce_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: if (unlikely(__pyx_nargs > 0)) { jpayne@68: __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} jpayne@68: if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9Tabixfile___reduce_cython__(((struct __pyx_obj_5pysam_9libctabix_Tabixfile *)__pyx_v_self)); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile___reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__52) jpayne@68: __Pyx_RefNannySetupContext("__reduce_cython__", 1); jpayne@68: __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":2 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); jpayne@68: __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Tabixfile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_9Tabixfile_2__setstate_cython__, "Tabixfile.__setstate_cython__(self, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9Tabixfile_3__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile_2__setstate_cython__}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__(PyObject *__pyx_v_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[1] = {0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setstate_cython__") < 0)) __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 1)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: } jpayne@68: __pyx_v___pyx_state = values[0]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Tabixfile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_9Tabixfile_2__setstate_cython__(((struct __pyx_obj_5pysam_9libctabix_Tabixfile *)__pyx_v_self), __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_9Tabixfile_2__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_9libctabix_Tabixfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__53) jpayne@68: __Pyx_RefNannySetupContext("__setstate_cython__", 1); jpayne@68: __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); jpayne@68: __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_AddTraceback("pysam.libctabix.Tabixfile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_7__pyx_unpickle_Parser(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_6__pyx_unpickle_Parser, "__pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_7__pyx_unpickle_Parser = {"__pyx_unpickle_Parser", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7__pyx_unpickle_Parser, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6__pyx_unpickle_Parser}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_7__pyx_unpickle_Parser(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_type = 0; jpayne@68: long __pyx_v___pyx_checksum; jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_Parser (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Parser", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Parser", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_Parser") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v___pyx_type = values[0]; jpayne@68: __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_v___pyx_state = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Parser", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_Parser", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_6__pyx_unpickle_Parser(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_6__pyx_unpickle_Parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_v___pyx_PickleError = 0; jpayne@68: PyObject *__pyx_v___pyx_result = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__54) jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_Parser", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_Parser", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = Parser.__new__(__pyx_type) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_n_s_PickleError); jpayne@68: __Pyx_GIVEREF(__pyx_n_s_PickleError); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __pyx_v___pyx_PickleError = __pyx_t_1; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<< jpayne@68: * __pyx_result = Parser.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = Parser.__new__(__pyx_type) # <<<<<<<<<<<<<< jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v___pyx_result = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = Parser.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v___pyx_state != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * __pyx_result = Parser.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(((struct __pyx_obj_5pysam_9libctabix_Parser *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = Parser.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":10 jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result # <<<<<<<<<<<<<< jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v___pyx_result); jpayne@68: __pyx_r = __pyx_v___pyx_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_Parser", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_PickleError); jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_Parser__set_state(struct __pyx_obj_5pysam_9libctabix_Parser *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: Py_ssize_t __pyx_t_3; jpayne@68: int __pyx_t_4; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: unsigned int __pyx_t_8; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_Parser__set_state", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_Parser__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<< jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF(__pyx_v___pyx_result->encoding); jpayne@68: __Pyx_DECREF(__pyx_v___pyx_result->encoding); jpayne@68: __pyx_v___pyx_result->encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); jpayne@68: __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_4 = (__pyx_t_3 > 1); jpayne@68: if (__pyx_t_4) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":14 jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_8 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_6))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_6, function); jpayne@68: __pyx_t_8 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_Parser__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asTuple(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9__pyx_unpickle_asTuple(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_8__pyx_unpickle_asTuple, "__pyx_unpickle_asTuple(__pyx_type, long __pyx_checksum, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_9__pyx_unpickle_asTuple = {"__pyx_unpickle_asTuple", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9__pyx_unpickle_asTuple, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_8__pyx_unpickle_asTuple}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_9__pyx_unpickle_asTuple(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_type = 0; jpayne@68: long __pyx_v___pyx_checksum; jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asTuple (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asTuple", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asTuple", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asTuple") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v___pyx_type = values[0]; jpayne@68: __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_v___pyx_state = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asTuple", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asTuple", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_8__pyx_unpickle_asTuple(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_8__pyx_unpickle_asTuple(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_v___pyx_PickleError = 0; jpayne@68: PyObject *__pyx_v___pyx_result = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__57) jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asTuple", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asTuple", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asTuple.__new__(__pyx_type) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_n_s_PickleError); jpayne@68: __Pyx_GIVEREF(__pyx_n_s_PickleError); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __pyx_v___pyx_PickleError = __pyx_t_1; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<< jpayne@68: * __pyx_result = asTuple.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asTuple.__new__(__pyx_type) # <<<<<<<<<<<<<< jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asTuple), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v___pyx_result = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asTuple.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v___pyx_state != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * __pyx_result = asTuple.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(((struct __pyx_obj_5pysam_9libctabix_asTuple *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asTuple.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":10 jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result # <<<<<<<<<<<<<< jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v___pyx_result); jpayne@68: __pyx_r = __pyx_v___pyx_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asTuple(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asTuple", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_PickleError); jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asTuple__set_state(struct __pyx_obj_5pysam_9libctabix_asTuple *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: Py_ssize_t __pyx_t_3; jpayne@68: int __pyx_t_4; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: unsigned int __pyx_t_8; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asTuple__set_state", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asTuple__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<< jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); jpayne@68: __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_4 = (__pyx_t_3 > 1); jpayne@68: if (__pyx_t_4) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":14 jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_8 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_6))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_6, function); jpayne@68: __pyx_t_8 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asTuple__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asTuple__set_state(asTuple __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asTuple__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_11__pyx_unpickle_asGFF3(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_10__pyx_unpickle_asGFF3, "__pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_11__pyx_unpickle_asGFF3 = {"__pyx_unpickle_asGFF3", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_11__pyx_unpickle_asGFF3, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10__pyx_unpickle_asGFF3}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_11__pyx_unpickle_asGFF3(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_type = 0; jpayne@68: long __pyx_v___pyx_checksum; jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asGFF3 (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGFF3", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGFF3", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asGFF3") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v___pyx_type = values[0]; jpayne@68: __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_v___pyx_state = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGFF3", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGFF3", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_10__pyx_unpickle_asGFF3(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_10__pyx_unpickle_asGFF3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_v___pyx_PickleError = 0; jpayne@68: PyObject *__pyx_v___pyx_result = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__58) jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asGFF3", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asGFF3", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGFF3.__new__(__pyx_type) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_n_s_PickleError); jpayne@68: __Pyx_GIVEREF(__pyx_n_s_PickleError); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __pyx_v___pyx_PickleError = __pyx_t_1; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<< jpayne@68: * __pyx_result = asGFF3.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGFF3.__new__(__pyx_type) # <<<<<<<<<<<<<< jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asGFF3), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v___pyx_result = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGFF3.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v___pyx_state != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * __pyx_result = asGFF3.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGFF3.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":10 jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result # <<<<<<<<<<<<<< jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v___pyx_result); jpayne@68: __pyx_r = __pyx_v___pyx_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGFF3", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_PickleError); jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGFF3__set_state(struct __pyx_obj_5pysam_9libctabix_asGFF3 *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: Py_ssize_t __pyx_t_3; jpayne@68: int __pyx_t_4; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: unsigned int __pyx_t_8; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asGFF3__set_state", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asGFF3__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<< jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); jpayne@68: __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_4 = (__pyx_t_3 > 1); jpayne@68: if (__pyx_t_4) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":14 jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_8 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_6))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_6, function); jpayne@68: __pyx_t_8 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGFF3__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asGTF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13__pyx_unpickle_asGTF(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_12__pyx_unpickle_asGTF, "__pyx_unpickle_asGTF(__pyx_type, long __pyx_checksum, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_13__pyx_unpickle_asGTF = {"__pyx_unpickle_asGTF", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13__pyx_unpickle_asGTF, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_12__pyx_unpickle_asGTF}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_13__pyx_unpickle_asGTF(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_type = 0; jpayne@68: long __pyx_v___pyx_checksum; jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asGTF (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGTF", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGTF", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asGTF") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v___pyx_type = values[0]; jpayne@68: __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_v___pyx_state = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asGTF", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGTF", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_12__pyx_unpickle_asGTF(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_12__pyx_unpickle_asGTF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_v___pyx_PickleError = 0; jpayne@68: PyObject *__pyx_v___pyx_result = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__59) jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asGTF", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asGTF", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGTF.__new__(__pyx_type) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_n_s_PickleError); jpayne@68: __Pyx_GIVEREF(__pyx_n_s_PickleError); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __pyx_v___pyx_PickleError = __pyx_t_1; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<< jpayne@68: * __pyx_result = asGTF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGTF.__new__(__pyx_type) # <<<<<<<<<<<<<< jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asGTF), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v___pyx_result = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGTF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v___pyx_state != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * __pyx_result = asGTF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(((struct __pyx_obj_5pysam_9libctabix_asGTF *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asGTF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":10 jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result # <<<<<<<<<<<<<< jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v___pyx_result); jpayne@68: __pyx_r = __pyx_v___pyx_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asGTF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGTF", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_PickleError); jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asGTF__set_state(struct __pyx_obj_5pysam_9libctabix_asGTF *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: Py_ssize_t __pyx_t_3; jpayne@68: int __pyx_t_4; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: unsigned int __pyx_t_8; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asGTF__set_state", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asGTF__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<< jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); jpayne@68: __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_4 = (__pyx_t_3 > 1); jpayne@68: if (__pyx_t_4) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":14 jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_8 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_6))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_6, function); jpayne@68: __pyx_t_8 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asGTF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGTF__set_state(asGTF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asGTF__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_15__pyx_unpickle_asBed(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_14__pyx_unpickle_asBed, "__pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_15__pyx_unpickle_asBed = {"__pyx_unpickle_asBed", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_15__pyx_unpickle_asBed, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14__pyx_unpickle_asBed}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_15__pyx_unpickle_asBed(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_type = 0; jpayne@68: long __pyx_v___pyx_checksum; jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asBed (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asBed", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asBed", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asBed") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v___pyx_type = values[0]; jpayne@68: __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_v___pyx_state = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asBed", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asBed", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_14__pyx_unpickle_asBed(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_14__pyx_unpickle_asBed(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_v___pyx_PickleError = 0; jpayne@68: PyObject *__pyx_v___pyx_result = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__60) jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asBed", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asBed", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asBed.__new__(__pyx_type) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_n_s_PickleError); jpayne@68: __Pyx_GIVEREF(__pyx_n_s_PickleError); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __pyx_v___pyx_PickleError = __pyx_t_1; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<< jpayne@68: * __pyx_result = asBed.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asBed.__new__(__pyx_type) # <<<<<<<<<<<<<< jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asBed), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v___pyx_result = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asBed.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v___pyx_state != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * __pyx_result = asBed.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(((struct __pyx_obj_5pysam_9libctabix_asBed *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asBed.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":10 jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result # <<<<<<<<<<<<<< jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v___pyx_result); jpayne@68: __pyx_r = __pyx_v___pyx_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asBed", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_PickleError); jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asBed__set_state(struct __pyx_obj_5pysam_9libctabix_asBed *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: Py_ssize_t __pyx_t_3; jpayne@68: int __pyx_t_4; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: unsigned int __pyx_t_8; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asBed__set_state", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asBed__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<< jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); jpayne@68: __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_4 = (__pyx_t_3 > 1); jpayne@68: if (__pyx_t_4) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":14 jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_8 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_6))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_6, function); jpayne@68: __pyx_t_8 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asBed__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asVCF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* Python wrapper */ jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_17__pyx_unpickle_asVCF(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ); /*proto*/ jpayne@68: PyDoc_STRVAR(__pyx_doc_5pysam_9libctabix_16__pyx_unpickle_asVCF, "__pyx_unpickle_asVCF(__pyx_type, long __pyx_checksum, __pyx_state)"); jpayne@68: static PyMethodDef __pyx_mdef_5pysam_9libctabix_17__pyx_unpickle_asVCF = {"__pyx_unpickle_asVCF", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_17__pyx_unpickle_asVCF, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16__pyx_unpickle_asVCF}; jpayne@68: static PyObject *__pyx_pw_5pysam_9libctabix_17__pyx_unpickle_asVCF(PyObject *__pyx_self, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds jpayne@68: #else jpayne@68: PyObject *__pyx_args, PyObject *__pyx_kwds jpayne@68: #endif jpayne@68: ) { jpayne@68: PyObject *__pyx_v___pyx_type = 0; jpayne@68: long __pyx_v___pyx_checksum; jpayne@68: PyObject *__pyx_v___pyx_state = 0; jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: CYTHON_UNUSED Py_ssize_t __pyx_nargs; jpayne@68: #endif jpayne@68: CYTHON_UNUSED PyObject *const *__pyx_kwvalues; jpayne@68: PyObject* values[3] = {0,0,0}; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: PyObject *__pyx_r = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asVCF (wrapper)", 0); jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); jpayne@68: #else jpayne@68: __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; jpayne@68: #endif jpayne@68: #endif jpayne@68: __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); jpayne@68: { jpayne@68: PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; jpayne@68: if (__pyx_kwds) { jpayne@68: Py_ssize_t kw_args; jpayne@68: switch (__pyx_nargs) { jpayne@68: case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 0: break; jpayne@68: default: goto __pyx_L5_argtuple_error; jpayne@68: } jpayne@68: kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); jpayne@68: switch (__pyx_nargs) { jpayne@68: case 0: jpayne@68: if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_type)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else goto __pyx_L5_argtuple_error; jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 1: jpayne@68: if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_checksum)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCF", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { jpayne@68: (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); jpayne@68: kw_args--; jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: else { jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCF", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } jpayne@68: if (unlikely(kw_args > 0)) { jpayne@68: const Py_ssize_t kwd_pos_args = __pyx_nargs; jpayne@68: if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__pyx_unpickle_asVCF") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: } jpayne@68: } else if (unlikely(__pyx_nargs != 3)) { jpayne@68: goto __pyx_L5_argtuple_error; jpayne@68: } else { jpayne@68: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); jpayne@68: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); jpayne@68: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); jpayne@68: } jpayne@68: __pyx_v___pyx_type = values[0]; jpayne@68: __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_v___pyx_state = values[2]; jpayne@68: } jpayne@68: goto __pyx_L6_skip; jpayne@68: __pyx_L5_argtuple_error:; jpayne@68: __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_asVCF", 1, 3, 3, __pyx_nargs); __PYX_ERR(1, 1, __pyx_L3_error) jpayne@68: __pyx_L6_skip:; jpayne@68: goto __pyx_L4_argument_unpacking_done; jpayne@68: __pyx_L3_error:; jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asVCF", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return NULL; jpayne@68: __pyx_L4_argument_unpacking_done:; jpayne@68: __pyx_r = __pyx_pf_5pysam_9libctabix_16__pyx_unpickle_asVCF(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); jpayne@68: jpayne@68: /* function exit code */ jpayne@68: { jpayne@68: Py_ssize_t __pyx_temp; jpayne@68: for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { jpayne@68: __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); jpayne@68: } jpayne@68: } jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_pf_5pysam_9libctabix_16__pyx_unpickle_asVCF(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_v___pyx_PickleError = 0; jpayne@68: PyObject *__pyx_v___pyx_result = 0; jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: unsigned int __pyx_t_5; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_TraceFrameInit(__pyx_codeobj__61) jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asVCF", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asVCF", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__55, Py_NE)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":5 jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asVCF.__new__(__pyx_type) jpayne@68: */ jpayne@68: __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_n_s_PickleError); jpayne@68: __Pyx_GIVEREF(__pyx_n_s_PickleError); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError)) __PYX_ERR(1, 5, __pyx_L1_error); jpayne@68: __pyx_t_3 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_INCREF(__pyx_t_1); jpayne@68: __pyx_v___pyx_PickleError = __pyx_t_1; jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":6 jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum # <<<<<<<<<<<<<< jpayne@68: * __pyx_result = asVCF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_Raise(__pyx_v___pyx_PickleError, __pyx_t_1, 0, 0); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __PYX_ERR(1, 6, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":7 jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asVCF.__new__(__pyx_type) # <<<<<<<<<<<<<< jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_5pysam_9libctabix_asVCF), __pyx_n_s_new); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __pyx_t_4 = NULL; jpayne@68: __pyx_t_5 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_3))) { jpayne@68: __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); jpayne@68: if (likely(__pyx_t_4)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_3, function); jpayne@68: __pyx_t_5 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v___pyx_type}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: } jpayne@68: __pyx_v___pyx_result = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asVCF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: __pyx_t_2 = (__pyx_v___pyx_state != Py_None); jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":9 jpayne@68: * __pyx_result = asVCF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) # <<<<<<<<<<<<<< jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): jpayne@68: */ jpayne@68: if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None) || __Pyx_RaiseUnexpectedTypeError("tuple", __pyx_v___pyx_state))) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __pyx_t_1 = __pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(((struct __pyx_obj_5pysam_9libctabix_asVCF *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":8 jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: * __pyx_result = asVCF.__new__(__pyx_type) jpayne@68: * if __pyx_state is not None: # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":10 jpayne@68: * if __pyx_state is not None: jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result # <<<<<<<<<<<<<< jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: */ jpayne@68: __Pyx_XDECREF(__pyx_r); jpayne@68: __Pyx_INCREF(__pyx_v___pyx_result); jpayne@68: __pyx_r = __pyx_v___pyx_result; jpayne@68: goto __pyx_L0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asVCF(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asVCF", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = NULL; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_PickleError); jpayne@68: __Pyx_XDECREF(__pyx_v___pyx_result); jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: static PyObject *__pyx_f_5pysam_9libctabix___pyx_unpickle_asVCF__set_state(struct __pyx_obj_5pysam_9libctabix_asVCF *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { jpayne@68: PyObject *__pyx_r = NULL; jpayne@68: __Pyx_TraceDeclarations jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_t_2; jpayne@68: Py_ssize_t __pyx_t_3; jpayne@68: int __pyx_t_4; jpayne@68: PyObject *__pyx_t_5 = NULL; jpayne@68: PyObject *__pyx_t_6 = NULL; jpayne@68: PyObject *__pyx_t_7 = NULL; jpayne@68: unsigned int __pyx_t_8; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__pyx_unpickle_asVCF__set_state", 1); jpayne@68: __Pyx_TraceCall("__pyx_unpickle_asVCF__set_state", __pyx_f[1], 11, 0, __PYX_ERR(1, 11, __pyx_L1_error)); jpayne@68: jpayne@68: /* "(tree fragment)":12 jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] # <<<<<<<<<<<<<< jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_GIVEREF(__pyx_t_1); jpayne@68: __Pyx_GOTREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __Pyx_DECREF(__pyx_v___pyx_result->__pyx_base.encoding); jpayne@68: __pyx_v___pyx_result->__pyx_base.encoding = __pyx_t_1; jpayne@68: __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); jpayne@68: __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_3 = __Pyx_PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_4 = (__pyx_t_3 > 1); jpayne@68: if (__pyx_t_4) { jpayne@68: } else { jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: goto __pyx_L4_bool_binop_done; jpayne@68: } jpayne@68: __pyx_t_4 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) jpayne@68: __pyx_t_2 = __pyx_t_4; jpayne@68: __pyx_L4_bool_binop_done:; jpayne@68: if (__pyx_t_2) { jpayne@68: jpayne@68: /* "(tree fragment)":14 jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) # <<<<<<<<<<<<<< jpayne@68: */ jpayne@68: __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_update); if (unlikely(!__pyx_t_6)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_6); jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(__pyx_v___pyx_state == Py_None)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); jpayne@68: __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: } jpayne@68: __pyx_t_5 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_5); jpayne@68: __pyx_t_7 = NULL; jpayne@68: __pyx_t_8 = 0; jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(PyMethod_Check(__pyx_t_6))) { jpayne@68: __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_6); jpayne@68: if (likely(__pyx_t_7)) { jpayne@68: PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); jpayne@68: __Pyx_INCREF(__pyx_t_7); jpayne@68: __Pyx_INCREF(function); jpayne@68: __Pyx_DECREF_SET(__pyx_t_6, function); jpayne@68: __pyx_t_8 = 1; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *__pyx_callargs[2] = {__pyx_t_7, __pyx_t_5}; jpayne@68: __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_8, 1+__pyx_t_8); jpayne@68: __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; jpayne@68: if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; jpayne@68: } jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":13 jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.__dict__.update(__pyx_state[1]) jpayne@68: */ jpayne@68: } jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asVCF__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asVCF__set_state(asVCF __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: jpayne@68: /* function exit code */ jpayne@68: __pyx_r = Py_None; __Pyx_INCREF(Py_None); jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_5); jpayne@68: __Pyx_XDECREF(__pyx_t_6); jpayne@68: __Pyx_XDECREF(__pyx_t_7); jpayne@68: __Pyx_AddTraceback("pysam.libctabix.__pyx_unpickle_asVCF__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: __pyx_r = 0; jpayne@68: __pyx_L0:; jpayne@68: __Pyx_XGIVEREF(__pyx_r); jpayne@68: __Pyx_TraceReturn(__pyx_r, 0); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return __pyx_r; jpayne@68: } jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_tabix_file_iterator __pyx_vtable_5pysam_9libctabix_tabix_file_iterator; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p; jpayne@68: PyObject *o; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc); jpayne@68: o = alloc_func(t, 0); jpayne@68: #else jpayne@68: if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) { jpayne@68: o = (*t->tp_alloc)(t, 0); jpayne@68: } else { jpayne@68: o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); jpayne@68: } jpayne@68: if (unlikely(!o)) return 0; jpayne@68: #endif jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o); jpayne@68: p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator; jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: p->infile = Py_None; Py_INCREF(Py_None); jpayne@68: if (unlikely(__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_1__cinit__(o, a, k) < 0)) goto bad; jpayne@68: return o; jpayne@68: bad: jpayne@68: Py_DECREF(o); o = 0; jpayne@68: return NULL; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: { jpayne@68: PyObject *etype, *eval, *etb; jpayne@68: PyErr_Fetch(&etype, &eval, &etb); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); jpayne@68: __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_5__dealloc__(o); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); jpayne@68: PyErr_Restore(etype, eval, etb); jpayne@68: } jpayne@68: Py_CLEAR(p->parser); jpayne@68: Py_CLEAR(p->infile); jpayne@68: #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY jpayne@68: (*Py_TYPE(o)->tp_free)(o); jpayne@68: #else jpayne@68: { jpayne@68: freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free); jpayne@68: if (tp_free) tp_free(o); jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_tabix_file_iterator(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o; jpayne@68: if (p->parser) { jpayne@68: e = (*v)(((PyObject *)p->parser), a); if (e) return e; jpayne@68: } jpayne@68: if (p->infile) { jpayne@68: e = (*v)(p->infile, a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_tabix_file_iterator(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *)o; jpayne@68: tmp = ((PyObject*)p->parser); jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: tmp = ((PyObject*)p->infile); jpayne@68: p->infile = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { jpayne@68: PyObject *res = __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__(self); jpayne@68: if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } jpayne@68: return res; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_tabix_file_iterator[] = { jpayne@68: {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__, METH_NOARGS|METH_COEXIST, 0}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_8__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19tabix_file_iterator_10__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_tabix_file_iterator_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("iterate over a compressed or uncompressed ``infile``.\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_tabix_file_iterator}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_tabix_file_iterator}, jpayne@68: {Py_tp_iter, (void *)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__}, jpayne@68: {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_tabix_file_iterator}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_tabix_file_iterator_spec = { jpayne@68: "pysam.libctabix.tabix_file_iterator", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_tabix_file_iterator_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_tabix_file_iterator = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""tabix_file_iterator", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_tabix_file_iterator, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("iterate over a compressed or uncompressed ``infile``.\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_tabix_file_iterator, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_tabix_file_iterator, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_3__iter__, /*tp_iter*/ jpayne@68: __pyx_pw_5pysam_9libctabix_19tabix_file_iterator_7__next__, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_tabix_file_iterator, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: 0, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_tabix_file_iterator, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_TabixFile __pyx_vtable_5pysam_9libctabix_TabixFile; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixFile(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile *p; jpayne@68: PyObject *o = __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_10libchtslib_HTSFile, tp_new, newfunc)(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__pyx_vtabptr_5pysam_9libctabix_TabixFile; jpayne@68: p->filename_index = Py_None; Py_INCREF(Py_None); jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: if (unlikely(__pyx_pw_5pysam_9libctabix_9TabixFile_1__cinit__(o, a, k) < 0)) goto bad; jpayne@68: return o; jpayne@68: bad: jpayne@68: Py_DECREF(o); o = 0; jpayne@68: return NULL; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_TabixFile(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile *p = (struct __pyx_obj_5pysam_9libctabix_TabixFile *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_TabixFile) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: { jpayne@68: PyObject *etype, *eval, *etb; jpayne@68: PyErr_Fetch(&etype, &eval, &etb); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); jpayne@68: __pyx_pw_5pysam_9libctabix_9TabixFile_11__dealloc__(o); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); jpayne@68: PyErr_Restore(etype, eval, etb); jpayne@68: } jpayne@68: Py_CLEAR(p->filename_index); jpayne@68: Py_CLEAR(p->parser); jpayne@68: Py_CLEAR(p->encoding); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (!(__pyx_ptype_5pysam_10libchtslib_HTSFile) || PyType_IS_GC(__pyx_ptype_5pysam_10libchtslib_HTSFile)) PyObject_GC_Track(o); jpayne@68: #else jpayne@68: if (PyType_IS_GC(__pyx_ptype_5pysam_10libchtslib_HTSFile)) PyObject_GC_Track(o); jpayne@68: #endif jpayne@68: if (likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_10libchtslib_HTSFile, tp_dealloc, destructor)(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_9libctabix_TabixFile); jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_TabixFile(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile *p = (struct __pyx_obj_5pysam_9libctabix_TabixFile *)o; jpayne@68: e = ((likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) ? ((__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_traverse) ? __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9libctabix_TabixFile)); if (e) return e; jpayne@68: if (p->filename_index) { jpayne@68: e = (*v)(p->filename_index, a); if (e) return e; jpayne@68: } jpayne@68: if (p->parser) { jpayne@68: e = (*v)(((PyObject *)p->parser), a); if (e) return e; jpayne@68: } jpayne@68: if (p->encoding) { jpayne@68: e = (*v)(p->encoding, a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_TabixFile(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixFile *p = (struct __pyx_obj_5pysam_9libctabix_TabixFile *)o; jpayne@68: if (likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) { if (__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_clear) __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9libctabix_TabixFile); jpayne@68: tmp = ((PyObject*)p->filename_index); jpayne@68: p->filename_index = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: tmp = ((PyObject*)p->parser); jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: tmp = ((PyObject*)p->encoding); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_getprop_5pysam_9libctabix_9TabixFile_header(PyObject *o, CYTHON_UNUSED void *x) { jpayne@68: return __pyx_pw_5pysam_9libctabix_9TabixFile_6header_1__get__(o); jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_getprop_5pysam_9libctabix_9TabixFile_contigs(PyObject *o, CYTHON_UNUSED void *x) { jpayne@68: return __pyx_pw_5pysam_9libctabix_9TabixFile_7contigs_1__get__(o); jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_getprop_5pysam_9libctabix_9TabixFile_filename_index(PyObject *o, CYTHON_UNUSED void *x) { jpayne@68: return __pyx_pw_5pysam_9libctabix_9TabixFile_14filename_index_1__get__(o); jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_TabixFile[] = { jpayne@68: {"_open", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_3_open, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_2_open}, jpayne@68: {"_dup", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_5_dup, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_4_dup}, jpayne@68: {"fetch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_7fetch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_6fetch}, jpayne@68: {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_9close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_8close}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_13__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_12__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9TabixFile_15__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9TabixFile_14__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: jpayne@68: static struct PyGetSetDef __pyx_getsets_5pysam_9libctabix_TabixFile[] = { jpayne@68: {(char *)"header", __pyx_getprop_5pysam_9libctabix_9TabixFile_header, 0, (char *)PyDoc_STR("the file header.\n\n The file header consists of the lines at the beginning of a\n file that are prefixed by the comment character ``#``.\n \n .. note::\n The header is returned as an iterator presenting lines\n without the newline character.\n "), 0}, jpayne@68: {(char *)"contigs", __pyx_getprop_5pysam_9libctabix_9TabixFile_contigs, 0, (char *)PyDoc_STR("list of chromosome names"), 0}, jpayne@68: {(char *)"filename_index", __pyx_getprop_5pysam_9libctabix_9TabixFile_filename_index, 0, (char *)0, 0}, jpayne@68: {0, 0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_TabixFile_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("Random access to bgzf formatted files that\n have been indexed by :term:`tabix`.\n\n The file is automatically opened. The index file of file\n ```` is expected to be called ``.tbi``\n by default (see parameter `index`).\n \n Parameters\n ----------\n \n filename : string\n Filename of bgzf file to be opened.\n\n index : string\n The filename of the index. If not set, the default is to\n assume that the index is called ``filename.tbi``\n\n mode : char\n The file opening mode. Currently, only ``r`` is permitted.\n \n parser : :class:`pysam.Parser`\n \n sets the default parser for this tabix file. If `parser`\n is None, the results are returned as an unparsed string.\n Otherwise, `parser` is assumed to be a functor that will return\n parsed data (see for example :class:`~pysam.asTuple` and\n :class:`~pysam.asGTF`).\n\n encoding : string\n\n The encoding passed to the parser\n\n threads: integer\n Number of threads to use for decompressing Tabix files.\n (Default=1)\n\n\n Raises\n ------\n \n ValueError\n if index file is missing.\n\n IOError\n if file could not be opened\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_getset, (void *)__pyx_getsets_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_TabixFile}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_TabixFile_spec = { jpayne@68: "pysam.libctabix.TabixFile", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_TabixFile), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, jpayne@68: __pyx_type_5pysam_9libctabix_TabixFile_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_TabixFile = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""TabixFile", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_TabixFile), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_TabixFile, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/ jpayne@68: PyDoc_STR("Random access to bgzf formatted files that\n have been indexed by :term:`tabix`.\n\n The file is automatically opened. The index file of file\n ```` is expected to be called ``.tbi``\n by default (see parameter `index`).\n \n Parameters\n ----------\n \n filename : string\n Filename of bgzf file to be opened.\n\n index : string\n The filename of the index. If not set, the default is to\n assume that the index is called ``filename.tbi``\n\n mode : char\n The file opening mode. Currently, only ``r`` is permitted.\n \n parser : :class:`pysam.Parser`\n \n sets the default parser for this tabix file. If `parser`\n is None, the results are returned as an unparsed string.\n Otherwise, `parser` is assumed to be a functor that will return\n parsed data (see for example :class:`~pysam.asTuple` and\n :class:`~pysam.asGTF`).\n\n encoding : string\n\n The encoding passed to the parser\n\n threads: integer\n Number of threads to use for decompressing Tabix files.\n (Default=1)\n\n\n Raises\n ------\n \n ValueError\n if index file is missing.\n\n IOError\n if file could not be opened\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_TabixFile, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_TabixFile, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_TabixFile, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: __pyx_getsets_5pysam_9libctabix_TabixFile, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: 0, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_TabixFile, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_Parser __pyx_vtable_5pysam_9libctabix_Parser; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *p; jpayne@68: PyObject *o; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc); jpayne@68: o = alloc_func(t, 0); jpayne@68: #else jpayne@68: if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) { jpayne@68: o = (*t->tp_alloc)(t, 0); jpayne@68: } else { jpayne@68: o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); jpayne@68: } jpayne@68: if (unlikely(!o)) return 0; jpayne@68: #endif jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_Parser *)o); jpayne@68: p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_Parser(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *p = (struct __pyx_obj_5pysam_9libctabix_Parser *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_Parser) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: Py_CLEAR(p->encoding); jpayne@68: #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY jpayne@68: (*Py_TYPE(o)->tp_free)(o); jpayne@68: #else jpayne@68: { jpayne@68: freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free); jpayne@68: if (tp_free) tp_free(o); jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_Parser(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *p = (struct __pyx_obj_5pysam_9libctabix_Parser *)o; jpayne@68: if (p->encoding) { jpayne@68: e = (*v)(p->encoding, a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_Parser(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_Parser *p = (struct __pyx_obj_5pysam_9libctabix_Parser *)o; jpayne@68: tmp = ((PyObject*)p->encoding); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_Parser[] = { jpayne@68: {"set_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_3set_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_2set_encoding}, jpayne@68: {"get_encoding", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_5get_encoding, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_4get_encoding}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_8__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6Parser_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6Parser_10__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_Parser_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_call, (void *)__pyx_pw_5pysam_9libctabix_6Parser_7__call__}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("Parser(encoding=u'ascii')")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_6Parser_1__init__}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_Parser}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_Parser_spec = { jpayne@68: "pysam.libctabix.Parser", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_Parser), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_Parser_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_Parser = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""Parser", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_Parser), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("Parser(encoding=u'ascii')"), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_Parser, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_Parser, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asTuple __pyx_vtable_5pysam_9libctabix_asTuple; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_asTuple *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_asTuple *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asTuple; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_asTuple[] = { jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple___reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_7asTuple_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_7asTuple_2__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_asTuple_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a python tuple.\n\n A field in a row is accessed by numeric index.\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asTuple}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asTuple}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_asTuple_spec = { jpayne@68: "pysam.libctabix.asTuple", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asTuple), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_asTuple_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_asTuple = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""asTuple", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asTuple), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/ jpayne@68: #else jpayne@68: 0, /*tp_call*/ jpayne@68: #endif jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("converts a :term:`tabix row` into a python tuple.\n\n A field in a row is accessed by numeric index.\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_asTuple, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/ jpayne@68: #else jpayne@68: 0, /*tp_init*/ jpayne@68: #endif jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_asTuple, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asGTF __pyx_vtable_5pysam_9libctabix_asGTF; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_asGTF *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_asGTF *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asGTF; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_asGTF[] = { jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF___reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asGTF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asGTF_2__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_asGTF_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a GTF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n GTF formatted entries also define the following fields that\n are derived from the attributes field:\n\n +--------------------+------------------------------+\n |*Name* |*Content* |\n +--------------------+------------------------------+\n |gene_id |the gene identifier |\n +--------------------+------------------------------+\n |transcript_id |the transcript identifier |\n +--------------------+-------------------""-----------+\n\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asGTF}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asGTF}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_asGTF_spec = { jpayne@68: "pysam.libctabix.asGTF", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asGTF), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_asGTF_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_asGTF = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""asGTF", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asGTF), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/ jpayne@68: #else jpayne@68: 0, /*tp_call*/ jpayne@68: #endif jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("converts a :term:`tabix row` into a GTF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n GTF formatted entries also define the following fields that\n are derived from the attributes field:\n\n +--------------------+------------------------------+\n |*Name* |*Content* |\n +--------------------+------------------------------+\n |gene_id |the gene identifier |\n +--------------------+------------------------------+\n |transcript_id |the transcript identifier |\n +--------------------+-------------------""-----------+\n\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_asGTF, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/ jpayne@68: #else jpayne@68: 0, /*tp_init*/ jpayne@68: #endif jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_asGTF, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asGFF3 __pyx_vtable_5pysam_9libctabix_asGFF3; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asGFF3(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_asGFF3 *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_asGFF3 *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asGFF3; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_asGFF3[] = { jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3___reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_6asGFF3_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_6asGFF3_2__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_asGFF3_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a GFF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asGFF3}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asGFF3}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_asGFF3_spec = { jpayne@68: "pysam.libctabix.asGFF3", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asGFF3), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_asGFF3_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_asGFF3 = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""asGFF3", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asGFF3), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/ jpayne@68: #else jpayne@68: 0, /*tp_call*/ jpayne@68: #endif jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("converts a :term:`tabix row` into a GFF record with the following\n fields:\n \n +----------+----------+-------------------------------+\n |*Column* |*Name* |*Content* |\n +----------+----------+-------------------------------+\n |1 |contig |the chromosome name |\n +----------+----------+-------------------------------+\n |2 |feature |The feature type |\n +----------+----------+-------------------------------+\n |3 |source |The feature source |\n +----------+----------+-------------------------------+\n |4 |start |genomic start coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |5 |end |genomic end coordinate |\n | | |(0-based) |\n +----------+----------+-------------------------------+\n |6 |score |feature score |\n +----------+----------+-------------------------------+\n |7 |strand |strand |\n +----------+----------+-------------------------------+\n |8 |frame |frame |\n +----------+----------+-------------------------------+\n |9 |attributes|the attribute field |\n +----------+----------+-------------------------------+\n\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_asGFF3, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/ jpayne@68: #else jpayne@68: 0, /*tp_init*/ jpayne@68: #endif jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_asGFF3, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asBed __pyx_vtable_5pysam_9libctabix_asBed; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_asBed *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_asBed *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asBed; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_asBed[] = { jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed___reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asBed_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asBed_2__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_asBed_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n +-----------+-----------+------------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +-----------+-----------+------------------------------------------+\n |1 |contig |contig |\n | | | |\n +-----------+-----------+------------------------------------------+\n |2 |start |genomic start coordinate (zero-based) |\n +-----------+-----------+------------------------------------------+\n |3 |end |genomic end coordinate plus one |\n | | |(zero-based) |\n +-----------+-----------+------------------------------------------+\n |4 |name |name of feature. |\n +-----------+-----------+------------------------------------------+\n |5 |score |score of feature |\n +-----------+-----------+------------------------------------------+\n |6 |strand |strand of feature |\n +-----------+-----------+------------------------------------------+\n |7 |thickStart |thickStart |\n +-----------+-----------+------------------------------------------+\n |8 |thickEnd |thickEnd |\n +-----------+-----------+------------------------------------------+\n |9 |itemRGB |itemRGB |\n +-----------+-----------+------------------------------------------+\n |10 |blockCount |number of bocks |\n +-----------+-----------+---------------------------------------""---+\n |11 |blockSizes |',' separated string of block sizes |\n +-----------+-----------+------------------------------------------+\n |12 |blockStarts|',' separated string of block genomic |\n | | |start positions |\n +-----------+-----------+------------------------------------------+\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceding\n need to be defined as well.\n\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asBed}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asBed}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_asBed_spec = { jpayne@68: "pysam.libctabix.asBed", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asBed), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_asBed_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_asBed = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""asBed", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asBed), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/ jpayne@68: #else jpayne@68: 0, /*tp_call*/ jpayne@68: #endif jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n +-----------+-----------+------------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +-----------+-----------+------------------------------------------+\n |1 |contig |contig |\n | | | |\n +-----------+-----------+------------------------------------------+\n |2 |start |genomic start coordinate (zero-based) |\n +-----------+-----------+------------------------------------------+\n |3 |end |genomic end coordinate plus one |\n | | |(zero-based) |\n +-----------+-----------+------------------------------------------+\n |4 |name |name of feature. |\n +-----------+-----------+------------------------------------------+\n |5 |score |score of feature |\n +-----------+-----------+------------------------------------------+\n |6 |strand |strand of feature |\n +-----------+-----------+------------------------------------------+\n |7 |thickStart |thickStart |\n +-----------+-----------+------------------------------------------+\n |8 |thickEnd |thickEnd |\n +-----------+-----------+------------------------------------------+\n |9 |itemRGB |itemRGB |\n +-----------+-----------+------------------------------------------+\n |10 |blockCount |number of bocks |\n +-----------+-----------+---------------------------------------""---+\n |11 |blockSizes |',' separated string of block sizes |\n +-----------+-----------+------------------------------------------+\n |12 |blockStarts|',' separated string of block genomic |\n | | |start positions |\n +-----------+-----------+------------------------------------------+\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceding\n need to be defined as well.\n\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_asBed, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/ jpayne@68: #else jpayne@68: 0, /*tp_init*/ jpayne@68: #endif jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_asBed, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_asVCF __pyx_vtable_5pysam_9libctabix_asVCF; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_asVCF *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_Parser(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_asVCF *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_Parser*)__pyx_vtabptr_5pysam_9libctabix_asVCF; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_asVCF[] = { jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF___reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_5asVCF_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_5asVCF_2__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_asVCF_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n +----------+---------+------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +----------+---------+------------------------------------+\n |1 |contig |chromosome |\n +----------+---------+------------------------------------+\n |2 |pos |chromosomal position, zero-based |\n +----------+---------+------------------------------------+\n |3 |id |id |\n +----------+---------+------------------------------------+\n |4 |ref |reference allele |\n +----------+---------+------------------------------------+\n |5 |alt |alternate alleles |\n +----------+---------+------------------------------------+\n |6 |qual |quality |\n +----------+---------+------------------------------------+\n |7 |filter |filter |\n +----------+---------+------------------------------------+\n |8 |info |info |\n +----------+---------+------------------------------------+\n |9 |format |format specifier. |\n +----------+---------+------------------------------------+\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_Parser}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_asVCF}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_asVCF}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_asVCF_spec = { jpayne@68: "pysam.libctabix.asVCF", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asVCF), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_asVCF_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_asVCF = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""asVCF", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_asVCF), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_Parser, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_7__call__, /*tp_call*/ jpayne@68: #else jpayne@68: 0, /*tp_call*/ jpayne@68: #endif jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n +----------+---------+------------------------------------+\n |*Column* |*Field* |*Contents* |\n | | | |\n +----------+---------+------------------------------------+\n |1 |contig |chromosome |\n +----------+---------+------------------------------------+\n |2 |pos |chromosomal position, zero-based |\n +----------+---------+------------------------------------+\n |3 |id |id |\n +----------+---------+------------------------------------+\n |4 |ref |reference allele |\n +----------+---------+------------------------------------+\n |5 |alt |alternate alleles |\n +----------+---------+------------------------------------+\n |6 |qual |quality |\n +----------+---------+------------------------------------+\n |7 |filter |filter |\n +----------+---------+------------------------------------+\n |8 |info |info |\n +----------+---------+------------------------------------+\n |9 |format |format specifier. |\n +----------+---------+------------------------------------+\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_Parser, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_Parser, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_asVCF, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_6Parser_1__init__, /*tp_init*/ jpayne@68: #else jpayne@68: 0, /*tp_init*/ jpayne@68: #endif jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_asVCF, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator __pyx_vtable_5pysam_9libctabix_TabixIterator; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator *p; jpayne@68: PyObject *o; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc); jpayne@68: o = alloc_func(t, 0); jpayne@68: #else jpayne@68: if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) { jpayne@68: o = (*t->tp_alloc)(t, 0); jpayne@68: } else { jpayne@68: o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); jpayne@68: } jpayne@68: if (unlikely(!o)) return 0; jpayne@68: #endif jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o); jpayne@68: p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_TabixIterator; jpayne@68: p->tabixfile = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)Py_None); Py_INCREF(Py_None); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator *p = (struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: { jpayne@68: PyObject *etype, *eval, *etb; jpayne@68: PyErr_Fetch(&etype, &eval, &etb); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); jpayne@68: __pyx_pw_5pysam_9libctabix_13TabixIterator_7__dealloc__(o); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); jpayne@68: PyErr_Restore(etype, eval, etb); jpayne@68: } jpayne@68: Py_CLEAR(p->tabixfile); jpayne@68: Py_CLEAR(p->encoding); jpayne@68: #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY jpayne@68: (*Py_TYPE(o)->tp_free)(o); jpayne@68: #else jpayne@68: { jpayne@68: freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free); jpayne@68: if (tp_free) tp_free(o); jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_TabixIterator(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator *p = (struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o; jpayne@68: if (p->tabixfile) { jpayne@68: e = (*v)(((PyObject *)p->tabixfile), a); if (e) return e; jpayne@68: } jpayne@68: if (p->encoding) { jpayne@68: e = (*v)(p->encoding, a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_TabixIterator(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIterator *p = (struct __pyx_obj_5pysam_9libctabix_TabixIterator *)o; jpayne@68: tmp = ((PyObject*)p->tabixfile); jpayne@68: p->tabixfile = ((struct __pyx_obj_5pysam_9libctabix_TabixFile *)Py_None); Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: tmp = ((PyObject*)p->encoding); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { jpayne@68: PyObject *res = __pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__(self); jpayne@68: if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } jpayne@68: return res; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_TabixIterator[] = { jpayne@68: {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_13TabixIterator_4__next__}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_8__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_13TabixIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_13TabixIterator_10__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_TabixIterator_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_TabixIterator}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("TabixIterator(encoding=u'ascii')\niterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixIterator}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixIterator}, jpayne@68: {Py_tp_iter, (void *)__pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__}, jpayne@68: {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_TabixIterator}, jpayne@68: {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_TabixIterator}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_TabixIterator_spec = { jpayne@68: "pysam.libctabix.TabixIterator", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIterator), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_TabixIterator_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_TabixIterator = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""TabixIterator", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIterator), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("TabixIterator(encoding=u'ascii')\niterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_TabixIterator, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_TabixIterator, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: __pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__, /*tp_iter*/ jpayne@68: __pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_TabixIterator, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_13TabixIterator_1__init__, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_TabixIterator, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_TabixIteratorParsed __pyx_vtable_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_TabixIterator(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_TabixIterator*)__pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: Py_CLEAR(p->parser); jpayne@68: PyObject_GC_Track(o); jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_TabixIterator(o); jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o; jpayne@68: e = __pyx_tp_traverse_5pysam_9libctabix_TabixIterator(o, v, a); if (e) return e; jpayne@68: if (p->parser) { jpayne@68: e = (*v)(((PyObject *)p->parser), a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_TabixIteratorParsed(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed *)o; jpayne@68: __pyx_tp_clear_5pysam_9libctabix_TabixIterator(o); jpayne@68: tmp = ((PyObject*)p->parser); jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { jpayne@68: PyObject *res = __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__(self); jpayne@68: if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } jpayne@68: return res; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_TabixIteratorParsed[] = { jpayne@68: {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_2__next__}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_4__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_6__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_TabixIteratorParsed_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("TabixIteratorParsed(Parser parser)\niterates over mapped reads in a region.\n\n The *parser* determines the encoding.\n\n Returns parsed data.\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixIteratorParsed}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixIteratorParsed}, jpayne@68: {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_TabixIteratorParsed}, jpayne@68: {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_TabixIteratorParsed_spec = { jpayne@68: "pysam.libctabix.TabixIteratorParsed", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_TabixIteratorParsed_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_TabixIteratorParsed = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""TabixIteratorParsed", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_TabixIteratorParsed), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_TabixIteratorParsed, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("TabixIteratorParsed(Parser parser)\niterates over mapped reads in a region.\n\n The *parser* determines the encoding.\n\n Returns parsed data.\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_TabixIteratorParsed, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_TabixIteratorParsed, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_13TabixIterator_3__iter__, /*tp_iter*/ jpayne@68: #else jpayne@68: 0, /*tp_iter*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_3__next__, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_TabixIteratorParsed, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_19TabixIteratorParsed_1__init__, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_TabixIteratorParsed, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator __pyx_vtable_5pysam_9libctabix_GZIterator; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator *p; jpayne@68: PyObject *o; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc); jpayne@68: o = alloc_func(t, 0); jpayne@68: #else jpayne@68: if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) { jpayne@68: o = (*t->tp_alloc)(t, 0); jpayne@68: } else { jpayne@68: o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); jpayne@68: } jpayne@68: if (unlikely(!o)) return 0; jpayne@68: #endif jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_GZIterator *)o); jpayne@68: p->__pyx_vtab = __pyx_vtabptr_5pysam_9libctabix_GZIterator; jpayne@68: p->_filename = Py_None; Py_INCREF(Py_None); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_GZIterator(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator *p = (struct __pyx_obj_5pysam_9libctabix_GZIterator *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_GZIterator) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: { jpayne@68: PyObject *etype, *eval, *etb; jpayne@68: PyErr_Fetch(&etype, &eval, &etb); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_3__dealloc__(o); jpayne@68: __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); jpayne@68: PyErr_Restore(etype, eval, etb); jpayne@68: } jpayne@68: Py_CLEAR(p->_filename); jpayne@68: Py_CLEAR(p->encoding); jpayne@68: #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY jpayne@68: (*Py_TYPE(o)->tp_free)(o); jpayne@68: #else jpayne@68: { jpayne@68: freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free); jpayne@68: if (tp_free) tp_free(o); jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_GZIterator(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator *p = (struct __pyx_obj_5pysam_9libctabix_GZIterator *)o; jpayne@68: if (p->_filename) { jpayne@68: e = (*v)(p->_filename, a); if (e) return e; jpayne@68: } jpayne@68: if (p->encoding) { jpayne@68: e = (*v)(p->encoding, a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_GZIterator(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIterator *p = (struct __pyx_obj_5pysam_9libctabix_GZIterator *)o; jpayne@68: tmp = ((PyObject*)p->_filename); jpayne@68: p->_filename = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: tmp = ((PyObject*)p->encoding); jpayne@68: p->encoding = Py_None; Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { jpayne@68: PyObject *res = __pyx_pw_5pysam_9libctabix_10GZIterator_7__next__(self); jpayne@68: if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } jpayne@68: return res; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_GZIterator[] = { jpayne@68: {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_10GZIterator_7__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_10GZIterator_6__next__}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_8__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_10GZIterator_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_10GZIterator_10__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_GZIterator_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_GZIterator}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("GZIterator(filename, int buffer_size=65536, encoding=u'ascii')")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_GZIterator}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_GZIterator}, jpayne@68: {Py_tp_iter, (void *)__pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__}, jpayne@68: {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_10GZIterator_7__next__}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_GZIterator}, jpayne@68: {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_10GZIterator_1__init__}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_GZIterator}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_GZIterator_spec = { jpayne@68: "pysam.libctabix.GZIterator", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_GZIterator), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_GZIterator_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_GZIterator = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""GZIterator", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_GZIterator), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_GZIterator, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("GZIterator(filename, int buffer_size=65536, encoding=u'ascii')"), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_GZIterator, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_GZIterator, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__, /*tp_iter*/ jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_7__next__, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_GZIterator, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_GZIterator, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorHead __pyx_vtable_5pysam_9libctabix_GZIteratorHead; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorHead(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_GZIterator(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_GZIteratorHead *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator*)__pyx_vtabptr_5pysam_9libctabix_GZIteratorHead; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { jpayne@68: PyObject *res = __pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__(self); jpayne@68: if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } jpayne@68: return res; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_GZIteratorHead[] = { jpayne@68: {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_14GZIteratorHead___next__}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_2__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_14GZIteratorHead_4__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_GZIteratorHead_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("iterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_GZIterator}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_GZIterator}, jpayne@68: {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_GZIteratorHead}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_GZIteratorHead}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_GZIteratorHead_spec = { jpayne@68: "pysam.libctabix.GZIteratorHead", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_GZIteratorHead_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_GZIteratorHead = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""GZIteratorHead", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorHead), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_GZIterator, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("iterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_GZIterator, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_GZIterator, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__, /*tp_iter*/ jpayne@68: #else jpayne@68: 0, /*tp_iter*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_14GZIteratorHead_1__next__, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_GZIteratorHead, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_1__init__, /*tp_init*/ jpayne@68: #else jpayne@68: 0, /*tp_init*/ jpayne@68: #endif jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_GZIteratorHead, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_GZIteratorParsed __pyx_vtable_5pysam_9libctabix_GZIteratorParsed; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_GZIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_GZIterator(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o); jpayne@68: p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9libctabix_GZIterator*)__pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed; jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static void __pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed(PyObject *o) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o; jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: if (unlikely((PY_VERSION_HEX >= 0x03080000 || __Pyx_PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE)) && __Pyx_PyObject_GetSlot(o, tp_finalize, destructor)) && !__Pyx_PyObject_GC_IsFinalized(o)) { jpayne@68: if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed) { jpayne@68: if (PyObject_CallFinalizerFromDealloc(o)) return; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: PyObject_GC_UnTrack(o); jpayne@68: Py_CLEAR(p->parser); jpayne@68: PyObject_GC_Track(o); jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_GZIterator(o); jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_traverse_5pysam_9libctabix_GZIteratorParsed(PyObject *o, visitproc v, void *a) { jpayne@68: int e; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o; jpayne@68: e = __pyx_tp_traverse_5pysam_9libctabix_GZIterator(o, v, a); if (e) return e; jpayne@68: if (p->parser) { jpayne@68: e = (*v)(((PyObject *)p->parser), a); if (e) return e; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __pyx_tp_clear_5pysam_9libctabix_GZIteratorParsed(PyObject *o) { jpayne@68: PyObject* tmp; jpayne@68: struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed *)o; jpayne@68: __pyx_tp_clear_5pysam_9libctabix_GZIterator(o); jpayne@68: tmp = ((PyObject*)p->parser); jpayne@68: p->parser = ((struct __pyx_obj_5pysam_9libctabix_Parser *)Py_None); Py_INCREF(Py_None); jpayne@68: Py_XDECREF(tmp); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static PyObject *__pyx_specialmethod___pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { jpayne@68: PyObject *res = __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__(self); jpayne@68: if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } jpayne@68: return res; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_GZIteratorParsed[] = { jpayne@68: {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__, METH_NOARGS|METH_COEXIST, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_2__next__}, jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_4__reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_6__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_GZIteratorParsed_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed}, jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("GZIteratorParsed(parser)\niterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n ")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_GZIteratorParsed}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_GZIteratorParsed}, jpayne@68: {Py_tp_iternext, (void *)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_GZIteratorParsed}, jpayne@68: {Py_tp_init, (void *)__pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_GZIteratorParsed}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_GZIteratorParsed_spec = { jpayne@68: "pysam.libctabix.GZIteratorParsed", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, jpayne@68: __pyx_type_5pysam_9libctabix_GZIteratorParsed_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_GZIteratorParsed = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""GZIteratorParsed", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_GZIteratorParsed), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_GZIteratorParsed, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ jpayne@68: PyDoc_STR("GZIteratorParsed(parser)\niterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n "), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_GZIteratorParsed, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_GZIteratorParsed, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: #if CYTHON_COMPILING_IN_PYPY || 0 jpayne@68: __pyx_pw_5pysam_9libctabix_10GZIterator_5__iter__, /*tp_iter*/ jpayne@68: #else jpayne@68: 0, /*tp_iter*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_3__next__, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_GZIteratorParsed, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: __pyx_pw_5pysam_9libctabix_16GZIteratorParsed_1__init__, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_GZIteratorParsed, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static struct __pyx_vtabstruct_5pysam_9libctabix_Tabixfile __pyx_vtable_5pysam_9libctabix_Tabixfile; jpayne@68: jpayne@68: static PyObject *__pyx_tp_new_5pysam_9libctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) { jpayne@68: struct __pyx_obj_5pysam_9libctabix_Tabixfile *p; jpayne@68: PyObject *o = __pyx_tp_new_5pysam_9libctabix_TabixFile(t, a, k); jpayne@68: if (unlikely(!o)) return 0; jpayne@68: p = ((struct __pyx_obj_5pysam_9libctabix_Tabixfile *)o); jpayne@68: p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__pyx_vtabptr_5pysam_9libctabix_Tabixfile; jpayne@68: return o; jpayne@68: } jpayne@68: jpayne@68: static PyMethodDef __pyx_methods_5pysam_9libctabix_Tabixfile[] = { jpayne@68: {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_1__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile___reduce_cython__}, jpayne@68: {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_9libctabix_9Tabixfile_3__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_9libctabix_9Tabixfile_2__setstate_cython__}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_type_5pysam_9libctabix_Tabixfile_slots[] = { jpayne@68: {Py_tp_doc, (void *)PyDoc_STR("Tabixfile is deprecated: use TabixFile instead")}, jpayne@68: {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_9libctabix_TabixFile}, jpayne@68: {Py_tp_methods, (void *)__pyx_methods_5pysam_9libctabix_Tabixfile}, jpayne@68: {Py_tp_new, (void *)__pyx_tp_new_5pysam_9libctabix_Tabixfile}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_type_5pysam_9libctabix_Tabixfile_spec = { jpayne@68: "pysam.libctabix.Tabixfile", jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_Tabixfile), jpayne@68: 0, jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, jpayne@68: __pyx_type_5pysam_9libctabix_Tabixfile_slots, jpayne@68: }; jpayne@68: #else jpayne@68: jpayne@68: static PyTypeObject __pyx_type_5pysam_9libctabix_Tabixfile = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: "pysam.libctabix.""Tabixfile", /*tp_name*/ jpayne@68: sizeof(struct __pyx_obj_5pysam_9libctabix_Tabixfile), /*tp_basicsize*/ jpayne@68: 0, /*tp_itemsize*/ jpayne@68: __pyx_tp_dealloc_5pysam_9libctabix_TabixFile, /*tp_dealloc*/ jpayne@68: #if PY_VERSION_HEX < 0x030800b4 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: 0, /*tp_vectorcall_offset*/ jpayne@68: #endif jpayne@68: 0, /*tp_getattr*/ jpayne@68: 0, /*tp_setattr*/ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, /*tp_compare*/ jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: 0, /*tp_as_async*/ jpayne@68: #endif jpayne@68: 0, /*tp_repr*/ jpayne@68: 0, /*tp_as_number*/ jpayne@68: 0, /*tp_as_sequence*/ jpayne@68: 0, /*tp_as_mapping*/ jpayne@68: 0, /*tp_hash*/ jpayne@68: 0, /*tp_call*/ jpayne@68: 0, /*tp_str*/ jpayne@68: 0, /*tp_getattro*/ jpayne@68: 0, /*tp_setattro*/ jpayne@68: 0, /*tp_as_buffer*/ jpayne@68: Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/ jpayne@68: PyDoc_STR("Tabixfile is deprecated: use TabixFile instead"), /*tp_doc*/ jpayne@68: __pyx_tp_traverse_5pysam_9libctabix_TabixFile, /*tp_traverse*/ jpayne@68: __pyx_tp_clear_5pysam_9libctabix_TabixFile, /*tp_clear*/ jpayne@68: 0, /*tp_richcompare*/ jpayne@68: 0, /*tp_weaklistoffset*/ jpayne@68: 0, /*tp_iter*/ jpayne@68: 0, /*tp_iternext*/ jpayne@68: __pyx_methods_5pysam_9libctabix_Tabixfile, /*tp_methods*/ jpayne@68: 0, /*tp_members*/ jpayne@68: 0, /*tp_getset*/ jpayne@68: 0, /*tp_base*/ jpayne@68: 0, /*tp_dict*/ jpayne@68: 0, /*tp_descr_get*/ jpayne@68: 0, /*tp_descr_set*/ jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: 0, /*tp_dictoffset*/ jpayne@68: #endif jpayne@68: 0, /*tp_init*/ jpayne@68: 0, /*tp_alloc*/ jpayne@68: __pyx_tp_new_5pysam_9libctabix_Tabixfile, /*tp_new*/ jpayne@68: 0, /*tp_free*/ jpayne@68: 0, /*tp_is_gc*/ jpayne@68: 0, /*tp_bases*/ jpayne@68: 0, /*tp_mro*/ jpayne@68: 0, /*tp_cache*/ jpayne@68: 0, /*tp_subclasses*/ jpayne@68: 0, /*tp_weaklist*/ jpayne@68: 0, /*tp_del*/ jpayne@68: 0, /*tp_version_tag*/ jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: #if CYTHON_USE_TP_FINALIZE jpayne@68: 0, /*tp_finalize*/ jpayne@68: #else jpayne@68: NULL, /*tp_finalize*/ jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, /*tp_vectorcall*/ jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT == 1 jpayne@68: 0, /*tp_print*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, /*tp_watched*/ jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, /*tp_versions_used*/ jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, /*tp_pypy_flags*/ jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: jpayne@68: static PyMethodDef __pyx_methods[] = { jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #ifndef CYTHON_SMALL_CODE jpayne@68: #if defined(__clang__) jpayne@68: #define CYTHON_SMALL_CODE jpayne@68: #elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)) jpayne@68: #define CYTHON_SMALL_CODE __attribute__((cold)) jpayne@68: #else jpayne@68: #define CYTHON_SMALL_CODE jpayne@68: #endif jpayne@68: #endif jpayne@68: /* #### Code section: pystring_table ### */ jpayne@68: jpayne@68: static int __Pyx_CreateStringTabAndInitStrings(void) { jpayne@68: __Pyx_StringTabEntry __pyx_string_tab[] = { jpayne@68: {&__pyx_n_s_AssertionError, __pyx_k_AssertionError, sizeof(__pyx_k_AssertionError), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_Could_not_open_file, __pyx_k_Could_not_open_file, sizeof(__pyx_k_Could_not_open_file), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_EmptyIterator, __pyx_k_EmptyIterator, sizeof(__pyx_k_EmptyIterator), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_EmptyIterator___iter, __pyx_k_EmptyIterator___iter, sizeof(__pyx_k_EmptyIterator___iter), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_EmptyIterator___next, __pyx_k_EmptyIterator___next, sizeof(__pyx_k_EmptyIterator___next), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_Filename_s_already_exists_use_fo, __pyx_k_Filename_s_already_exists_use_fo, sizeof(__pyx_k_Filename_s_already_exists_use_fo), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_GZIterator, __pyx_k_GZIterator, sizeof(__pyx_k_GZIterator), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_GZIterator, __pyx_k_GZIterator, sizeof(__pyx_k_GZIterator), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_GZIteratorHead, __pyx_k_GZIteratorHead, sizeof(__pyx_k_GZIteratorHead), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_GZIteratorHead, __pyx_k_GZIteratorHead, sizeof(__pyx_k_GZIteratorHead), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_GZIteratorHead___reduce_cython, __pyx_k_GZIteratorHead___reduce_cython, sizeof(__pyx_k_GZIteratorHead___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_GZIteratorHead___setstate_cython, __pyx_k_GZIteratorHead___setstate_cython, sizeof(__pyx_k_GZIteratorHead___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_GZIteratorParsed, __pyx_k_GZIteratorParsed, sizeof(__pyx_k_GZIteratorParsed), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_GZIteratorParsed___reduce_cython, __pyx_k_GZIteratorParsed___reduce_cython, sizeof(__pyx_k_GZIteratorParsed___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_GZIteratorParsed___setstate_cyth, __pyx_k_GZIteratorParsed___setstate_cyth, sizeof(__pyx_k_GZIteratorParsed___setstate_cyth), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_GZIterator___reduce_cython, __pyx_k_GZIterator___reduce_cython, sizeof(__pyx_k_GZIterator___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_GZIterator___setstate_cython, __pyx_k_GZIterator___setstate_cython, sizeof(__pyx_k_GZIterator___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_I_O_operation_on_closed_file, __pyx_k_I_O_operation_on_closed_file, sizeof(__pyx_k_I_O_operation_on_closed_file), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_I_O_operation_on_closed_file_2, __pyx_k_I_O_operation_on_closed_file_2, sizeof(__pyx_k_I_O_operation_on_closed_file_2), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_k_Incompatible_checksums_0x_x_vs_0, sizeof(__pyx_k_Incompatible_checksums_0x_x_vs_0), 0, 0, 1, 0}, jpayne@68: {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1}, jpayne@68: {&__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@68: {&__pyx_n_s_NotImplementedError, __pyx_k_NotImplementedError, sizeof(__pyx_k_NotImplementedError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_OSError, __pyx_k_OSError, sizeof(__pyx_k_OSError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_O_RDONLY, __pyx_k_O_RDONLY, sizeof(__pyx_k_O_RDONLY), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Parser, __pyx_k_Parser, sizeof(__pyx_k_Parser), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Parser___reduce_cython, __pyx_k_Parser___reduce_cython, sizeof(__pyx_k_Parser___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Parser___setstate_cython, __pyx_k_Parser___setstate_cython, sizeof(__pyx_k_Parser___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Parser_get_encoding, __pyx_k_Parser_get_encoding, sizeof(__pyx_k_Parser_get_encoding), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Parser_set_encoding, __pyx_k_Parser_set_encoding, sizeof(__pyx_k_Parser_set_encoding), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixFile, __pyx_k_TabixFile, sizeof(__pyx_k_TabixFile), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_TabixFile, __pyx_k_TabixFile, sizeof(__pyx_k_TabixFile), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_TabixFile___reduce_cython, __pyx_k_TabixFile___reduce_cython, sizeof(__pyx_k_TabixFile___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixFile___setstate_cython, __pyx_k_TabixFile___setstate_cython, sizeof(__pyx_k_TabixFile___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixFile__dup, __pyx_k_TabixFile__dup, sizeof(__pyx_k_TabixFile__dup), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixFile__open, __pyx_k_TabixFile__open, sizeof(__pyx_k_TabixFile__open), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixFile_close, __pyx_k_TabixFile_close, sizeof(__pyx_k_TabixFile_close), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixFile_fetch, __pyx_k_TabixFile_fetch, sizeof(__pyx_k_TabixFile_fetch), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixIterator, __pyx_k_TabixIterator, sizeof(__pyx_k_TabixIterator), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixIteratorParsed, __pyx_k_TabixIteratorParsed, sizeof(__pyx_k_TabixIteratorParsed), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixIteratorParsed___reduce_cyt, __pyx_k_TabixIteratorParsed___reduce_cyt, sizeof(__pyx_k_TabixIteratorParsed___reduce_cyt), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixIteratorParsed___setstate_c, __pyx_k_TabixIteratorParsed___setstate_c, sizeof(__pyx_k_TabixIteratorParsed___setstate_c), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixIterator___reduce_cython, __pyx_k_TabixIterator___reduce_cython, sizeof(__pyx_k_TabixIterator___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TabixIterator___setstate_cython, __pyx_k_TabixIterator___setstate_cython, sizeof(__pyx_k_TabixIterator___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Tabixfile, __pyx_k_Tabixfile, sizeof(__pyx_k_Tabixfile), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_Tabixfile, __pyx_k_Tabixfile, sizeof(__pyx_k_Tabixfile), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_Tabixfile___reduce_cython, __pyx_k_Tabixfile___reduce_cython, sizeof(__pyx_k_Tabixfile___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_Tabixfile___setstate_cython, __pyx_k_Tabixfile___setstate_cython, sizeof(__pyx_k_Tabixfile___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_WINDOW_SIZE, __pyx_k_WINDOW_SIZE, sizeof(__pyx_k_WINDOW_SIZE), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_b__16, __pyx_k__16, sizeof(__pyx_k__16), 0, 0, 0, 0}, jpayne@68: {&__pyx_kp_u__39, __pyx_k__39, sizeof(__pyx_k__39), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u__42, __pyx_k__42, sizeof(__pyx_k__42), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u__43, __pyx_k__43, sizeof(__pyx_k__43), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u__44, __pyx_k__44, sizeof(__pyx_k__44), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u__56, __pyx_k__56, sizeof(__pyx_k__56), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s__62, __pyx_k__62, sizeof(__pyx_k__62), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s__78, __pyx_k__78, sizeof(__pyx_k__78), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asBed, __pyx_k_asBed, sizeof(__pyx_k_asBed), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_asBed, __pyx_k_asBed, sizeof(__pyx_k_asBed), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_asBed___reduce_cython, __pyx_k_asBed___reduce_cython, sizeof(__pyx_k_asBed___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asBed___setstate_cython, __pyx_k_asBed___setstate_cython, sizeof(__pyx_k_asBed___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asGFF3, __pyx_k_asGFF3, sizeof(__pyx_k_asGFF3), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_asGFF3, __pyx_k_asGFF3, sizeof(__pyx_k_asGFF3), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_asGFF3___reduce_cython, __pyx_k_asGFF3___reduce_cython, sizeof(__pyx_k_asGFF3___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asGFF3___setstate_cython, __pyx_k_asGFF3___setstate_cython, sizeof(__pyx_k_asGFF3___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asGTF, __pyx_k_asGTF, sizeof(__pyx_k_asGTF), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_asGTF, __pyx_k_asGTF, sizeof(__pyx_k_asGTF), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_asGTF___reduce_cython, __pyx_k_asGTF___reduce_cython, sizeof(__pyx_k_asGTF___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asGTF___setstate_cython, __pyx_k_asGTF___setstate_cython, sizeof(__pyx_k_asGTF___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asTuple, __pyx_k_asTuple, sizeof(__pyx_k_asTuple), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_asTuple, __pyx_k_asTuple, sizeof(__pyx_k_asTuple), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_asTuple___reduce_cython, __pyx_k_asTuple___reduce_cython, sizeof(__pyx_k_asTuple___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asTuple___setstate_cython, __pyx_k_asTuple___setstate_cython, sizeof(__pyx_k_asTuple___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asVCF, __pyx_k_asVCF, sizeof(__pyx_k_asVCF), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_asVCF, __pyx_k_asVCF, sizeof(__pyx_k_asVCF), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_asVCF___reduce_cython, __pyx_k_asVCF___reduce_cython, sizeof(__pyx_k_asVCF___reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_asVCF___setstate_cython, __pyx_k_asVCF___setstate_cython, sizeof(__pyx_k_asVCF___setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_ascii, __pyx_k_ascii, sizeof(__pyx_k_ascii), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_asyncio_coroutines, __pyx_k_asyncio_coroutines, sizeof(__pyx_k_asyncio_coroutines), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_bcf, __pyx_k_bcf, sizeof(__pyx_k_bcf), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_u_bed, __pyx_k_bed, sizeof(__pyx_k_bed), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_buffer, __pyx_k_buffer, sizeof(__pyx_k_buffer), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_buffer_size, __pyx_k_buffer_size, sizeof(__pyx_k_buffer_size), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_building_of_index_for_failed, __pyx_k_building_of_index_for_failed, sizeof(__pyx_k_building_of_index_for_failed), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_bytes_cpy, __pyx_k_bytes_cpy, sizeof(__pyx_k_bytes_cpy), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_cfilename, __pyx_k_cfilename, sizeof(__pyx_k_cfilename), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_cfilename_index, __pyx_k_cfilename_index, sizeof(__pyx_k_cfilename_index), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_cfn, __pyx_k_cfn, sizeof(__pyx_k_cfn), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_closed, __pyx_k_closed, sizeof(__pyx_k_closed), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_conf, __pyx_k_conf, sizeof(__pyx_k_conf), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_conf_data, __pyx_k_conf_data, sizeof(__pyx_k_conf_data), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_contigs, __pyx_k_contigs, sizeof(__pyx_k_contigs), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_could_not_create_iterator_for_re, __pyx_k_could_not_create_iterator_for_re, sizeof(__pyx_k_could_not_create_iterator_for_re), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_create_iterator_possib, __pyx_k_could_not_create_iterator_possib, sizeof(__pyx_k_could_not_create_iterator_possib), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_load_tbi_csi_index_of, __pyx_k_could_not_load_tbi_csi_index_of, sizeof(__pyx_k_could_not_load_tbi_csi_index_of), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_open_file_s, __pyx_k_could_not_open_file_s, sizeof(__pyx_k_could_not_open_file_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_open_for_reading_heade, __pyx_k_could_not_open_for_reading_heade, sizeof(__pyx_k_could_not_open_for_reading_heade), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_open_index_for_s, __pyx_k_could_not_open_index_for_s, sizeof(__pyx_k_could_not_open_index_for_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_open_s_for_reading, __pyx_k_could_not_open_s_for_reading, sizeof(__pyx_k_could_not_open_s_for_reading), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_could_not_open_s_for_writing, __pyx_k_could_not_open_s_for_writing, sizeof(__pyx_k_could_not_open_s_for_writing), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_cpy, __pyx_k_cpy, sizeof(__pyx_k_cpy), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_csi, __pyx_k_csi, sizeof(__pyx_k_csi), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_csi_2, __pyx_k_csi_2, sizeof(__pyx_k_csi_2), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_cstr, __pyx_k_cstr, sizeof(__pyx_k_cstr), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_dict_2, __pyx_k_dict_2, sizeof(__pyx_k_dict_2), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_disable, __pyx_k_disable, sizeof(__pyx_k_disable), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_dup, __pyx_k_dup, sizeof(__pyx_k_dup), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_s_empty_iterator, __pyx_k_empty_iterator, sizeof(__pyx_k_empty_iterator), 0, 0, 1, 0}, jpayne@68: {&__pyx_kp_u_enable, __pyx_k_enable, sizeof(__pyx_k_enable), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_encoding, __pyx_k_encoding, sizeof(__pyx_k_encoding), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_end_col, __pyx_k_end_col, sizeof(__pyx_k_end_col), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_end_out_of_range_i, __pyx_k_end_out_of_range_i, sizeof(__pyx_k_end_out_of_range_i), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_error_i_when_closing_file_s, __pyx_k_error_i_when_closing_file_s, sizeof(__pyx_k_error_i_when_closing_file_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_error_i_when_writing_to_file_s, __pyx_k_error_i_when_writing_to_file_s, sizeof(__pyx_k_error_i_when_writing_to_file_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_exists, __pyx_k_exists, sizeof(__pyx_k_exists), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fd_src, __pyx_k_fd_src, sizeof(__pyx_k_fd_src), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fetch, __pyx_k_fetch, sizeof(__pyx_k_fetch), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_file_s_not_found, __pyx_k_file_s_not_found, sizeof(__pyx_k_file_s_not_found), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_filename, __pyx_k_filename, sizeof(__pyx_k_filename), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_filename_in, __pyx_k_filename_in, sizeof(__pyx_k_filename_in), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_filename_index, __pyx_k_filename_index, sizeof(__pyx_k_filename_index), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_filename_out, __pyx_k_filename_out, sizeof(__pyx_k_filename_out), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_filename_s_already_exists_use_fo, __pyx_k_filename_s_already_exists_use_fo, sizeof(__pyx_k_filename_s_already_exists_use_fo), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_fileobj, __pyx_k_fileobj, sizeof(__pyx_k_fileobj), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fmt, __pyx_k_fmt, sizeof(__pyx_k_fmt), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fn, __pyx_k_fn, sizeof(__pyx_k_fn), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fn_index, __pyx_k_fn_index, sizeof(__pyx_k_fn_index), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fnidx, __pyx_k_fnidx, sizeof(__pyx_k_fnidx), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_force, __pyx_k_force, sizeof(__pyx_k_force), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_fp, __pyx_k_fp, sizeof(__pyx_k_fp), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_gc, __pyx_k_gc, sizeof(__pyx_k_gc), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_get_encoding, __pyx_k_get_encoding, sizeof(__pyx_k_get_encoding), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_gff, __pyx_k_gff, sizeof(__pyx_k_gff), 0, 1, 0, 1}, jpayne@68: {&__pyx_kp_u_gz, __pyx_k_gz, sizeof(__pyx_k_gz), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_incomplete_line_at_s, __pyx_k_incomplete_line_at_s, sizeof(__pyx_k_incomplete_line_at_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_index, __pyx_k_index, sizeof(__pyx_k_index), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_index_s_not_found, __pyx_k_index_s_not_found, sizeof(__pyx_k_index_s_not_found), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_infile, __pyx_k_infile, sizeof(__pyx_k_infile), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_init_subclass, __pyx_k_init_subclass, sizeof(__pyx_k_init_subclass), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_initializing, __pyx_k_initializing, sizeof(__pyx_k_initializing), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_invalid_file_opening_mode_s, __pyx_k_invalid_file_opening_mode_s, sizeof(__pyx_k_invalid_file_opening_mode_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_is_coroutine, __pyx_k_is_coroutine, sizeof(__pyx_k_is_coroutine), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_is_empty, __pyx_k_is_empty, sizeof(__pyx_k_is_empty), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_is_open, __pyx_k_is_open, sizeof(__pyx_k_is_open), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_isenabled, __pyx_k_isenabled, sizeof(__pyx_k_isenabled), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_iter, __pyx_k_iter, sizeof(__pyx_k_iter), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_s_iterate_over_infile_Permits_the, __pyx_k_iterate_over_infile_Permits_the, sizeof(__pyx_k_iterate_over_infile_Permits_the), 0, 0, 1, 0}, jpayne@68: {&__pyx_kp_u_iteration_on_closed_file, __pyx_k_iteration_on_closed_file, sizeof(__pyx_k_iteration_on_closed_file), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_itr, __pyx_k_itr, sizeof(__pyx_k_itr), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_keep_original, __pyx_k_keep_original, sizeof(__pyx_k_keep_original), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_keys, __pyx_k_keys, sizeof(__pyx_k_keys), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_length, __pyx_k_length, sizeof(__pyx_k_length), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_line, __pyx_k_line, sizeof(__pyx_k_line), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_line_skip, __pyx_k_line_skip, sizeof(__pyx_k_line_skip), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_meta_char, __pyx_k_meta_char, sizeof(__pyx_k_meta_char), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_min_shift, __pyx_k_min_shift, sizeof(__pyx_k_min_shift), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_mode, __pyx_k_mode, sizeof(__pyx_k_mode), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_multiple_iterators, __pyx_k_multiple_iterators, sizeof(__pyx_k_multiple_iterators), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_nbytes, __pyx_k_nbytes, sizeof(__pyx_k_nbytes), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_neither_preset_nor_seq_col_start, __pyx_k_neither_preset_nor_seq_col_start, sizeof(__pyx_k_neither_preset_nor_seq_col_start), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_new, __pyx_k_new, sizeof(__pyx_k_new), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_next, __pyx_k_next, sizeof(__pyx_k_next), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_s_no_default___reduce___due_to_non, __pyx_k_no_default___reduce___due_to_non, sizeof(__pyx_k_no_default___reduce___due_to_non), 0, 0, 1, 0}, jpayne@68: {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_os, __pyx_k_os, sizeof(__pyx_k_os), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_parse_method_of_s_not_implemente, __pyx_k_parse_method_of_s_not_implemente, sizeof(__pyx_k_parse_method_of_s_not_implemente), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_parser, __pyx_k_parser, sizeof(__pyx_k_parser), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pickle, __pyx_k_pickle, sizeof(__pyx_k_pickle), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_preset, __pyx_k_preset, sizeof(__pyx_k_preset), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_preset2conf, __pyx_k_preset2conf, sizeof(__pyx_k_preset2conf), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_psltbl, __pyx_k_psltbl, sizeof(__pyx_k_psltbl), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_pysam_libctabix, __pyx_k_pysam_libctabix, sizeof(__pyx_k_pysam_libctabix), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_s_pysam_libctabix_pyx, __pyx_k_pysam_libctabix_pyx, sizeof(__pyx_k_pysam_libctabix_pyx), 0, 0, 1, 0}, jpayne@68: {&__pyx_n_s_pyx_PickleError, __pyx_k_pyx_PickleError, sizeof(__pyx_k_pyx_PickleError), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_checksum, __pyx_k_pyx_checksum, sizeof(__pyx_k_pyx_checksum), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_result, __pyx_k_pyx_result, sizeof(__pyx_k_pyx_result), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_type, __pyx_k_pyx_type, sizeof(__pyx_k_pyx_type), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_unpickle_Parser, __pyx_k_pyx_unpickle_Parser, sizeof(__pyx_k_pyx_unpickle_Parser), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_unpickle_asBed, __pyx_k_pyx_unpickle_asBed, sizeof(__pyx_k_pyx_unpickle_asBed), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_unpickle_asGFF3, __pyx_k_pyx_unpickle_asGFF3, sizeof(__pyx_k_pyx_unpickle_asGFF3), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_unpickle_asGTF, __pyx_k_pyx_unpickle_asGTF, sizeof(__pyx_k_pyx_unpickle_asGTF), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_unpickle_asTuple, __pyx_k_pyx_unpickle_asTuple, sizeof(__pyx_k_pyx_unpickle_asTuple), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_unpickle_asVCF, __pyx_k_pyx_unpickle_asVCF, sizeof(__pyx_k_pyx_unpickle_asVCF), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_readline, __pyx_k_readline, sizeof(__pyx_k_readline), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_reference, __pyx_k_reference, sizeof(__pyx_k_reference), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_region, __pyx_k_region, sizeof(__pyx_k_region), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_retval, __pyx_k_retval, sizeof(__pyx_k_retval), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_s_2, __pyx_k_s_2, sizeof(__pyx_k_s_2), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_s_i, __pyx_k_s_i, sizeof(__pyx_k_s_i), 0, 1, 0, 0}, jpayne@68: {&__pyx_kp_u_s_i_i, __pyx_k_s_i_i, sizeof(__pyx_k_s_i_i), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_u_sam, __pyx_k_sam, sizeof(__pyx_k_sam), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_s_self_gzipfile_self_kstream_canno, __pyx_k_self_gzipfile_self_kstream_canno, sizeof(__pyx_k_self_gzipfile_self_kstream_canno), 0, 0, 1, 0}, jpayne@68: {&__pyx_kp_s_self_iterator_cannot_be_converte, __pyx_k_self_iterator_cannot_be_converte, sizeof(__pyx_k_self_iterator_cannot_be_converte), 0, 0, 1, 0}, jpayne@68: {&__pyx_n_s_seq_col, __pyx_k_seq_col, sizeof(__pyx_k_seq_col), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_set_encoding, __pyx_k_set_encoding, sizeof(__pyx_k_set_encoding), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_set_name, __pyx_k_set_name, sizeof(__pyx_k_set_name), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_spec, __pyx_k_spec, sizeof(__pyx_k_spec), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_start_col, __pyx_k_start_col, sizeof(__pyx_k_start_col), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_start_i_end_i, __pyx_k_start_i_end_i, sizeof(__pyx_k_start_i_end_i), 0, 1, 0, 0}, jpayne@68: {&__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@68: {&__pyx_n_s_state, __pyx_k_state, sizeof(__pyx_k_state), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0}, jpayne@68: {&__pyx_n_s_suffix, __pyx_k_suffix, sizeof(__pyx_k_suffix), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_super, __pyx_k_super, sizeof(__pyx_k_super), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_tabix_compress, __pyx_k_tabix_compress, sizeof(__pyx_k_tabix_compress), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_tabix_compress, __pyx_k_tabix_compress, sizeof(__pyx_k_tabix_compress), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_tabix_file_iterator, __pyx_k_tabix_file_iterator, sizeof(__pyx_k_tabix_file_iterator), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_tabix_file_iterator, __pyx_k_tabix_file_iterator, sizeof(__pyx_k_tabix_file_iterator), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_tabix_file_iterator___reduce_cyt, __pyx_k_tabix_file_iterator___reduce_cyt, sizeof(__pyx_k_tabix_file_iterator___reduce_cyt), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_tabix_file_iterator___setstate_c, __pyx_k_tabix_file_iterator___setstate_c, sizeof(__pyx_k_tabix_file_iterator___setstate_c), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_tabix_generic_iterator, __pyx_k_tabix_generic_iterator, sizeof(__pyx_k_tabix_generic_iterator), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_tabix_generic_iterator, __pyx_k_tabix_generic_iterator, sizeof(__pyx_k_tabix_generic_iterator), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_tabix_generic_iterator___init, __pyx_k_tabix_generic_iterator___init, sizeof(__pyx_k_tabix_generic_iterator___init), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_tabix_generic_iterator___iter, __pyx_k_tabix_generic_iterator___iter, sizeof(__pyx_k_tabix_generic_iterator___iter), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_tabix_generic_iterator___next, __pyx_k_tabix_generic_iterator___next, sizeof(__pyx_k_tabix_generic_iterator___next), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_tabix_index, __pyx_k_tabix_index, sizeof(__pyx_k_tabix_index), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_tabix_index, __pyx_k_tabix_index, sizeof(__pyx_k_tabix_index), 0, 1, 0, 1}, jpayne@68: {&__pyx_n_s_tabix_iterator, __pyx_k_tabix_iterator, sizeof(__pyx_k_tabix_iterator), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_u_tabix_iterator, __pyx_k_tabix_iterator, sizeof(__pyx_k_tabix_iterator), 0, 1, 0, 1}, jpayne@68: {&__pyx_kp_u_tbi, __pyx_k_tbi, sizeof(__pyx_k_tbi), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_tell, __pyx_k_tell, sizeof(__pyx_k_tell), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_threads, __pyx_k_threads, sizeof(__pyx_k_threads), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_unknown_preset, __pyx_k_unknown_preset, sizeof(__pyx_k_unknown_preset), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_unlink, __pyx_k_unlink, sizeof(__pyx_k_unlink), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_update, __pyx_k_update, sizeof(__pyx_k_update), 0, 0, 1, 1}, jpayne@68: {&__pyx_n_s_use_setstate, __pyx_k_use_setstate, sizeof(__pyx_k_use_setstate), 0, 0, 1, 1}, jpayne@68: {&__pyx_kp_u_valid_presets_are, __pyx_k_valid_presets_are, sizeof(__pyx_k_valid_presets_are), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_u_vcf, __pyx_k_vcf, sizeof(__pyx_k_vcf), 0, 1, 0, 1}, jpayne@68: {&__pyx_kp_u_writing_failed, __pyx_k_writing_failed, sizeof(__pyx_k_writing_failed), 0, 1, 0, 0}, jpayne@68: {&__pyx_n_s_zerobased, __pyx_k_zerobased, sizeof(__pyx_k_zerobased), 0, 0, 1, 1}, jpayne@68: {0, 0, 0, 0, 0, 0, 0} jpayne@68: }; jpayne@68: return __Pyx_InitStrings(__pyx_string_tab); jpayne@68: } jpayne@68: /* #### Code section: cached_builtins ### */ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) { jpayne@68: __pyx_builtin_NotImplementedError = __Pyx_GetBuiltinName(__pyx_n_s_NotImplementedError); if (!__pyx_builtin_NotImplementedError) __PYX_ERR(0, 94, __pyx_L1_error) jpayne@68: __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 361, __pyx_L1_error) jpayne@68: __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) __PYX_ERR(0, 378, __pyx_L1_error) jpayne@68: __pyx_builtin_OSError = __Pyx_GetBuiltinName(__pyx_n_s_OSError); if (!__pyx_builtin_OSError) __PYX_ERR(0, 560, __pyx_L1_error) jpayne@68: __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error) jpayne@68: __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) __PYX_ERR(0, 671, __pyx_L1_error) jpayne@68: __pyx_builtin_super = __Pyx_GetBuiltinName(__pyx_n_s_super); if (!__pyx_builtin_super) __PYX_ERR(0, 701, __pyx_L1_error) jpayne@68: __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) __PYX_ERR(0, 969, __pyx_L1_error) jpayne@68: __pyx_builtin_AssertionError = __Pyx_GetBuiltinName(__pyx_n_s_AssertionError); if (!__pyx_builtin_AssertionError) __PYX_ERR(0, 1216, __pyx_L1_error) jpayne@68: __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) __PYX_ERR(3, 120, __pyx_L1_error) jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: return -1; jpayne@68: } jpayne@68: /* #### Code section: cached_constants ### */ jpayne@68: jpayne@68: static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":444 jpayne@68: * ''' jpayne@68: * if not self.is_open(): jpayne@68: * raise ValueError("I/O operation on closed file") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * # convert coordinates to region string, which is one-based jpayne@68: */ jpayne@68: __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_u_I_O_operation_on_closed_file); if (unlikely(!__pyx_tuple__19)) __PYX_ERR(0, 444, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__19); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__19); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":499 jpayne@68: * # when accessing a tabix file created prior tabix 1.0 jpayne@68: * # the full-file iterator is empty. jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * "could not create iterator, possible " jpayne@68: * "tabix version mismatch") jpayne@68: */ jpayne@68: __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_u_could_not_create_iterator_possib); if (unlikely(!__pyx_tuple__20)) __PYX_ERR(0, 499, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__20); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__20); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":669 jpayne@68: * cdef int retval = self.__cnext__() jpayne@68: * if retval == -5: jpayne@68: * raise IOError("iteration on closed file") # <<<<<<<<<<<<<< jpayne@68: * elif retval < 0: jpayne@68: * raise StopIteration jpayne@68: */ jpayne@68: __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_u_iteration_on_closed_file); if (unlikely(!__pyx_tuple__24)) __PYX_ERR(0, 669, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__24); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__24); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":859 jpayne@68: * if r < 0: jpayne@68: * free(buffer) jpayne@68: * raise IOError("writing failed") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * free(buffer) jpayne@68: */ jpayne@68: __pyx_tuple__38 = PyTuple_Pack(1, __pyx_kp_u_writing_failed); if (unlikely(!__pyx_tuple__38)) __PYX_ERR(0, 859, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__38); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__38); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":930 jpayne@68: * if preset is None and \ jpayne@68: * (seq_col is None or start_col is None or end_col is None): jpayne@68: * raise ValueError( # <<<<<<<<<<<<<< jpayne@68: * "neither preset nor seq_col,start_col and end_col given") jpayne@68: * jpayne@68: */ jpayne@68: __pyx_tuple__41 = PyTuple_Pack(1, __pyx_kp_u_neither_preset_nor_seq_col_start); if (unlikely(!__pyx_tuple__41)) __PYX_ERR(0, 930, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__41); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__41); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1108 jpayne@68: * jpayne@68: * if infile.closed: jpayne@68: * raise ValueError("I/O operation on closed file.") # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: */ jpayne@68: __pyx_tuple__45 = PyTuple_Pack(1, __pyx_kp_u_I_O_operation_on_closed_file_2); if (unlikely(!__pyx_tuple__45)) __PYX_ERR(0, 1108, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__45); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__45); jpayne@68: jpayne@68: /* "(tree fragment)":4 jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: * if __pyx_checksum not in (0xe8424ea, 0x14a9dc0, 0x84bea1f): # <<<<<<<<<<<<<< jpayne@68: * from pickle import PickleError as __pyx_PickleError jpayne@68: * raise __pyx_PickleError, "Incompatible checksums (0x%x vs (0xe8424ea, 0x14a9dc0, 0x84bea1f) = (encoding))" % __pyx_checksum jpayne@68: */ jpayne@68: __pyx_tuple__55 = PyTuple_Pack(3, __pyx_int_243541226, __pyx_int_21667264, __pyx_int_139192863); if (unlikely(!__pyx_tuple__55)) __PYX_ERR(1, 4, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__55); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__55); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":87 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def set_encoding(self, encoding): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: __pyx_tuple__63 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_encoding); if (unlikely(!__pyx_tuple__63)) __PYX_ERR(0, 87, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__63); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__63); jpayne@68: __pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_set_encoding, 87, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 87, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":90 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def get_encoding(self): # <<<<<<<<<<<<<< jpayne@68: * return self.encoding jpayne@68: * jpayne@68: */ jpayne@68: __pyx_tuple__64 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__64)) __PYX_ERR(0, 90, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__64); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__64); jpayne@68: __pyx_codeobj__2 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_get_encoding, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__2)) __PYX_ERR(0, 90, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_tuple__65 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_state, __pyx_n_s_dict_2, __pyx_n_s_use_setstate); if (unlikely(!__pyx_tuple__65)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__65); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__65); jpayne@68: __pyx_codeobj__3 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_Parser__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_tuple__66 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_pyx_state); if (unlikely(!__pyx_tuple__66)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__66); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__66); jpayne@68: __pyx_codeobj__4 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__4)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_codeobj__5 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__5)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asTuple__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_codeobj__6 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__6)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_codeobj__7 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__7)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGTF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asBed__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_codeobj__13 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__13)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asVCF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_codeobj__14 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 16, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__14)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":352 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def _open( self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: __pyx_tuple__67 = PyTuple_Pack(8, __pyx_n_s_self, __pyx_n_s_filename, __pyx_n_s_mode, __pyx_n_s_index, __pyx_n_s_threads, __pyx_n_s_filename_index, __pyx_n_s_cfilename, __pyx_n_s_cfilename_index); if (unlikely(!__pyx_tuple__67)) __PYX_ERR(0, 352, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__67); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__67); jpayne@68: __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(5, 0, 0, 8, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_open, 352, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) __PYX_ERR(0, 352, __pyx_L1_error) jpayne@68: __pyx_tuple__68 = PyTuple_Pack(3, __pyx_n_u_r, Py_None, __pyx_int_1); if (unlikely(!__pyx_tuple__68)) __PYX_ERR(0, 352, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__68); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__68); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":404 jpayne@68: * self.start_offset = self.tell() jpayne@68: * jpayne@68: * def _dup(self): # <<<<<<<<<<<<<< jpayne@68: * '''return a copy of this tabix file. jpayne@68: * jpayne@68: */ jpayne@68: __pyx_codeobj__17 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_dup, 404, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) __PYX_ERR(0, 404, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":416 jpayne@68: * encoding=self.encoding) jpayne@68: * jpayne@68: * def fetch(self, # <<<<<<<<<<<<<< jpayne@68: * reference=None, jpayne@68: * start=None, jpayne@68: */ jpayne@68: __pyx_tuple__69 = PyTuple_Pack(12, __pyx_n_s_self, __pyx_n_s_reference, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_region, __pyx_n_s_parser, __pyx_n_s_multiple_iterators, __pyx_n_s_itr, __pyx_n_s_cstr, __pyx_n_s_fileobj, __pyx_n_s_s_2, __pyx_n_s_a); if (unlikely(!__pyx_tuple__69)) __PYX_ERR(0, 416, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__69); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__69); jpayne@68: __pyx_codeobj__18 = (PyObject*)__Pyx_PyCode_New(7, 0, 0, 12, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_fetch, 416, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__18)) __PYX_ERR(0, 416, __pyx_L1_error) jpayne@68: __pyx_tuple__70 = PyTuple_Pack(6, Py_None, Py_None, Py_None, Py_None, Py_None, Py_False); if (unlikely(!__pyx_tuple__70)) __PYX_ERR(0, 416, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__70); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__70); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":598 jpayne@68: * return result jpayne@68: * jpayne@68: * def close(self): # <<<<<<<<<<<<<< jpayne@68: * ''' jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: */ jpayne@68: __pyx_codeobj__21 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_close, 598, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__21)) __PYX_ERR(0, 598, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__22 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__22)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__25 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__25)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_codeobj__26 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__26)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":685 jpayne@68: * '''empty iterator''' jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: __pyx_codeobj__27 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_iter, 685, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__27)) __PYX_ERR(0, 685, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":688 jpayne@68: * return self jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration() jpayne@68: * jpayne@68: */ jpayne@68: __pyx_codeobj__28 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_next, 688, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__28)) __PYX_ERR(0, 688, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__29 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__29)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_codeobj__30 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__30)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__31 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__31)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_codeobj__32 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__32)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__33 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__33)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_codeobj__34 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__34)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__35 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__35)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_codeobj__36 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__36)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":811 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_compress(filename_in, # <<<<<<<<<<<<<< jpayne@68: * filename_out, jpayne@68: * force=False): jpayne@68: */ jpayne@68: __pyx_tuple__71 = PyTuple_Pack(13, __pyx_n_s_filename_in, __pyx_n_s_filename_out, __pyx_n_s_force, __pyx_n_s_WINDOW_SIZE, __pyx_n_s_c, __pyx_n_s_r, __pyx_n_s_buffer, __pyx_n_s_fp, __pyx_n_s_fd_src, __pyx_n_s_is_empty, __pyx_n_s_O_RDONLY, __pyx_n_s_fn, __pyx_n_s_cfn); if (unlikely(!__pyx_tuple__71)) __PYX_ERR(0, 811, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__71); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__71); jpayne@68: __pyx_codeobj__37 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 13, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_tabix_compress, 811, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__37)) __PYX_ERR(0, 811, __pyx_L1_error) jpayne@68: __pyx_tuple__72 = PyTuple_Pack(1, ((PyObject *)Py_False)); if (unlikely(!__pyx_tuple__72)) __PYX_ERR(0, 811, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__72); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__72); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":873 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_index(filename, # <<<<<<<<<<<<<< jpayne@68: * force=False, jpayne@68: * seq_col=None, jpayne@68: */ jpayne@68: __pyx_tuple__73 = PyTuple_Pack(24, __pyx_n_s_filename, __pyx_n_s_force, __pyx_n_s_seq_col, __pyx_n_s_start_col, __pyx_n_s_end_col, __pyx_n_s_preset, __pyx_n_s_meta_char, __pyx_n_s_line_skip, __pyx_n_s_zerobased, __pyx_n_s_min_shift, __pyx_n_s_index, __pyx_n_s_keep_original, __pyx_n_s_csi, __pyx_n_s_fn, __pyx_n_s_cfn, __pyx_n_s_fp, __pyx_n_s_fmt, __pyx_n_s_preset2conf, __pyx_n_s_conf_data, __pyx_n_s_conf, __pyx_n_s_suffix, __pyx_n_s_fn_index, __pyx_n_s_fnidx, __pyx_n_s_retval); if (unlikely(!__pyx_tuple__73)) __PYX_ERR(0, 873, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__73); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__73); jpayne@68: __pyx_codeobj__40 = (PyObject*)__Pyx_PyCode_New(13, 0, 0, 24, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__73, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_tabix_index, 873, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__40)) __PYX_ERR(0, 873, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__46 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__46)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __pyx_codeobj__47 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__47)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1183 jpayne@68: * Permits the use of file-like objects for example from the gzip module. jpayne@68: * ''' jpayne@68: * def __init__(self, infile, parser): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: */ jpayne@68: __pyx_tuple__74 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_infile, __pyx_n_s_parser); if (unlikely(!__pyx_tuple__74)) __PYX_ERR(0, 1183, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__74); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__74); jpayne@68: __pyx_codeobj__48 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_init, 1183, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__48)) __PYX_ERR(0, 1183, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1190 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: __pyx_codeobj__49 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_iter, 1190, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__49)) __PYX_ERR(0, 1190, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1194 jpayne@68: * jpayne@68: * # cython version - required for python 3 jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char * b jpayne@68: */ jpayne@68: __pyx_tuple__75 = PyTuple_Pack(8, __pyx_n_s_self, __pyx_n_s_b, __pyx_n_s_cpy, __pyx_n_s_nbytes, __pyx_n_s_encoding, __pyx_n_s_line, __pyx_n_s_s_2, __pyx_n_s_bytes_cpy); if (unlikely(!__pyx_tuple__75)) __PYX_ERR(0, 1194, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__75); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__75); jpayne@68: __pyx_codeobj__50 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 8, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_next, 1194, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__50)) __PYX_ERR(0, 1194, __pyx_L1_error) jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1238 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<< jpayne@68: * """return an iterator over all entries in a file. jpayne@68: * jpayne@68: */ jpayne@68: __pyx_tuple__76 = PyTuple_Pack(2, __pyx_n_s_infile, __pyx_n_s_parser); if (unlikely(!__pyx_tuple__76)) __PYX_ERR(0, 1238, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__76); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__76); jpayne@68: __pyx_codeobj__51 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libctabix_pyx, __pyx_n_s_tabix_iterator, 1238, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__51)) __PYX_ERR(0, 1238, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_codeobj__52 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__52)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __pyx_codeobj__53 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__53)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: __pyx_tuple__77 = PyTuple_Pack(5, __pyx_n_s_pyx_type, __pyx_n_s_pyx_checksum, __pyx_n_s_pyx_state, __pyx_n_s_pyx_PickleError, __pyx_n_s_pyx_result); if (unlikely(!__pyx_tuple__77)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_tuple__77); jpayne@68: __Pyx_GIVEREF(__pyx_tuple__77); jpayne@68: __pyx_codeobj__54 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_Parser, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__54)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __pyx_codeobj__57 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asTuple, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__57)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __pyx_codeobj__58 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asGFF3, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__58)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __pyx_codeobj__59 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asGTF, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__59)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __pyx_codeobj__60 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asBed, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__60)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __pyx_codeobj__61 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_asVCF, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__61)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: } jpayne@68: /* #### Code section: init_constants ### */ jpayne@68: jpayne@68: static CYTHON_SMALL_CODE int __Pyx_InitConstants(void) { jpayne@68: __pyx_umethod_PyDict_Type_keys.type = (PyObject*)&PyDict_Type; jpayne@68: __pyx_umethod_PyDict_Type_keys.method_name = &__pyx_n_s_keys; jpayne@68: if (__Pyx_CreateStringTabAndInitStrings() < 0) __PYX_ERR(0, 1, __pyx_L1_error); jpayne@68: __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_17 = PyInt_FromLong(17); if (unlikely(!__pyx_int_17)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_18 = PyInt_FromLong(18); if (unlikely(!__pyx_int_18)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_35 = PyInt_FromLong(35); if (unlikely(!__pyx_int_35)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_64 = PyInt_FromLong(64); if (unlikely(!__pyx_int_64)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_21667264 = PyInt_FromLong(21667264L); if (unlikely(!__pyx_int_21667264)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_139192863 = PyInt_FromLong(139192863L); if (unlikely(!__pyx_int_139192863)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_243541226 = PyInt_FromLong(243541226L); if (unlikely(!__pyx_int_243541226)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: return -1; jpayne@68: } jpayne@68: /* #### Code section: init_globals ### */ jpayne@68: jpayne@68: static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) { jpayne@68: /* AssertionsEnabled.init */ jpayne@68: if (likely(__Pyx_init_assertions_enabled() == 0)); else jpayne@68: jpayne@68: if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: return -1; jpayne@68: } jpayne@68: /* #### Code section: init_module ### */ jpayne@68: jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/ jpayne@68: static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/ jpayne@68: jpayne@68: static int __Pyx_modinit_global_init_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0); jpayne@68: /*--- Global init code ---*/ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __Pyx_modinit_variable_export_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0); jpayne@68: /*--- Variable export code ---*/ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __Pyx_modinit_function_export_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0); jpayne@68: /*--- Function export code ---*/ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __Pyx_modinit_type_init_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0); jpayne@68: /*--- Type init code ---*/ jpayne@68: __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator = &__pyx_vtable_5pysam_9libctabix_tabix_file_iterator; jpayne@68: __pyx_vtable_5pysam_9libctabix_tabix_file_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_tabix_file_iterator *))__pyx_f_5pysam_9libctabix_19tabix_file_iterator___cnext__; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_ptype_5pysam_9libctabix_tabix_file_iterator = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_tabix_file_iterator_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_tabix_file_iterator)) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_tabix_file_iterator_spec, __pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_tabix_file_iterator = &__pyx_type_5pysam_9libctabix_tabix_file_iterator; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_tabix_file_iterator->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator, __pyx_vtabptr_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_tabix_file_iterator, (PyObject *) __pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_tabix_file_iterator) < 0) __PYX_ERR(0, 1098, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_t_1 = PyImport_ImportModule("pysam.libchtslib"); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_ptype_5pysam_10libchtslib_HTSFile = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libchtslib", "HTSFile", sizeof(struct __pyx_obj_5pysam_10libchtslib_HTSFile), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_10libchtslib_HTSFile),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_10libchtslib_HTSFile) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_10libchtslib_HTSFile = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__Pyx_GetVtable(__pyx_ptype_5pysam_10libchtslib_HTSFile); if (unlikely(!__pyx_vtabptr_5pysam_10libchtslib_HTSFile)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_9libctabix_TabixFile = &__pyx_vtable_5pysam_9libctabix_TabixFile; jpayne@68: __pyx_vtable_5pysam_9libctabix_TabixFile.__pyx_base = *__pyx_vtabptr_5pysam_10libchtslib_HTSFile; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixFile = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_TabixFile_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_TabixFile)) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_TabixFile_spec, __pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixFile = &__pyx_type_5pysam_9libctabix_TabixFile; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixFile->tp_base = __pyx_ptype_5pysam_10libchtslib_HTSFile; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixFile->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_TabixFile->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_TabixFile->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixFile->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_vtabptr_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_TabixFile, (PyObject *) __pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_TabixFile) < 0) __PYX_ERR(0, 287, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_Parser = &__pyx_vtable_5pysam_9libctabix_Parser; jpayne@68: __pyx_vtable_5pysam_9libctabix_Parser.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_6Parser_parse; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_ptype_5pysam_9libctabix_Parser = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_Parser_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_Parser)) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_Parser_spec, __pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_Parser = &__pyx_type_5pysam_9libctabix_Parser; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_Parser->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_Parser->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_Parser->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_Parser->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_Parser, __pyx_vtabptr_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Parser, (PyObject *) __pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_Parser) < 0) __PYX_ERR(0, 82, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_asTuple = &__pyx_vtable_5pysam_9libctabix_asTuple; jpayne@68: __pyx_vtable_5pysam_9libctabix_asTuple.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: __pyx_vtable_5pysam_9libctabix_asTuple.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_7asTuple_parse; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_asTuple = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asTuple_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_asTuple)) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asTuple_spec, __pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_asTuple = &__pyx_type_5pysam_9libctabix_asTuple; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_asTuple->tp_base = __pyx_ptype_5pysam_9libctabix_Parser; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_asTuple->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asTuple->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asTuple->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_asTuple->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asTuple, __pyx_vtabptr_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asTuple, (PyObject *) __pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asTuple) < 0) __PYX_ERR(0, 101, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_asGTF = &__pyx_vtable_5pysam_9libctabix_asGTF; jpayne@68: __pyx_vtable_5pysam_9libctabix_asGTF.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: __pyx_vtable_5pysam_9libctabix_asGTF.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_5asGTF_parse; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_asGTF = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asGTF_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_asGTF)) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asGTF_spec, __pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_asGTF = &__pyx_type_5pysam_9libctabix_asGTF; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_asGTF->tp_base = __pyx_ptype_5pysam_9libctabix_Parser; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_asGTF->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asGTF->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asGTF->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_asGTF->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asGTF, __pyx_vtabptr_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asGTF, (PyObject *) __pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asGTF) < 0) __PYX_ERR(0, 151, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_asGFF3 = &__pyx_vtable_5pysam_9libctabix_asGFF3; jpayne@68: __pyx_vtable_5pysam_9libctabix_asGFF3.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: __pyx_vtable_5pysam_9libctabix_asGFF3.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_6asGFF3_parse; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_asGFF3 = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asGFF3_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_asGFF3)) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asGFF3_spec, __pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_asGFF3 = &__pyx_type_5pysam_9libctabix_asGFF3; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_asGFF3->tp_base = __pyx_ptype_5pysam_9libctabix_Parser; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_asGFF3->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asGFF3->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asGFF3->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_asGFF3->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asGFF3, __pyx_vtabptr_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asGFF3, (PyObject *) __pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asGFF3) < 0) __PYX_ERR(0, 115, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_asBed = &__pyx_vtable_5pysam_9libctabix_asBed; jpayne@68: __pyx_vtable_5pysam_9libctabix_asBed.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: __pyx_vtable_5pysam_9libctabix_asBed.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_5asBed_parse; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_asBed = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asBed_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_asBed)) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asBed_spec, __pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_asBed = &__pyx_type_5pysam_9libctabix_asBed; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_asBed->tp_base = __pyx_ptype_5pysam_9libctabix_Parser; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_asBed->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asBed->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asBed->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_asBed->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asBed, __pyx_vtabptr_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asBed, (PyObject *) __pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asBed) < 0) __PYX_ERR(0, 198, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_asVCF = &__pyx_vtable_5pysam_9libctabix_asVCF; jpayne@68: __pyx_vtable_5pysam_9libctabix_asVCF.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_Parser; jpayne@68: __pyx_vtable_5pysam_9libctabix_asVCF.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_9libctabix_Parser *, char *, int))__pyx_f_5pysam_9libctabix_5asVCF_parse; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_Parser); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_asVCF = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_asVCF_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_asVCF)) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_asVCF_spec, __pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_asVCF = &__pyx_type_5pysam_9libctabix_asVCF; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_asVCF->tp_base = __pyx_ptype_5pysam_9libctabix_Parser; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_asVCF->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_asVCF->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_asVCF->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_asVCF->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_asVCF, __pyx_vtabptr_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_asVCF, (PyObject *) __pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_asVCF) < 0) __PYX_ERR(0, 246, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_TabixIterator = &__pyx_vtable_5pysam_9libctabix_TabixIterator; jpayne@68: __pyx_vtable_5pysam_9libctabix_TabixIterator.__pyx___cnext__ = (int (*)(struct __pyx_obj_5pysam_9libctabix_TabixIterator *))__pyx_f_5pysam_9libctabix_13TabixIterator___cnext__; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIterator = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_TabixIterator_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_TabixIterator)) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_TabixIterator_spec, __pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIterator = &__pyx_type_5pysam_9libctabix_TabixIterator; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIterator->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_TabixIterator->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_TabixIterator->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIterator->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: { jpayne@68: PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) { jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__.doc = __pyx_doc_5pysam_9libctabix_13TabixIterator_4__next__; jpayne@68: ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_13TabixIterator_4__next__; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_TabixIterator, __pyx_vtabptr_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_TabixIterator, (PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIterator) < 0) __PYX_ERR(0, 619, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed = &__pyx_vtable_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: __pyx_vtable_5pysam_9libctabix_TabixIteratorParsed.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_TabixIterator; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_TabixIteratorParsed_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed)) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_TabixIteratorParsed_spec, __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed = &__pyx_type_5pysam_9libctabix_TabixIteratorParsed; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_base = __pyx_ptype_5pysam_9libctabix_TabixIterator; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: { jpayne@68: PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) { jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__.doc = __pyx_doc_5pysam_9libctabix_19TabixIteratorParsed_2__next__; jpayne@68: ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_19TabixIteratorParsed_2__next__; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed, __pyx_vtabptr_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_TabixIteratorParsed, (PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_TabixIteratorParsed) < 0) __PYX_ERR(0, 692, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_GZIterator = &__pyx_vtable_5pysam_9libctabix_GZIterator; jpayne@68: __pyx_vtable_5pysam_9libctabix_GZIterator.__pyx___cnext__ = (int (*)(struct __pyx_obj_5pysam_9libctabix_GZIterator *))__pyx_f_5pysam_9libctabix_10GZIterator___cnext__; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIterator = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_GZIterator_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_9libctabix_GZIterator)) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_GZIterator_spec, __pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIterator = &__pyx_type_5pysam_9libctabix_GZIterator; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIterator->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_GZIterator->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_GZIterator->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIterator->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: { jpayne@68: PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator, "__init__"); if (unlikely(!wrapper)) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) { jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__.doc = __pyx_doc_5pysam_9libctabix_10GZIterator___init__; jpayne@68: ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_10GZIterator___init__; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: { jpayne@68: PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) { jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__.doc = __pyx_doc_5pysam_9libctabix_10GZIterator_6__next__; jpayne@68: ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_10GZIterator_6__next__; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_GZIterator, __pyx_vtabptr_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GZIterator, (PyObject *) __pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_GZIterator) < 0) __PYX_ERR(0, 720, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_GZIteratorHead = &__pyx_vtable_5pysam_9libctabix_GZIteratorHead; jpayne@68: __pyx_vtable_5pysam_9libctabix_GZIteratorHead.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_GZIterator; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorHead = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_GZIteratorHead_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_GZIteratorHead)) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_GZIteratorHead_spec, __pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorHead = &__pyx_type_5pysam_9libctabix_GZIteratorHead; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_base = __pyx_ptype_5pysam_9libctabix_GZIterator; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorHead->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: { jpayne@68: PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIteratorHead, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) { jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__.doc = __pyx_doc_5pysam_9libctabix_14GZIteratorHead___next__; jpayne@68: ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_14GZIteratorHead___next__; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_GZIteratorHead, __pyx_vtabptr_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GZIteratorHead, (PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorHead) < 0) __PYX_ERR(0, 775, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed = &__pyx_vtable_5pysam_9libctabix_GZIteratorParsed; jpayne@68: __pyx_vtable_5pysam_9libctabix_GZIteratorParsed.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_GZIterator; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_GZIterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorParsed = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_GZIteratorParsed_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_GZIteratorParsed)) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_GZIteratorParsed_spec, __pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorParsed = &__pyx_type_5pysam_9libctabix_GZIteratorParsed; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_base = __pyx_ptype_5pysam_9libctabix_GZIterator; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_GZIteratorParsed->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_UPDATE_DESCRIPTOR_DOC jpayne@68: { jpayne@68: PyObject *wrapper = PyObject_GetAttrString((PyObject *)__pyx_ptype_5pysam_9libctabix_GZIteratorParsed, "__next__"); if (unlikely(!wrapper)) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: if (__Pyx_IS_TYPE(wrapper, &PyWrapperDescr_Type)) { jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; jpayne@68: __pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__.doc = __pyx_doc_5pysam_9libctabix_16GZIteratorParsed_2__next__; jpayne@68: ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9libctabix_16GZIteratorParsed_2__next__; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed, __pyx_vtabptr_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_GZIteratorParsed, (PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_GZIteratorParsed) < 0) __PYX_ERR(0, 792, __pyx_L1_error) jpayne@68: #endif jpayne@68: __pyx_vtabptr_5pysam_9libctabix_Tabixfile = &__pyx_vtable_5pysam_9libctabix_Tabixfile; jpayne@68: __pyx_vtable_5pysam_9libctabix_Tabixfile.__pyx_base = *__pyx_vtabptr_5pysam_9libctabix_TabixFile; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_t_2 = PyTuple_Pack(1, (PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __pyx_ptype_5pysam_9libctabix_Tabixfile = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_9libctabix_Tabixfile_spec, __pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: if (unlikely(!__pyx_ptype_5pysam_9libctabix_Tabixfile)) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_9libctabix_Tabixfile_spec, __pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: #else jpayne@68: __pyx_ptype_5pysam_9libctabix_Tabixfile = &__pyx_type_5pysam_9libctabix_Tabixfile; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_base = __pyx_ptype_5pysam_9libctabix_TabixFile; jpayne@68: #endif jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_print = 0; jpayne@68: #endif jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_9libctabix_Tabixfile->tp_dictoffset && __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: __pyx_ptype_5pysam_9libctabix_Tabixfile->tp_getattro = __Pyx_PyObject_GenericGetAttr; jpayne@68: } jpayne@68: #endif jpayne@68: if (__Pyx_SetVtable(__pyx_ptype_5pysam_9libctabix_Tabixfile, __pyx_vtabptr_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_MergeVtables(__pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Tabixfile, (PyObject *) __pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_9libctabix_Tabixfile) < 0) __PYX_ERR(0, 1251, __pyx_L1_error) jpayne@68: #endif jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: } jpayne@68: jpayne@68: static int __Pyx_modinit_type_import_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0); jpayne@68: /*--- Type import code ---*/ jpayne@68: __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(5, 9, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", jpayne@68: #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000 jpayne@68: sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject), jpayne@68: #elif CYTHON_COMPILING_IN_LIMITED_API jpayne@68: sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject), jpayne@68: #else jpayne@68: sizeof(PyHeapTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyHeapTypeObject), jpayne@68: #endif jpayne@68: __Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(5, 9, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(6, 8, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyBoolObject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4bool_bool) __PYX_ERR(6, 8, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(7, 15, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyComplexObject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_7complex_complex) __PYX_ERR(7, 15, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = PyImport_ImportModule("pysam.libctabixproxies"); if (unlikely(!__pyx_t_1)) __PYX_ERR(8, 5, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_TupleProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_TupleProxy) __PYX_ERR(8, 5, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_TupleProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_TupleProxy)) __PYX_ERR(8, 5, __pyx_L1_error) jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "TupleProxyIterator", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_TupleProxyIterator),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_TupleProxyIterator) __PYX_ERR(8, 27, __pyx_L1_error) jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "NamedTupleProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_NamedTupleProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy) __PYX_ERR(8, 32, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_NamedTupleProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_NamedTupleProxy)) __PYX_ERR(8, 32, __pyx_L1_error) jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_GTFProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_GTFProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_GTFProxy) __PYX_ERR(8, 36, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_GTFProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_GTFProxy)) __PYX_ERR(8, 36, __pyx_L1_error) jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "GFF3Proxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_GFF3Proxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy) __PYX_ERR(8, 42, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_GFF3Proxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_GFF3Proxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_GFF3Proxy)) __PYX_ERR(8, 42, __pyx_L1_error) jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_BedProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "BedProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_BedProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_BedProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_BedProxy) __PYX_ERR(8, 46, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_16libctabixproxies_BedProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_BedProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_BedProxy)) __PYX_ERR(8, 46, __pyx_L1_error) jpayne@68: __pyx_ptype_5pysam_16libctabixproxies_VCFProxy = __Pyx_ImportType_3_0_11(__pyx_t_1, "pysam.libctabixproxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(struct __pyx_obj_5pysam_16libctabixproxies_VCFProxy),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_5pysam_16libctabixproxies_VCFProxy) __PYX_ERR(8, 58, __pyx_L1_error) jpayne@68: __pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_16libctabixproxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_16libctabixproxies_VCFProxy); if (unlikely(!__pyx_vtabptr_5pysam_16libctabixproxies_VCFProxy)) __PYX_ERR(8, 58, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __pyx_t_1 = PyImport_ImportModule("array"); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 69, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: __pyx_ptype_7cpython_5array_array = __Pyx_ImportType_3_0_11(__pyx_t_1, "array", "array", sizeof(arrayobject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(arrayobject),__Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_5array_array) __PYX_ERR(3, 69, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: } jpayne@68: jpayne@68: static int __Pyx_modinit_variable_import_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0); jpayne@68: /*--- Variable import code ---*/ jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: static int __Pyx_modinit_function_import_code(void) { jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0); jpayne@68: /*--- Function import code ---*/ jpayne@68: __pyx_t_1 = PyImport_ImportModule("pysam.libcutils"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_1); jpayne@68: if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "charptr_to_str", (void (**)(void))&__pyx_f_5pysam_9libcutils_charptr_to_str, "PyObject *(char const *, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "force_str", (void (**)(void))&__pyx_f_5pysam_9libcutils_force_str, "PyObject *(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "force_bytes", (void (**)(void))&__pyx_f_5pysam_9libcutils_force_bytes, "PyObject *(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_bytes *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "encode_filename", (void (**)(void))&__pyx_f_5pysam_9libcutils_encode_filename, "PyObject *(PyObject *)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "from_string_and_size", (void (**)(void))&__pyx_f_5pysam_9libcutils_from_string_and_size, "PyObject *(char const *, size_t)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return 0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_1); jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: return -1; jpayne@68: } jpayne@68: jpayne@68: jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/ jpayne@68: static int __pyx_pymod_exec_libctabix(PyObject* module); /*proto*/ jpayne@68: static PyModuleDef_Slot __pyx_moduledef_slots[] = { jpayne@68: {Py_mod_create, (void*)__pyx_pymod_create}, jpayne@68: {Py_mod_exec, (void*)__pyx_pymod_exec_libctabix}, jpayne@68: {0, NULL} jpayne@68: }; jpayne@68: #endif jpayne@68: jpayne@68: #ifdef __cplusplus jpayne@68: namespace { jpayne@68: struct PyModuleDef __pyx_moduledef = jpayne@68: #else jpayne@68: static struct PyModuleDef __pyx_moduledef = jpayne@68: #endif jpayne@68: { jpayne@68: PyModuleDef_HEAD_INIT, jpayne@68: "libctabix", jpayne@68: 0, /* m_doc */ jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: 0, /* m_size */ jpayne@68: #elif CYTHON_USE_MODULE_STATE jpayne@68: sizeof(__pyx_mstate), /* m_size */ jpayne@68: #else jpayne@68: -1, /* m_size */ jpayne@68: #endif jpayne@68: __pyx_methods /* m_methods */, jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: __pyx_moduledef_slots, /* m_slots */ jpayne@68: #else jpayne@68: NULL, /* m_reload */ jpayne@68: #endif jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: __pyx_m_traverse, /* m_traverse */ jpayne@68: __pyx_m_clear, /* m_clear */ jpayne@68: NULL /* m_free */ jpayne@68: #else jpayne@68: NULL, /* m_traverse */ jpayne@68: NULL, /* m_clear */ jpayne@68: NULL /* m_free */ jpayne@68: #endif jpayne@68: }; jpayne@68: #ifdef __cplusplus jpayne@68: } /* anonymous namespace */ jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: #ifndef CYTHON_NO_PYINIT_EXPORT jpayne@68: #define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC jpayne@68: #elif PY_MAJOR_VERSION < 3 jpayne@68: #ifdef __cplusplus jpayne@68: #define __Pyx_PyMODINIT_FUNC extern "C" void jpayne@68: #else jpayne@68: #define __Pyx_PyMODINIT_FUNC void jpayne@68: #endif jpayne@68: #else jpayne@68: #ifdef __cplusplus jpayne@68: #define __Pyx_PyMODINIT_FUNC extern "C" PyObject * jpayne@68: #else jpayne@68: #define __Pyx_PyMODINIT_FUNC PyObject * jpayne@68: #endif jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __Pyx_PyMODINIT_FUNC initlibctabix(void) CYTHON_SMALL_CODE; /*proto*/ jpayne@68: __Pyx_PyMODINIT_FUNC initlibctabix(void) jpayne@68: #else jpayne@68: __Pyx_PyMODINIT_FUNC PyInit_libctabix(void) CYTHON_SMALL_CODE; /*proto*/ jpayne@68: __Pyx_PyMODINIT_FUNC PyInit_libctabix(void) jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: { jpayne@68: return PyModuleDef_Init(&__pyx_moduledef); jpayne@68: } jpayne@68: static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) { jpayne@68: #if PY_VERSION_HEX >= 0x030700A1 jpayne@68: static PY_INT64_T main_interpreter_id = -1; jpayne@68: PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp); jpayne@68: if (main_interpreter_id == -1) { jpayne@68: main_interpreter_id = current_id; jpayne@68: return (unlikely(current_id == -1)) ? -1 : 0; jpayne@68: } else if (unlikely(main_interpreter_id != current_id)) jpayne@68: #else jpayne@68: static PyInterpreterState *main_interpreter = NULL; jpayne@68: PyInterpreterState *current_interpreter = PyThreadState_Get()->interp; jpayne@68: if (!main_interpreter) { jpayne@68: main_interpreter = current_interpreter; jpayne@68: } else if (unlikely(main_interpreter != current_interpreter)) jpayne@68: #endif jpayne@68: { jpayne@68: PyErr_SetString( jpayne@68: PyExc_ImportError, jpayne@68: "Interpreter change detected - this module can only be loaded into one interpreter per process."); jpayne@68: return -1; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: 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@68: #else jpayne@68: 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@68: #endif jpayne@68: { jpayne@68: PyObject *value = PyObject_GetAttrString(spec, from_name); jpayne@68: int result = 0; jpayne@68: if (likely(value)) { jpayne@68: if (allow_none || value != Py_None) { jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: result = PyModule_AddObject(module, to_name, value); jpayne@68: #else jpayne@68: result = PyDict_SetItemString(moddict, to_name, value); jpayne@68: #endif jpayne@68: } jpayne@68: Py_DECREF(value); jpayne@68: } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) { jpayne@68: PyErr_Clear(); jpayne@68: } else { jpayne@68: result = -1; jpayne@68: } jpayne@68: return result; jpayne@68: } jpayne@68: static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def) { jpayne@68: PyObject *module = NULL, *moddict, *modname; jpayne@68: CYTHON_UNUSED_VAR(def); jpayne@68: if (__Pyx_check_single_interpreter()) jpayne@68: return NULL; jpayne@68: if (__pyx_m) jpayne@68: return __Pyx_NewRef(__pyx_m); jpayne@68: modname = PyObject_GetAttrString(spec, "name"); jpayne@68: if (unlikely(!modname)) goto bad; jpayne@68: module = PyModule_NewObject(modname); jpayne@68: Py_DECREF(modname); jpayne@68: if (unlikely(!module)) goto bad; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: moddict = module; jpayne@68: #else jpayne@68: moddict = PyModule_GetDict(module); jpayne@68: if (unlikely(!moddict)) goto bad; jpayne@68: #endif jpayne@68: if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad; jpayne@68: if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad; jpayne@68: if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad; jpayne@68: if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad; jpayne@68: return module; jpayne@68: bad: jpayne@68: Py_XDECREF(module); jpayne@68: return NULL; jpayne@68: } jpayne@68: jpayne@68: jpayne@68: static CYTHON_SMALL_CODE int __pyx_pymod_exec_libctabix(PyObject *__pyx_pyinit_module) jpayne@68: #endif jpayne@68: #endif jpayne@68: { jpayne@68: int stringtab_initialized = 0; jpayne@68: #if CYTHON_USE_MODULE_STATE jpayne@68: int pystate_addmodule_run = 0; jpayne@68: #endif jpayne@68: __Pyx_TraceDeclarations jpayne@68: PyObject *__pyx_t_1 = NULL; jpayne@68: PyObject *__pyx_t_2 = NULL; jpayne@68: PyObject *__pyx_t_3 = NULL; jpayne@68: PyObject *__pyx_t_4 = NULL; jpayne@68: int __pyx_lineno = 0; jpayne@68: const char *__pyx_filename = NULL; jpayne@68: int __pyx_clineno = 0; jpayne@68: __Pyx_RefNannyDeclarations jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: if (__pyx_m) { jpayne@68: if (__pyx_m == __pyx_pyinit_module) return 0; jpayne@68: PyErr_SetString(PyExc_RuntimeError, "Module 'libctabix' has already been imported. Re-initialisation is not supported."); jpayne@68: return -1; jpayne@68: } jpayne@68: #elif PY_MAJOR_VERSION >= 3 jpayne@68: if (__pyx_m) return __Pyx_NewRef(__pyx_m); jpayne@68: #endif jpayne@68: /*--- Module creation code ---*/ jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: __pyx_m = __pyx_pyinit_module; jpayne@68: Py_INCREF(__pyx_m); jpayne@68: #else jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: __pyx_m = Py_InitModule4("libctabix", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); jpayne@68: if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #elif CYTHON_USE_MODULE_STATE jpayne@68: __pyx_t_1 = PyModule_Create(&__pyx_moduledef); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: { jpayne@68: int add_module_result = PyState_AddModule(__pyx_t_1, &__pyx_moduledef); jpayne@68: __pyx_t_1 = 0; /* transfer ownership from __pyx_t_1 to "libctabix" pseudovariable */ jpayne@68: if (unlikely((add_module_result < 0))) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: pystate_addmodule_run = 1; jpayne@68: } jpayne@68: #else jpayne@68: __pyx_m = PyModule_Create(&__pyx_moduledef); jpayne@68: if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: #endif jpayne@68: CYTHON_UNUSED_VAR(__pyx_t_1); jpayne@68: __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: Py_INCREF(__pyx_d); jpayne@68: __pyx_b = __Pyx_PyImport_AddModuleRef(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_cython_runtime = __Pyx_PyImport_AddModuleRef((const char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #if CYTHON_REFNANNY jpayne@68: __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); jpayne@68: if (!__Pyx_RefNanny) { jpayne@68: PyErr_Clear(); jpayne@68: __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); jpayne@68: if (!__Pyx_RefNanny) jpayne@68: Py_FatalError("failed to import 'refnanny' module"); jpayne@68: } jpayne@68: #endif jpayne@68: __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_libctabix(void)", 0); jpayne@68: 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@68: #ifdef __Pxy_PyFrame_Initialize_Offsets jpayne@68: __Pxy_PyFrame_Initialize_Offsets(); jpayne@68: #endif jpayne@68: __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: if (__pyx_CyFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: #ifdef __Pyx_FusedFunction_USED jpayne@68: if (__pyx_FusedFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: #ifdef __Pyx_Coroutine_USED jpayne@68: if (__pyx_Coroutine_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: #ifdef __Pyx_Generator_USED jpayne@68: if (__pyx_Generator_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: #ifdef __Pyx_AsyncGen_USED jpayne@68: if (__pyx_AsyncGen_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: #ifdef __Pyx_StopAsyncIteration_USED jpayne@68: if (__pyx_StopAsyncIteration_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: /*--- Library function declarations ---*/ jpayne@68: /*--- Threads initialization code ---*/ jpayne@68: #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS jpayne@68: PyEval_InitThreads(); jpayne@68: #endif jpayne@68: /*--- Initialize various global constants etc. ---*/ jpayne@68: if (__Pyx_InitConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: stringtab_initialized = 1; jpayne@68: if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) jpayne@68: if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: if (__pyx_module_is_main_pysam__libctabix) { jpayne@68: if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: } jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: { jpayne@68: PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (!PyDict_GetItemString(modules, "pysam.libctabix")) { jpayne@68: if (unlikely((PyDict_SetItemString(modules, "pysam.libctabix", __pyx_m) < 0))) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: /*--- Builtin init code ---*/ jpayne@68: if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: /*--- Constants init code ---*/ jpayne@68: if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: /*--- Global type/function init code ---*/ jpayne@68: (void)__Pyx_modinit_global_init_code(); jpayne@68: (void)__Pyx_modinit_variable_export_code(); jpayne@68: (void)__Pyx_modinit_function_export_code(); jpayne@68: if (unlikely((__Pyx_modinit_type_init_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: if (unlikely((__Pyx_modinit_type_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: (void)__Pyx_modinit_variable_import_code(); jpayne@68: if (unlikely((__Pyx_modinit_function_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: /*--- Execution code ---*/ jpayne@68: #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) jpayne@68: if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: #endif jpayne@68: __Pyx_TraceCall("__Pyx_PyMODINIT_FUNC PyInit_libctabix(void)", __pyx_f[0], 1, 0, __PYX_ERR(0, 1, __pyx_L1_error)); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":57 jpayne@68: * # jpayne@68: * ############################################################################### jpayne@68: * import os # <<<<<<<<<<<<<< jpayne@68: * import sys jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_os, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 57, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_os, __pyx_t_2) < 0) __PYX_ERR(0, 57, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":58 jpayne@68: * ############################################################################### jpayne@68: * import os jpayne@68: * import sys # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * from libc.stdio cimport printf, fprintf, stderr jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_sys, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 58, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_sys, __pyx_t_2) < 0) __PYX_ERR(0, 58, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":87 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def set_encoding(self, encoding): # <<<<<<<<<<<<<< jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6Parser_3set_encoding, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Parser_set_encoding, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj_)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 87, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser, __pyx_n_s_set_encoding, __pyx_t_2) < 0) __PYX_ERR(0, 87, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":90 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def get_encoding(self): # <<<<<<<<<<<<<< jpayne@68: * return self.encoding jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6Parser_5get_encoding, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Parser_get_encoding, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__2)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 90, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser, __pyx_n_s_get_encoding, __pyx_t_2) < 0) __PYX_ERR(0, 90, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6Parser_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Parser___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__3)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser); jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_Parser, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_Parser__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6Parser_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Parser___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__4)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_Parser, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_Parser); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_7asTuple_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asTuple___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__5)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asTuple, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asTuple); jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asTuple, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asTuple__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_7asTuple_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asTuple___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__6)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asTuple, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asTuple); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6asGFF3_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGFF3___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__7)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGFF3, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGFF3); jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGFF3, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGFF3__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_6asGFF3_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGFF3___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__8)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGFF3, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGFF3); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asGTF_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGTF___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__9)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGTF, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGTF); jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asGTF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asGTF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asGTF_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asGTF___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asGTF, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asGTF); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asBed_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asBed___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__11)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asBed, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asBed); jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asBed, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asBed__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asBed_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asBed___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__12)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asBed, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asBed); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * cdef tuple state jpayne@68: * cdef object _dict jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asVCF_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asVCF___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__13)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asVCF, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asVCF); jpayne@68: jpayne@68: /* "(tree fragment)":16 jpayne@68: * else: jpayne@68: * return __pyx_unpickle_asVCF, (type(self), 0xe8424ea, state) jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_unpickle_asVCF__set_state(self, __pyx_state) jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5asVCF_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_asVCF___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__14)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_asVCF, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 16, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_asVCF); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":352 jpayne@68: * self.encoding = encoding jpayne@68: * jpayne@68: * def _open( self, # <<<<<<<<<<<<<< jpayne@68: * filename, jpayne@68: * mode='r', jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_3_open, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile__open, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__15)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 352, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__68); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_open, __pyx_t_2) < 0) __PYX_ERR(0, 352, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":404 jpayne@68: * self.start_offset = self.tell() jpayne@68: * jpayne@68: * def _dup(self): # <<<<<<<<<<<<<< jpayne@68: * '''return a copy of this tabix file. jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_5_dup, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile__dup, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__17)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 404, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_dup, __pyx_t_2) < 0) __PYX_ERR(0, 404, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":416 jpayne@68: * encoding=self.encoding) jpayne@68: * jpayne@68: * def fetch(self, # <<<<<<<<<<<<<< jpayne@68: * reference=None, jpayne@68: * start=None, jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_7fetch, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile_fetch, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__18)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 416, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__70); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_fetch, __pyx_t_2) < 0) __PYX_ERR(0, 416, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":598 jpayne@68: * return result jpayne@68: * jpayne@68: * def close(self): # <<<<<<<<<<<<<< jpayne@68: * ''' jpayne@68: * closes the :class:`pysam.TabixFile`.''' jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_9close, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile_close, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__21)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 598, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_9libctabix_TabixFile, __pyx_n_s_close, __pyx_t_2) < 0) __PYX_ERR(0, 598, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: PyType_Modified(__pyx_ptype_5pysam_9libctabix_TabixFile); jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_13__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__22)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9TabixFile_15__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixFile___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__23)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13TabixIterator_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIterator___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__25)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13TabixIterator_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIterator___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__26)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":682 jpayne@68: * jpayne@68: * jpayne@68: * class EmptyIterator: # <<<<<<<<<<<<<< jpayne@68: * '''empty iterator''' jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_EmptyIterator, __pyx_n_s_EmptyIterator, (PyObject *) NULL, __pyx_n_s_pysam_libctabix, __pyx_kp_s_empty_iterator); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 682, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":685 jpayne@68: * '''empty iterator''' jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13EmptyIterator_1__iter__, 0, __pyx_n_s_EmptyIterator___iter, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__27)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 685, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_iter, __pyx_t_3) < 0) __PYX_ERR(0, 685, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":688 jpayne@68: * return self jpayne@68: * jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * raise StopIteration() jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13EmptyIterator_3__next__, 0, __pyx_n_s_EmptyIterator___next, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__28)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 688, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_next, __pyx_t_3) < 0) __PYX_ERR(0, 688, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":682 jpayne@68: * jpayne@68: * jpayne@68: * class EmptyIterator: # <<<<<<<<<<<<<< jpayne@68: * '''empty iterator''' jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_Py3ClassCreate(((PyObject*)&PyType_Type), __pyx_n_s_EmptyIterator, __pyx_empty_tuple, __pyx_t_2, NULL, 0, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 682, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_EmptyIterator, __pyx_t_3) < 0) __PYX_ERR(0, 682, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_5__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIteratorParsed___reduce_cyt, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__29)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.iterator cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19TabixIteratorParsed_7__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_TabixIteratorParsed___setstate_c, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__30)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_10GZIterator_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIterator___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__31)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_10GZIterator_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIterator___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__32)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_14GZIteratorHead_3__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorHead___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__33)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_14GZIteratorHead_5__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorHead___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__34)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_5__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorParsed___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__35)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "self.gzipfile,self.kstream cannot be converted to a Python object for pickling" jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_16GZIteratorParsed_7__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_GZIteratorParsed___setstate_cyth, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__36)); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_2) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":811 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_compress(filename_in, # <<<<<<<<<<<<<< jpayne@68: * filename_out, jpayne@68: * force=False): jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_1tabix_compress, 0, __pyx_n_s_tabix_compress, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__37)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 811, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_2, __pyx_tuple__72); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_compress, __pyx_t_2) < 0) __PYX_ERR(0, 811, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":880 jpayne@68: * preset=None, jpayne@68: * meta_char="#", jpayne@68: * int line_skip=0, # <<<<<<<<<<<<<< jpayne@68: * zerobased=False, jpayne@68: * int min_shift=-1, jpayne@68: */ jpayne@68: __pyx_t_2 = __Pyx_PyInt_From_int(((int)0)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 880, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_2); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":882 jpayne@68: * int line_skip=0, jpayne@68: * zerobased=False, jpayne@68: * int min_shift=-1, # <<<<<<<<<<<<<< jpayne@68: * index=None, jpayne@68: * keep_original=False, jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyInt_From_int(((int)-1)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 882, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":873 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_index(filename, # <<<<<<<<<<<<<< jpayne@68: * force=False, jpayne@68: * seq_col=None, jpayne@68: */ jpayne@68: __pyx_t_4 = PyTuple_New(12); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 873, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: __Pyx_INCREF(((PyObject *)Py_False)); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_False)); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 3, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 4, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(((PyObject*)__pyx_kp_u__39)); jpayne@68: __Pyx_GIVEREF(((PyObject*)__pyx_kp_u__39)); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 5, ((PyObject*)__pyx_kp_u__39))) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_2); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 6, __pyx_t_2)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(((PyObject *)Py_False)); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_False)); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 7, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_GIVEREF(__pyx_t_3); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 8, __pyx_t_3)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(Py_None); jpayne@68: __Pyx_GIVEREF(Py_None); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 9, Py_None)) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(((PyObject *)Py_False)); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_False)); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 10, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __Pyx_INCREF(((PyObject *)Py_False)); jpayne@68: __Pyx_GIVEREF(((PyObject *)Py_False)); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 11, ((PyObject *)Py_False))) __PYX_ERR(0, 873, __pyx_L1_error); jpayne@68: __pyx_t_2 = 0; jpayne@68: __pyx_t_3 = 0; jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_3tabix_index, 0, __pyx_n_s_tabix_index, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__40)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 873, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_t_4); jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_index, __pyx_t_3) < 0) __PYX_ERR(0, 873, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_9__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_tabix_file_iterator___reduce_cyt, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__46)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_19tabix_file_iterator_11__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_tabix_file_iterator___setstate_c, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__47)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1178 jpayne@68: * jpayne@68: * jpayne@68: * class tabix_generic_iterator: # <<<<<<<<<<<<<< jpayne@68: * '''iterate over ``infile``. jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_tabix_generic_iterator, __pyx_n_s_tabix_generic_iterator, (PyObject *) NULL, __pyx_n_s_pysam_libctabix, __pyx_kp_s_iterate_over_infile_Permits_the); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1178, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1183 jpayne@68: * Permits the use of file-like objects for example from the gzip module. jpayne@68: * ''' jpayne@68: * def __init__(self, infile, parser): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * self.infile = infile jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_1__init__, 0, __pyx_n_s_tabix_generic_iterator___init, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__48)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1183, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: if (__Pyx_SetNameInClass(__pyx_t_3, __pyx_n_s_init, __pyx_t_4) < 0) __PYX_ERR(0, 1183, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1190 jpayne@68: * self.parser = parser jpayne@68: * jpayne@68: * def __iter__(self): # <<<<<<<<<<<<<< jpayne@68: * return self jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_3__iter__, 0, __pyx_n_s_tabix_generic_iterator___iter, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__49)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1190, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: if (__Pyx_SetNameInClass(__pyx_t_3, __pyx_n_s_iter, __pyx_t_4) < 0) __PYX_ERR(0, 1190, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1194 jpayne@68: * jpayne@68: * # cython version - required for python 3 jpayne@68: * def __next__(self): # <<<<<<<<<<<<<< jpayne@68: * jpayne@68: * cdef char * b jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_22tabix_generic_iterator_5__next__, 0, __pyx_n_s_tabix_generic_iterator___next, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__50)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1194, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: if (__Pyx_SetNameInClass(__pyx_t_3, __pyx_n_s_next, __pyx_t_4) < 0) __PYX_ERR(0, 1194, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1178 jpayne@68: * jpayne@68: * jpayne@68: * class tabix_generic_iterator: # <<<<<<<<<<<<<< jpayne@68: * '''iterate over ``infile``. jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_4 = __Pyx_Py3ClassCreate(((PyObject*)&PyType_Type), __pyx_n_s_tabix_generic_iterator, __pyx_empty_tuple, __pyx_t_3, NULL, 0, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 1178, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_4); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_generic_iterator, __pyx_t_4) < 0) __PYX_ERR(0, 1178, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1238 jpayne@68: * jpayne@68: * jpayne@68: * def tabix_iterator(infile, parser): # <<<<<<<<<<<<<< jpayne@68: * """return an iterator over all entries in a file. jpayne@68: * jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_5tabix_iterator, 0, __pyx_n_s_tabix_iterator, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__51)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1238, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_tabix_iterator, __pyx_t_3) < 0) __PYX_ERR(0, 1238, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __reduce_cython__(self): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9Tabixfile_1__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Tabixfile___reduce_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__52)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":3 jpayne@68: * def __reduce_cython__(self): jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9Tabixfile_3__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_Tabixfile___setstate_cython, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__53)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1256 jpayne@68: * jpayne@68: * jpayne@68: * __all__ = [ # <<<<<<<<<<<<<< jpayne@68: * "tabix_index", jpayne@68: * "tabix_compress", jpayne@68: */ jpayne@68: __pyx_t_3 = PyList_New(14); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1256, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: __Pyx_INCREF(__pyx_n_u_tabix_index); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_tabix_index); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_u_tabix_index)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_tabix_compress); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_tabix_compress); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 1, __pyx_n_u_tabix_compress)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_TabixFile); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_TabixFile); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 2, __pyx_n_u_TabixFile)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_Tabixfile); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_Tabixfile); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 3, __pyx_n_u_Tabixfile)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_asTuple); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_asTuple); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 4, __pyx_n_u_asTuple)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_asGTF); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_asGTF); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 5, __pyx_n_u_asGTF)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_asGFF3); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_asGFF3); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 6, __pyx_n_u_asGFF3)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_asVCF); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_asVCF); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 7, __pyx_n_u_asVCF)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_asBed); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_asBed); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 8, __pyx_n_u_asBed)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_GZIterator); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_GZIterator); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 9, __pyx_n_u_GZIterator)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_GZIteratorHead); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_GZIteratorHead); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 10, __pyx_n_u_GZIteratorHead)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_tabix_iterator); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_tabix_iterator); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 11, __pyx_n_u_tabix_iterator)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_tabix_generic_iterator); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_tabix_generic_iterator); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 12, __pyx_n_u_tabix_generic_iterator)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: __Pyx_INCREF(__pyx_n_u_tabix_file_iterator); jpayne@68: __Pyx_GIVEREF(__pyx_n_u_tabix_file_iterator); jpayne@68: if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 13, __pyx_n_u_tabix_file_iterator)) __PYX_ERR(0, 1256, __pyx_L1_error); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_all, __pyx_t_3) < 0) __PYX_ERR(0, 1256, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_Parser(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_7__pyx_unpickle_Parser, 0, __pyx_n_s_pyx_unpickle_Parser, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__54)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_Parser, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_Parser__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_Parser__set_state(Parser __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_9__pyx_unpickle_asTuple, 0, __pyx_n_s_pyx_unpickle_asTuple, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__57)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asTuple, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asGFF3(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_11__pyx_unpickle_asGFF3, 0, __pyx_n_s_pyx_unpickle_asGFF3, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__58)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asGFF3, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asGFF3__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asGFF3__set_state(asGFF3 __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_13__pyx_unpickle_asGTF, 0, __pyx_n_s_pyx_unpickle_asGTF, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__59)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asGTF, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":1 jpayne@68: * def __pyx_unpickle_asBed(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * cdef object __pyx_PickleError jpayne@68: * cdef object __pyx_result jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_15__pyx_unpickle_asBed, 0, __pyx_n_s_pyx_unpickle_asBed, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__60)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asBed, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "(tree fragment)":11 jpayne@68: * __pyx_unpickle_asBed__set_state( __pyx_result, __pyx_state) jpayne@68: * return __pyx_result jpayne@68: * cdef __pyx_unpickle_asBed__set_state(asBed __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< jpayne@68: * __pyx_result.encoding = __pyx_state[0] jpayne@68: * if len(__pyx_state) > 1 and hasattr(__pyx_result, '__dict__'): jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_9libctabix_17__pyx_unpickle_asVCF, 0, __pyx_n_s_pyx_unpickle_asVCF, NULL, __pyx_n_s_pysam_libctabix, __pyx_d, ((PyObject *)__pyx_codeobj__61)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_asVCF, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: jpayne@68: /* "pysam/libctabix.pyx":1 jpayne@68: * # cython: language_level=3 # <<<<<<<<<<<<<< jpayne@68: * # cython: embedsignature=True jpayne@68: * # cython: profile=True jpayne@68: */ jpayne@68: __pyx_t_3 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __Pyx_GOTREF(__pyx_t_3); jpayne@68: if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error) jpayne@68: __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; jpayne@68: __Pyx_TraceReturn(Py_None, 0); jpayne@68: jpayne@68: /*--- Wrapped vars code ---*/ jpayne@68: jpayne@68: goto __pyx_L0; jpayne@68: __pyx_L1_error:; jpayne@68: __Pyx_XDECREF(__pyx_t_2); jpayne@68: __Pyx_XDECREF(__pyx_t_3); jpayne@68: __Pyx_XDECREF(__pyx_t_4); jpayne@68: if (__pyx_m) { jpayne@68: if (__pyx_d && stringtab_initialized) { jpayne@68: __Pyx_AddTraceback("init pysam.libctabix", __pyx_clineno, __pyx_lineno, __pyx_filename); jpayne@68: } jpayne@68: #if !CYTHON_USE_MODULE_STATE jpayne@68: Py_CLEAR(__pyx_m); jpayne@68: #else jpayne@68: Py_DECREF(__pyx_m); jpayne@68: if (pystate_addmodule_run) { jpayne@68: PyObject *tp, *value, *tb; jpayne@68: PyErr_Fetch(&tp, &value, &tb); jpayne@68: PyState_RemoveModule(&__pyx_moduledef); jpayne@68: PyErr_Restore(tp, value, tb); jpayne@68: } jpayne@68: #endif jpayne@68: } else if (!PyErr_Occurred()) { jpayne@68: PyErr_SetString(PyExc_ImportError, "init pysam.libctabix"); jpayne@68: } jpayne@68: __pyx_L0:; jpayne@68: __Pyx_RefNannyFinishContext(); jpayne@68: #if CYTHON_PEP489_MULTI_PHASE_INIT jpayne@68: return (__pyx_m != NULL) ? 0 : -1; jpayne@68: #elif PY_MAJOR_VERSION >= 3 jpayne@68: return __pyx_m; jpayne@68: #else jpayne@68: return; jpayne@68: #endif jpayne@68: } jpayne@68: /* #### Code section: cleanup_globals ### */ jpayne@68: /* #### Code section: cleanup_module ### */ jpayne@68: /* #### Code section: main_method ### */ jpayne@68: /* #### Code section: utility_code_pragmas ### */ jpayne@68: #ifdef _MSC_VER jpayne@68: #pragma warning( push ) jpayne@68: /* Warning 4127: conditional expression is constant jpayne@68: * Cython uses constant conditional expressions to allow in inline functions to be optimized at jpayne@68: * compile-time, so this warning is not useful jpayne@68: */ jpayne@68: #pragma warning( disable : 4127 ) jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: jpayne@68: /* #### Code section: utility_code_def ### */ jpayne@68: jpayne@68: /* --- Runtime support code --- */ jpayne@68: /* Refnanny */ jpayne@68: #if CYTHON_REFNANNY jpayne@68: static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { jpayne@68: PyObject *m = NULL, *p = NULL; jpayne@68: void *r = NULL; jpayne@68: m = PyImport_ImportModule(modname); jpayne@68: if (!m) goto end; jpayne@68: p = PyObject_GetAttrString(m, "RefNannyAPI"); jpayne@68: if (!p) goto end; jpayne@68: r = PyLong_AsVoidPtr(p); jpayne@68: end: jpayne@68: Py_XDECREF(p); jpayne@68: Py_XDECREF(m); jpayne@68: return (__Pyx_RefNannyAPIStruct *)r; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyErrExceptionMatches */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { jpayne@68: Py_ssize_t i, n; jpayne@68: n = PyTuple_GET_SIZE(tuple); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: for (i=0; i= 0x030C00A6 jpayne@68: PyObject *current_exception = tstate->current_exception; jpayne@68: if (unlikely(!current_exception)) return 0; jpayne@68: exc_type = (PyObject*) Py_TYPE(current_exception); jpayne@68: if (exc_type == err) return 1; jpayne@68: #else jpayne@68: exc_type = tstate->curexc_type; jpayne@68: if (exc_type == err) return 1; jpayne@68: if (unlikely(!exc_type)) return 0; jpayne@68: #endif jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_INCREF(exc_type); jpayne@68: #endif jpayne@68: if (unlikely(PyTuple_Check(err))) { jpayne@68: result = __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); jpayne@68: } else { jpayne@68: result = __Pyx_PyErr_GivenExceptionMatches(exc_type, err); jpayne@68: } jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_DECREF(exc_type); jpayne@68: #endif jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyErrFetchRestore */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { jpayne@68: #if PY_VERSION_HEX >= 0x030C00A6 jpayne@68: PyObject *tmp_value; jpayne@68: assert(type == NULL || (value != NULL && type == (PyObject*) Py_TYPE(value))); jpayne@68: if (value) { jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: if (unlikely(((PyBaseExceptionObject*) value)->traceback != tb)) jpayne@68: #endif jpayne@68: PyException_SetTraceback(value, tb); jpayne@68: } jpayne@68: tmp_value = tstate->current_exception; jpayne@68: tstate->current_exception = value; jpayne@68: Py_XDECREF(tmp_value); jpayne@68: Py_XDECREF(type); jpayne@68: Py_XDECREF(tb); jpayne@68: #else jpayne@68: PyObject *tmp_type, *tmp_value, *tmp_tb; jpayne@68: tmp_type = tstate->curexc_type; jpayne@68: tmp_value = tstate->curexc_value; jpayne@68: tmp_tb = tstate->curexc_traceback; jpayne@68: tstate->curexc_type = type; jpayne@68: tstate->curexc_value = value; jpayne@68: tstate->curexc_traceback = tb; jpayne@68: Py_XDECREF(tmp_type); jpayne@68: Py_XDECREF(tmp_value); jpayne@68: Py_XDECREF(tmp_tb); jpayne@68: #endif jpayne@68: } jpayne@68: static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { jpayne@68: #if PY_VERSION_HEX >= 0x030C00A6 jpayne@68: PyObject* exc_value; jpayne@68: exc_value = tstate->current_exception; jpayne@68: tstate->current_exception = 0; jpayne@68: *value = exc_value; jpayne@68: *type = NULL; jpayne@68: *tb = NULL; jpayne@68: if (exc_value) { jpayne@68: *type = (PyObject*) Py_TYPE(exc_value); jpayne@68: Py_INCREF(*type); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: *tb = ((PyBaseExceptionObject*) exc_value)->traceback; jpayne@68: Py_XINCREF(*tb); jpayne@68: #else jpayne@68: *tb = PyException_GetTraceback(exc_value); jpayne@68: #endif jpayne@68: } jpayne@68: #else jpayne@68: *type = tstate->curexc_type; jpayne@68: *value = tstate->curexc_value; jpayne@68: *tb = tstate->curexc_traceback; jpayne@68: tstate->curexc_type = 0; jpayne@68: tstate->curexc_value = 0; jpayne@68: tstate->curexc_traceback = 0; jpayne@68: #endif jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectGetAttrStr */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { jpayne@68: PyTypeObject* tp = Py_TYPE(obj); jpayne@68: if (likely(tp->tp_getattro)) jpayne@68: return tp->tp_getattro(obj, attr_name); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(tp->tp_getattr)) jpayne@68: return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); jpayne@68: #endif jpayne@68: return PyObject_GetAttr(obj, attr_name); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectGetAttrStrNoError */ jpayne@68: #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1 jpayne@68: static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { jpayne@68: __Pyx_PyThreadState_declare jpayne@68: __Pyx_PyThreadState_assign jpayne@68: if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) jpayne@68: __Pyx_PyErr_Clear(); jpayne@68: } jpayne@68: #endif jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { jpayne@68: PyObject *result; jpayne@68: #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 jpayne@68: (void) PyObject_GetOptionalAttr(obj, attr_name, &result); jpayne@68: return result; jpayne@68: #else jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 jpayne@68: PyTypeObject* tp = Py_TYPE(obj); jpayne@68: if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { jpayne@68: return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); jpayne@68: } jpayne@68: #endif jpayne@68: result = __Pyx_PyObject_GetAttrStr(obj, attr_name); jpayne@68: if (unlikely(!result)) { jpayne@68: __Pyx_PyObject_GetAttrStr_ClearAttributeError(); jpayne@68: } jpayne@68: return result; jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* GetBuiltinName */ jpayne@68: static PyObject *__Pyx_GetBuiltinName(PyObject *name) { jpayne@68: PyObject* result = __Pyx_PyObject_GetAttrStrNoError(__pyx_b, name); jpayne@68: if (unlikely(!result) && !PyErr_Occurred()) { jpayne@68: PyErr_Format(PyExc_NameError, jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: "name '%U' is not defined", name); jpayne@68: #else jpayne@68: "name '%.200s' is not defined", PyString_AS_STRING(name)); jpayne@68: #endif jpayne@68: } jpayne@68: return result; jpayne@68: } jpayne@68: jpayne@68: /* TupleAndListFromArray */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static CYTHON_INLINE void __Pyx_copy_object_array(PyObject *const *CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) { jpayne@68: PyObject *v; jpayne@68: Py_ssize_t i; jpayne@68: for (i = 0; i < length; i++) { jpayne@68: v = dest[i] = src[i]; jpayne@68: Py_INCREF(v); jpayne@68: } jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject * jpayne@68: __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n) jpayne@68: { jpayne@68: PyObject *res; jpayne@68: if (n <= 0) { jpayne@68: Py_INCREF(__pyx_empty_tuple); jpayne@68: return __pyx_empty_tuple; jpayne@68: } jpayne@68: res = PyTuple_New(n); jpayne@68: if (unlikely(res == NULL)) return NULL; jpayne@68: __Pyx_copy_object_array(src, ((PyTupleObject*)res)->ob_item, n); jpayne@68: return res; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject * jpayne@68: __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n) jpayne@68: { jpayne@68: PyObject *res; jpayne@68: if (n <= 0) { jpayne@68: return PyList_New(0); jpayne@68: } jpayne@68: res = PyList_New(n); jpayne@68: if (unlikely(res == NULL)) return NULL; jpayne@68: __Pyx_copy_object_array(src, ((PyListObject*)res)->ob_item, n); jpayne@68: return res; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* BytesEquals */ jpayne@68: static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { jpayne@68: #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: return PyObject_RichCompareBool(s1, s2, equals); jpayne@68: #else jpayne@68: if (s1 == s2) { jpayne@68: return (equals == Py_EQ); jpayne@68: } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { jpayne@68: const char *ps1, *ps2; jpayne@68: Py_ssize_t length = PyBytes_GET_SIZE(s1); jpayne@68: if (length != PyBytes_GET_SIZE(s2)) jpayne@68: return (equals == Py_NE); jpayne@68: ps1 = PyBytes_AS_STRING(s1); jpayne@68: ps2 = PyBytes_AS_STRING(s2); jpayne@68: if (ps1[0] != ps2[0]) { jpayne@68: return (equals == Py_NE); jpayne@68: } else if (length == 1) { jpayne@68: return (equals == Py_EQ); jpayne@68: } else { jpayne@68: int result; jpayne@68: #if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) jpayne@68: Py_hash_t hash1, hash2; jpayne@68: hash1 = ((PyBytesObject*)s1)->ob_shash; jpayne@68: hash2 = ((PyBytesObject*)s2)->ob_shash; jpayne@68: if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { jpayne@68: return (equals == Py_NE); jpayne@68: } jpayne@68: #endif jpayne@68: result = memcmp(ps1, ps2, (size_t)length); jpayne@68: return (equals == Py_EQ) ? (result == 0) : (result != 0); jpayne@68: } jpayne@68: } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { jpayne@68: return (equals == Py_NE); jpayne@68: } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { jpayne@68: return (equals == Py_NE); jpayne@68: } else { jpayne@68: int result; jpayne@68: PyObject* py_result = PyObject_RichCompare(s1, s2, equals); jpayne@68: if (!py_result) jpayne@68: return -1; jpayne@68: result = __Pyx_PyObject_IsTrue(py_result); jpayne@68: Py_DECREF(py_result); jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* UnicodeEquals */ jpayne@68: static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { jpayne@68: #if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: return PyObject_RichCompareBool(s1, s2, equals); jpayne@68: #else jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyObject* owned_ref = NULL; jpayne@68: #endif jpayne@68: int s1_is_unicode, s2_is_unicode; jpayne@68: if (s1 == s2) { jpayne@68: goto return_eq; jpayne@68: } jpayne@68: s1_is_unicode = PyUnicode_CheckExact(s1); jpayne@68: s2_is_unicode = PyUnicode_CheckExact(s2); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { jpayne@68: owned_ref = PyUnicode_FromObject(s2); jpayne@68: if (unlikely(!owned_ref)) jpayne@68: return -1; jpayne@68: s2 = owned_ref; jpayne@68: s2_is_unicode = 1; jpayne@68: } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { jpayne@68: owned_ref = PyUnicode_FromObject(s1); jpayne@68: if (unlikely(!owned_ref)) jpayne@68: return -1; jpayne@68: s1 = owned_ref; jpayne@68: s1_is_unicode = 1; jpayne@68: } else if (((!s2_is_unicode) & (!s1_is_unicode))) { jpayne@68: return __Pyx_PyBytes_Equals(s1, s2, equals); jpayne@68: } jpayne@68: #endif jpayne@68: if (s1_is_unicode & s2_is_unicode) { jpayne@68: Py_ssize_t length; jpayne@68: int kind; jpayne@68: void *data1, *data2; jpayne@68: if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) jpayne@68: return -1; jpayne@68: length = __Pyx_PyUnicode_GET_LENGTH(s1); jpayne@68: if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { jpayne@68: goto return_ne; jpayne@68: } jpayne@68: #if CYTHON_USE_UNICODE_INTERNALS jpayne@68: { jpayne@68: Py_hash_t hash1, hash2; jpayne@68: #if CYTHON_PEP393_ENABLED jpayne@68: hash1 = ((PyASCIIObject*)s1)->hash; jpayne@68: hash2 = ((PyASCIIObject*)s2)->hash; jpayne@68: #else jpayne@68: hash1 = ((PyUnicodeObject*)s1)->hash; jpayne@68: hash2 = ((PyUnicodeObject*)s2)->hash; jpayne@68: #endif jpayne@68: if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { jpayne@68: goto return_ne; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: kind = __Pyx_PyUnicode_KIND(s1); jpayne@68: if (kind != __Pyx_PyUnicode_KIND(s2)) { jpayne@68: goto return_ne; jpayne@68: } jpayne@68: data1 = __Pyx_PyUnicode_DATA(s1); jpayne@68: data2 = __Pyx_PyUnicode_DATA(s2); jpayne@68: if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { jpayne@68: goto return_ne; jpayne@68: } else if (length == 1) { jpayne@68: goto return_eq; jpayne@68: } else { jpayne@68: int result = memcmp(data1, data2, (size_t)(length * kind)); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: Py_XDECREF(owned_ref); jpayne@68: #endif jpayne@68: return (equals == Py_EQ) ? (result == 0) : (result != 0); jpayne@68: } jpayne@68: } else if ((s1 == Py_None) & s2_is_unicode) { jpayne@68: goto return_ne; jpayne@68: } else if ((s2 == Py_None) & s1_is_unicode) { jpayne@68: goto return_ne; jpayne@68: } else { jpayne@68: int result; jpayne@68: PyObject* py_result = PyObject_RichCompare(s1, s2, equals); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: Py_XDECREF(owned_ref); jpayne@68: #endif jpayne@68: if (!py_result) jpayne@68: return -1; jpayne@68: result = __Pyx_PyObject_IsTrue(py_result); jpayne@68: Py_DECREF(py_result); jpayne@68: return result; jpayne@68: } jpayne@68: return_eq: jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: Py_XDECREF(owned_ref); jpayne@68: #endif jpayne@68: return (equals == Py_EQ); jpayne@68: return_ne: jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: Py_XDECREF(owned_ref); jpayne@68: #endif jpayne@68: return (equals == Py_NE); jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* fastcall */ jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s) jpayne@68: { jpayne@68: Py_ssize_t i, n = PyTuple_GET_SIZE(kwnames); jpayne@68: for (i = 0; i < n; i++) jpayne@68: { jpayne@68: if (s == PyTuple_GET_ITEM(kwnames, i)) return kwvalues[i]; jpayne@68: } jpayne@68: for (i = 0; i < n; i++) jpayne@68: { jpayne@68: int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ); jpayne@68: if (unlikely(eq != 0)) { jpayne@68: if (unlikely(eq < 0)) return NULL; jpayne@68: return kwvalues[i]; jpayne@68: } jpayne@68: } jpayne@68: return NULL; jpayne@68: } jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000 jpayne@68: CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) { jpayne@68: Py_ssize_t i, nkwargs = PyTuple_GET_SIZE(kwnames); jpayne@68: PyObject *dict; jpayne@68: dict = PyDict_New(); jpayne@68: if (unlikely(!dict)) jpayne@68: return NULL; jpayne@68: for (i=0; i= 3 jpayne@68: "%s() got multiple values for keyword argument '%U'", func_name, kw_name); jpayne@68: #else jpayne@68: "%s() got multiple values for keyword argument '%s'", func_name, jpayne@68: PyString_AsString(kw_name)); jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* ParseKeywords */ jpayne@68: static int __Pyx_ParseOptionalKeywords( jpayne@68: PyObject *kwds, jpayne@68: PyObject *const *kwvalues, jpayne@68: PyObject **argnames[], jpayne@68: PyObject *kwds2, jpayne@68: PyObject *values[], jpayne@68: Py_ssize_t num_pos_args, jpayne@68: const char* function_name) jpayne@68: { jpayne@68: PyObject *key = 0, *value = 0; jpayne@68: Py_ssize_t pos = 0; jpayne@68: PyObject*** name; jpayne@68: PyObject*** first_kw_arg = argnames + num_pos_args; jpayne@68: int kwds_is_tuple = CYTHON_METH_FASTCALL && likely(PyTuple_Check(kwds)); jpayne@68: while (1) { jpayne@68: Py_XDECREF(key); key = NULL; jpayne@68: Py_XDECREF(value); value = NULL; jpayne@68: if (kwds_is_tuple) { jpayne@68: Py_ssize_t size; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: size = PyTuple_GET_SIZE(kwds); jpayne@68: #else jpayne@68: size = PyTuple_Size(kwds); jpayne@68: if (size < 0) goto bad; jpayne@68: #endif jpayne@68: if (pos >= size) break; jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: key = __Pyx_PySequence_ITEM(kwds, pos); jpayne@68: if (!key) goto bad; jpayne@68: #elif CYTHON_ASSUME_SAFE_MACROS jpayne@68: key = PyTuple_GET_ITEM(kwds, pos); jpayne@68: #else jpayne@68: key = PyTuple_GetItem(kwds, pos); jpayne@68: if (!key) goto bad; jpayne@68: #endif jpayne@68: value = kwvalues[pos]; jpayne@68: pos++; jpayne@68: } jpayne@68: else jpayne@68: { jpayne@68: if (!PyDict_Next(kwds, &pos, &key, &value)) break; jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_INCREF(key); jpayne@68: #endif jpayne@68: } jpayne@68: name = first_kw_arg; jpayne@68: while (*name && (**name != key)) name++; jpayne@68: if (*name) { jpayne@68: values[name-argnames] = value; jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_INCREF(value); jpayne@68: Py_DECREF(key); jpayne@68: #endif jpayne@68: key = NULL; jpayne@68: value = NULL; jpayne@68: continue; jpayne@68: } jpayne@68: #if !CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_INCREF(key); jpayne@68: #endif jpayne@68: Py_INCREF(value); jpayne@68: name = first_kw_arg; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyString_Check(key))) { jpayne@68: while (*name) { jpayne@68: if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) jpayne@68: && _PyString_Eq(**name, key)) { jpayne@68: values[name-argnames] = value; jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: value = NULL; jpayne@68: #endif jpayne@68: break; jpayne@68: } jpayne@68: name++; jpayne@68: } jpayne@68: if (*name) continue; jpayne@68: else { jpayne@68: PyObject*** argname = argnames; jpayne@68: while (argname != first_kw_arg) { jpayne@68: if ((**argname == key) || ( jpayne@68: (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) jpayne@68: && _PyString_Eq(**argname, key))) { jpayne@68: goto arg_passed_twice; jpayne@68: } jpayne@68: argname++; jpayne@68: } jpayne@68: } jpayne@68: } else jpayne@68: #endif jpayne@68: if (likely(PyUnicode_Check(key))) { jpayne@68: while (*name) { jpayne@68: int cmp = ( jpayne@68: #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 jpayne@68: (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : jpayne@68: #endif jpayne@68: PyUnicode_Compare(**name, key) jpayne@68: ); jpayne@68: if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; jpayne@68: if (cmp == 0) { jpayne@68: values[name-argnames] = value; jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: value = NULL; jpayne@68: #endif jpayne@68: break; jpayne@68: } jpayne@68: name++; jpayne@68: } jpayne@68: if (*name) continue; jpayne@68: else { jpayne@68: PyObject*** argname = argnames; jpayne@68: while (argname != first_kw_arg) { jpayne@68: int cmp = (**argname == key) ? 0 : jpayne@68: #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 jpayne@68: (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : jpayne@68: #endif jpayne@68: PyUnicode_Compare(**argname, key); jpayne@68: if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; jpayne@68: if (cmp == 0) goto arg_passed_twice; jpayne@68: argname++; jpayne@68: } jpayne@68: } jpayne@68: } else jpayne@68: goto invalid_keyword_type; jpayne@68: if (kwds2) { jpayne@68: if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; jpayne@68: } else { jpayne@68: goto invalid_keyword; jpayne@68: } jpayne@68: } jpayne@68: Py_XDECREF(key); jpayne@68: Py_XDECREF(value); jpayne@68: return 0; jpayne@68: arg_passed_twice: jpayne@68: __Pyx_RaiseDoubleKeywordsError(function_name, key); jpayne@68: goto bad; jpayne@68: invalid_keyword_type: jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() keywords must be strings", function_name); jpayne@68: goto bad; jpayne@68: invalid_keyword: jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() got an unexpected keyword argument '%.200s'", jpayne@68: function_name, PyString_AsString(key)); jpayne@68: #else jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%s() got an unexpected keyword argument '%U'", jpayne@68: function_name, key); jpayne@68: #endif jpayne@68: bad: jpayne@68: Py_XDECREF(key); jpayne@68: Py_XDECREF(value); jpayne@68: return -1; jpayne@68: } jpayne@68: jpayne@68: /* RaiseArgTupleInvalid */ jpayne@68: static void __Pyx_RaiseArgtupleInvalid( jpayne@68: const char* func_name, jpayne@68: int exact, jpayne@68: Py_ssize_t num_min, jpayne@68: Py_ssize_t num_max, jpayne@68: Py_ssize_t num_found) jpayne@68: { jpayne@68: Py_ssize_t num_expected; jpayne@68: const char *more_or_less; jpayne@68: if (num_found < num_min) { jpayne@68: num_expected = num_min; jpayne@68: more_or_less = "at least"; jpayne@68: } else { jpayne@68: num_expected = num_max; jpayne@68: more_or_less = "at most"; jpayne@68: } jpayne@68: if (exact) { jpayne@68: more_or_less = "exactly"; jpayne@68: } jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: func_name, more_or_less, num_expected, jpayne@68: (num_expected == 1) ? "" : "s", num_found); jpayne@68: } jpayne@68: jpayne@68: /* Profile */ jpayne@68: #if CYTHON_PROFILE jpayne@68: static int __Pyx_TraceSetupAndCall(PyCodeObject** code, jpayne@68: PyFrameObject** frame, jpayne@68: PyThreadState* tstate, jpayne@68: const char *funcname, jpayne@68: const char *srcfile, jpayne@68: int firstlineno) { jpayne@68: PyObject *type, *value, *traceback; jpayne@68: int retval; jpayne@68: if (*frame == NULL || !CYTHON_PROFILE_REUSE_FRAME) { jpayne@68: if (*code == NULL) { jpayne@68: *code = __Pyx_createFrameCodeObject(funcname, srcfile, firstlineno); jpayne@68: if (*code == NULL) return 0; jpayne@68: } jpayne@68: *frame = PyFrame_New( jpayne@68: tstate, /*PyThreadState *tstate*/ jpayne@68: *code, /*PyCodeObject *code*/ jpayne@68: __pyx_d, /*PyObject *globals*/ jpayne@68: 0 /*PyObject *locals*/ jpayne@68: ); jpayne@68: if (*frame == NULL) return 0; jpayne@68: if (CYTHON_TRACE && (*frame)->f_trace == NULL) { jpayne@68: Py_INCREF(Py_None); jpayne@68: (*frame)->f_trace = Py_None; jpayne@68: } jpayne@68: #if PY_VERSION_HEX < 0x030400B1 jpayne@68: } else { jpayne@68: (*frame)->f_tstate = tstate; jpayne@68: #endif jpayne@68: } jpayne@68: __Pyx_PyFrame_SetLineNumber(*frame, firstlineno); jpayne@68: retval = 1; jpayne@68: __Pyx_EnterTracing(tstate); jpayne@68: __Pyx_ErrFetchInState(tstate, &type, &value, &traceback); jpayne@68: #if CYTHON_TRACE jpayne@68: if (tstate->c_tracefunc) jpayne@68: retval = tstate->c_tracefunc(tstate->c_traceobj, *frame, PyTrace_CALL, NULL) == 0; jpayne@68: if (retval && tstate->c_profilefunc) jpayne@68: #endif jpayne@68: retval = tstate->c_profilefunc(tstate->c_profileobj, *frame, PyTrace_CALL, NULL) == 0; jpayne@68: __Pyx_LeaveTracing(tstate); jpayne@68: if (retval) { jpayne@68: __Pyx_ErrRestoreInState(tstate, type, value, traceback); jpayne@68: return __Pyx_IsTracing(tstate, 0, 0) && retval; jpayne@68: } else { jpayne@68: Py_XDECREF(type); jpayne@68: Py_XDECREF(value); jpayne@68: Py_XDECREF(traceback); jpayne@68: return -1; jpayne@68: } jpayne@68: } jpayne@68: static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) { jpayne@68: PyCodeObject *py_code = 0; jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: py_code = PyCode_NewEmpty(srcfile, funcname, firstlineno); jpayne@68: if (likely(py_code)) { jpayne@68: py_code->co_flags |= CO_OPTIMIZED | CO_NEWLOCALS; jpayne@68: } jpayne@68: #else jpayne@68: PyObject *py_srcfile = 0; jpayne@68: PyObject *py_funcname = 0; jpayne@68: py_funcname = PyString_FromString(funcname); jpayne@68: if (unlikely(!py_funcname)) goto bad; jpayne@68: py_srcfile = PyString_FromString(srcfile); jpayne@68: if (unlikely(!py_srcfile)) goto bad; jpayne@68: py_code = PyCode_New( jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: CO_OPTIMIZED | CO_NEWLOCALS, jpayne@68: __pyx_empty_bytes, /*PyObject *code,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *consts,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *names,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *varnames,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *freevars,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *cellvars,*/ jpayne@68: py_srcfile, /*PyObject *filename,*/ jpayne@68: py_funcname, /*PyObject *name,*/ jpayne@68: firstlineno, jpayne@68: __pyx_empty_bytes /*PyObject *lnotab*/ jpayne@68: ); jpayne@68: bad: jpayne@68: Py_XDECREF(py_srcfile); jpayne@68: Py_XDECREF(py_funcname); jpayne@68: #endif jpayne@68: return py_code; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* KeywordStringCheck */ jpayne@68: static int __Pyx_CheckKeywordStrings( jpayne@68: PyObject *kw, jpayne@68: const char* function_name, jpayne@68: int kw_allowed) jpayne@68: { jpayne@68: PyObject* key = 0; jpayne@68: Py_ssize_t pos = 0; jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: if (!kw_allowed && PyDict_Next(kw, &pos, &key, 0)) jpayne@68: goto invalid_keyword; jpayne@68: return 1; jpayne@68: #else jpayne@68: if (CYTHON_METH_FASTCALL && likely(PyTuple_Check(kw))) { jpayne@68: Py_ssize_t kwsize; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: kwsize = PyTuple_GET_SIZE(kw); jpayne@68: #else jpayne@68: kwsize = PyTuple_Size(kw); jpayne@68: if (kwsize < 0) return 0; jpayne@68: #endif jpayne@68: if (unlikely(kwsize == 0)) jpayne@68: return 1; jpayne@68: if (!kw_allowed) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: key = PyTuple_GET_ITEM(kw, 0); jpayne@68: #else jpayne@68: key = PyTuple_GetItem(kw, pos); jpayne@68: if (!key) return 0; jpayne@68: #endif jpayne@68: goto invalid_keyword; jpayne@68: } jpayne@68: #if PY_VERSION_HEX < 0x03090000 jpayne@68: for (pos = 0; pos < kwsize; pos++) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: key = PyTuple_GET_ITEM(kw, pos); jpayne@68: #else jpayne@68: key = PyTuple_GetItem(kw, pos); jpayne@68: if (!key) return 0; jpayne@68: #endif jpayne@68: if (unlikely(!PyUnicode_Check(key))) jpayne@68: goto invalid_keyword_type; jpayne@68: } jpayne@68: #endif jpayne@68: return 1; jpayne@68: } jpayne@68: while (PyDict_Next(kw, &pos, &key, 0)) { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (unlikely(!PyString_Check(key))) jpayne@68: #endif jpayne@68: if (unlikely(!PyUnicode_Check(key))) jpayne@68: goto invalid_keyword_type; jpayne@68: } jpayne@68: if (!kw_allowed && unlikely(key)) jpayne@68: goto invalid_keyword; jpayne@68: return 1; jpayne@68: invalid_keyword_type: jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() keywords must be strings", function_name); jpayne@68: return 0; jpayne@68: #endif jpayne@68: invalid_keyword: jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() got an unexpected keyword argument '%.200s'", jpayne@68: function_name, PyString_AsString(key)); jpayne@68: #else jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%s() got an unexpected keyword argument '%U'", jpayne@68: function_name, key); jpayne@68: #endif jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* PyFunctionFastCall */ jpayne@68: #if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL jpayne@68: static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, jpayne@68: PyObject *globals) { jpayne@68: PyFrameObject *f; jpayne@68: PyThreadState *tstate = __Pyx_PyThreadState_Current; jpayne@68: PyObject **fastlocals; jpayne@68: Py_ssize_t i; jpayne@68: PyObject *result; jpayne@68: assert(globals != NULL); jpayne@68: /* XXX Perhaps we should create a specialized jpayne@68: PyFrame_New() that doesn't take locals, but does jpayne@68: take builtins without sanity checking them. jpayne@68: */ jpayne@68: assert(tstate != NULL); jpayne@68: f = PyFrame_New(tstate, co, globals, NULL); jpayne@68: if (f == NULL) { jpayne@68: return NULL; jpayne@68: } jpayne@68: fastlocals = __Pyx_PyFrame_GetLocalsplus(f); jpayne@68: for (i = 0; i < na; i++) { jpayne@68: Py_INCREF(*args); jpayne@68: fastlocals[i] = *args++; jpayne@68: } jpayne@68: result = PyEval_EvalFrameEx(f,0); jpayne@68: ++tstate->recursion_depth; jpayne@68: Py_DECREF(f); jpayne@68: --tstate->recursion_depth; jpayne@68: return result; jpayne@68: } jpayne@68: static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { jpayne@68: PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); jpayne@68: PyObject *globals = PyFunction_GET_GLOBALS(func); jpayne@68: PyObject *argdefs = PyFunction_GET_DEFAULTS(func); jpayne@68: PyObject *closure; jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: PyObject *kwdefs; jpayne@68: #endif jpayne@68: PyObject *kwtuple, **k; jpayne@68: PyObject **d; jpayne@68: Py_ssize_t nd; jpayne@68: Py_ssize_t nk; jpayne@68: PyObject *result; jpayne@68: assert(kwargs == NULL || PyDict_Check(kwargs)); jpayne@68: nk = kwargs ? PyDict_Size(kwargs) : 0; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) { jpayne@68: return NULL; jpayne@68: } jpayne@68: #else jpayne@68: if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) { jpayne@68: return NULL; jpayne@68: } jpayne@68: #endif jpayne@68: if ( jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: co->co_kwonlyargcount == 0 && jpayne@68: #endif jpayne@68: likely(kwargs == NULL || nk == 0) && jpayne@68: co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { jpayne@68: if (argdefs == NULL && co->co_argcount == nargs) { jpayne@68: result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); jpayne@68: goto done; jpayne@68: } jpayne@68: else if (nargs == 0 && argdefs != NULL jpayne@68: && co->co_argcount == Py_SIZE(argdefs)) { jpayne@68: /* function called with no arguments, but all parameters have jpayne@68: a default value: use default values as arguments .*/ jpayne@68: args = &PyTuple_GET_ITEM(argdefs, 0); jpayne@68: result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); jpayne@68: goto done; jpayne@68: } jpayne@68: } jpayne@68: if (kwargs != NULL) { jpayne@68: Py_ssize_t pos, i; jpayne@68: kwtuple = PyTuple_New(2 * nk); jpayne@68: if (kwtuple == NULL) { jpayne@68: result = NULL; jpayne@68: goto done; jpayne@68: } jpayne@68: k = &PyTuple_GET_ITEM(kwtuple, 0); jpayne@68: pos = i = 0; jpayne@68: while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { jpayne@68: Py_INCREF(k[i]); jpayne@68: Py_INCREF(k[i+1]); jpayne@68: i += 2; jpayne@68: } jpayne@68: nk = i / 2; jpayne@68: } jpayne@68: else { jpayne@68: kwtuple = NULL; jpayne@68: k = NULL; jpayne@68: } jpayne@68: closure = PyFunction_GET_CLOSURE(func); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: kwdefs = PyFunction_GET_KW_DEFAULTS(func); jpayne@68: #endif jpayne@68: if (argdefs != NULL) { jpayne@68: d = &PyTuple_GET_ITEM(argdefs, 0); jpayne@68: nd = Py_SIZE(argdefs); jpayne@68: } jpayne@68: else { jpayne@68: d = NULL; jpayne@68: nd = 0; jpayne@68: } jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, jpayne@68: args, (int)nargs, jpayne@68: k, (int)nk, jpayne@68: d, (int)nd, kwdefs, closure); jpayne@68: #else jpayne@68: result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, jpayne@68: args, (int)nargs, jpayne@68: k, (int)nk, jpayne@68: d, (int)nd, closure); jpayne@68: #endif jpayne@68: Py_XDECREF(kwtuple); jpayne@68: done: jpayne@68: Py_LeaveRecursiveCall(); jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectCall */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { jpayne@68: PyObject *result; jpayne@68: ternaryfunc call = Py_TYPE(func)->tp_call; jpayne@68: if (unlikely(!call)) jpayne@68: return PyObject_Call(func, arg, kw); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) jpayne@68: return NULL; jpayne@68: #else jpayne@68: if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) jpayne@68: return NULL; jpayne@68: #endif jpayne@68: result = (*call)(func, arg, kw); jpayne@68: Py_LeaveRecursiveCall(); jpayne@68: if (unlikely(!result) && unlikely(!PyErr_Occurred())) { jpayne@68: PyErr_SetString( jpayne@68: PyExc_SystemError, jpayne@68: "NULL result without error in PyObject_Call"); jpayne@68: } jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectCallMethO */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { jpayne@68: PyObject *self, *result; jpayne@68: PyCFunction cfunc; jpayne@68: cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func); jpayne@68: self = __Pyx_CyOrPyCFunction_GET_SELF(func); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) jpayne@68: return NULL; jpayne@68: #else jpayne@68: if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) jpayne@68: return NULL; jpayne@68: #endif jpayne@68: result = cfunc(self, arg); jpayne@68: Py_LeaveRecursiveCall(); jpayne@68: if (unlikely(!result) && unlikely(!PyErr_Occurred())) { jpayne@68: PyErr_SetString( jpayne@68: PyExc_SystemError, jpayne@68: "NULL result without error in PyObject_Call"); jpayne@68: } jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectFastCall */ jpayne@68: #if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) { jpayne@68: PyObject *argstuple; jpayne@68: PyObject *result = 0; jpayne@68: size_t i; jpayne@68: argstuple = PyTuple_New((Py_ssize_t)nargs); jpayne@68: if (unlikely(!argstuple)) return NULL; jpayne@68: for (i = 0; i < nargs; i++) { jpayne@68: Py_INCREF(args[i]); jpayne@68: if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad; jpayne@68: } jpayne@68: result = __Pyx_PyObject_Call(func, argstuple, kwargs); jpayne@68: bad: jpayne@68: Py_DECREF(argstuple); jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) { jpayne@68: Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: if (nargs == 0 && kwargs == NULL) { jpayne@68: if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS)) jpayne@68: return __Pyx_PyObject_CallMethO(func, NULL); jpayne@68: } jpayne@68: else if (nargs == 1 && kwargs == NULL) { jpayne@68: if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O)) jpayne@68: return __Pyx_PyObject_CallMethO(func, args[0]); jpayne@68: } jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030800B1 jpayne@68: #if CYTHON_FAST_PYCCALL jpayne@68: if (PyCFunction_Check(func)) { jpayne@68: if (kwargs) { jpayne@68: return _PyCFunction_FastCallDict(func, args, nargs, kwargs); jpayne@68: } else { jpayne@68: return _PyCFunction_FastCallKeywords(func, args, nargs, NULL); jpayne@68: } jpayne@68: } jpayne@68: #if PY_VERSION_HEX >= 0x030700A1 jpayne@68: if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) { jpayne@68: return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL); jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: #if CYTHON_FAST_PYCALL jpayne@68: if (PyFunction_Check(func)) { jpayne@68: return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs); jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: if (kwargs == NULL) { jpayne@68: #if CYTHON_VECTORCALL jpayne@68: #if PY_VERSION_HEX < 0x03090000 jpayne@68: vectorcallfunc f = _PyVectorcall_Function(func); jpayne@68: #else jpayne@68: vectorcallfunc f = PyVectorcall_Function(func); jpayne@68: #endif jpayne@68: if (f) { jpayne@68: return f(func, args, (size_t)nargs, NULL); jpayne@68: } jpayne@68: #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL jpayne@68: if (__Pyx_CyFunction_CheckExact(func)) { jpayne@68: __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func); jpayne@68: if (f) return f(func, args, (size_t)nargs, NULL); jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: if (nargs == 0) { jpayne@68: return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs); jpayne@68: } jpayne@68: #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs); jpayne@68: #else jpayne@68: return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs); jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* PyObjectCallOneArg */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { jpayne@68: PyObject *args[2] = {NULL, arg}; jpayne@68: return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); jpayne@68: } jpayne@68: jpayne@68: /* RaiseException */ jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { jpayne@68: __Pyx_PyThreadState_declare jpayne@68: CYTHON_UNUSED_VAR(cause); jpayne@68: Py_XINCREF(type); jpayne@68: if (!value || value == Py_None) jpayne@68: value = NULL; jpayne@68: else jpayne@68: Py_INCREF(value); jpayne@68: if (!tb || tb == Py_None) jpayne@68: tb = NULL; jpayne@68: else { jpayne@68: Py_INCREF(tb); jpayne@68: if (!PyTraceBack_Check(tb)) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "raise: arg 3 must be a traceback or None"); jpayne@68: goto raise_error; jpayne@68: } jpayne@68: } jpayne@68: if (PyType_Check(type)) { jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: if (!value) { jpayne@68: Py_INCREF(Py_None); jpayne@68: value = Py_None; jpayne@68: } jpayne@68: #endif jpayne@68: PyErr_NormalizeException(&type, &value, &tb); jpayne@68: } else { jpayne@68: if (value) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "instance exception may not have a separate value"); jpayne@68: goto raise_error; jpayne@68: } jpayne@68: value = type; jpayne@68: type = (PyObject*) Py_TYPE(type); jpayne@68: Py_INCREF(type); jpayne@68: if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "raise: exception class must be a subclass of BaseException"); jpayne@68: goto raise_error; jpayne@68: } jpayne@68: } jpayne@68: __Pyx_PyThreadState_assign jpayne@68: __Pyx_ErrRestore(type, value, tb); jpayne@68: return; jpayne@68: raise_error: jpayne@68: Py_XDECREF(value); jpayne@68: Py_XDECREF(type); jpayne@68: Py_XDECREF(tb); jpayne@68: return; jpayne@68: } jpayne@68: #else jpayne@68: static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { jpayne@68: PyObject* owned_instance = NULL; jpayne@68: if (tb == Py_None) { jpayne@68: tb = 0; jpayne@68: } else if (tb && !PyTraceBack_Check(tb)) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "raise: arg 3 must be a traceback or None"); jpayne@68: goto bad; jpayne@68: } jpayne@68: if (value == Py_None) jpayne@68: value = 0; jpayne@68: if (PyExceptionInstance_Check(type)) { jpayne@68: if (value) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "instance exception may not have a separate value"); jpayne@68: goto bad; jpayne@68: } jpayne@68: value = type; jpayne@68: type = (PyObject*) Py_TYPE(value); jpayne@68: } else if (PyExceptionClass_Check(type)) { jpayne@68: PyObject *instance_class = NULL; jpayne@68: if (value && PyExceptionInstance_Check(value)) { jpayne@68: instance_class = (PyObject*) Py_TYPE(value); jpayne@68: if (instance_class != type) { jpayne@68: int is_subclass = PyObject_IsSubclass(instance_class, type); jpayne@68: if (!is_subclass) { jpayne@68: instance_class = NULL; jpayne@68: } else if (unlikely(is_subclass == -1)) { jpayne@68: goto bad; jpayne@68: } else { jpayne@68: type = instance_class; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: if (!instance_class) { jpayne@68: PyObject *args; jpayne@68: if (!value) jpayne@68: args = PyTuple_New(0); jpayne@68: else if (PyTuple_Check(value)) { jpayne@68: Py_INCREF(value); jpayne@68: args = value; jpayne@68: } else jpayne@68: args = PyTuple_Pack(1, value); jpayne@68: if (!args) jpayne@68: goto bad; jpayne@68: owned_instance = PyObject_Call(type, args, NULL); jpayne@68: Py_DECREF(args); jpayne@68: if (!owned_instance) jpayne@68: goto bad; jpayne@68: value = owned_instance; jpayne@68: if (!PyExceptionInstance_Check(value)) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "calling %R should have returned an instance of " jpayne@68: "BaseException, not %R", jpayne@68: type, Py_TYPE(value)); jpayne@68: goto bad; jpayne@68: } jpayne@68: } jpayne@68: } else { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "raise: exception class must be a subclass of BaseException"); jpayne@68: goto bad; jpayne@68: } jpayne@68: if (cause) { jpayne@68: PyObject *fixed_cause; jpayne@68: if (cause == Py_None) { jpayne@68: fixed_cause = NULL; jpayne@68: } else if (PyExceptionClass_Check(cause)) { jpayne@68: fixed_cause = PyObject_CallObject(cause, NULL); jpayne@68: if (fixed_cause == NULL) jpayne@68: goto bad; jpayne@68: } else if (PyExceptionInstance_Check(cause)) { jpayne@68: fixed_cause = cause; jpayne@68: Py_INCREF(fixed_cause); jpayne@68: } else { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "exception causes must derive from " jpayne@68: "BaseException"); jpayne@68: goto bad; jpayne@68: } jpayne@68: PyException_SetCause(value, fixed_cause); jpayne@68: } jpayne@68: PyErr_SetObject(type, value); jpayne@68: if (tb) { jpayne@68: #if PY_VERSION_HEX >= 0x030C00A6 jpayne@68: PyException_SetTraceback(value, tb); jpayne@68: #elif CYTHON_FAST_THREAD_STATE jpayne@68: PyThreadState *tstate = __Pyx_PyThreadState_Current; jpayne@68: PyObject* tmp_tb = tstate->curexc_traceback; jpayne@68: if (tb != tmp_tb) { jpayne@68: Py_INCREF(tb); jpayne@68: tstate->curexc_traceback = tb; jpayne@68: Py_XDECREF(tmp_tb); jpayne@68: } jpayne@68: #else jpayne@68: PyObject *tmp_type, *tmp_value, *tmp_tb; jpayne@68: PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); jpayne@68: Py_INCREF(tb); jpayne@68: PyErr_Restore(tmp_type, tmp_value, tb); jpayne@68: Py_XDECREF(tmp_tb); jpayne@68: #endif jpayne@68: } jpayne@68: bad: jpayne@68: Py_XDECREF(owned_instance); jpayne@68: return; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* GetAttr3 */ jpayne@68: #if __PYX_LIMITED_VERSION_HEX < 0x030d00A1 jpayne@68: static PyObject *__Pyx_GetAttr3Default(PyObject *d) { jpayne@68: __Pyx_PyThreadState_declare jpayne@68: __Pyx_PyThreadState_assign jpayne@68: if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) jpayne@68: return NULL; jpayne@68: __Pyx_PyErr_Clear(); jpayne@68: Py_INCREF(d); jpayne@68: return d; jpayne@68: } jpayne@68: #endif jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { jpayne@68: PyObject *r; jpayne@68: #if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 jpayne@68: int res = PyObject_GetOptionalAttr(o, n, &r); jpayne@68: return (res != 0) ? r : __Pyx_NewRef(d); jpayne@68: #else jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: if (likely(PyString_Check(n))) { jpayne@68: r = __Pyx_PyObject_GetAttrStrNoError(o, n); jpayne@68: if (unlikely(!r) && likely(!PyErr_Occurred())) { jpayne@68: r = __Pyx_NewRef(d); jpayne@68: } jpayne@68: return r; jpayne@68: } jpayne@68: #endif jpayne@68: r = PyObject_GetAttr(o, n); jpayne@68: return (likely(r)) ? r : __Pyx_GetAttr3Default(d); jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* PyDictVersioning */ jpayne@68: #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS jpayne@68: static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { jpayne@68: PyObject *dict = Py_TYPE(obj)->tp_dict; jpayne@68: return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; jpayne@68: } jpayne@68: static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { jpayne@68: PyObject **dictptr = NULL; jpayne@68: Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; jpayne@68: if (offset) { jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); jpayne@68: #else jpayne@68: dictptr = _PyObject_GetDictPtr(obj); jpayne@68: #endif jpayne@68: } jpayne@68: return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; jpayne@68: } jpayne@68: static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { jpayne@68: PyObject *dict = Py_TYPE(obj)->tp_dict; jpayne@68: if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) jpayne@68: return 0; jpayne@68: return obj_dict_version == __Pyx_get_object_dict_version(obj); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* GetModuleGlobalName */ jpayne@68: #if CYTHON_USE_DICT_VERSIONS jpayne@68: static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) jpayne@68: #else jpayne@68: static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *result; jpayne@68: #if !CYTHON_AVOID_BORROWED_REFS jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000 jpayne@68: result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); jpayne@68: __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) jpayne@68: if (likely(result)) { jpayne@68: return __Pyx_NewRef(result); jpayne@68: } else if (unlikely(PyErr_Occurred())) { jpayne@68: return NULL; jpayne@68: } jpayne@68: #elif CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (unlikely(!__pyx_m)) { jpayne@68: return NULL; jpayne@68: } jpayne@68: result = PyObject_GetAttr(__pyx_m, name); jpayne@68: if (likely(result)) { jpayne@68: return result; jpayne@68: } jpayne@68: #else jpayne@68: result = PyDict_GetItem(__pyx_d, name); jpayne@68: __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) jpayne@68: if (likely(result)) { jpayne@68: return __Pyx_NewRef(result); jpayne@68: } jpayne@68: #endif jpayne@68: #else jpayne@68: result = PyObject_GetItem(__pyx_d, name); jpayne@68: __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) jpayne@68: if (likely(result)) { jpayne@68: return __Pyx_NewRef(result); jpayne@68: } jpayne@68: PyErr_Clear(); jpayne@68: #endif jpayne@68: return __Pyx_GetBuiltinName(name); jpayne@68: } jpayne@68: jpayne@68: /* RaiseUnexpectedTypeError */ jpayne@68: static int jpayne@68: __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj) jpayne@68: { jpayne@68: __Pyx_TypeName obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); jpayne@68: PyErr_Format(PyExc_TypeError, "Expected %s, got " __Pyx_FMT_TYPENAME, jpayne@68: expected, obj_type_name); jpayne@68: __Pyx_DECREF_TypeName(obj_type_name); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* ExtTypeTest */ jpayne@68: static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { jpayne@68: __Pyx_TypeName obj_type_name; jpayne@68: __Pyx_TypeName type_name; jpayne@68: if (unlikely(!type)) { jpayne@68: PyErr_SetString(PyExc_SystemError, "Missing type object"); jpayne@68: return 0; jpayne@68: } jpayne@68: if (likely(__Pyx_TypeCheck(obj, type))) jpayne@68: return 1; jpayne@68: obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); jpayne@68: type_name = __Pyx_PyType_GetName(type); jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "Cannot convert " __Pyx_FMT_TYPENAME " to " __Pyx_FMT_TYPENAME, jpayne@68: obj_type_name, type_name); jpayne@68: __Pyx_DECREF_TypeName(obj_type_name); jpayne@68: __Pyx_DECREF_TypeName(type_name); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* PyIntBinop */ jpayne@68: #if !CYTHON_COMPILING_IN_PYPY jpayne@68: static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) { jpayne@68: CYTHON_MAYBE_UNUSED_VAR(intval); jpayne@68: CYTHON_MAYBE_UNUSED_VAR(inplace); jpayne@68: CYTHON_UNUSED_VAR(zerodivision_check); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_CheckExact(op1))) { jpayne@68: const long b = intval; jpayne@68: long x; jpayne@68: long a = PyInt_AS_LONG(op1); jpayne@68: jpayne@68: x = (long)((unsigned long)a + (unsigned long)b); jpayne@68: if (likely((x^a) >= 0 || (x^b) >= 0)) jpayne@68: return PyInt_FromLong(x); jpayne@68: return PyLong_Type.tp_as_number->nb_add(op1, op2); jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (likely(PyLong_CheckExact(op1))) { jpayne@68: const long b = intval; jpayne@68: long a, x; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: const PY_LONG_LONG llb = intval; jpayne@68: PY_LONG_LONG lla, llx; jpayne@68: #endif jpayne@68: if (unlikely(__Pyx_PyLong_IsZero(op1))) { jpayne@68: return __Pyx_NewRef(op2); jpayne@68: } jpayne@68: if (likely(__Pyx_PyLong_IsCompact(op1))) { jpayne@68: a = __Pyx_PyLong_CompactValue(op1); jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(op1); jpayne@68: const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1); jpayne@68: switch (size) { jpayne@68: case -2: jpayne@68: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { jpayne@68: a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); jpayne@68: break; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { jpayne@68: lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); jpayne@68: goto long_long; jpayne@68: #endif jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 2: jpayne@68: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { jpayne@68: a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); jpayne@68: break; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { jpayne@68: lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); jpayne@68: goto long_long; jpayne@68: #endif jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case -3: jpayne@68: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { jpayne@68: a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); jpayne@68: break; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { jpayne@68: 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@68: goto long_long; jpayne@68: #endif jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 3: jpayne@68: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { jpayne@68: a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); jpayne@68: break; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { jpayne@68: 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@68: goto long_long; jpayne@68: #endif jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case -4: jpayne@68: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { jpayne@68: 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@68: break; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { jpayne@68: 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@68: goto long_long; jpayne@68: #endif jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: case 4: jpayne@68: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { jpayne@68: 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@68: break; jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { jpayne@68: 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@68: goto long_long; jpayne@68: #endif jpayne@68: } jpayne@68: CYTHON_FALLTHROUGH; jpayne@68: default: return PyLong_Type.tp_as_number->nb_add(op1, op2); jpayne@68: } jpayne@68: } jpayne@68: x = a + b; jpayne@68: return PyLong_FromLong(x); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: long_long: jpayne@68: llx = lla + llb; jpayne@68: return PyLong_FromLongLong(llx); jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: } jpayne@68: #endif jpayne@68: if (PyFloat_CheckExact(op1)) { jpayne@68: const long b = intval; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: double a = __pyx_PyFloat_AsDouble(op1); jpayne@68: #else jpayne@68: double a = PyFloat_AS_DOUBLE(op1); jpayne@68: #endif jpayne@68: double result; jpayne@68: jpayne@68: PyFPE_START_PROTECT("add", return NULL) jpayne@68: result = ((double)a) + (double)b; jpayne@68: PyFPE_END_PROTECT(result) jpayne@68: return PyFloat_FromDouble(result); jpayne@68: } jpayne@68: return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* WriteUnraisableException */ jpayne@68: static void __Pyx_WriteUnraisable(const char *name, int clineno, jpayne@68: int lineno, const char *filename, jpayne@68: int full_traceback, int nogil) { jpayne@68: PyObject *old_exc, *old_val, *old_tb; jpayne@68: PyObject *ctx; jpayne@68: __Pyx_PyThreadState_declare jpayne@68: #ifdef WITH_THREAD jpayne@68: PyGILState_STATE state; jpayne@68: if (nogil) jpayne@68: state = PyGILState_Ensure(); jpayne@68: else state = (PyGILState_STATE)0; jpayne@68: #endif jpayne@68: CYTHON_UNUSED_VAR(clineno); jpayne@68: CYTHON_UNUSED_VAR(lineno); jpayne@68: CYTHON_UNUSED_VAR(filename); jpayne@68: CYTHON_MAYBE_UNUSED_VAR(nogil); jpayne@68: __Pyx_PyThreadState_assign jpayne@68: __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); jpayne@68: if (full_traceback) { jpayne@68: Py_XINCREF(old_exc); jpayne@68: Py_XINCREF(old_val); jpayne@68: Py_XINCREF(old_tb); jpayne@68: __Pyx_ErrRestore(old_exc, old_val, old_tb); jpayne@68: PyErr_PrintEx(0); jpayne@68: } jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: ctx = PyString_FromString(name); jpayne@68: #else jpayne@68: ctx = PyUnicode_FromString(name); jpayne@68: #endif jpayne@68: __Pyx_ErrRestore(old_exc, old_val, old_tb); jpayne@68: if (!ctx) { jpayne@68: PyErr_WriteUnraisable(Py_None); jpayne@68: } else { jpayne@68: PyErr_WriteUnraisable(ctx); jpayne@68: Py_DECREF(ctx); jpayne@68: } jpayne@68: #ifdef WITH_THREAD jpayne@68: if (nogil) jpayne@68: PyGILState_Release(state); jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* PyObjectCallNoArg */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { jpayne@68: PyObject *arg[2] = {NULL, NULL}; jpayne@68: return __Pyx_PyObject_FastCall(func, arg + 1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); jpayne@68: } jpayne@68: jpayne@68: /* ArgTypeTest */ jpayne@68: static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) jpayne@68: { jpayne@68: __Pyx_TypeName type_name; jpayne@68: __Pyx_TypeName obj_type_name; jpayne@68: if (unlikely(!type)) { jpayne@68: PyErr_SetString(PyExc_SystemError, "Missing type object"); jpayne@68: return 0; jpayne@68: } jpayne@68: else if (exact) { jpayne@68: #if PY_MAJOR_VERSION == 2 jpayne@68: if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; jpayne@68: #endif jpayne@68: } jpayne@68: else { jpayne@68: if (likely(__Pyx_TypeCheck(obj, type))) return 1; jpayne@68: } jpayne@68: type_name = __Pyx_PyType_GetName(type); jpayne@68: obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "Argument '%.200s' has incorrect type (expected " __Pyx_FMT_TYPENAME jpayne@68: ", got " __Pyx_FMT_TYPENAME ")", name, type_name, obj_type_name); jpayne@68: __Pyx_DECREF_TypeName(type_name); jpayne@68: __Pyx_DECREF_TypeName(obj_type_name); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* PyObjectFormatAndDecref */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f) { jpayne@68: if (unlikely(!s)) return NULL; jpayne@68: if (likely(PyUnicode_CheckExact(s))) return s; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyString_CheckExact(s))) { jpayne@68: PyObject *result = PyUnicode_FromEncodedObject(s, NULL, "strict"); jpayne@68: Py_DECREF(s); jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: return __Pyx_PyObject_FormatAndDecref(s, f); jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f) { jpayne@68: PyObject *result; jpayne@68: if (unlikely(!s)) return NULL; jpayne@68: result = PyObject_Format(s, f); jpayne@68: Py_DECREF(s); jpayne@68: return result; jpayne@68: } jpayne@68: jpayne@68: /* JoinPyUnicode */ jpayne@68: static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength, jpayne@68: Py_UCS4 max_char) { jpayne@68: #if CYTHON_USE_UNICODE_INTERNALS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: PyObject *result_uval; jpayne@68: int result_ukind, kind_shift; jpayne@68: Py_ssize_t i, char_pos; jpayne@68: void *result_udata; jpayne@68: CYTHON_MAYBE_UNUSED_VAR(max_char); jpayne@68: #if CYTHON_PEP393_ENABLED jpayne@68: result_uval = PyUnicode_New(result_ulength, max_char); jpayne@68: if (unlikely(!result_uval)) return NULL; jpayne@68: result_ukind = (max_char <= 255) ? PyUnicode_1BYTE_KIND : (max_char <= 65535) ? PyUnicode_2BYTE_KIND : PyUnicode_4BYTE_KIND; jpayne@68: kind_shift = (result_ukind == PyUnicode_4BYTE_KIND) ? 2 : result_ukind - 1; jpayne@68: result_udata = PyUnicode_DATA(result_uval); jpayne@68: #else jpayne@68: result_uval = PyUnicode_FromUnicode(NULL, result_ulength); jpayne@68: if (unlikely(!result_uval)) return NULL; jpayne@68: result_ukind = sizeof(Py_UNICODE); jpayne@68: kind_shift = (result_ukind == 4) ? 2 : result_ukind - 1; jpayne@68: result_udata = PyUnicode_AS_UNICODE(result_uval); jpayne@68: #endif jpayne@68: assert(kind_shift == 2 || kind_shift == 1 || kind_shift == 0); jpayne@68: char_pos = 0; jpayne@68: for (i=0; i < value_count; i++) { jpayne@68: int ukind; jpayne@68: Py_ssize_t ulength; jpayne@68: void *udata; jpayne@68: PyObject *uval = PyTuple_GET_ITEM(value_tuple, i); jpayne@68: if (unlikely(__Pyx_PyUnicode_READY(uval))) jpayne@68: goto bad; jpayne@68: ulength = __Pyx_PyUnicode_GET_LENGTH(uval); jpayne@68: if (unlikely(!ulength)) jpayne@68: continue; jpayne@68: if (unlikely((PY_SSIZE_T_MAX >> kind_shift) - ulength < char_pos)) jpayne@68: goto overflow; jpayne@68: ukind = __Pyx_PyUnicode_KIND(uval); jpayne@68: udata = __Pyx_PyUnicode_DATA(uval); jpayne@68: if (!CYTHON_PEP393_ENABLED || ukind == result_ukind) { jpayne@68: memcpy((char *)result_udata + (char_pos << kind_shift), udata, (size_t) (ulength << kind_shift)); jpayne@68: } else { jpayne@68: #if PY_VERSION_HEX >= 0x030d0000 jpayne@68: if (unlikely(PyUnicode_CopyCharacters(result_uval, char_pos, uval, 0, ulength) < 0)) goto bad; jpayne@68: #elif CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030300F0 || defined(_PyUnicode_FastCopyCharacters) jpayne@68: _PyUnicode_FastCopyCharacters(result_uval, char_pos, uval, 0, ulength); jpayne@68: #else jpayne@68: Py_ssize_t j; jpayne@68: for (j=0; j < ulength; j++) { jpayne@68: Py_UCS4 uchar = __Pyx_PyUnicode_READ(ukind, udata, j); jpayne@68: __Pyx_PyUnicode_WRITE(result_ukind, result_udata, char_pos+j, uchar); jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: char_pos += ulength; jpayne@68: } jpayne@68: return result_uval; jpayne@68: overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, "join() result is too long for a Python string"); jpayne@68: bad: jpayne@68: Py_DECREF(result_uval); jpayne@68: return NULL; jpayne@68: #else jpayne@68: CYTHON_UNUSED_VAR(max_char); jpayne@68: CYTHON_UNUSED_VAR(result_ulength); jpayne@68: CYTHON_UNUSED_VAR(value_count); jpayne@68: return PyUnicode_Join(__pyx_empty_unicode, value_tuple); jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* DictGetItem */ jpayne@68: #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY jpayne@68: static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { jpayne@68: PyObject *value; jpayne@68: value = PyDict_GetItemWithError(d, key); jpayne@68: if (unlikely(!value)) { jpayne@68: if (!PyErr_Occurred()) { jpayne@68: if (unlikely(PyTuple_Check(key))) { jpayne@68: PyObject* args = PyTuple_Pack(1, key); jpayne@68: if (likely(args)) { jpayne@68: PyErr_SetObject(PyExc_KeyError, args); jpayne@68: Py_DECREF(args); jpayne@68: } jpayne@68: } else { jpayne@68: PyErr_SetObject(PyExc_KeyError, key); jpayne@68: } jpayne@68: } jpayne@68: return NULL; jpayne@68: } jpayne@68: Py_INCREF(value); jpayne@68: return value; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* GetTopmostException */ jpayne@68: #if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE jpayne@68: static _PyErr_StackItem * jpayne@68: __Pyx_PyErr_GetTopmostException(PyThreadState *tstate) jpayne@68: { jpayne@68: _PyErr_StackItem *exc_info = tstate->exc_info; jpayne@68: while ((exc_info->exc_value == NULL || exc_info->exc_value == Py_None) && jpayne@68: exc_info->previous_item != NULL) jpayne@68: { jpayne@68: exc_info = exc_info->previous_item; jpayne@68: } jpayne@68: return exc_info; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* SaveResetException */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { jpayne@68: #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4 jpayne@68: _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); jpayne@68: PyObject *exc_value = exc_info->exc_value; jpayne@68: if (exc_value == NULL || exc_value == Py_None) { jpayne@68: *value = NULL; jpayne@68: *type = NULL; jpayne@68: *tb = NULL; jpayne@68: } else { jpayne@68: *value = exc_value; jpayne@68: Py_INCREF(*value); jpayne@68: *type = (PyObject*) Py_TYPE(exc_value); jpayne@68: Py_INCREF(*type); jpayne@68: *tb = PyException_GetTraceback(exc_value); jpayne@68: } jpayne@68: #elif CYTHON_USE_EXC_INFO_STACK jpayne@68: _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); jpayne@68: *type = exc_info->exc_type; jpayne@68: *value = exc_info->exc_value; jpayne@68: *tb = exc_info->exc_traceback; jpayne@68: Py_XINCREF(*type); jpayne@68: Py_XINCREF(*value); jpayne@68: Py_XINCREF(*tb); jpayne@68: #else jpayne@68: *type = tstate->exc_type; jpayne@68: *value = tstate->exc_value; jpayne@68: *tb = tstate->exc_traceback; jpayne@68: Py_XINCREF(*type); jpayne@68: Py_XINCREF(*value); jpayne@68: Py_XINCREF(*tb); jpayne@68: #endif jpayne@68: } jpayne@68: static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { jpayne@68: #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4 jpayne@68: _PyErr_StackItem *exc_info = tstate->exc_info; jpayne@68: PyObject *tmp_value = exc_info->exc_value; jpayne@68: exc_info->exc_value = value; jpayne@68: Py_XDECREF(tmp_value); jpayne@68: Py_XDECREF(type); jpayne@68: Py_XDECREF(tb); jpayne@68: #else jpayne@68: PyObject *tmp_type, *tmp_value, *tmp_tb; jpayne@68: #if CYTHON_USE_EXC_INFO_STACK jpayne@68: _PyErr_StackItem *exc_info = tstate->exc_info; jpayne@68: tmp_type = exc_info->exc_type; jpayne@68: tmp_value = exc_info->exc_value; jpayne@68: tmp_tb = exc_info->exc_traceback; jpayne@68: exc_info->exc_type = type; jpayne@68: exc_info->exc_value = value; jpayne@68: exc_info->exc_traceback = tb; jpayne@68: #else jpayne@68: tmp_type = tstate->exc_type; jpayne@68: tmp_value = tstate->exc_value; jpayne@68: tmp_tb = tstate->exc_traceback; jpayne@68: tstate->exc_type = type; jpayne@68: tstate->exc_value = value; jpayne@68: tstate->exc_traceback = tb; jpayne@68: #endif jpayne@68: Py_XDECREF(tmp_type); jpayne@68: Py_XDECREF(tmp_value); jpayne@68: Py_XDECREF(tmp_tb); jpayne@68: #endif jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* GetException */ jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) jpayne@68: #else jpayne@68: static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *local_type = NULL, *local_value, *local_tb = NULL; jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: PyObject *tmp_type, *tmp_value, *tmp_tb; jpayne@68: #if PY_VERSION_HEX >= 0x030C00A6 jpayne@68: local_value = tstate->current_exception; jpayne@68: tstate->current_exception = 0; jpayne@68: if (likely(local_value)) { jpayne@68: local_type = (PyObject*) Py_TYPE(local_value); jpayne@68: Py_INCREF(local_type); jpayne@68: local_tb = PyException_GetTraceback(local_value); jpayne@68: } jpayne@68: #else jpayne@68: local_type = tstate->curexc_type; jpayne@68: local_value = tstate->curexc_value; jpayne@68: local_tb = tstate->curexc_traceback; jpayne@68: tstate->curexc_type = 0; jpayne@68: tstate->curexc_value = 0; jpayne@68: tstate->curexc_traceback = 0; jpayne@68: #endif jpayne@68: #else jpayne@68: PyErr_Fetch(&local_type, &local_value, &local_tb); jpayne@68: #endif jpayne@68: PyErr_NormalizeException(&local_type, &local_value, &local_tb); jpayne@68: #if CYTHON_FAST_THREAD_STATE && PY_VERSION_HEX >= 0x030C00A6 jpayne@68: if (unlikely(tstate->current_exception)) jpayne@68: #elif CYTHON_FAST_THREAD_STATE jpayne@68: if (unlikely(tstate->curexc_type)) jpayne@68: #else jpayne@68: if (unlikely(PyErr_Occurred())) jpayne@68: #endif jpayne@68: goto bad; jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (local_tb) { jpayne@68: if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) jpayne@68: goto bad; jpayne@68: } jpayne@68: #endif jpayne@68: Py_XINCREF(local_tb); jpayne@68: Py_XINCREF(local_type); jpayne@68: Py_XINCREF(local_value); jpayne@68: *type = local_type; jpayne@68: *value = local_value; jpayne@68: *tb = local_tb; jpayne@68: #if CYTHON_FAST_THREAD_STATE jpayne@68: #if CYTHON_USE_EXC_INFO_STACK jpayne@68: { jpayne@68: _PyErr_StackItem *exc_info = tstate->exc_info; jpayne@68: #if PY_VERSION_HEX >= 0x030B00a4 jpayne@68: tmp_value = exc_info->exc_value; jpayne@68: exc_info->exc_value = local_value; jpayne@68: tmp_type = NULL; jpayne@68: tmp_tb = NULL; jpayne@68: Py_XDECREF(local_type); jpayne@68: Py_XDECREF(local_tb); jpayne@68: #else jpayne@68: tmp_type = exc_info->exc_type; jpayne@68: tmp_value = exc_info->exc_value; jpayne@68: tmp_tb = exc_info->exc_traceback; jpayne@68: exc_info->exc_type = local_type; jpayne@68: exc_info->exc_value = local_value; jpayne@68: exc_info->exc_traceback = local_tb; jpayne@68: #endif jpayne@68: } jpayne@68: #else jpayne@68: tmp_type = tstate->exc_type; jpayne@68: tmp_value = tstate->exc_value; jpayne@68: tmp_tb = tstate->exc_traceback; jpayne@68: tstate->exc_type = local_type; jpayne@68: tstate->exc_value = local_value; jpayne@68: tstate->exc_traceback = local_tb; jpayne@68: #endif jpayne@68: Py_XDECREF(tmp_type); jpayne@68: Py_XDECREF(tmp_value); jpayne@68: Py_XDECREF(tmp_tb); jpayne@68: #else jpayne@68: PyErr_SetExcInfo(local_type, local_value, local_tb); jpayne@68: #endif jpayne@68: return 0; jpayne@68: bad: jpayne@68: *type = 0; jpayne@68: *value = 0; jpayne@68: *tb = 0; jpayne@68: Py_XDECREF(local_type); jpayne@68: Py_XDECREF(local_value); jpayne@68: Py_XDECREF(local_tb); jpayne@68: return -1; jpayne@68: } jpayne@68: jpayne@68: /* UnpackUnboundCMethod */ jpayne@68: static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) { jpayne@68: PyObject *result; jpayne@68: PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args)); jpayne@68: if (unlikely(!selfless_args)) return NULL; jpayne@68: result = PyObject_Call(method, selfless_args, kwargs); jpayne@68: Py_DECREF(selfless_args); jpayne@68: return result; jpayne@68: } jpayne@68: static PyMethodDef __Pyx_UnboundCMethod_Def = { jpayne@68: "CythonUnboundCMethod", jpayne@68: __PYX_REINTERPRET_FUNCION(PyCFunction, __Pyx_SelflessCall), jpayne@68: METH_VARARGS | METH_KEYWORDS, jpayne@68: NULL jpayne@68: }; jpayne@68: static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) { jpayne@68: PyObject *method; jpayne@68: method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name); jpayne@68: if (unlikely(!method)) jpayne@68: return -1; jpayne@68: target->method = method; jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (likely(__Pyx_TypeCheck(method, &PyMethodDescr_Type))) jpayne@68: #else jpayne@68: if (likely(!__Pyx_CyOrPyCFunction_Check(method))) jpayne@68: #endif jpayne@68: { jpayne@68: PyMethodDescrObject *descr = (PyMethodDescrObject*) method; jpayne@68: target->func = descr->d_method->ml_meth; jpayne@68: target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_STACKLESS); jpayne@68: } else jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY jpayne@68: #else jpayne@68: if (PyCFunction_Check(method)) jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *self; jpayne@68: int self_found; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY jpayne@68: self = PyObject_GetAttrString(method, "__self__"); jpayne@68: if (!self) { jpayne@68: PyErr_Clear(); jpayne@68: } jpayne@68: #else jpayne@68: self = PyCFunction_GET_SELF(method); jpayne@68: #endif jpayne@68: self_found = (self && self != Py_None); jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY jpayne@68: Py_XDECREF(self); jpayne@68: #endif jpayne@68: if (self_found) { jpayne@68: PyObject *unbound_method = PyCFunction_New(&__Pyx_UnboundCMethod_Def, method); jpayne@68: if (unlikely(!unbound_method)) return -1; jpayne@68: Py_DECREF(method); jpayne@68: target->method = unbound_method; jpayne@68: } jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* CallUnboundCMethod0 */ jpayne@68: static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) { jpayne@68: PyObject *args, *result = NULL; jpayne@68: if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: args = PyTuple_New(1); jpayne@68: if (unlikely(!args)) goto bad; jpayne@68: Py_INCREF(self); jpayne@68: PyTuple_SET_ITEM(args, 0, self); jpayne@68: #else jpayne@68: args = PyTuple_Pack(1, self); jpayne@68: if (unlikely(!args)) goto bad; jpayne@68: #endif jpayne@68: result = __Pyx_PyObject_Call(cfunc->method, args, NULL); jpayne@68: Py_DECREF(args); jpayne@68: bad: jpayne@68: return result; jpayne@68: } jpayne@68: jpayne@68: /* py_dict_keys */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) { jpayne@68: if (PY_MAJOR_VERSION >= 3) jpayne@68: return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_keys, d); jpayne@68: else jpayne@68: return PyDict_Keys(d); jpayne@68: } jpayne@68: jpayne@68: /* UnicodeAsUCS4 */ jpayne@68: static CYTHON_INLINE Py_UCS4 __Pyx_PyUnicode_AsPy_UCS4(PyObject* x) { jpayne@68: Py_ssize_t length; jpayne@68: #if CYTHON_PEP393_ENABLED jpayne@68: length = PyUnicode_GET_LENGTH(x); jpayne@68: if (likely(length == 1)) { jpayne@68: return PyUnicode_READ_CHAR(x, 0); jpayne@68: } jpayne@68: #else jpayne@68: length = PyUnicode_GET_SIZE(x); jpayne@68: if (likely(length == 1)) { jpayne@68: return PyUnicode_AS_UNICODE(x)[0]; jpayne@68: } jpayne@68: #if Py_UNICODE_SIZE == 2 jpayne@68: else if (PyUnicode_GET_SIZE(x) == 2) { jpayne@68: Py_UCS4 high_val = PyUnicode_AS_UNICODE(x)[0]; jpayne@68: if (high_val >= 0xD800 && high_val <= 0xDBFF) { jpayne@68: Py_UCS4 low_val = PyUnicode_AS_UNICODE(x)[1]; jpayne@68: if (low_val >= 0xDC00 && low_val <= 0xDFFF) { jpayne@68: return 0x10000 + (((high_val & ((1<<10)-1)) << 10) | (low_val & ((1<<10)-1))); jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: PyErr_Format(PyExc_ValueError, jpayne@68: "only single character unicode strings can be converted to Py_UCS4, " jpayne@68: "got length %" CYTHON_FORMAT_SSIZE_T "d", length); jpayne@68: return (Py_UCS4)-1; jpayne@68: } jpayne@68: jpayne@68: /* object_ord */ jpayne@68: static long __Pyx__PyObject_Ord(PyObject* c) { jpayne@68: Py_ssize_t size; jpayne@68: if (PyBytes_Check(c)) { jpayne@68: size = PyBytes_GET_SIZE(c); jpayne@68: if (likely(size == 1)) { jpayne@68: return (unsigned char) PyBytes_AS_STRING(c)[0]; jpayne@68: } jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: } else if (PyUnicode_Check(c)) { jpayne@68: return (long)__Pyx_PyUnicode_AsPy_UCS4(c); jpayne@68: #endif jpayne@68: #if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) jpayne@68: } else if (PyByteArray_Check(c)) { jpayne@68: size = PyByteArray_GET_SIZE(c); jpayne@68: if (likely(size == 1)) { jpayne@68: return (unsigned char) PyByteArray_AS_STRING(c)[0]; jpayne@68: } jpayne@68: #endif jpayne@68: } else { jpayne@68: __Pyx_TypeName c_type_name = __Pyx_PyType_GetName(Py_TYPE(c)); jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "ord() expected string of length 1, but " __Pyx_FMT_TYPENAME " found", jpayne@68: c_type_name); jpayne@68: __Pyx_DECREF_TypeName(c_type_name); jpayne@68: return (long)(Py_UCS4)-1; jpayne@68: } jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "ord() expected a character, but string of length %zd found", size); jpayne@68: return (long)(Py_UCS4)-1; jpayne@68: } jpayne@68: jpayne@68: /* RaiseTooManyValuesToUnpack */ jpayne@68: static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { jpayne@68: PyErr_Format(PyExc_ValueError, jpayne@68: "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); jpayne@68: } jpayne@68: jpayne@68: /* RaiseNeedMoreValuesToUnpack */ jpayne@68: static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { jpayne@68: PyErr_Format(PyExc_ValueError, jpayne@68: "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", jpayne@68: index, (index == 1) ? "" : "s"); jpayne@68: } jpayne@68: jpayne@68: /* IterFinish */ jpayne@68: static CYTHON_INLINE int __Pyx_IterFinish(void) { jpayne@68: PyObject* exc_type; jpayne@68: __Pyx_PyThreadState_declare jpayne@68: __Pyx_PyThreadState_assign jpayne@68: exc_type = __Pyx_PyErr_CurrentExceptionType(); jpayne@68: if (unlikely(exc_type)) { jpayne@68: if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) jpayne@68: return -1; jpayne@68: __Pyx_PyErr_Clear(); jpayne@68: return 0; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* UnpackItemEndCheck */ jpayne@68: static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { jpayne@68: if (unlikely(retval)) { jpayne@68: Py_DECREF(retval); jpayne@68: __Pyx_RaiseTooManyValuesError(expected); jpayne@68: return -1; jpayne@68: } jpayne@68: return __Pyx_IterFinish(); jpayne@68: } jpayne@68: jpayne@68: /* PyObjectSetAttrStr */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { jpayne@68: PyTypeObject* tp = Py_TYPE(obj); jpayne@68: if (likely(tp->tp_setattro)) jpayne@68: return tp->tp_setattro(obj, attr_name, value); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(tp->tp_setattr)) jpayne@68: return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); jpayne@68: #endif jpayne@68: return PyObject_SetAttr(obj, attr_name, value); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* Import */ jpayne@68: static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { jpayne@68: PyObject *module = 0; jpayne@68: PyObject *empty_dict = 0; jpayne@68: PyObject *empty_list = 0; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyObject *py_import; jpayne@68: py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); jpayne@68: if (unlikely(!py_import)) jpayne@68: goto bad; jpayne@68: if (!from_list) { jpayne@68: empty_list = PyList_New(0); jpayne@68: if (unlikely(!empty_list)) jpayne@68: goto bad; jpayne@68: from_list = empty_list; jpayne@68: } jpayne@68: #endif jpayne@68: empty_dict = PyDict_New(); jpayne@68: if (unlikely(!empty_dict)) jpayne@68: goto bad; jpayne@68: { jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (level == -1) { jpayne@68: if (strchr(__Pyx_MODULE_NAME, '.') != NULL) { jpayne@68: module = PyImport_ImportModuleLevelObject( jpayne@68: name, __pyx_d, empty_dict, from_list, 1); jpayne@68: if (unlikely(!module)) { jpayne@68: if (unlikely(!PyErr_ExceptionMatches(PyExc_ImportError))) jpayne@68: goto bad; jpayne@68: PyErr_Clear(); jpayne@68: } jpayne@68: } jpayne@68: level = 0; jpayne@68: } jpayne@68: #endif jpayne@68: if (!module) { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyObject *py_level = PyInt_FromLong(level); jpayne@68: if (unlikely(!py_level)) jpayne@68: goto bad; jpayne@68: module = PyObject_CallFunctionObjArgs(py_import, jpayne@68: name, __pyx_d, empty_dict, from_list, py_level, (PyObject *)NULL); jpayne@68: Py_DECREF(py_level); jpayne@68: #else jpayne@68: module = PyImport_ImportModuleLevelObject( jpayne@68: name, __pyx_d, empty_dict, from_list, level); jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: bad: jpayne@68: Py_XDECREF(empty_dict); jpayne@68: Py_XDECREF(empty_list); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: Py_XDECREF(py_import); jpayne@68: #endif jpayne@68: return module; jpayne@68: } jpayne@68: jpayne@68: /* ImportFrom */ jpayne@68: static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { jpayne@68: PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); jpayne@68: if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { jpayne@68: const char* module_name_str = 0; jpayne@68: PyObject* module_name = 0; jpayne@68: PyObject* module_dot = 0; jpayne@68: PyObject* full_name = 0; jpayne@68: PyErr_Clear(); jpayne@68: module_name_str = PyModule_GetName(module); jpayne@68: if (unlikely(!module_name_str)) { goto modbad; } jpayne@68: module_name = PyUnicode_FromString(module_name_str); jpayne@68: if (unlikely(!module_name)) { goto modbad; } jpayne@68: module_dot = PyUnicode_Concat(module_name, __pyx_kp_u__56); jpayne@68: if (unlikely(!module_dot)) { goto modbad; } jpayne@68: full_name = PyUnicode_Concat(module_dot, name); jpayne@68: if (unlikely(!full_name)) { goto modbad; } jpayne@68: #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400) jpayne@68: { jpayne@68: PyObject *modules = PyImport_GetModuleDict(); jpayne@68: if (unlikely(!modules)) jpayne@68: goto modbad; jpayne@68: value = PyObject_GetItem(modules, full_name); jpayne@68: } jpayne@68: #else jpayne@68: value = PyImport_GetModule(full_name); jpayne@68: #endif jpayne@68: modbad: jpayne@68: Py_XDECREF(full_name); jpayne@68: Py_XDECREF(module_dot); jpayne@68: Py_XDECREF(module_name); jpayne@68: } jpayne@68: if (unlikely(!value)) { jpayne@68: PyErr_Format(PyExc_ImportError, jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: "cannot import name %.230s", PyString_AS_STRING(name)); jpayne@68: #else jpayne@68: "cannot import name %S", name); jpayne@68: #endif jpayne@68: } jpayne@68: return value; jpayne@68: } jpayne@68: jpayne@68: /* GetItemInt */ jpayne@68: static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { jpayne@68: PyObject *r; jpayne@68: if (unlikely(!j)) return NULL; jpayne@68: r = PyObject_GetItem(o, j); jpayne@68: Py_DECREF(j); jpayne@68: return r; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, jpayne@68: CYTHON_NCP_UNUSED int wraparound, jpayne@68: CYTHON_NCP_UNUSED int boundscheck) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_ssize_t wrapped_i = i; jpayne@68: if (wraparound & unlikely(i < 0)) { jpayne@68: wrapped_i += PyList_GET_SIZE(o); jpayne@68: } jpayne@68: if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { jpayne@68: PyObject *r = PyList_GET_ITEM(o, wrapped_i); jpayne@68: Py_INCREF(r); jpayne@68: return r; jpayne@68: } jpayne@68: return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); jpayne@68: #else jpayne@68: return PySequence_GetItem(o, i); jpayne@68: #endif jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, jpayne@68: CYTHON_NCP_UNUSED int wraparound, jpayne@68: CYTHON_NCP_UNUSED int boundscheck) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_ssize_t wrapped_i = i; jpayne@68: if (wraparound & unlikely(i < 0)) { jpayne@68: wrapped_i += PyTuple_GET_SIZE(o); jpayne@68: } jpayne@68: if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { jpayne@68: PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); jpayne@68: Py_INCREF(r); jpayne@68: return r; jpayne@68: } jpayne@68: return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); jpayne@68: #else jpayne@68: return PySequence_GetItem(o, i); jpayne@68: #endif jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, jpayne@68: CYTHON_NCP_UNUSED int wraparound, jpayne@68: CYTHON_NCP_UNUSED int boundscheck) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS jpayne@68: if (is_list || PyList_CheckExact(o)) { jpayne@68: Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); jpayne@68: if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { jpayne@68: PyObject *r = PyList_GET_ITEM(o, n); jpayne@68: Py_INCREF(r); jpayne@68: return r; jpayne@68: } jpayne@68: } jpayne@68: else if (PyTuple_CheckExact(o)) { jpayne@68: Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); jpayne@68: if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { jpayne@68: PyObject *r = PyTuple_GET_ITEM(o, n); jpayne@68: Py_INCREF(r); jpayne@68: return r; jpayne@68: } jpayne@68: } else { jpayne@68: PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping; jpayne@68: PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence; jpayne@68: if (mm && mm->mp_subscript) { jpayne@68: PyObject *r, *key = PyInt_FromSsize_t(i); jpayne@68: if (unlikely(!key)) return NULL; jpayne@68: r = mm->mp_subscript(o, key); jpayne@68: Py_DECREF(key); jpayne@68: return r; jpayne@68: } jpayne@68: if (likely(sm && sm->sq_item)) { jpayne@68: if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) { jpayne@68: Py_ssize_t l = sm->sq_length(o); jpayne@68: if (likely(l >= 0)) { jpayne@68: i += l; jpayne@68: } else { jpayne@68: if (!PyErr_ExceptionMatches(PyExc_OverflowError)) jpayne@68: return NULL; jpayne@68: PyErr_Clear(); jpayne@68: } jpayne@68: } jpayne@68: return sm->sq_item(o, i); jpayne@68: } jpayne@68: } jpayne@68: #else jpayne@68: if (is_list || !PyMapping_Check(o)) { jpayne@68: return PySequence_GetItem(o, i); jpayne@68: } jpayne@68: #endif jpayne@68: return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); jpayne@68: } jpayne@68: jpayne@68: /* GetAttr */ jpayne@68: static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (likely(PyUnicode_Check(n))) jpayne@68: #else jpayne@68: if (likely(PyString_Check(n))) jpayne@68: #endif jpayne@68: return __Pyx_PyObject_GetAttrStr(o, n); jpayne@68: #endif jpayne@68: return PyObject_GetAttr(o, n); jpayne@68: } jpayne@68: jpayne@68: /* HasAttr */ jpayne@68: static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { jpayne@68: PyObject *r; jpayne@68: if (unlikely(!__Pyx_PyBaseString_Check(n))) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "hasattr(): attribute name must be string"); jpayne@68: return -1; jpayne@68: } jpayne@68: r = __Pyx_GetAttr(o, n); jpayne@68: if (!r) { jpayne@68: PyErr_Clear(); jpayne@68: return 0; jpayne@68: } else { jpayne@68: Py_DECREF(r); jpayne@68: return 1; jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* CallNextTpDealloc */ jpayne@68: static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) { jpayne@68: PyTypeObject* type = Py_TYPE(obj); jpayne@68: destructor tp_dealloc = NULL; jpayne@68: while (type && __Pyx_PyType_GetSlot(type, tp_dealloc, destructor) != current_tp_dealloc) jpayne@68: type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); jpayne@68: while (type && (tp_dealloc = __Pyx_PyType_GetSlot(type, tp_dealloc, destructor)) == current_tp_dealloc) jpayne@68: type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); jpayne@68: if (type) jpayne@68: tp_dealloc(obj); jpayne@68: } jpayne@68: jpayne@68: /* CallNextTpTraverse */ jpayne@68: static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { jpayne@68: PyTypeObject* type = Py_TYPE(obj); jpayne@68: traverseproc tp_traverse = NULL; jpayne@68: while (type && __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc) != current_tp_traverse) jpayne@68: type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); jpayne@68: while (type && (tp_traverse = __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc)) == current_tp_traverse) jpayne@68: type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); jpayne@68: if (type && tp_traverse) jpayne@68: return tp_traverse(obj, v, a); jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* CallNextTpClear */ jpayne@68: static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { jpayne@68: PyTypeObject* type = Py_TYPE(obj); jpayne@68: inquiry tp_clear = NULL; jpayne@68: while (type && __Pyx_PyType_GetSlot(type, tp_clear, inquiry) != current_tp_clear) jpayne@68: type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); jpayne@68: while (type && (tp_clear = __Pyx_PyType_GetSlot(type, tp_clear, inquiry)) == current_tp_clear) jpayne@68: type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); jpayne@68: if (type && tp_clear) jpayne@68: tp_clear(obj); jpayne@68: } jpayne@68: jpayne@68: /* FixUpExtensionType */ jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type) { jpayne@68: #if PY_VERSION_HEX > 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: CYTHON_UNUSED_VAR(spec); jpayne@68: CYTHON_UNUSED_VAR(type); jpayne@68: #else jpayne@68: const PyType_Slot *slot = spec->slots; jpayne@68: while (slot && slot->slot && slot->slot != Py_tp_members) jpayne@68: slot++; jpayne@68: if (slot && slot->slot == Py_tp_members) { jpayne@68: int changed = 0; jpayne@68: #if !(PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON) jpayne@68: const jpayne@68: #endif jpayne@68: PyMemberDef *memb = (PyMemberDef*) slot->pfunc; jpayne@68: while (memb && memb->name) { jpayne@68: if (memb->name[0] == '_' && memb->name[1] == '_') { jpayne@68: #if PY_VERSION_HEX < 0x030900b1 jpayne@68: if (strcmp(memb->name, "__weaklistoffset__") == 0) { jpayne@68: assert(memb->type == T_PYSSIZET); jpayne@68: assert(memb->flags == READONLY); jpayne@68: type->tp_weaklistoffset = memb->offset; jpayne@68: changed = 1; jpayne@68: } jpayne@68: else if (strcmp(memb->name, "__dictoffset__") == 0) { jpayne@68: assert(memb->type == T_PYSSIZET); jpayne@68: assert(memb->flags == READONLY); jpayne@68: type->tp_dictoffset = memb->offset; jpayne@68: changed = 1; jpayne@68: } jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: else if (strcmp(memb->name, "__vectorcalloffset__") == 0) { jpayne@68: assert(memb->type == T_PYSSIZET); jpayne@68: assert(memb->flags == READONLY); jpayne@68: #if PY_VERSION_HEX >= 0x030800b4 jpayne@68: type->tp_vectorcall_offset = memb->offset; jpayne@68: #else jpayne@68: type->tp_print = (printfunc) memb->offset; jpayne@68: #endif jpayne@68: changed = 1; jpayne@68: } jpayne@68: #endif jpayne@68: #else jpayne@68: if ((0)); jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON jpayne@68: else if (strcmp(memb->name, "__module__") == 0) { jpayne@68: PyObject *descr; jpayne@68: assert(memb->type == T_OBJECT); jpayne@68: assert(memb->flags == 0 || memb->flags == READONLY); jpayne@68: descr = PyDescr_NewMember(type, memb); jpayne@68: if (unlikely(!descr)) jpayne@68: return -1; jpayne@68: if (unlikely(PyDict_SetItem(type->tp_dict, PyDescr_NAME(descr), descr) < 0)) { jpayne@68: Py_DECREF(descr); jpayne@68: return -1; jpayne@68: } jpayne@68: Py_DECREF(descr); jpayne@68: changed = 1; jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: memb++; jpayne@68: } jpayne@68: if (changed) jpayne@68: PyType_Modified(type); jpayne@68: } jpayne@68: #endif jpayne@68: return 0; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObjectGetMethod */ jpayne@68: static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) { jpayne@68: PyObject *attr; jpayne@68: #if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP jpayne@68: __Pyx_TypeName type_name; jpayne@68: PyTypeObject *tp = Py_TYPE(obj); jpayne@68: PyObject *descr; jpayne@68: descrgetfunc f = NULL; jpayne@68: PyObject **dictptr, *dict; jpayne@68: int meth_found = 0; jpayne@68: assert (*method == NULL); jpayne@68: if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) { jpayne@68: attr = __Pyx_PyObject_GetAttrStr(obj, name); jpayne@68: goto try_unpack; jpayne@68: } jpayne@68: if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) { jpayne@68: return 0; jpayne@68: } jpayne@68: descr = _PyType_Lookup(tp, name); jpayne@68: if (likely(descr != NULL)) { jpayne@68: Py_INCREF(descr); jpayne@68: #if defined(Py_TPFLAGS_METHOD_DESCRIPTOR) && Py_TPFLAGS_METHOD_DESCRIPTOR jpayne@68: if (__Pyx_PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_METHOD_DESCRIPTOR)) jpayne@68: #elif PY_MAJOR_VERSION >= 3 jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr))) jpayne@68: #else jpayne@68: if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type))) jpayne@68: #endif jpayne@68: #else jpayne@68: #ifdef __Pyx_CyFunction_USED jpayne@68: if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr))) jpayne@68: #else jpayne@68: if (likely(PyFunction_Check(descr))) jpayne@68: #endif jpayne@68: #endif jpayne@68: { jpayne@68: meth_found = 1; jpayne@68: } else { jpayne@68: f = Py_TYPE(descr)->tp_descr_get; jpayne@68: if (f != NULL && PyDescr_IsData(descr)) { jpayne@68: attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); jpayne@68: Py_DECREF(descr); jpayne@68: goto try_unpack; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: dictptr = _PyObject_GetDictPtr(obj); jpayne@68: if (dictptr != NULL && (dict = *dictptr) != NULL) { jpayne@68: Py_INCREF(dict); jpayne@68: attr = __Pyx_PyDict_GetItemStr(dict, name); jpayne@68: if (attr != NULL) { jpayne@68: Py_INCREF(attr); jpayne@68: Py_DECREF(dict); jpayne@68: Py_XDECREF(descr); jpayne@68: goto try_unpack; jpayne@68: } jpayne@68: Py_DECREF(dict); jpayne@68: } jpayne@68: if (meth_found) { jpayne@68: *method = descr; jpayne@68: return 1; jpayne@68: } jpayne@68: if (f != NULL) { jpayne@68: attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); jpayne@68: Py_DECREF(descr); jpayne@68: goto try_unpack; jpayne@68: } jpayne@68: if (likely(descr != NULL)) { jpayne@68: *method = descr; jpayne@68: return 0; jpayne@68: } jpayne@68: type_name = __Pyx_PyType_GetName(tp); jpayne@68: PyErr_Format(PyExc_AttributeError, jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'", jpayne@68: type_name, name); jpayne@68: #else jpayne@68: "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'", jpayne@68: type_name, PyString_AS_STRING(name)); jpayne@68: #endif jpayne@68: __Pyx_DECREF_TypeName(type_name); jpayne@68: return 0; jpayne@68: #else jpayne@68: attr = __Pyx_PyObject_GetAttrStr(obj, name); jpayne@68: goto try_unpack; jpayne@68: #endif jpayne@68: try_unpack: jpayne@68: #if CYTHON_UNPACK_METHODS jpayne@68: if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) { jpayne@68: PyObject *function = PyMethod_GET_FUNCTION(attr); jpayne@68: Py_INCREF(function); jpayne@68: Py_DECREF(attr); jpayne@68: *method = function; jpayne@68: return 1; jpayne@68: } jpayne@68: #endif jpayne@68: *method = attr; jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: /* PyObjectCallMethod0 */ jpayne@68: static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { jpayne@68: PyObject *method = NULL, *result = NULL; jpayne@68: int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); jpayne@68: if (likely(is_method)) { jpayne@68: result = __Pyx_PyObject_CallOneArg(method, obj); jpayne@68: Py_DECREF(method); jpayne@68: return result; jpayne@68: } jpayne@68: if (unlikely(!method)) goto bad; jpayne@68: result = __Pyx_PyObject_CallNoArg(method); jpayne@68: Py_DECREF(method); jpayne@68: bad: jpayne@68: return result; jpayne@68: } jpayne@68: jpayne@68: /* ValidateBasesTuple */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS jpayne@68: static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases) { jpayne@68: Py_ssize_t i, n; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: n = PyTuple_GET_SIZE(bases); jpayne@68: #else jpayne@68: n = PyTuple_Size(bases); jpayne@68: if (n < 0) return -1; jpayne@68: #endif jpayne@68: for (i = 1; i < n; i++) jpayne@68: { jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: PyObject *b0 = PySequence_GetItem(bases, i); jpayne@68: if (!b0) return -1; jpayne@68: #elif CYTHON_ASSUME_SAFE_MACROS jpayne@68: PyObject *b0 = PyTuple_GET_ITEM(bases, i); jpayne@68: #else jpayne@68: PyObject *b0 = PyTuple_GetItem(bases, i); jpayne@68: if (!b0) return -1; jpayne@68: #endif jpayne@68: PyTypeObject *b; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (PyClass_Check(b0)) jpayne@68: { jpayne@68: PyErr_Format(PyExc_TypeError, "base class '%.200s' is an old-style class", jpayne@68: PyString_AS_STRING(((PyClassObject*)b0)->cl_name)); jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_DECREF(b0); jpayne@68: #endif jpayne@68: return -1; jpayne@68: } jpayne@68: #endif jpayne@68: b = (PyTypeObject*) b0; jpayne@68: if (!__Pyx_PyType_HasFeature(b, Py_TPFLAGS_HEAPTYPE)) jpayne@68: { jpayne@68: __Pyx_TypeName b_name = __Pyx_PyType_GetName(b); jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "base class '" __Pyx_FMT_TYPENAME "' is not a heap type", b_name); jpayne@68: __Pyx_DECREF_TypeName(b_name); jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_DECREF(b0); jpayne@68: #endif jpayne@68: return -1; jpayne@68: } jpayne@68: if (dictoffset == 0) jpayne@68: { jpayne@68: Py_ssize_t b_dictoffset = 0; jpayne@68: #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY jpayne@68: b_dictoffset = b->tp_dictoffset; jpayne@68: #else jpayne@68: PyObject *py_b_dictoffset = PyObject_GetAttrString((PyObject*)b, "__dictoffset__"); jpayne@68: if (!py_b_dictoffset) goto dictoffset_return; jpayne@68: b_dictoffset = PyLong_AsSsize_t(py_b_dictoffset); jpayne@68: Py_DECREF(py_b_dictoffset); jpayne@68: if (b_dictoffset == -1 && PyErr_Occurred()) goto dictoffset_return; jpayne@68: #endif jpayne@68: if (b_dictoffset) { jpayne@68: { jpayne@68: __Pyx_TypeName b_name = __Pyx_PyType_GetName(b); jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "extension type '%.200s' has no __dict__ slot, " jpayne@68: "but base type '" __Pyx_FMT_TYPENAME "' has: " jpayne@68: "either add 'cdef dict __dict__' to the extension type " jpayne@68: "or add '__slots__ = [...]' to the base type", jpayne@68: type_name, b_name); jpayne@68: __Pyx_DECREF_TypeName(b_name); jpayne@68: } jpayne@68: #if !(CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY) jpayne@68: dictoffset_return: jpayne@68: #endif jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_DECREF(b0); jpayne@68: #endif jpayne@68: return -1; jpayne@68: } jpayne@68: } jpayne@68: #if CYTHON_AVOID_BORROWED_REFS jpayne@68: Py_DECREF(b0); jpayne@68: #endif jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyType_Ready */ jpayne@68: static int __Pyx_PyType_Ready(PyTypeObject *t) { jpayne@68: #if CYTHON_USE_TYPE_SPECS || !(CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API) || defined(PYSTON_MAJOR_VERSION) jpayne@68: (void)__Pyx_PyObject_CallMethod0; jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: (void)__Pyx_validate_bases_tuple; jpayne@68: #endif jpayne@68: return PyType_Ready(t); jpayne@68: #else jpayne@68: int r; jpayne@68: PyObject *bases = __Pyx_PyType_GetSlot(t, tp_bases, PyObject*); jpayne@68: if (bases && unlikely(__Pyx_validate_bases_tuple(t->tp_name, t->tp_dictoffset, bases) == -1)) jpayne@68: return -1; jpayne@68: #if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION) jpayne@68: { jpayne@68: int gc_was_enabled; jpayne@68: #if PY_VERSION_HEX >= 0x030A00b1 jpayne@68: gc_was_enabled = PyGC_Disable(); jpayne@68: (void)__Pyx_PyObject_CallMethod0; jpayne@68: #else jpayne@68: PyObject *ret, *py_status; jpayne@68: PyObject *gc = NULL; jpayne@68: #if PY_VERSION_HEX >= 0x030700a1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM+0 >= 0x07030400) jpayne@68: gc = PyImport_GetModule(__pyx_kp_u_gc); jpayne@68: #endif jpayne@68: if (unlikely(!gc)) gc = PyImport_Import(__pyx_kp_u_gc); jpayne@68: if (unlikely(!gc)) return -1; jpayne@68: py_status = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_isenabled); jpayne@68: if (unlikely(!py_status)) { jpayne@68: Py_DECREF(gc); jpayne@68: return -1; jpayne@68: } jpayne@68: gc_was_enabled = __Pyx_PyObject_IsTrue(py_status); jpayne@68: Py_DECREF(py_status); jpayne@68: if (gc_was_enabled > 0) { jpayne@68: ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_disable); jpayne@68: if (unlikely(!ret)) { jpayne@68: Py_DECREF(gc); jpayne@68: return -1; jpayne@68: } jpayne@68: Py_DECREF(ret); jpayne@68: } else if (unlikely(gc_was_enabled == -1)) { jpayne@68: Py_DECREF(gc); jpayne@68: return -1; jpayne@68: } jpayne@68: #endif jpayne@68: t->tp_flags |= Py_TPFLAGS_HEAPTYPE; jpayne@68: #if PY_VERSION_HEX >= 0x030A0000 jpayne@68: t->tp_flags |= Py_TPFLAGS_IMMUTABLETYPE; jpayne@68: #endif jpayne@68: #else jpayne@68: (void)__Pyx_PyObject_CallMethod0; jpayne@68: #endif jpayne@68: r = PyType_Ready(t); jpayne@68: #if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION) jpayne@68: t->tp_flags &= ~Py_TPFLAGS_HEAPTYPE; jpayne@68: #if PY_VERSION_HEX >= 0x030A00b1 jpayne@68: if (gc_was_enabled) jpayne@68: PyGC_Enable(); jpayne@68: #else jpayne@68: if (gc_was_enabled) { jpayne@68: PyObject *tp, *v, *tb; jpayne@68: PyErr_Fetch(&tp, &v, &tb); jpayne@68: ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_enable); jpayne@68: if (likely(ret || r == -1)) { jpayne@68: Py_XDECREF(ret); jpayne@68: PyErr_Restore(tp, v, tb); jpayne@68: } else { jpayne@68: Py_XDECREF(tp); jpayne@68: Py_XDECREF(v); jpayne@68: Py_XDECREF(tb); jpayne@68: r = -1; jpayne@68: } jpayne@68: } jpayne@68: Py_DECREF(gc); jpayne@68: #endif jpayne@68: } jpayne@68: #endif jpayne@68: return r; jpayne@68: #endif jpayne@68: } jpayne@68: jpayne@68: /* PyObject_GenericGetAttrNoDict */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 jpayne@68: static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { jpayne@68: __Pyx_TypeName type_name = __Pyx_PyType_GetName(tp); jpayne@68: PyErr_Format(PyExc_AttributeError, jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'", jpayne@68: type_name, attr_name); jpayne@68: #else jpayne@68: "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'", jpayne@68: type_name, PyString_AS_STRING(attr_name)); jpayne@68: #endif jpayne@68: __Pyx_DECREF_TypeName(type_name); jpayne@68: return NULL; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { jpayne@68: PyObject *descr; jpayne@68: PyTypeObject *tp = Py_TYPE(obj); jpayne@68: if (unlikely(!PyString_Check(attr_name))) { jpayne@68: return PyObject_GenericGetAttr(obj, attr_name); jpayne@68: } jpayne@68: assert(!tp->tp_dictoffset); jpayne@68: descr = _PyType_Lookup(tp, attr_name); jpayne@68: if (unlikely(!descr)) { jpayne@68: return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); jpayne@68: } jpayne@68: Py_INCREF(descr); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) jpayne@68: #endif jpayne@68: { jpayne@68: descrgetfunc f = Py_TYPE(descr)->tp_descr_get; jpayne@68: if (unlikely(f)) { jpayne@68: PyObject *res = f(descr, obj, (PyObject *)tp); jpayne@68: Py_DECREF(descr); jpayne@68: return res; jpayne@68: } jpayne@68: } jpayne@68: return descr; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyObject_GenericGetAttr */ jpayne@68: #if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 jpayne@68: static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { jpayne@68: if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { jpayne@68: return PyObject_GenericGetAttr(obj, attr_name); jpayne@68: } jpayne@68: return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* SetVTable */ jpayne@68: static int __Pyx_SetVtable(PyTypeObject *type, void *vtable) { jpayne@68: PyObject *ob = PyCapsule_New(vtable, 0, 0); jpayne@68: if (unlikely(!ob)) jpayne@68: goto bad; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: if (unlikely(PyObject_SetAttr((PyObject *) type, __pyx_n_s_pyx_vtable, ob) < 0)) jpayne@68: #else jpayne@68: if (unlikely(PyDict_SetItem(type->tp_dict, __pyx_n_s_pyx_vtable, ob) < 0)) jpayne@68: #endif jpayne@68: goto bad; jpayne@68: Py_DECREF(ob); jpayne@68: return 0; jpayne@68: bad: jpayne@68: Py_XDECREF(ob); jpayne@68: return -1; jpayne@68: } jpayne@68: jpayne@68: /* GetVTable */ jpayne@68: static void* __Pyx_GetVtable(PyTypeObject *type) { jpayne@68: void* ptr; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject *ob = PyObject_GetAttr((PyObject *)type, __pyx_n_s_pyx_vtable); jpayne@68: #else jpayne@68: PyObject *ob = PyObject_GetItem(type->tp_dict, __pyx_n_s_pyx_vtable); jpayne@68: #endif jpayne@68: if (!ob) jpayne@68: goto bad; jpayne@68: ptr = PyCapsule_GetPointer(ob, 0); jpayne@68: if (!ptr && !PyErr_Occurred()) jpayne@68: PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type"); jpayne@68: Py_DECREF(ob); jpayne@68: return ptr; jpayne@68: bad: jpayne@68: Py_XDECREF(ob); jpayne@68: return NULL; jpayne@68: } jpayne@68: jpayne@68: /* MergeVTables */ jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static int __Pyx_MergeVtables(PyTypeObject *type) { jpayne@68: int i; jpayne@68: void** base_vtables; jpayne@68: __Pyx_TypeName tp_base_name; jpayne@68: __Pyx_TypeName base_name; jpayne@68: void* unknown = (void*)-1; jpayne@68: PyObject* bases = type->tp_bases; jpayne@68: int base_depth = 0; jpayne@68: { jpayne@68: PyTypeObject* base = type->tp_base; jpayne@68: while (base) { jpayne@68: base_depth += 1; jpayne@68: base = base->tp_base; jpayne@68: } jpayne@68: } jpayne@68: base_vtables = (void**) malloc(sizeof(void*) * (size_t)(base_depth + 1)); jpayne@68: base_vtables[0] = unknown; jpayne@68: for (i = 1; i < PyTuple_GET_SIZE(bases); i++) { jpayne@68: void* base_vtable = __Pyx_GetVtable(((PyTypeObject*)PyTuple_GET_ITEM(bases, i))); jpayne@68: if (base_vtable != NULL) { jpayne@68: int j; jpayne@68: PyTypeObject* base = type->tp_base; jpayne@68: for (j = 0; j < base_depth; j++) { jpayne@68: if (base_vtables[j] == unknown) { jpayne@68: base_vtables[j] = __Pyx_GetVtable(base); jpayne@68: base_vtables[j + 1] = unknown; jpayne@68: } jpayne@68: if (base_vtables[j] == base_vtable) { jpayne@68: break; jpayne@68: } else if (base_vtables[j] == NULL) { jpayne@68: goto bad; jpayne@68: } jpayne@68: base = base->tp_base; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: PyErr_Clear(); jpayne@68: free(base_vtables); jpayne@68: return 0; jpayne@68: bad: jpayne@68: tp_base_name = __Pyx_PyType_GetName(type->tp_base); jpayne@68: base_name = __Pyx_PyType_GetName((PyTypeObject*)PyTuple_GET_ITEM(bases, i)); jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "multiple bases have vtable conflict: '" __Pyx_FMT_TYPENAME "' and '" __Pyx_FMT_TYPENAME "'", tp_base_name, base_name); jpayne@68: __Pyx_DECREF_TypeName(tp_base_name); jpayne@68: __Pyx_DECREF_TypeName(base_name); jpayne@68: free(base_vtables); jpayne@68: return -1; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* SetupReduce */ jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { jpayne@68: int ret; jpayne@68: PyObject *name_attr; jpayne@68: name_attr = __Pyx_PyObject_GetAttrStrNoError(meth, __pyx_n_s_name); jpayne@68: if (likely(name_attr)) { jpayne@68: ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); jpayne@68: } else { jpayne@68: ret = -1; jpayne@68: } jpayne@68: if (unlikely(ret < 0)) { jpayne@68: PyErr_Clear(); jpayne@68: ret = 0; jpayne@68: } jpayne@68: Py_XDECREF(name_attr); jpayne@68: return ret; jpayne@68: } jpayne@68: static int __Pyx_setup_reduce(PyObject* type_obj) { jpayne@68: int ret = 0; jpayne@68: PyObject *object_reduce = NULL; jpayne@68: PyObject *object_getstate = NULL; jpayne@68: PyObject *object_reduce_ex = NULL; jpayne@68: PyObject *reduce = NULL; jpayne@68: PyObject *reduce_ex = NULL; jpayne@68: PyObject *reduce_cython = NULL; jpayne@68: PyObject *setstate = NULL; jpayne@68: PyObject *setstate_cython = NULL; jpayne@68: PyObject *getstate = NULL; jpayne@68: #if CYTHON_USE_PYTYPE_LOOKUP jpayne@68: getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); jpayne@68: #else jpayne@68: getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); jpayne@68: if (!getstate && PyErr_Occurred()) { jpayne@68: goto __PYX_BAD; jpayne@68: } jpayne@68: #endif jpayne@68: if (getstate) { jpayne@68: #if CYTHON_USE_PYTYPE_LOOKUP jpayne@68: object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); jpayne@68: #else jpayne@68: object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); jpayne@68: if (!object_getstate && PyErr_Occurred()) { jpayne@68: goto __PYX_BAD; jpayne@68: } jpayne@68: #endif jpayne@68: if (object_getstate != getstate) { jpayne@68: goto __PYX_GOOD; jpayne@68: } jpayne@68: } jpayne@68: #if CYTHON_USE_PYTYPE_LOOKUP jpayne@68: object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; jpayne@68: #else jpayne@68: object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; jpayne@68: #endif jpayne@68: reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; jpayne@68: if (reduce_ex == object_reduce_ex) { jpayne@68: #if CYTHON_USE_PYTYPE_LOOKUP jpayne@68: object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; jpayne@68: #else jpayne@68: object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; jpayne@68: #endif jpayne@68: reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; jpayne@68: if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { jpayne@68: reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); jpayne@68: if (likely(reduce_cython)) { jpayne@68: ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; jpayne@68: ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; jpayne@68: } else if (reduce == object_reduce || PyErr_Occurred()) { jpayne@68: goto __PYX_BAD; jpayne@68: } jpayne@68: setstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate); jpayne@68: if (!setstate) PyErr_Clear(); jpayne@68: if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { jpayne@68: setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); jpayne@68: if (likely(setstate_cython)) { jpayne@68: ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; jpayne@68: ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; jpayne@68: } else if (!setstate || PyErr_Occurred()) { jpayne@68: goto __PYX_BAD; jpayne@68: } jpayne@68: } jpayne@68: PyType_Modified((PyTypeObject*)type_obj); jpayne@68: } jpayne@68: } jpayne@68: goto __PYX_GOOD; jpayne@68: __PYX_BAD: jpayne@68: if (!PyErr_Occurred()) { jpayne@68: __Pyx_TypeName type_obj_name = jpayne@68: __Pyx_PyType_GetName((PyTypeObject*)type_obj); jpayne@68: PyErr_Format(PyExc_RuntimeError, jpayne@68: "Unable to initialize pickling for " __Pyx_FMT_TYPENAME, type_obj_name); jpayne@68: __Pyx_DECREF_TypeName(type_obj_name); jpayne@68: } jpayne@68: ret = -1; jpayne@68: __PYX_GOOD: jpayne@68: #if !CYTHON_USE_PYTYPE_LOOKUP jpayne@68: Py_XDECREF(object_reduce); jpayne@68: Py_XDECREF(object_reduce_ex); jpayne@68: Py_XDECREF(object_getstate); jpayne@68: Py_XDECREF(getstate); jpayne@68: #endif jpayne@68: Py_XDECREF(reduce); jpayne@68: Py_XDECREF(reduce_ex); jpayne@68: Py_XDECREF(reduce_cython); jpayne@68: Py_XDECREF(setstate); jpayne@68: Py_XDECREF(setstate_cython); jpayne@68: return ret; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* TypeImport */ jpayne@68: #ifndef __PYX_HAVE_RT_ImportType_3_0_11 jpayne@68: #define __PYX_HAVE_RT_ImportType_3_0_11 jpayne@68: static PyTypeObject *__Pyx_ImportType_3_0_11(PyObject *module, const char *module_name, const char *class_name, jpayne@68: size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_11 check_size) jpayne@68: { jpayne@68: PyObject *result = 0; jpayne@68: char warning[200]; jpayne@68: Py_ssize_t basicsize; jpayne@68: Py_ssize_t itemsize; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject *py_basicsize; jpayne@68: PyObject *py_itemsize; jpayne@68: #endif jpayne@68: result = PyObject_GetAttrString(module, class_name); jpayne@68: if (!result) jpayne@68: goto bad; jpayne@68: if (!PyType_Check(result)) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s.%.200s is not a type object", jpayne@68: module_name, class_name); jpayne@68: goto bad; jpayne@68: } jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: basicsize = ((PyTypeObject *)result)->tp_basicsize; jpayne@68: itemsize = ((PyTypeObject *)result)->tp_itemsize; jpayne@68: #else jpayne@68: py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); jpayne@68: if (!py_basicsize) jpayne@68: goto bad; jpayne@68: basicsize = PyLong_AsSsize_t(py_basicsize); jpayne@68: Py_DECREF(py_basicsize); jpayne@68: py_basicsize = 0; jpayne@68: if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) jpayne@68: goto bad; jpayne@68: py_itemsize = PyObject_GetAttrString(result, "__itemsize__"); jpayne@68: if (!py_itemsize) jpayne@68: goto bad; jpayne@68: itemsize = PyLong_AsSsize_t(py_itemsize); jpayne@68: Py_DECREF(py_itemsize); jpayne@68: py_itemsize = 0; jpayne@68: if (itemsize == (Py_ssize_t)-1 && PyErr_Occurred()) jpayne@68: goto bad; jpayne@68: #endif jpayne@68: if (itemsize) { jpayne@68: if (size % alignment) { jpayne@68: alignment = size % alignment; jpayne@68: } jpayne@68: if (itemsize < (Py_ssize_t)alignment) jpayne@68: itemsize = (Py_ssize_t)alignment; jpayne@68: } jpayne@68: if ((size_t)(basicsize + itemsize) < size) { jpayne@68: PyErr_Format(PyExc_ValueError, jpayne@68: "%.200s.%.200s size changed, may indicate binary incompatibility. " jpayne@68: "Expected %zd from C header, got %zd from PyObject", jpayne@68: module_name, class_name, size, basicsize+itemsize); jpayne@68: goto bad; jpayne@68: } jpayne@68: if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 && jpayne@68: ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) { jpayne@68: PyErr_Format(PyExc_ValueError, jpayne@68: "%.200s.%.200s size changed, may indicate binary incompatibility. " jpayne@68: "Expected %zd from C header, got %zd-%zd from PyObject", jpayne@68: module_name, class_name, size, basicsize, basicsize+itemsize); jpayne@68: goto bad; jpayne@68: } jpayne@68: else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_11 && (size_t)basicsize > size) { jpayne@68: PyOS_snprintf(warning, sizeof(warning), jpayne@68: "%s.%s size changed, may indicate binary incompatibility. " jpayne@68: "Expected %zd from C header, got %zd from PyObject", jpayne@68: module_name, class_name, size, basicsize); jpayne@68: if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; jpayne@68: } jpayne@68: return (PyTypeObject *)result; jpayne@68: bad: jpayne@68: Py_XDECREF(result); jpayne@68: return NULL; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* ImportDottedModule */ jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: static PyObject *__Pyx__ImportDottedModule_Error(PyObject *name, PyObject *parts_tuple, Py_ssize_t count) { jpayne@68: PyObject *partial_name = NULL, *slice = NULL, *sep = NULL; jpayne@68: if (unlikely(PyErr_Occurred())) { jpayne@68: PyErr_Clear(); jpayne@68: } jpayne@68: if (likely(PyTuple_GET_SIZE(parts_tuple) == count)) { jpayne@68: partial_name = name; jpayne@68: } else { jpayne@68: slice = PySequence_GetSlice(parts_tuple, 0, count); jpayne@68: if (unlikely(!slice)) jpayne@68: goto bad; jpayne@68: sep = PyUnicode_FromStringAndSize(".", 1); jpayne@68: if (unlikely(!sep)) jpayne@68: goto bad; jpayne@68: partial_name = PyUnicode_Join(sep, slice); jpayne@68: } jpayne@68: PyErr_Format( jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyExc_ImportError, jpayne@68: "No module named '%s'", PyString_AS_STRING(partial_name)); jpayne@68: #else jpayne@68: #if PY_VERSION_HEX >= 0x030600B1 jpayne@68: PyExc_ModuleNotFoundError, jpayne@68: #else jpayne@68: PyExc_ImportError, jpayne@68: #endif jpayne@68: "No module named '%U'", partial_name); jpayne@68: #endif jpayne@68: bad: jpayne@68: Py_XDECREF(sep); jpayne@68: Py_XDECREF(slice); jpayne@68: Py_XDECREF(partial_name); jpayne@68: return NULL; jpayne@68: } jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: static PyObject *__Pyx__ImportDottedModule_Lookup(PyObject *name) { jpayne@68: PyObject *imported_module; jpayne@68: #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400) jpayne@68: PyObject *modules = PyImport_GetModuleDict(); jpayne@68: if (unlikely(!modules)) jpayne@68: return NULL; jpayne@68: imported_module = __Pyx_PyDict_GetItemStr(modules, name); jpayne@68: Py_XINCREF(imported_module); jpayne@68: #else jpayne@68: imported_module = PyImport_GetModule(name); jpayne@68: #endif jpayne@68: return imported_module; jpayne@68: } jpayne@68: #endif jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple) { jpayne@68: Py_ssize_t i, nparts; jpayne@68: nparts = PyTuple_GET_SIZE(parts_tuple); jpayne@68: for (i=1; i < nparts && module; i++) { jpayne@68: PyObject *part, *submodule; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: part = PyTuple_GET_ITEM(parts_tuple, i); jpayne@68: #else jpayne@68: part = PySequence_ITEM(parts_tuple, i); jpayne@68: #endif jpayne@68: submodule = __Pyx_PyObject_GetAttrStrNoError(module, part); jpayne@68: #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) jpayne@68: Py_DECREF(part); jpayne@68: #endif jpayne@68: Py_DECREF(module); jpayne@68: module = submodule; jpayne@68: } jpayne@68: if (unlikely(!module)) { jpayne@68: return __Pyx__ImportDottedModule_Error(name, parts_tuple, i); jpayne@68: } jpayne@68: return module; jpayne@68: } jpayne@68: #endif jpayne@68: static PyObject *__Pyx__ImportDottedModule(PyObject *name, PyObject *parts_tuple) { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyObject *module, *from_list, *star = __pyx_n_s__62; jpayne@68: CYTHON_UNUSED_VAR(parts_tuple); jpayne@68: from_list = PyList_New(1); jpayne@68: if (unlikely(!from_list)) jpayne@68: return NULL; jpayne@68: Py_INCREF(star); jpayne@68: PyList_SET_ITEM(from_list, 0, star); jpayne@68: module = __Pyx_Import(name, from_list, 0); jpayne@68: Py_DECREF(from_list); jpayne@68: return module; jpayne@68: #else jpayne@68: PyObject *imported_module; jpayne@68: PyObject *module = __Pyx_Import(name, NULL, 0); jpayne@68: if (!parts_tuple || unlikely(!module)) jpayne@68: return module; jpayne@68: imported_module = __Pyx__ImportDottedModule_Lookup(name); jpayne@68: if (likely(imported_module)) { jpayne@68: Py_DECREF(module); jpayne@68: return imported_module; jpayne@68: } jpayne@68: PyErr_Clear(); jpayne@68: return __Pyx_ImportDottedModule_WalkParts(module, name, parts_tuple); jpayne@68: #endif jpayne@68: } jpayne@68: static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple) { jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030400B1 jpayne@68: PyObject *module = __Pyx__ImportDottedModule_Lookup(name); jpayne@68: if (likely(module)) { jpayne@68: PyObject *spec = __Pyx_PyObject_GetAttrStrNoError(module, __pyx_n_s_spec); jpayne@68: if (likely(spec)) { jpayne@68: PyObject *unsafe = __Pyx_PyObject_GetAttrStrNoError(spec, __pyx_n_s_initializing); jpayne@68: if (likely(!unsafe || !__Pyx_PyObject_IsTrue(unsafe))) { jpayne@68: Py_DECREF(spec); jpayne@68: spec = NULL; jpayne@68: } jpayne@68: Py_XDECREF(unsafe); jpayne@68: } jpayne@68: if (likely(!spec)) { jpayne@68: PyErr_Clear(); jpayne@68: return module; jpayne@68: } jpayne@68: Py_DECREF(spec); jpayne@68: Py_DECREF(module); jpayne@68: } else if (PyErr_Occurred()) { jpayne@68: PyErr_Clear(); jpayne@68: } jpayne@68: #endif jpayne@68: return __Pyx__ImportDottedModule(name, parts_tuple); jpayne@68: } jpayne@68: jpayne@68: /* FetchSharedCythonModule */ jpayne@68: static PyObject *__Pyx_FetchSharedCythonABIModule(void) { jpayne@68: return __Pyx_PyImport_AddModuleRef((char*) __PYX_ABI_MODULE_NAME); jpayne@68: } jpayne@68: jpayne@68: /* FetchCommonType */ jpayne@68: static int __Pyx_VerifyCachedType(PyObject *cached_type, jpayne@68: const char *name, jpayne@68: Py_ssize_t basicsize, jpayne@68: Py_ssize_t expected_basicsize) { jpayne@68: if (!PyType_Check(cached_type)) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "Shared Cython type %.200s is not a type object", name); jpayne@68: return -1; jpayne@68: } jpayne@68: if (basicsize != expected_basicsize) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "Shared Cython type %.200s has the wrong size, try recompiling", jpayne@68: name); jpayne@68: return -1; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: #if !CYTHON_USE_TYPE_SPECS jpayne@68: static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { jpayne@68: PyObject* abi_module; jpayne@68: const char* object_name; jpayne@68: PyTypeObject *cached_type = NULL; jpayne@68: abi_module = __Pyx_FetchSharedCythonABIModule(); jpayne@68: if (!abi_module) return NULL; jpayne@68: object_name = strrchr(type->tp_name, '.'); jpayne@68: object_name = object_name ? object_name+1 : type->tp_name; jpayne@68: cached_type = (PyTypeObject*) PyObject_GetAttrString(abi_module, object_name); jpayne@68: if (cached_type) { jpayne@68: if (__Pyx_VerifyCachedType( jpayne@68: (PyObject *)cached_type, jpayne@68: object_name, jpayne@68: cached_type->tp_basicsize, jpayne@68: type->tp_basicsize) < 0) { jpayne@68: goto bad; jpayne@68: } jpayne@68: goto done; jpayne@68: } jpayne@68: if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; jpayne@68: PyErr_Clear(); jpayne@68: if (PyType_Ready(type) < 0) goto bad; jpayne@68: if (PyObject_SetAttrString(abi_module, object_name, (PyObject *)type) < 0) jpayne@68: goto bad; jpayne@68: Py_INCREF(type); jpayne@68: cached_type = type; jpayne@68: done: jpayne@68: Py_DECREF(abi_module); jpayne@68: return cached_type; jpayne@68: bad: jpayne@68: Py_XDECREF(cached_type); jpayne@68: cached_type = NULL; jpayne@68: goto done; jpayne@68: } jpayne@68: #else jpayne@68: static PyTypeObject *__Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases) { jpayne@68: PyObject *abi_module, *cached_type = NULL; jpayne@68: const char* object_name = strrchr(spec->name, '.'); jpayne@68: object_name = object_name ? object_name+1 : spec->name; jpayne@68: abi_module = __Pyx_FetchSharedCythonABIModule(); jpayne@68: if (!abi_module) return NULL; jpayne@68: cached_type = PyObject_GetAttrString(abi_module, object_name); jpayne@68: if (cached_type) { jpayne@68: Py_ssize_t basicsize; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject *py_basicsize; jpayne@68: py_basicsize = PyObject_GetAttrString(cached_type, "__basicsize__"); jpayne@68: if (unlikely(!py_basicsize)) goto bad; jpayne@68: basicsize = PyLong_AsSsize_t(py_basicsize); jpayne@68: Py_DECREF(py_basicsize); jpayne@68: py_basicsize = 0; jpayne@68: if (unlikely(basicsize == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; jpayne@68: #else jpayne@68: basicsize = likely(PyType_Check(cached_type)) ? ((PyTypeObject*) cached_type)->tp_basicsize : -1; jpayne@68: #endif jpayne@68: if (__Pyx_VerifyCachedType( jpayne@68: cached_type, jpayne@68: object_name, jpayne@68: basicsize, jpayne@68: spec->basicsize) < 0) { jpayne@68: goto bad; jpayne@68: } jpayne@68: goto done; jpayne@68: } jpayne@68: if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; jpayne@68: PyErr_Clear(); jpayne@68: CYTHON_UNUSED_VAR(module); jpayne@68: cached_type = __Pyx_PyType_FromModuleAndSpec(abi_module, spec, bases); jpayne@68: if (unlikely(!cached_type)) goto bad; jpayne@68: if (unlikely(__Pyx_fix_up_extension_type_from_spec(spec, (PyTypeObject *) cached_type) < 0)) goto bad; jpayne@68: if (PyObject_SetAttrString(abi_module, object_name, cached_type) < 0) goto bad; jpayne@68: done: jpayne@68: Py_DECREF(abi_module); jpayne@68: assert(cached_type == NULL || PyType_Check(cached_type)); jpayne@68: return (PyTypeObject *) cached_type; jpayne@68: bad: jpayne@68: Py_XDECREF(cached_type); jpayne@68: cached_type = NULL; jpayne@68: goto done; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* PyVectorcallFastCallDict */ jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: static PyObject *__Pyx_PyVectorcall_FastCallDict_kw(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw) jpayne@68: { jpayne@68: PyObject *res = NULL; jpayne@68: PyObject *kwnames; jpayne@68: PyObject **newargs; jpayne@68: PyObject **kwvalues; jpayne@68: Py_ssize_t i, pos; jpayne@68: size_t j; jpayne@68: PyObject *key, *value; jpayne@68: unsigned long keys_are_strings; jpayne@68: Py_ssize_t nkw = PyDict_GET_SIZE(kw); jpayne@68: newargs = (PyObject **)PyMem_Malloc((nargs + (size_t)nkw) * sizeof(args[0])); jpayne@68: if (unlikely(newargs == NULL)) { jpayne@68: PyErr_NoMemory(); jpayne@68: return NULL; jpayne@68: } jpayne@68: for (j = 0; j < nargs; j++) newargs[j] = args[j]; jpayne@68: kwnames = PyTuple_New(nkw); jpayne@68: if (unlikely(kwnames == NULL)) { jpayne@68: PyMem_Free(newargs); jpayne@68: return NULL; jpayne@68: } jpayne@68: kwvalues = newargs + nargs; jpayne@68: pos = i = 0; jpayne@68: keys_are_strings = Py_TPFLAGS_UNICODE_SUBCLASS; jpayne@68: while (PyDict_Next(kw, &pos, &key, &value)) { jpayne@68: keys_are_strings &= Py_TYPE(key)->tp_flags; jpayne@68: Py_INCREF(key); jpayne@68: Py_INCREF(value); jpayne@68: PyTuple_SET_ITEM(kwnames, i, key); jpayne@68: kwvalues[i] = value; jpayne@68: i++; jpayne@68: } jpayne@68: if (unlikely(!keys_are_strings)) { jpayne@68: PyErr_SetString(PyExc_TypeError, "keywords must be strings"); jpayne@68: goto cleanup; jpayne@68: } jpayne@68: res = vc(func, newargs, nargs, kwnames); jpayne@68: cleanup: jpayne@68: Py_DECREF(kwnames); jpayne@68: for (i = 0; i < nkw; i++) jpayne@68: Py_DECREF(kwvalues[i]); jpayne@68: PyMem_Free(newargs); jpayne@68: return res; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw) jpayne@68: { jpayne@68: if (likely(kw == NULL) || PyDict_GET_SIZE(kw) == 0) { jpayne@68: return vc(func, args, nargs, NULL); jpayne@68: } jpayne@68: return __Pyx_PyVectorcall_FastCallDict_kw(func, vc, args, nargs, kw); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* CythonFunctionShared */ jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) { jpayne@68: if (__Pyx_CyFunction_Check(func)) { jpayne@68: return PyCFunction_GetFunction(((__pyx_CyFunctionObject*)func)->func) == (PyCFunction) cfunc; jpayne@68: } else if (PyCFunction_Check(func)) { jpayne@68: return PyCFunction_GetFunction(func) == (PyCFunction) cfunc; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: #else jpayne@68: static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) { jpayne@68: return __Pyx_CyOrPyCFunction_Check(func) && __Pyx_CyOrPyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc; jpayne@68: } jpayne@68: #endif jpayne@68: static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj) { jpayne@68: #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: __Pyx_Py_XDECREF_SET( jpayne@68: __Pyx_CyFunction_GetClassObj(f), jpayne@68: ((classobj) ? __Pyx_NewRef(classobj) : NULL)); jpayne@68: #else jpayne@68: __Pyx_Py_XDECREF_SET( jpayne@68: ((PyCMethodObject *) (f))->mm_class, jpayne@68: (PyTypeObject*)((classobj) ? __Pyx_NewRef(classobj) : NULL)); jpayne@68: #endif jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, void *closure) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(closure); jpayne@68: if (unlikely(op->func_doc == NULL)) { jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: op->func_doc = PyObject_GetAttrString(op->func, "__doc__"); jpayne@68: if (unlikely(!op->func_doc)) return NULL; jpayne@68: #else jpayne@68: if (((PyCFunctionObject*)op)->m_ml->ml_doc) { jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: op->func_doc = PyUnicode_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc); jpayne@68: #else jpayne@68: op->func_doc = PyString_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc); jpayne@68: #endif jpayne@68: if (unlikely(op->func_doc == NULL)) jpayne@68: return NULL; jpayne@68: } else { jpayne@68: Py_INCREF(Py_None); jpayne@68: return Py_None; jpayne@68: } jpayne@68: #endif jpayne@68: } jpayne@68: Py_INCREF(op->func_doc); jpayne@68: return op->func_doc; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (value == NULL) { jpayne@68: value = Py_None; jpayne@68: } jpayne@68: Py_INCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->func_doc, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (unlikely(op->func_name == NULL)) { jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: op->func_name = PyObject_GetAttrString(op->func, "__name__"); jpayne@68: #elif PY_MAJOR_VERSION >= 3 jpayne@68: op->func_name = PyUnicode_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name); jpayne@68: #else jpayne@68: op->func_name = PyString_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name); jpayne@68: #endif jpayne@68: if (unlikely(op->func_name == NULL)) jpayne@68: return NULL; jpayne@68: } jpayne@68: Py_INCREF(op->func_name); jpayne@68: return op->func_name; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (unlikely(value == NULL || !PyUnicode_Check(value))) jpayne@68: #else jpayne@68: if (unlikely(value == NULL || !PyString_Check(value))) jpayne@68: #endif jpayne@68: { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "__name__ must be set to a string object"); jpayne@68: return -1; jpayne@68: } jpayne@68: Py_INCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->func_name, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: Py_INCREF(op->func_qualname); jpayne@68: return op->func_qualname; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (unlikely(value == NULL || !PyUnicode_Check(value))) jpayne@68: #else jpayne@68: if (unlikely(value == NULL || !PyString_Check(value))) jpayne@68: #endif jpayne@68: { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "__qualname__ must be set to a string object"); jpayne@68: return -1; jpayne@68: } jpayne@68: Py_INCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->func_qualname, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (unlikely(op->func_dict == NULL)) { jpayne@68: op->func_dict = PyDict_New(); jpayne@68: if (unlikely(op->func_dict == NULL)) jpayne@68: return NULL; jpayne@68: } jpayne@68: Py_INCREF(op->func_dict); jpayne@68: return op->func_dict; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (unlikely(value == NULL)) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "function's dictionary may not be deleted"); jpayne@68: return -1; jpayne@68: } jpayne@68: if (unlikely(!PyDict_Check(value))) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "setting function's dictionary to a non-dict"); jpayne@68: return -1; jpayne@68: } jpayne@68: Py_INCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->func_dict, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: Py_INCREF(op->func_globals); jpayne@68: return op->func_globals; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_closure(__pyx_CyFunctionObject *op, void *context) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(op); jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: Py_INCREF(Py_None); jpayne@68: return Py_None; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op, void *context) jpayne@68: { jpayne@68: PyObject* result = (op->func_code) ? op->func_code : Py_None; jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: Py_INCREF(result); jpayne@68: return result; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) { jpayne@68: int result = 0; jpayne@68: PyObject *res = op->defaults_getter((PyObject *) op); jpayne@68: if (unlikely(!res)) jpayne@68: return -1; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: op->defaults_tuple = PyTuple_GET_ITEM(res, 0); jpayne@68: Py_INCREF(op->defaults_tuple); jpayne@68: op->defaults_kwdict = PyTuple_GET_ITEM(res, 1); jpayne@68: Py_INCREF(op->defaults_kwdict); jpayne@68: #else jpayne@68: op->defaults_tuple = __Pyx_PySequence_ITEM(res, 0); jpayne@68: if (unlikely(!op->defaults_tuple)) result = -1; jpayne@68: else { jpayne@68: op->defaults_kwdict = __Pyx_PySequence_ITEM(res, 1); jpayne@68: if (unlikely(!op->defaults_kwdict)) result = -1; jpayne@68: } jpayne@68: #endif jpayne@68: Py_DECREF(res); jpayne@68: return result; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (!value) { jpayne@68: value = Py_None; jpayne@68: } else if (unlikely(value != Py_None && !PyTuple_Check(value))) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "__defaults__ must be set to a tuple object"); jpayne@68: return -1; jpayne@68: } jpayne@68: PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__defaults__ will not " jpayne@68: "currently affect the values used in function calls", 1); jpayne@68: Py_INCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->defaults_tuple, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op, void *context) { jpayne@68: PyObject* result = op->defaults_tuple; jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (unlikely(!result)) { jpayne@68: if (op->defaults_getter) { jpayne@68: if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL; jpayne@68: result = op->defaults_tuple; jpayne@68: } else { jpayne@68: result = Py_None; jpayne@68: } jpayne@68: } jpayne@68: Py_INCREF(result); jpayne@68: return result; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (!value) { jpayne@68: value = Py_None; jpayne@68: } else if (unlikely(value != Py_None && !PyDict_Check(value))) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "__kwdefaults__ must be set to a dict object"); jpayne@68: return -1; jpayne@68: } jpayne@68: PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__kwdefaults__ will not " jpayne@68: "currently affect the values used in function calls", 1); jpayne@68: Py_INCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->defaults_kwdict, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op, void *context) { jpayne@68: PyObject* result = op->defaults_kwdict; jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (unlikely(!result)) { jpayne@68: if (op->defaults_getter) { jpayne@68: if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL; jpayne@68: result = op->defaults_kwdict; jpayne@68: } else { jpayne@68: result = Py_None; jpayne@68: } jpayne@68: } jpayne@68: Py_INCREF(result); jpayne@68: return result; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value, void *context) { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (!value || value == Py_None) { jpayne@68: value = NULL; jpayne@68: } else if (unlikely(!PyDict_Check(value))) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "__annotations__ must be set to a dict object"); jpayne@68: return -1; jpayne@68: } jpayne@68: Py_XINCREF(value); jpayne@68: __Pyx_Py_XDECREF_SET(op->func_annotations, value); jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op, void *context) { jpayne@68: PyObject* result = op->func_annotations; jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (unlikely(!result)) { jpayne@68: result = PyDict_New(); jpayne@68: if (unlikely(!result)) return NULL; jpayne@68: op->func_annotations = result; jpayne@68: } jpayne@68: Py_INCREF(result); jpayne@68: return result; jpayne@68: } jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_is_coroutine(__pyx_CyFunctionObject *op, void *context) { jpayne@68: int is_coroutine; jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: if (op->func_is_coroutine) { jpayne@68: return __Pyx_NewRef(op->func_is_coroutine); jpayne@68: } jpayne@68: is_coroutine = op->flags & __Pyx_CYFUNCTION_COROUTINE; jpayne@68: #if PY_VERSION_HEX >= 0x03050000 jpayne@68: if (is_coroutine) { jpayne@68: PyObject *module, *fromlist, *marker = __pyx_n_s_is_coroutine; jpayne@68: fromlist = PyList_New(1); jpayne@68: if (unlikely(!fromlist)) return NULL; jpayne@68: Py_INCREF(marker); jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: PyList_SET_ITEM(fromlist, 0, marker); jpayne@68: #else jpayne@68: if (unlikely(PyList_SetItem(fromlist, 0, marker) < 0)) { jpayne@68: Py_DECREF(marker); jpayne@68: Py_DECREF(fromlist); jpayne@68: return NULL; jpayne@68: } jpayne@68: #endif jpayne@68: module = PyImport_ImportModuleLevelObject(__pyx_n_s_asyncio_coroutines, NULL, NULL, fromlist, 0); jpayne@68: Py_DECREF(fromlist); jpayne@68: if (unlikely(!module)) goto ignore; jpayne@68: op->func_is_coroutine = __Pyx_PyObject_GetAttrStr(module, marker); jpayne@68: Py_DECREF(module); jpayne@68: if (likely(op->func_is_coroutine)) { jpayne@68: return __Pyx_NewRef(op->func_is_coroutine); jpayne@68: } jpayne@68: ignore: jpayne@68: PyErr_Clear(); jpayne@68: } jpayne@68: #endif jpayne@68: op->func_is_coroutine = __Pyx_PyBool_FromLong(is_coroutine); jpayne@68: return __Pyx_NewRef(op->func_is_coroutine); jpayne@68: } jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_get_module(__pyx_CyFunctionObject *op, void *context) { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: return PyObject_GetAttrString(op->func, "__module__"); jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_set_module(__pyx_CyFunctionObject *op, PyObject* value, void *context) { jpayne@68: CYTHON_UNUSED_VAR(context); jpayne@68: return PyObject_SetAttrString(op->func, "__module__", value); jpayne@68: } jpayne@68: #endif jpayne@68: static PyGetSetDef __pyx_CyFunction_getsets[] = { jpayne@68: {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, jpayne@68: {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, jpayne@68: {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, jpayne@68: {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, jpayne@68: {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, jpayne@68: {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, jpayne@68: {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, jpayne@68: {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, jpayne@68: {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, jpayne@68: {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, jpayne@68: {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, jpayne@68: {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, jpayne@68: {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, jpayne@68: {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, jpayne@68: {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, jpayne@68: {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0}, jpayne@68: {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0}, jpayne@68: {(char *) "_is_coroutine", (getter)__Pyx_CyFunction_get_is_coroutine, 0, 0, 0}, jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: {"__module__", (getter)__Pyx_CyFunction_get_module, (setter)__Pyx_CyFunction_set_module, 0, 0}, jpayne@68: #endif jpayne@68: {0, 0, 0, 0, 0} jpayne@68: }; jpayne@68: static PyMemberDef __pyx_CyFunction_members[] = { jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: {(char *) "__module__", T_OBJECT, offsetof(PyCFunctionObject, m_module), 0, 0}, jpayne@68: #endif jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: {(char *) "__dictoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_dict), READONLY, 0}, jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_vectorcall), READONLY, 0}, jpayne@68: #else jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(PyCFunctionObject, vectorcall), READONLY, 0}, jpayne@68: #endif jpayne@68: #endif jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_weakreflist), READONLY, 0}, jpayne@68: #else jpayne@68: {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(PyCFunctionObject, m_weakreflist), READONLY, 0}, jpayne@68: #endif jpayne@68: #endif jpayne@68: {0, 0, 0, 0, 0} jpayne@68: }; jpayne@68: static PyObject * jpayne@68: __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, PyObject *args) jpayne@68: { jpayne@68: CYTHON_UNUSED_VAR(args); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: Py_INCREF(m->func_qualname); jpayne@68: return m->func_qualname; jpayne@68: #else jpayne@68: return PyString_FromString(((PyCFunctionObject*)m)->m_ml->ml_name); jpayne@68: #endif jpayne@68: } jpayne@68: static PyMethodDef __pyx_CyFunction_methods[] = { jpayne@68: {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, jpayne@68: {0, 0, 0, 0} jpayne@68: }; jpayne@68: #if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist) jpayne@68: #else jpayne@68: #define __Pyx_CyFunction_weakreflist(cyfunc) (((PyCFunctionObject*)cyfunc)->m_weakreflist) jpayne@68: #endif jpayne@68: static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname, jpayne@68: PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyCFunctionObject *cf = (PyCFunctionObject*) op; jpayne@68: #endif jpayne@68: if (unlikely(op == NULL)) jpayne@68: return NULL; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: op->func = PyCFunction_NewEx(ml, (PyObject*)op, module); jpayne@68: if (unlikely(!op->func)) return NULL; jpayne@68: #endif jpayne@68: op->flags = flags; jpayne@68: __Pyx_CyFunction_weakreflist(op) = NULL; jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: cf->m_ml = ml; jpayne@68: cf->m_self = (PyObject *) op; jpayne@68: #endif jpayne@68: Py_XINCREF(closure); jpayne@68: op->func_closure = closure; jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_XINCREF(module); jpayne@68: cf->m_module = module; jpayne@68: #endif jpayne@68: op->func_dict = NULL; jpayne@68: op->func_name = NULL; jpayne@68: Py_INCREF(qualname); jpayne@68: op->func_qualname = qualname; jpayne@68: op->func_doc = NULL; jpayne@68: #if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API jpayne@68: op->func_classobj = NULL; jpayne@68: #else jpayne@68: ((PyCMethodObject*)op)->mm_class = NULL; jpayne@68: #endif jpayne@68: op->func_globals = globals; jpayne@68: Py_INCREF(op->func_globals); jpayne@68: Py_XINCREF(code); jpayne@68: op->func_code = code; jpayne@68: op->defaults_pyobjects = 0; jpayne@68: op->defaults_size = 0; jpayne@68: op->defaults = NULL; jpayne@68: op->defaults_tuple = NULL; jpayne@68: op->defaults_kwdict = NULL; jpayne@68: op->defaults_getter = NULL; jpayne@68: op->func_annotations = NULL; jpayne@68: op->func_is_coroutine = NULL; jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: switch (ml->ml_flags & (METH_VARARGS | METH_FASTCALL | METH_NOARGS | METH_O | METH_KEYWORDS | METH_METHOD)) { jpayne@68: case METH_NOARGS: jpayne@68: __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_NOARGS; jpayne@68: break; jpayne@68: case METH_O: jpayne@68: __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_O; jpayne@68: break; jpayne@68: case METH_METHOD | METH_FASTCALL | METH_KEYWORDS: jpayne@68: __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD; jpayne@68: break; jpayne@68: case METH_FASTCALL | METH_KEYWORDS: jpayne@68: __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS; jpayne@68: break; jpayne@68: case METH_VARARGS | METH_KEYWORDS: jpayne@68: __Pyx_CyFunction_func_vectorcall(op) = NULL; jpayne@68: break; jpayne@68: default: jpayne@68: PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction"); jpayne@68: Py_DECREF(op); jpayne@68: return NULL; jpayne@68: } jpayne@68: #endif jpayne@68: return (PyObject *) op; jpayne@68: } jpayne@68: static int jpayne@68: __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) jpayne@68: { jpayne@68: Py_CLEAR(m->func_closure); jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_CLEAR(m->func); jpayne@68: #else jpayne@68: Py_CLEAR(((PyCFunctionObject*)m)->m_module); jpayne@68: #endif jpayne@68: Py_CLEAR(m->func_dict); jpayne@68: Py_CLEAR(m->func_name); jpayne@68: Py_CLEAR(m->func_qualname); jpayne@68: Py_CLEAR(m->func_doc); jpayne@68: Py_CLEAR(m->func_globals); jpayne@68: Py_CLEAR(m->func_code); jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #if PY_VERSION_HEX < 0x030900B1 jpayne@68: Py_CLEAR(__Pyx_CyFunction_GetClassObj(m)); jpayne@68: #else jpayne@68: { jpayne@68: PyObject *cls = (PyObject*) ((PyCMethodObject *) (m))->mm_class; jpayne@68: ((PyCMethodObject *) (m))->mm_class = NULL; jpayne@68: Py_XDECREF(cls); jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: Py_CLEAR(m->defaults_tuple); jpayne@68: Py_CLEAR(m->defaults_kwdict); jpayne@68: Py_CLEAR(m->func_annotations); jpayne@68: Py_CLEAR(m->func_is_coroutine); jpayne@68: if (m->defaults) { jpayne@68: PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); jpayne@68: int i; jpayne@68: for (i = 0; i < m->defaults_pyobjects; i++) jpayne@68: Py_XDECREF(pydefaults[i]); jpayne@68: PyObject_Free(m->defaults); jpayne@68: m->defaults = NULL; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: static void __Pyx__CyFunction_dealloc(__pyx_CyFunctionObject *m) jpayne@68: { jpayne@68: if (__Pyx_CyFunction_weakreflist(m) != NULL) jpayne@68: PyObject_ClearWeakRefs((PyObject *) m); jpayne@68: __Pyx_CyFunction_clear(m); jpayne@68: __Pyx_PyHeapTypeObject_GC_Del(m); jpayne@68: } jpayne@68: static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) jpayne@68: { jpayne@68: PyObject_GC_UnTrack(m); jpayne@68: __Pyx__CyFunction_dealloc(m); jpayne@68: } jpayne@68: static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) jpayne@68: { jpayne@68: Py_VISIT(m->func_closure); jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_VISIT(m->func); jpayne@68: #else jpayne@68: Py_VISIT(((PyCFunctionObject*)m)->m_module); jpayne@68: #endif jpayne@68: Py_VISIT(m->func_dict); jpayne@68: Py_VISIT(m->func_name); jpayne@68: Py_VISIT(m->func_qualname); jpayne@68: Py_VISIT(m->func_doc); jpayne@68: Py_VISIT(m->func_globals); jpayne@68: Py_VISIT(m->func_code); jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_VISIT(__Pyx_CyFunction_GetClassObj(m)); jpayne@68: #endif jpayne@68: Py_VISIT(m->defaults_tuple); jpayne@68: Py_VISIT(m->defaults_kwdict); jpayne@68: Py_VISIT(m->func_is_coroutine); jpayne@68: if (m->defaults) { jpayne@68: PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); jpayne@68: int i; jpayne@68: for (i = 0; i < m->defaults_pyobjects; i++) jpayne@68: Py_VISIT(pydefaults[i]); jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: static PyObject* jpayne@68: __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) jpayne@68: { jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: return PyUnicode_FromFormat("", jpayne@68: op->func_qualname, (void *)op); jpayne@68: #else jpayne@68: return PyString_FromFormat("", jpayne@68: PyString_AsString(op->func_qualname), (void *)op); jpayne@68: #endif jpayne@68: } jpayne@68: static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) { jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: PyObject *f = ((__pyx_CyFunctionObject*)func)->func; jpayne@68: PyObject *py_name = NULL; jpayne@68: PyCFunction meth; jpayne@68: int flags; jpayne@68: meth = PyCFunction_GetFunction(f); jpayne@68: if (unlikely(!meth)) return NULL; jpayne@68: flags = PyCFunction_GetFlags(f); jpayne@68: if (unlikely(flags < 0)) return NULL; jpayne@68: #else jpayne@68: PyCFunctionObject* f = (PyCFunctionObject*)func; jpayne@68: PyCFunction meth = f->m_ml->ml_meth; jpayne@68: int flags = f->m_ml->ml_flags; jpayne@68: #endif jpayne@68: Py_ssize_t size; jpayne@68: switch (flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) { jpayne@68: case METH_VARARGS: jpayne@68: if (likely(kw == NULL || PyDict_Size(kw) == 0)) jpayne@68: return (*meth)(self, arg); jpayne@68: break; jpayne@68: case METH_VARARGS | METH_KEYWORDS: jpayne@68: return (*(PyCFunctionWithKeywords)(void*)meth)(self, arg, kw); jpayne@68: case METH_NOARGS: jpayne@68: if (likely(kw == NULL || PyDict_Size(kw) == 0)) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: size = PyTuple_GET_SIZE(arg); jpayne@68: #else jpayne@68: size = PyTuple_Size(arg); jpayne@68: if (unlikely(size < 0)) return NULL; jpayne@68: #endif jpayne@68: if (likely(size == 0)) jpayne@68: return (*meth)(self, NULL); jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL); jpayne@68: if (!py_name) return NULL; jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200S() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: py_name, size); jpayne@68: Py_DECREF(py_name); jpayne@68: #else jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: f->m_ml->ml_name, size); jpayne@68: #endif jpayne@68: return NULL; jpayne@68: } jpayne@68: break; jpayne@68: case METH_O: jpayne@68: if (likely(kw == NULL || PyDict_Size(kw) == 0)) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: size = PyTuple_GET_SIZE(arg); jpayne@68: #else jpayne@68: size = PyTuple_Size(arg); jpayne@68: if (unlikely(size < 0)) return NULL; jpayne@68: #endif jpayne@68: if (likely(size == 1)) { jpayne@68: PyObject *result, *arg0; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: arg0 = PyTuple_GET_ITEM(arg, 0); jpayne@68: #else jpayne@68: arg0 = __Pyx_PySequence_ITEM(arg, 0); if (unlikely(!arg0)) return NULL; jpayne@68: #endif jpayne@68: result = (*meth)(self, arg0); jpayne@68: #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) jpayne@68: Py_DECREF(arg0); jpayne@68: #endif jpayne@68: return result; jpayne@68: } jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL); jpayne@68: if (!py_name) return NULL; jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200S() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: py_name, size); jpayne@68: Py_DECREF(py_name); jpayne@68: #else jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: f->m_ml->ml_name, size); jpayne@68: #endif jpayne@68: return NULL; jpayne@68: } jpayne@68: break; jpayne@68: default: jpayne@68: PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction"); jpayne@68: return NULL; jpayne@68: } jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL); jpayne@68: if (!py_name) return NULL; jpayne@68: PyErr_Format(PyExc_TypeError, "%.200S() takes no keyword arguments", jpayne@68: py_name); jpayne@68: Py_DECREF(py_name); jpayne@68: #else jpayne@68: PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", jpayne@68: f->m_ml->ml_name); jpayne@68: #endif jpayne@68: return NULL; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { jpayne@68: PyObject *self, *result; jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: self = PyCFunction_GetSelf(((__pyx_CyFunctionObject*)func)->func); jpayne@68: if (unlikely(!self) && PyErr_Occurred()) return NULL; jpayne@68: #else jpayne@68: self = ((PyCFunctionObject*)func)->m_self; jpayne@68: #endif jpayne@68: result = __Pyx_CyFunction_CallMethod(func, self, arg, kw); jpayne@68: return result; jpayne@68: } jpayne@68: static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) { jpayne@68: PyObject *result; jpayne@68: __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func; jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: __pyx_vectorcallfunc vc = __Pyx_CyFunction_func_vectorcall(cyfunc); jpayne@68: if (vc) { jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: return __Pyx_PyVectorcall_FastCallDict(func, vc, &PyTuple_GET_ITEM(args, 0), (size_t)PyTuple_GET_SIZE(args), kw); jpayne@68: #else jpayne@68: (void) &__Pyx_PyVectorcall_FastCallDict; jpayne@68: return PyVectorcall_Call(func, args, kw); jpayne@68: #endif jpayne@68: } jpayne@68: #endif jpayne@68: if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) { jpayne@68: Py_ssize_t argc; jpayne@68: PyObject *new_args; jpayne@68: PyObject *self; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: argc = PyTuple_GET_SIZE(args); jpayne@68: #else jpayne@68: argc = PyTuple_Size(args); jpayne@68: if (unlikely(!argc) < 0) return NULL; jpayne@68: #endif jpayne@68: new_args = PyTuple_GetSlice(args, 1, argc); jpayne@68: if (unlikely(!new_args)) jpayne@68: return NULL; jpayne@68: self = PyTuple_GetItem(args, 0); jpayne@68: if (unlikely(!self)) { jpayne@68: Py_DECREF(new_args); jpayne@68: #if PY_MAJOR_VERSION > 2 jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "unbound method %.200S() needs an argument", jpayne@68: cyfunc->func_qualname); jpayne@68: #else jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "unbound method needs an argument"); jpayne@68: #endif jpayne@68: return NULL; jpayne@68: } jpayne@68: result = __Pyx_CyFunction_CallMethod(func, self, new_args, kw); jpayne@68: Py_DECREF(new_args); jpayne@68: } else { jpayne@68: result = __Pyx_CyFunction_Call(func, args, kw); jpayne@68: } jpayne@68: return result; jpayne@68: } jpayne@68: #if CYTHON_METH_FASTCALL jpayne@68: static CYTHON_INLINE int __Pyx_CyFunction_Vectorcall_CheckArgs(__pyx_CyFunctionObject *cyfunc, Py_ssize_t nargs, PyObject *kwnames) jpayne@68: { jpayne@68: int ret = 0; jpayne@68: if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) { jpayne@68: if (unlikely(nargs < 1)) { jpayne@68: PyErr_Format(PyExc_TypeError, "%.200s() needs an argument", jpayne@68: ((PyCFunctionObject*)cyfunc)->m_ml->ml_name); jpayne@68: return -1; jpayne@68: } jpayne@68: ret = 1; jpayne@68: } jpayne@68: if (unlikely(kwnames) && unlikely(PyTuple_GET_SIZE(kwnames))) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() takes no keyword arguments", ((PyCFunctionObject*)cyfunc)->m_ml->ml_name); jpayne@68: return -1; jpayne@68: } jpayne@68: return ret; jpayne@68: } jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) jpayne@68: { jpayne@68: __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; jpayne@68: PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: Py_ssize_t nargs = (Py_ssize_t)nargsf; jpayne@68: #else jpayne@68: Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); jpayne@68: #endif jpayne@68: PyObject *self; jpayne@68: switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) { jpayne@68: case 1: jpayne@68: self = args[0]; jpayne@68: args += 1; jpayne@68: nargs -= 1; jpayne@68: break; jpayne@68: case 0: jpayne@68: self = ((PyCFunctionObject*)cyfunc)->m_self; jpayne@68: break; jpayne@68: default: jpayne@68: return NULL; jpayne@68: } jpayne@68: if (unlikely(nargs != 0)) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: def->ml_name, nargs); jpayne@68: return NULL; jpayne@68: } jpayne@68: return def->ml_meth(self, NULL); jpayne@68: } jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) jpayne@68: { jpayne@68: __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; jpayne@68: PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: Py_ssize_t nargs = (Py_ssize_t)nargsf; jpayne@68: #else jpayne@68: Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); jpayne@68: #endif jpayne@68: PyObject *self; jpayne@68: switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) { jpayne@68: case 1: jpayne@68: self = args[0]; jpayne@68: args += 1; jpayne@68: nargs -= 1; jpayne@68: break; jpayne@68: case 0: jpayne@68: self = ((PyCFunctionObject*)cyfunc)->m_self; jpayne@68: break; jpayne@68: default: jpayne@68: return NULL; jpayne@68: } jpayne@68: if (unlikely(nargs != 1)) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", jpayne@68: def->ml_name, nargs); jpayne@68: return NULL; jpayne@68: } jpayne@68: return def->ml_meth(self, args[0]); jpayne@68: } jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) jpayne@68: { jpayne@68: __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; jpayne@68: PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: Py_ssize_t nargs = (Py_ssize_t)nargsf; jpayne@68: #else jpayne@68: Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); jpayne@68: #endif jpayne@68: PyObject *self; jpayne@68: switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) { jpayne@68: case 1: jpayne@68: self = args[0]; jpayne@68: args += 1; jpayne@68: nargs -= 1; jpayne@68: break; jpayne@68: case 0: jpayne@68: self = ((PyCFunctionObject*)cyfunc)->m_self; jpayne@68: break; jpayne@68: default: jpayne@68: return NULL; jpayne@68: } jpayne@68: return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames); jpayne@68: } jpayne@68: static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) jpayne@68: { jpayne@68: __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; jpayne@68: PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; jpayne@68: PyTypeObject *cls = (PyTypeObject *) __Pyx_CyFunction_GetClassObj(cyfunc); jpayne@68: #if CYTHON_BACKPORT_VECTORCALL jpayne@68: Py_ssize_t nargs = (Py_ssize_t)nargsf; jpayne@68: #else jpayne@68: Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); jpayne@68: #endif jpayne@68: PyObject *self; jpayne@68: switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) { jpayne@68: case 1: jpayne@68: self = args[0]; jpayne@68: args += 1; jpayne@68: nargs -= 1; jpayne@68: break; jpayne@68: case 0: jpayne@68: self = ((PyCFunctionObject*)cyfunc)->m_self; jpayne@68: break; jpayne@68: default: jpayne@68: return NULL; jpayne@68: } jpayne@68: return ((__Pyx_PyCMethod)(void(*)(void))def->ml_meth)(self, cls, args, (size_t)nargs, kwnames); jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: static PyType_Slot __pyx_CyFunctionType_slots[] = { jpayne@68: {Py_tp_dealloc, (void *)__Pyx_CyFunction_dealloc}, jpayne@68: {Py_tp_repr, (void *)__Pyx_CyFunction_repr}, jpayne@68: {Py_tp_call, (void *)__Pyx_CyFunction_CallAsMethod}, jpayne@68: {Py_tp_traverse, (void *)__Pyx_CyFunction_traverse}, jpayne@68: {Py_tp_clear, (void *)__Pyx_CyFunction_clear}, jpayne@68: {Py_tp_methods, (void *)__pyx_CyFunction_methods}, jpayne@68: {Py_tp_members, (void *)__pyx_CyFunction_members}, jpayne@68: {Py_tp_getset, (void *)__pyx_CyFunction_getsets}, jpayne@68: {Py_tp_descr_get, (void *)__Pyx_PyMethod_New}, jpayne@68: {0, 0}, jpayne@68: }; jpayne@68: static PyType_Spec __pyx_CyFunctionType_spec = { jpayne@68: __PYX_TYPE_MODULE_PREFIX "cython_function_or_method", jpayne@68: sizeof(__pyx_CyFunctionObject), jpayne@68: 0, jpayne@68: #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR jpayne@68: Py_TPFLAGS_METHOD_DESCRIPTOR | jpayne@68: #endif jpayne@68: #if (defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL) jpayne@68: _Py_TPFLAGS_HAVE_VECTORCALL | jpayne@68: #endif jpayne@68: Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE, jpayne@68: __pyx_CyFunctionType_slots jpayne@68: }; jpayne@68: #else jpayne@68: static PyTypeObject __pyx_CyFunctionType_type = { jpayne@68: PyVarObject_HEAD_INIT(0, 0) jpayne@68: __PYX_TYPE_MODULE_PREFIX "cython_function_or_method", jpayne@68: sizeof(__pyx_CyFunctionObject), jpayne@68: 0, jpayne@68: (destructor) __Pyx_CyFunction_dealloc, jpayne@68: #if !CYTHON_METH_FASTCALL jpayne@68: 0, jpayne@68: #elif CYTHON_BACKPORT_VECTORCALL jpayne@68: (printfunc)offsetof(__pyx_CyFunctionObject, func_vectorcall), jpayne@68: #else jpayne@68: offsetof(PyCFunctionObject, vectorcall), jpayne@68: #endif jpayne@68: 0, jpayne@68: 0, jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: 0, jpayne@68: #else jpayne@68: 0, jpayne@68: #endif jpayne@68: (reprfunc) __Pyx_CyFunction_repr, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: __Pyx_CyFunction_CallAsMethod, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: #ifdef Py_TPFLAGS_METHOD_DESCRIPTOR jpayne@68: Py_TPFLAGS_METHOD_DESCRIPTOR | jpayne@68: #endif jpayne@68: #if defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL jpayne@68: _Py_TPFLAGS_HAVE_VECTORCALL | jpayne@68: #endif jpayne@68: Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE, jpayne@68: 0, jpayne@68: (traverseproc) __Pyx_CyFunction_traverse, jpayne@68: (inquiry) __Pyx_CyFunction_clear, jpayne@68: 0, jpayne@68: #if PY_VERSION_HEX < 0x030500A0 jpayne@68: offsetof(__pyx_CyFunctionObject, func_weakreflist), jpayne@68: #else jpayne@68: offsetof(PyCFunctionObject, m_weakreflist), jpayne@68: #endif jpayne@68: 0, jpayne@68: 0, jpayne@68: __pyx_CyFunction_methods, jpayne@68: __pyx_CyFunction_members, jpayne@68: __pyx_CyFunction_getsets, jpayne@68: 0, jpayne@68: 0, jpayne@68: __Pyx_PyMethod_New, jpayne@68: 0, jpayne@68: offsetof(__pyx_CyFunctionObject, func_dict), jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: #if PY_VERSION_HEX >= 0x030400a1 jpayne@68: 0, jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) jpayne@68: 0, jpayne@68: #endif jpayne@68: #if __PYX_NEED_TP_PRINT_SLOT jpayne@68: 0, jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030C0000 jpayne@68: 0, jpayne@68: #endif jpayne@68: #if PY_VERSION_HEX >= 0x030d00A4 jpayne@68: 0, jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 jpayne@68: 0, jpayne@68: #endif jpayne@68: }; jpayne@68: #endif jpayne@68: static int __pyx_CyFunction_init(PyObject *module) { jpayne@68: #if CYTHON_USE_TYPE_SPECS jpayne@68: __pyx_CyFunctionType = __Pyx_FetchCommonTypeFromSpec(module, &__pyx_CyFunctionType_spec, NULL); jpayne@68: #else jpayne@68: CYTHON_UNUSED_VAR(module); jpayne@68: __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); jpayne@68: #endif jpayne@68: if (unlikely(__pyx_CyFunctionType == NULL)) { jpayne@68: return -1; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { jpayne@68: __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; jpayne@68: m->defaults = PyObject_Malloc(size); jpayne@68: if (unlikely(!m->defaults)) jpayne@68: return PyErr_NoMemory(); jpayne@68: memset(m->defaults, 0, size); jpayne@68: m->defaults_pyobjects = pyobjects; jpayne@68: m->defaults_size = size; jpayne@68: return m->defaults; jpayne@68: } jpayne@68: static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { jpayne@68: __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; jpayne@68: m->defaults_tuple = tuple; jpayne@68: Py_INCREF(tuple); jpayne@68: } jpayne@68: static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) { jpayne@68: __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; jpayne@68: m->defaults_kwdict = dict; jpayne@68: Py_INCREF(dict); jpayne@68: } jpayne@68: static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) { jpayne@68: __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; jpayne@68: m->func_annotations = dict; jpayne@68: Py_INCREF(dict); jpayne@68: } jpayne@68: jpayne@68: /* CythonFunction */ jpayne@68: static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, int flags, PyObject* qualname, jpayne@68: PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { jpayne@68: PyObject *op = __Pyx_CyFunction_Init( jpayne@68: PyObject_GC_New(__pyx_CyFunctionObject, __pyx_CyFunctionType), jpayne@68: ml, flags, qualname, closure, module, globals, code jpayne@68: ); jpayne@68: if (likely(op)) { jpayne@68: PyObject_GC_Track(op); jpayne@68: } jpayne@68: return op; jpayne@68: } jpayne@68: jpayne@68: /* CalculateMetaclass */ jpayne@68: static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { jpayne@68: Py_ssize_t i, nbases; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: nbases = PyTuple_GET_SIZE(bases); jpayne@68: #else jpayne@68: nbases = PyTuple_Size(bases); jpayne@68: if (nbases < 0) return NULL; jpayne@68: #endif jpayne@68: for (i=0; i < nbases; i++) { jpayne@68: PyTypeObject *tmptype; jpayne@68: #if CYTHON_ASSUME_SAFE_MACROS jpayne@68: PyObject *tmp = PyTuple_GET_ITEM(bases, i); jpayne@68: #else jpayne@68: PyObject *tmp = PyTuple_GetItem(bases, i); jpayne@68: if (!tmp) return NULL; jpayne@68: #endif jpayne@68: tmptype = Py_TYPE(tmp); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (tmptype == &PyClass_Type) jpayne@68: continue; jpayne@68: #endif jpayne@68: if (!metaclass) { jpayne@68: metaclass = tmptype; jpayne@68: continue; jpayne@68: } jpayne@68: if (PyType_IsSubtype(metaclass, tmptype)) jpayne@68: continue; jpayne@68: if (PyType_IsSubtype(tmptype, metaclass)) { jpayne@68: metaclass = tmptype; jpayne@68: continue; jpayne@68: } jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "metaclass conflict: " jpayne@68: "the metaclass of a derived class " jpayne@68: "must be a (non-strict) subclass " jpayne@68: "of the metaclasses of all its bases"); jpayne@68: return NULL; jpayne@68: } jpayne@68: if (!metaclass) { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: metaclass = &PyClass_Type; jpayne@68: #else jpayne@68: metaclass = &PyType_Type; jpayne@68: #endif jpayne@68: } jpayne@68: Py_INCREF((PyObject*) metaclass); jpayne@68: return (PyObject*) metaclass; jpayne@68: } jpayne@68: jpayne@68: /* PyObjectCall2Args */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { jpayne@68: PyObject *args[3] = {NULL, arg1, arg2}; jpayne@68: return __Pyx_PyObject_FastCall(function, args+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); jpayne@68: } jpayne@68: jpayne@68: /* PyObjectLookupSpecial */ jpayne@68: #if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS jpayne@68: static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error) { jpayne@68: PyObject *res; jpayne@68: PyTypeObject *tp = Py_TYPE(obj); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (unlikely(PyInstance_Check(obj))) jpayne@68: return with_error ? __Pyx_PyObject_GetAttrStr(obj, attr_name) : __Pyx_PyObject_GetAttrStrNoError(obj, attr_name); jpayne@68: #endif jpayne@68: res = _PyType_Lookup(tp, attr_name); jpayne@68: if (likely(res)) { jpayne@68: descrgetfunc f = Py_TYPE(res)->tp_descr_get; jpayne@68: if (!f) { jpayne@68: Py_INCREF(res); jpayne@68: } else { jpayne@68: res = f(res, obj, (PyObject *)tp); jpayne@68: } jpayne@68: } else if (with_error) { jpayne@68: PyErr_SetObject(PyExc_AttributeError, attr_name); jpayne@68: } jpayne@68: return res; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* Py3ClassCreate */ jpayne@68: static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, jpayne@68: PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { jpayne@68: PyObject *ns; jpayne@68: if (metaclass) { jpayne@68: PyObject *prep = __Pyx_PyObject_GetAttrStrNoError(metaclass, __pyx_n_s_prepare); jpayne@68: if (prep) { jpayne@68: PyObject *pargs[3] = {NULL, name, bases}; jpayne@68: ns = __Pyx_PyObject_FastCallDict(prep, pargs+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, mkw); jpayne@68: Py_DECREF(prep); jpayne@68: } else { jpayne@68: if (unlikely(PyErr_Occurred())) jpayne@68: return NULL; jpayne@68: ns = PyDict_New(); jpayne@68: } jpayne@68: } else { jpayne@68: ns = PyDict_New(); jpayne@68: } jpayne@68: if (unlikely(!ns)) jpayne@68: return NULL; jpayne@68: if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad; jpayne@68: #if PY_VERSION_HEX >= 0x03030000 jpayne@68: if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad; jpayne@68: #else jpayne@68: CYTHON_MAYBE_UNUSED_VAR(qualname); jpayne@68: #endif jpayne@68: if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad; jpayne@68: return ns; jpayne@68: bad: jpayne@68: Py_DECREF(ns); jpayne@68: return NULL; jpayne@68: } jpayne@68: #if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS jpayne@68: static int __Pyx_SetNamesPEP487(PyObject *type_obj) { jpayne@68: PyTypeObject *type = (PyTypeObject*) type_obj; jpayne@68: PyObject *names_to_set, *key, *value, *set_name, *tmp; jpayne@68: Py_ssize_t i = 0; jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: names_to_set = PyDict_Copy(type->tp_dict); jpayne@68: #else jpayne@68: { jpayne@68: PyObject *d = PyObject_GetAttr(type_obj, __pyx_n_s_dict); jpayne@68: names_to_set = NULL; jpayne@68: if (likely(d)) { jpayne@68: PyObject *names_to_set = PyDict_New(); jpayne@68: int ret = likely(names_to_set) ? PyDict_Update(names_to_set, d) : -1; jpayne@68: Py_DECREF(d); jpayne@68: if (unlikely(ret < 0)) jpayne@68: Py_CLEAR(names_to_set); jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (unlikely(names_to_set == NULL)) jpayne@68: goto bad; jpayne@68: while (PyDict_Next(names_to_set, &i, &key, &value)) { jpayne@68: set_name = __Pyx_PyObject_LookupSpecialNoError(value, __pyx_n_s_set_name); jpayne@68: if (unlikely(set_name != NULL)) { jpayne@68: tmp = __Pyx_PyObject_Call2Args(set_name, type_obj, key); jpayne@68: Py_DECREF(set_name); jpayne@68: if (unlikely(tmp == NULL)) { jpayne@68: __Pyx_TypeName value_type_name = jpayne@68: __Pyx_PyType_GetName(Py_TYPE(value)); jpayne@68: __Pyx_TypeName type_name = __Pyx_PyType_GetName(type); jpayne@68: PyErr_Format(PyExc_RuntimeError, jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %R " "in '" __Pyx_FMT_TYPENAME "'", jpayne@68: value_type_name, key, type_name); jpayne@68: #else jpayne@68: "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %.100s in '" __Pyx_FMT_TYPENAME "'", jpayne@68: value_type_name, jpayne@68: PyString_Check(key) ? PyString_AS_STRING(key) : "?", jpayne@68: type_name); jpayne@68: #endif jpayne@68: goto bad; jpayne@68: } else { jpayne@68: Py_DECREF(tmp); jpayne@68: } jpayne@68: } jpayne@68: else if (unlikely(PyErr_Occurred())) { jpayne@68: goto bad; jpayne@68: } jpayne@68: } jpayne@68: Py_DECREF(names_to_set); jpayne@68: return 0; jpayne@68: bad: jpayne@68: Py_XDECREF(names_to_set); jpayne@68: return -1; jpayne@68: } jpayne@68: static PyObject *__Pyx_InitSubclassPEP487(PyObject *type_obj, PyObject *mkw) { jpayne@68: #if CYTHON_USE_TYPE_SLOTS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS jpayne@68: PyTypeObject *type = (PyTypeObject*) type_obj; jpayne@68: PyObject *mro = type->tp_mro; jpayne@68: Py_ssize_t i, nbases; jpayne@68: if (unlikely(!mro)) goto done; jpayne@68: (void) &__Pyx_GetBuiltinName; jpayne@68: Py_INCREF(mro); jpayne@68: nbases = PyTuple_GET_SIZE(mro); jpayne@68: assert(PyTuple_GET_ITEM(mro, 0) == type_obj); jpayne@68: for (i = 1; i < nbases-1; i++) { jpayne@68: PyObject *base, *dict, *meth; jpayne@68: base = PyTuple_GET_ITEM(mro, i); jpayne@68: dict = ((PyTypeObject *)base)->tp_dict; jpayne@68: meth = __Pyx_PyDict_GetItemStrWithError(dict, __pyx_n_s_init_subclass); jpayne@68: if (unlikely(meth)) { jpayne@68: descrgetfunc f = Py_TYPE(meth)->tp_descr_get; jpayne@68: PyObject *res; jpayne@68: Py_INCREF(meth); jpayne@68: if (likely(f)) { jpayne@68: res = f(meth, NULL, type_obj); jpayne@68: Py_DECREF(meth); jpayne@68: if (unlikely(!res)) goto bad; jpayne@68: meth = res; jpayne@68: } jpayne@68: res = __Pyx_PyObject_FastCallDict(meth, NULL, 0, mkw); jpayne@68: Py_DECREF(meth); jpayne@68: if (unlikely(!res)) goto bad; jpayne@68: Py_DECREF(res); jpayne@68: goto done; jpayne@68: } else if (unlikely(PyErr_Occurred())) { jpayne@68: goto bad; jpayne@68: } jpayne@68: } jpayne@68: done: jpayne@68: Py_XDECREF(mro); jpayne@68: return type_obj; jpayne@68: bad: jpayne@68: Py_XDECREF(mro); jpayne@68: Py_DECREF(type_obj); jpayne@68: return NULL; jpayne@68: #else jpayne@68: PyObject *super_type, *super, *func, *res; jpayne@68: #if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type) jpayne@68: super_type = __Pyx_GetBuiltinName(__pyx_n_s_super); jpayne@68: #else jpayne@68: super_type = (PyObject*) &PySuper_Type; jpayne@68: (void) &__Pyx_GetBuiltinName; jpayne@68: #endif jpayne@68: super = likely(super_type) ? __Pyx_PyObject_Call2Args(super_type, type_obj, type_obj) : NULL; jpayne@68: #if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type) jpayne@68: Py_XDECREF(super_type); jpayne@68: #endif jpayne@68: if (unlikely(!super)) { jpayne@68: Py_CLEAR(type_obj); jpayne@68: goto done; jpayne@68: } jpayne@68: func = __Pyx_PyObject_GetAttrStrNoError(super, __pyx_n_s_init_subclass); jpayne@68: Py_DECREF(super); jpayne@68: if (likely(!func)) { jpayne@68: if (unlikely(PyErr_Occurred())) jpayne@68: Py_CLEAR(type_obj); jpayne@68: goto done; jpayne@68: } jpayne@68: res = __Pyx_PyObject_FastCallDict(func, NULL, 0, mkw); jpayne@68: Py_DECREF(func); jpayne@68: if (unlikely(!res)) jpayne@68: Py_CLEAR(type_obj); jpayne@68: Py_XDECREF(res); jpayne@68: done: jpayne@68: return type_obj; jpayne@68: #endif jpayne@68: } jpayne@68: #endif jpayne@68: static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, jpayne@68: PyObject *dict, PyObject *mkw, jpayne@68: int calculate_metaclass, int allow_py2_metaclass) { jpayne@68: PyObject *result; jpayne@68: PyObject *owned_metaclass = NULL; jpayne@68: PyObject *margs[4] = {NULL, name, bases, dict}; jpayne@68: if (allow_py2_metaclass) { jpayne@68: owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass); jpayne@68: if (owned_metaclass) { jpayne@68: metaclass = owned_metaclass; jpayne@68: } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) { jpayne@68: PyErr_Clear(); jpayne@68: } else { jpayne@68: return NULL; jpayne@68: } jpayne@68: } jpayne@68: if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) { jpayne@68: metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases); jpayne@68: Py_XDECREF(owned_metaclass); jpayne@68: if (unlikely(!metaclass)) jpayne@68: return NULL; jpayne@68: owned_metaclass = metaclass; jpayne@68: } jpayne@68: result = __Pyx_PyObject_FastCallDict(metaclass, margs+1, 3 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, jpayne@68: #if PY_VERSION_HEX < 0x030600A4 jpayne@68: (metaclass == (PyObject*)&PyType_Type) ? NULL : mkw jpayne@68: #else jpayne@68: mkw jpayne@68: #endif jpayne@68: ); jpayne@68: Py_XDECREF(owned_metaclass); jpayne@68: #if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS jpayne@68: if (likely(result) && likely(PyType_Check(result))) { jpayne@68: if (unlikely(__Pyx_SetNamesPEP487(result) < 0)) { jpayne@68: Py_CLEAR(result); jpayne@68: } else { jpayne@68: result = __Pyx_InitSubclassPEP487(result, mkw); jpayne@68: } jpayne@68: } jpayne@68: #else jpayne@68: (void) &__Pyx_GetBuiltinName; jpayne@68: #endif jpayne@68: return result; jpayne@68: } jpayne@68: jpayne@68: /* CLineInTraceback */ jpayne@68: #ifndef CYTHON_CLINE_IN_TRACEBACK jpayne@68: static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) { jpayne@68: PyObject *use_cline; jpayne@68: PyObject *ptype, *pvalue, *ptraceback; jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: PyObject **cython_runtime_dict; jpayne@68: #endif jpayne@68: CYTHON_MAYBE_UNUSED_VAR(tstate); jpayne@68: if (unlikely(!__pyx_cython_runtime)) { jpayne@68: return c_line; jpayne@68: } jpayne@68: __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); jpayne@68: if (likely(cython_runtime_dict)) { jpayne@68: __PYX_PY_DICT_LOOKUP_IF_MODIFIED( jpayne@68: use_cline, *cython_runtime_dict, jpayne@68: __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) jpayne@68: } else jpayne@68: #endif jpayne@68: { jpayne@68: PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStrNoError(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); jpayne@68: if (use_cline_obj) { jpayne@68: use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; jpayne@68: Py_DECREF(use_cline_obj); jpayne@68: } else { jpayne@68: PyErr_Clear(); jpayne@68: use_cline = NULL; jpayne@68: } jpayne@68: } jpayne@68: if (!use_cline) { jpayne@68: c_line = 0; jpayne@68: (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); jpayne@68: } jpayne@68: else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { jpayne@68: c_line = 0; jpayne@68: } jpayne@68: __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); jpayne@68: return c_line; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* CodeObjectCache */ jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { jpayne@68: int start = 0, mid = 0, end = count - 1; jpayne@68: if (end >= 0 && code_line > entries[end].code_line) { jpayne@68: return count; jpayne@68: } jpayne@68: while (start < end) { jpayne@68: mid = start + (end - start) / 2; jpayne@68: if (code_line < entries[mid].code_line) { jpayne@68: end = mid; jpayne@68: } else if (code_line > entries[mid].code_line) { jpayne@68: start = mid + 1; jpayne@68: } else { jpayne@68: return mid; jpayne@68: } jpayne@68: } jpayne@68: if (code_line <= entries[mid].code_line) { jpayne@68: return mid; jpayne@68: } else { jpayne@68: return mid + 1; jpayne@68: } jpayne@68: } jpayne@68: static PyCodeObject *__pyx_find_code_object(int code_line) { jpayne@68: PyCodeObject* code_object; jpayne@68: int pos; jpayne@68: if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { jpayne@68: return NULL; jpayne@68: } jpayne@68: pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); jpayne@68: if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { jpayne@68: return NULL; jpayne@68: } jpayne@68: code_object = __pyx_code_cache.entries[pos].code_object; jpayne@68: Py_INCREF(code_object); jpayne@68: return code_object; jpayne@68: } jpayne@68: static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { jpayne@68: int pos, i; jpayne@68: __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; jpayne@68: if (unlikely(!code_line)) { jpayne@68: return; jpayne@68: } jpayne@68: if (unlikely(!entries)) { jpayne@68: entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); jpayne@68: if (likely(entries)) { jpayne@68: __pyx_code_cache.entries = entries; jpayne@68: __pyx_code_cache.max_count = 64; jpayne@68: __pyx_code_cache.count = 1; jpayne@68: entries[0].code_line = code_line; jpayne@68: entries[0].code_object = code_object; jpayne@68: Py_INCREF(code_object); jpayne@68: } jpayne@68: return; jpayne@68: } jpayne@68: pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); jpayne@68: if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { jpayne@68: PyCodeObject* tmp = entries[pos].code_object; jpayne@68: entries[pos].code_object = code_object; jpayne@68: Py_DECREF(tmp); jpayne@68: return; jpayne@68: } jpayne@68: if (__pyx_code_cache.count == __pyx_code_cache.max_count) { jpayne@68: int new_max = __pyx_code_cache.max_count + 64; jpayne@68: entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( jpayne@68: __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); jpayne@68: if (unlikely(!entries)) { jpayne@68: return; jpayne@68: } jpayne@68: __pyx_code_cache.entries = entries; jpayne@68: __pyx_code_cache.max_count = new_max; jpayne@68: } jpayne@68: for (i=__pyx_code_cache.count; i>pos; i--) { jpayne@68: entries[i] = entries[i-1]; jpayne@68: } jpayne@68: entries[pos].code_line = code_line; jpayne@68: entries[pos].code_object = code_object; jpayne@68: __pyx_code_cache.count++; jpayne@68: Py_INCREF(code_object); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* AddTraceback */ jpayne@68: #include "compile.h" jpayne@68: #include "frameobject.h" jpayne@68: #include "traceback.h" jpayne@68: #if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: #ifndef Py_BUILD_CORE jpayne@68: #define Py_BUILD_CORE 1 jpayne@68: #endif jpayne@68: #include "internal/pycore_frame.h" jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static PyObject *__Pyx_PyCode_Replace_For_AddTraceback(PyObject *code, PyObject *scratch_dict, jpayne@68: PyObject *firstlineno, PyObject *name) { jpayne@68: PyObject *replace = NULL; jpayne@68: if (unlikely(PyDict_SetItemString(scratch_dict, "co_firstlineno", firstlineno))) return NULL; jpayne@68: if (unlikely(PyDict_SetItemString(scratch_dict, "co_name", name))) return NULL; jpayne@68: replace = PyObject_GetAttrString(code, "replace"); jpayne@68: if (likely(replace)) { jpayne@68: PyObject *result; jpayne@68: result = PyObject_Call(replace, __pyx_empty_tuple, scratch_dict); jpayne@68: Py_DECREF(replace); jpayne@68: return result; jpayne@68: } jpayne@68: PyErr_Clear(); jpayne@68: #if __PYX_LIMITED_VERSION_HEX < 0x030780000 jpayne@68: { jpayne@68: PyObject *compiled = NULL, *result = NULL; jpayne@68: if (unlikely(PyDict_SetItemString(scratch_dict, "code", code))) return NULL; jpayne@68: if (unlikely(PyDict_SetItemString(scratch_dict, "type", (PyObject*)(&PyType_Type)))) return NULL; jpayne@68: compiled = Py_CompileString( jpayne@68: "out = type(code)(\n" jpayne@68: " code.co_argcount, code.co_kwonlyargcount, code.co_nlocals, code.co_stacksize,\n" jpayne@68: " code.co_flags, code.co_code, code.co_consts, code.co_names,\n" jpayne@68: " code.co_varnames, code.co_filename, co_name, co_firstlineno,\n" jpayne@68: " code.co_lnotab)\n", "", Py_file_input); jpayne@68: if (!compiled) return NULL; jpayne@68: result = PyEval_EvalCode(compiled, scratch_dict, scratch_dict); jpayne@68: Py_DECREF(compiled); jpayne@68: if (!result) PyErr_Print(); jpayne@68: Py_DECREF(result); jpayne@68: result = PyDict_GetItemString(scratch_dict, "out"); jpayne@68: if (result) Py_INCREF(result); jpayne@68: return result; jpayne@68: } jpayne@68: #else jpayne@68: return NULL; jpayne@68: #endif jpayne@68: } jpayne@68: static void __Pyx_AddTraceback(const char *funcname, int c_line, jpayne@68: int py_line, const char *filename) { jpayne@68: PyObject *code_object = NULL, *py_py_line = NULL, *py_funcname = NULL, *dict = NULL; jpayne@68: PyObject *replace = NULL, *getframe = NULL, *frame = NULL; jpayne@68: PyObject *exc_type, *exc_value, *exc_traceback; jpayne@68: int success = 0; jpayne@68: if (c_line) { jpayne@68: (void) __pyx_cfilenm; jpayne@68: (void) __Pyx_CLineForTraceback(__Pyx_PyThreadState_Current, c_line); jpayne@68: } jpayne@68: PyErr_Fetch(&exc_type, &exc_value, &exc_traceback); jpayne@68: code_object = Py_CompileString("_getframe()", filename, Py_eval_input); jpayne@68: if (unlikely(!code_object)) goto bad; jpayne@68: py_py_line = PyLong_FromLong(py_line); jpayne@68: if (unlikely(!py_py_line)) goto bad; jpayne@68: py_funcname = PyUnicode_FromString(funcname); jpayne@68: if (unlikely(!py_funcname)) goto bad; jpayne@68: dict = PyDict_New(); jpayne@68: if (unlikely(!dict)) goto bad; jpayne@68: { jpayne@68: PyObject *old_code_object = code_object; jpayne@68: code_object = __Pyx_PyCode_Replace_For_AddTraceback(code_object, dict, py_py_line, py_funcname); jpayne@68: Py_DECREF(old_code_object); jpayne@68: } jpayne@68: if (unlikely(!code_object)) goto bad; jpayne@68: getframe = PySys_GetObject("_getframe"); jpayne@68: if (unlikely(!getframe)) goto bad; jpayne@68: if (unlikely(PyDict_SetItemString(dict, "_getframe", getframe))) goto bad; jpayne@68: frame = PyEval_EvalCode(code_object, dict, dict); jpayne@68: if (unlikely(!frame) || frame == Py_None) goto bad; jpayne@68: success = 1; jpayne@68: bad: jpayne@68: PyErr_Restore(exc_type, exc_value, exc_traceback); jpayne@68: Py_XDECREF(code_object); jpayne@68: Py_XDECREF(py_py_line); jpayne@68: Py_XDECREF(py_funcname); jpayne@68: Py_XDECREF(dict); jpayne@68: Py_XDECREF(replace); jpayne@68: if (success) { jpayne@68: PyTraceBack_Here( jpayne@68: (struct _frame*)frame); jpayne@68: } jpayne@68: Py_XDECREF(frame); jpayne@68: } jpayne@68: #else jpayne@68: static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( jpayne@68: const char *funcname, int c_line, jpayne@68: int py_line, const char *filename) { jpayne@68: PyCodeObject *py_code = NULL; jpayne@68: PyObject *py_funcname = NULL; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: PyObject *py_srcfile = NULL; jpayne@68: py_srcfile = PyString_FromString(filename); jpayne@68: if (!py_srcfile) goto bad; jpayne@68: #endif jpayne@68: if (c_line) { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); jpayne@68: if (!py_funcname) goto bad; jpayne@68: #else jpayne@68: py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); jpayne@68: if (!py_funcname) goto bad; jpayne@68: funcname = PyUnicode_AsUTF8(py_funcname); jpayne@68: if (!funcname) goto bad; jpayne@68: #endif jpayne@68: } jpayne@68: else { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: py_funcname = PyString_FromString(funcname); jpayne@68: if (!py_funcname) goto bad; jpayne@68: #endif jpayne@68: } jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: py_code = __Pyx_PyCode_New( jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: 0, jpayne@68: __pyx_empty_bytes, /*PyObject *code,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *consts,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *names,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *varnames,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *freevars,*/ jpayne@68: __pyx_empty_tuple, /*PyObject *cellvars,*/ jpayne@68: py_srcfile, /*PyObject *filename,*/ jpayne@68: py_funcname, /*PyObject *name,*/ jpayne@68: py_line, jpayne@68: __pyx_empty_bytes /*PyObject *lnotab*/ jpayne@68: ); jpayne@68: Py_DECREF(py_srcfile); jpayne@68: #else jpayne@68: py_code = PyCode_NewEmpty(filename, funcname, py_line); jpayne@68: #endif jpayne@68: Py_XDECREF(py_funcname); jpayne@68: return py_code; jpayne@68: bad: jpayne@68: Py_XDECREF(py_funcname); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: Py_XDECREF(py_srcfile); jpayne@68: #endif jpayne@68: return NULL; jpayne@68: } jpayne@68: static void __Pyx_AddTraceback(const char *funcname, int c_line, jpayne@68: int py_line, const char *filename) { jpayne@68: PyCodeObject *py_code = 0; jpayne@68: PyFrameObject *py_frame = 0; jpayne@68: PyThreadState *tstate = __Pyx_PyThreadState_Current; jpayne@68: PyObject *ptype, *pvalue, *ptraceback; jpayne@68: if (c_line) { jpayne@68: c_line = __Pyx_CLineForTraceback(tstate, c_line); jpayne@68: } jpayne@68: py_code = __pyx_find_code_object(c_line ? -c_line : py_line); jpayne@68: if (!py_code) { jpayne@68: __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); jpayne@68: py_code = __Pyx_CreateCodeObjectForTraceback( jpayne@68: funcname, c_line, py_line, filename); jpayne@68: if (!py_code) { jpayne@68: /* If the code object creation fails, then we should clear the jpayne@68: fetched exception references and propagate the new exception */ jpayne@68: Py_XDECREF(ptype); jpayne@68: Py_XDECREF(pvalue); jpayne@68: Py_XDECREF(ptraceback); jpayne@68: goto bad; jpayne@68: } jpayne@68: __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); jpayne@68: __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); jpayne@68: } jpayne@68: py_frame = PyFrame_New( jpayne@68: tstate, /*PyThreadState *tstate,*/ jpayne@68: py_code, /*PyCodeObject *code,*/ jpayne@68: __pyx_d, /*PyObject *globals,*/ jpayne@68: 0 /*PyObject *locals*/ jpayne@68: ); jpayne@68: if (!py_frame) goto bad; jpayne@68: __Pyx_PyFrame_SetLineNumber(py_frame, py_line); jpayne@68: PyTraceBack_Here(py_frame); jpayne@68: bad: jpayne@68: Py_XDECREF(py_code); jpayne@68: Py_XDECREF(py_frame); jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* CIntFromPyVerify */ jpayne@68: #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ jpayne@68: __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) jpayne@68: #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ jpayne@68: __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) jpayne@68: #define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ jpayne@68: {\ jpayne@68: func_type value = func_value;\ jpayne@68: if (sizeof(target_type) < sizeof(func_type)) {\ jpayne@68: if (unlikely(value != (func_type) (target_type) value)) {\ jpayne@68: func_type zero = 0;\ jpayne@68: if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ jpayne@68: return (target_type) -1;\ jpayne@68: if (is_unsigned && unlikely(value < zero))\ jpayne@68: goto raise_neg_overflow;\ jpayne@68: else\ jpayne@68: goto raise_overflow;\ jpayne@68: }\ jpayne@68: }\ jpayne@68: return (target_type) value;\ jpayne@68: } jpayne@68: jpayne@68: /* CIntFromPy */ jpayne@68: static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const int neg_one = (int) -1, const_zero = (int) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_Check(x))) { jpayne@68: if ((sizeof(int) < sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) jpayne@68: } else { jpayne@68: long val = PyInt_AS_LONG(x); jpayne@68: if (is_unsigned && unlikely(val < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: return (int) val; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (unlikely(!PyLong_Check(x))) { jpayne@68: int val; jpayne@68: PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); jpayne@68: if (!tmp) return (int) -1; jpayne@68: val = __Pyx_PyInt_As_int(tmp); jpayne@68: Py_DECREF(tmp); jpayne@68: return val; jpayne@68: } jpayne@68: if (is_unsigned) { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (unlikely(__Pyx_PyLong_IsNeg(x))) { jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_DigitCount(x)) { jpayne@68: case 2: jpayne@68: if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) { jpayne@68: return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) { jpayne@68: return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) { jpayne@68: return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 jpayne@68: if (unlikely(Py_SIZE(x) < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #else jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(x, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) jpayne@68: return (int) -1; jpayne@68: if (unlikely(result == 1)) jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(int) <= sizeof(unsigned long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_SignedDigitCount(x)) { jpayne@68: case -2: jpayne@68: if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 2: jpayne@68: if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -3: jpayne@68: if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -4: jpayne@68: if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(int) <= sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: int val; jpayne@68: int ret = -1; jpayne@68: #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_ssize_t bytes_copied = PyLong_AsNativeBytes( jpayne@68: x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); jpayne@68: if (unlikely(bytes_copied == -1)) { jpayne@68: } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { jpayne@68: goto raise_overflow; jpayne@68: } else { jpayne@68: ret = 0; jpayne@68: } jpayne@68: #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) jpayne@68: int one = 1; int is_little = (int)*(unsigned char *)&one; jpayne@68: unsigned char *bytes = (unsigned char *)&val; jpayne@68: ret = _PyLong_AsByteArray((PyLongObject *)x, jpayne@68: bytes, sizeof(val), jpayne@68: is_little, !is_unsigned); jpayne@68: #else jpayne@68: PyObject *v; jpayne@68: PyObject *stepval = NULL, *mask = NULL, *shift = NULL; jpayne@68: int bits, remaining_bits, is_negative = 0; jpayne@68: int chunk_size = (sizeof(long) < 8) ? 30 : 62; jpayne@68: if (likely(PyLong_CheckExact(x))) { jpayne@68: v = __Pyx_NewRef(x); jpayne@68: } else { jpayne@68: v = PyNumber_Long(x); jpayne@68: if (unlikely(!v)) return (int) -1; jpayne@68: assert(PyLong_CheckExact(v)); jpayne@68: } jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(v, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) { jpayne@68: Py_DECREF(v); jpayne@68: return (int) -1; jpayne@68: } jpayne@68: is_negative = result == 1; jpayne@68: } jpayne@68: if (is_unsigned && unlikely(is_negative)) { jpayne@68: Py_DECREF(v); jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (is_negative) { jpayne@68: stepval = PyNumber_Invert(v); jpayne@68: Py_DECREF(v); jpayne@68: if (unlikely(!stepval)) jpayne@68: return (int) -1; jpayne@68: } else { jpayne@68: stepval = v; jpayne@68: } jpayne@68: v = NULL; jpayne@68: val = (int) 0; jpayne@68: mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; jpayne@68: shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; jpayne@68: for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) { jpayne@68: PyObject *tmp, *digit; jpayne@68: long idigit; jpayne@68: digit = PyNumber_And(stepval, mask); jpayne@68: if (unlikely(!digit)) goto done; jpayne@68: idigit = PyLong_AsLong(digit); jpayne@68: Py_DECREF(digit); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: val |= ((int) idigit) << bits; jpayne@68: tmp = PyNumber_Rshift(stepval, shift); jpayne@68: if (unlikely(!tmp)) goto done; jpayne@68: Py_DECREF(stepval); stepval = tmp; jpayne@68: } jpayne@68: Py_DECREF(shift); shift = NULL; jpayne@68: Py_DECREF(mask); mask = NULL; jpayne@68: { jpayne@68: long idigit = PyLong_AsLong(stepval); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1); jpayne@68: if (unlikely(idigit >= (1L << remaining_bits))) jpayne@68: goto raise_overflow; jpayne@68: val |= ((int) idigit) << bits; jpayne@68: } jpayne@68: if (!is_unsigned) { jpayne@68: if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1)))) jpayne@68: goto raise_overflow; jpayne@68: if (is_negative) jpayne@68: val = ~val; jpayne@68: } jpayne@68: ret = 0; jpayne@68: done: jpayne@68: Py_XDECREF(shift); jpayne@68: Py_XDECREF(mask); jpayne@68: Py_XDECREF(stepval); jpayne@68: #endif jpayne@68: if (unlikely(ret)) jpayne@68: return (int) -1; jpayne@68: return val; jpayne@68: } jpayne@68: raise_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "value too large to convert to int"); jpayne@68: return (int) -1; jpayne@68: raise_neg_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "can't convert negative value to int"); jpayne@68: return (int) -1; jpayne@68: } jpayne@68: jpayne@68: /* CIntToPy */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const int neg_one = (int) -1, const_zero = (int) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: if (is_unsigned) { jpayne@68: if (sizeof(int) < sizeof(long)) { jpayne@68: return PyInt_FromLong((long) value); jpayne@68: } else if (sizeof(int) <= sizeof(unsigned long)) { jpayne@68: return PyLong_FromUnsignedLong((unsigned long) value); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { jpayne@68: return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: if (sizeof(int) <= sizeof(long)) { jpayne@68: return PyInt_FromLong((long) value); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { jpayne@68: return PyLong_FromLongLong((PY_LONG_LONG) value); jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: unsigned char *bytes = (unsigned char *)&value; jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 jpayne@68: if (is_unsigned) { jpayne@68: return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); jpayne@68: } else { jpayne@68: return PyLong_FromNativeBytes(bytes, sizeof(value), -1); jpayne@68: } jpayne@68: #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 jpayne@68: int one = 1; int little = (int)*(unsigned char *)&one; jpayne@68: return _PyLong_FromByteArray(bytes, sizeof(int), jpayne@68: little, !is_unsigned); jpayne@68: #else jpayne@68: int one = 1; int little = (int)*(unsigned char *)&one; jpayne@68: PyObject *from_bytes, *result = NULL; jpayne@68: PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; jpayne@68: from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); jpayne@68: if (!from_bytes) return NULL; jpayne@68: py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int)); jpayne@68: if (!py_bytes) goto limited_bad; jpayne@68: order_str = PyUnicode_FromString(little ? "little" : "big"); jpayne@68: if (!order_str) goto limited_bad; jpayne@68: arg_tuple = PyTuple_Pack(2, py_bytes, order_str); jpayne@68: if (!arg_tuple) goto limited_bad; jpayne@68: if (!is_unsigned) { jpayne@68: kwds = PyDict_New(); jpayne@68: if (!kwds) goto limited_bad; jpayne@68: if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; jpayne@68: } jpayne@68: result = PyObject_Call(from_bytes, arg_tuple, kwds); jpayne@68: limited_bad: jpayne@68: Py_XDECREF(kwds); jpayne@68: Py_XDECREF(arg_tuple); jpayne@68: Py_XDECREF(order_str); jpayne@68: Py_XDECREF(py_bytes); jpayne@68: Py_XDECREF(from_bytes); jpayne@68: return result; jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* CIntFromPy */ jpayne@68: static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const long neg_one = (long) -1, const_zero = (long) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_Check(x))) { jpayne@68: if ((sizeof(long) < sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) jpayne@68: } else { jpayne@68: long val = PyInt_AS_LONG(x); jpayne@68: if (is_unsigned && unlikely(val < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: return (long) val; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (unlikely(!PyLong_Check(x))) { jpayne@68: long val; jpayne@68: PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); jpayne@68: if (!tmp) return (long) -1; jpayne@68: val = __Pyx_PyInt_As_long(tmp); jpayne@68: Py_DECREF(tmp); jpayne@68: return val; jpayne@68: } jpayne@68: if (is_unsigned) { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (unlikely(__Pyx_PyLong_IsNeg(x))) { jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_DigitCount(x)) { jpayne@68: case 2: jpayne@68: if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) { jpayne@68: return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) { jpayne@68: return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) { jpayne@68: return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 jpayne@68: if (unlikely(Py_SIZE(x) < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #else jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(x, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) jpayne@68: return (long) -1; jpayne@68: if (unlikely(result == 1)) jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(long) <= sizeof(unsigned long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_SignedDigitCount(x)) { jpayne@68: case -2: jpayne@68: if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 2: jpayne@68: if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -3: jpayne@68: if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -4: jpayne@68: if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(long) <= sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: long val; jpayne@68: int ret = -1; jpayne@68: #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_ssize_t bytes_copied = PyLong_AsNativeBytes( jpayne@68: x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); jpayne@68: if (unlikely(bytes_copied == -1)) { jpayne@68: } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { jpayne@68: goto raise_overflow; jpayne@68: } else { jpayne@68: ret = 0; jpayne@68: } jpayne@68: #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) jpayne@68: int one = 1; int is_little = (int)*(unsigned char *)&one; jpayne@68: unsigned char *bytes = (unsigned char *)&val; jpayne@68: ret = _PyLong_AsByteArray((PyLongObject *)x, jpayne@68: bytes, sizeof(val), jpayne@68: is_little, !is_unsigned); jpayne@68: #else jpayne@68: PyObject *v; jpayne@68: PyObject *stepval = NULL, *mask = NULL, *shift = NULL; jpayne@68: int bits, remaining_bits, is_negative = 0; jpayne@68: int chunk_size = (sizeof(long) < 8) ? 30 : 62; jpayne@68: if (likely(PyLong_CheckExact(x))) { jpayne@68: v = __Pyx_NewRef(x); jpayne@68: } else { jpayne@68: v = PyNumber_Long(x); jpayne@68: if (unlikely(!v)) return (long) -1; jpayne@68: assert(PyLong_CheckExact(v)); jpayne@68: } jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(v, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) { jpayne@68: Py_DECREF(v); jpayne@68: return (long) -1; jpayne@68: } jpayne@68: is_negative = result == 1; jpayne@68: } jpayne@68: if (is_unsigned && unlikely(is_negative)) { jpayne@68: Py_DECREF(v); jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (is_negative) { jpayne@68: stepval = PyNumber_Invert(v); jpayne@68: Py_DECREF(v); jpayne@68: if (unlikely(!stepval)) jpayne@68: return (long) -1; jpayne@68: } else { jpayne@68: stepval = v; jpayne@68: } jpayne@68: v = NULL; jpayne@68: val = (long) 0; jpayne@68: mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; jpayne@68: shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; jpayne@68: for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) { jpayne@68: PyObject *tmp, *digit; jpayne@68: long idigit; jpayne@68: digit = PyNumber_And(stepval, mask); jpayne@68: if (unlikely(!digit)) goto done; jpayne@68: idigit = PyLong_AsLong(digit); jpayne@68: Py_DECREF(digit); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: val |= ((long) idigit) << bits; jpayne@68: tmp = PyNumber_Rshift(stepval, shift); jpayne@68: if (unlikely(!tmp)) goto done; jpayne@68: Py_DECREF(stepval); stepval = tmp; jpayne@68: } jpayne@68: Py_DECREF(shift); shift = NULL; jpayne@68: Py_DECREF(mask); mask = NULL; jpayne@68: { jpayne@68: long idigit = PyLong_AsLong(stepval); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1); jpayne@68: if (unlikely(idigit >= (1L << remaining_bits))) jpayne@68: goto raise_overflow; jpayne@68: val |= ((long) idigit) << bits; jpayne@68: } jpayne@68: if (!is_unsigned) { jpayne@68: if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1)))) jpayne@68: goto raise_overflow; jpayne@68: if (is_negative) jpayne@68: val = ~val; jpayne@68: } jpayne@68: ret = 0; jpayne@68: done: jpayne@68: Py_XDECREF(shift); jpayne@68: Py_XDECREF(mask); jpayne@68: Py_XDECREF(stepval); jpayne@68: #endif jpayne@68: if (unlikely(ret)) jpayne@68: return (long) -1; jpayne@68: return val; jpayne@68: } jpayne@68: raise_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "value too large to convert to long"); jpayne@68: return (long) -1; jpayne@68: raise_neg_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "can't convert negative value to long"); jpayne@68: return (long) -1; jpayne@68: } jpayne@68: jpayne@68: /* CIntFromPy */ jpayne@68: static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_Check(x))) { jpayne@68: if ((sizeof(int64_t) < sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x)) jpayne@68: } else { jpayne@68: long val = PyInt_AS_LONG(x); jpayne@68: if (is_unsigned && unlikely(val < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: return (int64_t) val; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (unlikely(!PyLong_Check(x))) { jpayne@68: int64_t val; jpayne@68: PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); jpayne@68: if (!tmp) return (int64_t) -1; jpayne@68: val = __Pyx_PyInt_As_int64_t(tmp); jpayne@68: Py_DECREF(tmp); jpayne@68: return val; jpayne@68: } jpayne@68: if (is_unsigned) { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (unlikely(__Pyx_PyLong_IsNeg(x))) { jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_DigitCount(x)) { jpayne@68: case 2: jpayne@68: if ((8 * sizeof(int64_t) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) >= 2 * PyLong_SHIFT)) { jpayne@68: return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(int64_t) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) >= 3 * PyLong_SHIFT)) { jpayne@68: return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(int64_t) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) >= 4 * PyLong_SHIFT)) { jpayne@68: return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 jpayne@68: if (unlikely(Py_SIZE(x) < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #else jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(x, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) jpayne@68: return (int64_t) -1; jpayne@68: if (unlikely(result == 1)) jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(int64_t) <= sizeof(unsigned long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_SignedDigitCount(x)) { jpayne@68: case -2: jpayne@68: if ((8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 2: jpayne@68: if ((8 * sizeof(int64_t) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -3: jpayne@68: if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(int64_t) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -4: jpayne@68: if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(int64_t) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(int64_t) <= sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(int64_t) <= sizeof(PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: int64_t val; jpayne@68: int ret = -1; jpayne@68: #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_ssize_t bytes_copied = PyLong_AsNativeBytes( jpayne@68: x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); jpayne@68: if (unlikely(bytes_copied == -1)) { jpayne@68: } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { jpayne@68: goto raise_overflow; jpayne@68: } else { jpayne@68: ret = 0; jpayne@68: } jpayne@68: #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) jpayne@68: int one = 1; int is_little = (int)*(unsigned char *)&one; jpayne@68: unsigned char *bytes = (unsigned char *)&val; jpayne@68: ret = _PyLong_AsByteArray((PyLongObject *)x, jpayne@68: bytes, sizeof(val), jpayne@68: is_little, !is_unsigned); jpayne@68: #else jpayne@68: PyObject *v; jpayne@68: PyObject *stepval = NULL, *mask = NULL, *shift = NULL; jpayne@68: int bits, remaining_bits, is_negative = 0; jpayne@68: int chunk_size = (sizeof(long) < 8) ? 30 : 62; jpayne@68: if (likely(PyLong_CheckExact(x))) { jpayne@68: v = __Pyx_NewRef(x); jpayne@68: } else { jpayne@68: v = PyNumber_Long(x); jpayne@68: if (unlikely(!v)) return (int64_t) -1; jpayne@68: assert(PyLong_CheckExact(v)); jpayne@68: } jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(v, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) { jpayne@68: Py_DECREF(v); jpayne@68: return (int64_t) -1; jpayne@68: } jpayne@68: is_negative = result == 1; jpayne@68: } jpayne@68: if (is_unsigned && unlikely(is_negative)) { jpayne@68: Py_DECREF(v); jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (is_negative) { jpayne@68: stepval = PyNumber_Invert(v); jpayne@68: Py_DECREF(v); jpayne@68: if (unlikely(!stepval)) jpayne@68: return (int64_t) -1; jpayne@68: } else { jpayne@68: stepval = v; jpayne@68: } jpayne@68: v = NULL; jpayne@68: val = (int64_t) 0; jpayne@68: mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; jpayne@68: shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; jpayne@68: for (bits = 0; bits < (int) sizeof(int64_t) * 8 - chunk_size; bits += chunk_size) { jpayne@68: PyObject *tmp, *digit; jpayne@68: long idigit; jpayne@68: digit = PyNumber_And(stepval, mask); jpayne@68: if (unlikely(!digit)) goto done; jpayne@68: idigit = PyLong_AsLong(digit); jpayne@68: Py_DECREF(digit); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: val |= ((int64_t) idigit) << bits; jpayne@68: tmp = PyNumber_Rshift(stepval, shift); jpayne@68: if (unlikely(!tmp)) goto done; jpayne@68: Py_DECREF(stepval); stepval = tmp; jpayne@68: } jpayne@68: Py_DECREF(shift); shift = NULL; jpayne@68: Py_DECREF(mask); mask = NULL; jpayne@68: { jpayne@68: long idigit = PyLong_AsLong(stepval); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: remaining_bits = ((int) sizeof(int64_t) * 8) - bits - (is_unsigned ? 0 : 1); jpayne@68: if (unlikely(idigit >= (1L << remaining_bits))) jpayne@68: goto raise_overflow; jpayne@68: val |= ((int64_t) idigit) << bits; jpayne@68: } jpayne@68: if (!is_unsigned) { jpayne@68: if (unlikely(val & (((int64_t) 1) << (sizeof(int64_t) * 8 - 1)))) jpayne@68: goto raise_overflow; jpayne@68: if (is_negative) jpayne@68: val = ~val; jpayne@68: } jpayne@68: ret = 0; jpayne@68: done: jpayne@68: Py_XDECREF(shift); jpayne@68: Py_XDECREF(mask); jpayne@68: Py_XDECREF(stepval); jpayne@68: #endif jpayne@68: if (unlikely(ret)) jpayne@68: return (int64_t) -1; jpayne@68: return val; jpayne@68: } jpayne@68: raise_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "value too large to convert to int64_t"); jpayne@68: return (int64_t) -1; jpayne@68: raise_neg_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "can't convert negative value to int64_t"); jpayne@68: return (int64_t) -1; jpayne@68: } jpayne@68: jpayne@68: /* CIntToPy */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: if (is_unsigned) { jpayne@68: if (sizeof(int32_t) < sizeof(long)) { jpayne@68: return PyInt_FromLong((long) value); jpayne@68: } else if (sizeof(int32_t) <= sizeof(unsigned long)) { jpayne@68: return PyLong_FromUnsignedLong((unsigned long) value); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) { jpayne@68: return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: if (sizeof(int32_t) <= sizeof(long)) { jpayne@68: return PyInt_FromLong((long) value); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) { jpayne@68: return PyLong_FromLongLong((PY_LONG_LONG) value); jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: unsigned char *bytes = (unsigned char *)&value; jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 jpayne@68: if (is_unsigned) { jpayne@68: return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); jpayne@68: } else { jpayne@68: return PyLong_FromNativeBytes(bytes, sizeof(value), -1); jpayne@68: } jpayne@68: #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 jpayne@68: int one = 1; int little = (int)*(unsigned char *)&one; jpayne@68: return _PyLong_FromByteArray(bytes, sizeof(int32_t), jpayne@68: little, !is_unsigned); jpayne@68: #else jpayne@68: int one = 1; int little = (int)*(unsigned char *)&one; jpayne@68: PyObject *from_bytes, *result = NULL; jpayne@68: PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; jpayne@68: from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); jpayne@68: if (!from_bytes) return NULL; jpayne@68: py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int32_t)); jpayne@68: if (!py_bytes) goto limited_bad; jpayne@68: order_str = PyUnicode_FromString(little ? "little" : "big"); jpayne@68: if (!order_str) goto limited_bad; jpayne@68: arg_tuple = PyTuple_Pack(2, py_bytes, order_str); jpayne@68: if (!arg_tuple) goto limited_bad; jpayne@68: if (!is_unsigned) { jpayne@68: kwds = PyDict_New(); jpayne@68: if (!kwds) goto limited_bad; jpayne@68: if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; jpayne@68: } jpayne@68: result = PyObject_Call(from_bytes, arg_tuple, kwds); jpayne@68: limited_bad: jpayne@68: Py_XDECREF(kwds); jpayne@68: Py_XDECREF(arg_tuple); jpayne@68: Py_XDECREF(order_str); jpayne@68: Py_XDECREF(py_bytes); jpayne@68: Py_XDECREF(from_bytes); jpayne@68: return result; jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* CIntToPy */ jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const long neg_one = (long) -1, const_zero = (long) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: if (is_unsigned) { jpayne@68: if (sizeof(long) < sizeof(long)) { jpayne@68: return PyInt_FromLong((long) value); jpayne@68: } else if (sizeof(long) <= sizeof(unsigned long)) { jpayne@68: return PyLong_FromUnsignedLong((unsigned long) value); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { jpayne@68: return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: if (sizeof(long) <= sizeof(long)) { jpayne@68: return PyInt_FromLong((long) value); jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { jpayne@68: return PyLong_FromLongLong((PY_LONG_LONG) value); jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: unsigned char *bytes = (unsigned char *)&value; jpayne@68: #if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 jpayne@68: if (is_unsigned) { jpayne@68: return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); jpayne@68: } else { jpayne@68: return PyLong_FromNativeBytes(bytes, sizeof(value), -1); jpayne@68: } jpayne@68: #elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 jpayne@68: int one = 1; int little = (int)*(unsigned char *)&one; jpayne@68: return _PyLong_FromByteArray(bytes, sizeof(long), jpayne@68: little, !is_unsigned); jpayne@68: #else jpayne@68: int one = 1; int little = (int)*(unsigned char *)&one; jpayne@68: PyObject *from_bytes, *result = NULL; jpayne@68: PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; jpayne@68: from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); jpayne@68: if (!from_bytes) return NULL; jpayne@68: py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(long)); jpayne@68: if (!py_bytes) goto limited_bad; jpayne@68: order_str = PyUnicode_FromString(little ? "little" : "big"); jpayne@68: if (!order_str) goto limited_bad; jpayne@68: arg_tuple = PyTuple_Pack(2, py_bytes, order_str); jpayne@68: if (!arg_tuple) goto limited_bad; jpayne@68: if (!is_unsigned) { jpayne@68: kwds = PyDict_New(); jpayne@68: if (!kwds) goto limited_bad; jpayne@68: if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; jpayne@68: } jpayne@68: result = PyObject_Call(from_bytes, arg_tuple, kwds); jpayne@68: limited_bad: jpayne@68: Py_XDECREF(kwds); jpayne@68: Py_XDECREF(arg_tuple); jpayne@68: Py_XDECREF(order_str); jpayne@68: Py_XDECREF(py_bytes); jpayne@68: Py_XDECREF(from_bytes); jpayne@68: return result; jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* CIntFromPy */ jpayne@68: static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) { jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic push jpayne@68: #pragma GCC diagnostic ignored "-Wconversion" jpayne@68: #endif jpayne@68: const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0; jpayne@68: #ifdef __Pyx_HAS_GCC_DIAGNOSTIC jpayne@68: #pragma GCC diagnostic pop jpayne@68: #endif jpayne@68: const int is_unsigned = neg_one > const_zero; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_Check(x))) { jpayne@68: if ((sizeof(int32_t) < sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT(int32_t, long, PyInt_AS_LONG(x)) jpayne@68: } else { jpayne@68: long val = PyInt_AS_LONG(x); jpayne@68: if (is_unsigned && unlikely(val < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: return (int32_t) val; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if (unlikely(!PyLong_Check(x))) { jpayne@68: int32_t val; jpayne@68: PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); jpayne@68: if (!tmp) return (int32_t) -1; jpayne@68: val = __Pyx_PyInt_As_int32_t(tmp); jpayne@68: Py_DECREF(tmp); jpayne@68: return val; jpayne@68: } jpayne@68: if (is_unsigned) { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (unlikely(__Pyx_PyLong_IsNeg(x))) { jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_DigitCount(x)) { jpayne@68: case 2: jpayne@68: if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int32_t) >= 2 * PyLong_SHIFT)) { jpayne@68: return (int32_t) (((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int32_t) >= 3 * PyLong_SHIFT)) { jpayne@68: return (int32_t) (((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int32_t) >= 4 * PyLong_SHIFT)) { jpayne@68: 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@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 jpayne@68: if (unlikely(Py_SIZE(x) < 0)) { jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #else jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(x, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) jpayne@68: return (int32_t) -1; jpayne@68: if (unlikely(result == 1)) jpayne@68: goto raise_neg_overflow; jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(int32_t) <= sizeof(unsigned long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned long, PyLong_AsUnsignedLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } else { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (__Pyx_PyLong_IsCompact(x)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(x); jpayne@68: assert(__Pyx_PyLong_DigitCount(x) > 1); jpayne@68: switch (__Pyx_PyLong_SignedDigitCount(x)) { jpayne@68: case -2: jpayne@68: if ((8 * sizeof(int32_t) - 1 > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (int32_t) (((int32_t)-1)*(((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 2: jpayne@68: if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { jpayne@68: __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) jpayne@68: } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: return (int32_t) ((((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -3: jpayne@68: if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (int32_t) (((int32_t)-1)*(((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: return (int32_t) ((((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); jpayne@68: } jpayne@68: } jpayne@68: break; jpayne@68: case -4: jpayne@68: if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: 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@68: } jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) { jpayne@68: if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { jpayne@68: __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@68: } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) { jpayne@68: 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@68: } jpayne@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: if ((sizeof(int32_t) <= sizeof(long))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int32_t, long, PyLong_AsLong(x)) jpayne@68: #ifdef HAVE_LONG_LONG jpayne@68: } else if ((sizeof(int32_t) <= sizeof(PY_LONG_LONG))) { jpayne@68: __PYX_VERIFY_RETURN_INT_EXC(int32_t, PY_LONG_LONG, PyLong_AsLongLong(x)) jpayne@68: #endif jpayne@68: } jpayne@68: } jpayne@68: { jpayne@68: int32_t val; jpayne@68: int ret = -1; jpayne@68: #if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API jpayne@68: Py_ssize_t bytes_copied = PyLong_AsNativeBytes( jpayne@68: x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); jpayne@68: if (unlikely(bytes_copied == -1)) { jpayne@68: } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { jpayne@68: goto raise_overflow; jpayne@68: } else { jpayne@68: ret = 0; jpayne@68: } jpayne@68: #elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) jpayne@68: int one = 1; int is_little = (int)*(unsigned char *)&one; jpayne@68: unsigned char *bytes = (unsigned char *)&val; jpayne@68: ret = _PyLong_AsByteArray((PyLongObject *)x, jpayne@68: bytes, sizeof(val), jpayne@68: is_little, !is_unsigned); jpayne@68: #else jpayne@68: PyObject *v; jpayne@68: PyObject *stepval = NULL, *mask = NULL, *shift = NULL; jpayne@68: int bits, remaining_bits, is_negative = 0; jpayne@68: int chunk_size = (sizeof(long) < 8) ? 30 : 62; jpayne@68: if (likely(PyLong_CheckExact(x))) { jpayne@68: v = __Pyx_NewRef(x); jpayne@68: } else { jpayne@68: v = PyNumber_Long(x); jpayne@68: if (unlikely(!v)) return (int32_t) -1; jpayne@68: assert(PyLong_CheckExact(v)); jpayne@68: } jpayne@68: { jpayne@68: int result = PyObject_RichCompareBool(v, Py_False, Py_LT); jpayne@68: if (unlikely(result < 0)) { jpayne@68: Py_DECREF(v); jpayne@68: return (int32_t) -1; jpayne@68: } jpayne@68: is_negative = result == 1; jpayne@68: } jpayne@68: if (is_unsigned && unlikely(is_negative)) { jpayne@68: Py_DECREF(v); jpayne@68: goto raise_neg_overflow; jpayne@68: } else if (is_negative) { jpayne@68: stepval = PyNumber_Invert(v); jpayne@68: Py_DECREF(v); jpayne@68: if (unlikely(!stepval)) jpayne@68: return (int32_t) -1; jpayne@68: } else { jpayne@68: stepval = v; jpayne@68: } jpayne@68: v = NULL; jpayne@68: val = (int32_t) 0; jpayne@68: mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; jpayne@68: shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; jpayne@68: for (bits = 0; bits < (int) sizeof(int32_t) * 8 - chunk_size; bits += chunk_size) { jpayne@68: PyObject *tmp, *digit; jpayne@68: long idigit; jpayne@68: digit = PyNumber_And(stepval, mask); jpayne@68: if (unlikely(!digit)) goto done; jpayne@68: idigit = PyLong_AsLong(digit); jpayne@68: Py_DECREF(digit); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: val |= ((int32_t) idigit) << bits; jpayne@68: tmp = PyNumber_Rshift(stepval, shift); jpayne@68: if (unlikely(!tmp)) goto done; jpayne@68: Py_DECREF(stepval); stepval = tmp; jpayne@68: } jpayne@68: Py_DECREF(shift); shift = NULL; jpayne@68: Py_DECREF(mask); mask = NULL; jpayne@68: { jpayne@68: long idigit = PyLong_AsLong(stepval); jpayne@68: if (unlikely(idigit < 0)) goto done; jpayne@68: remaining_bits = ((int) sizeof(int32_t) * 8) - bits - (is_unsigned ? 0 : 1); jpayne@68: if (unlikely(idigit >= (1L << remaining_bits))) jpayne@68: goto raise_overflow; jpayne@68: val |= ((int32_t) idigit) << bits; jpayne@68: } jpayne@68: if (!is_unsigned) { jpayne@68: if (unlikely(val & (((int32_t) 1) << (sizeof(int32_t) * 8 - 1)))) jpayne@68: goto raise_overflow; jpayne@68: if (is_negative) jpayne@68: val = ~val; jpayne@68: } jpayne@68: ret = 0; jpayne@68: done: jpayne@68: Py_XDECREF(shift); jpayne@68: Py_XDECREF(mask); jpayne@68: Py_XDECREF(stepval); jpayne@68: #endif jpayne@68: if (unlikely(ret)) jpayne@68: return (int32_t) -1; jpayne@68: return val; jpayne@68: } jpayne@68: raise_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "value too large to convert to int32_t"); jpayne@68: return (int32_t) -1; jpayne@68: raise_neg_overflow: jpayne@68: PyErr_SetString(PyExc_OverflowError, jpayne@68: "can't convert negative value to int32_t"); jpayne@68: return (int32_t) -1; jpayne@68: } jpayne@68: jpayne@68: /* FormatTypeName */ jpayne@68: #if CYTHON_COMPILING_IN_LIMITED_API jpayne@68: static __Pyx_TypeName jpayne@68: __Pyx_PyType_GetName(PyTypeObject* tp) jpayne@68: { jpayne@68: PyObject *name = __Pyx_PyObject_GetAttrStr((PyObject *)tp, jpayne@68: __pyx_n_s_name); jpayne@68: if (unlikely(name == NULL) || unlikely(!PyUnicode_Check(name))) { jpayne@68: PyErr_Clear(); jpayne@68: Py_XDECREF(name); jpayne@68: name = __Pyx_NewRef(__pyx_n_s__78); jpayne@68: } jpayne@68: return name; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* FastTypeChecks */ jpayne@68: #if CYTHON_COMPILING_IN_CPYTHON jpayne@68: static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { jpayne@68: while (a) { jpayne@68: a = __Pyx_PyType_GetSlot(a, tp_base, PyTypeObject*); jpayne@68: if (a == b) jpayne@68: return 1; jpayne@68: } jpayne@68: return b == &PyBaseObject_Type; jpayne@68: } jpayne@68: static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { jpayne@68: PyObject *mro; jpayne@68: if (a == b) return 1; jpayne@68: mro = a->tp_mro; jpayne@68: if (likely(mro)) { jpayne@68: Py_ssize_t i, n; jpayne@68: n = PyTuple_GET_SIZE(mro); jpayne@68: for (i = 0; i < n; i++) { jpayne@68: if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) jpayne@68: return 1; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: return __Pyx_InBases(a, b); jpayne@68: } jpayne@68: static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b) { jpayne@68: PyObject *mro; jpayne@68: if (cls == a || cls == b) return 1; jpayne@68: mro = cls->tp_mro; jpayne@68: if (likely(mro)) { jpayne@68: Py_ssize_t i, n; jpayne@68: n = PyTuple_GET_SIZE(mro); jpayne@68: for (i = 0; i < n; i++) { jpayne@68: PyObject *base = PyTuple_GET_ITEM(mro, i); jpayne@68: if (base == (PyObject *)a || base == (PyObject *)b) jpayne@68: return 1; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: return __Pyx_InBases(cls, a) || __Pyx_InBases(cls, b); jpayne@68: } jpayne@68: #if PY_MAJOR_VERSION == 2 jpayne@68: static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { jpayne@68: PyObject *exception, *value, *tb; jpayne@68: int res; jpayne@68: __Pyx_PyThreadState_declare jpayne@68: __Pyx_PyThreadState_assign jpayne@68: __Pyx_ErrFetch(&exception, &value, &tb); jpayne@68: res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; jpayne@68: if (unlikely(res == -1)) { jpayne@68: PyErr_WriteUnraisable(err); jpayne@68: res = 0; jpayne@68: } jpayne@68: if (!res) { jpayne@68: res = PyObject_IsSubclass(err, exc_type2); jpayne@68: if (unlikely(res == -1)) { jpayne@68: PyErr_WriteUnraisable(err); jpayne@68: res = 0; jpayne@68: } jpayne@68: } jpayne@68: __Pyx_ErrRestore(exception, value, tb); jpayne@68: return res; jpayne@68: } jpayne@68: #else jpayne@68: static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { jpayne@68: if (exc_type1) { jpayne@68: return __Pyx_IsAnySubtype2((PyTypeObject*)err, (PyTypeObject*)exc_type1, (PyTypeObject*)exc_type2); jpayne@68: } else { jpayne@68: return __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { jpayne@68: Py_ssize_t i, n; jpayne@68: assert(PyExceptionClass_Check(exc_type)); jpayne@68: n = PyTuple_GET_SIZE(tuple); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: for (i=0; i= 0x030B00A4 jpayne@68: return Py_Version & ~0xFFUL; jpayne@68: #else jpayne@68: const char* rt_version = Py_GetVersion(); jpayne@68: unsigned long version = 0; jpayne@68: unsigned long factor = 0x01000000UL; jpayne@68: unsigned int digit = 0; jpayne@68: int i = 0; jpayne@68: while (factor) { jpayne@68: while ('0' <= rt_version[i] && rt_version[i] <= '9') { jpayne@68: digit = digit * 10 + (unsigned int) (rt_version[i] - '0'); jpayne@68: ++i; jpayne@68: } jpayne@68: version += factor * digit; jpayne@68: if (rt_version[i] != '.') jpayne@68: break; jpayne@68: digit = 0; jpayne@68: factor >>= 8; jpayne@68: ++i; jpayne@68: } jpayne@68: return version; jpayne@68: #endif jpayne@68: } jpayne@68: static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer) { jpayne@68: const unsigned long MAJOR_MINOR = 0xFFFF0000UL; jpayne@68: if ((rt_version & MAJOR_MINOR) == (ct_version & MAJOR_MINOR)) jpayne@68: return 0; jpayne@68: if (likely(allow_newer && (rt_version & MAJOR_MINOR) > (ct_version & MAJOR_MINOR))) jpayne@68: return 1; jpayne@68: { jpayne@68: char message[200]; jpayne@68: PyOS_snprintf(message, sizeof(message), jpayne@68: "compile time Python version %d.%d " jpayne@68: "of module '%.100s' " jpayne@68: "%s " jpayne@68: "runtime version %d.%d", jpayne@68: (int) (ct_version >> 24), (int) ((ct_version >> 16) & 0xFF), jpayne@68: __Pyx_MODULE_NAME, jpayne@68: (allow_newer) ? "was newer than" : "does not match", jpayne@68: (int) (rt_version >> 24), (int) ((rt_version >> 16) & 0xFF) jpayne@68: ); jpayne@68: return PyErr_WarnEx(NULL, message, 1); jpayne@68: } jpayne@68: } jpayne@68: jpayne@68: /* FunctionImport */ jpayne@68: #ifndef __PYX_HAVE_RT_ImportFunction_3_0_11 jpayne@68: #define __PYX_HAVE_RT_ImportFunction_3_0_11 jpayne@68: static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { jpayne@68: PyObject *d = 0; jpayne@68: PyObject *cobj = 0; jpayne@68: union { jpayne@68: void (*fp)(void); jpayne@68: void *p; jpayne@68: } tmp; jpayne@68: d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); jpayne@68: if (!d) jpayne@68: goto bad; jpayne@68: cobj = PyDict_GetItemString(d, funcname); jpayne@68: if (!cobj) { jpayne@68: PyErr_Format(PyExc_ImportError, jpayne@68: "%.200s does not export expected C function %.200s", jpayne@68: PyModule_GetName(module), funcname); jpayne@68: goto bad; jpayne@68: } jpayne@68: if (!PyCapsule_IsValid(cobj, sig)) { jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", jpayne@68: PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); jpayne@68: goto bad; jpayne@68: } jpayne@68: tmp.p = PyCapsule_GetPointer(cobj, sig); jpayne@68: *f = tmp.fp; jpayne@68: if (!(*f)) jpayne@68: goto bad; jpayne@68: Py_DECREF(d); jpayne@68: return 0; jpayne@68: bad: jpayne@68: Py_XDECREF(d); jpayne@68: return -1; jpayne@68: } jpayne@68: #endif jpayne@68: jpayne@68: /* InitStrings */ jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: static int __Pyx_InitString(__Pyx_StringTabEntry t, PyObject **str) { jpayne@68: if (t.is_unicode | t.is_str) { jpayne@68: if (t.intern) { jpayne@68: *str = PyUnicode_InternFromString(t.s); jpayne@68: } else if (t.encoding) { jpayne@68: *str = PyUnicode_Decode(t.s, t.n - 1, t.encoding, NULL); jpayne@68: } else { jpayne@68: *str = PyUnicode_FromStringAndSize(t.s, t.n - 1); jpayne@68: } jpayne@68: } else { jpayne@68: *str = PyBytes_FromStringAndSize(t.s, t.n - 1); jpayne@68: } jpayne@68: if (!*str) jpayne@68: return -1; jpayne@68: if (PyObject_Hash(*str) == -1) jpayne@68: return -1; jpayne@68: return 0; jpayne@68: } jpayne@68: #endif jpayne@68: static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { jpayne@68: while (t->p) { jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: __Pyx_InitString(*t, t->p); jpayne@68: #else jpayne@68: if (t->is_unicode) { jpayne@68: *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); jpayne@68: } else if (t->intern) { jpayne@68: *t->p = PyString_InternFromString(t->s); jpayne@68: } else { jpayne@68: *t->p = PyString_FromStringAndSize(t->s, t->n - 1); jpayne@68: } jpayne@68: if (!*t->p) jpayne@68: return -1; jpayne@68: if (PyObject_Hash(*t->p) == -1) jpayne@68: return -1; jpayne@68: #endif jpayne@68: ++t; jpayne@68: } jpayne@68: return 0; jpayne@68: } jpayne@68: jpayne@68: #include jpayne@68: static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s) { jpayne@68: size_t len = strlen(s); jpayne@68: if (unlikely(len > (size_t) PY_SSIZE_T_MAX)) { jpayne@68: PyErr_SetString(PyExc_OverflowError, "byte string is too long"); jpayne@68: return -1; jpayne@68: } jpayne@68: return (Py_ssize_t) len; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { jpayne@68: Py_ssize_t len = __Pyx_ssize_strlen(c_str); jpayne@68: if (unlikely(len < 0)) return NULL; jpayne@68: return __Pyx_PyUnicode_FromStringAndSize(c_str, len); jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char* c_str) { jpayne@68: Py_ssize_t len = __Pyx_ssize_strlen(c_str); jpayne@68: if (unlikely(len < 0)) return NULL; jpayne@68: return PyByteArray_FromStringAndSize(c_str, len); jpayne@68: } jpayne@68: static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { jpayne@68: Py_ssize_t ignore; jpayne@68: return __Pyx_PyObject_AsStringAndSize(o, &ignore); jpayne@68: } jpayne@68: #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT jpayne@68: #if !CYTHON_PEP393_ENABLED jpayne@68: static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { jpayne@68: char* defenc_c; jpayne@68: PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); jpayne@68: if (!defenc) return NULL; jpayne@68: defenc_c = PyBytes_AS_STRING(defenc); jpayne@68: #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII jpayne@68: { jpayne@68: char* end = defenc_c + PyBytes_GET_SIZE(defenc); jpayne@68: char* c; jpayne@68: for (c = defenc_c; c < end; c++) { jpayne@68: if ((unsigned char) (*c) >= 128) { jpayne@68: PyUnicode_AsASCIIString(o); jpayne@68: return NULL; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: *length = PyBytes_GET_SIZE(defenc); jpayne@68: return defenc_c; jpayne@68: } jpayne@68: #else jpayne@68: static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { jpayne@68: if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; jpayne@68: #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII jpayne@68: if (likely(PyUnicode_IS_ASCII(o))) { jpayne@68: *length = PyUnicode_GET_LENGTH(o); jpayne@68: return PyUnicode_AsUTF8(o); jpayne@68: } else { jpayne@68: PyUnicode_AsASCIIString(o); jpayne@68: return NULL; jpayne@68: } jpayne@68: #else jpayne@68: return PyUnicode_AsUTF8AndSize(o, length); jpayne@68: #endif jpayne@68: } jpayne@68: #endif jpayne@68: #endif jpayne@68: static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { jpayne@68: #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT jpayne@68: if ( jpayne@68: #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII jpayne@68: __Pyx_sys_getdefaultencoding_not_ascii && jpayne@68: #endif jpayne@68: PyUnicode_Check(o)) { jpayne@68: return __Pyx_PyUnicode_AsStringAndSize(o, length); jpayne@68: } else jpayne@68: #endif jpayne@68: #if (!CYTHON_COMPILING_IN_PYPY && !CYTHON_COMPILING_IN_LIMITED_API) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) jpayne@68: if (PyByteArray_Check(o)) { jpayne@68: *length = PyByteArray_GET_SIZE(o); jpayne@68: return PyByteArray_AS_STRING(o); jpayne@68: } else jpayne@68: #endif jpayne@68: { jpayne@68: char* result; jpayne@68: int r = PyBytes_AsStringAndSize(o, &result, length); jpayne@68: if (unlikely(r < 0)) { jpayne@68: return NULL; jpayne@68: } else { jpayne@68: return result; jpayne@68: } jpayne@68: } jpayne@68: } jpayne@68: static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { jpayne@68: int is_true = x == Py_True; jpayne@68: if (is_true | (x == Py_False) | (x == Py_None)) return is_true; jpayne@68: else return PyObject_IsTrue(x); jpayne@68: } jpayne@68: static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { jpayne@68: int retval; jpayne@68: if (unlikely(!x)) return -1; jpayne@68: retval = __Pyx_PyObject_IsTrue(x); jpayne@68: Py_DECREF(x); jpayne@68: return retval; jpayne@68: } jpayne@68: static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { jpayne@68: __Pyx_TypeName result_type_name = __Pyx_PyType_GetName(Py_TYPE(result)); jpayne@68: #if PY_MAJOR_VERSION >= 3 jpayne@68: if (PyLong_Check(result)) { jpayne@68: if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, jpayne@68: "__int__ returned non-int (type " __Pyx_FMT_TYPENAME "). " jpayne@68: "The ability to return an instance of a strict subclass of int is deprecated, " jpayne@68: "and may be removed in a future version of Python.", jpayne@68: result_type_name)) { jpayne@68: __Pyx_DECREF_TypeName(result_type_name); jpayne@68: Py_DECREF(result); jpayne@68: return NULL; jpayne@68: } jpayne@68: __Pyx_DECREF_TypeName(result_type_name); jpayne@68: return result; jpayne@68: } jpayne@68: #endif jpayne@68: PyErr_Format(PyExc_TypeError, jpayne@68: "__%.4s__ returned non-%.4s (type " __Pyx_FMT_TYPENAME ")", jpayne@68: type_name, type_name, result_type_name); jpayne@68: __Pyx_DECREF_TypeName(result_type_name); jpayne@68: Py_DECREF(result); jpayne@68: return NULL; jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: PyNumberMethods *m; jpayne@68: #endif jpayne@68: const char *name = NULL; jpayne@68: PyObject *res = NULL; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_Check(x) || PyLong_Check(x))) jpayne@68: #else jpayne@68: if (likely(PyLong_Check(x))) jpayne@68: #endif jpayne@68: return __Pyx_NewRef(x); jpayne@68: #if CYTHON_USE_TYPE_SLOTS jpayne@68: m = Py_TYPE(x)->tp_as_number; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (m && m->nb_int) { jpayne@68: name = "int"; jpayne@68: res = m->nb_int(x); jpayne@68: } jpayne@68: else if (m && m->nb_long) { jpayne@68: name = "long"; jpayne@68: res = m->nb_long(x); jpayne@68: } jpayne@68: #else jpayne@68: if (likely(m && m->nb_int)) { jpayne@68: name = "int"; jpayne@68: res = m->nb_int(x); jpayne@68: } jpayne@68: #endif jpayne@68: #else jpayne@68: if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { jpayne@68: res = PyNumber_Int(x); jpayne@68: } jpayne@68: #endif jpayne@68: if (likely(res)) { jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { jpayne@68: #else jpayne@68: if (unlikely(!PyLong_CheckExact(res))) { jpayne@68: #endif jpayne@68: return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); jpayne@68: } jpayne@68: } jpayne@68: else if (!PyErr_Occurred()) { jpayne@68: PyErr_SetString(PyExc_TypeError, jpayne@68: "an integer is required"); jpayne@68: } jpayne@68: return res; jpayne@68: } jpayne@68: static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { jpayne@68: Py_ssize_t ival; jpayne@68: PyObject *x; jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: if (likely(PyInt_CheckExact(b))) { jpayne@68: if (sizeof(Py_ssize_t) >= sizeof(long)) jpayne@68: return PyInt_AS_LONG(b); jpayne@68: else jpayne@68: return PyInt_AsSsize_t(b); jpayne@68: } jpayne@68: #endif jpayne@68: if (likely(PyLong_CheckExact(b))) { jpayne@68: #if CYTHON_USE_PYLONG_INTERNALS jpayne@68: if (likely(__Pyx_PyLong_IsCompact(b))) { jpayne@68: return __Pyx_PyLong_CompactValue(b); jpayne@68: } else { jpayne@68: const digit* digits = __Pyx_PyLong_Digits(b); jpayne@68: const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(b); jpayne@68: switch (size) { jpayne@68: case 2: jpayne@68: if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { jpayne@68: return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); jpayne@68: } jpayne@68: break; jpayne@68: case -2: jpayne@68: if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { jpayne@68: return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); jpayne@68: } jpayne@68: break; jpayne@68: case 3: jpayne@68: if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { jpayne@68: return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); jpayne@68: } jpayne@68: break; jpayne@68: case -3: jpayne@68: if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { jpayne@68: return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); jpayne@68: } jpayne@68: break; jpayne@68: case 4: jpayne@68: if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { jpayne@68: 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@68: } jpayne@68: break; jpayne@68: case -4: jpayne@68: if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { jpayne@68: 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@68: } jpayne@68: break; jpayne@68: } jpayne@68: } jpayne@68: #endif jpayne@68: return PyLong_AsSsize_t(b); jpayne@68: } jpayne@68: x = PyNumber_Index(b); jpayne@68: if (!x) return -1; jpayne@68: ival = PyInt_AsSsize_t(x); jpayne@68: Py_DECREF(x); jpayne@68: return ival; jpayne@68: } jpayne@68: static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) { jpayne@68: if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) { jpayne@68: return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o); jpayne@68: #if PY_MAJOR_VERSION < 3 jpayne@68: } else if (likely(PyInt_CheckExact(o))) { jpayne@68: return PyInt_AS_LONG(o); jpayne@68: #endif jpayne@68: } else { jpayne@68: Py_ssize_t ival; jpayne@68: PyObject *x; jpayne@68: x = PyNumber_Index(o); jpayne@68: if (!x) return -1; jpayne@68: ival = PyInt_AsLong(x); jpayne@68: Py_DECREF(x); jpayne@68: return ival; jpayne@68: } jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { jpayne@68: return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); jpayne@68: } jpayne@68: static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { jpayne@68: return PyInt_FromSize_t(ival); jpayne@68: } jpayne@68: jpayne@68: jpayne@68: /* #### Code section: utility_code_pragmas_end ### */ jpayne@68: #ifdef _MSC_VER jpayne@68: #pragma warning( pop ) jpayne@68: #endif jpayne@68: jpayne@68: jpayne@68: jpayne@68: /* #### Code section: end ### */ jpayne@68: #endif /* Py_PYTHON_H */