Mercurial > repos > rliterman > csp2
diff CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.c @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libchtslib.c Tue Mar 18 17:55:14 2025 -0400 @@ -0,0 +1,29751 @@ +/* Generated by Cython 3.0.11 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "define_macros": [ + [ + "BUILDING_WHEEL", + null + ] + ], + "depends": [ + "/project/htslib/htslib/bgzf.h", + "/project/htslib/htslib/cram.h", + "/project/htslib/htslib/faidx.h", + "/project/htslib/htslib/hfile.h", + "/project/htslib/htslib/hts.h", + "/project/htslib/htslib/kstring.h", + "/project/htslib/htslib/sam.h", + "/project/htslib/htslib/tbx.h", + "/project/htslib/htslib/vcf.h", + "/project/htslib/htslib/vcfutils.h", + "/project/pysam/htslib_util.h" + ], + "extra_compile_args": [ + "-Wno-unused", + "-Wno-strict-prototypes", + "-Wno-sign-compare", + "-Wno-error=declaration-after-statement" + ], + "extra_link_args": [ + "-Wl,-rpath,$ORIGIN" + ], + "extra_objects": [ + "htslib/kfunc.o", + "htslib/kstring.o", + "htslib/bcf_sr_sort.o", + "htslib/bgzf.o", + "htslib/errmod.o", + "htslib/faidx.o", + "htslib/header.o", + "htslib/hfile.o", + "htslib/hts.o", + "htslib/hts_expr.o", + "htslib/hts_os.o", + "htslib/md5.o", + "htslib/multipart.o", + "htslib/probaln.o", + "htslib/realn.o", + "htslib/regidx.o", + "htslib/region.o", + "htslib/sam.o", + "htslib/sam_mods.o", + "htslib/simd.o", + "htslib/synced_bcf_reader.o", + "htslib/vcf_sweep.o", + "htslib/tbx.o", + "htslib/textutils.o", + "htslib/thread_pool.o", + "htslib/vcf.o", + "htslib/vcfutils.o", + "htslib/cram/cram_codecs.o", + "htslib/cram/cram_decode.o", + "htslib/cram/cram_encode.o", + "htslib/cram/cram_external.o", + "htslib/cram/cram_index.o", + "htslib/cram/cram_io.o", + "htslib/cram/cram_stats.o", + "htslib/cram/mFILE.o", + "htslib/cram/open_trace_file.o", + "htslib/cram/pooled_alloc.o", + "htslib/cram/string_alloc.o", + "htslib/htscodecs/htscodecs/arith_dynamic.o", + "htslib/htscodecs/htscodecs/fqzcomp_qual.o", + "htslib/htscodecs/htscodecs/htscodecs.o", + "htslib/htscodecs/htscodecs/pack.o", + "htslib/htscodecs/htscodecs/rANS_static4x16pr.o", + "htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o", + "htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o", + "htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o", + "htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.o", + "htslib/htscodecs/htscodecs/rANS_static32x16pr.o", + "htslib/htscodecs/htscodecs/rANS_static.o", + "htslib/htscodecs/htscodecs/rle.o", + "htslib/htscodecs/htscodecs/tokenise_name3.o", + "htslib/htscodecs/htscodecs/utils.o", + "htslib/hfile_libcurl.o", + "htslib/hfile_gcs.o", + "htslib/hfile_s3.o", + "htslib/hfile_s3_write.o" + ], + "include_dirs": [ + "pysam", + "/project/pysam", + "/project/htslib", + "/project/samtools", + "/project/samtools/lz4", + "/project/bcftools", + "/project" + ], + "language": "c", + "libraries": [ + "z", + "lzma", + "bz2", + "z", + "m", + "curl", + "crypto" + ], + "library_dirs": [ + "/project/pysam", + "/project", + "build/lib.linux-x86_64-cpython-37/pysam" + ], + "name": "pysam.libchtslib", + "sources": [ + "pysam/libchtslib.pyx", + "pysam/htslib_util.c" + ] + }, + "module_name": "pysam.libchtslib" +} +END: Cython Metadata */ + +#ifndef PY_SSIZE_T_CLEAN +#define PY_SSIZE_T_CLEAN +#endif /* PY_SSIZE_T_CLEAN */ +#if defined(CYTHON_LIMITED_API) && 0 + #ifndef Py_LIMITED_API + #if CYTHON_LIMITED_API+0 > 0x03030000 + #define Py_LIMITED_API CYTHON_LIMITED_API + #else + #define Py_LIMITED_API 0x03030000 + #endif + #endif +#endif + +#include "Python.h" + + #if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj) + #else + #define __Pyx_PyFloat_FromString(obj) PyFloat_FromString(obj, NULL) + #endif + + + #if PY_MAJOR_VERSION <= 2 + #define PyDict_GetItemWithError _PyDict_GetItemWithError + #endif + + + #if (PY_VERSION_HEX < 0x030700b1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030600)) && !defined(PyContextVar_Get) + #define PyContextVar_Get(var, d, v) ((d) ? ((void)(var), Py_INCREF(d), (v)[0] = (d), 0) : ((v)[0] = NULL, 0) ) + #endif + +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02070000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) + #error Cython requires Python 2.7+ or Python 3.3+. +#else +#if defined(CYTHON_LIMITED_API) && CYTHON_LIMITED_API +#define __PYX_EXTRA_ABI_MODULE_NAME "limited" +#else +#define __PYX_EXTRA_ABI_MODULE_NAME "" +#endif +#define CYTHON_ABI "3_0_11" __PYX_EXTRA_ABI_MODULE_NAME +#define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI +#define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "." +#define CYTHON_HEX_VERSION 0x03000BF0 +#define CYTHON_FUTURE_DIVISION 1 +#include <stddef.h> +#ifndef offsetof + #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(_WIN32) && !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#define __PYX_COMMA , +#ifndef HAVE_LONG_LONG + #define HAVE_LONG_LONG +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#define __PYX_LIMITED_VERSION_HEX PY_VERSION_HEX +#if defined(GRAALVM_PYTHON) + /* For very preliminary testing purposes. Most variables are set the same as PyPy. + The existence of this section does not imply that anything works or is even tested */ + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_LIMITED_API 0 + #define CYTHON_COMPILING_IN_GRAAL 1 + #define CYTHON_COMPILING_IN_NOGIL 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #undef CYTHON_USE_TYPE_SPECS + #define CYTHON_USE_TYPE_SPECS 0 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #if PY_VERSION_HEX < 0x03050000 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #undef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 1 + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_GIL + #define CYTHON_FAST_GIL 0 + #undef CYTHON_METH_FASTCALL + #define CYTHON_METH_FASTCALL 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #ifndef CYTHON_PEP487_INIT_SUBCLASS + #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3) + #endif + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 1 + #undef CYTHON_USE_MODULE_STATE + #define CYTHON_USE_MODULE_STATE 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 + #undef CYTHON_USE_DICT_VERSIONS + #define CYTHON_USE_DICT_VERSIONS 0 + #undef CYTHON_USE_EXC_INFO_STACK + #define CYTHON_USE_EXC_INFO_STACK 0 + #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC + #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 + #endif + #undef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 +#elif defined(PYPY_VERSION) + #define CYTHON_COMPILING_IN_PYPY 1 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_LIMITED_API 0 + #define CYTHON_COMPILING_IN_GRAAL 0 + #define CYTHON_COMPILING_IN_NOGIL 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #ifndef CYTHON_USE_TYPE_SPECS + #define CYTHON_USE_TYPE_SPECS 0 + #endif + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #if PY_VERSION_HEX < 0x03050000 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #undef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 1 + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_GIL + #define CYTHON_FAST_GIL 0 + #undef CYTHON_METH_FASTCALL + #define CYTHON_METH_FASTCALL 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #ifndef CYTHON_PEP487_INIT_SUBCLASS + #define CYTHON_PEP487_INIT_SUBCLASS (PY_MAJOR_VERSION >= 3) + #endif + #if PY_VERSION_HEX < 0x03090000 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT) + #define CYTHON_PEP489_MULTI_PHASE_INIT 1 + #endif + #undef CYTHON_USE_MODULE_STATE + #define CYTHON_USE_MODULE_STATE 0 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1 && PYPY_VERSION_NUM >= 0x07030C00) + #undef CYTHON_USE_DICT_VERSIONS + #define CYTHON_USE_DICT_VERSIONS 0 + #undef CYTHON_USE_EXC_INFO_STACK + #define CYTHON_USE_EXC_INFO_STACK 0 + #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC + #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 + #endif + #undef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 +#elif defined(CYTHON_LIMITED_API) + #ifdef Py_LIMITED_API + #undef __PYX_LIMITED_VERSION_HEX + #define __PYX_LIMITED_VERSION_HEX Py_LIMITED_API + #endif + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_LIMITED_API 1 + #define CYTHON_COMPILING_IN_GRAAL 0 + #define CYTHON_COMPILING_IN_NOGIL 0 + #undef CYTHON_CLINE_IN_TRACEBACK + #define CYTHON_CLINE_IN_TRACEBACK 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #undef CYTHON_USE_TYPE_SPECS + #define CYTHON_USE_TYPE_SPECS 1 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #ifndef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #endif + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_GIL + #define CYTHON_FAST_GIL 0 + #undef CYTHON_METH_FASTCALL + #define CYTHON_METH_FASTCALL 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #ifndef CYTHON_PEP487_INIT_SUBCLASS + #define CYTHON_PEP487_INIT_SUBCLASS 1 + #endif + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #undef CYTHON_USE_MODULE_STATE + #define CYTHON_USE_MODULE_STATE 1 + #ifndef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 + #endif + #undef CYTHON_USE_DICT_VERSIONS + #define CYTHON_USE_DICT_VERSIONS 0 + #undef CYTHON_USE_EXC_INFO_STACK + #define CYTHON_USE_EXC_INFO_STACK 0 + #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC + #define CYTHON_UPDATE_DESCRIPTOR_DOC 0 + #endif + #undef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 +#elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_LIMITED_API 0 + #define CYTHON_COMPILING_IN_GRAAL 0 + #define CYTHON_COMPILING_IN_NOGIL 1 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #ifndef CYTHON_USE_TYPE_SPECS + #define CYTHON_USE_TYPE_SPECS 0 + #endif + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #ifndef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #ifndef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #endif + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_GIL + #define CYTHON_FAST_GIL 0 + #ifndef CYTHON_METH_FASTCALL + #define CYTHON_METH_FASTCALL 1 + #endif + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 + #ifndef CYTHON_PEP487_INIT_SUBCLASS + #define CYTHON_PEP487_INIT_SUBCLASS 1 + #endif + #ifndef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 1 + #endif + #ifndef CYTHON_USE_MODULE_STATE + #define CYTHON_USE_MODULE_STATE 0 + #endif + #ifndef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 1 + #endif + #undef CYTHON_USE_DICT_VERSIONS + #define CYTHON_USE_DICT_VERSIONS 0 + #undef CYTHON_USE_EXC_INFO_STACK + #define CYTHON_USE_EXC_INFO_STACK 0 + #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC + #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 + #endif + #ifndef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 0 + #endif +#else + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_CPYTHON 1 + #define CYTHON_COMPILING_IN_LIMITED_API 0 + #define CYTHON_COMPILING_IN_GRAAL 0 + #define CYTHON_COMPILING_IN_NOGIL 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #ifndef CYTHON_USE_TYPE_SPECS + #define CYTHON_USE_TYPE_SPECS 0 + #endif + #ifndef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 1 + #endif + #if PY_MAJOR_VERSION < 3 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #ifndef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 1 + #endif + #ifndef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 1 + #endif + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #elif !defined(CYTHON_USE_UNICODE_WRITER) + #define CYTHON_USE_UNICODE_WRITER 1 + #endif + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #ifndef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 1 + #endif + #ifndef CYTHON_FAST_GIL + #define CYTHON_FAST_GIL (PY_MAJOR_VERSION < 3 || PY_VERSION_HEX >= 0x03060000 && PY_VERSION_HEX < 0x030C00A6) + #endif + #ifndef CYTHON_METH_FASTCALL + #define CYTHON_METH_FASTCALL (PY_VERSION_HEX >= 0x030700A1) + #endif + #ifndef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 1 + #endif + #ifndef CYTHON_PEP487_INIT_SUBCLASS + #define CYTHON_PEP487_INIT_SUBCLASS 1 + #endif + #if PY_VERSION_HEX < 0x03050000 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 0 + #elif !defined(CYTHON_PEP489_MULTI_PHASE_INIT) + #define CYTHON_PEP489_MULTI_PHASE_INIT 1 + #endif + #ifndef CYTHON_USE_MODULE_STATE + #define CYTHON_USE_MODULE_STATE 0 + #endif + #if PY_VERSION_HEX < 0x030400a1 + #undef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE 0 + #elif !defined(CYTHON_USE_TP_FINALIZE) + #define CYTHON_USE_TP_FINALIZE 1 + #endif + #if PY_VERSION_HEX < 0x030600B1 + #undef CYTHON_USE_DICT_VERSIONS + #define CYTHON_USE_DICT_VERSIONS 0 + #elif !defined(CYTHON_USE_DICT_VERSIONS) + #define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX < 0x030C00A5) + #endif + #if PY_VERSION_HEX < 0x030700A3 + #undef CYTHON_USE_EXC_INFO_STACK + #define CYTHON_USE_EXC_INFO_STACK 0 + #elif !defined(CYTHON_USE_EXC_INFO_STACK) + #define CYTHON_USE_EXC_INFO_STACK 1 + #endif + #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC + #define CYTHON_UPDATE_DESCRIPTOR_DOC 1 + #endif + #ifndef CYTHON_USE_FREELISTS + #define CYTHON_USE_FREELISTS 1 + #endif +#endif +#if !defined(CYTHON_FAST_PYCCALL) +#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) +#endif +#if !defined(CYTHON_VECTORCALL) +#define CYTHON_VECTORCALL (CYTHON_FAST_PYCCALL && PY_VERSION_HEX >= 0x030800B1) +#endif +#define CYTHON_BACKPORT_VECTORCALL (CYTHON_METH_FASTCALL && PY_VERSION_HEX < 0x030800B1) +#if CYTHON_USE_PYLONG_INTERNALS + #if PY_MAJOR_VERSION < 3 + #include "longintrepr.h" + #endif + #undef SHIFT + #undef BASE + #undef MASK + #ifdef SIZEOF_VOID_P + enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; + #endif +#endif +#ifndef __has_attribute + #define __has_attribute(x) 0 +#endif +#ifndef __has_cpp_attribute + #define __has_cpp_attribute(x) 0 +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifndef CYTHON_UNUSED + #if defined(__cplusplus) + /* for clang __has_cpp_attribute(maybe_unused) is true even before C++17 + * but leads to warnings with -pedantic, since it is a C++17 feature */ + #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L) + #if __has_cpp_attribute(maybe_unused) + #define CYTHON_UNUSED [[maybe_unused]] + #endif + #endif + #endif +#endif +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_UNUSED_VAR +# if defined(__cplusplus) + template<class T> void CYTHON_UNUSED_VAR( const T& ) { } +# else +# define CYTHON_UNUSED_VAR(x) (void)(x) +# endif +#endif +#ifndef CYTHON_MAYBE_UNUSED_VAR + #define CYTHON_MAYBE_UNUSED_VAR(x) CYTHON_UNUSED_VAR(x) +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_USE_CPP_STD_MOVE + #if defined(__cplusplus) && (\ + __cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1600)) + #define CYTHON_USE_CPP_STD_MOVE 1 + #else + #define CYTHON_USE_CPP_STD_MOVE 0 + #endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#ifdef _MSC_VER + #ifndef _MSC_STDINT_H_ + #if _MSC_VER < 1300 + typedef unsigned char uint8_t; + typedef unsigned short uint16_t; + typedef unsigned int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int16 uint16_t; + typedef unsigned __int32 uint32_t; + #endif + #endif + #if _MSC_VER < 1300 + #ifdef _WIN64 + typedef unsigned long long __pyx_uintptr_t; + #else + typedef unsigned int __pyx_uintptr_t; + #endif + #else + #ifdef _WIN64 + typedef unsigned __int64 __pyx_uintptr_t; + #else + typedef unsigned __int32 __pyx_uintptr_t; + #endif + #endif +#else + #include <stdint.h> + typedef uintptr_t __pyx_uintptr_t; +#endif +#ifndef CYTHON_FALLTHROUGH + #if defined(__cplusplus) + /* for clang __has_cpp_attribute(fallthrough) is true even before C++17 + * but leads to warnings with -pedantic, since it is a C++17 feature */ + #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L) + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #elif __has_cpp_attribute(gnu::fallthrough) + #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] + #endif + #endif + #endif + #ifndef CYTHON_FALLTHROUGH + #if __has_attribute(fallthrough) + #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) + #else + #define CYTHON_FALLTHROUGH + #endif + #endif + #if defined(__clang__) && defined(__apple_build_version__) + #if __apple_build_version__ < 7000000 + #undef CYTHON_FALLTHROUGH + #define CYTHON_FALLTHROUGH + #endif + #endif +#endif +#ifdef __cplusplus + template <typename T> + struct __PYX_IS_UNSIGNED_IMPL {static const bool value = T(0) < T(-1);}; + #define __PYX_IS_UNSIGNED(type) (__PYX_IS_UNSIGNED_IMPL<type>::value) +#else + #define __PYX_IS_UNSIGNED(type) (((type)-1) > 0) +#endif +#if CYTHON_COMPILING_IN_PYPY == 1 + #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x030A0000) +#else + #define __PYX_NEED_TP_PRINT_SLOT (PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000) +#endif +#define __PYX_REINTERPRET_FUNCION(func_pointer, other_pointer) ((func_pointer)(void(*)(void))(other_pointer)) + +#ifndef CYTHON_INLINE + #if defined(__clang__) + #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) + #elif defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif + +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_DefaultClassType PyClass_Type + #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_DefaultClassType PyType_Type +#if CYTHON_COMPILING_IN_LIMITED_API + static CYTHON_INLINE PyObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f, + PyObject *code, PyObject *c, PyObject* n, PyObject *v, + PyObject *fv, PyObject *cell, PyObject* fn, + PyObject *name, int fline, PyObject *lnos) { + PyObject *exception_table = NULL; + PyObject *types_module=NULL, *code_type=NULL, *result=NULL; + #if __PYX_LIMITED_VERSION_HEX < 0x030B0000 + PyObject *version_info; + PyObject *py_minor_version = NULL; + #endif + long minor_version = 0; + PyObject *type, *value, *traceback; + PyErr_Fetch(&type, &value, &traceback); + #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000 + minor_version = 11; + #else + if (!(version_info = PySys_GetObject("version_info"))) goto end; + if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end; + minor_version = PyLong_AsLong(py_minor_version); + Py_DECREF(py_minor_version); + if (minor_version == -1 && PyErr_Occurred()) goto end; + #endif + if (!(types_module = PyImport_ImportModule("types"))) goto end; + if (!(code_type = PyObject_GetAttrString(types_module, "CodeType"))) goto end; + if (minor_version <= 7) { + (void)p; + result = PyObject_CallFunction(code_type, "iiiiiOOOOOOiOO", a, k, l, s, f, code, + c, n, v, fn, name, fline, lnos, fv, cell); + } else if (minor_version <= 10) { + result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOiOO", a,p, k, l, s, f, code, + c, n, v, fn, name, fline, lnos, fv, cell); + } else { + if (!(exception_table = PyBytes_FromStringAndSize(NULL, 0))) goto end; + result = PyObject_CallFunction(code_type, "iiiiiiOOOOOOOiOO", a,p, k, l, s, f, code, + c, n, v, fn, name, name, fline, lnos, exception_table, fv, cell); + } + end: + Py_XDECREF(code_type); + Py_XDECREF(exception_table); + Py_XDECREF(types_module); + if (type) { + PyErr_Restore(type, value, traceback); + } + return result; + } + #ifndef CO_OPTIMIZED + #define CO_OPTIMIZED 0x0001 + #endif + #ifndef CO_NEWLOCALS + #define CO_NEWLOCALS 0x0002 + #endif + #ifndef CO_VARARGS + #define CO_VARARGS 0x0004 + #endif + #ifndef CO_VARKEYWORDS + #define CO_VARKEYWORDS 0x0008 + #endif + #ifndef CO_ASYNC_GENERATOR + #define CO_ASYNC_GENERATOR 0x0200 + #endif + #ifndef CO_GENERATOR + #define CO_GENERATOR 0x0020 + #endif + #ifndef CO_COROUTINE + #define CO_COROUTINE 0x0080 + #endif +#elif PY_VERSION_HEX >= 0x030B0000 + static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int p, int k, int l, int s, int f, + PyObject *code, PyObject *c, PyObject* n, PyObject *v, + PyObject *fv, PyObject *cell, PyObject* fn, + PyObject *name, int fline, PyObject *lnos) { + PyCodeObject *result; + PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0); + if (!empty_bytes) return NULL; + result = + #if PY_VERSION_HEX >= 0x030C0000 + PyUnstable_Code_NewWithPosOnlyArgs + #else + PyCode_NewWithPosOnlyArgs + #endif + (a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, name, fline, lnos, empty_bytes); + Py_DECREF(empty_bytes); + return result; + } +#elif PY_VERSION_HEX >= 0x030800B2 && !CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_NewWithPosOnlyArgs(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) +#else + #define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) +#endif +#endif +#if PY_VERSION_HEX >= 0x030900A4 || defined(Py_IS_TYPE) + #define __Pyx_IS_TYPE(ob, type) Py_IS_TYPE(ob, type) +#else + #define __Pyx_IS_TYPE(ob, type) (((const PyObject*)ob)->ob_type == (type)) +#endif +#if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_Is) + #define __Pyx_Py_Is(x, y) Py_Is(x, y) +#else + #define __Pyx_Py_Is(x, y) ((x) == (y)) +#endif +#if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsNone) + #define __Pyx_Py_IsNone(ob) Py_IsNone(ob) +#else + #define __Pyx_Py_IsNone(ob) __Pyx_Py_Is((ob), Py_None) +#endif +#if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsTrue) + #define __Pyx_Py_IsTrue(ob) Py_IsTrue(ob) +#else + #define __Pyx_Py_IsTrue(ob) __Pyx_Py_Is((ob), Py_True) +#endif +#if PY_VERSION_HEX >= 0x030A00B1 || defined(Py_IsFalse) + #define __Pyx_Py_IsFalse(ob) Py_IsFalse(ob) +#else + #define __Pyx_Py_IsFalse(ob) __Pyx_Py_Is((ob), Py_False) +#endif +#define __Pyx_NoneAsNull(obj) (__Pyx_Py_IsNone(obj) ? NULL : (obj)) +#if PY_VERSION_HEX >= 0x030900F0 && !CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyObject_GC_IsFinalized(o) PyObject_GC_IsFinalized(o) +#else + #define __Pyx_PyObject_GC_IsFinalized(o) _PyGC_FINALIZED(o) +#endif +#ifndef CO_COROUTINE + #define CO_COROUTINE 0x80 +#endif +#ifndef CO_ASYNC_GENERATOR + #define CO_ASYNC_GENERATOR 0x200 +#endif +#ifndef Py_TPFLAGS_CHECKTYPES + #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#ifndef Py_TPFLAGS_HAVE_FINALIZE + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#ifndef Py_TPFLAGS_SEQUENCE + #define Py_TPFLAGS_SEQUENCE 0 +#endif +#ifndef Py_TPFLAGS_MAPPING + #define Py_TPFLAGS_MAPPING 0 +#endif +#ifndef METH_STACKLESS + #define METH_STACKLESS 0 +#endif +#if PY_VERSION_HEX <= 0x030700A3 || !defined(METH_FASTCALL) + #ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + #endif + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject *const *args, Py_ssize_t nargs); + typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args, + Py_ssize_t nargs, PyObject *kwnames); +#else + #if PY_VERSION_HEX >= 0x030d00A4 + # define __Pyx_PyCFunctionFast PyCFunctionFast + # define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords + #else + # define __Pyx_PyCFunctionFast _PyCFunctionFast + # define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords + #endif +#endif +#if CYTHON_METH_FASTCALL + #define __Pyx_METH_FASTCALL METH_FASTCALL + #define __Pyx_PyCFunction_FastCall __Pyx_PyCFunctionFast + #define __Pyx_PyCFunction_FastCallWithKeywords __Pyx_PyCFunctionFastWithKeywords +#else + #define __Pyx_METH_FASTCALL METH_VARARGS + #define __Pyx_PyCFunction_FastCall PyCFunction + #define __Pyx_PyCFunction_FastCallWithKeywords PyCFunctionWithKeywords +#endif +#if CYTHON_VECTORCALL + #define __pyx_vectorcallfunc vectorcallfunc + #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET PY_VECTORCALL_ARGUMENTS_OFFSET + #define __Pyx_PyVectorcall_NARGS(n) PyVectorcall_NARGS((size_t)(n)) +#elif CYTHON_BACKPORT_VECTORCALL + typedef PyObject *(*__pyx_vectorcallfunc)(PyObject *callable, PyObject *const *args, + size_t nargsf, PyObject *kwnames); + #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET ((size_t)1 << (8 * sizeof(size_t) - 1)) + #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(((size_t)(n)) & ~__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET)) +#else + #define __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET 0 + #define __Pyx_PyVectorcall_NARGS(n) ((Py_ssize_t)(n)) +#endif +#if PY_MAJOR_VERSION >= 0x030900B1 +#define __Pyx_PyCFunction_CheckExact(func) PyCFunction_CheckExact(func) +#else +#define __Pyx_PyCFunction_CheckExact(func) PyCFunction_Check(func) +#endif +#define __Pyx_CyOrPyCFunction_Check(func) PyCFunction_Check(func) +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) (((PyCFunctionObject*)(func))->m_ml->ml_meth) +#elif !CYTHON_COMPILING_IN_LIMITED_API +#define __Pyx_CyOrPyCFunction_GET_FUNCTION(func) PyCFunction_GET_FUNCTION(func) +#endif +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_CyOrPyCFunction_GET_FLAGS(func) (((PyCFunctionObject*)(func))->m_ml->ml_flags) +static CYTHON_INLINE PyObject* __Pyx_CyOrPyCFunction_GET_SELF(PyObject *func) { + return (__Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_STATIC) ? NULL : ((PyCFunctionObject*)func)->m_self; +} +#endif +static CYTHON_INLINE int __Pyx__IsSameCFunction(PyObject *func, void *cfunc) { +#if CYTHON_COMPILING_IN_LIMITED_API + return PyCFunction_Check(func) && PyCFunction_GetFunction(func) == (PyCFunction) cfunc; +#else + return PyCFunction_Check(func) && PyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc; +#endif +} +#define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCFunction(func, cfunc) +#if __PYX_LIMITED_VERSION_HEX < 0x030900B1 + #define __Pyx_PyType_FromModuleAndSpec(m, s, b) ((void)m, PyType_FromSpecWithBases(s, b)) + typedef PyObject *(*__Pyx_PyCMethod)(PyObject *, PyTypeObject *, PyObject *const *, size_t, PyObject *); +#else + #define __Pyx_PyType_FromModuleAndSpec(m, s, b) PyType_FromModuleAndSpec(m, s, b) + #define __Pyx_PyCMethod PyCMethod +#endif +#ifndef METH_METHOD + #define METH_METHOD 0x200 +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) + #define PyObject_Malloc(s) PyMem_Malloc(s) + #define PyObject_Free(p) PyMem_Free(p) + #define PyObject_Realloc(p) PyMem_Realloc(p) +#endif +#if CYTHON_COMPILING_IN_LIMITED_API + #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) +#else + #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) +#endif +#if CYTHON_COMPILING_IN_LIMITED_API + #define __Pyx_PyThreadState_Current PyThreadState_Get() +#elif !CYTHON_FAST_THREAD_STATE + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#elif PY_VERSION_HEX >= 0x030d00A1 + #define __Pyx_PyThreadState_Current PyThreadState_GetUnchecked() +#elif PY_VERSION_HEX >= 0x03060000 + #define __Pyx_PyThreadState_Current _PyThreadState_UncheckedGet() +#elif PY_VERSION_HEX >= 0x03000000 + #define __Pyx_PyThreadState_Current PyThreadState_GET() +#else + #define __Pyx_PyThreadState_Current _PyThreadState_Current +#endif +#if CYTHON_COMPILING_IN_LIMITED_API +static CYTHON_INLINE void *__Pyx_PyModule_GetState(PyObject *op) +{ + void *result; + result = PyModule_GetState(op); + if (!result) + Py_FatalError("Couldn't find the module state"); + return result; +} +#endif +#define __Pyx_PyObject_GetSlot(obj, name, func_ctype) __Pyx_PyType_GetSlot(Py_TYPE(obj), name, func_ctype) +#if CYTHON_COMPILING_IN_LIMITED_API + #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((func_ctype) PyType_GetSlot((type), Py_##name)) +#else + #define __Pyx_PyType_GetSlot(type, name, func_ctype) ((type)->name) +#endif +#if PY_VERSION_HEX < 0x030700A2 && !defined(PyThread_tss_create) && !defined(Py_tss_NEEDS_INIT) +#include "pythread.h" +#define Py_tss_NEEDS_INIT 0 +typedef int Py_tss_t; +static CYTHON_INLINE int PyThread_tss_create(Py_tss_t *key) { + *key = PyThread_create_key(); + return 0; +} +static CYTHON_INLINE Py_tss_t * PyThread_tss_alloc(void) { + Py_tss_t *key = (Py_tss_t *)PyObject_Malloc(sizeof(Py_tss_t)); + *key = Py_tss_NEEDS_INIT; + return key; +} +static CYTHON_INLINE void PyThread_tss_free(Py_tss_t *key) { + PyObject_Free(key); +} +static CYTHON_INLINE int PyThread_tss_is_created(Py_tss_t *key) { + return *key != Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE void PyThread_tss_delete(Py_tss_t *key) { + PyThread_delete_key(*key); + *key = Py_tss_NEEDS_INIT; +} +static CYTHON_INLINE int PyThread_tss_set(Py_tss_t *key, void *value) { + return PyThread_set_key_value(*key, value); +} +static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { + return PyThread_get_key_value(*key); +} +#endif +#if PY_MAJOR_VERSION < 3 + #if CYTHON_COMPILING_IN_PYPY + #if PYPY_VERSION_NUM < 0x07030600 + #if defined(__cplusplus) && __cplusplus >= 201402L + [[deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")]] + #elif defined(__GNUC__) || defined(__clang__) + __attribute__ ((__deprecated__("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6"))) + #elif defined(_MSC_VER) + __declspec(deprecated("`with nogil:` inside a nogil function will not release the GIL in PyPy2 < 7.3.6")) + #endif + static CYTHON_INLINE int PyGILState_Check(void) { + return 0; + } + #else // PYPY_VERSION_NUM < 0x07030600 + #endif // PYPY_VERSION_NUM < 0x07030600 + #else + static CYTHON_INLINE int PyGILState_Check(void) { + PyThreadState * tstate = _PyThreadState_Current; + return tstate && (tstate == PyGILState_GetThisThreadState()); + } + #endif +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030d0000 || defined(_PyDict_NewPresized) +#define __Pyx_PyDict_NewPresized(n) ((n <= 8) ? PyDict_New() : _PyDict_NewPresized(n)) +#else +#define __Pyx_PyDict_NewPresized(n) PyDict_New() +#endif +#if PY_MAJOR_VERSION >= 3 || CYTHON_FUTURE_DIVISION + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX > 0x030600B4 && PY_VERSION_HEX < 0x030d0000 && CYTHON_USE_UNICODE_INTERNALS +#define __Pyx_PyDict_GetItemStrWithError(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) +static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStr(PyObject *dict, PyObject *name) { + PyObject *res = __Pyx_PyDict_GetItemStrWithError(dict, name); + if (res == NULL) PyErr_Clear(); + return res; +} +#elif PY_MAJOR_VERSION >= 3 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07020000) +#define __Pyx_PyDict_GetItemStrWithError PyDict_GetItemWithError +#define __Pyx_PyDict_GetItemStr PyDict_GetItem +#else +static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict, PyObject *name) { +#if CYTHON_COMPILING_IN_PYPY + return PyDict_GetItem(dict, name); +#else + PyDictEntry *ep; + PyDictObject *mp = (PyDictObject*) dict; + long hash = ((PyStringObject *) name)->ob_shash; + assert(hash != -1); + ep = (mp->ma_lookup)(mp, name, hash); + if (ep == NULL) { + return NULL; + } + return ep->me_value; +#endif +} +#define __Pyx_PyDict_GetItemStr PyDict_GetItem +#endif +#if CYTHON_USE_TYPE_SLOTS + #define __Pyx_PyType_GetFlags(tp) (((PyTypeObject *)tp)->tp_flags) + #define __Pyx_PyType_HasFeature(type, feature) ((__Pyx_PyType_GetFlags(type) & (feature)) != 0) + #define __Pyx_PyObject_GetIterNextFunc(obj) (Py_TYPE(obj)->tp_iternext) +#else + #define __Pyx_PyType_GetFlags(tp) (PyType_GetFlags((PyTypeObject *)tp)) + #define __Pyx_PyType_HasFeature(type, feature) PyType_HasFeature(type, feature) + #define __Pyx_PyObject_GetIterNextFunc(obj) PyIter_Next +#endif +#if CYTHON_COMPILING_IN_LIMITED_API + #define __Pyx_SetItemOnTypeDict(tp, k, v) PyObject_GenericSetAttr((PyObject*)tp, k, v) +#else + #define __Pyx_SetItemOnTypeDict(tp, k, v) PyDict_SetItem(tp->tp_dict, k, v) +#endif +#if CYTHON_USE_TYPE_SPECS && PY_VERSION_HEX >= 0x03080000 +#define __Pyx_PyHeapTypeObject_GC_Del(obj) {\ + PyTypeObject *type = Py_TYPE((PyObject*)obj);\ + assert(__Pyx_PyType_HasFeature(type, Py_TPFLAGS_HEAPTYPE));\ + PyObject_GC_Del(obj);\ + Py_DECREF(type);\ +} +#else +#define __Pyx_PyHeapTypeObject_GC_Del(obj) PyObject_GC_Del(obj) +#endif +#if CYTHON_COMPILING_IN_LIMITED_API + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GetLength(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_ReadChar(u, i) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((void)u, 1114111U) + #define __Pyx_PyUnicode_KIND(u) ((void)u, (0)) + #define __Pyx_PyUnicode_DATA(u) ((void*)u) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)k, PyUnicode_ReadChar((PyObject*)(d), i)) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GetLength(u)) +#elif PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #if PY_VERSION_HEX >= 0x030C0000 + #define __Pyx_PyUnicode_READY(op) (0) + #else + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #endif + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) + #define __Pyx_PyUnicode_KIND(u) ((int)PyUnicode_KIND(u)) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, (Py_UCS4) ch) + #if PY_VERSION_HEX >= 0x030C0000 + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) + #else + #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x03090000 + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : ((PyCompactUnicodeObject *)(u))->wstr_length)) + #else + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) + #endif + #endif +#else + #define CYTHON_PEP393_ENABLED 0 + #define PyUnicode_1BYTE_KIND 1 + #define PyUnicode_2BYTE_KIND 2 + #define PyUnicode_4BYTE_KIND 4 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535U : 1114111U) + #define __Pyx_PyUnicode_KIND(u) ((int)sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = (Py_UNICODE) ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#if CYTHON_COMPILING_IN_PYPY + #if !defined(PyUnicode_DecodeUnicodeEscape) + #define PyUnicode_DecodeUnicodeEscape(s, size, errors) PyUnicode_Decode(s, size, "unicode_escape", errors) + #endif + #if !defined(PyUnicode_Contains) || (PY_MAJOR_VERSION == 2 && PYPY_VERSION_NUM < 0x07030500) + #undef PyUnicode_Contains + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) + #endif + #if !defined(PyByteArray_Check) + #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) + #endif + #if !defined(PyObject_Format) + #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) + #endif +#endif +#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)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None || (PyUnicode_Check(b) && !PyUnicode_CheckExact(b)))) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) + #define PyObject_ASCII(o) PyObject_Repr(o) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact +#ifndef PyObject_Unicode + #define PyObject_Unicode PyObject_Str +#endif +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#if CYTHON_COMPILING_IN_CPYTHON + #define __Pyx_PySequence_ListKeepNew(obj)\ + (likely(PyList_CheckExact(obj) && Py_REFCNT(obj) == 1) ? __Pyx_NewRef(obj) : PySequence_List(obj)) +#else + #define __Pyx_PySequence_ListKeepNew(obj) PySequence_List(obj) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) __Pyx_IS_TYPE(obj, &PySet_Type) +#endif +#if PY_VERSION_HEX >= 0x030900A4 + #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) +#else + #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) +#endif +#if CYTHON_ASSUME_SAFE_MACROS + #define __Pyx_PySequence_ITEM(o, i) PySequence_ITEM(o, i) + #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) + #define __Pyx_PyTuple_SET_ITEM(o, i, v) (PyTuple_SET_ITEM(o, i, v), (0)) + #define __Pyx_PyList_SET_ITEM(o, i, v) (PyList_SET_ITEM(o, i, v), (0)) + #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_GET_SIZE(o) + #define __Pyx_PyList_GET_SIZE(o) PyList_GET_SIZE(o) + #define __Pyx_PySet_GET_SIZE(o) PySet_GET_SIZE(o) + #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_GET_SIZE(o) + #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_GET_SIZE(o) +#else + #define __Pyx_PySequence_ITEM(o, i) PySequence_GetItem(o, i) + #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) + #define __Pyx_PyTuple_SET_ITEM(o, i, v) PyTuple_SetItem(o, i, v) + #define __Pyx_PyList_SET_ITEM(o, i, v) PyList_SetItem(o, i, v) + #define __Pyx_PyTuple_GET_SIZE(o) PyTuple_Size(o) + #define __Pyx_PyList_GET_SIZE(o) PyList_Size(o) + #define __Pyx_PySet_GET_SIZE(o) PySet_Size(o) + #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o) + #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o) +#endif +#if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 + #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name) +#else + static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) { + PyObject *module = PyImport_AddModule(name); + Py_XINCREF(module); + return module; + } +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define __Pyx_Py3Int_Check(op) PyLong_Check(op) + #define __Pyx_Py3Int_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#else + #define __Pyx_Py3Int_Check(op) (PyLong_Check(op) || PyInt_Check(op)) + #define __Pyx_Py3Int_CheckExact(op) (PyLong_CheckExact(op) || PyInt_CheckExact(op)) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t +#endif +#if CYTHON_USE_ASYNC_SLOTS + #if PY_VERSION_HEX >= 0x030500B1 + #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods + #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) + #else + #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) + #endif +#else + #define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef __Pyx_PyAsyncMethodsStruct + typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; + } __Pyx_PyAsyncMethodsStruct; +#endif + +#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS) + #if !defined(_USE_MATH_DEFINES) + #define _USE_MATH_DEFINES + #endif +#endif +#include <math.h> +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) +#define __Pyx_truncl trunc +#else +#define __Pyx_truncl truncl +#endif + +#define __PYX_MARK_ERR_POS(f_index, lineno) \ + { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } +#define __PYX_ERR(f_index, lineno, Ln_error) \ + { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } + +#ifdef CYTHON_EXTERN_C + #undef __PYX_EXTERN_C + #define __PYX_EXTERN_C CYTHON_EXTERN_C +#elif defined(__PYX_EXTERN_C) + #ifdef _MSC_VER + #pragma message ("Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead.") + #else + #warning Please do not define the '__PYX_EXTERN_C' macro externally. Use 'CYTHON_EXTERN_C' instead. + #endif +#else + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__pysam__libchtslib +#define __PYX_HAVE_API__pysam__libchtslib +/* Early includes */ +#include <stdint.h> +#include <string.h> +#include <stdlib.h> +#include <stdio.h> +#include <sys/types.h> +#include "stdarg.h" +#include "htslib/kstring.h" +#include "htslib_util.h" +#include "htslib/hfile.h" +#include "htslib/bgzf.h" +#include "htslib/hts.h" +#include "htslib/sam.h" +#include "htslib/faidx.h" +#include "htslib/tbx.h" +#include "htslib/vcf.h" +#include "htslib/vcfutils.h" +#include "htslib/cram.h" +#include <unistd.h> +#include <errno.h> +#include <stddef.h> +#include "pythread.h" + + #if CYTHON_COMPILING_IN_PYPY + #ifdef _MSC_VER + #pragma message ("This module uses CPython specific internals of 'array.array', which are not available in PyPy.") + #else + #warning This module uses CPython specific internals of 'array.array', which are not available in PyPy. + #endif + #endif + +#ifdef _OPENMP +#include <omp.h> +#endif /* _OPENMP */ + +#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8) +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) { + return (size_t) i < (size_t) limit; +} +#if defined (__cplusplus) && __cplusplus >= 201103L + #include <cstdlib> + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) + #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s); +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char*); +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s)) +#define __Pyx_PyObject_AsWritableString(s) ((char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*)(__pyx_uintptr_t) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +#define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o) +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b); +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); +#define __Pyx_PySequence_Tuple(obj)\ + (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj)) +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); +#if CYTHON_ASSUME_SAFE_MACROS +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) +#else +#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) +#endif +#if CYTHON_USE_PYLONG_INTERNALS + #if PY_VERSION_HEX >= 0x030C00A7 + #ifndef _PyLong_SIGN_MASK + #define _PyLong_SIGN_MASK 3 + #endif + #ifndef _PyLong_NON_SIZE_BITS + #define _PyLong_NON_SIZE_BITS 3 + #endif + #define __Pyx_PyLong_Sign(x) (((PyLongObject*)x)->long_value.lv_tag & _PyLong_SIGN_MASK) + #define __Pyx_PyLong_IsNeg(x) ((__Pyx_PyLong_Sign(x) & 2) != 0) + #define __Pyx_PyLong_IsNonNeg(x) (!__Pyx_PyLong_IsNeg(x)) + #define __Pyx_PyLong_IsZero(x) (__Pyx_PyLong_Sign(x) & 1) + #define __Pyx_PyLong_IsPos(x) (__Pyx_PyLong_Sign(x) == 0) + #define __Pyx_PyLong_CompactValueUnsigned(x) (__Pyx_PyLong_Digits(x)[0]) + #define __Pyx_PyLong_DigitCount(x) ((Py_ssize_t) (((PyLongObject*)x)->long_value.lv_tag >> _PyLong_NON_SIZE_BITS)) + #define __Pyx_PyLong_SignedDigitCount(x)\ + ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * __Pyx_PyLong_DigitCount(x)) + #if defined(PyUnstable_Long_IsCompact) && defined(PyUnstable_Long_CompactValue) + #define __Pyx_PyLong_IsCompact(x) PyUnstable_Long_IsCompact((PyLongObject*) x) + #define __Pyx_PyLong_CompactValue(x) PyUnstable_Long_CompactValue((PyLongObject*) x) + #else + #define __Pyx_PyLong_IsCompact(x) (((PyLongObject*)x)->long_value.lv_tag < (2 << _PyLong_NON_SIZE_BITS)) + #define __Pyx_PyLong_CompactValue(x) ((1 - (Py_ssize_t) __Pyx_PyLong_Sign(x)) * (Py_ssize_t) __Pyx_PyLong_Digits(x)[0]) + #endif + typedef Py_ssize_t __Pyx_compact_pylong; + typedef size_t __Pyx_compact_upylong; + #else + #define __Pyx_PyLong_IsNeg(x) (Py_SIZE(x) < 0) + #define __Pyx_PyLong_IsNonNeg(x) (Py_SIZE(x) >= 0) + #define __Pyx_PyLong_IsZero(x) (Py_SIZE(x) == 0) + #define __Pyx_PyLong_IsPos(x) (Py_SIZE(x) > 0) + #define __Pyx_PyLong_CompactValueUnsigned(x) ((Py_SIZE(x) == 0) ? 0 : __Pyx_PyLong_Digits(x)[0]) + #define __Pyx_PyLong_DigitCount(x) __Pyx_sst_abs(Py_SIZE(x)) + #define __Pyx_PyLong_SignedDigitCount(x) Py_SIZE(x) + #define __Pyx_PyLong_IsCompact(x) (Py_SIZE(x) == 0 || Py_SIZE(x) == 1 || Py_SIZE(x) == -1) + #define __Pyx_PyLong_CompactValue(x)\ + ((Py_SIZE(x) == 0) ? (sdigit) 0 : ((Py_SIZE(x) < 0) ? -(sdigit)__Pyx_PyLong_Digits(x)[0] : (sdigit)__Pyx_PyLong_Digits(x)[0])) + typedef sdigit __Pyx_compact_pylong; + typedef digit __Pyx_compact_upylong; + #endif + #if PY_VERSION_HEX >= 0x030C00A5 + #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->long_value.ob_digit) + #else + #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->ob_digit) + #endif +#endif +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +#include <string.h> +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = (char) c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +#include <string.h> +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ +static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; } + +#if !CYTHON_USE_MODULE_STATE +static PyObject *__pyx_m = NULL; +#endif +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm = __FILE__; +static const char *__pyx_filename; + +/* #### Code section: filename_table ### */ + +static const char *__pyx_f[] = { + "pysam/libchtslib.pyx", + "<stringsource>", + "contextvars.pxd", + "array.pxd", + "pysam/libchtslib.pxd", + "type.pxd", + "bool.pxd", + "complex.pxd", +}; +/* #### Code section: utility_code_proto_before_types ### */ +/* ForceInitThreads.proto */ +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +/* NoFastGil.proto */ +#define __Pyx_PyGILState_Ensure PyGILState_Ensure +#define __Pyx_PyGILState_Release PyGILState_Release +#define __Pyx_FastGIL_Remember() +#define __Pyx_FastGIL_Forget() +#define __Pyx_FastGilFuncInit() + +/* #### Code section: numeric_typedefs ### */ +/* #### Code section: complex_type_declarations ### */ +/* #### Code section: type_declarations ### */ + +/*--- Type declarations ---*/ +#ifndef _ARRAYARRAY_H +struct arrayobject; +typedef struct arrayobject arrayobject; +#endif +struct __pyx_obj_5pysam_10libchtslib_HTSFile; +struct __pyx_obj_5pysam_10libchtslib_HFile; +struct __pyx_opt_args_7cpython_11contextvars_get_value; +struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default; + +/* "cpython/contextvars.pxd":112 + * + * + * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<< + * """Return a new reference to the value of the context variable, + * or the default value of the context variable, + */ +struct __pyx_opt_args_7cpython_11contextvars_get_value { + int __pyx_n; + PyObject *default_value; +}; + +/* "cpython/contextvars.pxd":129 + * + * + * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<< + * """Return a new reference to the value of the context variable, + * or the provided default value if no such value was found. + */ +struct __pyx_opt_args_7cpython_11contextvars_get_value_no_default { + int __pyx_n; + PyObject *default_value; +}; +struct __pyx_opt_args_5pysam_9libcutils_parse_region; +struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array; +struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring; +struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring; +struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str; +struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes; +struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len; +struct __pyx_opt_args_5pysam_9libcutils_force_str; +struct __pyx_opt_args_5pysam_9libcutils_force_bytes; +struct __pyx_opt_args_5pysam_9libcutils_decode_bytes; + +/* "pysam/libcutils.pxd":8 + * from cpython cimport array as c_array + * + * cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*) # <<<<<<<<<<<<<< + * + * cdef int libc_whence_from_io(int whence) + */ +struct __pyx_opt_args_5pysam_9libcutils_parse_region { + int __pyx_n; + PyObject *contig; + PyObject *start; + PyObject *stop; + PyObject *region; + PyObject *reference; + PyObject *end; +}; + +/* "pysam/libcutils.pxd":15 + * # Utility functions for quality string conversions + * + * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) # <<<<<<<<<<<<<< + * cpdef array_to_qualitystring(c_array.array arr, int offset=*) + * cpdef qualities_to_qualitystring(qualities, int offset=*) + */ +struct __pyx_opt_args_5pysam_9libcutils_qualitystring_to_array { + int __pyx_n; + int offset; +}; + +/* "pysam/libcutils.pxd":16 + * + * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) + * cpdef array_to_qualitystring(c_array.array arr, int offset=*) # <<<<<<<<<<<<<< + * cpdef qualities_to_qualitystring(qualities, int offset=*) + * + */ +struct __pyx_opt_args_5pysam_9libcutils_array_to_qualitystring { + int __pyx_n; + int offset; +}; + +/* "pysam/libcutils.pxd":17 + * cpdef c_array.array qualitystring_to_array(input_str, int offset=*) + * cpdef array_to_qualitystring(c_array.array arr, int offset=*) + * cpdef qualities_to_qualitystring(qualities, int offset=*) # <<<<<<<<<<<<<< + * + * ######################################################################## + */ +struct __pyx_opt_args_5pysam_9libcutils_qualities_to_qualitystring { + int __pyx_n; + int offset; +}; + +/* "pysam/libcutils.pxd":29 + * ## Python 3 compatibility functions + * ######################################################################## + * cdef charptr_to_str(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<< + * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) + * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) + */ +struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str { + int __pyx_n; + PyObject *encoding; + PyObject *errors; +}; + +/* "pysam/libcutils.pxd":30 + * ######################################################################## + * cdef charptr_to_str(const char *s, encoding=*, errors=*) + * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) # <<<<<<<<<<<<<< + * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) + * cdef force_str(object s, encoding=*, errors=*) + */ +struct __pyx_opt_args_5pysam_9libcutils_charptr_to_bytes { + int __pyx_n; + PyObject *encoding; + PyObject *errors; +}; + +/* "pysam/libcutils.pxd":31 + * cdef charptr_to_str(const char *s, encoding=*, errors=*) + * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) + * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) # <<<<<<<<<<<<<< + * cdef force_str(object s, encoding=*, errors=*) + * cdef bytes force_bytes(object s, encoding=*, errors=*) + */ +struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len { + int __pyx_n; + PyObject *encoding; + PyObject *errors; +}; + +/* "pysam/libcutils.pxd":32 + * cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*) + * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) + * cdef force_str(object s, encoding=*, errors=*) # <<<<<<<<<<<<<< + * cdef bytes force_bytes(object s, encoding=*, errors=*) + * cdef decode_bytes(bytes s, encoding=*, errors=*) + */ +struct __pyx_opt_args_5pysam_9libcutils_force_str { + int __pyx_n; + PyObject *encoding; + PyObject *errors; +}; + +/* "pysam/libcutils.pxd":33 + * cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*) + * cdef force_str(object s, encoding=*, errors=*) + * cdef bytes force_bytes(object s, encoding=*, errors=*) # <<<<<<<<<<<<<< + * cdef decode_bytes(bytes s, encoding=*, errors=*) + * cdef bytes encode_filename(object filename) + */ +struct __pyx_opt_args_5pysam_9libcutils_force_bytes { + int __pyx_n; + PyObject *encoding; + PyObject *errors; +}; + +/* "pysam/libcutils.pxd":34 + * cdef force_str(object s, encoding=*, errors=*) + * cdef bytes force_bytes(object s, encoding=*, errors=*) + * cdef decode_bytes(bytes s, encoding=*, errors=*) # <<<<<<<<<<<<<< + * cdef bytes encode_filename(object filename) + * cdef from_string_and_size(const char *s, size_t length) + */ +struct __pyx_opt_args_5pysam_9libcutils_decode_bytes { + int __pyx_n; + PyObject *encoding; + PyObject *errors; +}; +struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open; + +/* "pysam/libchtslib.pyx":81 + * return self.fp == NULL + * + * cdef _open(self, name, mode, closefd=True): # <<<<<<<<<<<<<< + * self.name = name + * self.mode = mode + */ +struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open { + int __pyx_n; + PyObject *closefd; +}; + +/* "pysam/libchtslib.pxd":2706 + * + * + * cdef class HTSFile(object): # <<<<<<<<<<<<<< + * cdef htsFile *htsfile # pointer to htsFile structure + * cdef int64_t start_offset # BGZF offset of first record + */ +struct __pyx_obj_5pysam_10libchtslib_HTSFile { + PyObject_HEAD + struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtab; + htsFile *htsfile; + int64_t start_offset; + PyObject *filename; + PyObject *mode; + PyObject *threads; + PyObject *index_filename; + int is_stream; + int is_remote; + int duplicate_filehandle; +}; + + +/* "pysam/libchtslib.pyx":67 + * ######################################################################## + * + * cdef class HFile(object): # <<<<<<<<<<<<<< + * cdef hFILE *fp + * cdef readonly object name, mode + */ +struct __pyx_obj_5pysam_10libchtslib_HFile { + PyObject_HEAD + struct __pyx_vtabstruct_5pysam_10libchtslib_HFile *__pyx_vtab; + hFILE *fp; + PyObject *name; + PyObject *mode; +}; + + + +/* "pysam/libchtslib.pyx":321 + * ######################################################################## + * + * cdef class HTSFile(object): # <<<<<<<<<<<<<< + * """ + * Base class for HTS file types + */ + +struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile { + htsFile *(*_open_htsfile)(struct __pyx_obj_5pysam_10libchtslib_HTSFile *); +}; +static struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile *__pyx_vtabptr_5pysam_10libchtslib_HTSFile; + + +/* "pysam/libchtslib.pyx":67 + * ######################################################################## + * + * cdef class HFile(object): # <<<<<<<<<<<<<< + * cdef hFILE *fp + * cdef readonly object name, mode + */ + +struct __pyx_vtabstruct_5pysam_10libchtslib_HFile { + PyObject *(*_open)(struct __pyx_obj_5pysam_10libchtslib_HFile *, PyObject *, PyObject *, struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open *__pyx_optional_args); +}; +static struct __pyx_vtabstruct_5pysam_10libchtslib_HFile *__pyx_vtabptr_5pysam_10libchtslib_HFile; +/* #### Code section: utility_code_proto ### */ + +/* --- Runtime support code (head) --- */ +/* Refnanny.proto */ +#ifndef CYTHON_REFNANNY + #define CYTHON_REFNANNY 0 +#endif +#if CYTHON_REFNANNY + typedef struct { + void (*INCREF)(void*, PyObject*, Py_ssize_t); + void (*DECREF)(void*, PyObject*, Py_ssize_t); + void (*GOTREF)(void*, PyObject*, Py_ssize_t); + void (*GIVEREF)(void*, PyObject*, Py_ssize_t); + void* (*SetupContext)(const char*, Py_ssize_t, const char*); + void (*FinishContext)(void**); + } __Pyx_RefNannyAPIStruct; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); + #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; +#ifdef WITH_THREAD + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__));\ + } + #define __Pyx_RefNannyFinishContextNogil() {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __Pyx_RefNannyFinishContext();\ + PyGILState_Release(__pyx_gilstate_save);\ + } +#else + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), (__LINE__), (__FILE__)) + #define __Pyx_RefNannyFinishContextNogil() __Pyx_RefNannyFinishContext() +#endif + #define __Pyx_RefNannyFinishContextNogil() {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __Pyx_RefNannyFinishContext();\ + PyGILState_Release(__pyx_gilstate_save);\ + } + #define __Pyx_RefNannyFinishContext()\ + __Pyx_RefNanny->FinishContext(&__pyx_refnanny) + #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) + #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) + #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) + #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), (__LINE__)) + #define __Pyx_XINCREF(r) do { if((r) == NULL); else {__Pyx_INCREF(r); }} while(0) + #define __Pyx_XDECREF(r) do { if((r) == NULL); else {__Pyx_DECREF(r); }} while(0) + #define __Pyx_XGOTREF(r) do { if((r) == NULL); else {__Pyx_GOTREF(r); }} while(0) + #define __Pyx_XGIVEREF(r) do { if((r) == NULL); else {__Pyx_GIVEREF(r);}} while(0) +#else + #define __Pyx_RefNannyDeclarations + #define __Pyx_RefNannySetupContext(name, acquire_gil) + #define __Pyx_RefNannyFinishContextNogil() + #define __Pyx_RefNannyFinishContext() + #define __Pyx_INCREF(r) Py_INCREF(r) + #define __Pyx_DECREF(r) Py_DECREF(r) + #define __Pyx_GOTREF(r) + #define __Pyx_GIVEREF(r) + #define __Pyx_XINCREF(r) Py_XINCREF(r) + #define __Pyx_XDECREF(r) Py_XDECREF(r) + #define __Pyx_XGOTREF(r) + #define __Pyx_XGIVEREF(r) +#endif +#define __Pyx_Py_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; Py_XDECREF(tmp);\ + } while (0) +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ + } while (0) +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ + } while (0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) + +/* PyErrExceptionMatches.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); +#else +#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) +#endif + +/* PyThreadStateGet.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; +#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; +#if PY_VERSION_HEX >= 0x030C00A6 +#define __Pyx_PyErr_Occurred() (__pyx_tstate->current_exception != NULL) +#define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->current_exception ? (PyObject*) Py_TYPE(__pyx_tstate->current_exception) : (PyObject*) NULL) +#else +#define __Pyx_PyErr_Occurred() (__pyx_tstate->curexc_type != NULL) +#define __Pyx_PyErr_CurrentExceptionType() (__pyx_tstate->curexc_type) +#endif +#else +#define __Pyx_PyThreadState_declare +#define __Pyx_PyThreadState_assign +#define __Pyx_PyErr_Occurred() (PyErr_Occurred() != NULL) +#define __Pyx_PyErr_CurrentExceptionType() PyErr_Occurred() +#endif + +/* PyErrFetchRestore.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) +#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A6 +#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) +#else +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#endif +#else +#define __Pyx_PyErr_Clear() PyErr_Clear() +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) +#endif + +/* PyObjectGetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +/* PyObjectGetAttrStrNoError.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); + +/* GetBuiltinName.proto */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +/* TupleAndListFromArray.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n); +static CYTHON_INLINE PyObject* __Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n); +#endif + +/* IncludeStringH.proto */ +#include <string.h> + +/* BytesEquals.proto */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +/* UnicodeEquals.proto */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +/* fastcall.proto */ +#if CYTHON_AVOID_BORROWED_REFS + #define __Pyx_Arg_VARARGS(args, i) PySequence_GetItem(args, i) +#elif CYTHON_ASSUME_SAFE_MACROS + #define __Pyx_Arg_VARARGS(args, i) PyTuple_GET_ITEM(args, i) +#else + #define __Pyx_Arg_VARARGS(args, i) PyTuple_GetItem(args, i) +#endif +#if CYTHON_AVOID_BORROWED_REFS + #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg) + #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg) +#else + #define __Pyx_Arg_NewRef_VARARGS(arg) arg + #define __Pyx_Arg_XDECREF_VARARGS(arg) +#endif +#define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds) +#define __Pyx_KwValues_VARARGS(args, nargs) NULL +#define __Pyx_GetKwValue_VARARGS(kw, kwvalues, s) __Pyx_PyDict_GetItemStrWithError(kw, s) +#define __Pyx_KwargsAsDict_VARARGS(kw, kwvalues) PyDict_Copy(kw) +#if CYTHON_METH_FASTCALL + #define __Pyx_Arg_FASTCALL(args, i) args[i] + #define __Pyx_NumKwargs_FASTCALL(kwds) PyTuple_GET_SIZE(kwds) + #define __Pyx_KwValues_FASTCALL(args, nargs) ((args) + (nargs)) + static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s); +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000 + CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues); + #else + #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw) + #endif + #define __Pyx_Arg_NewRef_FASTCALL(arg) arg /* no-op, __Pyx_Arg_FASTCALL is direct and this needs + to have the same reference counting */ + #define __Pyx_Arg_XDECREF_FASTCALL(arg) +#else + #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS + #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS + #define __Pyx_KwValues_FASTCALL __Pyx_KwValues_VARARGS + #define __Pyx_GetKwValue_FASTCALL __Pyx_GetKwValue_VARARGS + #define __Pyx_KwargsAsDict_FASTCALL __Pyx_KwargsAsDict_VARARGS + #define __Pyx_Arg_NewRef_FASTCALL(arg) __Pyx_Arg_NewRef_VARARGS(arg) + #define __Pyx_Arg_XDECREF_FASTCALL(arg) __Pyx_Arg_XDECREF_VARARGS(arg) +#endif +#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS +#define __Pyx_ArgsSlice_VARARGS(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_VARARGS(args, start), stop - start) +#define __Pyx_ArgsSlice_FASTCALL(args, start, stop) __Pyx_PyTuple_FromArray(&__Pyx_Arg_FASTCALL(args, start), stop - start) +#else +#define __Pyx_ArgsSlice_VARARGS(args, start, stop) PyTuple_GetSlice(args, start, stop) +#define __Pyx_ArgsSlice_FASTCALL(args, start, stop) PyTuple_GetSlice(args, start, stop) +#endif + +/* Profile.proto */ +#ifndef CYTHON_PROFILE +#if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY + #define CYTHON_PROFILE 0 +#else + #define CYTHON_PROFILE 1 +#endif +#endif +#ifndef CYTHON_TRACE_NOGIL + #define CYTHON_TRACE_NOGIL 0 +#else + #if CYTHON_TRACE_NOGIL && !defined(CYTHON_TRACE) + #define CYTHON_TRACE 1 + #endif +#endif +#ifndef CYTHON_TRACE + #define CYTHON_TRACE 0 +#endif +#if CYTHON_TRACE + #undef CYTHON_PROFILE_REUSE_FRAME +#endif +#ifndef CYTHON_PROFILE_REUSE_FRAME + #define CYTHON_PROFILE_REUSE_FRAME 0 +#endif +#if CYTHON_PROFILE || CYTHON_TRACE + #include "compile.h" + #include "frameobject.h" + #include "traceback.h" +#if PY_VERSION_HEX >= 0x030b00a6 + #ifndef Py_BUILD_CORE + #define Py_BUILD_CORE 1 + #endif + #include "internal/pycore_frame.h" +#endif + #if CYTHON_PROFILE_REUSE_FRAME + #define CYTHON_FRAME_MODIFIER static + #define CYTHON_FRAME_DEL(frame) + #else + #define CYTHON_FRAME_MODIFIER + #define CYTHON_FRAME_DEL(frame) Py_CLEAR(frame) + #endif + #define __Pyx_TraceDeclarations\ + static PyCodeObject *__pyx_frame_code = NULL;\ + CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL;\ + int __Pyx_use_tracing = 0; + #define __Pyx_TraceFrameInit(codeobj)\ + if (codeobj) __pyx_frame_code = (PyCodeObject*) codeobj; +#if PY_VERSION_HEX >= 0x030b00a2 + #if PY_VERSION_HEX >= 0x030C00b1 + #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ + ((!(check_tracing) || !(tstate)->tracing) &&\ + (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) + #else + #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ + (unlikely((tstate)->cframe->use_tracing) &&\ + (!(check_tracing) || !(tstate)->tracing) &&\ + (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) + #endif + #define __Pyx_EnterTracing(tstate) PyThreadState_EnterTracing(tstate) + #define __Pyx_LeaveTracing(tstate) PyThreadState_LeaveTracing(tstate) +#elif PY_VERSION_HEX >= 0x030a00b1 + #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ + (unlikely((tstate)->cframe->use_tracing) &&\ + (!(check_tracing) || !(tstate)->tracing) &&\ + (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) + #define __Pyx_EnterTracing(tstate)\ + do { tstate->tracing++; tstate->cframe->use_tracing = 0; } while (0) + #define __Pyx_LeaveTracing(tstate)\ + do {\ + tstate->tracing--;\ + tstate->cframe->use_tracing = ((CYTHON_TRACE && tstate->c_tracefunc != NULL)\ + || tstate->c_profilefunc != NULL);\ + } while (0) +#else + #define __Pyx_IsTracing(tstate, check_tracing, check_funcs)\ + (unlikely((tstate)->use_tracing) &&\ + (!(check_tracing) || !(tstate)->tracing) &&\ + (!(check_funcs) || (tstate)->c_profilefunc || (CYTHON_TRACE && (tstate)->c_tracefunc))) + #define __Pyx_EnterTracing(tstate)\ + do { tstate->tracing++; tstate->use_tracing = 0; } while (0) + #define __Pyx_LeaveTracing(tstate)\ + do {\ + tstate->tracing--;\ + tstate->use_tracing = ((CYTHON_TRACE && tstate->c_tracefunc != NULL)\ + || tstate->c_profilefunc != NULL);\ + } while (0) +#endif + #ifdef WITH_THREAD + #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\ + if (nogil) {\ + if (CYTHON_TRACE_NOGIL) {\ + PyThreadState *tstate;\ + PyGILState_STATE state = PyGILState_Ensure();\ + tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 1, 1)) {\ + __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\ + }\ + PyGILState_Release(state);\ + if (unlikely(__Pyx_use_tracing < 0)) goto_error;\ + }\ + } else {\ + PyThreadState* tstate = PyThreadState_GET();\ + if (__Pyx_IsTracing(tstate, 1, 1)) {\ + __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\ + if (unlikely(__Pyx_use_tracing < 0)) goto_error;\ + }\ + } + #else + #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error)\ + { PyThreadState* tstate = PyThreadState_GET();\ + if (__Pyx_IsTracing(tstate, 1, 1)) {\ + __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, tstate, funcname, srcfile, firstlineno);\ + if (unlikely(__Pyx_use_tracing < 0)) goto_error;\ + }\ + } + #endif + #define __Pyx_TraceException()\ + if (likely(!__Pyx_use_tracing)); else {\ + PyThreadState* tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 1)) {\ + __Pyx_EnterTracing(tstate);\ + PyObject *exc_info = __Pyx_GetExceptionTuple(tstate);\ + if (exc_info) {\ + if (CYTHON_TRACE && tstate->c_tracefunc)\ + tstate->c_tracefunc(\ + tstate->c_traceobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\ + tstate->c_profilefunc(\ + tstate->c_profileobj, __pyx_frame, PyTrace_EXCEPTION, exc_info);\ + Py_DECREF(exc_info);\ + }\ + __Pyx_LeaveTracing(tstate);\ + }\ + } + static void __Pyx_call_return_trace_func(PyThreadState *tstate, PyFrameObject *frame, PyObject *result) { + PyObject *type, *value, *traceback; + __Pyx_ErrFetchInState(tstate, &type, &value, &traceback); + __Pyx_EnterTracing(tstate); + if (CYTHON_TRACE && tstate->c_tracefunc) + tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_RETURN, result); + if (tstate->c_profilefunc) + tstate->c_profilefunc(tstate->c_profileobj, frame, PyTrace_RETURN, result); + CYTHON_FRAME_DEL(frame); + __Pyx_LeaveTracing(tstate); + __Pyx_ErrRestoreInState(tstate, type, value, traceback); + } + #ifdef WITH_THREAD + #define __Pyx_TraceReturn(result, nogil)\ + if (likely(!__Pyx_use_tracing)); else {\ + if (nogil) {\ + if (CYTHON_TRACE_NOGIL) {\ + PyThreadState *tstate;\ + PyGILState_STATE state = PyGILState_Ensure();\ + tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 0)) {\ + __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\ + }\ + PyGILState_Release(state);\ + }\ + } else {\ + PyThreadState* tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 0)) {\ + __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\ + }\ + }\ + } + #else + #define __Pyx_TraceReturn(result, nogil)\ + if (likely(!__Pyx_use_tracing)); else {\ + PyThreadState* tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 0)) {\ + __Pyx_call_return_trace_func(tstate, __pyx_frame, (PyObject*)result);\ + }\ + } + #endif + static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); + static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, PyThreadState* tstate, const char *funcname, const char *srcfile, int firstlineno); +#else + #define __Pyx_TraceDeclarations + #define __Pyx_TraceFrameInit(codeobj) + #define __Pyx_TraceCall(funcname, srcfile, firstlineno, nogil, goto_error) if ((1)); else goto_error; + #define __Pyx_TraceException() + #define __Pyx_TraceReturn(result, nogil) +#endif +#if CYTHON_TRACE + static int __Pyx_call_line_trace_func(PyThreadState *tstate, PyFrameObject *frame, int lineno) { + int ret; + PyObject *type, *value, *traceback; + __Pyx_ErrFetchInState(tstate, &type, &value, &traceback); + __Pyx_PyFrame_SetLineNumber(frame, lineno); + __Pyx_EnterTracing(tstate); + ret = tstate->c_tracefunc(tstate->c_traceobj, frame, PyTrace_LINE, NULL); + __Pyx_LeaveTracing(tstate); + if (likely(!ret)) { + __Pyx_ErrRestoreInState(tstate, type, value, traceback); + } else { + Py_XDECREF(type); + Py_XDECREF(value); + Py_XDECREF(traceback); + } + return ret; + } + #ifdef WITH_THREAD + #define __Pyx_TraceLine(lineno, nogil, goto_error)\ + if (likely(!__Pyx_use_tracing)); else {\ + if (nogil) {\ + if (CYTHON_TRACE_NOGIL) {\ + int ret = 0;\ + PyThreadState *tstate;\ + PyGILState_STATE state = __Pyx_PyGILState_Ensure();\ + tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\ + ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\ + }\ + __Pyx_PyGILState_Release(state);\ + if (unlikely(ret)) goto_error;\ + }\ + } else {\ + PyThreadState* tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\ + int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\ + if (unlikely(ret)) goto_error;\ + }\ + }\ + } + #else + #define __Pyx_TraceLine(lineno, nogil, goto_error)\ + if (likely(!__Pyx_use_tracing)); else {\ + PyThreadState* tstate = __Pyx_PyThreadState_Current;\ + if (__Pyx_IsTracing(tstate, 0, 0) && tstate->c_tracefunc && __pyx_frame->f_trace) {\ + int ret = __Pyx_call_line_trace_func(tstate, __pyx_frame, lineno);\ + if (unlikely(ret)) goto_error;\ + }\ + } + #endif +#else + #define __Pyx_TraceLine(lineno, nogil, goto_error) if ((1)); else goto_error; +#endif + +/* RaiseDoubleKeywords.proto */ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +/* ParseKeywords.proto */ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject *const *kwvalues, + PyObject **argnames[], + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, + const char* function_name); + +/* RaiseArgTupleInvalid.proto */ +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +/* PyFunctionFastCall.proto */ +#if CYTHON_FAST_PYCALL +#if !CYTHON_VECTORCALL +#define __Pyx_PyFunction_FastCall(func, args, nargs)\ + __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); +#endif +#define __Pyx_BUILD_ASSERT_EXPR(cond)\ + (sizeof(char [1 - 2*!(cond)]) - 1) +#ifndef Py_MEMBER_SIZE +#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) +#endif +#if !CYTHON_VECTORCALL +#if PY_VERSION_HEX >= 0x03080000 + #include "frameobject.h" +#if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API + #ifndef Py_BUILD_CORE + #define Py_BUILD_CORE 1 + #endif + #include "internal/pycore_frame.h" +#endif + #define __Pxy_PyFrame_Initialize_Offsets() + #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus) +#else + static size_t __pyx_pyframe_localsplus_offset = 0; + #include "frameobject.h" + #define __Pxy_PyFrame_Initialize_Offsets()\ + ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ + (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) + #define __Pyx_PyFrame_GetLocalsplus(frame)\ + (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) +#endif +#endif +#endif + +/* PyObjectCall.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +/* PyObjectCallMethO.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +/* PyObjectFastCall.proto */ +#define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL) +static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs); + +/* WriteUnraisableException.proto */ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback, int nogil); + +/* RaiseException.proto */ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +/* KeywordStringCheck.proto */ +static int __Pyx_CheckKeywordStrings(PyObject *kw, const char* function_name, int kw_allowed); + +/* PySequenceContains.proto */ +static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { + int result = PySequence_Contains(seq, item); + return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); +} + +/* ListAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000 + L->ob_item[len] = x; + #else + PyList_SET_ITEM(list, len, x); + #endif + __Pyx_SET_SIZE(list, len + 1); + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +/* PyObjectCall2Args.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); + +/* PyObjectCallOneArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +/* PyObjectGetMethod.proto */ +static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method); + +/* PyObjectCallMethod1.proto */ +static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); + +/* StringJoin.proto */ +#if PY_MAJOR_VERSION < 3 +#define __Pyx_PyString_Join __Pyx_PyBytes_Join +#define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v)) +#else +#define __Pyx_PyString_Join PyUnicode_Join +#define __Pyx_PyBaseString_Join PyUnicode_Join +#endif +static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values); + +/* PyObjectCallNoArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); + +/* ArgTypeTest.proto */ +#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ + ((likely(__Pyx_IS_TYPE(obj, type) | (none_allowed && (obj == Py_None)))) ? 1 :\ + __Pyx__ArgTypeTest(obj, type, name, exact)) +static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); + +/* PyObjectSetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS +#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL) +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value); +#else +#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) +#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) +#endif + +/* PyObjectFormatSimple.proto */ +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyObject_FormatSimple(s, f) (\ + likely(PyUnicode_CheckExact(s)) ? (Py_INCREF(s), s) :\ + PyObject_Format(s, f)) +#elif PY_MAJOR_VERSION < 3 + #define __Pyx_PyObject_FormatSimple(s, f) (\ + likely(PyUnicode_CheckExact(s)) ? (Py_INCREF(s), s) :\ + likely(PyString_CheckExact(s)) ? PyUnicode_FromEncodedObject(s, NULL, "strict") :\ + PyObject_Format(s, f)) +#elif CYTHON_USE_TYPE_SLOTS + #define __Pyx_PyObject_FormatSimple(s, f) (\ + likely(PyUnicode_CheckExact(s)) ? (Py_INCREF(s), s) :\ + likely(PyLong_CheckExact(s)) ? PyLong_Type.tp_repr(s) :\ + likely(PyFloat_CheckExact(s)) ? PyFloat_Type.tp_repr(s) :\ + PyObject_Format(s, f)) +#else + #define __Pyx_PyObject_FormatSimple(s, f) (\ + likely(PyUnicode_CheckExact(s)) ? (Py_INCREF(s), s) :\ + PyObject_Format(s, f)) +#endif + +/* JoinPyUnicode.proto */ +static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength, + Py_UCS4 max_char); + +/* PyDictVersioning.proto */ +#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS +#define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1) +#define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) +#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var)\ + (version_var) = __PYX_GET_DICT_VERSION(dict);\ + (cache_var) = (value); +#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) {\ + static PY_UINT64_T __pyx_dict_version = 0;\ + static PyObject *__pyx_dict_cached_value = NULL;\ + if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ + (VAR) = __pyx_dict_cached_value;\ + } else {\ + (VAR) = __pyx_dict_cached_value = (LOOKUP);\ + __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ + }\ +} +static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj); +static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj); +static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version); +#else +#define __PYX_GET_DICT_VERSION(dict) (0) +#define __PYX_UPDATE_DICT_CACHE(dict, value, cache_var, version_var) +#define __PYX_PY_DICT_LOOKUP_IF_MODIFIED(VAR, DICT, LOOKUP) (VAR) = (LOOKUP); +#endif + +/* GetModuleGlobalName.proto */ +#if CYTHON_USE_DICT_VERSIONS +#define __Pyx_GetModuleGlobalName(var, name) do {\ + static PY_UINT64_T __pyx_dict_version = 0;\ + static PyObject *__pyx_dict_cached_value = NULL;\ + (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ + (likely(__pyx_dict_cached_value) ? __Pyx_NewRef(__pyx_dict_cached_value) : __Pyx_GetBuiltinName(name)) :\ + __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ +} while(0) +#define __Pyx_GetModuleGlobalNameUncached(var, name) do {\ + PY_UINT64_T __pyx_dict_version;\ + PyObject *__pyx_dict_cached_value;\ + (var) = __Pyx__GetModuleGlobalName(name, &__pyx_dict_version, &__pyx_dict_cached_value);\ +} while(0) +static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value); +#else +#define __Pyx_GetModuleGlobalName(var, name) (var) = __Pyx__GetModuleGlobalName(name) +#define __Pyx_GetModuleGlobalNameUncached(var, name) (var) = __Pyx__GetModuleGlobalName(name) +static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); +#endif + +/* GetItemInt.proto */ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +/* ObjectGetItem.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject *key); +#else +#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) +#endif + +/* GetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* SwapException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* GetTopmostException.proto */ +#if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE +static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); +#endif + +/* SaveResetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +#else +#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) +#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) +#endif + +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); +#else +#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\ + (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) +#endif + +/* PyObject_Unicode.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyObject_Unicode(obj)\ + (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj)) +#else +#define __Pyx_PyObject_Unicode(obj)\ + (likely(PyUnicode_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Unicode(obj)) +#endif + +/* RaiseTooManyValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +/* RaiseNeedMoreValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +/* IterFinish.proto */ +static CYTHON_INLINE int __Pyx_IterFinish(void); + +/* UnpackItemEndCheck.proto */ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); + +/* PyIntCompare.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_NeObjC(PyObject *op1, PyObject *op2, long intval, long inplace); + +/* IncludeStructmemberH.proto */ +#include <structmember.h> + +/* FixUpExtensionType.proto */ +#if CYTHON_USE_TYPE_SPECS +static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type); +#endif + +/* PyObjectCallMethod0.proto */ +static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); + +/* ValidateBasesTuple.proto */ +#if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS +static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases); +#endif + +/* PyType_Ready.proto */ +CYTHON_UNUSED static int __Pyx_PyType_Ready(PyTypeObject *t); + +/* PyObject_GenericGetAttrNoDict.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr +#endif + +/* PyObject_GenericGetAttr.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr +#endif + +/* SetVTable.proto */ +static int __Pyx_SetVtable(PyTypeObject* typeptr , void* vtable); + +/* GetVTable.proto */ +static void* __Pyx_GetVtable(PyTypeObject *type); + +/* MergeVTables.proto */ +#if !CYTHON_COMPILING_IN_LIMITED_API +static int __Pyx_MergeVtables(PyTypeObject *type); +#endif + +/* SetupReduce.proto */ +#if !CYTHON_COMPILING_IN_LIMITED_API +static int __Pyx_setup_reduce(PyObject* type_obj); +#endif + +/* TypeImport.proto */ +#ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11 +#define __PYX_HAVE_RT_ImportType_proto_3_0_11 +#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L +#include <stdalign.h> +#endif +#if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L +#define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) alignof(s) +#else +#define __PYX_GET_STRUCT_ALIGNMENT_3_0_11(s) sizeof(void*) +#endif +enum __Pyx_ImportType_CheckSize_3_0_11 { + __Pyx_ImportType_CheckSize_Error_3_0_11 = 0, + __Pyx_ImportType_CheckSize_Warn_3_0_11 = 1, + __Pyx_ImportType_CheckSize_Ignore_3_0_11 = 2 +}; +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); +#endif + +/* Import.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +/* ImportDottedModule.proto */ +static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple); +#if PY_MAJOR_VERSION >= 3 +static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple); +#endif + +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + +/* FetchSharedCythonModule.proto */ +static PyObject *__Pyx_FetchSharedCythonABIModule(void); + +/* FetchCommonType.proto */ +#if !CYTHON_USE_TYPE_SPECS +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); +#else +static PyTypeObject* __Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases); +#endif + +/* PyMethodNew.proto */ +#if CYTHON_COMPILING_IN_LIMITED_API +static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) { + PyObject *typesModule=NULL, *methodType=NULL, *result=NULL; + CYTHON_UNUSED_VAR(typ); + if (!self) + return __Pyx_NewRef(func); + typesModule = PyImport_ImportModule("types"); + if (!typesModule) return NULL; + methodType = PyObject_GetAttrString(typesModule, "MethodType"); + Py_DECREF(typesModule); + if (!methodType) return NULL; + result = PyObject_CallFunctionObjArgs(methodType, func, self, NULL); + Py_DECREF(methodType); + return result; +} +#elif PY_MAJOR_VERSION >= 3 +static PyObject *__Pyx_PyMethod_New(PyObject *func, PyObject *self, PyObject *typ) { + CYTHON_UNUSED_VAR(typ); + if (!self) + return __Pyx_NewRef(func); + return PyMethod_New(func, self); +} +#else + #define __Pyx_PyMethod_New PyMethod_New +#endif + +/* PyVectorcallFastCallDict.proto */ +#if CYTHON_METH_FASTCALL +static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw); +#endif + +/* CythonFunctionShared.proto */ +#define __Pyx_CyFunction_USED +#define __Pyx_CYFUNCTION_STATICMETHOD 0x01 +#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 +#define __Pyx_CYFUNCTION_CCLASS 0x04 +#define __Pyx_CYFUNCTION_COROUTINE 0x08 +#define __Pyx_CyFunction_GetClosure(f)\ + (((__pyx_CyFunctionObject *) (f))->func_closure) +#if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API + #define __Pyx_CyFunction_GetClassObj(f)\ + (((__pyx_CyFunctionObject *) (f))->func_classobj) +#else + #define __Pyx_CyFunction_GetClassObj(f)\ + ((PyObject*) ((PyCMethodObject *) (f))->mm_class) +#endif +#define __Pyx_CyFunction_SetClassObj(f, classobj)\ + __Pyx__CyFunction_SetClassObj((__pyx_CyFunctionObject *) (f), (classobj)) +#define __Pyx_CyFunction_Defaults(type, f)\ + ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) +#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\ + ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) +typedef struct { +#if CYTHON_COMPILING_IN_LIMITED_API + PyObject_HEAD + PyObject *func; +#elif PY_VERSION_HEX < 0x030900B1 + PyCFunctionObject func; +#else + PyCMethodObject func; +#endif +#if CYTHON_BACKPORT_VECTORCALL + __pyx_vectorcallfunc func_vectorcall; +#endif +#if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API + PyObject *func_weakreflist; +#endif + PyObject *func_dict; + PyObject *func_name; + PyObject *func_qualname; + PyObject *func_doc; + PyObject *func_globals; + PyObject *func_code; + PyObject *func_closure; +#if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API + PyObject *func_classobj; +#endif + void *defaults; + int defaults_pyobjects; + size_t defaults_size; + int flags; + PyObject *defaults_tuple; + PyObject *defaults_kwdict; + PyObject *(*defaults_getter)(PyObject *); + PyObject *func_annotations; + PyObject *func_is_coroutine; +} __pyx_CyFunctionObject; +#undef __Pyx_CyOrPyCFunction_Check +#define __Pyx_CyFunction_Check(obj) __Pyx_TypeCheck(obj, __pyx_CyFunctionType) +#define __Pyx_CyOrPyCFunction_Check(obj) __Pyx_TypeCheck2(obj, __pyx_CyFunctionType, &PyCFunction_Type) +#define __Pyx_CyFunction_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_CyFunctionType) +static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc); +#undef __Pyx_IsSameCFunction +#define __Pyx_IsSameCFunction(func, cfunc) __Pyx__IsSameCyOrCFunction(func, cfunc) +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml, + int flags, PyObject* qualname, + PyObject *closure, + PyObject *module, PyObject *globals, + PyObject* code); +static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj); +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, + size_t size, + int pyobjects); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, + PyObject *tuple); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, + PyObject *dict); +static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, + PyObject *dict); +static int __pyx_CyFunction_init(PyObject *module); +#if CYTHON_METH_FASTCALL +static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); +static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); +static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); +static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames); +#if CYTHON_BACKPORT_VECTORCALL +#define __Pyx_CyFunction_func_vectorcall(f) (((__pyx_CyFunctionObject*)f)->func_vectorcall) +#else +#define __Pyx_CyFunction_func_vectorcall(f) (((PyCFunctionObject*)f)->vectorcall) +#endif +#endif + +/* CythonFunction.proto */ +static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, + int flags, PyObject* qualname, + PyObject *closure, + PyObject *module, PyObject *globals, + PyObject* code); + +/* Py3UpdateBases.proto */ +static PyObject* __Pyx_PEP560_update_bases(PyObject *bases); + +/* CalculateMetaclass.proto */ +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); + +/* SetNameInClass.proto */ +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000 +#define __Pyx_SetNameInClass(ns, name, value)\ + (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value)) +#elif CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_SetNameInClass(ns, name, value)\ + (likely(PyDict_CheckExact(ns)) ? PyDict_SetItem(ns, name, value) : PyObject_SetItem(ns, name, value)) +#else +#define __Pyx_SetNameInClass(ns, name, value) PyObject_SetItem(ns, name, value) +#endif + +/* PyObjectLookupSpecial.proto */ +#if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS +#define __Pyx_PyObject_LookupSpecialNoError(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 0) +#define __Pyx_PyObject_LookupSpecial(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 1) +static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error); +#else +#define __Pyx_PyObject_LookupSpecialNoError(o,n) __Pyx_PyObject_GetAttrStrNoError(o,n) +#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) +#endif + +/* Py3ClassCreate.proto */ +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, + PyObject *mkw, PyObject *modname, PyObject *doc); +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, + PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); + +/* CLineInTraceback.proto */ +#ifdef CYTHON_CLINE_IN_TRACEBACK +#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) +#else +static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line); +#endif + +/* CodeObjectCache.proto */ +#if !CYTHON_COMPILING_IN_LIMITED_API +typedef struct { + PyCodeObject* code_object; + int code_line; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); +#endif + +/* AddTraceback.proto */ +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +/* GCCDiagnostics.proto */ +#if !defined(__INTEL_COMPILER) && defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) +#define __Pyx_HAS_GCC_DIAGNOSTIC +#endif + +/* ArrayAPI.proto */ +#ifndef _ARRAYARRAY_H +#define _ARRAYARRAY_H +typedef struct arraydescr { + int typecode; + int itemsize; + PyObject * (*getitem)(struct arrayobject *, Py_ssize_t); + int (*setitem)(struct arrayobject *, Py_ssize_t, PyObject *); +#if PY_MAJOR_VERSION >= 3 + char *formats; +#endif +} arraydescr; +struct arrayobject { + PyObject_HEAD + Py_ssize_t ob_size; + union { + char *ob_item; + float *as_floats; + double *as_doubles; + int *as_ints; + unsigned int *as_uints; + unsigned char *as_uchars; + signed char *as_schars; + char *as_chars; + unsigned long *as_ulongs; + long *as_longs; +#if PY_MAJOR_VERSION >= 3 + unsigned long long *as_ulonglongs; + long long *as_longlongs; +#endif + short *as_shorts; + unsigned short *as_ushorts; + Py_UNICODE *as_pyunicodes; + void *as_voidptr; + } data; + Py_ssize_t allocated; + struct arraydescr *ob_descr; + PyObject *weakreflist; +#if PY_MAJOR_VERSION >= 3 + int ob_exports; +#endif +}; +#ifndef NO_NEWARRAY_INLINE +static CYTHON_INLINE PyObject * newarrayobject(PyTypeObject *type, Py_ssize_t size, + struct arraydescr *descr) { + arrayobject *op; + size_t nbytes; + if (size < 0) { + PyErr_BadInternalCall(); + return NULL; + } + nbytes = size * descr->itemsize; + if (nbytes / descr->itemsize != (size_t)size) { + return PyErr_NoMemory(); + } + op = (arrayobject *) type->tp_alloc(type, 0); + if (op == NULL) { + return NULL; + } + op->ob_descr = descr; + op->allocated = size; + op->weakreflist = NULL; + __Pyx_SET_SIZE(op, size); + if (size <= 0) { + op->data.ob_item = NULL; + } + else { + op->data.ob_item = PyMem_NEW(char, nbytes); + if (op->data.ob_item == NULL) { + Py_DECREF(op); + return PyErr_NoMemory(); + } + } + return (PyObject *) op; +} +#else +PyObject* newarrayobject(PyTypeObject *type, Py_ssize_t size, + struct arraydescr *descr); +#endif +static CYTHON_INLINE int resize(arrayobject *self, Py_ssize_t n) { + void *items = (void*) self->data.ob_item; + PyMem_Resize(items, char, (size_t)(n * self->ob_descr->itemsize)); + if (items == NULL) { + PyErr_NoMemory(); + return -1; + } + self->data.ob_item = (char*) items; + __Pyx_SET_SIZE(self, n); + self->allocated = n; + return 0; +} +static CYTHON_INLINE int resize_smart(arrayobject *self, Py_ssize_t n) { + void *items = (void*) self->data.ob_item; + Py_ssize_t newsize; + if (n < self->allocated && n*4 > self->allocated) { + __Pyx_SET_SIZE(self, n); + return 0; + } + newsize = n + (n / 2) + 1; + if (newsize <= n) { + PyErr_NoMemory(); + return -1; + } + PyMem_Resize(items, char, (size_t)(newsize * self->ob_descr->itemsize)); + if (items == NULL) { + PyErr_NoMemory(); + return -1; + } + self->data.ob_item = (char*) items; + __Pyx_SET_SIZE(self, n); + self->allocated = newsize; + return 0; +} +#endif + +/* CIntFromPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +/* CIntFromPy.proto */ +static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_off_t(off_t value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__htsFormatCategory(enum htsFormatCategory value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__htsExactFormat(enum htsExactFormat value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__htsCompression(enum htsCompression value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value); + +/* CIntFromPy.proto */ +static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value); + +/* FormatTypeName.proto */ +#if CYTHON_COMPILING_IN_LIMITED_API +typedef PyObject *__Pyx_TypeName; +#define __Pyx_FMT_TYPENAME "%U" +static __Pyx_TypeName __Pyx_PyType_GetName(PyTypeObject* tp); +#define __Pyx_DECREF_TypeName(obj) Py_XDECREF(obj) +#else +typedef const char *__Pyx_TypeName; +#define __Pyx_FMT_TYPENAME "%.200s" +#define __Pyx_PyType_GetName(tp) ((tp)->tp_name) +#define __Pyx_DECREF_TypeName(obj) +#endif + +/* CIntFromPy.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +/* FastTypeChecks.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) +#define __Pyx_TypeCheck2(obj, type1, type2) __Pyx_IsAnySubtype2(Py_TYPE(obj), (PyTypeObject *)type1, (PyTypeObject *)type2) +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b); +static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type); +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2); +#else +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#define __Pyx_TypeCheck2(obj, type1, type2) (PyObject_TypeCheck(obj, (PyTypeObject *)type1) || PyObject_TypeCheck(obj, (PyTypeObject *)type2)) +#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type) +#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2)) +#endif +#define __Pyx_PyErr_ExceptionMatches2(err1, err2) __Pyx_PyErr_GivenExceptionMatches2(__Pyx_PyErr_CurrentExceptionType(), err1, err2) +#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) + +/* CheckBinaryVersion.proto */ +static unsigned long __Pyx_get_runtime_version(void); +static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer); + +/* FunctionImport.proto */ +static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig); + +/* InitStrings.proto */ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +/* #### Code section: module_declarations ### */ +static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self); /* proto*/ +static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self); /* proto*/ +static PyObject *__pyx_f_5pysam_10libchtslib_5HFile__open(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_mode, struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open *__pyx_optional_args); /* proto*/ +static htsFile *__pyx_f_5pysam_10libchtslib_7HTSFile__open_htsfile(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto*/ + +/* Module declarations from "libc.stdint" */ + +/* Module declarations from "libc.string" */ + +/* Module declarations from "libc.stdlib" */ + +/* Module declarations from "libc.stdio" */ + +/* Module declarations from "posix.types" */ + +/* Module declarations from "posix.unistd" */ + +/* Module declarations from "libc.errno" */ + +/* Module declarations from "cpython.version" */ + +/* Module declarations from "__builtin__" */ + +/* Module declarations from "cpython.type" */ + +/* Module declarations from "cpython.object" */ + +/* Module declarations from "cpython.ref" */ + +/* Module declarations from "cpython.exc" */ + +/* Module declarations from "cpython.module" */ + +/* Module declarations from "cpython.mem" */ + +/* Module declarations from "cpython.tuple" */ + +/* Module declarations from "cpython.list" */ + +/* Module declarations from "cpython.sequence" */ + +/* Module declarations from "cpython.mapping" */ + +/* Module declarations from "cpython.iterator" */ + +/* Module declarations from "cpython.number" */ + +/* Module declarations from "cpython.int" */ + +/* Module declarations from "__builtin__" */ + +/* Module declarations from "cpython.bool" */ + +/* Module declarations from "cpython.long" */ + +/* Module declarations from "cpython.float" */ + +/* Module declarations from "__builtin__" */ + +/* Module declarations from "cpython.complex" */ + +/* Module declarations from "cpython.string" */ + +/* Module declarations from "libc.stddef" */ + +/* Module declarations from "cpython.unicode" */ + +/* Module declarations from "cpython.pyport" */ + +/* Module declarations from "cpython.dict" */ + +/* Module declarations from "cpython.instance" */ + +/* Module declarations from "cpython.function" */ + +/* Module declarations from "cpython.method" */ + +/* Module declarations from "cpython.weakref" */ + +/* Module declarations from "cpython.getargs" */ + +/* Module declarations from "cpython.pythread" */ + +/* Module declarations from "cpython.pystate" */ + +/* Module declarations from "cpython.cobject" */ + +/* Module declarations from "cpython.oldbuffer" */ + +/* Module declarations from "cpython.set" */ + +/* Module declarations from "cpython.buffer" */ + +/* Module declarations from "cpython.bytes" */ + +/* Module declarations from "cpython.pycapsule" */ + +/* Module declarations from "cpython.contextvars" */ + +/* Module declarations from "cpython" */ + +/* Module declarations from "cython" */ + +/* Module declarations from "array" */ + +/* Module declarations from "cpython.array" */ +static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *, char *, Py_ssize_t); /*proto*/ + +/* Module declarations from "pysam.libcutils" */ +static int (*__pyx_f_5pysam_9libcutils_libc_whence_from_io)(int); /*proto*/ +static PyObject *(*__pyx_f_5pysam_9libcutils_charptr_to_str)(char const *, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str *__pyx_optional_args); /*proto*/ +static PyObject *(*__pyx_f_5pysam_9libcutils_charptr_to_str_w_len)(char const *, size_t, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len *__pyx_optional_args); /*proto*/ +static PyObject *(*__pyx_f_5pysam_9libcutils_force_str)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_str *__pyx_optional_args); /*proto*/ +static PyObject *(*__pyx_f_5pysam_9libcutils_force_bytes)(PyObject *, struct __pyx_opt_args_5pysam_9libcutils_force_bytes *__pyx_optional_args); /*proto*/ +static PyObject *(*__pyx_f_5pysam_9libcutils_encode_filename)(PyObject *); /*proto*/ +static PyObject *(*__pyx_f_5pysam_9libcutils_from_string_and_size)(char const *, size_t); /*proto*/ + +/* Module declarations from "pysam.libchtslib" */ +static int __pyx_v_5pysam_10libchtslib_MAX_POS; +static PyObject *__pyx_v_5pysam_10libchtslib_FORMAT_CATEGORIES = 0; +static PyObject *__pyx_v_5pysam_10libchtslib_FORMATS = 0; +static PyObject *__pyx_v_5pysam_10libchtslib_COMPRESSION = 0; +static PyObject *__pyx_f_5pysam_10libchtslib_set_verbosity(int, int __pyx_skip_dispatch); /*proto*/ +static PyObject *__pyx_f_5pysam_10libchtslib_get_verbosity(int __pyx_skip_dispatch); /*proto*/ +/* #### Code section: typeinfo ### */ +/* #### Code section: before_global_var ### */ +#define __Pyx_MODULE_NAME "pysam.libchtslib" +extern int __pyx_module_is_main_pysam__libchtslib; +int __pyx_module_is_main_pysam__libchtslib = 0; + +/* Implementation of "pysam.libchtslib" */ +/* #### Code section: global_var ### */ +static PyObject *__pyx_builtin_object; +static PyObject *__pyx_builtin_IOError; +static PyObject *__pyx_builtin_AttributeError; +static PyObject *__pyx_builtin_StopIteration; +static PyObject *__pyx_builtin_NotImplementedError; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_OSError; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_OverflowError; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_builtin_MemoryError; +/* #### Code section: string_decls ### */ +static const char __pyx_k_b[] = "b"; +static const char __pyx_k_c[] = "c"; +static const char __pyx_k_r[] = "r"; +static const char __pyx_k_w[] = "w"; +static const char __pyx_k_eq[] = "__eq__"; +static const char __pyx_k_fd[] = "<fd:{}>"; +static const char __pyx_k_fp[] = "fp"; +static const char __pyx_k_gc[] = "gc"; +static const char __pyx_k_io[] = "io"; +static const char __pyx_k_mv[] = "mv"; +static const char __pyx_k_ne[] = "__ne__"; +static const char __pyx_k_os[] = "os"; +static const char __pyx_k_re[] = "re"; +static const char __pyx_k_tb[] = "tb"; +static const char __pyx_k_BAI[] = "BAI"; +static const char __pyx_k_BAM[] = "BAM"; +static const char __pyx_k_BCF[] = "BCF"; +static const char __pyx_k_BED[] = "BED"; +static const char __pyx_k_CSI[] = "CSI"; +static const char __pyx_k_GZI[] = "GZI"; +static const char __pyx_k_SAM[] = "SAM"; +static const char __pyx_k_TBI[] = "TBI"; +static const char __pyx_k_VCF[] = "VCF"; +static const char __pyx_k__13[] = ""; +static const char __pyx_k__55[] = ":"; +static const char __pyx_k__56[] = "-"; +static const char __pyx_k__58[] = "*"; +static const char __pyx_k__59[] = "."; +static const char __pyx_k__97[] = "?"; +static const char __pyx_k_all[] = "__all__"; +static const char __pyx_k_buf[] = "buf"; +static const char __pyx_k_doc[] = "__doc__"; +static const char __pyx_k_end[] = "end"; +static const char __pyx_k_got[] = "got"; +static const char __pyx_k_msg[] = "msg"; +static const char __pyx_k_off[] = "off"; +static const char __pyx_k_ret[] = "ret"; +static const char __pyx_k_tid[] = "tid"; +static const char __pyx_k_BGZF[] = "BGZF"; +static const char __pyx_k_CRAI[] = "CRAI"; +static const char __pyx_k_CRAM[] = "CRAM"; +static const char __pyx_k_GZIP[] = "GZIP"; +static const char __pyx_k_NONE[] = "NONE"; +static const char __pyx_k_bool[] = "__bool__"; +static const char __pyx_k_call[] = "__call__"; +static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_exit[] = "__exit__"; +static const char __pyx_k_init[] = "__init__"; +static const char __pyx_k_join[] = "join"; +static const char __pyx_k_line[] = "line"; +static const char __pyx_k_main[] = "__main__"; +static const char __pyx_k_mode[] = "mode"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_opts[] = "opts"; +static const char __pyx_k_part[] = "part"; +static const char __pyx_k_read[] = "read"; +static const char __pyx_k_rtid[] = "rtid"; +static const char __pyx_k_rval[] = "rval"; +static const char __pyx_k_seek[] = "seek"; +static const char __pyx_k_self[] = "self"; +static const char __pyx_k_size[] = "size"; +static const char __pyx_k_spec[] = "__spec__"; +static const char __pyx_k_stop[] = "stop"; +static const char __pyx_k_tell[] = "tell"; +static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_type[] = "type"; +static const char __pyx_k_warn[] = "warn"; +static const char __pyx_k_CTrue[] = "CTrue"; +static const char __pyx_k_HFile[] = "HFile"; +static const char __pyx_k_INDEX[] = "INDEX"; +static const char __pyx_k_bgzfp[] = "bgzfp"; +static const char __pyx_k_close[] = "close"; +static const char __pyx_k_coord[] = "coord"; +static const char __pyx_k_cpart[] = "cpart"; +static const char __pyx_k_enter[] = "__enter__"; +static const char __pyx_k_flush[] = "flush"; +static const char __pyx_k_lines[] = "lines"; +static const char __pyx_k_other[] = "other"; +static const char __pyx_k_parts[] = "parts"; +static const char __pyx_k_reset[] = "reset"; +static const char __pyx_k_rstop[] = "rstop"; +static const char __pyx_k_split[] = "split"; +static const char __pyx_k_start[] = "start"; +static const char __pyx_k_super[] = "super"; +static const char __pyx_k_value[] = "value"; +static const char __pyx_k_write[] = "write"; +static const char __pyx_k_CFalse[] = "CFalse"; +static const char __pyx_k_CUSTOM[] = "CUSTOM"; +static const char __pyx_k_contig[] = "contig"; +static const char __pyx_k_enable[] = "enable"; +static const char __pyx_k_failed[] = " failed"; +static const char __pyx_k_fileno[] = "fileno"; +static const char __pyx_k_format[] = "format"; +static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_isatty[] = "isatty"; +static const char __pyx_k_module[] = "__module__"; +static const char __pyx_k_name_2[] = "__name__"; +static const char __pyx_k_object[] = "object"; +static const char __pyx_k_offset[] = "offset"; +static const char __pyx_k_reduce[] = "__reduce__"; +static const char __pyx_k_region[] = "region"; +static const char __pyx_k_rstart[] = "rstart"; +static const char __pyx_k_whence[] = "whence"; +static const char __pyx_k_HTSFile[] = "HTSFile"; +static const char __pyx_k_IOError[] = "IOError"; +static const char __pyx_k_OSError[] = "OSError"; +static const char __pyx_k_REGIONS[] = "REGIONS"; +static const char __pyx_k_UNKNOWN[] = "UNKNOWN"; +static const char __pyx_k_closefd[] = "closefd"; +static const char __pyx_k_disable[] = "disable"; +static const char __pyx_k_get_tid[] = "get_tid"; +static const char __pyx_k_is_open[] = "is_open"; +static const char __pyx_k_nonzero[] = "__nonzero__"; +static const char __pyx_k_prepare[] = "__prepare__"; +static const char __pyx_k_readall[] = "readall"; +static const char __pyx_k_replace[] = "replace"; +static const char __pyx_k_Flushing[] = "Flushing "; +static const char __pyx_k_SEEK_SET[] = "SEEK_SET"; +static const char __pyx_k_VARIANTS[] = "VARIANTS"; +static const char __pyx_k_exc_type[] = "exc_type"; +static const char __pyx_k_getstate[] = "__getstate__"; +static const char __pyx_k_qualname[] = "__qualname__"; +static const char __pyx_k_readable[] = "readable"; +static const char __pyx_k_readinto[] = "readinto"; +static const char __pyx_k_readline[] = "readline"; +static const char __pyx_k_seekable[] = "seekable"; +static const char __pyx_k_set_name[] = "__set_name__"; +static const char __pyx_k_setstate[] = "__setstate__"; +static const char __pyx_k_truncate[] = "truncate"; +static const char __pyx_k_warnings[] = "warnings"; +static const char __pyx_k_writable[] = "writable"; +static const char __pyx_k_TypeError[] = "TypeError"; +static const char __pyx_k_exc_value[] = "exc_value"; +static const char __pyx_k_isenabled[] = "isenabled"; +static const char __pyx_k_metaclass[] = "__metaclass__"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; +static const char __pyx_k_readlines[] = "readlines"; +static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; +static const char __pyx_k_reference[] = "reference"; +static const char __pyx_k_traceback[] = "traceback"; +static const char __pyx_k_verbosity[] = "verbosity"; +static const char __pyx_k_ALIGNMENTS[] = "ALIGNMENTS"; +static const char __pyx_k_HFile_read[] = "HFile.read"; +static const char __pyx_k_HFile_seek[] = "HFile.seek"; +static const char __pyx_k_HFile_tell[] = "HFile.tell"; +static const char __pyx_k_IndexError[] = "IndexError"; +static const char __pyx_k_ValueError[] = "ValueError"; +static const char __pyx_k_bytes_read[] = "bytes_read"; +static const char __pyx_k_chunk_size[] = "chunk_size"; +static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static const char __pyx_k_writelines[] = "writelines"; +static const char __pyx_k_HFile_close[] = "HFile.close"; +static const char __pyx_k_HFile_flush[] = "HFile.flush"; +static const char __pyx_k_HFile_write[] = "HFile.write"; +static const char __pyx_k_MemoryError[] = "MemoryError"; +static const char __pyx_k_TEXT_FORMAT[] = "TEXT_FORMAT"; +static const char __pyx_k_invalid_tid[] = "invalid tid"; +static const char __pyx_k_mro_entries[] = "__mro_entries__"; +static const char __pyx_k_HFile___exit[] = "HFile.__exit__"; +static const char __pyx_k_HFile_fileno[] = "HFile.fileno"; +static const char __pyx_k_HFile_isatty[] = "HFile.isatty"; +static const char __pyx_k_HTSFile_seek[] = "HTSFile.seek"; +static const char __pyx_k_HTSFile_tell[] = "HTSFile.tell"; +static const char __pyx_k_RuntimeError[] = "RuntimeError"; +static const char __pyx_k_initializing[] = "_initializing"; +static const char __pyx_k_is_coroutine[] = "_is_coroutine"; +static const char __pyx_k_is_valid_tid[] = "is_valid_tid"; +static const char __pyx_k_parse_region[] = "parse_region"; +static const char __pyx_k_stringsource[] = "<stringsource>"; +static const char __pyx_k_BINARY_FORMAT[] = "BINARY_FORMAT"; +static const char __pyx_k_CallableValue[] = "CallableValue"; +static const char __pyx_k_HFile___enter[] = "HFile.__enter__"; +static const char __pyx_k_HFile_readall[] = "HFile.readall"; +static const char __pyx_k_HTSFile_close[] = "HTSFile.close"; +static const char __pyx_k_HTSFile_flush[] = "HTSFile.flush"; +static const char __pyx_k_HTSFile_reset[] = "HTSFile.reset"; +static const char __pyx_k_OverflowError[] = "OverflowError"; +static const char __pyx_k_StopIteration[] = "StopIteration"; +static const char __pyx_k_class_getitem[] = "__class_getitem__"; +static const char __pyx_k_format_option[] = "format_option"; +static const char __pyx_k_get_verbosity[] = "get_verbosity"; +static const char __pyx_k_init_subclass[] = "__init_subclass__"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; +static const char __pyx_k_set_verbosity[] = "set_verbosity"; +static const char __pyx_k_AttributeError[] = "AttributeError"; +static const char __pyx_k_HFile_readable[] = "HFile.readable"; +static const char __pyx_k_HFile_readinto[] = "HFile.readinto"; +static const char __pyx_k_HFile_readline[] = "HFile.readline"; +static const char __pyx_k_HFile_seekable[] = "HFile.seekable"; +static const char __pyx_k_HFile_truncate[] = "HFile.truncate"; +static const char __pyx_k_HFile_writable[] = "HFile.writable"; +static const char __pyx_k_HTSFile___exit[] = "HTSFile.__exit__"; +static const char __pyx_k_format_options[] = "format_options"; +static const char __pyx_k_HFile_readlines[] = "HFile.readlines"; +static const char __pyx_k_HTSFile___enter[] = "HTSFile.__enter__"; +static const char __pyx_k_HTSFile_get_tid[] = "HTSFile.get_tid"; +static const char __pyx_k_add_hts_options[] = "add_hts_options"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; +static const char __pyx_k_HFile_writelines[] = "HFile.writelines"; +static const char __pyx_k_check_truncation[] = "check_truncation"; +static const char __pyx_k_invalid_contig_s[] = "invalid contig `%s`"; +static const char __pyx_k_pysam_libchtslib[] = "pysam.libchtslib"; +static const char __pyx_k_ignore_truncation[] = "ignore_truncation"; +static const char __pyx_k_CallableValue___eq[] = "CallableValue.__eq__"; +static const char __pyx_k_CallableValue___ne[] = "CallableValue.__ne__"; +static const char __pyx_k_asyncio_coroutines[] = "asyncio.coroutines"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; +static const char __pyx_k_get_reference_name[] = "get_reference_name"; +static const char __pyx_k_Cannot_create_hfile[] = "Cannot create hfile"; +static const char __pyx_k_NotImplementedError[] = "NotImplementedError"; +static const char __pyx_k_stop_out_of_range_i[] = "stop out of range (%i)"; +static const char __pyx_k_CallableValue___bool[] = "CallableValue.__bool__"; +static const char __pyx_k_CallableValue___call[] = "CallableValue.__call__"; +static const char __pyx_k_CallableValue___init[] = "CallableValue.__init__"; +static const char __pyx_k_HTSFile_is_valid_tid[] = "HTSFile.is_valid_tid"; +static const char __pyx_k_HTSFile_parse_region[] = "HTSFile.parse_region"; +static const char __pyx_k_failed_to_open_HFile[] = "failed to open HFile"; +static const char __pyx_k_failed_to_read_HFile[] = "failed to read HFile"; +static const char __pyx_k_fileno_not_available[] = "fileno not available"; +static const char __pyx_k_pysam_libchtslib_pyx[] = "pysam/libchtslib.pyx"; +static const char __pyx_k_seek_failed_on_HFile[] = "seek failed on HFile"; +static const char __pyx_k_start_out_of_range_i[] = "start out of range (%i)"; +static const char __pyx_k_tell_failed_on_HFile[] = "tell failed on HFile"; +static const char __pyx_k_HFile___reduce_cython[] = "HFile.__reduce_cython__"; +static const char __pyx_k_failed_to_close_HFile[] = "failed to close HFile"; +static const char __pyx_k_failed_to_flush_HFile[] = "failed to flush HFile"; +static const char __pyx_k_write_failed_on_HFile[] = "write failed on HFile"; +static const char __pyx_k_CallableValue___nonzero[] = "CallableValue.__nonzero__"; +static const char __pyx_k_HFile___setstate_cython[] = "HFile.__setstate_cython__"; +static const char __pyx_k_HTSFile___reduce_cython[] = "HTSFile.__reduce_cython__"; +static const char __pyx_k_HTSFile_add_hts_options[] = "HTSFile.add_hts_options"; +static const char __pyx_k_is_valid_reference_name[] = "is_valid_reference_name"; +static const char __pyx_k_HTSFile_check_truncation[] = "HTSFile.check_truncation"; +static const char __pyx_k_HTSFile___setstate_cython[] = "HTSFile.__setstate_cython__"; +static const char __pyx_k_operation_on_closed_HFile[] = "operation on closed HFile"; +static const char __pyx_k_HTSFile_get_reference_name[] = "HTSFile.get_reference_name"; +static const char __pyx_k_I_O_operation_on_closed_file[] = "I/O operation on closed file"; +static const char __pyx_k_error_checking_for_EOF_marker[] = "error checking for EOF marker"; +static const char __pyx_k_seek_not_available_in_streams[] = "seek not available in streams"; +static const char __pyx_k_tell_not_available_in_streams[] = "tell not available in streams"; +static const char __pyx_k_HTSFile_is_valid_reference_name[] = "HTSFile.is_valid_reference_name"; +static const char __pyx_k_Invalid_format_option_specified[] = "Invalid format option ({}) specified"; +static const char __pyx_k_contig_and_reference_should_not[] = "contig and reference should not both be specified"; +static const char __pyx_k_stop_and_end_should_not_both_be[] = "stop and end should not both be specified"; +static const char __pyx_k_An_error_occurred_while_applying[] = "An error occurred while applying the requested format options"; +static const char __pyx_k_invalid_coordinates_start_i_stop[] = "invalid coordinates: start (%i) > stop (%i)"; +static const char __pyx_k_metadata_not_available_on_closed[] = "metadata not available on closed file"; +static const char __pyx_k_no_BGZF_EOF_marker_file_may_be_t[] = "no BGZF EOF marker; file may be truncated"; +static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; +static const char __pyx_k_seek_not_implemented_in_files_co[] = "seek not implemented in files compressed by method {}"; +static const char __pyx_k_self_fp_cannot_be_converted_to_a[] = "self.fp cannot be converted to a Python object for pickling"; +/* #### Code section: decls ### */ +static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags); /* proto */ +static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_set_verbosity(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_verbosity); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_2get_verbosity(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static int __pyx_pf_5pysam_10libchtslib_5HFile___init__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_mode, CYTHON_UNUSED PyObject *__pyx_v_closefd); /* proto */ +static void __pyx_pf_5pysam_10libchtslib_5HFile_2__dealloc__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_6closed___get__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_4close(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_6fileno(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_8__enter__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_10__exit__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_type, CYTHON_UNUSED PyObject *__pyx_v_value, CYTHON_UNUSED PyObject *__pyx_v_tb); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_12__iter__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_14__next__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_16flush(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_18isatty(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_20readable(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_22read(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, Py_ssize_t __pyx_v_size); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_24readall(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_26readinto(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_buf); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_28readline(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, Py_ssize_t __pyx_v_size); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_30readlines(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_32seek(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, Py_ssize_t __pyx_v_offset, int __pyx_v_whence); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_34tell(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_36seekable(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_38truncate(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_size); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_40writable(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_42write(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_b); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_44writelines(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_lines); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_4name___get__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_4mode___get__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_46__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_48__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_2__call__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_4__bool__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_6__nonzero__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_8__eq__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_other); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_10__ne__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_other); /* proto */ +static int __pyx_pf_5pysam_10libchtslib_7HTSFile___cinit__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_args, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_2close(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static void __pyx_pf_5pysam_10libchtslib_7HTSFile_4__dealloc__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6flush(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8check_truncation(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_ignore_truncation); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_10__enter__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_12__exit__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8category___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6format___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7version___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_11compression___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_11description___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_open___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_closed___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6closed___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8is_write___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_read___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_sam___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bam___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_cram___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_vcf___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bcf___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_14reset(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_16seek(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_whence); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_18tell(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_20add_hts_options(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_format_options); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_22parse_region(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_tid, PyObject *__pyx_v_reference, PyObject *__pyx_v_end); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_24is_valid_tid(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_tid); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_26is_valid_reference_name(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_contig); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_28get_tid(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_contig); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_30get_reference_name(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_tid); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8filename___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_4mode___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7threads___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_14index_filename___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_stream___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_remote___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_32__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_34__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_tp_new_5pysam_10libchtslib_HTSFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_5pysam_10libchtslib_HFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +/* #### Code section: late_includes ### */ +/* #### Code section: module_state ### */ +typedef struct { + PyObject *__pyx_d; + PyObject *__pyx_b; + PyObject *__pyx_cython_runtime; + PyObject *__pyx_empty_tuple; + PyObject *__pyx_empty_bytes; + PyObject *__pyx_empty_unicode; + #ifdef __Pyx_CyFunction_USED + PyTypeObject *__pyx_CyFunctionType; + #endif + #ifdef __Pyx_FusedFunction_USED + PyTypeObject *__pyx_FusedFunctionType; + #endif + #ifdef __Pyx_Generator_USED + PyTypeObject *__pyx_GeneratorType; + #endif + #ifdef __Pyx_IterableCoroutine_USED + PyTypeObject *__pyx_IterableCoroutineType; + #endif + #ifdef __Pyx_Coroutine_USED + PyTypeObject *__pyx_CoroutineAwaitType; + #endif + #ifdef __Pyx_Coroutine_USED + PyTypeObject *__pyx_CoroutineType; + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + PyTypeObject *__pyx_ptype_7cpython_4type_type; + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + PyTypeObject *__pyx_ptype_7cpython_4bool_bool; + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + PyTypeObject *__pyx_ptype_7cpython_7complex_complex; + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + #endif + PyTypeObject *__pyx_ptype_7cpython_5array_array; + #if CYTHON_USE_MODULE_STATE + #endif + #if CYTHON_USE_MODULE_STATE + PyObject *__pyx_type_5pysam_10libchtslib_HTSFile; + PyObject *__pyx_type_5pysam_10libchtslib_HFile; + #endif + PyTypeObject *__pyx_ptype_5pysam_10libchtslib_HTSFile; + PyTypeObject *__pyx_ptype_5pysam_10libchtslib_HFile; + PyObject *__pyx_n_u_ALIGNMENTS; + PyObject *__pyx_kp_u_An_error_occurred_while_applying; + PyObject *__pyx_n_s_AttributeError; + PyObject *__pyx_n_u_BAI; + PyObject *__pyx_n_u_BAM; + PyObject *__pyx_n_u_BCF; + PyObject *__pyx_n_u_BED; + PyObject *__pyx_n_u_BGZF; + PyObject *__pyx_n_u_BINARY_FORMAT; + PyObject *__pyx_n_s_CFalse; + PyObject *__pyx_n_u_CRAI; + PyObject *__pyx_n_u_CRAM; + PyObject *__pyx_n_u_CSI; + PyObject *__pyx_n_s_CTrue; + PyObject *__pyx_n_u_CUSTOM; + PyObject *__pyx_n_s_CallableValue; + PyObject *__pyx_n_s_CallableValue___bool; + PyObject *__pyx_n_s_CallableValue___call; + PyObject *__pyx_n_s_CallableValue___eq; + PyObject *__pyx_n_s_CallableValue___init; + PyObject *__pyx_n_s_CallableValue___ne; + PyObject *__pyx_n_s_CallableValue___nonzero; + PyObject *__pyx_kp_u_Cannot_create_hfile; + PyObject *__pyx_kp_u_Flushing; + PyObject *__pyx_n_u_GZI; + PyObject *__pyx_n_u_GZIP; + PyObject *__pyx_n_s_HFile; + PyObject *__pyx_n_u_HFile; + PyObject *__pyx_n_s_HFile___enter; + PyObject *__pyx_n_s_HFile___exit; + PyObject *__pyx_n_s_HFile___reduce_cython; + PyObject *__pyx_n_s_HFile___setstate_cython; + PyObject *__pyx_n_s_HFile_close; + PyObject *__pyx_n_s_HFile_fileno; + PyObject *__pyx_n_s_HFile_flush; + PyObject *__pyx_n_s_HFile_isatty; + PyObject *__pyx_n_s_HFile_read; + PyObject *__pyx_n_s_HFile_readable; + PyObject *__pyx_n_s_HFile_readall; + PyObject *__pyx_n_s_HFile_readinto; + PyObject *__pyx_n_s_HFile_readline; + PyObject *__pyx_n_s_HFile_readlines; + PyObject *__pyx_n_s_HFile_seek; + PyObject *__pyx_n_s_HFile_seekable; + PyObject *__pyx_n_s_HFile_tell; + PyObject *__pyx_n_s_HFile_truncate; + PyObject *__pyx_n_s_HFile_writable; + PyObject *__pyx_n_s_HFile_write; + PyObject *__pyx_n_s_HFile_writelines; + PyObject *__pyx_n_s_HTSFile; + PyObject *__pyx_n_u_HTSFile; + PyObject *__pyx_n_s_HTSFile___enter; + PyObject *__pyx_n_s_HTSFile___exit; + PyObject *__pyx_n_s_HTSFile___reduce_cython; + PyObject *__pyx_n_s_HTSFile___setstate_cython; + PyObject *__pyx_n_s_HTSFile_add_hts_options; + PyObject *__pyx_n_s_HTSFile_check_truncation; + PyObject *__pyx_n_s_HTSFile_close; + PyObject *__pyx_n_s_HTSFile_flush; + PyObject *__pyx_n_s_HTSFile_get_reference_name; + PyObject *__pyx_n_s_HTSFile_get_tid; + PyObject *__pyx_n_s_HTSFile_is_valid_reference_name; + PyObject *__pyx_n_s_HTSFile_is_valid_tid; + PyObject *__pyx_n_s_HTSFile_parse_region; + PyObject *__pyx_n_s_HTSFile_reset; + PyObject *__pyx_n_s_HTSFile_seek; + PyObject *__pyx_n_s_HTSFile_tell; + PyObject *__pyx_n_u_INDEX; + PyObject *__pyx_n_s_IOError; + PyObject *__pyx_kp_u_I_O_operation_on_closed_file; + PyObject *__pyx_n_s_IndexError; + PyObject *__pyx_kp_u_Invalid_format_option_specified; + PyObject *__pyx_n_s_MemoryError; + PyObject *__pyx_n_u_NONE; + PyObject *__pyx_n_s_NotImplementedError; + PyObject *__pyx_n_s_OSError; + PyObject *__pyx_n_s_OverflowError; + PyObject *__pyx_n_u_REGIONS; + PyObject *__pyx_n_s_RuntimeError; + PyObject *__pyx_n_u_SAM; + PyObject *__pyx_n_s_SEEK_SET; + PyObject *__pyx_n_s_StopIteration; + PyObject *__pyx_n_u_TBI; + PyObject *__pyx_n_u_TEXT_FORMAT; + PyObject *__pyx_n_s_TypeError; + PyObject *__pyx_n_u_UNKNOWN; + PyObject *__pyx_n_u_VARIANTS; + PyObject *__pyx_n_u_VCF; + PyObject *__pyx_n_s_ValueError; + PyObject *__pyx_kp_b__13; + PyObject *__pyx_kp_u__55; + PyObject *__pyx_kp_u__56; + PyObject *__pyx_n_s__58; + PyObject *__pyx_kp_u__58; + PyObject *__pyx_kp_u__59; + PyObject *__pyx_n_s__97; + PyObject *__pyx_n_s_add_hts_options; + PyObject *__pyx_n_s_all; + PyObject *__pyx_n_s_asyncio_coroutines; + PyObject *__pyx_n_b_b; + PyObject *__pyx_n_s_b; + PyObject *__pyx_n_s_bgzfp; + PyObject *__pyx_n_s_bool; + PyObject *__pyx_n_s_buf; + PyObject *__pyx_n_s_bytes_read; + PyObject *__pyx_n_b_c; + PyObject *__pyx_n_s_call; + PyObject *__pyx_n_s_check_truncation; + PyObject *__pyx_n_s_chunk_size; + PyObject *__pyx_n_s_class_getitem; + PyObject *__pyx_n_s_cline_in_traceback; + PyObject *__pyx_n_s_close; + PyObject *__pyx_n_s_closefd; + PyObject *__pyx_n_s_contig; + PyObject *__pyx_kp_u_contig_and_reference_should_not; + PyObject *__pyx_n_s_coord; + PyObject *__pyx_n_s_cpart; + PyObject *__pyx_n_s_dict; + PyObject *__pyx_kp_u_disable; + PyObject *__pyx_n_s_doc; + PyObject *__pyx_kp_u_enable; + PyObject *__pyx_n_s_end; + PyObject *__pyx_n_s_enter; + PyObject *__pyx_n_s_eq; + PyObject *__pyx_kp_u_error_checking_for_EOF_marker; + PyObject *__pyx_n_s_exc_type; + PyObject *__pyx_n_s_exc_value; + PyObject *__pyx_n_s_exit; + PyObject *__pyx_kp_u_failed; + PyObject *__pyx_kp_u_failed_to_close_HFile; + PyObject *__pyx_kp_u_failed_to_flush_HFile; + PyObject *__pyx_kp_u_failed_to_open_HFile; + PyObject *__pyx_kp_u_failed_to_read_HFile; + PyObject *__pyx_kp_u_fd; + PyObject *__pyx_n_s_fileno; + PyObject *__pyx_kp_u_fileno_not_available; + PyObject *__pyx_n_s_flush; + PyObject *__pyx_n_s_format; + PyObject *__pyx_n_s_format_option; + PyObject *__pyx_n_s_format_options; + PyObject *__pyx_n_s_fp; + PyObject *__pyx_kp_u_gc; + PyObject *__pyx_n_s_get_reference_name; + PyObject *__pyx_n_s_get_tid; + PyObject *__pyx_n_s_get_verbosity; + PyObject *__pyx_n_u_get_verbosity; + PyObject *__pyx_n_s_getstate; + PyObject *__pyx_n_s_got; + PyObject *__pyx_n_s_ignore_truncation; + PyObject *__pyx_n_s_import; + PyObject *__pyx_n_s_init; + PyObject *__pyx_n_s_init_subclass; + PyObject *__pyx_n_s_initializing; + PyObject *__pyx_kp_u_invalid_contig_s; + PyObject *__pyx_kp_u_invalid_coordinates_start_i_stop; + PyObject *__pyx_kp_u_invalid_tid; + PyObject *__pyx_n_s_io; + PyObject *__pyx_n_s_is_coroutine; + PyObject *__pyx_n_s_is_open; + PyObject *__pyx_n_s_is_valid_reference_name; + PyObject *__pyx_n_s_is_valid_tid; + PyObject *__pyx_n_s_isatty; + PyObject *__pyx_kp_u_isenabled; + PyObject *__pyx_n_s_join; + PyObject *__pyx_n_s_line; + PyObject *__pyx_n_s_lines; + PyObject *__pyx_n_s_main; + PyObject *__pyx_n_s_metaclass; + PyObject *__pyx_kp_u_metadata_not_available_on_closed; + PyObject *__pyx_n_s_mode; + PyObject *__pyx_n_s_module; + PyObject *__pyx_n_s_mro_entries; + PyObject *__pyx_n_s_msg; + PyObject *__pyx_n_s_mv; + PyObject *__pyx_n_s_name; + PyObject *__pyx_n_s_name_2; + PyObject *__pyx_n_s_ne; + PyObject *__pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t; + PyObject *__pyx_kp_s_no_default___reduce___due_to_non; + PyObject *__pyx_n_s_nonzero; + PyObject *__pyx_n_s_object; + PyObject *__pyx_n_s_off; + PyObject *__pyx_n_s_offset; + PyObject *__pyx_kp_u_operation_on_closed_HFile; + PyObject *__pyx_n_s_opts; + PyObject *__pyx_n_s_os; + PyObject *__pyx_n_s_other; + PyObject *__pyx_n_s_parse_region; + PyObject *__pyx_n_s_part; + PyObject *__pyx_n_s_parts; + PyObject *__pyx_n_s_prepare; + PyObject *__pyx_n_s_pysam_libchtslib; + PyObject *__pyx_kp_s_pysam_libchtslib_pyx; + PyObject *__pyx_n_s_pyx_state; + PyObject *__pyx_n_s_pyx_vtable; + PyObject *__pyx_n_s_qualname; + PyObject *__pyx_n_u_r; + PyObject *__pyx_n_s_re; + PyObject *__pyx_n_s_read; + PyObject *__pyx_n_s_readable; + PyObject *__pyx_n_s_readall; + PyObject *__pyx_n_s_readinto; + PyObject *__pyx_n_s_readline; + PyObject *__pyx_n_s_readlines; + PyObject *__pyx_n_s_reduce; + PyObject *__pyx_n_s_reduce_cython; + PyObject *__pyx_n_s_reduce_ex; + PyObject *__pyx_n_s_reference; + PyObject *__pyx_n_s_region; + PyObject *__pyx_n_s_replace; + PyObject *__pyx_n_s_reset; + PyObject *__pyx_n_s_ret; + PyObject *__pyx_n_s_rstart; + PyObject *__pyx_n_s_rstop; + PyObject *__pyx_n_s_rtid; + PyObject *__pyx_n_s_rval; + PyObject *__pyx_n_s_seek; + PyObject *__pyx_kp_u_seek_failed_on_HFile; + PyObject *__pyx_kp_u_seek_not_available_in_streams; + PyObject *__pyx_kp_u_seek_not_implemented_in_files_co; + PyObject *__pyx_n_s_seekable; + PyObject *__pyx_n_s_self; + PyObject *__pyx_kp_s_self_fp_cannot_be_converted_to_a; + PyObject *__pyx_n_s_set_name; + PyObject *__pyx_n_s_set_verbosity; + PyObject *__pyx_n_u_set_verbosity; + PyObject *__pyx_n_s_setstate; + PyObject *__pyx_n_s_setstate_cython; + PyObject *__pyx_n_s_size; + PyObject *__pyx_n_s_spec; + PyObject *__pyx_n_s_split; + PyObject *__pyx_n_s_start; + PyObject *__pyx_kp_u_start_out_of_range_i; + PyObject *__pyx_n_s_stop; + PyObject *__pyx_kp_u_stop_and_end_should_not_both_be; + PyObject *__pyx_kp_u_stop_out_of_range_i; + PyObject *__pyx_kp_s_stringsource; + PyObject *__pyx_n_s_super; + PyObject *__pyx_n_s_tb; + PyObject *__pyx_n_s_tell; + PyObject *__pyx_kp_u_tell_failed_on_HFile; + PyObject *__pyx_kp_u_tell_not_available_in_streams; + PyObject *__pyx_n_s_test; + PyObject *__pyx_n_s_tid; + PyObject *__pyx_n_s_traceback; + PyObject *__pyx_n_s_truncate; + PyObject *__pyx_n_s_type; + PyObject *__pyx_n_s_value; + PyObject *__pyx_n_s_verbosity; + PyObject *__pyx_n_u_w; + PyObject *__pyx_n_s_warn; + PyObject *__pyx_n_s_warnings; + PyObject *__pyx_n_s_whence; + PyObject *__pyx_n_s_writable; + PyObject *__pyx_n_s_write; + PyObject *__pyx_kp_u_write_failed_on_HFile; + PyObject *__pyx_n_s_writelines; + PyObject *__pyx_int_0; + PyObject *__pyx_int_1; + PyObject *__pyx_int_neg_1; + int __pyx_k__18; + int __pyx_k__41; + PyObject *__pyx_codeobj_; + PyObject *__pyx_tuple__5; + PyObject *__pyx_tuple__6; + PyObject *__pyx_tuple__39; + PyObject *__pyx_tuple__43; + PyObject *__pyx_tuple__44; + PyObject *__pyx_tuple__46; + PyObject *__pyx_tuple__47; + PyObject *__pyx_tuple__48; + PyObject *__pyx_tuple__49; + PyObject *__pyx_tuple__51; + PyObject *__pyx_tuple__53; + PyObject *__pyx_tuple__54; + PyObject *__pyx_tuple__57; + PyObject *__pyx_tuple__66; + PyObject *__pyx_tuple__67; + PyObject *__pyx_tuple__68; + PyObject *__pyx_tuple__69; + PyObject *__pyx_tuple__70; + PyObject *__pyx_tuple__71; + PyObject *__pyx_tuple__72; + PyObject *__pyx_tuple__73; + PyObject *__pyx_tuple__74; + PyObject *__pyx_tuple__75; + PyObject *__pyx_tuple__76; + PyObject *__pyx_tuple__77; + PyObject *__pyx_tuple__78; + PyObject *__pyx_tuple__79; + PyObject *__pyx_tuple__80; + PyObject *__pyx_tuple__81; + PyObject *__pyx_tuple__82; + PyObject *__pyx_tuple__83; + PyObject *__pyx_tuple__84; + PyObject *__pyx_tuple__85; + PyObject *__pyx_tuple__86; + PyObject *__pyx_tuple__87; + PyObject *__pyx_tuple__88; + PyObject *__pyx_tuple__89; + PyObject *__pyx_tuple__90; + PyObject *__pyx_tuple__91; + PyObject *__pyx_tuple__92; + PyObject *__pyx_tuple__93; + PyObject *__pyx_tuple__94; + PyObject *__pyx_tuple__95; + PyObject *__pyx_tuple__96; + PyObject *__pyx_codeobj__2; + PyObject *__pyx_codeobj__3; + PyObject *__pyx_codeobj__4; + PyObject *__pyx_codeobj__7; + PyObject *__pyx_codeobj__8; + PyObject *__pyx_codeobj__9; + PyObject *__pyx_codeobj__10; + PyObject *__pyx_codeobj__11; + PyObject *__pyx_codeobj__12; + PyObject *__pyx_codeobj__14; + PyObject *__pyx_codeobj__15; + PyObject *__pyx_codeobj__16; + PyObject *__pyx_codeobj__17; + PyObject *__pyx_codeobj__19; + PyObject *__pyx_codeobj__20; + PyObject *__pyx_codeobj__21; + PyObject *__pyx_codeobj__22; + PyObject *__pyx_codeobj__23; + PyObject *__pyx_codeobj__24; + PyObject *__pyx_codeobj__25; + PyObject *__pyx_codeobj__26; + PyObject *__pyx_codeobj__27; + PyObject *__pyx_codeobj__28; + PyObject *__pyx_codeobj__29; + PyObject *__pyx_codeobj__30; + PyObject *__pyx_codeobj__31; + PyObject *__pyx_codeobj__32; + PyObject *__pyx_codeobj__33; + PyObject *__pyx_codeobj__34; + PyObject *__pyx_codeobj__35; + PyObject *__pyx_codeobj__36; + PyObject *__pyx_codeobj__37; + PyObject *__pyx_codeobj__38; + PyObject *__pyx_codeobj__40; + PyObject *__pyx_codeobj__42; + PyObject *__pyx_codeobj__45; + PyObject *__pyx_codeobj__50; + PyObject *__pyx_codeobj__52; + PyObject *__pyx_codeobj__60; + PyObject *__pyx_codeobj__61; + PyObject *__pyx_codeobj__62; + PyObject *__pyx_codeobj__63; + PyObject *__pyx_codeobj__64; + PyObject *__pyx_codeobj__65; +} __pyx_mstate; + +#if CYTHON_USE_MODULE_STATE +#ifdef __cplusplus +namespace { + extern struct PyModuleDef __pyx_moduledef; +} /* anonymous namespace */ +#else +static struct PyModuleDef __pyx_moduledef; +#endif + +#define __pyx_mstate(o) ((__pyx_mstate *)__Pyx_PyModule_GetState(o)) + +#define __pyx_mstate_global (__pyx_mstate(PyState_FindModule(&__pyx_moduledef))) + +#define __pyx_m (PyState_FindModule(&__pyx_moduledef)) +#else +static __pyx_mstate __pyx_mstate_global_static = +#ifdef __cplusplus + {}; +#else + {0}; +#endif +static __pyx_mstate *__pyx_mstate_global = &__pyx_mstate_global_static; +#endif +/* #### Code section: module_state_clear ### */ +#if CYTHON_USE_MODULE_STATE +static int __pyx_m_clear(PyObject *m) { + __pyx_mstate *clear_module_state = __pyx_mstate(m); + if (!clear_module_state) return 0; + Py_CLEAR(clear_module_state->__pyx_d); + Py_CLEAR(clear_module_state->__pyx_b); + Py_CLEAR(clear_module_state->__pyx_cython_runtime); + Py_CLEAR(clear_module_state->__pyx_empty_tuple); + Py_CLEAR(clear_module_state->__pyx_empty_bytes); + Py_CLEAR(clear_module_state->__pyx_empty_unicode); + #ifdef __Pyx_CyFunction_USED + Py_CLEAR(clear_module_state->__pyx_CyFunctionType); + #endif + #ifdef __Pyx_FusedFunction_USED + Py_CLEAR(clear_module_state->__pyx_FusedFunctionType); + #endif + Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4type_type); + Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_4bool_bool); + Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_7complex_complex); + Py_CLEAR(clear_module_state->__pyx_ptype_7cpython_5array_array); + Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile); + Py_CLEAR(clear_module_state->__pyx_type_5pysam_10libchtslib_HTSFile); + Py_CLEAR(clear_module_state->__pyx_ptype_5pysam_10libchtslib_HFile); + Py_CLEAR(clear_module_state->__pyx_type_5pysam_10libchtslib_HFile); + Py_CLEAR(clear_module_state->__pyx_n_u_ALIGNMENTS); + Py_CLEAR(clear_module_state->__pyx_kp_u_An_error_occurred_while_applying); + Py_CLEAR(clear_module_state->__pyx_n_s_AttributeError); + Py_CLEAR(clear_module_state->__pyx_n_u_BAI); + Py_CLEAR(clear_module_state->__pyx_n_u_BAM); + Py_CLEAR(clear_module_state->__pyx_n_u_BCF); + Py_CLEAR(clear_module_state->__pyx_n_u_BED); + Py_CLEAR(clear_module_state->__pyx_n_u_BGZF); + Py_CLEAR(clear_module_state->__pyx_n_u_BINARY_FORMAT); + Py_CLEAR(clear_module_state->__pyx_n_s_CFalse); + Py_CLEAR(clear_module_state->__pyx_n_u_CRAI); + Py_CLEAR(clear_module_state->__pyx_n_u_CRAM); + Py_CLEAR(clear_module_state->__pyx_n_u_CSI); + Py_CLEAR(clear_module_state->__pyx_n_s_CTrue); + Py_CLEAR(clear_module_state->__pyx_n_u_CUSTOM); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue___bool); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue___call); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue___eq); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue___init); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue___ne); + Py_CLEAR(clear_module_state->__pyx_n_s_CallableValue___nonzero); + Py_CLEAR(clear_module_state->__pyx_kp_u_Cannot_create_hfile); + Py_CLEAR(clear_module_state->__pyx_kp_u_Flushing); + Py_CLEAR(clear_module_state->__pyx_n_u_GZI); + Py_CLEAR(clear_module_state->__pyx_n_u_GZIP); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile); + Py_CLEAR(clear_module_state->__pyx_n_u_HFile); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile___enter); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile___exit); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile___reduce_cython); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile___setstate_cython); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_close); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_fileno); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_flush); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_isatty); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_read); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_readable); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_readall); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_readinto); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_readline); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_readlines); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_seek); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_seekable); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_tell); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_truncate); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_writable); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_write); + Py_CLEAR(clear_module_state->__pyx_n_s_HFile_writelines); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile); + Py_CLEAR(clear_module_state->__pyx_n_u_HTSFile); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile___enter); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile___exit); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile___reduce_cython); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile___setstate_cython); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_add_hts_options); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_check_truncation); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_close); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_flush); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_get_reference_name); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_get_tid); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_is_valid_reference_name); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_is_valid_tid); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_parse_region); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_reset); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_seek); + Py_CLEAR(clear_module_state->__pyx_n_s_HTSFile_tell); + Py_CLEAR(clear_module_state->__pyx_n_u_INDEX); + Py_CLEAR(clear_module_state->__pyx_n_s_IOError); + Py_CLEAR(clear_module_state->__pyx_kp_u_I_O_operation_on_closed_file); + Py_CLEAR(clear_module_state->__pyx_n_s_IndexError); + Py_CLEAR(clear_module_state->__pyx_kp_u_Invalid_format_option_specified); + Py_CLEAR(clear_module_state->__pyx_n_s_MemoryError); + Py_CLEAR(clear_module_state->__pyx_n_u_NONE); + Py_CLEAR(clear_module_state->__pyx_n_s_NotImplementedError); + Py_CLEAR(clear_module_state->__pyx_n_s_OSError); + Py_CLEAR(clear_module_state->__pyx_n_s_OverflowError); + Py_CLEAR(clear_module_state->__pyx_n_u_REGIONS); + Py_CLEAR(clear_module_state->__pyx_n_s_RuntimeError); + Py_CLEAR(clear_module_state->__pyx_n_u_SAM); + Py_CLEAR(clear_module_state->__pyx_n_s_SEEK_SET); + Py_CLEAR(clear_module_state->__pyx_n_s_StopIteration); + Py_CLEAR(clear_module_state->__pyx_n_u_TBI); + Py_CLEAR(clear_module_state->__pyx_n_u_TEXT_FORMAT); + Py_CLEAR(clear_module_state->__pyx_n_s_TypeError); + Py_CLEAR(clear_module_state->__pyx_n_u_UNKNOWN); + Py_CLEAR(clear_module_state->__pyx_n_u_VARIANTS); + Py_CLEAR(clear_module_state->__pyx_n_u_VCF); + Py_CLEAR(clear_module_state->__pyx_n_s_ValueError); + Py_CLEAR(clear_module_state->__pyx_kp_b__13); + Py_CLEAR(clear_module_state->__pyx_kp_u__55); + Py_CLEAR(clear_module_state->__pyx_kp_u__56); + Py_CLEAR(clear_module_state->__pyx_n_s__58); + Py_CLEAR(clear_module_state->__pyx_kp_u__58); + Py_CLEAR(clear_module_state->__pyx_kp_u__59); + Py_CLEAR(clear_module_state->__pyx_n_s__97); + Py_CLEAR(clear_module_state->__pyx_n_s_add_hts_options); + Py_CLEAR(clear_module_state->__pyx_n_s_all); + Py_CLEAR(clear_module_state->__pyx_n_s_asyncio_coroutines); + Py_CLEAR(clear_module_state->__pyx_n_b_b); + Py_CLEAR(clear_module_state->__pyx_n_s_b); + Py_CLEAR(clear_module_state->__pyx_n_s_bgzfp); + Py_CLEAR(clear_module_state->__pyx_n_s_bool); + Py_CLEAR(clear_module_state->__pyx_n_s_buf); + Py_CLEAR(clear_module_state->__pyx_n_s_bytes_read); + Py_CLEAR(clear_module_state->__pyx_n_b_c); + Py_CLEAR(clear_module_state->__pyx_n_s_call); + Py_CLEAR(clear_module_state->__pyx_n_s_check_truncation); + Py_CLEAR(clear_module_state->__pyx_n_s_chunk_size); + Py_CLEAR(clear_module_state->__pyx_n_s_class_getitem); + Py_CLEAR(clear_module_state->__pyx_n_s_cline_in_traceback); + Py_CLEAR(clear_module_state->__pyx_n_s_close); + Py_CLEAR(clear_module_state->__pyx_n_s_closefd); + Py_CLEAR(clear_module_state->__pyx_n_s_contig); + Py_CLEAR(clear_module_state->__pyx_kp_u_contig_and_reference_should_not); + Py_CLEAR(clear_module_state->__pyx_n_s_coord); + Py_CLEAR(clear_module_state->__pyx_n_s_cpart); + Py_CLEAR(clear_module_state->__pyx_n_s_dict); + Py_CLEAR(clear_module_state->__pyx_kp_u_disable); + Py_CLEAR(clear_module_state->__pyx_n_s_doc); + Py_CLEAR(clear_module_state->__pyx_kp_u_enable); + Py_CLEAR(clear_module_state->__pyx_n_s_end); + Py_CLEAR(clear_module_state->__pyx_n_s_enter); + Py_CLEAR(clear_module_state->__pyx_n_s_eq); + Py_CLEAR(clear_module_state->__pyx_kp_u_error_checking_for_EOF_marker); + Py_CLEAR(clear_module_state->__pyx_n_s_exc_type); + Py_CLEAR(clear_module_state->__pyx_n_s_exc_value); + Py_CLEAR(clear_module_state->__pyx_n_s_exit); + Py_CLEAR(clear_module_state->__pyx_kp_u_failed); + Py_CLEAR(clear_module_state->__pyx_kp_u_failed_to_close_HFile); + Py_CLEAR(clear_module_state->__pyx_kp_u_failed_to_flush_HFile); + Py_CLEAR(clear_module_state->__pyx_kp_u_failed_to_open_HFile); + Py_CLEAR(clear_module_state->__pyx_kp_u_failed_to_read_HFile); + Py_CLEAR(clear_module_state->__pyx_kp_u_fd); + Py_CLEAR(clear_module_state->__pyx_n_s_fileno); + Py_CLEAR(clear_module_state->__pyx_kp_u_fileno_not_available); + Py_CLEAR(clear_module_state->__pyx_n_s_flush); + Py_CLEAR(clear_module_state->__pyx_n_s_format); + Py_CLEAR(clear_module_state->__pyx_n_s_format_option); + Py_CLEAR(clear_module_state->__pyx_n_s_format_options); + Py_CLEAR(clear_module_state->__pyx_n_s_fp); + Py_CLEAR(clear_module_state->__pyx_kp_u_gc); + Py_CLEAR(clear_module_state->__pyx_n_s_get_reference_name); + Py_CLEAR(clear_module_state->__pyx_n_s_get_tid); + Py_CLEAR(clear_module_state->__pyx_n_s_get_verbosity); + Py_CLEAR(clear_module_state->__pyx_n_u_get_verbosity); + Py_CLEAR(clear_module_state->__pyx_n_s_getstate); + Py_CLEAR(clear_module_state->__pyx_n_s_got); + Py_CLEAR(clear_module_state->__pyx_n_s_ignore_truncation); + Py_CLEAR(clear_module_state->__pyx_n_s_import); + Py_CLEAR(clear_module_state->__pyx_n_s_init); + Py_CLEAR(clear_module_state->__pyx_n_s_init_subclass); + Py_CLEAR(clear_module_state->__pyx_n_s_initializing); + Py_CLEAR(clear_module_state->__pyx_kp_u_invalid_contig_s); + Py_CLEAR(clear_module_state->__pyx_kp_u_invalid_coordinates_start_i_stop); + Py_CLEAR(clear_module_state->__pyx_kp_u_invalid_tid); + Py_CLEAR(clear_module_state->__pyx_n_s_io); + Py_CLEAR(clear_module_state->__pyx_n_s_is_coroutine); + Py_CLEAR(clear_module_state->__pyx_n_s_is_open); + Py_CLEAR(clear_module_state->__pyx_n_s_is_valid_reference_name); + Py_CLEAR(clear_module_state->__pyx_n_s_is_valid_tid); + Py_CLEAR(clear_module_state->__pyx_n_s_isatty); + Py_CLEAR(clear_module_state->__pyx_kp_u_isenabled); + Py_CLEAR(clear_module_state->__pyx_n_s_join); + Py_CLEAR(clear_module_state->__pyx_n_s_line); + Py_CLEAR(clear_module_state->__pyx_n_s_lines); + Py_CLEAR(clear_module_state->__pyx_n_s_main); + Py_CLEAR(clear_module_state->__pyx_n_s_metaclass); + Py_CLEAR(clear_module_state->__pyx_kp_u_metadata_not_available_on_closed); + Py_CLEAR(clear_module_state->__pyx_n_s_mode); + Py_CLEAR(clear_module_state->__pyx_n_s_module); + Py_CLEAR(clear_module_state->__pyx_n_s_mro_entries); + Py_CLEAR(clear_module_state->__pyx_n_s_msg); + Py_CLEAR(clear_module_state->__pyx_n_s_mv); + Py_CLEAR(clear_module_state->__pyx_n_s_name); + Py_CLEAR(clear_module_state->__pyx_n_s_name_2); + Py_CLEAR(clear_module_state->__pyx_n_s_ne); + Py_CLEAR(clear_module_state->__pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t); + Py_CLEAR(clear_module_state->__pyx_kp_s_no_default___reduce___due_to_non); + Py_CLEAR(clear_module_state->__pyx_n_s_nonzero); + Py_CLEAR(clear_module_state->__pyx_n_s_object); + Py_CLEAR(clear_module_state->__pyx_n_s_off); + Py_CLEAR(clear_module_state->__pyx_n_s_offset); + Py_CLEAR(clear_module_state->__pyx_kp_u_operation_on_closed_HFile); + Py_CLEAR(clear_module_state->__pyx_n_s_opts); + Py_CLEAR(clear_module_state->__pyx_n_s_os); + Py_CLEAR(clear_module_state->__pyx_n_s_other); + Py_CLEAR(clear_module_state->__pyx_n_s_parse_region); + Py_CLEAR(clear_module_state->__pyx_n_s_part); + Py_CLEAR(clear_module_state->__pyx_n_s_parts); + Py_CLEAR(clear_module_state->__pyx_n_s_prepare); + Py_CLEAR(clear_module_state->__pyx_n_s_pysam_libchtslib); + Py_CLEAR(clear_module_state->__pyx_kp_s_pysam_libchtslib_pyx); + Py_CLEAR(clear_module_state->__pyx_n_s_pyx_state); + Py_CLEAR(clear_module_state->__pyx_n_s_pyx_vtable); + Py_CLEAR(clear_module_state->__pyx_n_s_qualname); + Py_CLEAR(clear_module_state->__pyx_n_u_r); + Py_CLEAR(clear_module_state->__pyx_n_s_re); + Py_CLEAR(clear_module_state->__pyx_n_s_read); + Py_CLEAR(clear_module_state->__pyx_n_s_readable); + Py_CLEAR(clear_module_state->__pyx_n_s_readall); + Py_CLEAR(clear_module_state->__pyx_n_s_readinto); + Py_CLEAR(clear_module_state->__pyx_n_s_readline); + Py_CLEAR(clear_module_state->__pyx_n_s_readlines); + Py_CLEAR(clear_module_state->__pyx_n_s_reduce); + Py_CLEAR(clear_module_state->__pyx_n_s_reduce_cython); + Py_CLEAR(clear_module_state->__pyx_n_s_reduce_ex); + Py_CLEAR(clear_module_state->__pyx_n_s_reference); + Py_CLEAR(clear_module_state->__pyx_n_s_region); + Py_CLEAR(clear_module_state->__pyx_n_s_replace); + Py_CLEAR(clear_module_state->__pyx_n_s_reset); + Py_CLEAR(clear_module_state->__pyx_n_s_ret); + Py_CLEAR(clear_module_state->__pyx_n_s_rstart); + Py_CLEAR(clear_module_state->__pyx_n_s_rstop); + Py_CLEAR(clear_module_state->__pyx_n_s_rtid); + Py_CLEAR(clear_module_state->__pyx_n_s_rval); + Py_CLEAR(clear_module_state->__pyx_n_s_seek); + Py_CLEAR(clear_module_state->__pyx_kp_u_seek_failed_on_HFile); + Py_CLEAR(clear_module_state->__pyx_kp_u_seek_not_available_in_streams); + Py_CLEAR(clear_module_state->__pyx_kp_u_seek_not_implemented_in_files_co); + Py_CLEAR(clear_module_state->__pyx_n_s_seekable); + Py_CLEAR(clear_module_state->__pyx_n_s_self); + Py_CLEAR(clear_module_state->__pyx_kp_s_self_fp_cannot_be_converted_to_a); + Py_CLEAR(clear_module_state->__pyx_n_s_set_name); + Py_CLEAR(clear_module_state->__pyx_n_s_set_verbosity); + Py_CLEAR(clear_module_state->__pyx_n_u_set_verbosity); + Py_CLEAR(clear_module_state->__pyx_n_s_setstate); + Py_CLEAR(clear_module_state->__pyx_n_s_setstate_cython); + Py_CLEAR(clear_module_state->__pyx_n_s_size); + Py_CLEAR(clear_module_state->__pyx_n_s_spec); + Py_CLEAR(clear_module_state->__pyx_n_s_split); + Py_CLEAR(clear_module_state->__pyx_n_s_start); + Py_CLEAR(clear_module_state->__pyx_kp_u_start_out_of_range_i); + Py_CLEAR(clear_module_state->__pyx_n_s_stop); + Py_CLEAR(clear_module_state->__pyx_kp_u_stop_and_end_should_not_both_be); + Py_CLEAR(clear_module_state->__pyx_kp_u_stop_out_of_range_i); + Py_CLEAR(clear_module_state->__pyx_kp_s_stringsource); + Py_CLEAR(clear_module_state->__pyx_n_s_super); + Py_CLEAR(clear_module_state->__pyx_n_s_tb); + Py_CLEAR(clear_module_state->__pyx_n_s_tell); + Py_CLEAR(clear_module_state->__pyx_kp_u_tell_failed_on_HFile); + Py_CLEAR(clear_module_state->__pyx_kp_u_tell_not_available_in_streams); + Py_CLEAR(clear_module_state->__pyx_n_s_test); + Py_CLEAR(clear_module_state->__pyx_n_s_tid); + Py_CLEAR(clear_module_state->__pyx_n_s_traceback); + Py_CLEAR(clear_module_state->__pyx_n_s_truncate); + Py_CLEAR(clear_module_state->__pyx_n_s_type); + Py_CLEAR(clear_module_state->__pyx_n_s_value); + Py_CLEAR(clear_module_state->__pyx_n_s_verbosity); + Py_CLEAR(clear_module_state->__pyx_n_u_w); + Py_CLEAR(clear_module_state->__pyx_n_s_warn); + Py_CLEAR(clear_module_state->__pyx_n_s_warnings); + Py_CLEAR(clear_module_state->__pyx_n_s_whence); + Py_CLEAR(clear_module_state->__pyx_n_s_writable); + Py_CLEAR(clear_module_state->__pyx_n_s_write); + Py_CLEAR(clear_module_state->__pyx_kp_u_write_failed_on_HFile); + Py_CLEAR(clear_module_state->__pyx_n_s_writelines); + Py_CLEAR(clear_module_state->__pyx_int_0); + Py_CLEAR(clear_module_state->__pyx_int_1); + Py_CLEAR(clear_module_state->__pyx_int_neg_1); + Py_CLEAR(clear_module_state->__pyx_codeobj_); + Py_CLEAR(clear_module_state->__pyx_tuple__5); + Py_CLEAR(clear_module_state->__pyx_tuple__6); + Py_CLEAR(clear_module_state->__pyx_tuple__39); + Py_CLEAR(clear_module_state->__pyx_tuple__43); + Py_CLEAR(clear_module_state->__pyx_tuple__44); + Py_CLEAR(clear_module_state->__pyx_tuple__46); + Py_CLEAR(clear_module_state->__pyx_tuple__47); + Py_CLEAR(clear_module_state->__pyx_tuple__48); + Py_CLEAR(clear_module_state->__pyx_tuple__49); + Py_CLEAR(clear_module_state->__pyx_tuple__51); + Py_CLEAR(clear_module_state->__pyx_tuple__53); + Py_CLEAR(clear_module_state->__pyx_tuple__54); + Py_CLEAR(clear_module_state->__pyx_tuple__57); + Py_CLEAR(clear_module_state->__pyx_tuple__66); + Py_CLEAR(clear_module_state->__pyx_tuple__67); + Py_CLEAR(clear_module_state->__pyx_tuple__68); + Py_CLEAR(clear_module_state->__pyx_tuple__69); + Py_CLEAR(clear_module_state->__pyx_tuple__70); + Py_CLEAR(clear_module_state->__pyx_tuple__71); + Py_CLEAR(clear_module_state->__pyx_tuple__72); + Py_CLEAR(clear_module_state->__pyx_tuple__73); + Py_CLEAR(clear_module_state->__pyx_tuple__74); + Py_CLEAR(clear_module_state->__pyx_tuple__75); + Py_CLEAR(clear_module_state->__pyx_tuple__76); + Py_CLEAR(clear_module_state->__pyx_tuple__77); + Py_CLEAR(clear_module_state->__pyx_tuple__78); + Py_CLEAR(clear_module_state->__pyx_tuple__79); + Py_CLEAR(clear_module_state->__pyx_tuple__80); + Py_CLEAR(clear_module_state->__pyx_tuple__81); + Py_CLEAR(clear_module_state->__pyx_tuple__82); + Py_CLEAR(clear_module_state->__pyx_tuple__83); + Py_CLEAR(clear_module_state->__pyx_tuple__84); + Py_CLEAR(clear_module_state->__pyx_tuple__85); + Py_CLEAR(clear_module_state->__pyx_tuple__86); + Py_CLEAR(clear_module_state->__pyx_tuple__87); + Py_CLEAR(clear_module_state->__pyx_tuple__88); + Py_CLEAR(clear_module_state->__pyx_tuple__89); + Py_CLEAR(clear_module_state->__pyx_tuple__90); + Py_CLEAR(clear_module_state->__pyx_tuple__91); + Py_CLEAR(clear_module_state->__pyx_tuple__92); + Py_CLEAR(clear_module_state->__pyx_tuple__93); + Py_CLEAR(clear_module_state->__pyx_tuple__94); + Py_CLEAR(clear_module_state->__pyx_tuple__95); + Py_CLEAR(clear_module_state->__pyx_tuple__96); + Py_CLEAR(clear_module_state->__pyx_codeobj__2); + Py_CLEAR(clear_module_state->__pyx_codeobj__3); + Py_CLEAR(clear_module_state->__pyx_codeobj__4); + Py_CLEAR(clear_module_state->__pyx_codeobj__7); + Py_CLEAR(clear_module_state->__pyx_codeobj__8); + Py_CLEAR(clear_module_state->__pyx_codeobj__9); + Py_CLEAR(clear_module_state->__pyx_codeobj__10); + Py_CLEAR(clear_module_state->__pyx_codeobj__11); + Py_CLEAR(clear_module_state->__pyx_codeobj__12); + Py_CLEAR(clear_module_state->__pyx_codeobj__14); + Py_CLEAR(clear_module_state->__pyx_codeobj__15); + Py_CLEAR(clear_module_state->__pyx_codeobj__16); + Py_CLEAR(clear_module_state->__pyx_codeobj__17); + Py_CLEAR(clear_module_state->__pyx_codeobj__19); + Py_CLEAR(clear_module_state->__pyx_codeobj__20); + Py_CLEAR(clear_module_state->__pyx_codeobj__21); + Py_CLEAR(clear_module_state->__pyx_codeobj__22); + Py_CLEAR(clear_module_state->__pyx_codeobj__23); + Py_CLEAR(clear_module_state->__pyx_codeobj__24); + Py_CLEAR(clear_module_state->__pyx_codeobj__25); + Py_CLEAR(clear_module_state->__pyx_codeobj__26); + Py_CLEAR(clear_module_state->__pyx_codeobj__27); + Py_CLEAR(clear_module_state->__pyx_codeobj__28); + Py_CLEAR(clear_module_state->__pyx_codeobj__29); + Py_CLEAR(clear_module_state->__pyx_codeobj__30); + Py_CLEAR(clear_module_state->__pyx_codeobj__31); + Py_CLEAR(clear_module_state->__pyx_codeobj__32); + Py_CLEAR(clear_module_state->__pyx_codeobj__33); + Py_CLEAR(clear_module_state->__pyx_codeobj__34); + Py_CLEAR(clear_module_state->__pyx_codeobj__35); + Py_CLEAR(clear_module_state->__pyx_codeobj__36); + Py_CLEAR(clear_module_state->__pyx_codeobj__37); + Py_CLEAR(clear_module_state->__pyx_codeobj__38); + Py_CLEAR(clear_module_state->__pyx_codeobj__40); + Py_CLEAR(clear_module_state->__pyx_codeobj__42); + Py_CLEAR(clear_module_state->__pyx_codeobj__45); + Py_CLEAR(clear_module_state->__pyx_codeobj__50); + Py_CLEAR(clear_module_state->__pyx_codeobj__52); + Py_CLEAR(clear_module_state->__pyx_codeobj__60); + Py_CLEAR(clear_module_state->__pyx_codeobj__61); + Py_CLEAR(clear_module_state->__pyx_codeobj__62); + Py_CLEAR(clear_module_state->__pyx_codeobj__63); + Py_CLEAR(clear_module_state->__pyx_codeobj__64); + Py_CLEAR(clear_module_state->__pyx_codeobj__65); + return 0; +} +#endif +/* #### Code section: module_state_traverse ### */ +#if CYTHON_USE_MODULE_STATE +static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { + __pyx_mstate *traverse_module_state = __pyx_mstate(m); + if (!traverse_module_state) return 0; + Py_VISIT(traverse_module_state->__pyx_d); + Py_VISIT(traverse_module_state->__pyx_b); + Py_VISIT(traverse_module_state->__pyx_cython_runtime); + Py_VISIT(traverse_module_state->__pyx_empty_tuple); + Py_VISIT(traverse_module_state->__pyx_empty_bytes); + Py_VISIT(traverse_module_state->__pyx_empty_unicode); + #ifdef __Pyx_CyFunction_USED + Py_VISIT(traverse_module_state->__pyx_CyFunctionType); + #endif + #ifdef __Pyx_FusedFunction_USED + Py_VISIT(traverse_module_state->__pyx_FusedFunctionType); + #endif + Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4type_type); + Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_4bool_bool); + Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_7complex_complex); + Py_VISIT(traverse_module_state->__pyx_ptype_7cpython_5array_array); + Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_10libchtslib_HTSFile); + Py_VISIT(traverse_module_state->__pyx_type_5pysam_10libchtslib_HTSFile); + Py_VISIT(traverse_module_state->__pyx_ptype_5pysam_10libchtslib_HFile); + Py_VISIT(traverse_module_state->__pyx_type_5pysam_10libchtslib_HFile); + Py_VISIT(traverse_module_state->__pyx_n_u_ALIGNMENTS); + Py_VISIT(traverse_module_state->__pyx_kp_u_An_error_occurred_while_applying); + Py_VISIT(traverse_module_state->__pyx_n_s_AttributeError); + Py_VISIT(traverse_module_state->__pyx_n_u_BAI); + Py_VISIT(traverse_module_state->__pyx_n_u_BAM); + Py_VISIT(traverse_module_state->__pyx_n_u_BCF); + Py_VISIT(traverse_module_state->__pyx_n_u_BED); + Py_VISIT(traverse_module_state->__pyx_n_u_BGZF); + Py_VISIT(traverse_module_state->__pyx_n_u_BINARY_FORMAT); + Py_VISIT(traverse_module_state->__pyx_n_s_CFalse); + Py_VISIT(traverse_module_state->__pyx_n_u_CRAI); + Py_VISIT(traverse_module_state->__pyx_n_u_CRAM); + Py_VISIT(traverse_module_state->__pyx_n_u_CSI); + Py_VISIT(traverse_module_state->__pyx_n_s_CTrue); + Py_VISIT(traverse_module_state->__pyx_n_u_CUSTOM); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue___bool); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue___call); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue___eq); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue___init); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue___ne); + Py_VISIT(traverse_module_state->__pyx_n_s_CallableValue___nonzero); + Py_VISIT(traverse_module_state->__pyx_kp_u_Cannot_create_hfile); + Py_VISIT(traverse_module_state->__pyx_kp_u_Flushing); + Py_VISIT(traverse_module_state->__pyx_n_u_GZI); + Py_VISIT(traverse_module_state->__pyx_n_u_GZIP); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile); + Py_VISIT(traverse_module_state->__pyx_n_u_HFile); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile___enter); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile___exit); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile___reduce_cython); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile___setstate_cython); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_close); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_fileno); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_flush); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_isatty); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_read); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_readable); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_readall); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_readinto); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_readline); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_readlines); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_seek); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_seekable); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_tell); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_truncate); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_writable); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_write); + Py_VISIT(traverse_module_state->__pyx_n_s_HFile_writelines); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile); + Py_VISIT(traverse_module_state->__pyx_n_u_HTSFile); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile___enter); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile___exit); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile___reduce_cython); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile___setstate_cython); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_add_hts_options); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_check_truncation); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_close); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_flush); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_get_reference_name); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_get_tid); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_is_valid_reference_name); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_is_valid_tid); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_parse_region); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_reset); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_seek); + Py_VISIT(traverse_module_state->__pyx_n_s_HTSFile_tell); + Py_VISIT(traverse_module_state->__pyx_n_u_INDEX); + Py_VISIT(traverse_module_state->__pyx_n_s_IOError); + Py_VISIT(traverse_module_state->__pyx_kp_u_I_O_operation_on_closed_file); + Py_VISIT(traverse_module_state->__pyx_n_s_IndexError); + Py_VISIT(traverse_module_state->__pyx_kp_u_Invalid_format_option_specified); + Py_VISIT(traverse_module_state->__pyx_n_s_MemoryError); + Py_VISIT(traverse_module_state->__pyx_n_u_NONE); + Py_VISIT(traverse_module_state->__pyx_n_s_NotImplementedError); + Py_VISIT(traverse_module_state->__pyx_n_s_OSError); + Py_VISIT(traverse_module_state->__pyx_n_s_OverflowError); + Py_VISIT(traverse_module_state->__pyx_n_u_REGIONS); + Py_VISIT(traverse_module_state->__pyx_n_s_RuntimeError); + Py_VISIT(traverse_module_state->__pyx_n_u_SAM); + Py_VISIT(traverse_module_state->__pyx_n_s_SEEK_SET); + Py_VISIT(traverse_module_state->__pyx_n_s_StopIteration); + Py_VISIT(traverse_module_state->__pyx_n_u_TBI); + Py_VISIT(traverse_module_state->__pyx_n_u_TEXT_FORMAT); + Py_VISIT(traverse_module_state->__pyx_n_s_TypeError); + Py_VISIT(traverse_module_state->__pyx_n_u_UNKNOWN); + Py_VISIT(traverse_module_state->__pyx_n_u_VARIANTS); + Py_VISIT(traverse_module_state->__pyx_n_u_VCF); + Py_VISIT(traverse_module_state->__pyx_n_s_ValueError); + Py_VISIT(traverse_module_state->__pyx_kp_b__13); + Py_VISIT(traverse_module_state->__pyx_kp_u__55); + Py_VISIT(traverse_module_state->__pyx_kp_u__56); + Py_VISIT(traverse_module_state->__pyx_n_s__58); + Py_VISIT(traverse_module_state->__pyx_kp_u__58); + Py_VISIT(traverse_module_state->__pyx_kp_u__59); + Py_VISIT(traverse_module_state->__pyx_n_s__97); + Py_VISIT(traverse_module_state->__pyx_n_s_add_hts_options); + Py_VISIT(traverse_module_state->__pyx_n_s_all); + Py_VISIT(traverse_module_state->__pyx_n_s_asyncio_coroutines); + Py_VISIT(traverse_module_state->__pyx_n_b_b); + Py_VISIT(traverse_module_state->__pyx_n_s_b); + Py_VISIT(traverse_module_state->__pyx_n_s_bgzfp); + Py_VISIT(traverse_module_state->__pyx_n_s_bool); + Py_VISIT(traverse_module_state->__pyx_n_s_buf); + Py_VISIT(traverse_module_state->__pyx_n_s_bytes_read); + Py_VISIT(traverse_module_state->__pyx_n_b_c); + Py_VISIT(traverse_module_state->__pyx_n_s_call); + Py_VISIT(traverse_module_state->__pyx_n_s_check_truncation); + Py_VISIT(traverse_module_state->__pyx_n_s_chunk_size); + Py_VISIT(traverse_module_state->__pyx_n_s_class_getitem); + Py_VISIT(traverse_module_state->__pyx_n_s_cline_in_traceback); + Py_VISIT(traverse_module_state->__pyx_n_s_close); + Py_VISIT(traverse_module_state->__pyx_n_s_closefd); + Py_VISIT(traverse_module_state->__pyx_n_s_contig); + Py_VISIT(traverse_module_state->__pyx_kp_u_contig_and_reference_should_not); + Py_VISIT(traverse_module_state->__pyx_n_s_coord); + Py_VISIT(traverse_module_state->__pyx_n_s_cpart); + Py_VISIT(traverse_module_state->__pyx_n_s_dict); + Py_VISIT(traverse_module_state->__pyx_kp_u_disable); + Py_VISIT(traverse_module_state->__pyx_n_s_doc); + Py_VISIT(traverse_module_state->__pyx_kp_u_enable); + Py_VISIT(traverse_module_state->__pyx_n_s_end); + Py_VISIT(traverse_module_state->__pyx_n_s_enter); + Py_VISIT(traverse_module_state->__pyx_n_s_eq); + Py_VISIT(traverse_module_state->__pyx_kp_u_error_checking_for_EOF_marker); + Py_VISIT(traverse_module_state->__pyx_n_s_exc_type); + Py_VISIT(traverse_module_state->__pyx_n_s_exc_value); + Py_VISIT(traverse_module_state->__pyx_n_s_exit); + Py_VISIT(traverse_module_state->__pyx_kp_u_failed); + Py_VISIT(traverse_module_state->__pyx_kp_u_failed_to_close_HFile); + Py_VISIT(traverse_module_state->__pyx_kp_u_failed_to_flush_HFile); + Py_VISIT(traverse_module_state->__pyx_kp_u_failed_to_open_HFile); + Py_VISIT(traverse_module_state->__pyx_kp_u_failed_to_read_HFile); + Py_VISIT(traverse_module_state->__pyx_kp_u_fd); + Py_VISIT(traverse_module_state->__pyx_n_s_fileno); + Py_VISIT(traverse_module_state->__pyx_kp_u_fileno_not_available); + Py_VISIT(traverse_module_state->__pyx_n_s_flush); + Py_VISIT(traverse_module_state->__pyx_n_s_format); + Py_VISIT(traverse_module_state->__pyx_n_s_format_option); + Py_VISIT(traverse_module_state->__pyx_n_s_format_options); + Py_VISIT(traverse_module_state->__pyx_n_s_fp); + Py_VISIT(traverse_module_state->__pyx_kp_u_gc); + Py_VISIT(traverse_module_state->__pyx_n_s_get_reference_name); + Py_VISIT(traverse_module_state->__pyx_n_s_get_tid); + Py_VISIT(traverse_module_state->__pyx_n_s_get_verbosity); + Py_VISIT(traverse_module_state->__pyx_n_u_get_verbosity); + Py_VISIT(traverse_module_state->__pyx_n_s_getstate); + Py_VISIT(traverse_module_state->__pyx_n_s_got); + Py_VISIT(traverse_module_state->__pyx_n_s_ignore_truncation); + Py_VISIT(traverse_module_state->__pyx_n_s_import); + Py_VISIT(traverse_module_state->__pyx_n_s_init); + Py_VISIT(traverse_module_state->__pyx_n_s_init_subclass); + Py_VISIT(traverse_module_state->__pyx_n_s_initializing); + Py_VISIT(traverse_module_state->__pyx_kp_u_invalid_contig_s); + Py_VISIT(traverse_module_state->__pyx_kp_u_invalid_coordinates_start_i_stop); + Py_VISIT(traverse_module_state->__pyx_kp_u_invalid_tid); + Py_VISIT(traverse_module_state->__pyx_n_s_io); + Py_VISIT(traverse_module_state->__pyx_n_s_is_coroutine); + Py_VISIT(traverse_module_state->__pyx_n_s_is_open); + Py_VISIT(traverse_module_state->__pyx_n_s_is_valid_reference_name); + Py_VISIT(traverse_module_state->__pyx_n_s_is_valid_tid); + Py_VISIT(traverse_module_state->__pyx_n_s_isatty); + Py_VISIT(traverse_module_state->__pyx_kp_u_isenabled); + Py_VISIT(traverse_module_state->__pyx_n_s_join); + Py_VISIT(traverse_module_state->__pyx_n_s_line); + Py_VISIT(traverse_module_state->__pyx_n_s_lines); + Py_VISIT(traverse_module_state->__pyx_n_s_main); + Py_VISIT(traverse_module_state->__pyx_n_s_metaclass); + Py_VISIT(traverse_module_state->__pyx_kp_u_metadata_not_available_on_closed); + Py_VISIT(traverse_module_state->__pyx_n_s_mode); + Py_VISIT(traverse_module_state->__pyx_n_s_module); + Py_VISIT(traverse_module_state->__pyx_n_s_mro_entries); + Py_VISIT(traverse_module_state->__pyx_n_s_msg); + Py_VISIT(traverse_module_state->__pyx_n_s_mv); + Py_VISIT(traverse_module_state->__pyx_n_s_name); + Py_VISIT(traverse_module_state->__pyx_n_s_name_2); + Py_VISIT(traverse_module_state->__pyx_n_s_ne); + Py_VISIT(traverse_module_state->__pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t); + Py_VISIT(traverse_module_state->__pyx_kp_s_no_default___reduce___due_to_non); + Py_VISIT(traverse_module_state->__pyx_n_s_nonzero); + Py_VISIT(traverse_module_state->__pyx_n_s_object); + Py_VISIT(traverse_module_state->__pyx_n_s_off); + Py_VISIT(traverse_module_state->__pyx_n_s_offset); + Py_VISIT(traverse_module_state->__pyx_kp_u_operation_on_closed_HFile); + Py_VISIT(traverse_module_state->__pyx_n_s_opts); + Py_VISIT(traverse_module_state->__pyx_n_s_os); + Py_VISIT(traverse_module_state->__pyx_n_s_other); + Py_VISIT(traverse_module_state->__pyx_n_s_parse_region); + Py_VISIT(traverse_module_state->__pyx_n_s_part); + Py_VISIT(traverse_module_state->__pyx_n_s_parts); + Py_VISIT(traverse_module_state->__pyx_n_s_prepare); + Py_VISIT(traverse_module_state->__pyx_n_s_pysam_libchtslib); + Py_VISIT(traverse_module_state->__pyx_kp_s_pysam_libchtslib_pyx); + Py_VISIT(traverse_module_state->__pyx_n_s_pyx_state); + Py_VISIT(traverse_module_state->__pyx_n_s_pyx_vtable); + Py_VISIT(traverse_module_state->__pyx_n_s_qualname); + Py_VISIT(traverse_module_state->__pyx_n_u_r); + Py_VISIT(traverse_module_state->__pyx_n_s_re); + Py_VISIT(traverse_module_state->__pyx_n_s_read); + Py_VISIT(traverse_module_state->__pyx_n_s_readable); + Py_VISIT(traverse_module_state->__pyx_n_s_readall); + Py_VISIT(traverse_module_state->__pyx_n_s_readinto); + Py_VISIT(traverse_module_state->__pyx_n_s_readline); + Py_VISIT(traverse_module_state->__pyx_n_s_readlines); + Py_VISIT(traverse_module_state->__pyx_n_s_reduce); + Py_VISIT(traverse_module_state->__pyx_n_s_reduce_cython); + Py_VISIT(traverse_module_state->__pyx_n_s_reduce_ex); + Py_VISIT(traverse_module_state->__pyx_n_s_reference); + Py_VISIT(traverse_module_state->__pyx_n_s_region); + Py_VISIT(traverse_module_state->__pyx_n_s_replace); + Py_VISIT(traverse_module_state->__pyx_n_s_reset); + Py_VISIT(traverse_module_state->__pyx_n_s_ret); + Py_VISIT(traverse_module_state->__pyx_n_s_rstart); + Py_VISIT(traverse_module_state->__pyx_n_s_rstop); + Py_VISIT(traverse_module_state->__pyx_n_s_rtid); + Py_VISIT(traverse_module_state->__pyx_n_s_rval); + Py_VISIT(traverse_module_state->__pyx_n_s_seek); + Py_VISIT(traverse_module_state->__pyx_kp_u_seek_failed_on_HFile); + Py_VISIT(traverse_module_state->__pyx_kp_u_seek_not_available_in_streams); + Py_VISIT(traverse_module_state->__pyx_kp_u_seek_not_implemented_in_files_co); + Py_VISIT(traverse_module_state->__pyx_n_s_seekable); + Py_VISIT(traverse_module_state->__pyx_n_s_self); + Py_VISIT(traverse_module_state->__pyx_kp_s_self_fp_cannot_be_converted_to_a); + Py_VISIT(traverse_module_state->__pyx_n_s_set_name); + Py_VISIT(traverse_module_state->__pyx_n_s_set_verbosity); + Py_VISIT(traverse_module_state->__pyx_n_u_set_verbosity); + Py_VISIT(traverse_module_state->__pyx_n_s_setstate); + Py_VISIT(traverse_module_state->__pyx_n_s_setstate_cython); + Py_VISIT(traverse_module_state->__pyx_n_s_size); + Py_VISIT(traverse_module_state->__pyx_n_s_spec); + Py_VISIT(traverse_module_state->__pyx_n_s_split); + Py_VISIT(traverse_module_state->__pyx_n_s_start); + Py_VISIT(traverse_module_state->__pyx_kp_u_start_out_of_range_i); + Py_VISIT(traverse_module_state->__pyx_n_s_stop); + Py_VISIT(traverse_module_state->__pyx_kp_u_stop_and_end_should_not_both_be); + Py_VISIT(traverse_module_state->__pyx_kp_u_stop_out_of_range_i); + Py_VISIT(traverse_module_state->__pyx_kp_s_stringsource); + Py_VISIT(traverse_module_state->__pyx_n_s_super); + Py_VISIT(traverse_module_state->__pyx_n_s_tb); + Py_VISIT(traverse_module_state->__pyx_n_s_tell); + Py_VISIT(traverse_module_state->__pyx_kp_u_tell_failed_on_HFile); + Py_VISIT(traverse_module_state->__pyx_kp_u_tell_not_available_in_streams); + Py_VISIT(traverse_module_state->__pyx_n_s_test); + Py_VISIT(traverse_module_state->__pyx_n_s_tid); + Py_VISIT(traverse_module_state->__pyx_n_s_traceback); + Py_VISIT(traverse_module_state->__pyx_n_s_truncate); + Py_VISIT(traverse_module_state->__pyx_n_s_type); + Py_VISIT(traverse_module_state->__pyx_n_s_value); + Py_VISIT(traverse_module_state->__pyx_n_s_verbosity); + Py_VISIT(traverse_module_state->__pyx_n_u_w); + Py_VISIT(traverse_module_state->__pyx_n_s_warn); + Py_VISIT(traverse_module_state->__pyx_n_s_warnings); + Py_VISIT(traverse_module_state->__pyx_n_s_whence); + Py_VISIT(traverse_module_state->__pyx_n_s_writable); + Py_VISIT(traverse_module_state->__pyx_n_s_write); + Py_VISIT(traverse_module_state->__pyx_kp_u_write_failed_on_HFile); + Py_VISIT(traverse_module_state->__pyx_n_s_writelines); + Py_VISIT(traverse_module_state->__pyx_int_0); + Py_VISIT(traverse_module_state->__pyx_int_1); + Py_VISIT(traverse_module_state->__pyx_int_neg_1); + Py_VISIT(traverse_module_state->__pyx_codeobj_); + Py_VISIT(traverse_module_state->__pyx_tuple__5); + Py_VISIT(traverse_module_state->__pyx_tuple__6); + Py_VISIT(traverse_module_state->__pyx_tuple__39); + Py_VISIT(traverse_module_state->__pyx_tuple__43); + Py_VISIT(traverse_module_state->__pyx_tuple__44); + Py_VISIT(traverse_module_state->__pyx_tuple__46); + Py_VISIT(traverse_module_state->__pyx_tuple__47); + Py_VISIT(traverse_module_state->__pyx_tuple__48); + Py_VISIT(traverse_module_state->__pyx_tuple__49); + Py_VISIT(traverse_module_state->__pyx_tuple__51); + Py_VISIT(traverse_module_state->__pyx_tuple__53); + Py_VISIT(traverse_module_state->__pyx_tuple__54); + Py_VISIT(traverse_module_state->__pyx_tuple__57); + Py_VISIT(traverse_module_state->__pyx_tuple__66); + Py_VISIT(traverse_module_state->__pyx_tuple__67); + Py_VISIT(traverse_module_state->__pyx_tuple__68); + Py_VISIT(traverse_module_state->__pyx_tuple__69); + Py_VISIT(traverse_module_state->__pyx_tuple__70); + Py_VISIT(traverse_module_state->__pyx_tuple__71); + Py_VISIT(traverse_module_state->__pyx_tuple__72); + Py_VISIT(traverse_module_state->__pyx_tuple__73); + Py_VISIT(traverse_module_state->__pyx_tuple__74); + Py_VISIT(traverse_module_state->__pyx_tuple__75); + Py_VISIT(traverse_module_state->__pyx_tuple__76); + Py_VISIT(traverse_module_state->__pyx_tuple__77); + Py_VISIT(traverse_module_state->__pyx_tuple__78); + Py_VISIT(traverse_module_state->__pyx_tuple__79); + Py_VISIT(traverse_module_state->__pyx_tuple__80); + Py_VISIT(traverse_module_state->__pyx_tuple__81); + Py_VISIT(traverse_module_state->__pyx_tuple__82); + Py_VISIT(traverse_module_state->__pyx_tuple__83); + Py_VISIT(traverse_module_state->__pyx_tuple__84); + Py_VISIT(traverse_module_state->__pyx_tuple__85); + Py_VISIT(traverse_module_state->__pyx_tuple__86); + Py_VISIT(traverse_module_state->__pyx_tuple__87); + Py_VISIT(traverse_module_state->__pyx_tuple__88); + Py_VISIT(traverse_module_state->__pyx_tuple__89); + Py_VISIT(traverse_module_state->__pyx_tuple__90); + Py_VISIT(traverse_module_state->__pyx_tuple__91); + Py_VISIT(traverse_module_state->__pyx_tuple__92); + Py_VISIT(traverse_module_state->__pyx_tuple__93); + Py_VISIT(traverse_module_state->__pyx_tuple__94); + Py_VISIT(traverse_module_state->__pyx_tuple__95); + Py_VISIT(traverse_module_state->__pyx_tuple__96); + Py_VISIT(traverse_module_state->__pyx_codeobj__2); + Py_VISIT(traverse_module_state->__pyx_codeobj__3); + Py_VISIT(traverse_module_state->__pyx_codeobj__4); + Py_VISIT(traverse_module_state->__pyx_codeobj__7); + Py_VISIT(traverse_module_state->__pyx_codeobj__8); + Py_VISIT(traverse_module_state->__pyx_codeobj__9); + Py_VISIT(traverse_module_state->__pyx_codeobj__10); + Py_VISIT(traverse_module_state->__pyx_codeobj__11); + Py_VISIT(traverse_module_state->__pyx_codeobj__12); + Py_VISIT(traverse_module_state->__pyx_codeobj__14); + Py_VISIT(traverse_module_state->__pyx_codeobj__15); + Py_VISIT(traverse_module_state->__pyx_codeobj__16); + Py_VISIT(traverse_module_state->__pyx_codeobj__17); + Py_VISIT(traverse_module_state->__pyx_codeobj__19); + Py_VISIT(traverse_module_state->__pyx_codeobj__20); + Py_VISIT(traverse_module_state->__pyx_codeobj__21); + Py_VISIT(traverse_module_state->__pyx_codeobj__22); + Py_VISIT(traverse_module_state->__pyx_codeobj__23); + Py_VISIT(traverse_module_state->__pyx_codeobj__24); + Py_VISIT(traverse_module_state->__pyx_codeobj__25); + Py_VISIT(traverse_module_state->__pyx_codeobj__26); + Py_VISIT(traverse_module_state->__pyx_codeobj__27); + Py_VISIT(traverse_module_state->__pyx_codeobj__28); + Py_VISIT(traverse_module_state->__pyx_codeobj__29); + Py_VISIT(traverse_module_state->__pyx_codeobj__30); + Py_VISIT(traverse_module_state->__pyx_codeobj__31); + Py_VISIT(traverse_module_state->__pyx_codeobj__32); + Py_VISIT(traverse_module_state->__pyx_codeobj__33); + Py_VISIT(traverse_module_state->__pyx_codeobj__34); + Py_VISIT(traverse_module_state->__pyx_codeobj__35); + Py_VISIT(traverse_module_state->__pyx_codeobj__36); + Py_VISIT(traverse_module_state->__pyx_codeobj__37); + Py_VISIT(traverse_module_state->__pyx_codeobj__38); + Py_VISIT(traverse_module_state->__pyx_codeobj__40); + Py_VISIT(traverse_module_state->__pyx_codeobj__42); + Py_VISIT(traverse_module_state->__pyx_codeobj__45); + Py_VISIT(traverse_module_state->__pyx_codeobj__50); + Py_VISIT(traverse_module_state->__pyx_codeobj__52); + Py_VISIT(traverse_module_state->__pyx_codeobj__60); + Py_VISIT(traverse_module_state->__pyx_codeobj__61); + Py_VISIT(traverse_module_state->__pyx_codeobj__62); + Py_VISIT(traverse_module_state->__pyx_codeobj__63); + Py_VISIT(traverse_module_state->__pyx_codeobj__64); + Py_VISIT(traverse_module_state->__pyx_codeobj__65); + return 0; +} +#endif +/* #### Code section: module_state_defines ### */ +#define __pyx_d __pyx_mstate_global->__pyx_d +#define __pyx_b __pyx_mstate_global->__pyx_b +#define __pyx_cython_runtime __pyx_mstate_global->__pyx_cython_runtime +#define __pyx_empty_tuple __pyx_mstate_global->__pyx_empty_tuple +#define __pyx_empty_bytes __pyx_mstate_global->__pyx_empty_bytes +#define __pyx_empty_unicode __pyx_mstate_global->__pyx_empty_unicode +#ifdef __Pyx_CyFunction_USED +#define __pyx_CyFunctionType __pyx_mstate_global->__pyx_CyFunctionType +#endif +#ifdef __Pyx_FusedFunction_USED +#define __pyx_FusedFunctionType __pyx_mstate_global->__pyx_FusedFunctionType +#endif +#ifdef __Pyx_Generator_USED +#define __pyx_GeneratorType __pyx_mstate_global->__pyx_GeneratorType +#endif +#ifdef __Pyx_IterableCoroutine_USED +#define __pyx_IterableCoroutineType __pyx_mstate_global->__pyx_IterableCoroutineType +#endif +#ifdef __Pyx_Coroutine_USED +#define __pyx_CoroutineAwaitType __pyx_mstate_global->__pyx_CoroutineAwaitType +#endif +#ifdef __Pyx_Coroutine_USED +#define __pyx_CoroutineType __pyx_mstate_global->__pyx_CoroutineType +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#define __pyx_ptype_7cpython_4type_type __pyx_mstate_global->__pyx_ptype_7cpython_4type_type +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#define __pyx_ptype_7cpython_4bool_bool __pyx_mstate_global->__pyx_ptype_7cpython_4bool_bool +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#define __pyx_ptype_7cpython_7complex_complex __pyx_mstate_global->__pyx_ptype_7cpython_7complex_complex +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#endif +#define __pyx_ptype_7cpython_5array_array __pyx_mstate_global->__pyx_ptype_7cpython_5array_array +#if CYTHON_USE_MODULE_STATE +#endif +#if CYTHON_USE_MODULE_STATE +#define __pyx_type_5pysam_10libchtslib_HTSFile __pyx_mstate_global->__pyx_type_5pysam_10libchtslib_HTSFile +#define __pyx_type_5pysam_10libchtslib_HFile __pyx_mstate_global->__pyx_type_5pysam_10libchtslib_HFile +#endif +#define __pyx_ptype_5pysam_10libchtslib_HTSFile __pyx_mstate_global->__pyx_ptype_5pysam_10libchtslib_HTSFile +#define __pyx_ptype_5pysam_10libchtslib_HFile __pyx_mstate_global->__pyx_ptype_5pysam_10libchtslib_HFile +#define __pyx_n_u_ALIGNMENTS __pyx_mstate_global->__pyx_n_u_ALIGNMENTS +#define __pyx_kp_u_An_error_occurred_while_applying __pyx_mstate_global->__pyx_kp_u_An_error_occurred_while_applying +#define __pyx_n_s_AttributeError __pyx_mstate_global->__pyx_n_s_AttributeError +#define __pyx_n_u_BAI __pyx_mstate_global->__pyx_n_u_BAI +#define __pyx_n_u_BAM __pyx_mstate_global->__pyx_n_u_BAM +#define __pyx_n_u_BCF __pyx_mstate_global->__pyx_n_u_BCF +#define __pyx_n_u_BED __pyx_mstate_global->__pyx_n_u_BED +#define __pyx_n_u_BGZF __pyx_mstate_global->__pyx_n_u_BGZF +#define __pyx_n_u_BINARY_FORMAT __pyx_mstate_global->__pyx_n_u_BINARY_FORMAT +#define __pyx_n_s_CFalse __pyx_mstate_global->__pyx_n_s_CFalse +#define __pyx_n_u_CRAI __pyx_mstate_global->__pyx_n_u_CRAI +#define __pyx_n_u_CRAM __pyx_mstate_global->__pyx_n_u_CRAM +#define __pyx_n_u_CSI __pyx_mstate_global->__pyx_n_u_CSI +#define __pyx_n_s_CTrue __pyx_mstate_global->__pyx_n_s_CTrue +#define __pyx_n_u_CUSTOM __pyx_mstate_global->__pyx_n_u_CUSTOM +#define __pyx_n_s_CallableValue __pyx_mstate_global->__pyx_n_s_CallableValue +#define __pyx_n_s_CallableValue___bool __pyx_mstate_global->__pyx_n_s_CallableValue___bool +#define __pyx_n_s_CallableValue___call __pyx_mstate_global->__pyx_n_s_CallableValue___call +#define __pyx_n_s_CallableValue___eq __pyx_mstate_global->__pyx_n_s_CallableValue___eq +#define __pyx_n_s_CallableValue___init __pyx_mstate_global->__pyx_n_s_CallableValue___init +#define __pyx_n_s_CallableValue___ne __pyx_mstate_global->__pyx_n_s_CallableValue___ne +#define __pyx_n_s_CallableValue___nonzero __pyx_mstate_global->__pyx_n_s_CallableValue___nonzero +#define __pyx_kp_u_Cannot_create_hfile __pyx_mstate_global->__pyx_kp_u_Cannot_create_hfile +#define __pyx_kp_u_Flushing __pyx_mstate_global->__pyx_kp_u_Flushing +#define __pyx_n_u_GZI __pyx_mstate_global->__pyx_n_u_GZI +#define __pyx_n_u_GZIP __pyx_mstate_global->__pyx_n_u_GZIP +#define __pyx_n_s_HFile __pyx_mstate_global->__pyx_n_s_HFile +#define __pyx_n_u_HFile __pyx_mstate_global->__pyx_n_u_HFile +#define __pyx_n_s_HFile___enter __pyx_mstate_global->__pyx_n_s_HFile___enter +#define __pyx_n_s_HFile___exit __pyx_mstate_global->__pyx_n_s_HFile___exit +#define __pyx_n_s_HFile___reduce_cython __pyx_mstate_global->__pyx_n_s_HFile___reduce_cython +#define __pyx_n_s_HFile___setstate_cython __pyx_mstate_global->__pyx_n_s_HFile___setstate_cython +#define __pyx_n_s_HFile_close __pyx_mstate_global->__pyx_n_s_HFile_close +#define __pyx_n_s_HFile_fileno __pyx_mstate_global->__pyx_n_s_HFile_fileno +#define __pyx_n_s_HFile_flush __pyx_mstate_global->__pyx_n_s_HFile_flush +#define __pyx_n_s_HFile_isatty __pyx_mstate_global->__pyx_n_s_HFile_isatty +#define __pyx_n_s_HFile_read __pyx_mstate_global->__pyx_n_s_HFile_read +#define __pyx_n_s_HFile_readable __pyx_mstate_global->__pyx_n_s_HFile_readable +#define __pyx_n_s_HFile_readall __pyx_mstate_global->__pyx_n_s_HFile_readall +#define __pyx_n_s_HFile_readinto __pyx_mstate_global->__pyx_n_s_HFile_readinto +#define __pyx_n_s_HFile_readline __pyx_mstate_global->__pyx_n_s_HFile_readline +#define __pyx_n_s_HFile_readlines __pyx_mstate_global->__pyx_n_s_HFile_readlines +#define __pyx_n_s_HFile_seek __pyx_mstate_global->__pyx_n_s_HFile_seek +#define __pyx_n_s_HFile_seekable __pyx_mstate_global->__pyx_n_s_HFile_seekable +#define __pyx_n_s_HFile_tell __pyx_mstate_global->__pyx_n_s_HFile_tell +#define __pyx_n_s_HFile_truncate __pyx_mstate_global->__pyx_n_s_HFile_truncate +#define __pyx_n_s_HFile_writable __pyx_mstate_global->__pyx_n_s_HFile_writable +#define __pyx_n_s_HFile_write __pyx_mstate_global->__pyx_n_s_HFile_write +#define __pyx_n_s_HFile_writelines __pyx_mstate_global->__pyx_n_s_HFile_writelines +#define __pyx_n_s_HTSFile __pyx_mstate_global->__pyx_n_s_HTSFile +#define __pyx_n_u_HTSFile __pyx_mstate_global->__pyx_n_u_HTSFile +#define __pyx_n_s_HTSFile___enter __pyx_mstate_global->__pyx_n_s_HTSFile___enter +#define __pyx_n_s_HTSFile___exit __pyx_mstate_global->__pyx_n_s_HTSFile___exit +#define __pyx_n_s_HTSFile___reduce_cython __pyx_mstate_global->__pyx_n_s_HTSFile___reduce_cython +#define __pyx_n_s_HTSFile___setstate_cython __pyx_mstate_global->__pyx_n_s_HTSFile___setstate_cython +#define __pyx_n_s_HTSFile_add_hts_options __pyx_mstate_global->__pyx_n_s_HTSFile_add_hts_options +#define __pyx_n_s_HTSFile_check_truncation __pyx_mstate_global->__pyx_n_s_HTSFile_check_truncation +#define __pyx_n_s_HTSFile_close __pyx_mstate_global->__pyx_n_s_HTSFile_close +#define __pyx_n_s_HTSFile_flush __pyx_mstate_global->__pyx_n_s_HTSFile_flush +#define __pyx_n_s_HTSFile_get_reference_name __pyx_mstate_global->__pyx_n_s_HTSFile_get_reference_name +#define __pyx_n_s_HTSFile_get_tid __pyx_mstate_global->__pyx_n_s_HTSFile_get_tid +#define __pyx_n_s_HTSFile_is_valid_reference_name __pyx_mstate_global->__pyx_n_s_HTSFile_is_valid_reference_name +#define __pyx_n_s_HTSFile_is_valid_tid __pyx_mstate_global->__pyx_n_s_HTSFile_is_valid_tid +#define __pyx_n_s_HTSFile_parse_region __pyx_mstate_global->__pyx_n_s_HTSFile_parse_region +#define __pyx_n_s_HTSFile_reset __pyx_mstate_global->__pyx_n_s_HTSFile_reset +#define __pyx_n_s_HTSFile_seek __pyx_mstate_global->__pyx_n_s_HTSFile_seek +#define __pyx_n_s_HTSFile_tell __pyx_mstate_global->__pyx_n_s_HTSFile_tell +#define __pyx_n_u_INDEX __pyx_mstate_global->__pyx_n_u_INDEX +#define __pyx_n_s_IOError __pyx_mstate_global->__pyx_n_s_IOError +#define __pyx_kp_u_I_O_operation_on_closed_file __pyx_mstate_global->__pyx_kp_u_I_O_operation_on_closed_file +#define __pyx_n_s_IndexError __pyx_mstate_global->__pyx_n_s_IndexError +#define __pyx_kp_u_Invalid_format_option_specified __pyx_mstate_global->__pyx_kp_u_Invalid_format_option_specified +#define __pyx_n_s_MemoryError __pyx_mstate_global->__pyx_n_s_MemoryError +#define __pyx_n_u_NONE __pyx_mstate_global->__pyx_n_u_NONE +#define __pyx_n_s_NotImplementedError __pyx_mstate_global->__pyx_n_s_NotImplementedError +#define __pyx_n_s_OSError __pyx_mstate_global->__pyx_n_s_OSError +#define __pyx_n_s_OverflowError __pyx_mstate_global->__pyx_n_s_OverflowError +#define __pyx_n_u_REGIONS __pyx_mstate_global->__pyx_n_u_REGIONS +#define __pyx_n_s_RuntimeError __pyx_mstate_global->__pyx_n_s_RuntimeError +#define __pyx_n_u_SAM __pyx_mstate_global->__pyx_n_u_SAM +#define __pyx_n_s_SEEK_SET __pyx_mstate_global->__pyx_n_s_SEEK_SET +#define __pyx_n_s_StopIteration __pyx_mstate_global->__pyx_n_s_StopIteration +#define __pyx_n_u_TBI __pyx_mstate_global->__pyx_n_u_TBI +#define __pyx_n_u_TEXT_FORMAT __pyx_mstate_global->__pyx_n_u_TEXT_FORMAT +#define __pyx_n_s_TypeError __pyx_mstate_global->__pyx_n_s_TypeError +#define __pyx_n_u_UNKNOWN __pyx_mstate_global->__pyx_n_u_UNKNOWN +#define __pyx_n_u_VARIANTS __pyx_mstate_global->__pyx_n_u_VARIANTS +#define __pyx_n_u_VCF __pyx_mstate_global->__pyx_n_u_VCF +#define __pyx_n_s_ValueError __pyx_mstate_global->__pyx_n_s_ValueError +#define __pyx_kp_b__13 __pyx_mstate_global->__pyx_kp_b__13 +#define __pyx_kp_u__55 __pyx_mstate_global->__pyx_kp_u__55 +#define __pyx_kp_u__56 __pyx_mstate_global->__pyx_kp_u__56 +#define __pyx_n_s__58 __pyx_mstate_global->__pyx_n_s__58 +#define __pyx_kp_u__58 __pyx_mstate_global->__pyx_kp_u__58 +#define __pyx_kp_u__59 __pyx_mstate_global->__pyx_kp_u__59 +#define __pyx_n_s__97 __pyx_mstate_global->__pyx_n_s__97 +#define __pyx_n_s_add_hts_options __pyx_mstate_global->__pyx_n_s_add_hts_options +#define __pyx_n_s_all __pyx_mstate_global->__pyx_n_s_all +#define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines +#define __pyx_n_b_b __pyx_mstate_global->__pyx_n_b_b +#define __pyx_n_s_b __pyx_mstate_global->__pyx_n_s_b +#define __pyx_n_s_bgzfp __pyx_mstate_global->__pyx_n_s_bgzfp +#define __pyx_n_s_bool __pyx_mstate_global->__pyx_n_s_bool +#define __pyx_n_s_buf __pyx_mstate_global->__pyx_n_s_buf +#define __pyx_n_s_bytes_read __pyx_mstate_global->__pyx_n_s_bytes_read +#define __pyx_n_b_c __pyx_mstate_global->__pyx_n_b_c +#define __pyx_n_s_call __pyx_mstate_global->__pyx_n_s_call +#define __pyx_n_s_check_truncation __pyx_mstate_global->__pyx_n_s_check_truncation +#define __pyx_n_s_chunk_size __pyx_mstate_global->__pyx_n_s_chunk_size +#define __pyx_n_s_class_getitem __pyx_mstate_global->__pyx_n_s_class_getitem +#define __pyx_n_s_cline_in_traceback __pyx_mstate_global->__pyx_n_s_cline_in_traceback +#define __pyx_n_s_close __pyx_mstate_global->__pyx_n_s_close +#define __pyx_n_s_closefd __pyx_mstate_global->__pyx_n_s_closefd +#define __pyx_n_s_contig __pyx_mstate_global->__pyx_n_s_contig +#define __pyx_kp_u_contig_and_reference_should_not __pyx_mstate_global->__pyx_kp_u_contig_and_reference_should_not +#define __pyx_n_s_coord __pyx_mstate_global->__pyx_n_s_coord +#define __pyx_n_s_cpart __pyx_mstate_global->__pyx_n_s_cpart +#define __pyx_n_s_dict __pyx_mstate_global->__pyx_n_s_dict +#define __pyx_kp_u_disable __pyx_mstate_global->__pyx_kp_u_disable +#define __pyx_n_s_doc __pyx_mstate_global->__pyx_n_s_doc +#define __pyx_kp_u_enable __pyx_mstate_global->__pyx_kp_u_enable +#define __pyx_n_s_end __pyx_mstate_global->__pyx_n_s_end +#define __pyx_n_s_enter __pyx_mstate_global->__pyx_n_s_enter +#define __pyx_n_s_eq __pyx_mstate_global->__pyx_n_s_eq +#define __pyx_kp_u_error_checking_for_EOF_marker __pyx_mstate_global->__pyx_kp_u_error_checking_for_EOF_marker +#define __pyx_n_s_exc_type __pyx_mstate_global->__pyx_n_s_exc_type +#define __pyx_n_s_exc_value __pyx_mstate_global->__pyx_n_s_exc_value +#define __pyx_n_s_exit __pyx_mstate_global->__pyx_n_s_exit +#define __pyx_kp_u_failed __pyx_mstate_global->__pyx_kp_u_failed +#define __pyx_kp_u_failed_to_close_HFile __pyx_mstate_global->__pyx_kp_u_failed_to_close_HFile +#define __pyx_kp_u_failed_to_flush_HFile __pyx_mstate_global->__pyx_kp_u_failed_to_flush_HFile +#define __pyx_kp_u_failed_to_open_HFile __pyx_mstate_global->__pyx_kp_u_failed_to_open_HFile +#define __pyx_kp_u_failed_to_read_HFile __pyx_mstate_global->__pyx_kp_u_failed_to_read_HFile +#define __pyx_kp_u_fd __pyx_mstate_global->__pyx_kp_u_fd +#define __pyx_n_s_fileno __pyx_mstate_global->__pyx_n_s_fileno +#define __pyx_kp_u_fileno_not_available __pyx_mstate_global->__pyx_kp_u_fileno_not_available +#define __pyx_n_s_flush __pyx_mstate_global->__pyx_n_s_flush +#define __pyx_n_s_format __pyx_mstate_global->__pyx_n_s_format +#define __pyx_n_s_format_option __pyx_mstate_global->__pyx_n_s_format_option +#define __pyx_n_s_format_options __pyx_mstate_global->__pyx_n_s_format_options +#define __pyx_n_s_fp __pyx_mstate_global->__pyx_n_s_fp +#define __pyx_kp_u_gc __pyx_mstate_global->__pyx_kp_u_gc +#define __pyx_n_s_get_reference_name __pyx_mstate_global->__pyx_n_s_get_reference_name +#define __pyx_n_s_get_tid __pyx_mstate_global->__pyx_n_s_get_tid +#define __pyx_n_s_get_verbosity __pyx_mstate_global->__pyx_n_s_get_verbosity +#define __pyx_n_u_get_verbosity __pyx_mstate_global->__pyx_n_u_get_verbosity +#define __pyx_n_s_getstate __pyx_mstate_global->__pyx_n_s_getstate +#define __pyx_n_s_got __pyx_mstate_global->__pyx_n_s_got +#define __pyx_n_s_ignore_truncation __pyx_mstate_global->__pyx_n_s_ignore_truncation +#define __pyx_n_s_import __pyx_mstate_global->__pyx_n_s_import +#define __pyx_n_s_init __pyx_mstate_global->__pyx_n_s_init +#define __pyx_n_s_init_subclass __pyx_mstate_global->__pyx_n_s_init_subclass +#define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing +#define __pyx_kp_u_invalid_contig_s __pyx_mstate_global->__pyx_kp_u_invalid_contig_s +#define __pyx_kp_u_invalid_coordinates_start_i_stop __pyx_mstate_global->__pyx_kp_u_invalid_coordinates_start_i_stop +#define __pyx_kp_u_invalid_tid __pyx_mstate_global->__pyx_kp_u_invalid_tid +#define __pyx_n_s_io __pyx_mstate_global->__pyx_n_s_io +#define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine +#define __pyx_n_s_is_open __pyx_mstate_global->__pyx_n_s_is_open +#define __pyx_n_s_is_valid_reference_name __pyx_mstate_global->__pyx_n_s_is_valid_reference_name +#define __pyx_n_s_is_valid_tid __pyx_mstate_global->__pyx_n_s_is_valid_tid +#define __pyx_n_s_isatty __pyx_mstate_global->__pyx_n_s_isatty +#define __pyx_kp_u_isenabled __pyx_mstate_global->__pyx_kp_u_isenabled +#define __pyx_n_s_join __pyx_mstate_global->__pyx_n_s_join +#define __pyx_n_s_line __pyx_mstate_global->__pyx_n_s_line +#define __pyx_n_s_lines __pyx_mstate_global->__pyx_n_s_lines +#define __pyx_n_s_main __pyx_mstate_global->__pyx_n_s_main +#define __pyx_n_s_metaclass __pyx_mstate_global->__pyx_n_s_metaclass +#define __pyx_kp_u_metadata_not_available_on_closed __pyx_mstate_global->__pyx_kp_u_metadata_not_available_on_closed +#define __pyx_n_s_mode __pyx_mstate_global->__pyx_n_s_mode +#define __pyx_n_s_module __pyx_mstate_global->__pyx_n_s_module +#define __pyx_n_s_mro_entries __pyx_mstate_global->__pyx_n_s_mro_entries +#define __pyx_n_s_msg __pyx_mstate_global->__pyx_n_s_msg +#define __pyx_n_s_mv __pyx_mstate_global->__pyx_n_s_mv +#define __pyx_n_s_name __pyx_mstate_global->__pyx_n_s_name +#define __pyx_n_s_name_2 __pyx_mstate_global->__pyx_n_s_name_2 +#define __pyx_n_s_ne __pyx_mstate_global->__pyx_n_s_ne +#define __pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t __pyx_mstate_global->__pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t +#define __pyx_kp_s_no_default___reduce___due_to_non __pyx_mstate_global->__pyx_kp_s_no_default___reduce___due_to_non +#define __pyx_n_s_nonzero __pyx_mstate_global->__pyx_n_s_nonzero +#define __pyx_n_s_object __pyx_mstate_global->__pyx_n_s_object +#define __pyx_n_s_off __pyx_mstate_global->__pyx_n_s_off +#define __pyx_n_s_offset __pyx_mstate_global->__pyx_n_s_offset +#define __pyx_kp_u_operation_on_closed_HFile __pyx_mstate_global->__pyx_kp_u_operation_on_closed_HFile +#define __pyx_n_s_opts __pyx_mstate_global->__pyx_n_s_opts +#define __pyx_n_s_os __pyx_mstate_global->__pyx_n_s_os +#define __pyx_n_s_other __pyx_mstate_global->__pyx_n_s_other +#define __pyx_n_s_parse_region __pyx_mstate_global->__pyx_n_s_parse_region +#define __pyx_n_s_part __pyx_mstate_global->__pyx_n_s_part +#define __pyx_n_s_parts __pyx_mstate_global->__pyx_n_s_parts +#define __pyx_n_s_prepare __pyx_mstate_global->__pyx_n_s_prepare +#define __pyx_n_s_pysam_libchtslib __pyx_mstate_global->__pyx_n_s_pysam_libchtslib +#define __pyx_kp_s_pysam_libchtslib_pyx __pyx_mstate_global->__pyx_kp_s_pysam_libchtslib_pyx +#define __pyx_n_s_pyx_state __pyx_mstate_global->__pyx_n_s_pyx_state +#define __pyx_n_s_pyx_vtable __pyx_mstate_global->__pyx_n_s_pyx_vtable +#define __pyx_n_s_qualname __pyx_mstate_global->__pyx_n_s_qualname +#define __pyx_n_u_r __pyx_mstate_global->__pyx_n_u_r +#define __pyx_n_s_re __pyx_mstate_global->__pyx_n_s_re +#define __pyx_n_s_read __pyx_mstate_global->__pyx_n_s_read +#define __pyx_n_s_readable __pyx_mstate_global->__pyx_n_s_readable +#define __pyx_n_s_readall __pyx_mstate_global->__pyx_n_s_readall +#define __pyx_n_s_readinto __pyx_mstate_global->__pyx_n_s_readinto +#define __pyx_n_s_readline __pyx_mstate_global->__pyx_n_s_readline +#define __pyx_n_s_readlines __pyx_mstate_global->__pyx_n_s_readlines +#define __pyx_n_s_reduce __pyx_mstate_global->__pyx_n_s_reduce +#define __pyx_n_s_reduce_cython __pyx_mstate_global->__pyx_n_s_reduce_cython +#define __pyx_n_s_reduce_ex __pyx_mstate_global->__pyx_n_s_reduce_ex +#define __pyx_n_s_reference __pyx_mstate_global->__pyx_n_s_reference +#define __pyx_n_s_region __pyx_mstate_global->__pyx_n_s_region +#define __pyx_n_s_replace __pyx_mstate_global->__pyx_n_s_replace +#define __pyx_n_s_reset __pyx_mstate_global->__pyx_n_s_reset +#define __pyx_n_s_ret __pyx_mstate_global->__pyx_n_s_ret +#define __pyx_n_s_rstart __pyx_mstate_global->__pyx_n_s_rstart +#define __pyx_n_s_rstop __pyx_mstate_global->__pyx_n_s_rstop +#define __pyx_n_s_rtid __pyx_mstate_global->__pyx_n_s_rtid +#define __pyx_n_s_rval __pyx_mstate_global->__pyx_n_s_rval +#define __pyx_n_s_seek __pyx_mstate_global->__pyx_n_s_seek +#define __pyx_kp_u_seek_failed_on_HFile __pyx_mstate_global->__pyx_kp_u_seek_failed_on_HFile +#define __pyx_kp_u_seek_not_available_in_streams __pyx_mstate_global->__pyx_kp_u_seek_not_available_in_streams +#define __pyx_kp_u_seek_not_implemented_in_files_co __pyx_mstate_global->__pyx_kp_u_seek_not_implemented_in_files_co +#define __pyx_n_s_seekable __pyx_mstate_global->__pyx_n_s_seekable +#define __pyx_n_s_self __pyx_mstate_global->__pyx_n_s_self +#define __pyx_kp_s_self_fp_cannot_be_converted_to_a __pyx_mstate_global->__pyx_kp_s_self_fp_cannot_be_converted_to_a +#define __pyx_n_s_set_name __pyx_mstate_global->__pyx_n_s_set_name +#define __pyx_n_s_set_verbosity __pyx_mstate_global->__pyx_n_s_set_verbosity +#define __pyx_n_u_set_verbosity __pyx_mstate_global->__pyx_n_u_set_verbosity +#define __pyx_n_s_setstate __pyx_mstate_global->__pyx_n_s_setstate +#define __pyx_n_s_setstate_cython __pyx_mstate_global->__pyx_n_s_setstate_cython +#define __pyx_n_s_size __pyx_mstate_global->__pyx_n_s_size +#define __pyx_n_s_spec __pyx_mstate_global->__pyx_n_s_spec +#define __pyx_n_s_split __pyx_mstate_global->__pyx_n_s_split +#define __pyx_n_s_start __pyx_mstate_global->__pyx_n_s_start +#define __pyx_kp_u_start_out_of_range_i __pyx_mstate_global->__pyx_kp_u_start_out_of_range_i +#define __pyx_n_s_stop __pyx_mstate_global->__pyx_n_s_stop +#define __pyx_kp_u_stop_and_end_should_not_both_be __pyx_mstate_global->__pyx_kp_u_stop_and_end_should_not_both_be +#define __pyx_kp_u_stop_out_of_range_i __pyx_mstate_global->__pyx_kp_u_stop_out_of_range_i +#define __pyx_kp_s_stringsource __pyx_mstate_global->__pyx_kp_s_stringsource +#define __pyx_n_s_super __pyx_mstate_global->__pyx_n_s_super +#define __pyx_n_s_tb __pyx_mstate_global->__pyx_n_s_tb +#define __pyx_n_s_tell __pyx_mstate_global->__pyx_n_s_tell +#define __pyx_kp_u_tell_failed_on_HFile __pyx_mstate_global->__pyx_kp_u_tell_failed_on_HFile +#define __pyx_kp_u_tell_not_available_in_streams __pyx_mstate_global->__pyx_kp_u_tell_not_available_in_streams +#define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test +#define __pyx_n_s_tid __pyx_mstate_global->__pyx_n_s_tid +#define __pyx_n_s_traceback __pyx_mstate_global->__pyx_n_s_traceback +#define __pyx_n_s_truncate __pyx_mstate_global->__pyx_n_s_truncate +#define __pyx_n_s_type __pyx_mstate_global->__pyx_n_s_type +#define __pyx_n_s_value __pyx_mstate_global->__pyx_n_s_value +#define __pyx_n_s_verbosity __pyx_mstate_global->__pyx_n_s_verbosity +#define __pyx_n_u_w __pyx_mstate_global->__pyx_n_u_w +#define __pyx_n_s_warn __pyx_mstate_global->__pyx_n_s_warn +#define __pyx_n_s_warnings __pyx_mstate_global->__pyx_n_s_warnings +#define __pyx_n_s_whence __pyx_mstate_global->__pyx_n_s_whence +#define __pyx_n_s_writable __pyx_mstate_global->__pyx_n_s_writable +#define __pyx_n_s_write __pyx_mstate_global->__pyx_n_s_write +#define __pyx_kp_u_write_failed_on_HFile __pyx_mstate_global->__pyx_kp_u_write_failed_on_HFile +#define __pyx_n_s_writelines __pyx_mstate_global->__pyx_n_s_writelines +#define __pyx_int_0 __pyx_mstate_global->__pyx_int_0 +#define __pyx_int_1 __pyx_mstate_global->__pyx_int_1 +#define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1 +#define __pyx_k__18 __pyx_mstate_global->__pyx_k__18 +#define __pyx_k__41 __pyx_mstate_global->__pyx_k__41 +#define __pyx_codeobj_ __pyx_mstate_global->__pyx_codeobj_ +#define __pyx_tuple__5 __pyx_mstate_global->__pyx_tuple__5 +#define __pyx_tuple__6 __pyx_mstate_global->__pyx_tuple__6 +#define __pyx_tuple__39 __pyx_mstate_global->__pyx_tuple__39 +#define __pyx_tuple__43 __pyx_mstate_global->__pyx_tuple__43 +#define __pyx_tuple__44 __pyx_mstate_global->__pyx_tuple__44 +#define __pyx_tuple__46 __pyx_mstate_global->__pyx_tuple__46 +#define __pyx_tuple__47 __pyx_mstate_global->__pyx_tuple__47 +#define __pyx_tuple__48 __pyx_mstate_global->__pyx_tuple__48 +#define __pyx_tuple__49 __pyx_mstate_global->__pyx_tuple__49 +#define __pyx_tuple__51 __pyx_mstate_global->__pyx_tuple__51 +#define __pyx_tuple__53 __pyx_mstate_global->__pyx_tuple__53 +#define __pyx_tuple__54 __pyx_mstate_global->__pyx_tuple__54 +#define __pyx_tuple__57 __pyx_mstate_global->__pyx_tuple__57 +#define __pyx_tuple__66 __pyx_mstate_global->__pyx_tuple__66 +#define __pyx_tuple__67 __pyx_mstate_global->__pyx_tuple__67 +#define __pyx_tuple__68 __pyx_mstate_global->__pyx_tuple__68 +#define __pyx_tuple__69 __pyx_mstate_global->__pyx_tuple__69 +#define __pyx_tuple__70 __pyx_mstate_global->__pyx_tuple__70 +#define __pyx_tuple__71 __pyx_mstate_global->__pyx_tuple__71 +#define __pyx_tuple__72 __pyx_mstate_global->__pyx_tuple__72 +#define __pyx_tuple__73 __pyx_mstate_global->__pyx_tuple__73 +#define __pyx_tuple__74 __pyx_mstate_global->__pyx_tuple__74 +#define __pyx_tuple__75 __pyx_mstate_global->__pyx_tuple__75 +#define __pyx_tuple__76 __pyx_mstate_global->__pyx_tuple__76 +#define __pyx_tuple__77 __pyx_mstate_global->__pyx_tuple__77 +#define __pyx_tuple__78 __pyx_mstate_global->__pyx_tuple__78 +#define __pyx_tuple__79 __pyx_mstate_global->__pyx_tuple__79 +#define __pyx_tuple__80 __pyx_mstate_global->__pyx_tuple__80 +#define __pyx_tuple__81 __pyx_mstate_global->__pyx_tuple__81 +#define __pyx_tuple__82 __pyx_mstate_global->__pyx_tuple__82 +#define __pyx_tuple__83 __pyx_mstate_global->__pyx_tuple__83 +#define __pyx_tuple__84 __pyx_mstate_global->__pyx_tuple__84 +#define __pyx_tuple__85 __pyx_mstate_global->__pyx_tuple__85 +#define __pyx_tuple__86 __pyx_mstate_global->__pyx_tuple__86 +#define __pyx_tuple__87 __pyx_mstate_global->__pyx_tuple__87 +#define __pyx_tuple__88 __pyx_mstate_global->__pyx_tuple__88 +#define __pyx_tuple__89 __pyx_mstate_global->__pyx_tuple__89 +#define __pyx_tuple__90 __pyx_mstate_global->__pyx_tuple__90 +#define __pyx_tuple__91 __pyx_mstate_global->__pyx_tuple__91 +#define __pyx_tuple__92 __pyx_mstate_global->__pyx_tuple__92 +#define __pyx_tuple__93 __pyx_mstate_global->__pyx_tuple__93 +#define __pyx_tuple__94 __pyx_mstate_global->__pyx_tuple__94 +#define __pyx_tuple__95 __pyx_mstate_global->__pyx_tuple__95 +#define __pyx_tuple__96 __pyx_mstate_global->__pyx_tuple__96 +#define __pyx_codeobj__2 __pyx_mstate_global->__pyx_codeobj__2 +#define __pyx_codeobj__3 __pyx_mstate_global->__pyx_codeobj__3 +#define __pyx_codeobj__4 __pyx_mstate_global->__pyx_codeobj__4 +#define __pyx_codeobj__7 __pyx_mstate_global->__pyx_codeobj__7 +#define __pyx_codeobj__8 __pyx_mstate_global->__pyx_codeobj__8 +#define __pyx_codeobj__9 __pyx_mstate_global->__pyx_codeobj__9 +#define __pyx_codeobj__10 __pyx_mstate_global->__pyx_codeobj__10 +#define __pyx_codeobj__11 __pyx_mstate_global->__pyx_codeobj__11 +#define __pyx_codeobj__12 __pyx_mstate_global->__pyx_codeobj__12 +#define __pyx_codeobj__14 __pyx_mstate_global->__pyx_codeobj__14 +#define __pyx_codeobj__15 __pyx_mstate_global->__pyx_codeobj__15 +#define __pyx_codeobj__16 __pyx_mstate_global->__pyx_codeobj__16 +#define __pyx_codeobj__17 __pyx_mstate_global->__pyx_codeobj__17 +#define __pyx_codeobj__19 __pyx_mstate_global->__pyx_codeobj__19 +#define __pyx_codeobj__20 __pyx_mstate_global->__pyx_codeobj__20 +#define __pyx_codeobj__21 __pyx_mstate_global->__pyx_codeobj__21 +#define __pyx_codeobj__22 __pyx_mstate_global->__pyx_codeobj__22 +#define __pyx_codeobj__23 __pyx_mstate_global->__pyx_codeobj__23 +#define __pyx_codeobj__24 __pyx_mstate_global->__pyx_codeobj__24 +#define __pyx_codeobj__25 __pyx_mstate_global->__pyx_codeobj__25 +#define __pyx_codeobj__26 __pyx_mstate_global->__pyx_codeobj__26 +#define __pyx_codeobj__27 __pyx_mstate_global->__pyx_codeobj__27 +#define __pyx_codeobj__28 __pyx_mstate_global->__pyx_codeobj__28 +#define __pyx_codeobj__29 __pyx_mstate_global->__pyx_codeobj__29 +#define __pyx_codeobj__30 __pyx_mstate_global->__pyx_codeobj__30 +#define __pyx_codeobj__31 __pyx_mstate_global->__pyx_codeobj__31 +#define __pyx_codeobj__32 __pyx_mstate_global->__pyx_codeobj__32 +#define __pyx_codeobj__33 __pyx_mstate_global->__pyx_codeobj__33 +#define __pyx_codeobj__34 __pyx_mstate_global->__pyx_codeobj__34 +#define __pyx_codeobj__35 __pyx_mstate_global->__pyx_codeobj__35 +#define __pyx_codeobj__36 __pyx_mstate_global->__pyx_codeobj__36 +#define __pyx_codeobj__37 __pyx_mstate_global->__pyx_codeobj__37 +#define __pyx_codeobj__38 __pyx_mstate_global->__pyx_codeobj__38 +#define __pyx_codeobj__40 __pyx_mstate_global->__pyx_codeobj__40 +#define __pyx_codeobj__42 __pyx_mstate_global->__pyx_codeobj__42 +#define __pyx_codeobj__45 __pyx_mstate_global->__pyx_codeobj__45 +#define __pyx_codeobj__50 __pyx_mstate_global->__pyx_codeobj__50 +#define __pyx_codeobj__52 __pyx_mstate_global->__pyx_codeobj__52 +#define __pyx_codeobj__60 __pyx_mstate_global->__pyx_codeobj__60 +#define __pyx_codeobj__61 __pyx_mstate_global->__pyx_codeobj__61 +#define __pyx_codeobj__62 __pyx_mstate_global->__pyx_codeobj__62 +#define __pyx_codeobj__63 __pyx_mstate_global->__pyx_codeobj__63 +#define __pyx_codeobj__64 __pyx_mstate_global->__pyx_codeobj__64 +#define __pyx_codeobj__65 __pyx_mstate_global->__pyx_codeobj__65 +/* #### Code section: module_code ### */ + +/* "cpython/complex.pxd":19 + * + * @property + * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<< + * return self.cval.real + * + */ + +static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self) { + double __pyx_r; + + /* "cpython/complex.pxd":20 + * @property + * cdef inline double real(self) noexcept: + * return self.cval.real # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_r = __pyx_v_self->cval.real; + goto __pyx_L0; + + /* "cpython/complex.pxd":19 + * + * @property + * cdef inline double real(self) noexcept: # <<<<<<<<<<<<<< + * return self.cval.real + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "cpython/complex.pxd":23 + * + * @property + * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<< + * return self.cval.imag + * + */ + +static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4imag_imag(PyComplexObject *__pyx_v_self) { + double __pyx_r; + + /* "cpython/complex.pxd":24 + * @property + * cdef inline double imag(self) noexcept: + * return self.cval.imag # <<<<<<<<<<<<<< + * + * # PyTypeObject PyComplex_Type + */ + __pyx_r = __pyx_v_self->cval.imag; + goto __pyx_L0; + + /* "cpython/complex.pxd":23 + * + * @property + * cdef inline double imag(self) noexcept: # <<<<<<<<<<<<<< + * return self.cval.imag + * + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "cpython/contextvars.pxd":112 + * + * + * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<< + * """Return a new reference to the value of the context variable, + * or the default value of the context variable, + */ + +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) { + PyObject *__pyx_v_default_value = ((PyObject *)Py_None); + PyObject *__pyx_v_value; + PyObject *__pyx_v_pyvalue = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("get_value", 1); + if (__pyx_optional_args) { + if (__pyx_optional_args->__pyx_n > 0) { + __pyx_v_default_value = __pyx_optional_args->default_value; + } + } + + /* "cpython/contextvars.pxd":117 + * or None if no such value or default was found. + * """ + * cdef PyObject *value = NULL # <<<<<<<<<<<<<< + * PyContextVar_Get(var, NULL, &value) + * if value is NULL: + */ + __pyx_v_value = NULL; + + /* "cpython/contextvars.pxd":118 + * """ + * cdef PyObject *value = NULL + * PyContextVar_Get(var, NULL, &value) # <<<<<<<<<<<<<< + * if value is NULL: + * # context variable does not have a default + */ + __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) + + /* "cpython/contextvars.pxd":119 + * cdef PyObject *value = NULL + * PyContextVar_Get(var, NULL, &value) + * if value is NULL: # <<<<<<<<<<<<<< + * # context variable does not have a default + * pyvalue = default_value + */ + __pyx_t_2 = (__pyx_v_value == NULL); + if (__pyx_t_2) { + + /* "cpython/contextvars.pxd":121 + * if value is NULL: + * # context variable does not have a default + * pyvalue = default_value # <<<<<<<<<<<<<< + * else: + * # value or default value of context variable + */ + __Pyx_INCREF(__pyx_v_default_value); + __pyx_v_pyvalue = __pyx_v_default_value; + + /* "cpython/contextvars.pxd":119 + * cdef PyObject *value = NULL + * PyContextVar_Get(var, NULL, &value) + * if value is NULL: # <<<<<<<<<<<<<< + * # context variable does not have a default + * pyvalue = default_value + */ + goto __pyx_L3; + } + + /* "cpython/contextvars.pxd":124 + * else: + * # value or default value of context variable + * pyvalue = <object>value # <<<<<<<<<<<<<< + * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' + * return pyvalue + */ + /*else*/ { + __pyx_t_3 = ((PyObject *)__pyx_v_value); + __Pyx_INCREF(__pyx_t_3); + __pyx_v_pyvalue = __pyx_t_3; + __pyx_t_3 = 0; + + /* "cpython/contextvars.pxd":125 + * # value or default value of context variable + * pyvalue = <object>value + * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<< + * return pyvalue + * + */ + Py_XDECREF(__pyx_v_value); + } + __pyx_L3:; + + /* "cpython/contextvars.pxd":126 + * pyvalue = <object>value + * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' + * return pyvalue # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_pyvalue); + __pyx_r = __pyx_v_pyvalue; + goto __pyx_L0; + + /* "cpython/contextvars.pxd":112 + * + * + * cdef inline object get_value(var, default_value=None): # <<<<<<<<<<<<<< + * """Return a new reference to the value of the context variable, + * or the default value of the context variable, + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("cpython.contextvars.get_value", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_pyvalue); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "cpython/contextvars.pxd":129 + * + * + * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<< + * """Return a new reference to the value of the context variable, + * or the provided default value if no such value was found. + */ + +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) { + PyObject *__pyx_v_default_value = ((PyObject *)Py_None); + PyObject *__pyx_v_value; + PyObject *__pyx_v_pyvalue = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("get_value_no_default", 1); + if (__pyx_optional_args) { + if (__pyx_optional_args->__pyx_n > 0) { + __pyx_v_default_value = __pyx_optional_args->default_value; + } + } + + /* "cpython/contextvars.pxd":135 + * Ignores the default value of the context variable, if any. + * """ + * cdef PyObject *value = NULL # <<<<<<<<<<<<<< + * PyContextVar_Get(var, <PyObject*>default_value, &value) + * # value of context variable or 'default_value' + */ + __pyx_v_value = NULL; + + /* "cpython/contextvars.pxd":136 + * """ + * cdef PyObject *value = NULL + * PyContextVar_Get(var, <PyObject*>default_value, &value) # <<<<<<<<<<<<<< + * # value of context variable or 'default_value' + * pyvalue = <object>value + */ + __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) + + /* "cpython/contextvars.pxd":138 + * PyContextVar_Get(var, <PyObject*>default_value, &value) + * # value of context variable or 'default_value' + * pyvalue = <object>value # <<<<<<<<<<<<<< + * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' + * return pyvalue + */ + __pyx_t_2 = ((PyObject *)__pyx_v_value); + __Pyx_INCREF(__pyx_t_2); + __pyx_v_pyvalue = __pyx_t_2; + __pyx_t_2 = 0; + + /* "cpython/contextvars.pxd":139 + * # value of context variable or 'default_value' + * pyvalue = <object>value + * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' # <<<<<<<<<<<<<< + * return pyvalue + */ + Py_XDECREF(__pyx_v_value); + + /* "cpython/contextvars.pxd":140 + * pyvalue = <object>value + * Py_XDECREF(value) # PyContextVar_Get() returned an owned reference as 'PyObject*' + * return pyvalue # <<<<<<<<<<<<<< + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_pyvalue); + __pyx_r = __pyx_v_pyvalue; + goto __pyx_L0; + + /* "cpython/contextvars.pxd":129 + * + * + * cdef inline object get_value_no_default(var, default_value=None): # <<<<<<<<<<<<<< + * """Return a new reference to the value of the context variable, + * or the provided default value if no such value was found. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("cpython.contextvars.get_value_no_default", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_pyvalue); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "array.pxd":104 + * __data_union data + * + * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< + * # This implementation of getbuffer is geared towards Cython + * # requirements, and does not yet fulfill the PEP. + */ + +/* Python wrapper */ +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*/ +CYTHON_UNUSED static int __pyx_pw_7cpython_5array_5array_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_7cpython_5array_5array___getbuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_7cpython_5array_5array___getbuffer__(arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info, CYTHON_UNUSED int __pyx_v_flags) { + PyObject *__pyx_v_item_count = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + char *__pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + Py_ssize_t __pyx_t_5; + int __pyx_t_6; + char __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + if (unlikely(__pyx_v_info == NULL)) { + PyErr_SetString(PyExc_BufferError, "PyObject_GetBuffer: view==NULL argument is obsolete"); + return -1; + } + __Pyx_RefNannySetupContext("__getbuffer__", 0); + __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(__pyx_v_info->obj); + + /* "array.pxd":109 + * # In particular strided access is always provided regardless + * # of flags + * item_count = Py_SIZE(self) # <<<<<<<<<<<<<< + * + * info.suboffsets = NULL + */ + __pyx_t_1 = PyInt_FromSsize_t(Py_SIZE(((PyObject *)__pyx_v_self))); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 109, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_item_count = __pyx_t_1; + __pyx_t_1 = 0; + + /* "array.pxd":111 + * item_count = Py_SIZE(self) + * + * info.suboffsets = NULL # <<<<<<<<<<<<<< + * info.buf = self.data.as_chars + * info.readonly = 0 + */ + __pyx_v_info->suboffsets = NULL; + + /* "array.pxd":112 + * + * info.suboffsets = NULL + * info.buf = self.data.as_chars # <<<<<<<<<<<<<< + * info.readonly = 0 + * info.ndim = 1 + */ + __pyx_t_2 = __pyx_v_self->data.as_chars; + __pyx_v_info->buf = __pyx_t_2; + + /* "array.pxd":113 + * info.suboffsets = NULL + * info.buf = self.data.as_chars + * info.readonly = 0 # <<<<<<<<<<<<<< + * info.ndim = 1 + * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) + */ + __pyx_v_info->readonly = 0; + + /* "array.pxd":114 + * info.buf = self.data.as_chars + * info.readonly = 0 + * info.ndim = 1 # <<<<<<<<<<<<<< + * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) + * info.len = info.itemsize * item_count + */ + __pyx_v_info->ndim = 1; + + /* "array.pxd":115 + * info.readonly = 0 + * info.ndim = 1 + * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) # <<<<<<<<<<<<<< + * info.len = info.itemsize * item_count + * + */ + __pyx_t_3 = __pyx_v_self->ob_descr->itemsize; + __pyx_v_info->itemsize = __pyx_t_3; + + /* "array.pxd":116 + * info.ndim = 1 + * info.itemsize = self.ob_descr.itemsize # e.g. sizeof(float) + * info.len = info.itemsize * item_count # <<<<<<<<<<<<<< + * + * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) + */ + __pyx_t_1 = PyInt_FromSsize_t(__pyx_v_info->itemsize); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 116, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_4 = PyNumber_Multiply(__pyx_t_1, __pyx_v_item_count); if (unlikely(!__pyx_t_4)) __PYX_ERR(3, 116, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __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) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_v_info->len = __pyx_t_5; + + /* "array.pxd":118 + * info.len = info.itemsize * item_count + * + * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) # <<<<<<<<<<<<<< + * if not info.shape: + * raise MemoryError() + */ + __pyx_v_info->shape = ((Py_ssize_t *)PyObject_Malloc(((sizeof(Py_ssize_t)) + 2))); + + /* "array.pxd":119 + * + * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) + * if not info.shape: # <<<<<<<<<<<<<< + * raise MemoryError() + * info.shape[0] = item_count # constant regardless of resizing + */ + __pyx_t_6 = (!(__pyx_v_info->shape != 0)); + if (unlikely(__pyx_t_6)) { + + /* "array.pxd":120 + * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) + * if not info.shape: + * raise MemoryError() # <<<<<<<<<<<<<< + * info.shape[0] = item_count # constant regardless of resizing + * info.strides = &info.itemsize + */ + PyErr_NoMemory(); __PYX_ERR(3, 120, __pyx_L1_error) + + /* "array.pxd":119 + * + * info.shape = <Py_ssize_t*> PyObject_Malloc(sizeof(Py_ssize_t) + 2) + * if not info.shape: # <<<<<<<<<<<<<< + * raise MemoryError() + * info.shape[0] = item_count # constant regardless of resizing + */ + } + + /* "array.pxd":121 + * if not info.shape: + * raise MemoryError() + * info.shape[0] = item_count # constant regardless of resizing # <<<<<<<<<<<<<< + * info.strides = &info.itemsize + * + */ + __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) + (__pyx_v_info->shape[0]) = __pyx_t_5; + + /* "array.pxd":122 + * raise MemoryError() + * info.shape[0] = item_count # constant regardless of resizing + * info.strides = &info.itemsize # <<<<<<<<<<<<<< + * + * info.format = <char*> (info.shape + 1) + */ + __pyx_v_info->strides = (&__pyx_v_info->itemsize); + + /* "array.pxd":124 + * info.strides = &info.itemsize + * + * info.format = <char*> (info.shape + 1) # <<<<<<<<<<<<<< + * info.format[0] = self.ob_descr.typecode + * info.format[1] = 0 + */ + __pyx_v_info->format = ((char *)(__pyx_v_info->shape + 1)); + + /* "array.pxd":125 + * + * info.format = <char*> (info.shape + 1) + * info.format[0] = self.ob_descr.typecode # <<<<<<<<<<<<<< + * info.format[1] = 0 + * info.obj = self + */ + __pyx_t_7 = __pyx_v_self->ob_descr->typecode; + (__pyx_v_info->format[0]) = __pyx_t_7; + + /* "array.pxd":126 + * info.format = <char*> (info.shape + 1) + * info.format[0] = self.ob_descr.typecode + * info.format[1] = 0 # <<<<<<<<<<<<<< + * info.obj = self + * + */ + (__pyx_v_info->format[1]) = 0; + + /* "array.pxd":127 + * info.format[0] = self.ob_descr.typecode + * info.format[1] = 0 + * info.obj = self # <<<<<<<<<<<<<< + * + * def __releasebuffer__(self, Py_buffer* info): + */ + __Pyx_INCREF((PyObject *)__pyx_v_self); + __Pyx_GIVEREF((PyObject *)__pyx_v_self); + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); + __pyx_v_info->obj = ((PyObject *)__pyx_v_self); + + /* "array.pxd":104 + * __data_union data + * + * def __getbuffer__(self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< + * # This implementation of getbuffer is geared towards Cython + * # requirements, and does not yet fulfill the PEP. + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("cpython.array.array.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + if (__pyx_v_info->obj != NULL) { + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0; + } + goto __pyx_L2; + __pyx_L0:; + if (__pyx_v_info->obj == Py_None) { + __Pyx_GOTREF(__pyx_v_info->obj); + __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = 0; + } + __pyx_L2:; + __Pyx_XDECREF(__pyx_v_item_count); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "array.pxd":129 + * info.obj = self + * + * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<< + * PyObject_Free(info.shape) + * + */ + +/* Python wrapper */ +CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/ +CYTHON_UNUSED static void __pyx_pw_7cpython_5array_5array_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_pf_7cpython_5array_5array_2__releasebuffer__(((arrayobject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_7cpython_5array_5array_2__releasebuffer__(CYTHON_UNUSED arrayobject *__pyx_v_self, Py_buffer *__pyx_v_info) { + + /* "array.pxd":130 + * + * def __releasebuffer__(self, Py_buffer* info): + * PyObject_Free(info.shape) # <<<<<<<<<<<<<< + * + * array newarrayobject(PyTypeObject* type, Py_ssize_t size, arraydescr *descr) + */ + PyObject_Free(__pyx_v_info->shape); + + /* "array.pxd":129 + * info.obj = self + * + * def __releasebuffer__(self, Py_buffer* info): # <<<<<<<<<<<<<< + * PyObject_Free(info.shape) + * + */ + + /* function exit code */ +} + +/* "array.pxd":141 + * + * + * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<< + * """ fast creation of a new array, given a template array. + * type will be same as template. + */ + +static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_clone(arrayobject *__pyx_v_template, Py_ssize_t __pyx_v_length, int __pyx_v_zero) { + arrayobject *__pyx_v_op = 0; + arrayobject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("clone", 1); + + /* "array.pxd":145 + * type will be same as template. + * if zero is true, new array will be initialized with zeroes.""" + * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) # <<<<<<<<<<<<<< + * if zero and op is not None: + * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) + */ + __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) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_op = ((arrayobject *)__pyx_t_1); + __pyx_t_1 = 0; + + /* "array.pxd":146 + * if zero is true, new array will be initialized with zeroes.""" + * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) + * if zero and op is not None: # <<<<<<<<<<<<<< + * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) + * return op + */ + if (__pyx_v_zero) { + } else { + __pyx_t_2 = __pyx_v_zero; + goto __pyx_L4_bool_binop_done; + } + __pyx_t_3 = (((PyObject *)__pyx_v_op) != Py_None); + __pyx_t_2 = __pyx_t_3; + __pyx_L4_bool_binop_done:; + if (__pyx_t_2) { + + /* "array.pxd":147 + * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) + * if zero and op is not None: + * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) # <<<<<<<<<<<<<< + * return op + * + */ + (void)(memset(__pyx_v_op->data.as_chars, 0, (__pyx_v_length * __pyx_v_op->ob_descr->itemsize))); + + /* "array.pxd":146 + * if zero is true, new array will be initialized with zeroes.""" + * cdef array op = newarrayobject(Py_TYPE(template), length, template.ob_descr) + * if zero and op is not None: # <<<<<<<<<<<<<< + * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) + * return op + */ + } + + /* "array.pxd":148 + * if zero and op is not None: + * memset(op.data.as_chars, 0, length * op.ob_descr.itemsize) + * return op # <<<<<<<<<<<<<< + * + * cdef inline array copy(array self): + */ + __Pyx_XDECREF((PyObject *)__pyx_r); + __Pyx_INCREF((PyObject *)__pyx_v_op); + __pyx_r = __pyx_v_op; + goto __pyx_L0; + + /* "array.pxd":141 + * + * + * cdef inline array clone(array template, Py_ssize_t length, bint zero): # <<<<<<<<<<<<<< + * """ fast creation of a new array, given a template array. + * type will be same as template. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("cpython.array.clone", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_op); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "array.pxd":150 + * return op + * + * cdef inline array copy(array self): # <<<<<<<<<<<<<< + * """ make a copy of an array. """ + * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) + */ + +static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_copy(arrayobject *__pyx_v_self) { + arrayobject *__pyx_v_op = 0; + arrayobject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("copy", 1); + + /* "array.pxd":152 + * cdef inline array copy(array self): + * """ make a copy of an array. """ + * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) # <<<<<<<<<<<<<< + * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) + * return op + */ + __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) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_op = ((arrayobject *)__pyx_t_1); + __pyx_t_1 = 0; + + /* "array.pxd":153 + * """ make a copy of an array. """ + * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) + * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) # <<<<<<<<<<<<<< + * return op + * + */ + (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))); + + /* "array.pxd":154 + * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) + * memcpy(op.data.as_chars, self.data.as_chars, Py_SIZE(op) * op.ob_descr.itemsize) + * return op # <<<<<<<<<<<<<< + * + * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: + */ + __Pyx_XDECREF((PyObject *)__pyx_r); + __Pyx_INCREF((PyObject *)__pyx_v_op); + __pyx_r = __pyx_v_op; + goto __pyx_L0; + + /* "array.pxd":150 + * return op + * + * cdef inline array copy(array self): # <<<<<<<<<<<<<< + * """ make a copy of an array. """ + * cdef array op = newarrayobject(Py_TYPE(self), Py_SIZE(self), self.ob_descr) + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("cpython.array.copy", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_op); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "array.pxd":156 + * return op + * + * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<< + * """ efficient appending of new stuff of same type + * (e.g. of same array type) + */ + +static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *__pyx_v_self, char *__pyx_v_stuff, Py_ssize_t __pyx_v_n) { + Py_ssize_t __pyx_v_itemsize; + Py_ssize_t __pyx_v_origsize; + int __pyx_r; + int __pyx_t_1; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + + /* "array.pxd":160 + * (e.g. of same array type) + * n: number of elements (not number of bytes!) """ + * cdef Py_ssize_t itemsize = self.ob_descr.itemsize # <<<<<<<<<<<<<< + * cdef Py_ssize_t origsize = Py_SIZE(self) + * resize_smart(self, origsize + n) + */ + __pyx_t_1 = __pyx_v_self->ob_descr->itemsize; + __pyx_v_itemsize = __pyx_t_1; + + /* "array.pxd":161 + * n: number of elements (not number of bytes!) """ + * cdef Py_ssize_t itemsize = self.ob_descr.itemsize + * cdef Py_ssize_t origsize = Py_SIZE(self) # <<<<<<<<<<<<<< + * resize_smart(self, origsize + n) + * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) + */ + __pyx_v_origsize = Py_SIZE(((PyObject *)__pyx_v_self)); + + /* "array.pxd":162 + * cdef Py_ssize_t itemsize = self.ob_descr.itemsize + * cdef Py_ssize_t origsize = Py_SIZE(self) + * resize_smart(self, origsize + n) # <<<<<<<<<<<<<< + * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) + * return 0 + */ + __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) + + /* "array.pxd":163 + * cdef Py_ssize_t origsize = Py_SIZE(self) + * resize_smart(self, origsize + n) + * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) # <<<<<<<<<<<<<< + * return 0 + * + */ + (void)(memcpy((__pyx_v_self->data.as_chars + (__pyx_v_origsize * __pyx_v_itemsize)), __pyx_v_stuff, (__pyx_v_n * __pyx_v_itemsize))); + + /* "array.pxd":164 + * resize_smart(self, origsize + n) + * memcpy(self.data.as_chars + origsize * itemsize, stuff, n * itemsize) + * return 0 # <<<<<<<<<<<<<< + * + * cdef inline int extend(array self, array other) except -1: + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "array.pxd":156 + * return op + * + * cdef inline int extend_buffer(array self, char* stuff, Py_ssize_t n) except -1: # <<<<<<<<<<<<<< + * """ efficient appending of new stuff of same type + * (e.g. of same array type) + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("cpython.array.extend_buffer", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "array.pxd":166 + * return 0 + * + * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<< + * """ extend array with data from another array; types must match. """ + * if self.ob_descr.typecode != other.ob_descr.typecode: + */ + +static CYTHON_INLINE int __pyx_f_7cpython_5array_extend(arrayobject *__pyx_v_self, arrayobject *__pyx_v_other) { + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + + /* "array.pxd":168 + * cdef inline int extend(array self, array other) except -1: + * """ extend array with data from another array; types must match. """ + * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<< + * PyErr_BadArgument() + * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) + */ + __pyx_t_1 = (__pyx_v_self->ob_descr->typecode != __pyx_v_other->ob_descr->typecode); + if (__pyx_t_1) { + + /* "array.pxd":169 + * """ extend array with data from another array; types must match. """ + * if self.ob_descr.typecode != other.ob_descr.typecode: + * PyErr_BadArgument() # <<<<<<<<<<<<<< + * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) + * + */ + __pyx_t_2 = PyErr_BadArgument(); if (unlikely(__pyx_t_2 == ((int)0))) __PYX_ERR(3, 169, __pyx_L1_error) + + /* "array.pxd":168 + * cdef inline int extend(array self, array other) except -1: + * """ extend array with data from another array; types must match. """ + * if self.ob_descr.typecode != other.ob_descr.typecode: # <<<<<<<<<<<<<< + * PyErr_BadArgument() + * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) + */ + } + + /* "array.pxd":170 + * if self.ob_descr.typecode != other.ob_descr.typecode: + * PyErr_BadArgument() + * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) # <<<<<<<<<<<<<< + * + * cdef inline void zero(array self) noexcept: + */ + __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) + __pyx_r = __pyx_t_2; + goto __pyx_L0; + + /* "array.pxd":166 + * return 0 + * + * cdef inline int extend(array self, array other) except -1: # <<<<<<<<<<<<<< + * """ extend array with data from another array; types must match. """ + * if self.ob_descr.typecode != other.ob_descr.typecode: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("cpython.array.extend", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "array.pxd":172 + * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) + * + * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<< + * """ set all elements of array to zero. """ + * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) + */ + +static CYTHON_INLINE void __pyx_f_7cpython_5array_zero(arrayobject *__pyx_v_self) { + + /* "array.pxd":174 + * cdef inline void zero(array self) noexcept: + * """ set all elements of array to zero. """ + * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) # <<<<<<<<<<<<<< + */ + (void)(memset(__pyx_v_self->data.as_chars, 0, (Py_SIZE(((PyObject *)__pyx_v_self)) * __pyx_v_self->ob_descr->itemsize))); + + /* "array.pxd":172 + * return extend_buffer(self, other.data.as_chars, Py_SIZE(other)) + * + * cdef inline void zero(array self) noexcept: # <<<<<<<<<<<<<< + * """ set all elements of array to zero. """ + * memset(self.data.as_chars, 0, Py_SIZE(self) * self.ob_descr.itemsize) + */ + + /* function exit code */ +} + +/* "pysam/libchtslib.pyx":53 + * + * + * cpdef set_verbosity(int verbosity): # <<<<<<<<<<<<<< + * """Set htslib's hts_verbose global variable to the specified value.""" + * return hts_set_verbosity(verbosity) + */ + +static PyObject *__pyx_pw_5pysam_10libchtslib_1set_verbosity(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +static PyObject *__pyx_f_5pysam_10libchtslib_set_verbosity(int __pyx_v_verbosity, CYTHON_UNUSED int __pyx_skip_dispatch) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj_) + __Pyx_RefNannySetupContext("set_verbosity", 1); + __Pyx_TraceCall("set_verbosity", __pyx_f[0], 53, 0, __PYX_ERR(0, 53, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":55 + * cpdef set_verbosity(int verbosity): + * """Set htslib's hts_verbose global variable to the specified value.""" + * return hts_set_verbosity(verbosity) # <<<<<<<<<<<<<< + * + * cpdef get_verbosity(): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(hts_set_verbosity(__pyx_v_verbosity)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 55, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":53 + * + * + * cpdef set_verbosity(int verbosity): # <<<<<<<<<<<<<< + * """Set htslib's hts_verbose global variable to the specified value.""" + * return hts_set_verbosity(verbosity) + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.set_verbosity", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_1set_verbosity(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_set_verbosity, "set_verbosity(int verbosity)\nSet htslib's hts_verbose global variable to the specified value."); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_1set_verbosity = {"set_verbosity", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_1set_verbosity, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_set_verbosity}; +static PyObject *__pyx_pw_5pysam_10libchtslib_1set_verbosity(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + int __pyx_v_verbosity; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("set_verbosity (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_verbosity,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_verbosity)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 53, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "set_verbosity") < 0)) __PYX_ERR(0, 53, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_verbosity = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_verbosity == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 53, __pyx_L3_error) + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("set_verbosity", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 53, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.set_verbosity", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_set_verbosity(__pyx_self, __pyx_v_verbosity); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_set_verbosity(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_verbosity) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj_) + __Pyx_RefNannySetupContext("set_verbosity", 1); + __Pyx_TraceCall("set_verbosity (wrapper)", __pyx_f[0], 53, 0, __PYX_ERR(0, 53, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_5pysam_10libchtslib_set_verbosity(__pyx_v_verbosity, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.set_verbosity", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":57 + * return hts_set_verbosity(verbosity) + * + * cpdef get_verbosity(): # <<<<<<<<<<<<<< + * """Return the value of htslib's hts_verbose global variable.""" + * return hts_get_verbosity() + */ + +static PyObject *__pyx_pw_5pysam_10libchtslib_3get_verbosity(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_f_5pysam_10libchtslib_get_verbosity(CYTHON_UNUSED int __pyx_skip_dispatch) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__2) + __Pyx_RefNannySetupContext("get_verbosity", 1); + __Pyx_TraceCall("get_verbosity", __pyx_f[0], 57, 0, __PYX_ERR(0, 57, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":59 + * cpdef get_verbosity(): + * """Return the value of htslib's hts_verbose global variable.""" + * return hts_get_verbosity() # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(hts_get_verbosity()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":57 + * return hts_set_verbosity(verbosity) + * + * cpdef get_verbosity(): # <<<<<<<<<<<<<< + * """Return the value of htslib's hts_verbose global variable.""" + * return hts_get_verbosity() + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.get_verbosity", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_3get_verbosity(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_2get_verbosity, "get_verbosity()\nReturn the value of htslib's hts_verbose global variable."); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_3get_verbosity = {"get_verbosity", (PyCFunction)__pyx_pw_5pysam_10libchtslib_3get_verbosity, METH_NOARGS, __pyx_doc_5pysam_10libchtslib_2get_verbosity}; +static PyObject *__pyx_pw_5pysam_10libchtslib_3get_verbosity(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("get_verbosity (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_2get_verbosity(__pyx_self); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_2get_verbosity(CYTHON_UNUSED PyObject *__pyx_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__2) + __Pyx_RefNannySetupContext("get_verbosity", 1); + __Pyx_TraceCall("get_verbosity (wrapper)", __pyx_f[0], 57, 0, __PYX_ERR(0, 57, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_5pysam_10libchtslib_get_verbosity(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.get_verbosity", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":71 + * cdef readonly object name, mode + * + * def __init__(self, name, mode='r', closefd=True): # <<<<<<<<<<<<<< + * self._open(name, mode, closefd=True) + * + */ + +/* Python wrapper */ +static int __pyx_pw_5pysam_10libchtslib_5HFile_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_10libchtslib_5HFile_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_name = 0; + PyObject *__pyx_v_mode = 0; + CYTHON_UNUSED PyObject *__pyx_v_closefd = 0; + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[3] = {0,0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; + #endif + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_name,&__pyx_n_s_mode,&__pyx_n_s_closefd,0}; + values[1] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)__pyx_n_u_r)); + values[2] = __Pyx_Arg_NewRef_VARARGS(((PyObject *)Py_True)); + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_VARARGS(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_name)) != 0)) { + (void)__Pyx_Arg_NewRef_VARARGS(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 71, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_mode); + if (value) { values[1] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 71, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_VARARGS(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_closefd); + if (value) { values[2] = __Pyx_Arg_NewRef_VARARGS(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 71, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 71, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 3: values[2] = __Pyx_Arg_VARARGS(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_VARARGS(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_VARARGS(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_name = values[0]; + __pyx_v_mode = values[1]; + __pyx_v_closefd = values[2]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 3, __pyx_nargs); __PYX_ERR(0, 71, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile___init__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_name, __pyx_v_mode, __pyx_v_closefd); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_VARARGS(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_5pysam_10libchtslib_5HFile___init__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_mode, CYTHON_UNUSED PyObject *__pyx_v_closefd) { + int __pyx_r; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 1); + __Pyx_TraceCall("__init__", __pyx_f[0], 71, 0, __PYX_ERR(0, 71, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":72 + * + * def __init__(self, name, mode='r', closefd=True): + * self._open(name, mode, closefd=True) # <<<<<<<<<<<<<< + * + * def __dealloc__(self): + */ + __pyx_t_2.__pyx_n = 1; + __pyx_t_2.closefd = Py_True; + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10libchtslib_HFile *)__pyx_v_self->__pyx_vtab)->_open(__pyx_v_self, __pyx_v_name, __pyx_v_mode, &__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 72, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":71 + * cdef readonly object name, mode + * + * def __init__(self, name, mode='r', closefd=True): # <<<<<<<<<<<<<< + * self._open(name, mode, closefd=True) + * + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HFile.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_TraceReturn(Py_None, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":74 + * self._open(name, mode, closefd=True) + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * self.close() + * + */ + +/* Python wrapper */ +static void __pyx_pw_5pysam_10libchtslib_5HFile_3__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_10libchtslib_5HFile_3__dealloc__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_pf_5pysam_10libchtslib_5HFile_2__dealloc__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_5pysam_10libchtslib_5HFile_2__dealloc__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + unsigned int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__dealloc__", 1); + __Pyx_TraceCall("__dealloc__", __pyx_f[0], 74, 0, __PYX_ERR(0, 74, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":75 + * + * def __dealloc__(self): + * self.close() # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 75, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + __pyx_t_4 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_4 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 75, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":74 + * self._open(name, mode, closefd=True) + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * self.close() + * + */ + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_WriteUnraisable("pysam.libchtslib.HFile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); + __pyx_L0:; + __Pyx_TraceReturn(Py_None, 0); + __Pyx_RefNannyFinishContext(); +} + +/* "pysam/libchtslib.pyx":77 + * self.close() + * + * @property # <<<<<<<<<<<<<< + * def closed(self): + * return self.fp == NULL + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_6closed_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_6closed_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_6closed___get__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_6closed___get__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 77, 0, __PYX_ERR(0, 77, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":79 + * @property + * def closed(self): + * return self.fp == NULL # <<<<<<<<<<<<<< + * + * cdef _open(self, name, mode, closefd=True): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fp == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 79, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":77 + * self.close() + * + * @property # <<<<<<<<<<<<<< + * def closed(self): + * return self.fp == NULL + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HFile.closed.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":81 + * return self.fp == NULL + * + * cdef _open(self, name, mode, closefd=True): # <<<<<<<<<<<<<< + * self.name = name + * self.mode = mode + */ + +static PyObject *__pyx_f_5pysam_10libchtslib_5HFile__open(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_mode, struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open *__pyx_optional_args) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + char const *__pyx_t_4; + char const *__pyx_t_5; + char const *__pyx_t_6; + PyObject *__pyx_t_7 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_open", 0); + __Pyx_TraceCall("_open", __pyx_f[0], 81, 0, __PYX_ERR(0, 81, __pyx_L1_error)); + if (__pyx_optional_args) { + } + __Pyx_INCREF(__pyx_v_name); + __Pyx_INCREF(__pyx_v_mode); + + /* "pysam/libchtslib.pyx":82 + * + * cdef _open(self, name, mode, closefd=True): + * self.name = name # <<<<<<<<<<<<<< + * self.mode = mode + * + */ + __Pyx_INCREF(__pyx_v_name); + __Pyx_GIVEREF(__pyx_v_name); + __Pyx_GOTREF(__pyx_v_self->name); + __Pyx_DECREF(__pyx_v_self->name); + __pyx_v_self->name = __pyx_v_name; + + /* "pysam/libchtslib.pyx":83 + * cdef _open(self, name, mode, closefd=True): + * self.name = name + * self.mode = mode # <<<<<<<<<<<<<< + * + * mode = force_bytes(mode) + */ + __Pyx_INCREF(__pyx_v_mode); + __Pyx_GIVEREF(__pyx_v_mode); + __Pyx_GOTREF(__pyx_v_self->mode); + __Pyx_DECREF(__pyx_v_self->mode); + __pyx_v_self->mode = __pyx_v_mode; + + /* "pysam/libchtslib.pyx":85 + * self.mode = mode + * + * mode = force_bytes(mode) # <<<<<<<<<<<<<< + * + * if isinstance(name, int): + */ + __pyx_t_1 = __pyx_f_5pysam_9libcutils_force_bytes(__pyx_v_mode, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 85, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_mode, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":87 + * mode = force_bytes(mode) + * + * if isinstance(name, int): # <<<<<<<<<<<<<< + * if self.fp != NULL: + * name = dup(name) + */ + __pyx_t_2 = PyInt_Check(__pyx_v_name); + if (__pyx_t_2) { + + /* "pysam/libchtslib.pyx":88 + * + * if isinstance(name, int): + * if self.fp != NULL: # <<<<<<<<<<<<<< + * name = dup(name) + * self.fp = hdopen(name, mode) + */ + __pyx_t_2 = (__pyx_v_self->fp != NULL); + if (__pyx_t_2) { + + /* "pysam/libchtslib.pyx":89 + * if isinstance(name, int): + * if self.fp != NULL: + * name = dup(name) # <<<<<<<<<<<<<< + * self.fp = hdopen(name, mode) + * else: + */ + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_v_name); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 89, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_int(dup(__pyx_t_3)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 89, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_name, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":88 + * + * if isinstance(name, int): + * if self.fp != NULL: # <<<<<<<<<<<<<< + * name = dup(name) + * self.fp = hdopen(name, mode) + */ + } + + /* "pysam/libchtslib.pyx":90 + * if self.fp != NULL: + * name = dup(name) + * self.fp = hdopen(name, mode) # <<<<<<<<<<<<<< + * else: + * name = encode_filename(name) + */ + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_v_name); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 90, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 90, __pyx_L1_error) + __pyx_v_self->fp = hdopen(__pyx_t_3, __pyx_t_4); + + /* "pysam/libchtslib.pyx":87 + * mode = force_bytes(mode) + * + * if isinstance(name, int): # <<<<<<<<<<<<<< + * if self.fp != NULL: + * name = dup(name) + */ + goto __pyx_L3; + } + + /* "pysam/libchtslib.pyx":92 + * self.fp = hdopen(name, mode) + * else: + * name = encode_filename(name) # <<<<<<<<<<<<<< + * self.fp = hopen(name, mode) + * + */ + /*else*/ { + __pyx_t_1 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_name); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 92, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_name, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":93 + * else: + * name = encode_filename(name) + * self.fp = hopen(name, mode) # <<<<<<<<<<<<<< + * + * if not self.fp: + */ + __pyx_t_5 = __Pyx_PyObject_AsString(__pyx_v_name); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) __PYX_ERR(0, 93, __pyx_L1_error) + __pyx_t_6 = __Pyx_PyObject_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) __PYX_ERR(0, 93, __pyx_L1_error) + __pyx_v_self->fp = hopen(__pyx_t_5, __pyx_t_6); + } + __pyx_L3:; + + /* "pysam/libchtslib.pyx":95 + * self.fp = hopen(name, mode) + * + * if not self.fp: # <<<<<<<<<<<<<< + * raise IOError(errno, 'failed to open HFile', self.name) + * + */ + __pyx_t_2 = (!(__pyx_v_self->fp != 0)); + if (unlikely(__pyx_t_2)) { + + /* "pysam/libchtslib.pyx":96 + * + * if not self.fp: + * raise IOError(errno, 'failed to open HFile', self.name) # <<<<<<<<<<<<<< + * + * def close(self): + */ + __pyx_t_1 = __Pyx_PyInt_From_int(errno); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 96, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 96, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GIVEREF(__pyx_t_1); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_1)) __PYX_ERR(0, 96, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_failed_to_open_HFile); + __Pyx_GIVEREF(__pyx_kp_u_failed_to_open_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_kp_u_failed_to_open_HFile)) __PYX_ERR(0, 96, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_v_self->name)) __PYX_ERR(0, 96, __pyx_L1_error); + __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 96, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 96, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":95 + * self.fp = hopen(name, mode) + * + * if not self.fp: # <<<<<<<<<<<<<< + * raise IOError(errno, 'failed to open HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":81 + * return self.fp == NULL + * + * cdef _open(self, name, mode, closefd=True): # <<<<<<<<<<<<<< + * self.name = name + * self.mode = mode + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_AddTraceback("pysam.libchtslib.HFile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_name); + __Pyx_XDECREF(__pyx_v_mode); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":98 + * raise IOError(errno, 'failed to open HFile', self.name) + * + * def close(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * return + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_5close(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_4close, "HFile.close(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_5close = {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_5close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_4close}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_5close(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("close (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("close", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "close", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_4close(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_4close(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + hFILE *__pyx_v_fp; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + hFILE *__pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__3) + __Pyx_RefNannySetupContext("close", 1); + __Pyx_TraceCall("close", __pyx_f[0], 98, 0, __PYX_ERR(0, 98, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":99 + * + * def close(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * return + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":100 + * def close(self): + * if self.fp == NULL: + * return # <<<<<<<<<<<<<< + * + * cdef hFILE *fp = self.fp + */ + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":99 + * + * def close(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * return + * + */ + } + + /* "pysam/libchtslib.pyx":102 + * return + * + * cdef hFILE *fp = self.fp # <<<<<<<<<<<<<< + * self.fp = NULL + * + */ + __pyx_t_2 = __pyx_v_self->fp; + __pyx_v_fp = __pyx_t_2; + + /* "pysam/libchtslib.pyx":103 + * + * cdef hFILE *fp = self.fp + * self.fp = NULL # <<<<<<<<<<<<<< + * + * if hclose(fp) != 0: + */ + __pyx_v_self->fp = NULL; + + /* "pysam/libchtslib.pyx":105 + * self.fp = NULL + * + * if hclose(fp) != 0: # <<<<<<<<<<<<<< + * raise IOError(errno, 'failed to close HFile', self.name) + * + */ + __pyx_t_1 = (hclose(__pyx_v_fp) != 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":106 + * + * if hclose(fp) != 0: + * raise IOError(errno, 'failed to close HFile', self.name) # <<<<<<<<<<<<<< + * + * def fileno(self): + */ + __pyx_t_3 = __Pyx_PyInt_From_int(errno); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 106, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 106, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_3); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3)) __PYX_ERR(0, 106, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_failed_to_close_HFile); + __Pyx_GIVEREF(__pyx_kp_u_failed_to_close_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_kp_u_failed_to_close_HFile)) __PYX_ERR(0, 106, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_self->name)) __PYX_ERR(0, 106, __pyx_L1_error); + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 106, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __PYX_ERR(0, 106, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":105 + * self.fp = NULL + * + * if hclose(fp) != 0: # <<<<<<<<<<<<<< + * raise IOError(errno, 'failed to close HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":98 + * raise IOError(errno, 'failed to open HFile', self.name) + * + * def close(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * return + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HFile.close", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":108 + * raise IOError(errno, 'failed to close HFile', self.name) + * + * def fileno(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_7fileno(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_6fileno, "HFile.fileno(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_7fileno = {"fileno", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_7fileno, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_6fileno}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_7fileno(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("fileno (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("fileno", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "fileno", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_6fileno(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_6fileno(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__4) + __Pyx_RefNannySetupContext("fileno", 1); + __Pyx_TraceCall("fileno", __pyx_f[0], 108, 0, __PYX_ERR(0, 108, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":109 + * + * def fileno(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * if isinstance(self.name, int): + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":110 + * def fileno(self): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * if isinstance(self.name, int): + * return self.name + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 110, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 110, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":109 + * + * def fileno(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * if isinstance(self.name, int): + */ + } + + /* "pysam/libchtslib.pyx":111 + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + * if isinstance(self.name, int): # <<<<<<<<<<<<<< + * return self.name + * else: + */ + __pyx_t_2 = __pyx_v_self->name; + __Pyx_INCREF(__pyx_t_2); + __pyx_t_1 = PyInt_Check(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (likely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":112 + * raise IOError('operation on closed HFile') + * if isinstance(self.name, int): + * return self.name # <<<<<<<<<<<<<< + * else: + * raise AttributeError('fileno not available') + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->name); + __pyx_r = __pyx_v_self->name; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":111 + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + * if isinstance(self.name, int): # <<<<<<<<<<<<<< + * return self.name + * else: + */ + } + + /* "pysam/libchtslib.pyx":114 + * return self.name + * else: + * raise AttributeError('fileno not available') # <<<<<<<<<<<<<< + * + * def __enter__(self): + */ + /*else*/ { + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_AttributeError, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 114, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 114, __pyx_L1_error) + } + + /* "pysam/libchtslib.pyx":108 + * raise IOError(errno, 'failed to close HFile', self.name) + * + * def fileno(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pysam.libchtslib.HFile.fileno", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":116 + * raise AttributeError('fileno not available') + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_9__enter__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_8__enter__, "HFile.__enter__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_9__enter__ = {"__enter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_9__enter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_8__enter__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_9__enter__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__enter__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("__enter__", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__enter__", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_8__enter__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_8__enter__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__7) + __Pyx_RefNannySetupContext("__enter__", 1); + __Pyx_TraceCall("__enter__", __pyx_f[0], 116, 0, __PYX_ERR(0, 116, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":117 + * + * def __enter__(self): + * return self # <<<<<<<<<<<<<< + * + * def __exit__(self, type, value, tb): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF((PyObject *)__pyx_v_self); + __pyx_r = ((PyObject *)__pyx_v_self); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":116 + * raise AttributeError('fileno not available') + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HFile.__enter__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":119 + * return self + * + * def __exit__(self, type, value, tb): # <<<<<<<<<<<<<< + * self.close() + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_11__exit__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_10__exit__, "HFile.__exit__(self, type, value, tb)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_11__exit__ = {"__exit__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_11__exit__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_10__exit__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_11__exit__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v_type = 0; + CYTHON_UNUSED PyObject *__pyx_v_value = 0; + CYTHON_UNUSED PyObject *__pyx_v_tb = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[3] = {0,0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__exit__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_type,&__pyx_n_s_value,&__pyx_n_s_tb,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_type)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 119, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_value)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 119, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); __PYX_ERR(0, 119, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_tb)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 119, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); __PYX_ERR(0, 119, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__exit__") < 0)) __PYX_ERR(0, 119, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 3)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + } + __pyx_v_type = values[0]; + __pyx_v_value = values[1]; + __pyx_v_tb = values[2]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 119, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_10__exit__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_type, __pyx_v_value, __pyx_v_tb); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_10__exit__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_type, CYTHON_UNUSED PyObject *__pyx_v_value, CYTHON_UNUSED PyObject *__pyx_v_tb) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + unsigned int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__8) + __Pyx_RefNannySetupContext("__exit__", 1); + __Pyx_TraceCall("__exit__", __pyx_f[0], 119, 0, __PYX_ERR(0, 119, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":120 + * + * def __exit__(self, type, value, tb): + * self.close() # <<<<<<<<<<<<<< + * + * def __iter__(self): + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 120, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + __pyx_t_4 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_4 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 120, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":119 + * return self + * + * def __exit__(self, type, value, tb): # <<<<<<<<<<<<<< + * self.close() + * + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HFile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":122 + * self.close() + * + * def __iter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_13__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_13__iter__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_12__iter__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_12__iter__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__iter__", 1); + __Pyx_TraceCall("__iter__", __pyx_f[0], 122, 0, __PYX_ERR(0, 122, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":123 + * + * def __iter__(self): + * return self # <<<<<<<<<<<<<< + * + * def __next__(self): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF((PyObject *)__pyx_v_self); + __pyx_r = ((PyObject *)__pyx_v_self); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":122 + * self.close() + * + * def __iter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HFile.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":125 + * return self + * + * def __next__(self): # <<<<<<<<<<<<<< + * line = self.readline() + * if not line: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_15__next__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_15__next__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_14__next__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_14__next__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_v_line = NULL; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_error_without_exception = 0; /* StopIteration */ + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + unsigned int __pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__next__", 1); + __Pyx_TraceCall("__next__", __pyx_f[0], 125, 0, __PYX_ERR(0, 125, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":126 + * + * def __next__(self): + * line = self.readline() # <<<<<<<<<<<<<< + * if not line: + * raise StopIteration() + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_readline); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 126, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + __pyx_t_4 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_4 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 126, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __pyx_v_line = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":127 + * def __next__(self): + * line = self.readline() + * if not line: # <<<<<<<<<<<<<< + * raise StopIteration() + * return line + */ + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_line); if (unlikely((__pyx_t_5 < 0))) __PYX_ERR(0, 127, __pyx_L1_error) + __pyx_t_6 = (!__pyx_t_5); + if (unlikely(__pyx_t_6)) { + + /* "pysam/libchtslib.pyx":128 + * line = self.readline() + * if not line: + * raise StopIteration() # <<<<<<<<<<<<<< + * return line + * + */ + __pyx_error_without_exception = 1; + goto __pyx_L1_error;; + + /* "pysam/libchtslib.pyx":127 + * def __next__(self): + * line = self.readline() + * if not line: # <<<<<<<<<<<<<< + * raise StopIteration() + * return line + */ + } + + /* "pysam/libchtslib.pyx":129 + * if not line: + * raise StopIteration() + * return line # <<<<<<<<<<<<<< + * + * def flush(self): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_line); + __pyx_r = __pyx_v_line; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":125 + * return self + * + * def __next__(self): # <<<<<<<<<<<<<< + * line = self.readline() + * if not line: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + if (!__pyx_error_without_exception) { + __Pyx_AddTraceback("pysam.libchtslib.HFile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + } + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_line); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":131 + * return line + * + * def flush(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_17flush(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_16flush, "HFile.flush(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_17flush = {"flush", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_17flush, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_16flush}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_17flush(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("flush (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("flush", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "flush", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_16flush(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_16flush(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__9) + __Pyx_RefNannySetupContext("flush", 1); + __Pyx_TraceCall("flush", __pyx_f[0], 131, 0, __PYX_ERR(0, 131, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":132 + * + * def flush(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * if hflush(self.fp) != 0: + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":133 + * def flush(self): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * if hflush(self.fp) != 0: + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 133, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 133, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":132 + * + * def flush(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * if hflush(self.fp) != 0: + */ + } + + /* "pysam/libchtslib.pyx":134 + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + * if hflush(self.fp) != 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + * + */ + __pyx_t_1 = (hflush(__pyx_v_self->fp) != 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":135 + * raise IOError('operation on closed HFile') + * if hflush(self.fp) != 0: + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) # <<<<<<<<<<<<<< + * + * def isatty(self): + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 135, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 135, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2)) __PYX_ERR(0, 135, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_failed_to_flush_HFile); + __Pyx_GIVEREF(__pyx_kp_u_failed_to_flush_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_kp_u_failed_to_flush_HFile)) __PYX_ERR(0, 135, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_v_self->name)) __PYX_ERR(0, 135, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 135, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 135, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":134 + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + * if hflush(self.fp) != 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":131 + * return line + * + * def flush(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HFile.flush", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":137 + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + * + * def isatty(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_19isatty(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_18isatty, "HFile.isatty(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_19isatty = {"isatty", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_19isatty, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_18isatty}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_19isatty(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("isatty (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("isatty", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "isatty", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_18isatty(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_18isatty(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__10) + __Pyx_RefNannySetupContext("isatty", 1); + __Pyx_TraceCall("isatty", __pyx_f[0], 137, 0, __PYX_ERR(0, 137, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":138 + * + * def isatty(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * return False + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":139 + * def isatty(self): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * return False + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 139, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 139, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":138 + * + * def isatty(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * return False + */ + } + + /* "pysam/libchtslib.pyx":140 + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + * return False # <<<<<<<<<<<<<< + * + * def readable(self): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_False); + __pyx_r = Py_False; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":137 + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + * + * def isatty(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pysam.libchtslib.HFile.isatty", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":142 + * return False + * + * def readable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'r' in self.mode + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_21readable(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_20readable, "HFile.readable(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_21readable = {"readable", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_21readable, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_20readable}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_21readable(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("readable (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("readable", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "readable", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_20readable(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_20readable(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__11) + __Pyx_RefNannySetupContext("readable", 1); + __Pyx_TraceCall("readable", __pyx_f[0], 142, 0, __PYX_ERR(0, 142, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":143 + * + * def readable(self): + * return self.fp != NULL and 'r' in self.mode # <<<<<<<<<<<<<< + * + * def read(self, Py_ssize_t size=-1): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->fp != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 143, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_n_u_r, __pyx_v_self->mode, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 143, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 143, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":142 + * return False + * + * def readable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'r' in self.mode + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HFile.readable", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":145 + * return self.fp != NULL and 'r' in self.mode + * + * def read(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_23read(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_22read, "HFile.read(self, Py_ssize_t size=-1)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_23read = {"read", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_23read, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_22read}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_23read(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + Py_ssize_t __pyx_v_size; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("read (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_size,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_size); + if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 145, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "read") < 0)) __PYX_ERR(0, 145, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + } + if (values[0]) { + __pyx_v_size = __Pyx_PyIndex_AsSsize_t(values[0]); if (unlikely((__pyx_v_size == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 145, __pyx_L3_error) + } else { + __pyx_v_size = ((Py_ssize_t)-1L); + } + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("read", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 145, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.read", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_22read(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_size); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_22read(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, Py_ssize_t __pyx_v_size) { + PyObject *__pyx_v_parts = 0; + PyObject *__pyx_v_part = 0; + Py_ssize_t __pyx_v_chunk_size; + Py_ssize_t __pyx_v_ret; + Py_ssize_t __pyx_v_bytes_read; + char *__pyx_v_cpart; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + char *__pyx_t_7; + PyObject *__pyx_t_8 = NULL; + int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__12) + __Pyx_RefNannySetupContext("read", 1); + __Pyx_TraceCall("read", __pyx_f[0], 145, 0, __PYX_ERR(0, 145, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":146 + * + * def read(self, Py_ssize_t size=-1): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":147 + * def read(self, Py_ssize_t size=-1): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * + * if size == 0: + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 147, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 147, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":146 + * + * def read(self, Py_ssize_t size=-1): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + } + + /* "pysam/libchtslib.pyx":149 + * raise IOError('operation on closed HFile') + * + * if size == 0: # <<<<<<<<<<<<<< + * return b'' + * + */ + __pyx_t_1 = (__pyx_v_size == 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":150 + * + * if size == 0: + * return b'' # <<<<<<<<<<<<<< + * + * cdef list parts = [] + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_kp_b__13); + __pyx_r = __pyx_kp_b__13; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":149 + * raise IOError('operation on closed HFile') + * + * if size == 0: # <<<<<<<<<<<<<< + * return b'' + * + */ + } + + /* "pysam/libchtslib.pyx":152 + * return b'' + * + * cdef list parts = [] # <<<<<<<<<<<<<< + * cdef bytes part + * cdef Py_ssize_t chunk_size, ret, bytes_read = 0 + */ + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 152, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_parts = ((PyObject*)__pyx_t_2); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":154 + * cdef list parts = [] + * cdef bytes part + * cdef Py_ssize_t chunk_size, ret, bytes_read = 0 # <<<<<<<<<<<<<< + * cdef char *cpart + * + */ + __pyx_v_bytes_read = 0; + + /* "pysam/libchtslib.pyx":157 + * cdef char *cpart + * + * while size == -1 or bytes_read < size: # <<<<<<<<<<<<<< + * chunk_size = 4096 + * if size != -1: + */ + while (1) { + __pyx_t_3 = (__pyx_v_size == -1L); + if (!__pyx_t_3) { + } else { + __pyx_t_1 = __pyx_t_3; + goto __pyx_L7_bool_binop_done; + } + __pyx_t_3 = (__pyx_v_bytes_read < __pyx_v_size); + __pyx_t_1 = __pyx_t_3; + __pyx_L7_bool_binop_done:; + if (!__pyx_t_1) break; + + /* "pysam/libchtslib.pyx":158 + * + * while size == -1 or bytes_read < size: + * chunk_size = 4096 # <<<<<<<<<<<<<< + * if size != -1: + * chunk_size = min(chunk_size, size - bytes_read) + */ + __pyx_v_chunk_size = 0x1000; + + /* "pysam/libchtslib.pyx":159 + * while size == -1 or bytes_read < size: + * chunk_size = 4096 + * if size != -1: # <<<<<<<<<<<<<< + * chunk_size = min(chunk_size, size - bytes_read) + * + */ + __pyx_t_1 = (__pyx_v_size != -1L); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":160 + * chunk_size = 4096 + * if size != -1: + * chunk_size = min(chunk_size, size - bytes_read) # <<<<<<<<<<<<<< + * + * part = PyBytes_FromStringAndSize(NULL, chunk_size) + */ + __pyx_t_4 = (__pyx_v_size - __pyx_v_bytes_read); + __pyx_t_5 = __pyx_v_chunk_size; + __pyx_t_1 = (__pyx_t_4 < __pyx_t_5); + if (__pyx_t_1) { + __pyx_t_6 = __pyx_t_4; + } else { + __pyx_t_6 = __pyx_t_5; + } + __pyx_v_chunk_size = __pyx_t_6; + + /* "pysam/libchtslib.pyx":159 + * while size == -1 or bytes_read < size: + * chunk_size = 4096 + * if size != -1: # <<<<<<<<<<<<<< + * chunk_size = min(chunk_size, size - bytes_read) + * + */ + } + + /* "pysam/libchtslib.pyx":162 + * chunk_size = min(chunk_size, size - bytes_read) + * + * part = PyBytes_FromStringAndSize(NULL, chunk_size) # <<<<<<<<<<<<<< + * cpart = <char *>part + * ret = hread(self.fp, <void *>cpart, chunk_size) + */ + __pyx_t_2 = PyBytes_FromStringAndSize(NULL, __pyx_v_chunk_size); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 162, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_XDECREF_SET(__pyx_v_part, ((PyObject*)__pyx_t_2)); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":163 + * + * part = PyBytes_FromStringAndSize(NULL, chunk_size) + * cpart = <char *>part # <<<<<<<<<<<<<< + * ret = hread(self.fp, <void *>cpart, chunk_size) + * + */ + if (unlikely(__pyx_v_part == Py_None)) { + PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); + __PYX_ERR(0, 163, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_PyBytes_AsWritableString(__pyx_v_part); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) __PYX_ERR(0, 163, __pyx_L1_error) + __pyx_v_cpart = ((char *)__pyx_t_7); + + /* "pysam/libchtslib.pyx":164 + * part = PyBytes_FromStringAndSize(NULL, chunk_size) + * cpart = <char *>part + * ret = hread(self.fp, <void *>cpart, chunk_size) # <<<<<<<<<<<<<< + * + * if ret < 0: + */ + __pyx_v_ret = hread(__pyx_v_self->fp, ((void *)__pyx_v_cpart), __pyx_v_chunk_size); + + /* "pysam/libchtslib.pyx":166 + * ret = hread(self.fp, <void *>cpart, chunk_size) + * + * if ret < 0: # <<<<<<<<<<<<<< + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: + */ + __pyx_t_1 = (__pyx_v_ret < 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":167 + * + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) # <<<<<<<<<<<<<< + * elif not ret: + * break + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 167, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 167, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2)) __PYX_ERR(0, 167, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_failed_to_read_HFile); + __Pyx_GIVEREF(__pyx_kp_u_failed_to_read_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_kp_u_failed_to_read_HFile)) __PYX_ERR(0, 167, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_v_self->name)) __PYX_ERR(0, 167, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 167, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":166 + * ret = hread(self.fp, <void *>cpart, chunk_size) + * + * if ret < 0: # <<<<<<<<<<<<<< + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: + */ + goto __pyx_L10; + } + + /* "pysam/libchtslib.pyx":168 + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: # <<<<<<<<<<<<<< + * break + * + */ + __pyx_t_1 = (!(__pyx_v_ret != 0)); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":169 + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: + * break # <<<<<<<<<<<<<< + * + * bytes_read += ret + */ + goto __pyx_L6_break; + + /* "pysam/libchtslib.pyx":168 + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: # <<<<<<<<<<<<<< + * break + * + */ + } + __pyx_L10:; + + /* "pysam/libchtslib.pyx":171 + * break + * + * bytes_read += ret # <<<<<<<<<<<<<< + * + * if ret < chunk_size: + */ + __pyx_v_bytes_read = (__pyx_v_bytes_read + __pyx_v_ret); + + /* "pysam/libchtslib.pyx":173 + * bytes_read += ret + * + * if ret < chunk_size: # <<<<<<<<<<<<<< + * part = cpart[:ret] + * + */ + __pyx_t_1 = (__pyx_v_ret < __pyx_v_chunk_size); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":174 + * + * if ret < chunk_size: + * part = cpart[:ret] # <<<<<<<<<<<<<< + * + * parts.append(part) + */ + __pyx_t_2 = __Pyx_PyBytes_FromStringAndSize(__pyx_v_cpart + 0, __pyx_v_ret - 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 174, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF_SET(__pyx_v_part, ((PyObject*)__pyx_t_2)); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":173 + * bytes_read += ret + * + * if ret < chunk_size: # <<<<<<<<<<<<<< + * part = cpart[:ret] + * + */ + } + + /* "pysam/libchtslib.pyx":176 + * part = cpart[:ret] + * + * parts.append(part) # <<<<<<<<<<<<<< + * + * return b''.join(parts) + */ + __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_parts, __pyx_v_part); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 176, __pyx_L1_error) + } + __pyx_L6_break:; + + /* "pysam/libchtslib.pyx":178 + * parts.append(part) + * + * return b''.join(parts) # <<<<<<<<<<<<<< + * + * def readall(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyBytes_Join(__pyx_kp_b__13, __pyx_v_parts); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 178, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":145 + * return self.fp != NULL and 'r' in self.mode + * + * def read(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_AddTraceback("pysam.libchtslib.HFile.read", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_parts); + __Pyx_XDECREF(__pyx_v_part); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":180 + * return b''.join(parts) + * + * def readall(self): # <<<<<<<<<<<<<< + * return self.read() + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_25readall(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_24readall, "HFile.readall(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_25readall = {"readall", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_25readall, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_24readall}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_25readall(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("readall (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("readall", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "readall", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_24readall(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_24readall(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + unsigned int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__14) + __Pyx_RefNannySetupContext("readall", 1); + __Pyx_TraceCall("readall", __pyx_f[0], 180, 0, __PYX_ERR(0, 180, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":181 + * + * def readall(self): + * return self.read() # <<<<<<<<<<<<<< + * + * def readinto(self, buf): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_read); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 181, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + __pyx_t_4 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_4 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 181, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":180 + * return b''.join(parts) + * + * def readall(self): # <<<<<<<<<<<<<< + * return self.read() + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HFile.readall", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":183 + * return self.read() + * + * def readinto(self, buf): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_27readinto(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_26readinto, "HFile.readinto(self, buf)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_27readinto = {"readinto", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_27readinto, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_26readinto}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_27readinto(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_buf = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("readinto (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_buf,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_buf)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 183, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "readinto") < 0)) __PYX_ERR(0, 183, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_buf = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("readinto", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 183, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.readinto", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_26readinto(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_buf); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_26readinto(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_buf) { + Py_ssize_t __pyx_v_size; + PyObject *__pyx_v_mv = NULL; + Py_ssize_t __pyx_v_ret; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + Py_ssize_t __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__15) + __Pyx_RefNannySetupContext("readinto", 1); + __Pyx_TraceCall("readinto", __pyx_f[0], 183, 0, __PYX_ERR(0, 183, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":184 + * + * def readinto(self, buf): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":185 + * def readinto(self, buf): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * + * size = len(buf) + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 185, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":184 + * + * def readinto(self, buf): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + } + + /* "pysam/libchtslib.pyx":187 + * raise IOError('operation on closed HFile') + * + * size = len(buf) # <<<<<<<<<<<<<< + * + * if size == 0: + */ + __pyx_t_3 = PyObject_Length(__pyx_v_buf); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 187, __pyx_L1_error) + __pyx_v_size = __pyx_t_3; + + /* "pysam/libchtslib.pyx":189 + * size = len(buf) + * + * if size == 0: # <<<<<<<<<<<<<< + * return size + * + */ + __pyx_t_1 = (__pyx_v_size == 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":190 + * + * if size == 0: + * return size # <<<<<<<<<<<<<< + * + * mv = memoryview(buf) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_size); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 190, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":189 + * size = len(buf) + * + * if size == 0: # <<<<<<<<<<<<<< + * return size + * + */ + } + + /* "pysam/libchtslib.pyx":192 + * return size + * + * mv = memoryview(buf) # <<<<<<<<<<<<<< + * ret = hread(self.fp, <void *>mv, size) + * + */ + __pyx_t_2 = PyMemoryView_FromObject(__pyx_v_buf); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 192, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_mv = ((PyObject*)__pyx_t_2); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":193 + * + * mv = memoryview(buf) + * ret = hread(self.fp, <void *>mv, size) # <<<<<<<<<<<<<< + * + * if ret < 0: + */ + __pyx_v_ret = hread(__pyx_v_self->fp, ((void *)__pyx_v_mv), __pyx_v_size); + + /* "pysam/libchtslib.pyx":195 + * ret = hread(self.fp, <void *>mv, size) + * + * if ret < 0: # <<<<<<<<<<<<<< + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * + */ + __pyx_t_1 = (__pyx_v_ret < 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":196 + * + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) # <<<<<<<<<<<<<< + * + * return ret + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2)) __PYX_ERR(0, 196, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_failed_to_read_HFile); + __Pyx_GIVEREF(__pyx_kp_u_failed_to_read_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_kp_u_failed_to_read_HFile)) __PYX_ERR(0, 196, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_self->name)) __PYX_ERR(0, 196, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":195 + * ret = hread(self.fp, <void *>mv, size) + * + * if ret < 0: # <<<<<<<<<<<<<< + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":198 + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * + * return ret # <<<<<<<<<<<<<< + * + * def readline(self, Py_ssize_t size=-1): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_ret); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 198, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":183 + * return self.read() + * + * def readinto(self, buf): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HFile.readinto", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_mv); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":200 + * return ret + * + * def readline(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_29readline(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_28readline, "HFile.readline(self, Py_ssize_t size=-1)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_29readline = {"readline", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_29readline, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_28readline}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_29readline(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + Py_ssize_t __pyx_v_size; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("readline (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_size,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_size); + if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 200, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "readline") < 0)) __PYX_ERR(0, 200, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + } + if (values[0]) { + __pyx_v_size = __Pyx_PyIndex_AsSsize_t(values[0]); if (unlikely((__pyx_v_size == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 200, __pyx_L3_error) + } else { + __pyx_v_size = ((Py_ssize_t)-1L); + } + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("readline", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 200, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.readline", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_28readline(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_size); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_28readline(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, Py_ssize_t __pyx_v_size) { + PyObject *__pyx_v_parts = 0; + PyObject *__pyx_v_part = 0; + Py_ssize_t __pyx_v_chunk_size; + Py_ssize_t __pyx_v_ret; + Py_ssize_t __pyx_v_bytes_read; + char *__pyx_v_cpart; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + char *__pyx_t_7; + PyObject *__pyx_t_8 = NULL; + int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__16) + __Pyx_RefNannySetupContext("readline", 1); + __Pyx_TraceCall("readline", __pyx_f[0], 200, 0, __PYX_ERR(0, 200, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":201 + * + * def readline(self, Py_ssize_t size=-1): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":202 + * def readline(self, Py_ssize_t size=-1): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * + * if size == 0: + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 202, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 202, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":201 + * + * def readline(self, Py_ssize_t size=-1): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + } + + /* "pysam/libchtslib.pyx":204 + * raise IOError('operation on closed HFile') + * + * if size == 0: # <<<<<<<<<<<<<< + * return b'' + * + */ + __pyx_t_1 = (__pyx_v_size == 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":205 + * + * if size == 0: + * return b'' # <<<<<<<<<<<<<< + * + * cdef list parts = [] + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_kp_b__13); + __pyx_r = __pyx_kp_b__13; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":204 + * raise IOError('operation on closed HFile') + * + * if size == 0: # <<<<<<<<<<<<<< + * return b'' + * + */ + } + + /* "pysam/libchtslib.pyx":207 + * return b'' + * + * cdef list parts = [] # <<<<<<<<<<<<<< + * cdef bytes part + * cdef Py_ssize_t chunk_size, ret, bytes_read = 0 + */ + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 207, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_parts = ((PyObject*)__pyx_t_2); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":209 + * cdef list parts = [] + * cdef bytes part + * cdef Py_ssize_t chunk_size, ret, bytes_read = 0 # <<<<<<<<<<<<<< + * cdef char *cpart + * + */ + __pyx_v_bytes_read = 0; + + /* "pysam/libchtslib.pyx":212 + * cdef char *cpart + * + * while size == -1 or bytes_read < size: # <<<<<<<<<<<<<< + * chunk_size = 4096 + * if size != -1: + */ + while (1) { + __pyx_t_3 = (__pyx_v_size == -1L); + if (!__pyx_t_3) { + } else { + __pyx_t_1 = __pyx_t_3; + goto __pyx_L7_bool_binop_done; + } + __pyx_t_3 = (__pyx_v_bytes_read < __pyx_v_size); + __pyx_t_1 = __pyx_t_3; + __pyx_L7_bool_binop_done:; + if (!__pyx_t_1) break; + + /* "pysam/libchtslib.pyx":213 + * + * while size == -1 or bytes_read < size: + * chunk_size = 4096 # <<<<<<<<<<<<<< + * if size != -1: + * chunk_size = min(chunk_size, size - bytes_read) + */ + __pyx_v_chunk_size = 0x1000; + + /* "pysam/libchtslib.pyx":214 + * while size == -1 or bytes_read < size: + * chunk_size = 4096 + * if size != -1: # <<<<<<<<<<<<<< + * chunk_size = min(chunk_size, size - bytes_read) + * + */ + __pyx_t_1 = (__pyx_v_size != -1L); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":215 + * chunk_size = 4096 + * if size != -1: + * chunk_size = min(chunk_size, size - bytes_read) # <<<<<<<<<<<<<< + * + * part = PyBytes_FromStringAndSize(NULL, chunk_size) + */ + __pyx_t_4 = (__pyx_v_size - __pyx_v_bytes_read); + __pyx_t_5 = __pyx_v_chunk_size; + __pyx_t_1 = (__pyx_t_4 < __pyx_t_5); + if (__pyx_t_1) { + __pyx_t_6 = __pyx_t_4; + } else { + __pyx_t_6 = __pyx_t_5; + } + __pyx_v_chunk_size = __pyx_t_6; + + /* "pysam/libchtslib.pyx":214 + * while size == -1 or bytes_read < size: + * chunk_size = 4096 + * if size != -1: # <<<<<<<<<<<<<< + * chunk_size = min(chunk_size, size - bytes_read) + * + */ + } + + /* "pysam/libchtslib.pyx":217 + * chunk_size = min(chunk_size, size - bytes_read) + * + * part = PyBytes_FromStringAndSize(NULL, chunk_size) # <<<<<<<<<<<<<< + * cpart = <char *>part + * + */ + __pyx_t_2 = PyBytes_FromStringAndSize(NULL, __pyx_v_chunk_size); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 217, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_XDECREF_SET(__pyx_v_part, ((PyObject*)__pyx_t_2)); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":218 + * + * part = PyBytes_FromStringAndSize(NULL, chunk_size) + * cpart = <char *>part # <<<<<<<<<<<<<< + * + * # Python bytes objects allocate an extra byte for a null terminator + */ + if (unlikely(__pyx_v_part == Py_None)) { + PyErr_SetString(PyExc_TypeError, "expected bytes, NoneType found"); + __PYX_ERR(0, 218, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_PyBytes_AsWritableString(__pyx_v_part); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) __PYX_ERR(0, 218, __pyx_L1_error) + __pyx_v_cpart = ((char *)__pyx_t_7); + + /* "pysam/libchtslib.pyx":221 + * + * # Python bytes objects allocate an extra byte for a null terminator + * ret = hgetln(cpart, chunk_size+1, self.fp) # <<<<<<<<<<<<<< + * + * if ret < 0: + */ + __pyx_v_ret = hgetln(__pyx_v_cpart, (__pyx_v_chunk_size + 1), __pyx_v_self->fp); + + /* "pysam/libchtslib.pyx":223 + * ret = hgetln(cpart, chunk_size+1, self.fp) + * + * if ret < 0: # <<<<<<<<<<<<<< + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: + */ + __pyx_t_1 = (__pyx_v_ret < 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":224 + * + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) # <<<<<<<<<<<<<< + * elif not ret: + * break + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 224, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 224, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2)) __PYX_ERR(0, 224, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_failed_to_read_HFile); + __Pyx_GIVEREF(__pyx_kp_u_failed_to_read_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_kp_u_failed_to_read_HFile)) __PYX_ERR(0, 224, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_v_self->name)) __PYX_ERR(0, 224, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 224, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":223 + * ret = hgetln(cpart, chunk_size+1, self.fp) + * + * if ret < 0: # <<<<<<<<<<<<<< + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: + */ + goto __pyx_L10; + } + + /* "pysam/libchtslib.pyx":225 + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: # <<<<<<<<<<<<<< + * break + * + */ + __pyx_t_1 = (!(__pyx_v_ret != 0)); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":226 + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: + * break # <<<<<<<<<<<<<< + * + * bytes_read += ret + */ + goto __pyx_L6_break; + + /* "pysam/libchtslib.pyx":225 + * if ret < 0: + * IOError(herrno(self.fp), 'failed to read HFile', self.name) + * elif not ret: # <<<<<<<<<<<<<< + * break + * + */ + } + __pyx_L10:; + + /* "pysam/libchtslib.pyx":228 + * break + * + * bytes_read += ret # <<<<<<<<<<<<<< + * + * if ret < chunk_size: + */ + __pyx_v_bytes_read = (__pyx_v_bytes_read + __pyx_v_ret); + + /* "pysam/libchtslib.pyx":230 + * bytes_read += ret + * + * if ret < chunk_size: # <<<<<<<<<<<<<< + * part = cpart[:ret] + * cpart = <char *>part + */ + __pyx_t_1 = (__pyx_v_ret < __pyx_v_chunk_size); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":231 + * + * if ret < chunk_size: + * part = cpart[:ret] # <<<<<<<<<<<<<< + * cpart = <char *>part + * + */ + __pyx_t_2 = __Pyx_PyBytes_FromStringAndSize(__pyx_v_cpart + 0, __pyx_v_ret - 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 231, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF_SET(__pyx_v_part, ((PyObject*)__pyx_t_2)); + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":232 + * if ret < chunk_size: + * part = cpart[:ret] + * cpart = <char *>part # <<<<<<<<<<<<<< + * + * parts.append(part) + */ + __pyx_t_7 = __Pyx_PyBytes_AsWritableString(__pyx_v_part); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) __PYX_ERR(0, 232, __pyx_L1_error) + __pyx_v_cpart = ((char *)__pyx_t_7); + + /* "pysam/libchtslib.pyx":230 + * bytes_read += ret + * + * if ret < chunk_size: # <<<<<<<<<<<<<< + * part = cpart[:ret] + * cpart = <char *>part + */ + } + + /* "pysam/libchtslib.pyx":234 + * cpart = <char *>part + * + * parts.append(part) # <<<<<<<<<<<<<< + * + * if cpart[ret-1] == b'\n': + */ + __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_parts, __pyx_v_part); if (unlikely(__pyx_t_9 == ((int)-1))) __PYX_ERR(0, 234, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":236 + * parts.append(part) + * + * if cpart[ret-1] == b'\n': # <<<<<<<<<<<<<< + * break + * + */ + __pyx_t_1 = ((__pyx_v_cpart[(__pyx_v_ret - 1)]) == '\n'); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":237 + * + * if cpart[ret-1] == b'\n': + * break # <<<<<<<<<<<<<< + * + * return b''.join(parts) + */ + goto __pyx_L6_break; + + /* "pysam/libchtslib.pyx":236 + * parts.append(part) + * + * if cpart[ret-1] == b'\n': # <<<<<<<<<<<<<< + * break + * + */ + } + } + __pyx_L6_break:; + + /* "pysam/libchtslib.pyx":239 + * break + * + * return b''.join(parts) # <<<<<<<<<<<<<< + * + * def readlines(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyBytes_Join(__pyx_kp_b__13, __pyx_v_parts); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 239, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":200 + * return ret + * + * def readline(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_AddTraceback("pysam.libchtslib.HFile.readline", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_parts); + __Pyx_XDECREF(__pyx_v_part); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":241 + * return b''.join(parts) + * + * def readlines(self): # <<<<<<<<<<<<<< + * return list(self) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_31readlines(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_30readlines, "HFile.readlines(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_31readlines = {"readlines", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_31readlines, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_30readlines}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_31readlines(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("readlines (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("readlines", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "readlines", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_30readlines(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_30readlines(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__17) + __Pyx_RefNannySetupContext("readlines", 1); + __Pyx_TraceCall("readlines", __pyx_f[0], 241, 0, __PYX_ERR(0, 241, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":242 + * + * def readlines(self): + * return list(self) # <<<<<<<<<<<<<< + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PySequence_List(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 242, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":241 + * return b''.join(parts) + * + * def readlines(self): # <<<<<<<<<<<<<< + * return list(self) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HFile.readlines", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":244 + * return list(self) + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_33seek(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_32seek, "HFile.seek(self, Py_ssize_t offset, int whence=io.SEEK_SET)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_33seek = {"seek", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_33seek, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_32seek}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_33seek(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + Py_ssize_t __pyx_v_offset; + int __pyx_v_whence; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[2] = {0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("seek (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_offset,&__pyx_n_s_whence,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_offset)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_whence); + if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "seek") < 0)) __PYX_ERR(0, 244, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_offset = __Pyx_PyIndex_AsSsize_t(values[0]); if (unlikely((__pyx_v_offset == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L3_error) + if (values[1]) { + __pyx_v_whence = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_whence == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L3_error) + } else { + __pyx_v_whence = __pyx_k__18; + } + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, __pyx_nargs); __PYX_ERR(0, 244, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_32seek(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_offset, __pyx_v_whence); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_32seek(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, Py_ssize_t __pyx_v_offset, int __pyx_v_whence) { + Py_ssize_t __pyx_v_off; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__19) + __Pyx_RefNannySetupContext("seek", 1); + __Pyx_TraceCall("seek", __pyx_f[0], 244, 0, __PYX_ERR(0, 244, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":245 + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":246 + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * + * cdef Py_ssize_t off = hseek(self.fp, offset, libc_whence_from_io(whence)) + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 246, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 246, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":245 + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + } + + /* "pysam/libchtslib.pyx":248 + * raise IOError('operation on closed HFile') + * + * cdef Py_ssize_t off = hseek(self.fp, offset, libc_whence_from_io(whence)) # <<<<<<<<<<<<<< + * + * if off < 0: + */ + __pyx_t_3 = __pyx_f_5pysam_9libcutils_libc_whence_from_io(__pyx_v_whence); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 248, __pyx_L1_error) + __pyx_v_off = hseek(__pyx_v_self->fp, __pyx_v_offset, __pyx_t_3); + + /* "pysam/libchtslib.pyx":250 + * cdef Py_ssize_t off = hseek(self.fp, offset, libc_whence_from_io(whence)) + * + * if off < 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'seek failed on HFile', self.name) + * + */ + __pyx_t_1 = (__pyx_v_off < 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":251 + * + * if off < 0: + * raise IOError(herrno(self.fp), 'seek failed on HFile', self.name) # <<<<<<<<<<<<<< + * + * return off + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 251, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 251, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2)) __PYX_ERR(0, 251, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_seek_failed_on_HFile); + __Pyx_GIVEREF(__pyx_kp_u_seek_failed_on_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_kp_u_seek_failed_on_HFile)) __PYX_ERR(0, 251, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_self->name)) __PYX_ERR(0, 251, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 251, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 251, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":250 + * cdef Py_ssize_t off = hseek(self.fp, offset, libc_whence_from_io(whence)) + * + * if off < 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'seek failed on HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":253 + * raise IOError(herrno(self.fp), 'seek failed on HFile', self.name) + * + * return off # <<<<<<<<<<<<<< + * + * def tell(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_off); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 253, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":244 + * return list(self) + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HFile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":255 + * return off + * + * def tell(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_35tell(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_34tell, "HFile.tell(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_35tell = {"tell", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_35tell, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_34tell}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_35tell(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("tell (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("tell", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "tell", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_34tell(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_34tell(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + off_t __pyx_v_ret; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__20) + __Pyx_RefNannySetupContext("tell", 1); + __Pyx_TraceCall("tell", __pyx_f[0], 255, 0, __PYX_ERR(0, 255, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":256 + * + * def tell(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":257 + * def tell(self): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * + * ret = htell(self.fp) + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 257, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 257, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":256 + * + * def tell(self): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + } + + /* "pysam/libchtslib.pyx":259 + * raise IOError('operation on closed HFile') + * + * ret = htell(self.fp) # <<<<<<<<<<<<<< + * + * if ret < 0: + */ + __pyx_v_ret = htell(__pyx_v_self->fp); + + /* "pysam/libchtslib.pyx":261 + * ret = htell(self.fp) + * + * if ret < 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'tell failed on HFile', self.name) + * + */ + __pyx_t_1 = (__pyx_v_ret < 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":262 + * + * if ret < 0: + * raise IOError(herrno(self.fp), 'tell failed on HFile', self.name) # <<<<<<<<<<<<<< + * + * return ret + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 262, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 262, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2)) __PYX_ERR(0, 262, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_tell_failed_on_HFile); + __Pyx_GIVEREF(__pyx_kp_u_tell_failed_on_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_kp_u_tell_failed_on_HFile)) __PYX_ERR(0, 262, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_v_self->name)) __PYX_ERR(0, 262, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 262, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 262, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":261 + * ret = htell(self.fp) + * + * if ret < 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'tell failed on HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":264 + * raise IOError(herrno(self.fp), 'tell failed on HFile', self.name) + * + * return ret # <<<<<<<<<<<<<< + * + * def seekable(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyInt_From_off_t(__pyx_v_ret); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 264, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":255 + * return off + * + * def tell(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HFile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":266 + * return ret + * + * def seekable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_37seekable(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_36seekable, "HFile.seekable(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_37seekable = {"seekable", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_37seekable, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_36seekable}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_37seekable(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("seekable (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("seekable", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "seekable", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_36seekable(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_36seekable(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__21) + __Pyx_RefNannySetupContext("seekable", 1); + __Pyx_TraceCall("seekable", __pyx_f[0], 266, 0, __PYX_ERR(0, 266, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":267 + * + * def seekable(self): + * return self.fp != NULL # <<<<<<<<<<<<<< + * + * def truncate(self, size=None): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fp != NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 267, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":266 + * return ret + * + * def seekable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HFile.seekable", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":269 + * return self.fp != NULL + * + * def truncate(self, size=None): # <<<<<<<<<<<<<< + * raise NotImplementedError() + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_39truncate(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_38truncate, "HFile.truncate(self, size=None)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_39truncate = {"truncate", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_39truncate, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_38truncate}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_39truncate(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v_size = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("truncate (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_size,0}; + values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_size); + if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 269, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "truncate") < 0)) __PYX_ERR(0, 269, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_size = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("truncate", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 269, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.truncate", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_38truncate(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_size); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_38truncate(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_size) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__22) + __Pyx_RefNannySetupContext("truncate", 1); + __Pyx_TraceCall("truncate", __pyx_f[0], 269, 0, __PYX_ERR(0, 269, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":270 + * + * def truncate(self, size=None): + * raise NotImplementedError() # <<<<<<<<<<<<<< + * + * def writable(self): + */ + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_builtin_NotImplementedError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 270, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 270, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":269 + * return self.fp != NULL + * + * def truncate(self, size=None): # <<<<<<<<<<<<<< + * raise NotImplementedError() + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HFile.truncate", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":272 + * raise NotImplementedError() + * + * def writable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'w' in self.mode + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_41writable(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_40writable, "HFile.writable(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_41writable = {"writable", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_41writable, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_40writable}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_41writable(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("writable (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("writable", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "writable", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_40writable(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_40writable(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__23) + __Pyx_RefNannySetupContext("writable", 1); + __Pyx_TraceCall("writable", __pyx_f[0], 272, 0, __PYX_ERR(0, 272, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":273 + * + * def writable(self): + * return self.fp != NULL and 'w' in self.mode # <<<<<<<<<<<<<< + * + * def write(self, bytes b): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->fp != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 273, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_n_u_w, __pyx_v_self->mode, Py_EQ)); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 273, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 273, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":272 + * raise NotImplementedError() + * + * def writable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'w' in self.mode + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HFile.writable", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":275 + * return self.fp != NULL and 'w' in self.mode + * + * def write(self, bytes b): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_43write(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_42write, "HFile.write(self, bytes b)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_43write = {"write", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_43write, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_42write}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_43write(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_b = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("write (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_b,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_b)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 275, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "write") < 0)) __PYX_ERR(0, 275, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_b = ((PyObject*)values[0]); + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("write", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 275, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.write", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_b), (&PyBytes_Type), 1, "b", 1))) __PYX_ERR(0, 275, __pyx_L1_error) + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_42write(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_b); + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __pyx_r = NULL; + __pyx_L0:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_42write(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_b) { + Py_ssize_t __pyx_v_got; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + Py_ssize_t __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__24) + __Pyx_RefNannySetupContext("write", 1); + __Pyx_TraceCall("write", __pyx_f[0], 275, 0, __PYX_ERR(0, 275, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":276 + * + * def write(self, bytes b): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + __pyx_t_1 = (__pyx_v_self->fp == NULL); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":277 + * def write(self, bytes b): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * + * got = hwrite(self.fp, <void *>b, len(b)) + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 277, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 277, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":276 + * + * def write(self, bytes b): + * if self.fp == NULL: # <<<<<<<<<<<<<< + * raise IOError('operation on closed HFile') + * + */ + } + + /* "pysam/libchtslib.pyx":279 + * raise IOError('operation on closed HFile') + * + * got = hwrite(self.fp, <void *>b, len(b)) # <<<<<<<<<<<<<< + * + * if got < 0: + */ + if (unlikely(__pyx_v_b == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 279, __pyx_L1_error) + } + __pyx_t_3 = __Pyx_PyBytes_GET_SIZE(__pyx_v_b); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 279, __pyx_L1_error) + __pyx_v_got = hwrite(__pyx_v_self->fp, ((void *)__pyx_v_b), __pyx_t_3); + + /* "pysam/libchtslib.pyx":281 + * got = hwrite(self.fp, <void *>b, len(b)) + * + * if got < 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'write failed on HFile', self.name) + * + */ + __pyx_t_1 = (__pyx_v_got < 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":282 + * + * if got < 0: + * raise IOError(herrno(self.fp), 'write failed on HFile', self.name) # <<<<<<<<<<<<<< + * + * return got + */ + __pyx_t_2 = __Pyx_PyInt_From_int(herrno(__pyx_v_self->fp)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 282, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 282, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2)) __PYX_ERR(0, 282, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_write_failed_on_HFile); + __Pyx_GIVEREF(__pyx_kp_u_write_failed_on_HFile); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_kp_u_write_failed_on_HFile)) __PYX_ERR(0, 282, __pyx_L1_error); + __Pyx_INCREF(__pyx_v_self->name); + __Pyx_GIVEREF(__pyx_v_self->name); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_self->name)) __PYX_ERR(0, 282, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 282, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 282, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":281 + * got = hwrite(self.fp, <void *>b, len(b)) + * + * if got < 0: # <<<<<<<<<<<<<< + * raise IOError(herrno(self.fp), 'write failed on HFile', self.name) + * + */ + } + + /* "pysam/libchtslib.pyx":284 + * raise IOError(herrno(self.fp), 'write failed on HFile', self.name) + * + * return got # <<<<<<<<<<<<<< + * + * def writelines(self, lines): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = PyInt_FromSsize_t(__pyx_v_got); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 284, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":275 + * return self.fp != NULL and 'w' in self.mode + * + * def write(self, bytes b): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HFile.write", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":286 + * return got + * + * def writelines(self, lines): # <<<<<<<<<<<<<< + * for line in lines: + * self.write(line) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_45writelines(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_44writelines, "HFile.writelines(self, lines)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_45writelines = {"writelines", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_45writelines, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_44writelines}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_45writelines(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_lines = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("writelines (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_lines,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_lines)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 286, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "writelines") < 0)) __PYX_ERR(0, 286, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_lines = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("writelines", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 286, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.writelines", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_44writelines(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v_lines); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_44writelines(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, PyObject *__pyx_v_lines) { + PyObject *__pyx_v_line = NULL; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + Py_ssize_t __pyx_t_2; + PyObject *(*__pyx_t_3)(PyObject *); + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + unsigned int __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__25) + __Pyx_RefNannySetupContext("writelines", 1); + __Pyx_TraceCall("writelines", __pyx_f[0], 286, 0, __PYX_ERR(0, 286, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":287 + * + * def writelines(self, lines): + * for line in lines: # <<<<<<<<<<<<<< + * self.write(line) + * + */ + if (likely(PyList_CheckExact(__pyx_v_lines)) || PyTuple_CheckExact(__pyx_v_lines)) { + __pyx_t_1 = __pyx_v_lines; __Pyx_INCREF(__pyx_t_1); + __pyx_t_2 = 0; + __pyx_t_3 = NULL; + } else { + __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_lines); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 287, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 287, __pyx_L1_error) + } + for (;;) { + if (likely(!__pyx_t_3)) { + if (likely(PyList_CheckExact(__pyx_t_1))) { + { + Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1); + #if !CYTHON_ASSUME_SAFE_MACROS + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 287, __pyx_L1_error) + #endif + if (__pyx_t_2 >= __pyx_temp) break; + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 287, __pyx_L1_error) + #else + __pyx_t_4 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 287, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + #endif + } else { + { + Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1); + #if !CYTHON_ASSUME_SAFE_MACROS + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 287, __pyx_L1_error) + #endif + if (__pyx_t_2 >= __pyx_temp) break; + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 287, __pyx_L1_error) + #else + __pyx_t_4 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 287, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + #endif + } + } else { + __pyx_t_4 = __pyx_t_3(__pyx_t_1); + if (unlikely(!__pyx_t_4)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 287, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_4); + } + __Pyx_XDECREF_SET(__pyx_v_line, __pyx_t_4); + __pyx_t_4 = 0; + + /* "pysam/libchtslib.pyx":288 + * def writelines(self, lines): + * for line in lines: + * self.write(line) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_write); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 288, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = NULL; + __pyx_t_7 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_5))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_5, function); + __pyx_t_7 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_v_line}; + __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_7, 1+__pyx_t_7); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 288, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + } + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "pysam/libchtslib.pyx":287 + * + * def writelines(self, lines): + * for line in lines: # <<<<<<<<<<<<<< + * self.write(line) + * + */ + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":286 + * return got + * + * def writelines(self, lines): # <<<<<<<<<<<<<< + * for line in lines: + * self.write(line) + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("pysam.libchtslib.HFile.writelines", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_line); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":69 + * cdef class HFile(object): + * cdef hFILE *fp + * cdef readonly object name, mode # <<<<<<<<<<<<<< + * + * def __init__(self, name, mode='r', closefd=True): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_4name_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_4name_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_4name___get__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_4name___get__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 69, 0, __PYX_ERR(0, 69, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->name); + __pyx_r = __pyx_v_self->name; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HFile.name.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_4mode_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_4mode_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_4mode___get__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_4mode___get__(struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 69, 0, __PYX_ERR(0, 69, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->mode); + __pyx_r = __pyx_v_self->mode; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HFile.mode.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_47__reduce_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_46__reduce_cython__, "HFile.__reduce_cython__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_47__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_47__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_46__reduce_cython__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_47__reduce_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_46__reduce_cython__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_46__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__26) + __Pyx_RefNannySetupContext("__reduce_cython__", 1); + __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); + + /* "(tree fragment)":2 + * def __reduce_cython__(self): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + */ + __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_fp_cannot_be_converted_to_a, 0, 0); + __PYX_ERR(1, 2, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HFile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_49__setstate_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_5HFile_48__setstate_cython__, "HFile.__setstate_cython__(self, __pyx_state)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_5HFile_49__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_49__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_48__setstate_cython__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_5HFile_49__setstate_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + 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) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v___pyx_state = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_5HFile_48__setstate_cython__(((struct __pyx_obj_5pysam_10libchtslib_HFile *)__pyx_v_self), __pyx_v___pyx_state); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_5HFile_48__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__27) + __Pyx_RefNannySetupContext("__setstate_cython__", 1); + __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); + + /* "(tree fragment)":4 + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" # <<<<<<<<<<<<<< + */ + __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_self_fp_cannot_be_converted_to_a, 0, 0); + __PYX_ERR(1, 4, __pyx_L1_error) + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":298 + * + * class CallableValue(object): + * def __init__(self, value): # <<<<<<<<<<<<<< + * self.value = value + * def __call__(self): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_1__init__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_13CallableValue___init__, "CallableValue.__init__(self, value)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_13CallableValue_1__init__ = {"__init__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_13CallableValue_1__init__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_13CallableValue___init__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_1__init__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_value = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[2] = {0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_value,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 298, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_value)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 298, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); __PYX_ERR(0, 298, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 298, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 2)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_value = values[1]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 298, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_13CallableValue___init__(__pyx_self, __pyx_v_self, __pyx_v_value); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_value) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__28) + __Pyx_RefNannySetupContext("__init__", 1); + __Pyx_TraceCall("__init__", __pyx_f[0], 298, 0, __PYX_ERR(0, 298, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":299 + * class CallableValue(object): + * def __init__(self, value): + * self.value = value # <<<<<<<<<<<<<< + * def __call__(self): + * return self.value + */ + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_value, __pyx_v_value) < 0) __PYX_ERR(0, 299, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":298 + * + * class CallableValue(object): + * def __init__(self, value): # <<<<<<<<<<<<<< + * self.value = value + * def __call__(self): + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":300 + * def __init__(self, value): + * self.value = value + * def __call__(self): # <<<<<<<<<<<<<< + * return self.value + * def __bool__(self): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_3__call__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_13CallableValue_2__call__, "CallableValue.__call__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_13CallableValue_3__call__ = {"__call__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_13CallableValue_3__call__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_13CallableValue_2__call__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_3__call__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 300, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__call__") < 0)) __PYX_ERR(0, 300, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_self = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__call__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 300, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_13CallableValue_2__call__(__pyx_self, __pyx_v_self); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_2__call__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__29) + __Pyx_RefNannySetupContext("__call__", 1); + __Pyx_TraceCall("__call__", __pyx_f[0], 300, 0, __PYX_ERR(0, 300, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":301 + * self.value = value + * def __call__(self): + * return self.value # <<<<<<<<<<<<<< + * def __bool__(self): + * return self.value + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 301, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":300 + * def __init__(self, value): + * self.value = value + * def __call__(self): # <<<<<<<<<<<<<< + * return self.value + * def __bool__(self): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":302 + * def __call__(self): + * return self.value + * def __bool__(self): # <<<<<<<<<<<<<< + * return self.value + * def __nonzero__(self): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_5__bool__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_13CallableValue_4__bool__, "CallableValue.__bool__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_13CallableValue_5__bool__ = {"__bool__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_13CallableValue_5__bool__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_13CallableValue_4__bool__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_5__bool__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__bool__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 302, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__bool__") < 0)) __PYX_ERR(0, 302, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_self = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__bool__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 302, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__bool__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_13CallableValue_4__bool__(__pyx_self, __pyx_v_self); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_4__bool__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__30) + __Pyx_RefNannySetupContext("__bool__", 1); + __Pyx_TraceCall("__bool__", __pyx_f[0], 302, 0, __PYX_ERR(0, 302, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":303 + * return self.value + * def __bool__(self): + * return self.value # <<<<<<<<<<<<<< + * def __nonzero__(self): + * return self.value + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 303, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":302 + * def __call__(self): + * return self.value + * def __bool__(self): # <<<<<<<<<<<<<< + * return self.value + * def __nonzero__(self): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__bool__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":304 + * def __bool__(self): + * return self.value + * def __nonzero__(self): # <<<<<<<<<<<<<< + * return self.value + * def __eq__(self, other): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_7__nonzero__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_13CallableValue_6__nonzero__, "CallableValue.__nonzero__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_13CallableValue_7__nonzero__ = {"__nonzero__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_13CallableValue_7__nonzero__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_13CallableValue_6__nonzero__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_7__nonzero__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__nonzero__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 304, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__nonzero__") < 0)) __PYX_ERR(0, 304, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_self = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__nonzero__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 304, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__nonzero__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_13CallableValue_6__nonzero__(__pyx_self, __pyx_v_self); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_6__nonzero__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__31) + __Pyx_RefNannySetupContext("__nonzero__", 1); + __Pyx_TraceCall("__nonzero__", __pyx_f[0], 304, 0, __PYX_ERR(0, 304, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":305 + * return self.value + * def __nonzero__(self): + * return self.value # <<<<<<<<<<<<<< + * def __eq__(self, other): + * return self.value == other + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 305, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":304 + * def __bool__(self): + * return self.value + * def __nonzero__(self): # <<<<<<<<<<<<<< + * return self.value + * def __eq__(self, other): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__nonzero__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":306 + * def __nonzero__(self): + * return self.value + * def __eq__(self, other): # <<<<<<<<<<<<<< + * return self.value == other + * def __ne__(self, other): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_9__eq__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_13CallableValue_8__eq__, "CallableValue.__eq__(self, other)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_13CallableValue_9__eq__ = {"__eq__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_13CallableValue_9__eq__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_13CallableValue_8__eq__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_9__eq__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_other = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[2] = {0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__eq__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_other,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 306, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_other)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 306, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__eq__", 1, 2, 2, 1); __PYX_ERR(0, 306, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__eq__") < 0)) __PYX_ERR(0, 306, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 2)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_other = values[1]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__eq__", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 306, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__eq__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_13CallableValue_8__eq__(__pyx_self, __pyx_v_self, __pyx_v_other); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_8__eq__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_other) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__32) + __Pyx_RefNannySetupContext("__eq__", 1); + __Pyx_TraceCall("__eq__", __pyx_f[0], 306, 0, __PYX_ERR(0, 306, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":307 + * return self.value + * def __eq__(self, other): + * return self.value == other # <<<<<<<<<<<<<< + * def __ne__(self, other): + * return self.value != other + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 307, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_v_other, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 307, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":306 + * def __nonzero__(self): + * return self.value + * def __eq__(self, other): # <<<<<<<<<<<<<< + * return self.value == other + * def __ne__(self, other): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__eq__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":308 + * def __eq__(self, other): + * return self.value == other + * def __ne__(self, other): # <<<<<<<<<<<<<< + * return self.value != other + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_11__ne__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_13CallableValue_10__ne__, "CallableValue.__ne__(self, other)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_13CallableValue_11__ne__ = {"__ne__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_13CallableValue_11__ne__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_13CallableValue_10__ne__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_13CallableValue_11__ne__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_other = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[2] = {0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__ne__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_other,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 308, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_other)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 308, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__ne__", 1, 2, 2, 1); __PYX_ERR(0, 308, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__ne__") < 0)) __PYX_ERR(0, 308, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 2)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_other = values[1]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__ne__", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 308, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__ne__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_13CallableValue_10__ne__(__pyx_self, __pyx_v_self, __pyx_v_other); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_13CallableValue_10__ne__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_other) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__33) + __Pyx_RefNannySetupContext("__ne__", 1); + __Pyx_TraceCall("__ne__", __pyx_f[0], 308, 0, __PYX_ERR(0, 308, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":309 + * return self.value == other + * def __ne__(self, other): + * return self.value != other # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 309, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_v_other, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 309, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":308 + * def __eq__(self, other): + * return self.value == other + * def __ne__(self, other): # <<<<<<<<<<<<<< + * return self.value != other + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pysam.libchtslib.CallableValue.__ne__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":326 + * """ + * + * def __cinit__(self, *args, **kwargs): # <<<<<<<<<<<<<< + * self.htsfile = NULL + * self.threads = 1 + */ + +/* Python wrapper */ +static int __pyx_pw_5pysam_10libchtslib_7HTSFile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_10libchtslib_7HTSFile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + CYTHON_UNUSED PyObject *__pyx_v_args = 0; + CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0; + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return -1; + #endif + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1; + __Pyx_INCREF(__pyx_args); + __pyx_v_args = __pyx_args; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile___cinit__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs); + + /* function exit code */ + __Pyx_DECREF(__pyx_v_args); + __Pyx_XDECREF(__pyx_v_kwargs); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_5pysam_10libchtslib_7HTSFile___cinit__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_args, CYTHON_UNUSED PyObject *__pyx_v_kwargs) { + int __pyx_r; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__cinit__", 1); + __Pyx_TraceCall("__cinit__", __pyx_f[0], 326, 0, __PYX_ERR(0, 326, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":327 + * + * def __cinit__(self, *args, **kwargs): + * self.htsfile = NULL # <<<<<<<<<<<<<< + * self.threads = 1 + * self.duplicate_filehandle = True + */ + __pyx_v_self->htsfile = NULL; + + /* "pysam/libchtslib.pyx":328 + * def __cinit__(self, *args, **kwargs): + * self.htsfile = NULL + * self.threads = 1 # <<<<<<<<<<<<<< + * self.duplicate_filehandle = True + * + */ + __Pyx_INCREF(__pyx_int_1); + __Pyx_GIVEREF(__pyx_int_1); + __Pyx_GOTREF(__pyx_v_self->threads); + __Pyx_DECREF(__pyx_v_self->threads); + __pyx_v_self->threads = __pyx_int_1; + + /* "pysam/libchtslib.pyx":329 + * self.htsfile = NULL + * self.threads = 1 + * self.duplicate_filehandle = True # <<<<<<<<<<<<<< + * + * def close(self): + */ + __pyx_v_self->duplicate_filehandle = 1; + + /* "pysam/libchtslib.pyx":326 + * """ + * + * def __cinit__(self, *args, **kwargs): # <<<<<<<<<<<<<< + * self.htsfile = NULL + * self.threads = 1 + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_TraceReturn(Py_None, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":331 + * self.duplicate_filehandle = True + * + * def close(self): # <<<<<<<<<<<<<< + * if self.htsfile: + * hts_close(self.htsfile) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_3close(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_2close, "HTSFile.close(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_3close = {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_3close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_2close}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_3close(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("close (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("close", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "close", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_2close(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_2close(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__34) + __Pyx_RefNannySetupContext("close", 1); + __Pyx_TraceCall("close", __pyx_f[0], 331, 0, __PYX_ERR(0, 331, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":332 + * + * def close(self): + * if self.htsfile: # <<<<<<<<<<<<<< + * hts_close(self.htsfile) + * self.htsfile = NULL + */ + __pyx_t_1 = (__pyx_v_self->htsfile != 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":333 + * def close(self): + * if self.htsfile: + * hts_close(self.htsfile) # <<<<<<<<<<<<<< + * self.htsfile = NULL + * + */ + (void)(hts_close(__pyx_v_self->htsfile)); + + /* "pysam/libchtslib.pyx":334 + * if self.htsfile: + * hts_close(self.htsfile) + * self.htsfile = NULL # <<<<<<<<<<<<<< + * + * def __dealloc__(self): + */ + __pyx_v_self->htsfile = NULL; + + /* "pysam/libchtslib.pyx":332 + * + * def close(self): + * if self.htsfile: # <<<<<<<<<<<<<< + * hts_close(self.htsfile) + * self.htsfile = NULL + */ + } + + /* "pysam/libchtslib.pyx":331 + * self.duplicate_filehandle = True + * + * def close(self): # <<<<<<<<<<<<<< + * if self.htsfile: + * hts_close(self.htsfile) + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.close", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":336 + * self.htsfile = NULL + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * if self.htsfile: + * hts_close(self.htsfile) + */ + +/* Python wrapper */ +static void __pyx_pw_5pysam_10libchtslib_7HTSFile_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_10libchtslib_7HTSFile_5__dealloc__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_pf_5pysam_10libchtslib_7HTSFile_4__dealloc__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_5pysam_10libchtslib_7HTSFile_4__dealloc__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + __Pyx_TraceDeclarations + int __pyx_t_1; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceCall("__dealloc__", __pyx_f[0], 336, 0, __PYX_ERR(0, 336, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":337 + * + * def __dealloc__(self): + * if self.htsfile: # <<<<<<<<<<<<<< + * hts_close(self.htsfile) + * self.htsfile = NULL + */ + __pyx_t_1 = (__pyx_v_self->htsfile != 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":338 + * def __dealloc__(self): + * if self.htsfile: + * hts_close(self.htsfile) # <<<<<<<<<<<<<< + * self.htsfile = NULL + * + */ + (void)(hts_close(__pyx_v_self->htsfile)); + + /* "pysam/libchtslib.pyx":339 + * if self.htsfile: + * hts_close(self.htsfile) + * self.htsfile = NULL # <<<<<<<<<<<<<< + * + * def flush(self): + */ + __pyx_v_self->htsfile = NULL; + + /* "pysam/libchtslib.pyx":337 + * + * def __dealloc__(self): + * if self.htsfile: # <<<<<<<<<<<<<< + * hts_close(self.htsfile) + * self.htsfile = NULL + */ + } + + /* "pysam/libchtslib.pyx":336 + * self.htsfile = NULL + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * if self.htsfile: + * hts_close(self.htsfile) + */ + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_WriteUnraisable("pysam.libchtslib.HTSFile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); + __pyx_L0:; + __Pyx_TraceReturn(Py_None, 0); +} + +/* "pysam/libchtslib.pyx":341 + * self.htsfile = NULL + * + * def flush(self): # <<<<<<<<<<<<<< + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7flush(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_6flush, "HTSFile.flush(self)\nFlush any buffered data to the underlying output stream."); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_7flush = {"flush", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_7flush, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_6flush}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7flush(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("flush (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("flush", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "flush", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6flush(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6flush(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + Py_ssize_t __pyx_t_4; + Py_UCS4 __pyx_t_5; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__35) + __Pyx_RefNannySetupContext("flush", 1); + __Pyx_TraceCall("flush", __pyx_f[0], 341, 0, __PYX_ERR(0, 341, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":343 + * def flush(self): + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: # <<<<<<<<<<<<<< + * if hts_flush(self.htsfile) < 0: + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + */ + __pyx_t_1 = (__pyx_v_self->htsfile != 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":344 + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: + * if hts_flush(self.htsfile) < 0: # <<<<<<<<<<<<<< + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + * + */ + __pyx_t_1 = (hts_flush(__pyx_v_self->htsfile) < 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":345 + * if self.htsfile: + * if hts_flush(self.htsfile) < 0: + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) # <<<<<<<<<<<<<< + * + * def check_truncation(self, ignore_truncation=False): + */ + __pyx_t_2 = __Pyx_PyInt_From_int(errno); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = 0; + __pyx_t_5 = 127; + __Pyx_INCREF(__pyx_kp_u_Flushing); + __pyx_t_4 += 9; + __Pyx_GIVEREF(__pyx_kp_u_Flushing); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_kp_u_Flushing); + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))), __pyx_n_s_name_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __pyx_t_7 = __Pyx_PyObject_FormatSimple(__pyx_t_6, __pyx_empty_unicode); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_5 = (__Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) > __pyx_t_5) ? __Pyx_PyUnicode_MAX_CHAR_VALUE(__pyx_t_7) : __pyx_t_5; + __pyx_t_4 += __Pyx_PyUnicode_GET_LENGTH(__pyx_t_7); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_7); + __pyx_t_7 = 0; + __Pyx_INCREF(__pyx_kp_u_failed); + __pyx_t_4 += 7; + __Pyx_GIVEREF(__pyx_kp_u_failed); + PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_kp_u_failed); + __pyx_t_7 = __Pyx_PyUnicode_Join(__pyx_t_3, 3, __pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __pyx_v_self->filename; + __Pyx_INCREF(__pyx_t_3); + __pyx_t_6 = __pyx_f_5pysam_9libcutils_force_str(__pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2)) __PYX_ERR(0, 345, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_7); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_7)) __PYX_ERR(0, 345, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_6); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_6)) __PYX_ERR(0, 345, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_7 = 0; + __pyx_t_6 = 0; + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_OSError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_6, 0, 0, 0); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __PYX_ERR(0, 345, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":344 + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: + * if hts_flush(self.htsfile) < 0: # <<<<<<<<<<<<<< + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + * + */ + } + + /* "pysam/libchtslib.pyx":343 + * def flush(self): + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: # <<<<<<<<<<<<<< + * if hts_flush(self.htsfile) < 0: + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + */ + } + + /* "pysam/libchtslib.pyx":341 + * self.htsfile = NULL + * + * def flush(self): # <<<<<<<<<<<<<< + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.flush", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":347 + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + * + * def check_truncation(self, ignore_truncation=False): # <<<<<<<<<<<<<< + * """Check if file is truncated.""" + * if not self.htsfile: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9check_truncation(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_8check_truncation, "HTSFile.check_truncation(self, ignore_truncation=False)\nCheck if file is truncated."); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_9check_truncation = {"check_truncation", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_9check_truncation, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_8check_truncation}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9check_truncation(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_ignore_truncation = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("check_truncation (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_ignore_truncation,0}; + values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_False)); + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_ignore_truncation); + if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 347, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "check_truncation") < 0)) __PYX_ERR(0, 347, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_ignore_truncation = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("check_truncation", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 347, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.check_truncation", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_8check_truncation(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_ignore_truncation); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8check_truncation(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_ignore_truncation) { + BGZF *__pyx_v_bgzfp; + int __pyx_v_ret; + PyObject *__pyx_v_msg = NULL; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + unsigned int __pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__36) + __Pyx_RefNannySetupContext("check_truncation", 1); + __Pyx_TraceCall("check_truncation", __pyx_f[0], 347, 0, __PYX_ERR(0, 347, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":349 + * def check_truncation(self, ignore_truncation=False): + * """Check if file is truncated.""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * return + * + */ + __pyx_t_1 = (!(__pyx_v_self->htsfile != 0)); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":350 + * """Check if file is truncated.""" + * if not self.htsfile: + * return # <<<<<<<<<<<<<< + * + * if self.htsfile.format.compression != bgzf: + */ + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":349 + * def check_truncation(self, ignore_truncation=False): + * """Check if file is truncated.""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * return + * + */ + } + + /* "pysam/libchtslib.pyx":352 + * return + * + * if self.htsfile.format.compression != bgzf: # <<<<<<<<<<<<<< + * return + * + */ + __pyx_t_1 = (__pyx_v_self->htsfile->format.compression != bgzf); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":353 + * + * if self.htsfile.format.compression != bgzf: + * return # <<<<<<<<<<<<<< + * + * cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":352 + * return + * + * if self.htsfile.format.compression != bgzf: # <<<<<<<<<<<<<< + * return + * + */ + } + + /* "pysam/libchtslib.pyx":355 + * return + * + * cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile) # <<<<<<<<<<<<<< + * if not bgzfp: + * return + */ + __pyx_v_bgzfp = hts_get_bgzfp(__pyx_v_self->htsfile); + + /* "pysam/libchtslib.pyx":356 + * + * cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile) + * if not bgzfp: # <<<<<<<<<<<<<< + * return + * + */ + __pyx_t_1 = (!(__pyx_v_bgzfp != 0)); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":357 + * cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile) + * if not bgzfp: + * return # <<<<<<<<<<<<<< + * + * cdef int ret = bgzf_check_EOF(bgzfp) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":356 + * + * cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile) + * if not bgzfp: # <<<<<<<<<<<<<< + * return + * + */ + } + + /* "pysam/libchtslib.pyx":359 + * return + * + * cdef int ret = bgzf_check_EOF(bgzfp) # <<<<<<<<<<<<<< + * if ret < 0: + * raise IOError(errno, 'error checking for EOF marker') + */ + __pyx_v_ret = bgzf_check_EOF(__pyx_v_bgzfp); + + /* "pysam/libchtslib.pyx":360 + * + * cdef int ret = bgzf_check_EOF(bgzfp) + * if ret < 0: # <<<<<<<<<<<<<< + * raise IOError(errno, 'error checking for EOF marker') + * elif ret == 0: + */ + __pyx_t_1 = (__pyx_v_ret < 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":361 + * cdef int ret = bgzf_check_EOF(bgzfp) + * if ret < 0: + * raise IOError(errno, 'error checking for EOF marker') # <<<<<<<<<<<<<< + * elif ret == 0: + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) + */ + __pyx_t_2 = __Pyx_PyInt_From_int(errno); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 361, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 361, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2)) __PYX_ERR(0, 361, __pyx_L1_error); + __Pyx_INCREF(__pyx_kp_u_error_checking_for_EOF_marker); + __Pyx_GIVEREF(__pyx_kp_u_error_checking_for_EOF_marker); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_kp_u_error_checking_for_EOF_marker)) __PYX_ERR(0, 361, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 361, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 361, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":360 + * + * cdef int ret = bgzf_check_EOF(bgzfp) + * if ret < 0: # <<<<<<<<<<<<<< + * raise IOError(errno, 'error checking for EOF marker') + * elif ret == 0: + */ + } + + /* "pysam/libchtslib.pyx":362 + * if ret < 0: + * raise IOError(errno, 'error checking for EOF marker') + * elif ret == 0: # <<<<<<<<<<<<<< + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) + * if ignore_truncation: + */ + __pyx_t_1 = (__pyx_v_ret == 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":363 + * raise IOError(errno, 'error checking for EOF marker') + * elif ret == 0: + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) # <<<<<<<<<<<<<< + * if ignore_truncation: + * warn(msg) + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 363, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = NULL; + __pyx_t_5 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + __pyx_t_5 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v_self->filename}; + __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 363, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + } + __pyx_v_msg = __pyx_t_2; + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":364 + * elif ret == 0: + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) + * if ignore_truncation: # <<<<<<<<<<<<<< + * warn(msg) + * else: + */ + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_ignore_truncation); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 364, __pyx_L1_error) + if (likely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":365 + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) + * if ignore_truncation: + * warn(msg) # <<<<<<<<<<<<<< + * else: + * raise IOError(msg) + */ + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_warn); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 365, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = NULL; + __pyx_t_5 = 0; + #if CYTHON_UNPACK_METHODS + if (unlikely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + __pyx_t_5 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_v_msg}; + __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_3, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 365, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":364 + * elif ret == 0: + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) + * if ignore_truncation: # <<<<<<<<<<<<<< + * warn(msg) + * else: + */ + goto __pyx_L7; + } + + /* "pysam/libchtslib.pyx":367 + * warn(msg) + * else: + * raise IOError(msg) # <<<<<<<<<<<<<< + * + * def __enter__(self): + */ + /*else*/ { + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_IOError, __pyx_v_msg); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 367, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 367, __pyx_L1_error) + } + __pyx_L7:; + + /* "pysam/libchtslib.pyx":362 + * if ret < 0: + * raise IOError(errno, 'error checking for EOF marker') + * elif ret == 0: # <<<<<<<<<<<<<< + * msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename) + * if ignore_truncation: + */ + } + + /* "pysam/libchtslib.pyx":347 + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + * + * def check_truncation(self, ignore_truncation=False): # <<<<<<<<<<<<<< + * """Check if file is truncated.""" + * if not self.htsfile: + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.check_truncation", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_msg); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":369 + * raise IOError(msg) + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_11__enter__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_10__enter__, "HTSFile.__enter__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_11__enter__ = {"__enter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_11__enter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_10__enter__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_11__enter__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__enter__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("__enter__", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__enter__", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_10__enter__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_10__enter__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__37) + __Pyx_RefNannySetupContext("__enter__", 1); + __Pyx_TraceCall("__enter__", __pyx_f[0], 369, 0, __PYX_ERR(0, 369, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":370 + * + * def __enter__(self): + * return self # <<<<<<<<<<<<<< + * + * def __exit__(self, exc_type, exc_value, traceback): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF((PyObject *)__pyx_v_self); + __pyx_r = ((PyObject *)__pyx_v_self); + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":369 + * raise IOError(msg) + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__enter__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":372 + * return self + * + * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<< + * self.close() + * return False + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_13__exit__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_12__exit__, "HTSFile.__exit__(self, exc_type, exc_value, traceback)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_13__exit__ = {"__exit__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_13__exit__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_12__exit__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_13__exit__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v_exc_type = 0; + CYTHON_UNUSED PyObject *__pyx_v_exc_value = 0; + CYTHON_UNUSED PyObject *__pyx_v_traceback = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[3] = {0,0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__exit__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_exc_type,&__pyx_n_s_exc_value,&__pyx_n_s_traceback,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_exc_type)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 372, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_exc_value)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 372, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); __PYX_ERR(0, 372, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_traceback)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 372, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); __PYX_ERR(0, 372, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__exit__") < 0)) __PYX_ERR(0, 372, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 3)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + } + __pyx_v_exc_type = values[0]; + __pyx_v_exc_value = values[1]; + __pyx_v_traceback = values[2]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 372, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_12__exit__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_exc_type, __pyx_v_exc_value, __pyx_v_traceback); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_12__exit__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + unsigned int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__38) + __Pyx_RefNannySetupContext("__exit__", 1); + __Pyx_TraceCall("__exit__", __pyx_f[0], 372, 0, __PYX_ERR(0, 372, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":373 + * + * def __exit__(self, exc_type, exc_value, traceback): + * self.close() # <<<<<<<<<<<<<< + * return False + * + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 373, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + __pyx_t_4 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_4 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_3, NULL}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 0+__pyx_t_4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 373, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pysam/libchtslib.pyx":374 + * def __exit__(self, exc_type, exc_value, traceback): + * self.close() + * return False # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_False); + __pyx_r = Py_False; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":372 + * return self + * + * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<< + * self.close() + * return False + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":376 + * return False + * + * @property # <<<<<<<<<<<<<< + * def category(self): + * """General file format category. One of UNKNOWN, ALIGNMENTS, + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_8category_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_8category_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_8category___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8category___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 376, 0, __PYX_ERR(0, 376, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":380 + * """General file format category. One of UNKNOWN, ALIGNMENTS, + * VARIANTS, INDEX, REGIONS""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return FORMAT_CATEGORIES[self.htsfile.format.category] + */ + __pyx_t_1 = (!(__pyx_v_self->htsfile != 0)); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":381 + * VARIANTS, INDEX, REGIONS""" + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') # <<<<<<<<<<<<<< + * return FORMAT_CATEGORIES[self.htsfile.format.category] + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__39, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 381, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 381, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":380 + * """General file format category. One of UNKNOWN, ALIGNMENTS, + * VARIANTS, INDEX, REGIONS""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return FORMAT_CATEGORIES[self.htsfile.format.category] + */ + } + + /* "pysam/libchtslib.pyx":382 + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') + * return FORMAT_CATEGORIES[self.htsfile.format.category] # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + if (unlikely(__pyx_v_5pysam_10libchtslib_FORMAT_CATEGORIES == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 382, __pyx_L1_error) + } + __pyx_t_2 = __Pyx_PyInt_From_enum__htsFormatCategory(__pyx_v_self->htsfile->format.category); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 382, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_v_5pysam_10libchtslib_FORMAT_CATEGORIES, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 382, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":376 + * return False + * + * @property # <<<<<<<<<<<<<< + * def category(self): + * """General file format category. One of UNKNOWN, ALIGNMENTS, + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.category.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":384 + * return FORMAT_CATEGORIES[self.htsfile.format.category] + * + * @property # <<<<<<<<<<<<<< + * def format(self): + * """File format. + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6format_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6format_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6format___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6format___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 384, 0, __PYX_ERR(0, 384, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":391 + * BAI, CRAM, CRAI, VCF, BCF, CSI, GZI, TBI, BED. + * """ + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return FORMATS[self.htsfile.format.format] + */ + __pyx_t_1 = (!(__pyx_v_self->htsfile != 0)); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":392 + * """ + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') # <<<<<<<<<<<<<< + * return FORMATS[self.htsfile.format.format] + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__39, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 392, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 392, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":391 + * BAI, CRAM, CRAI, VCF, BCF, CSI, GZI, TBI, BED. + * """ + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return FORMATS[self.htsfile.format.format] + */ + } + + /* "pysam/libchtslib.pyx":393 + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') + * return FORMATS[self.htsfile.format.format] # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + if (unlikely(__pyx_v_5pysam_10libchtslib_FORMATS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 393, __pyx_L1_error) + } + __pyx_t_2 = __Pyx_PyInt_From_enum__htsExactFormat(__pyx_v_self->htsfile->format.format); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 393, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_v_5pysam_10libchtslib_FORMATS, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 393, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":384 + * return FORMAT_CATEGORIES[self.htsfile.format.category] + * + * @property # <<<<<<<<<<<<<< + * def format(self): + * """File format. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.format.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":395 + * return FORMATS[self.htsfile.format.format] + * + * @property # <<<<<<<<<<<<<< + * def version(self): + * """Tuple of file format version numbers (major, minor)""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7version_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7version_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_7version___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7version___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 395, 0, __PYX_ERR(0, 395, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":398 + * def version(self): + * """Tuple of file format version numbers (major, minor)""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return self.htsfile.format.version.major, self.htsfile.format.version.minor + */ + __pyx_t_1 = (!(__pyx_v_self->htsfile != 0)); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":399 + * """Tuple of file format version numbers (major, minor)""" + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') # <<<<<<<<<<<<<< + * return self.htsfile.format.version.major, self.htsfile.format.version.minor + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__39, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 399, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 399, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":398 + * def version(self): + * """Tuple of file format version numbers (major, minor)""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return self.htsfile.format.version.major, self.htsfile.format.version.minor + */ + } + + /* "pysam/libchtslib.pyx":400 + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') + * return self.htsfile.format.version.major, self.htsfile.format.version.minor # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyInt_From_short(__pyx_v_self->htsfile->format.version.major); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 400, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyInt_From_short(__pyx_v_self->htsfile->format.version.minor); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 400, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 400, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2)) __PYX_ERR(0, 400, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_3); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3)) __PYX_ERR(0, 400, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_3 = 0; + __pyx_r = __pyx_t_4; + __pyx_t_4 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":395 + * return FORMATS[self.htsfile.format.format] + * + * @property # <<<<<<<<<<<<<< + * def version(self): + * """Tuple of file format version numbers (major, minor)""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.version.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":402 + * return self.htsfile.format.version.major, self.htsfile.format.version.minor + * + * @property # <<<<<<<<<<<<<< + * def compression(self): + * """File compression. + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_11compression_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_11compression_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_11compression___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_11compression___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 402, 0, __PYX_ERR(0, 402, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":407 + * + * One of NONE, GZIP, BGZF, CUSTOM.""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return COMPRESSION[self.htsfile.format.compression] + */ + __pyx_t_1 = (!(__pyx_v_self->htsfile != 0)); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":408 + * One of NONE, GZIP, BGZF, CUSTOM.""" + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') # <<<<<<<<<<<<<< + * return COMPRESSION[self.htsfile.format.compression] + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__39, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 408, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 408, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":407 + * + * One of NONE, GZIP, BGZF, CUSTOM.""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * return COMPRESSION[self.htsfile.format.compression] + */ + } + + /* "pysam/libchtslib.pyx":409 + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') + * return COMPRESSION[self.htsfile.format.compression] # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + if (unlikely(__pyx_v_5pysam_10libchtslib_COMPRESSION == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 409, __pyx_L1_error) + } + __pyx_t_2 = __Pyx_PyInt_From_enum__htsCompression(__pyx_v_self->htsfile->format.compression); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 409, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetItem(__pyx_v_5pysam_10libchtslib_COMPRESSION, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 409, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":402 + * return self.htsfile.format.version.major, self.htsfile.format.version.minor + * + * @property # <<<<<<<<<<<<<< + * def compression(self): + * """File compression. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.compression.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":411 + * return COMPRESSION[self.htsfile.format.compression] + * + * @property # <<<<<<<<<<<<<< + * def description(self): + * """Vaguely human readable description of the file format""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_11description_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_11description_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_11description___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_11description___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + char *__pyx_v_desc; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + char const *__pyx_t_5; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 411, 0, __PYX_ERR(0, 411, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":414 + * def description(self): + * """Vaguely human readable description of the file format""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * cdef char *desc = hts_format_description(&self.htsfile.format) + */ + __pyx_t_1 = (!(__pyx_v_self->htsfile != 0)); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":415 + * """Vaguely human readable description of the file format""" + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') # <<<<<<<<<<<<<< + * cdef char *desc = hts_format_description(&self.htsfile.format) + * try: + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__39, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 415, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 415, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":414 + * def description(self): + * """Vaguely human readable description of the file format""" + * if not self.htsfile: # <<<<<<<<<<<<<< + * raise ValueError('metadata not available on closed file') + * cdef char *desc = hts_format_description(&self.htsfile.format) + */ + } + + /* "pysam/libchtslib.pyx":416 + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') + * cdef char *desc = hts_format_description(&self.htsfile.format) # <<<<<<<<<<<<<< + * try: + * return charptr_to_str(desc) + */ + __pyx_v_desc = hts_format_description((&__pyx_v_self->htsfile->format)); + + /* "pysam/libchtslib.pyx":417 + * raise ValueError('metadata not available on closed file') + * cdef char *desc = hts_format_description(&self.htsfile.format) + * try: # <<<<<<<<<<<<<< + * return charptr_to_str(desc) + * finally: + */ + /*try:*/ { + + /* "pysam/libchtslib.pyx":418 + * cdef char *desc = hts_format_description(&self.htsfile.format) + * try: + * return charptr_to_str(desc) # <<<<<<<<<<<<<< + * finally: + * free(desc) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __pyx_f_5pysam_9libcutils_charptr_to_str(__pyx_v_desc, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 418, __pyx_L5_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L4_return; + } + + /* "pysam/libchtslib.pyx":420 + * return charptr_to_str(desc) + * finally: + * free(desc) # <<<<<<<<<<<<<< + * + * @property + */ + /*finally:*/ { + __pyx_L5_error:; + /*exception exit:*/{ + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __pyx_t_6 = 0; __pyx_t_7 = 0; __pyx_t_8 = 0; __pyx_t_9 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + if (PY_MAJOR_VERSION >= 3) __Pyx_ExceptionSwap(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11); + if ((PY_MAJOR_VERSION < 3) || unlikely(__Pyx_GetException(&__pyx_t_6, &__pyx_t_7, &__pyx_t_8) < 0)) __Pyx_ErrFetch(&__pyx_t_6, &__pyx_t_7, &__pyx_t_8); + __Pyx_XGOTREF(__pyx_t_6); + __Pyx_XGOTREF(__pyx_t_7); + __Pyx_XGOTREF(__pyx_t_8); + __Pyx_XGOTREF(__pyx_t_9); + __Pyx_XGOTREF(__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_11); + __pyx_t_3 = __pyx_lineno; __pyx_t_4 = __pyx_clineno; __pyx_t_5 = __pyx_filename; + { + free(__pyx_v_desc); + } + if (PY_MAJOR_VERSION >= 3) { + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11); + } + __Pyx_XGIVEREF(__pyx_t_6); + __Pyx_XGIVEREF(__pyx_t_7); + __Pyx_XGIVEREF(__pyx_t_8); + __Pyx_ErrRestore(__pyx_t_6, __pyx_t_7, __pyx_t_8); + __pyx_t_6 = 0; __pyx_t_7 = 0; __pyx_t_8 = 0; __pyx_t_9 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0; + __pyx_lineno = __pyx_t_3; __pyx_clineno = __pyx_t_4; __pyx_filename = __pyx_t_5; + goto __pyx_L1_error; + } + __pyx_L4_return: { + __pyx_t_11 = __pyx_r; + __pyx_r = 0; + free(__pyx_v_desc); + __pyx_r = __pyx_t_11; + __pyx_t_11 = 0; + goto __pyx_L0; + } + } + + /* "pysam/libchtslib.pyx":411 + * return COMPRESSION[self.htsfile.format.compression] + * + * @property # <<<<<<<<<<<<<< + * def description(self): + * """Vaguely human readable description of the file format""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.description.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":422 + * free(desc) + * + * @property # <<<<<<<<<<<<<< + * def is_open(self): + * """return True if HTSFile is open and in a valid state.""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7is_open_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7is_open_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_7is_open___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_open___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 422, 0, __PYX_ERR(0, 422, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":425 + * def is_open(self): + * """return True if HTSFile is open and in a valid state.""" + * return CTrue if self.htsfile != NULL else CFalse # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_CTrue); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 425, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + } else { + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_CFalse); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 425, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + } + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":422 + * free(desc) + * + * @property # <<<<<<<<<<<<<< + * def is_open(self): + * """return True if HTSFile is open and in a valid state.""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_open.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":427 + * return CTrue if self.htsfile != NULL else CFalse + * + * @property # <<<<<<<<<<<<<< + * def is_closed(self): + * """return True if HTSFile is closed.""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9is_closed_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9is_closed_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_9is_closed___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_closed___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 427, 0, __PYX_ERR(0, 427, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":430 + * def is_closed(self): + * """return True if HTSFile is closed.""" + * return self.htsfile == NULL # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->htsfile == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 430, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":427 + * return CTrue if self.htsfile != NULL else CFalse + * + * @property # <<<<<<<<<<<<<< + * def is_closed(self): + * """return True if HTSFile is closed.""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_closed.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":432 + * return self.htsfile == NULL + * + * @property # <<<<<<<<<<<<<< + * def closed(self): + * """return True if HTSFile is closed.""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6closed_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6closed_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6closed___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6closed___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 432, 0, __PYX_ERR(0, 432, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":435 + * def closed(self): + * """return True if HTSFile is closed.""" + * return self.htsfile == NULL # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->htsfile == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 435, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":432 + * return self.htsfile == NULL + * + * @property # <<<<<<<<<<<<<< + * def closed(self): + * """return True if HTSFile is closed.""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.closed.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":437 + * return self.htsfile == NULL + * + * @property # <<<<<<<<<<<<<< + * def is_write(self): + * """return True if HTSFile is open for writing""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_8is_write_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_8is_write_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_8is_write___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8is_write___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 437, 0, __PYX_ERR(0, 437, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":440 + * def is_write(self): + * """return True if HTSFile is open for writing""" + * return self.htsfile != NULL and self.htsfile.is_write != 0 # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 440, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->is_write != 0); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 440, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":437 + * return self.htsfile == NULL + * + * @property # <<<<<<<<<<<<<< + * def is_write(self): + * """return True if HTSFile is open for writing""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_write.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":442 + * return self.htsfile != NULL and self.htsfile.is_write != 0 + * + * @property # <<<<<<<<<<<<<< + * def is_read(self): + * """return True if HTSFile is open for reading""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7is_read_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7is_read_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_7is_read___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_read___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 442, 0, __PYX_ERR(0, 442, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":445 + * def is_read(self): + * """return True if HTSFile is open for reading""" + * return self.htsfile != NULL and self.htsfile.is_write == 0 # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 445, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->is_write == 0); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 445, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":442 + * return self.htsfile != NULL and self.htsfile.is_write != 0 + * + * @property # <<<<<<<<<<<<<< + * def is_read(self): + * """return True if HTSFile is open for reading""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_read.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":447 + * return self.htsfile != NULL and self.htsfile.is_write == 0 + * + * @property # <<<<<<<<<<<<<< + * def is_sam(self): + * """return True if HTSFile is reading or writing a SAM alignment file""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_sam_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_sam_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6is_sam___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_sam___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 447, 0, __PYX_ERR(0, 447, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":450 + * def is_sam(self): + * """return True if HTSFile is reading or writing a SAM alignment file""" + * return self.htsfile != NULL and self.htsfile.format.format == sam # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 450, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->format.format == sam); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 450, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":447 + * return self.htsfile != NULL and self.htsfile.is_write == 0 + * + * @property # <<<<<<<<<<<<<< + * def is_sam(self): + * """return True if HTSFile is reading or writing a SAM alignment file""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_sam.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":452 + * return self.htsfile != NULL and self.htsfile.format.format == sam + * + * @property # <<<<<<<<<<<<<< + * def is_bam(self): + * """return True if HTSFile is reading or writing a BAM alignment file""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_bam_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_bam_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bam___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bam___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 452, 0, __PYX_ERR(0, 452, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":455 + * def is_bam(self): + * """return True if HTSFile is reading or writing a BAM alignment file""" + * return self.htsfile != NULL and self.htsfile.format.format == bam # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 455, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->format.format == bam); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 455, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":452 + * return self.htsfile != NULL and self.htsfile.format.format == sam + * + * @property # <<<<<<<<<<<<<< + * def is_bam(self): + * """return True if HTSFile is reading or writing a BAM alignment file""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_bam.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":457 + * return self.htsfile != NULL and self.htsfile.format.format == bam + * + * @property # <<<<<<<<<<<<<< + * def is_cram(self): + * """return True if HTSFile is reading or writing a BAM alignment file""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7is_cram_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7is_cram_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_7is_cram___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_cram___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 457, 0, __PYX_ERR(0, 457, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":460 + * def is_cram(self): + * """return True if HTSFile is reading or writing a BAM alignment file""" + * return self.htsfile != NULL and self.htsfile.format.format == cram # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 460, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->format.format == cram); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 460, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":457 + * return self.htsfile != NULL and self.htsfile.format.format == bam + * + * @property # <<<<<<<<<<<<<< + * def is_cram(self): + * """return True if HTSFile is reading or writing a BAM alignment file""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_cram.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":462 + * return self.htsfile != NULL and self.htsfile.format.format == cram + * + * @property # <<<<<<<<<<<<<< + * def is_vcf(self): + * """return True if HTSFile is reading or writing a VCF variant file""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_vcf_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_vcf_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6is_vcf___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_vcf___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 462, 0, __PYX_ERR(0, 462, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":465 + * def is_vcf(self): + * """return True if HTSFile is reading or writing a VCF variant file""" + * return self.htsfile != NULL and self.htsfile.format.format == vcf # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 465, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->format.format == vcf); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 465, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":462 + * return self.htsfile != NULL and self.htsfile.format.format == cram + * + * @property # <<<<<<<<<<<<<< + * def is_vcf(self): + * """return True if HTSFile is reading or writing a VCF variant file""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_vcf.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":467 + * return self.htsfile != NULL and self.htsfile.format.format == vcf + * + * @property # <<<<<<<<<<<<<< + * def is_bcf(self): + * """return True if HTSFile is reading or writing a BCF variant file""" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_bcf_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_6is_bcf_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bcf___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bcf___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[0], 467, 0, __PYX_ERR(0, 467, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":470 + * def is_bcf(self): + * """return True if HTSFile is reading or writing a BCF variant file""" + * return self.htsfile != NULL and self.htsfile.format.format == bcf # <<<<<<<<<<<<<< + * + * def reset(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = (__pyx_v_self->htsfile != NULL); + if (__pyx_t_2) { + } else { + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 470, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L3_bool_binop_done; + } + __pyx_t_2 = (__pyx_v_self->htsfile->format.format == bcf); + __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 470, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_t_3; + __pyx_t_3 = 0; + __pyx_L3_bool_binop_done:; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":467 + * return self.htsfile != NULL and self.htsfile.format.format == vcf + * + * @property # <<<<<<<<<<<<<< + * def is_bcf(self): + * """return True if HTSFile is reading or writing a BCF variant file""" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_bcf.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":472 + * return self.htsfile != NULL and self.htsfile.format.format == bcf + * + * def reset(self): # <<<<<<<<<<<<<< + * """reset file position to beginning of file just after the header. + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_15reset(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_14reset, "HTSFile.reset(self)\nreset file position to beginning of file just after the header.\n\n Returns\n -------\n\n The file position after moving the file pointer. : pointer\n\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_15reset = {"reset", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_15reset, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_14reset}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_15reset(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("reset (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("reset", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "reset", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_14reset(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_14reset(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + unsigned int __pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__40) + __Pyx_RefNannySetupContext("reset", 1); + __Pyx_TraceCall("reset", __pyx_f[0], 472, 0, __PYX_ERR(0, 472, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":481 + * + * """ + * return self.seek(self.start_offset) # <<<<<<<<<<<<<< + * + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_seek); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 481, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyInt_From_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 481, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = NULL; + __pyx_t_5 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_5 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_4, __pyx_t_3}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_5, 1+__pyx_t_5); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 481, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":472 + * return self.htsfile != NULL and self.htsfile.format.format == bcf + * + * def reset(self): # <<<<<<<<<<<<<< + * """reset file position to beginning of file just after the header. + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.reset", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":483 + * return self.seek(self.start_offset) + * + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_17seek(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_16seek, "HTSFile.seek(self, uint64_t offset, int whence=io.SEEK_SET)\nmove file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`."); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_17seek = {"seek", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_17seek, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_16seek}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_17seek(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + uint64_t __pyx_v_offset; + int __pyx_v_whence; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[2] = {0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("seek (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_offset,&__pyx_n_s_whence,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_offset)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 483, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_whence); + if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 483, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "seek") < 0)) __PYX_ERR(0, 483, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_offset = __Pyx_PyInt_As_uint64_t(values[0]); if (unlikely((__pyx_v_offset == ((uint64_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 483, __pyx_L3_error) + if (values[1]) { + __pyx_v_whence = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_whence == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 483, __pyx_L3_error) + } else { + __pyx_v_whence = __pyx_k__41; + } + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, __pyx_nargs); __PYX_ERR(0, 483, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_16seek(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_offset, __pyx_v_whence); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_16seek(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_whence) { + int64_t __pyx_v_ret; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + int64_t __pyx_t_5; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + unsigned int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__42) + __Pyx_RefNannySetupContext("seek", 1); + __Pyx_TraceCall("seek", __pyx_f[0], 483, 0, __PYX_ERR(0, 483, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":485 + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: # <<<<<<<<<<<<<< + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_is_open); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 485, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 485, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = (!__pyx_t_2); + if (unlikely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":486 + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: + * raise ValueError('I/O operation on closed file') # <<<<<<<<<<<<<< + * if self.is_stream: + * raise IOError('seek not available in streams') + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__43, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 486, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 486, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":485 + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: # <<<<<<<<<<<<<< + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + */ + } + + /* "pysam/libchtslib.pyx":487 + * if not self.is_open: + * raise ValueError('I/O operation on closed file') + * if self.is_stream: # <<<<<<<<<<<<<< + * raise IOError('seek not available in streams') + * + */ + if (unlikely(__pyx_v_self->is_stream)) { + + /* "pysam/libchtslib.pyx":488 + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + * raise IOError('seek not available in streams') # <<<<<<<<<<<<<< + * + * whence = libc_whence_from_io(whence) + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__44, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 488, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 488, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":487 + * if not self.is_open: + * raise ValueError('I/O operation on closed file') + * if self.is_stream: # <<<<<<<<<<<<<< + * raise IOError('seek not available in streams') + * + */ + } + + /* "pysam/libchtslib.pyx":490 + * raise IOError('seek not available in streams') + * + * whence = libc_whence_from_io(whence) # <<<<<<<<<<<<<< + * + * cdef int64_t ret + */ + __pyx_t_4 = __pyx_f_5pysam_9libcutils_libc_whence_from_io(__pyx_v_whence); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 490, __pyx_L1_error) + __pyx_v_whence = __pyx_t_4; + + /* "pysam/libchtslib.pyx":493 + * + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: # <<<<<<<<<<<<<< + * with nogil: + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) + */ + switch (__pyx_v_self->htsfile->format.compression) { + case bgzf: + + /* "pysam/libchtslib.pyx":494 + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: + * with nogil: # <<<<<<<<<<<<<< + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) + * elif self.htsfile.format.compression == no_compression: + */ + { + #ifdef WITH_THREAD + PyThreadState *_save; + _save = NULL; + Py_UNBLOCK_THREADS + __Pyx_FastGIL_Remember(); + #endif + /*try:*/ { + + /* "pysam/libchtslib.pyx":495 + * if self.htsfile.format.compression == bgzf: + * with nogil: + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) # <<<<<<<<<<<<<< + * elif self.htsfile.format.compression == no_compression: + * ret = 0 if (hseek(self.htsfile.fp.hfile, offset, whence) >= 0) else -1 + */ + __pyx_v_ret = bgzf_seek(hts_get_bgzfp(__pyx_v_self->htsfile), __pyx_v_offset, __pyx_v_whence); + } + + /* "pysam/libchtslib.pyx":494 + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: + * with nogil: # <<<<<<<<<<<<<< + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) + * elif self.htsfile.format.compression == no_compression: + */ + /*finally:*/ { + /*normal exit:*/{ + #ifdef WITH_THREAD + __Pyx_FastGIL_Forget(); + Py_BLOCK_THREADS + #endif + goto __pyx_L7; + } + __pyx_L7:; + } + } + + /* "pysam/libchtslib.pyx":493 + * + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: # <<<<<<<<<<<<<< + * with nogil: + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) + */ + break; + case no_compression: + + /* "pysam/libchtslib.pyx":497 + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) + * elif self.htsfile.format.compression == no_compression: + * ret = 0 if (hseek(self.htsfile.fp.hfile, offset, whence) >= 0) else -1 # <<<<<<<<<<<<<< + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( + */ + __pyx_t_3 = (hseek(__pyx_v_self->htsfile->fp.hfile, __pyx_v_offset, __pyx_v_whence) >= 0); + if (__pyx_t_3) { + __pyx_t_5 = 0; + } else { + __pyx_t_5 = -1L; + } + __pyx_v_ret = __pyx_t_5; + + /* "pysam/libchtslib.pyx":496 + * with nogil: + * ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, whence) + * elif self.htsfile.format.compression == no_compression: # <<<<<<<<<<<<<< + * ret = 0 if (hseek(self.htsfile.fp.hfile, offset, whence) >= 0) else -1 + * else: + */ + break; + default: + + /* "pysam/libchtslib.pyx":499 + * ret = 0 if (hseek(self.htsfile.fp.hfile, offset, whence) >= 0) else -1 + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( # <<<<<<<<<<<<<< + * self.htsfile.format.compression)) + * return ret + */ + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_seek_not_implemented_in_files_co, __pyx_n_s_format); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 499, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + + /* "pysam/libchtslib.pyx":500 + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( + * self.htsfile.format.compression)) # <<<<<<<<<<<<<< + * return ret + * + */ + __pyx_t_7 = __Pyx_PyInt_From_enum__htsCompression(__pyx_v_self->htsfile->format.compression); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 500, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_8 = NULL; + __pyx_t_9 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_6))) { + __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_6); + if (likely(__pyx_t_8)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6); + __Pyx_INCREF(__pyx_t_8); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_6, function); + __pyx_t_9 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_t_7}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_6, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9); + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 499, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + } + + /* "pysam/libchtslib.pyx":499 + * ret = 0 if (hseek(self.htsfile.fp.hfile, offset, whence) >= 0) else -1 + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( # <<<<<<<<<<<<<< + * self.htsfile.format.compression)) + * return ret + */ + __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_builtin_NotImplementedError, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 499, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_Raise(__pyx_t_6, 0, 0, 0); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __PYX_ERR(0, 499, __pyx_L1_error) + break; + } + + /* "pysam/libchtslib.pyx":501 + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( + * self.htsfile.format.compression)) + * return ret # <<<<<<<<<<<<<< + * + * def tell(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_6 = __Pyx_PyInt_From_int64_t(__pyx_v_ret); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 501, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __pyx_r = __pyx_t_6; + __pyx_t_6 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":483 + * return self.seek(self.start_offset) + * + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":503 + * return ret + * + * def tell(self): # <<<<<<<<<<<<<< + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_19tell(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_18tell, "HTSFile.tell(self)\nreturn current file position, see :meth:`pysam.HTSFile.seek`."); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_19tell = {"tell", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_19tell, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_18tell}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_19tell(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("tell (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("tell", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "tell", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_18tell(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_18tell(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + int64_t __pyx_v_ret; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + unsigned int __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__45) + __Pyx_RefNannySetupContext("tell", 1); + __Pyx_TraceCall("tell", __pyx_f[0], 503, 0, __PYX_ERR(0, 503, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":505 + * def tell(self): + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: # <<<<<<<<<<<<<< + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_is_open); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 505, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_2 < 0))) __PYX_ERR(0, 505, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = (!__pyx_t_2); + if (unlikely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":506 + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: + * raise ValueError('I/O operation on closed file') # <<<<<<<<<<<<<< + * if self.is_stream: + * raise IOError('tell not available in streams') + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__43, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 506, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 506, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":505 + * def tell(self): + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: # <<<<<<<<<<<<<< + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + */ + } + + /* "pysam/libchtslib.pyx":507 + * if not self.is_open: + * raise ValueError('I/O operation on closed file') + * if self.is_stream: # <<<<<<<<<<<<<< + * raise IOError('tell not available in streams') + * + */ + if (unlikely(__pyx_v_self->is_stream)) { + + /* "pysam/libchtslib.pyx":508 + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + * raise IOError('tell not available in streams') # <<<<<<<<<<<<<< + * + * cdef int64_t ret + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__46, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 508, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 508, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":507 + * if not self.is_open: + * raise ValueError('I/O operation on closed file') + * if self.is_stream: # <<<<<<<<<<<<<< + * raise IOError('tell not available in streams') + * + */ + } + + /* "pysam/libchtslib.pyx":511 + * + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: # <<<<<<<<<<<<<< + * with nogil: + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + */ + __pyx_t_3 = (__pyx_v_self->htsfile->format.compression == bgzf); + if (__pyx_t_3) { + + /* "pysam/libchtslib.pyx":512 + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: + * with nogil: # <<<<<<<<<<<<<< + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + * elif self.htsfile.format.compression == no_compression: + */ + { + #ifdef WITH_THREAD + PyThreadState *_save; + _save = NULL; + Py_UNBLOCK_THREADS + __Pyx_FastGIL_Remember(); + #endif + /*try:*/ { + + /* "pysam/libchtslib.pyx":513 + * if self.htsfile.format.compression == bgzf: + * with nogil: + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) # <<<<<<<<<<<<<< + * elif self.htsfile.format.compression == no_compression: + * ret = htell(self.htsfile.fp.hfile) + */ + __pyx_v_ret = bgzf_tell(hts_get_bgzfp(__pyx_v_self->htsfile)); + } + + /* "pysam/libchtslib.pyx":512 + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: + * with nogil: # <<<<<<<<<<<<<< + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + * elif self.htsfile.format.compression == no_compression: + */ + /*finally:*/ { + /*normal exit:*/{ + #ifdef WITH_THREAD + __Pyx_FastGIL_Forget(); + Py_BLOCK_THREADS + #endif + goto __pyx_L8; + } + __pyx_L8:; + } + } + + /* "pysam/libchtslib.pyx":511 + * + * cdef int64_t ret + * if self.htsfile.format.compression == bgzf: # <<<<<<<<<<<<<< + * with nogil: + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + */ + goto __pyx_L5; + } + + /* "pysam/libchtslib.pyx":514 + * with nogil: + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + * elif self.htsfile.format.compression == no_compression: # <<<<<<<<<<<<<< + * ret = htell(self.htsfile.fp.hfile) + * elif self.htsfile.format.format == cram: + */ + __pyx_t_3 = (__pyx_v_self->htsfile->format.compression == no_compression); + if (__pyx_t_3) { + + /* "pysam/libchtslib.pyx":515 + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + * elif self.htsfile.format.compression == no_compression: + * ret = htell(self.htsfile.fp.hfile) # <<<<<<<<<<<<<< + * elif self.htsfile.format.format == cram: + * with nogil: + */ + __pyx_v_ret = htell(__pyx_v_self->htsfile->fp.hfile); + + /* "pysam/libchtslib.pyx":514 + * with nogil: + * ret = bgzf_tell(hts_get_bgzfp(self.htsfile)) + * elif self.htsfile.format.compression == no_compression: # <<<<<<<<<<<<<< + * ret = htell(self.htsfile.fp.hfile) + * elif self.htsfile.format.format == cram: + */ + goto __pyx_L5; + } + + /* "pysam/libchtslib.pyx":516 + * elif self.htsfile.format.compression == no_compression: + * ret = htell(self.htsfile.fp.hfile) + * elif self.htsfile.format.format == cram: # <<<<<<<<<<<<<< + * with nogil: + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) + */ + __pyx_t_3 = (__pyx_v_self->htsfile->format.format == cram); + if (likely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":517 + * ret = htell(self.htsfile.fp.hfile) + * elif self.htsfile.format.format == cram: + * with nogil: # <<<<<<<<<<<<<< + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) + * else: + */ + { + #ifdef WITH_THREAD + PyThreadState *_save; + _save = NULL; + Py_UNBLOCK_THREADS + __Pyx_FastGIL_Remember(); + #endif + /*try:*/ { + + /* "pysam/libchtslib.pyx":518 + * elif self.htsfile.format.format == cram: + * with nogil: + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) # <<<<<<<<<<<<<< + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( + */ + __pyx_v_ret = htell(cram_fd_get_fp(__pyx_v_self->htsfile->fp.cram)); + } + + /* "pysam/libchtslib.pyx":517 + * ret = htell(self.htsfile.fp.hfile) + * elif self.htsfile.format.format == cram: + * with nogil: # <<<<<<<<<<<<<< + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) + * else: + */ + /*finally:*/ { + /*normal exit:*/{ + #ifdef WITH_THREAD + __Pyx_FastGIL_Forget(); + Py_BLOCK_THREADS + #endif + goto __pyx_L11; + } + __pyx_L11:; + } + } + + /* "pysam/libchtslib.pyx":516 + * elif self.htsfile.format.compression == no_compression: + * ret = htell(self.htsfile.fp.hfile) + * elif self.htsfile.format.format == cram: # <<<<<<<<<<<<<< + * with nogil: + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) + */ + goto __pyx_L5; + } + + /* "pysam/libchtslib.pyx":520 + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( # <<<<<<<<<<<<<< + * self.htsfile.format.compression)) + * + */ + /*else*/ { + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_seek_not_implemented_in_files_co, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 520, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + + /* "pysam/libchtslib.pyx":521 + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( + * self.htsfile.format.compression)) # <<<<<<<<<<<<<< + * + * return ret + */ + __pyx_t_5 = __Pyx_PyInt_From_enum__htsCompression(__pyx_v_self->htsfile->format.compression); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 521, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = NULL; + __pyx_t_7 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + __pyx_t_7 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_6, __pyx_t_5}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_7, 1+__pyx_t_7); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 520, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } + + /* "pysam/libchtslib.pyx":520 + * ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) + * else: + * raise NotImplementedError("seek not implemented in files compressed by method {}".format( # <<<<<<<<<<<<<< + * self.htsfile.format.compression)) + * + */ + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_NotImplementedError, __pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 520, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __PYX_ERR(0, 520, __pyx_L1_error) + } + __pyx_L5:; + + /* "pysam/libchtslib.pyx":523 + * self.htsfile.format.compression)) + * + * return ret # <<<<<<<<<<<<<< + * + * cdef htsFile *_open_htsfile(self) except? NULL: + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_4 = __Pyx_PyInt_From_int64_t(__pyx_v_ret); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 523, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_r = __pyx_t_4; + __pyx_t_4 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":503 + * return ret + * + * def tell(self): # <<<<<<<<<<<<<< + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":525 + * return ret + * + * cdef htsFile *_open_htsfile(self) except? NULL: # <<<<<<<<<<<<<< + * cdef char *cfilename + * cdef char *cmode = self.mode + */ + +static htsFile *__pyx_f_5pysam_10libchtslib_7HTSFile__open_htsfile(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + char *__pyx_v_cfilename; + char *__pyx_v_cmode; + int __pyx_v_fd; + int __pyx_v_dup_fd; + int __pyx_v_threads; + htsFile *__pyx_v_htsfile; + PyObject *__pyx_v_smode = NULL; + hFILE *__pyx_v_hfile; + PyObject *__pyx_v_filename = NULL; + htsFile *__pyx_r; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + char *__pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + unsigned int __pyx_t_7; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + PyObject *__pyx_t_12 = NULL; + PyObject *__pyx_t_13 = NULL; + PyObject *__pyx_t_14 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_open_htsfile", 1); + __Pyx_TraceCall("_open_htsfile", __pyx_f[0], 525, 0, __PYX_ERR(0, 525, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":527 + * cdef htsFile *_open_htsfile(self) except? NULL: + * cdef char *cfilename + * cdef char *cmode = self.mode # <<<<<<<<<<<<<< + * cdef int fd, dup_fd, threads + * + */ + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->mode); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 527, __pyx_L1_error) + __pyx_v_cmode = __pyx_t_1; + + /* "pysam/libchtslib.pyx":530 + * cdef int fd, dup_fd, threads + * + * threads = self.threads - 1 # <<<<<<<<<<<<<< + * if isinstance(self.filename, bytes): + * cfilename = self.filename + */ + __pyx_t_2 = __Pyx_PyInt_SubtractObjC(__pyx_v_self->threads, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 530, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 530, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_threads = __pyx_t_3; + + /* "pysam/libchtslib.pyx":531 + * + * threads = self.threads - 1 + * if isinstance(self.filename, bytes): # <<<<<<<<<<<<<< + * cfilename = self.filename + * with nogil: + */ + __pyx_t_2 = __pyx_v_self->filename; + __Pyx_INCREF(__pyx_t_2); + __pyx_t_4 = PyBytes_Check(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__pyx_t_4) { + + /* "pysam/libchtslib.pyx":532 + * threads = self.threads - 1 + * if isinstance(self.filename, bytes): + * cfilename = self.filename # <<<<<<<<<<<<<< + * with nogil: + * htsfile = hts_open(cfilename, cmode) + */ + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_self->filename); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 532, __pyx_L1_error) + __pyx_v_cfilename = __pyx_t_1; + + /* "pysam/libchtslib.pyx":533 + * if isinstance(self.filename, bytes): + * cfilename = self.filename + * with nogil: # <<<<<<<<<<<<<< + * htsfile = hts_open(cfilename, cmode) + * if htsfile != NULL: + */ + { + #ifdef WITH_THREAD + PyThreadState *_save; + _save = NULL; + Py_UNBLOCK_THREADS + __Pyx_FastGIL_Remember(); + #endif + /*try:*/ { + + /* "pysam/libchtslib.pyx":534 + * cfilename = self.filename + * with nogil: + * htsfile = hts_open(cfilename, cmode) # <<<<<<<<<<<<<< + * if htsfile != NULL: + * hts_set_threads(htsfile, threads) + */ + __pyx_v_htsfile = hts_open(__pyx_v_cfilename, __pyx_v_cmode); + + /* "pysam/libchtslib.pyx":535 + * with nogil: + * htsfile = hts_open(cfilename, cmode) + * if htsfile != NULL: # <<<<<<<<<<<<<< + * hts_set_threads(htsfile, threads) + * return htsfile + */ + __pyx_t_4 = (__pyx_v_htsfile != NULL); + if (__pyx_t_4) { + + /* "pysam/libchtslib.pyx":536 + * htsfile = hts_open(cfilename, cmode) + * if htsfile != NULL: + * hts_set_threads(htsfile, threads) # <<<<<<<<<<<<<< + * return htsfile + * else: + */ + (void)(hts_set_threads(__pyx_v_htsfile, __pyx_v_threads)); + + /* "pysam/libchtslib.pyx":535 + * with nogil: + * htsfile = hts_open(cfilename, cmode) + * if htsfile != NULL: # <<<<<<<<<<<<<< + * hts_set_threads(htsfile, threads) + * return htsfile + */ + } + + /* "pysam/libchtslib.pyx":537 + * if htsfile != NULL: + * hts_set_threads(htsfile, threads) + * return htsfile # <<<<<<<<<<<<<< + * else: + * if isinstance(self.filename, int): + */ + __pyx_r = __pyx_v_htsfile; + goto __pyx_L4_return; + } + + /* "pysam/libchtslib.pyx":533 + * if isinstance(self.filename, bytes): + * cfilename = self.filename + * with nogil: # <<<<<<<<<<<<<< + * htsfile = hts_open(cfilename, cmode) + * if htsfile != NULL: + */ + /*finally:*/ { + __pyx_L4_return: { + #ifdef WITH_THREAD + __Pyx_FastGIL_Forget(); + Py_BLOCK_THREADS + #endif + goto __pyx_L0; + } + } + } + + /* "pysam/libchtslib.pyx":531 + * + * threads = self.threads - 1 + * if isinstance(self.filename, bytes): # <<<<<<<<<<<<<< + * cfilename = self.filename + * with nogil: + */ + } + + /* "pysam/libchtslib.pyx":539 + * return htsfile + * else: + * if isinstance(self.filename, int): # <<<<<<<<<<<<<< + * fd = self.filename + * else: + */ + /*else*/ { + __pyx_t_2 = __pyx_v_self->filename; + __Pyx_INCREF(__pyx_t_2); + __pyx_t_4 = PyInt_Check(__pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__pyx_t_4) { + + /* "pysam/libchtslib.pyx":540 + * else: + * if isinstance(self.filename, int): + * fd = self.filename # <<<<<<<<<<<<<< + * else: + * fd = self.filename.fileno() + */ + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_v_self->filename); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 540, __pyx_L1_error) + __pyx_v_fd = __pyx_t_3; + + /* "pysam/libchtslib.pyx":539 + * return htsfile + * else: + * if isinstance(self.filename, int): # <<<<<<<<<<<<<< + * fd = self.filename + * else: + */ + goto __pyx_L8; + } + + /* "pysam/libchtslib.pyx":542 + * fd = self.filename + * else: + * fd = self.filename.fileno() # <<<<<<<<<<<<<< + * + * if self.duplicate_filehandle: + */ + /*else*/ { + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->filename, __pyx_n_s_fileno); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 542, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = NULL; + __pyx_t_7 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_5))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_5, function); + __pyx_t_7 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_6, NULL}; + __pyx_t_2 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_7, 0+__pyx_t_7); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 542, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + } + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 542, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_fd = __pyx_t_3; + } + __pyx_L8:; + + /* "pysam/libchtslib.pyx":544 + * fd = self.filename.fileno() + * + * if self.duplicate_filehandle: # <<<<<<<<<<<<<< + * dup_fd = dup(fd) + * else: + */ + if (__pyx_v_self->duplicate_filehandle) { + + /* "pysam/libchtslib.pyx":545 + * + * if self.duplicate_filehandle: + * dup_fd = dup(fd) # <<<<<<<<<<<<<< + * else: + * dup_fd = fd + */ + __pyx_v_dup_fd = dup(__pyx_v_fd); + + /* "pysam/libchtslib.pyx":544 + * fd = self.filename.fileno() + * + * if self.duplicate_filehandle: # <<<<<<<<<<<<<< + * dup_fd = dup(fd) + * else: + */ + goto __pyx_L9; + } + + /* "pysam/libchtslib.pyx":547 + * dup_fd = dup(fd) + * else: + * dup_fd = fd # <<<<<<<<<<<<<< + * + * # Replicate mode normalization done in hts_open_format + */ + /*else*/ { + __pyx_v_dup_fd = __pyx_v_fd; + } + __pyx_L9:; + + /* "pysam/libchtslib.pyx":550 + * + * # Replicate mode normalization done in hts_open_format + * smode = self.mode.replace(b'b', b'').replace(b'c', b'') # <<<<<<<<<<<<<< + * if b'b' in self.mode: + * smode += b'b' + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->mode, __pyx_n_s_replace); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__47, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_replace); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__48, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_smode = __pyx_t_5; + __pyx_t_5 = 0; + + /* "pysam/libchtslib.pyx":551 + * # Replicate mode normalization done in hts_open_format + * smode = self.mode.replace(b'b', b'').replace(b'c', b'') + * if b'b' in self.mode: # <<<<<<<<<<<<<< + * smode += b'b' + * elif b'c' in self.mode: + */ + __pyx_t_4 = (__Pyx_PySequence_ContainsTF(__pyx_n_b_b, __pyx_v_self->mode, Py_EQ)); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 551, __pyx_L1_error) + if (__pyx_t_4) { + + /* "pysam/libchtslib.pyx":552 + * smode = self.mode.replace(b'b', b'').replace(b'c', b'') + * if b'b' in self.mode: + * smode += b'b' # <<<<<<<<<<<<<< + * elif b'c' in self.mode: + * smode += b'c' + */ + __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_v_smode, __pyx_n_b_b); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 552, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF_SET(__pyx_v_smode, __pyx_t_5); + __pyx_t_5 = 0; + + /* "pysam/libchtslib.pyx":551 + * # Replicate mode normalization done in hts_open_format + * smode = self.mode.replace(b'b', b'').replace(b'c', b'') + * if b'b' in self.mode: # <<<<<<<<<<<<<< + * smode += b'b' + * elif b'c' in self.mode: + */ + goto __pyx_L10; + } + + /* "pysam/libchtslib.pyx":553 + * if b'b' in self.mode: + * smode += b'b' + * elif b'c' in self.mode: # <<<<<<<<<<<<<< + * smode += b'c' + * cmode = smode + */ + __pyx_t_4 = (__Pyx_PySequence_ContainsTF(__pyx_n_b_c, __pyx_v_self->mode, Py_EQ)); if (unlikely((__pyx_t_4 < 0))) __PYX_ERR(0, 553, __pyx_L1_error) + if (__pyx_t_4) { + + /* "pysam/libchtslib.pyx":554 + * smode += b'b' + * elif b'c' in self.mode: + * smode += b'c' # <<<<<<<<<<<<<< + * cmode = smode + * + */ + __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_v_smode, __pyx_n_b_c); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 554, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF_SET(__pyx_v_smode, __pyx_t_5); + __pyx_t_5 = 0; + + /* "pysam/libchtslib.pyx":553 + * if b'b' in self.mode: + * smode += b'b' + * elif b'c' in self.mode: # <<<<<<<<<<<<<< + * smode += b'c' + * cmode = smode + */ + } + __pyx_L10:; + + /* "pysam/libchtslib.pyx":555 + * elif b'c' in self.mode: + * smode += b'c' + * cmode = smode # <<<<<<<<<<<<<< + * + * hfile = hdopen(dup_fd, cmode) + */ + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_smode); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 555, __pyx_L1_error) + __pyx_v_cmode = __pyx_t_1; + + /* "pysam/libchtslib.pyx":557 + * cmode = smode + * + * hfile = hdopen(dup_fd, cmode) # <<<<<<<<<<<<<< + * if hfile == NULL: + * raise IOError('Cannot create hfile') + */ + __pyx_v_hfile = hdopen(__pyx_v_dup_fd, __pyx_v_cmode); + + /* "pysam/libchtslib.pyx":558 + * + * hfile = hdopen(dup_fd, cmode) + * if hfile == NULL: # <<<<<<<<<<<<<< + * raise IOError('Cannot create hfile') + * + */ + __pyx_t_4 = (__pyx_v_hfile == NULL); + if (unlikely(__pyx_t_4)) { + + /* "pysam/libchtslib.pyx":559 + * hfile = hdopen(dup_fd, cmode) + * if hfile == NULL: + * raise IOError('Cannot create hfile') # <<<<<<<<<<<<<< + * + * try: + */ + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__49, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 559, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_Raise(__pyx_t_5, 0, 0, 0); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __PYX_ERR(0, 559, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":558 + * + * hfile = hdopen(dup_fd, cmode) + * if hfile == NULL: # <<<<<<<<<<<<<< + * raise IOError('Cannot create hfile') + * + */ + } + + /* "pysam/libchtslib.pyx":561 + * raise IOError('Cannot create hfile') + * + * try: # <<<<<<<<<<<<<< + * # filename.name can be an int + * filename = str(self.filename.name) + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_8, &__pyx_t_9, &__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_8); + __Pyx_XGOTREF(__pyx_t_9); + __Pyx_XGOTREF(__pyx_t_10); + /*try:*/ { + + /* "pysam/libchtslib.pyx":563 + * try: + * # filename.name can be an int + * filename = str(self.filename.name) # <<<<<<<<<<<<<< + * except AttributeError: + * filename = '<fd:{}>'.format(fd) + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->filename, __pyx_n_s_name); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 563, __pyx_L12_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_2 = __Pyx_PyObject_Unicode(__pyx_t_5); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 563, __pyx_L12_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_v_filename = __pyx_t_2; + __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":561 + * raise IOError('Cannot create hfile') + * + * try: # <<<<<<<<<<<<<< + * # filename.name can be an int + * filename = str(self.filename.name) + */ + } + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + goto __pyx_L17_try_end; + __pyx_L12_error:; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":564 + * # filename.name can be an int + * filename = str(self.filename.name) + * except AttributeError: # <<<<<<<<<<<<<< + * filename = '<fd:{}>'.format(fd) + * + */ + __pyx_t_3 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_AttributeError); + if (__pyx_t_3) { + __Pyx_AddTraceback("pysam.libchtslib.HTSFile._open_htsfile", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_5, &__pyx_t_6) < 0) __PYX_ERR(0, 564, __pyx_L14_except_error) + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_5); + __Pyx_XGOTREF(__pyx_t_6); + + /* "pysam/libchtslib.pyx":565 + * filename = str(self.filename.name) + * except AttributeError: + * filename = '<fd:{}>'.format(fd) # <<<<<<<<<<<<<< + * + * filename = encode_filename(filename) + */ + __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_fd, __pyx_n_s_format); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 565, __pyx_L14_except_error) + __Pyx_GOTREF(__pyx_t_12); + __pyx_t_13 = __Pyx_PyInt_From_int(__pyx_v_fd); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 565, __pyx_L14_except_error) + __Pyx_GOTREF(__pyx_t_13); + __pyx_t_14 = NULL; + __pyx_t_7 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_12))) { + __pyx_t_14 = PyMethod_GET_SELF(__pyx_t_12); + if (likely(__pyx_t_14)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12); + __Pyx_INCREF(__pyx_t_14); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_12, function); + __pyx_t_7 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_14, __pyx_t_13}; + __pyx_t_11 = __Pyx_PyObject_FastCall(__pyx_t_12, __pyx_callargs+1-__pyx_t_7, 1+__pyx_t_7); + __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0; + __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; + if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 565, __pyx_L14_except_error) + __Pyx_GOTREF(__pyx_t_11); + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + } + __Pyx_XDECREF_SET(__pyx_v_filename, __pyx_t_11); + __pyx_t_11 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + goto __pyx_L13_exception_handled; + } + goto __pyx_L14_except_error; + + /* "pysam/libchtslib.pyx":561 + * raise IOError('Cannot create hfile') + * + * try: # <<<<<<<<<<<<<< + * # filename.name can be an int + * filename = str(self.filename.name) + */ + __pyx_L14_except_error:; + __Pyx_XGIVEREF(__pyx_t_8); + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_ExceptionReset(__pyx_t_8, __pyx_t_9, __pyx_t_10); + goto __pyx_L1_error; + __pyx_L13_exception_handled:; + __Pyx_XGIVEREF(__pyx_t_8); + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_ExceptionReset(__pyx_t_8, __pyx_t_9, __pyx_t_10); + __pyx_L17_try_end:; + } + + /* "pysam/libchtslib.pyx":567 + * filename = '<fd:{}>'.format(fd) + * + * filename = encode_filename(filename) # <<<<<<<<<<<<<< + * cfilename = filename + * with nogil: + */ + __pyx_t_6 = __pyx_f_5pysam_9libcutils_encode_filename(__pyx_v_filename); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 567, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF_SET(__pyx_v_filename, __pyx_t_6); + __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":568 + * + * filename = encode_filename(filename) + * cfilename = filename # <<<<<<<<<<<<<< + * with nogil: + * htsfile = hts_hopen(hfile, cfilename, cmode) + */ + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_filename); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 568, __pyx_L1_error) + __pyx_v_cfilename = __pyx_t_1; + + /* "pysam/libchtslib.pyx":569 + * filename = encode_filename(filename) + * cfilename = filename + * with nogil: # <<<<<<<<<<<<<< + * htsfile = hts_hopen(hfile, cfilename, cmode) + * if htsfile != NULL: + */ + { + #ifdef WITH_THREAD + PyThreadState *_save; + _save = NULL; + Py_UNBLOCK_THREADS + __Pyx_FastGIL_Remember(); + #endif + /*try:*/ { + + /* "pysam/libchtslib.pyx":570 + * cfilename = filename + * with nogil: + * htsfile = hts_hopen(hfile, cfilename, cmode) # <<<<<<<<<<<<<< + * if htsfile != NULL: + * hts_set_threads(htsfile, threads) + */ + __pyx_v_htsfile = hts_hopen(__pyx_v_hfile, __pyx_v_cfilename, __pyx_v_cmode); + + /* "pysam/libchtslib.pyx":571 + * with nogil: + * htsfile = hts_hopen(hfile, cfilename, cmode) + * if htsfile != NULL: # <<<<<<<<<<<<<< + * hts_set_threads(htsfile, threads) + * return htsfile + */ + __pyx_t_4 = (__pyx_v_htsfile != NULL); + if (__pyx_t_4) { + + /* "pysam/libchtslib.pyx":572 + * htsfile = hts_hopen(hfile, cfilename, cmode) + * if htsfile != NULL: + * hts_set_threads(htsfile, threads) # <<<<<<<<<<<<<< + * return htsfile + * + */ + (void)(hts_set_threads(__pyx_v_htsfile, __pyx_v_threads)); + + /* "pysam/libchtslib.pyx":571 + * with nogil: + * htsfile = hts_hopen(hfile, cfilename, cmode) + * if htsfile != NULL: # <<<<<<<<<<<<<< + * hts_set_threads(htsfile, threads) + * return htsfile + */ + } + + /* "pysam/libchtslib.pyx":573 + * if htsfile != NULL: + * hts_set_threads(htsfile, threads) + * return htsfile # <<<<<<<<<<<<<< + * + * def add_hts_options(self, format_options=None): + */ + __pyx_r = __pyx_v_htsfile; + goto __pyx_L20_return; + } + + /* "pysam/libchtslib.pyx":569 + * filename = encode_filename(filename) + * cfilename = filename + * with nogil: # <<<<<<<<<<<<<< + * htsfile = hts_hopen(hfile, cfilename, cmode) + * if htsfile != NULL: + */ + /*finally:*/ { + __pyx_L20_return: { + #ifdef WITH_THREAD + __Pyx_FastGIL_Forget(); + Py_BLOCK_THREADS + #endif + goto __pyx_L0; + } + } + } + } + + /* "pysam/libchtslib.pyx":525 + * return ret + * + * cdef htsFile *_open_htsfile(self) except? NULL: # <<<<<<<<<<<<<< + * cdef char *cfilename + * cdef char *cmode = self.mode + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_11); + __Pyx_XDECREF(__pyx_t_12); + __Pyx_XDECREF(__pyx_t_13); + __Pyx_XDECREF(__pyx_t_14); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile._open_htsfile", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_smode); + __Pyx_XDECREF(__pyx_v_filename); + __Pyx_TraceReturn(Py_None, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":575 + * return htsfile + * + * def add_hts_options(self, format_options=None): # <<<<<<<<<<<<<< + * """Given a list of key=value format option strings, add them to an open htsFile + * """ + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_21add_hts_options(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_20add_hts_options, "HTSFile.add_hts_options(self, format_options=None)\nGiven a list of key=value format option strings, add them to an open htsFile\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_21add_hts_options = {"add_hts_options", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_21add_hts_options, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_20add_hts_options}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_21add_hts_options(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_format_options = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("add_hts_options (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_format_options,0}; + values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_format_options); + if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 575, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "add_hts_options") < 0)) __PYX_ERR(0, 575, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_format_options = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("add_hts_options", 0, 0, 1, __pyx_nargs); __PYX_ERR(0, 575, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.add_hts_options", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_20add_hts_options(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_format_options); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_20add_hts_options(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_format_options) { + int __pyx_v_rval; + hts_opt *__pyx_v_opts; + PyObject *__pyx_v_format_option = NULL; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + Py_ssize_t __pyx_t_3; + PyObject *(*__pyx_t_4)(PyObject *); + PyObject *__pyx_t_5 = NULL; + char const *__pyx_t_6; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + unsigned int __pyx_t_9; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__50) + __Pyx_RefNannySetupContext("add_hts_options", 1); + __Pyx_TraceCall("add_hts_options", __pyx_f[0], 575, 0, __PYX_ERR(0, 575, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":579 + * """ + * cdef int rval + * cdef hts_opt *opts = NULL # <<<<<<<<<<<<<< + * + * if format_options: + */ + __pyx_v_opts = NULL; + + /* "pysam/libchtslib.pyx":581 + * cdef hts_opt *opts = NULL + * + * if format_options: # <<<<<<<<<<<<<< + * for format_option in format_options: + * rval = hts_opt_add(&opts, format_option) + */ + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_format_options); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 581, __pyx_L1_error) + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":582 + * + * if format_options: + * for format_option in format_options: # <<<<<<<<<<<<<< + * rval = hts_opt_add(&opts, format_option) + * if rval != 0: + */ + if (likely(PyList_CheckExact(__pyx_v_format_options)) || PyTuple_CheckExact(__pyx_v_format_options)) { + __pyx_t_2 = __pyx_v_format_options; __Pyx_INCREF(__pyx_t_2); + __pyx_t_3 = 0; + __pyx_t_4 = NULL; + } else { + __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_format_options); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 582, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 582, __pyx_L1_error) + } + for (;;) { + if (likely(!__pyx_t_4)) { + if (likely(PyList_CheckExact(__pyx_t_2))) { + { + Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_2); + #if !CYTHON_ASSUME_SAFE_MACROS + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 582, __pyx_L1_error) + #endif + if (__pyx_t_3 >= __pyx_temp) break; + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 582, __pyx_L1_error) + #else + __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 582, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + #endif + } else { + { + Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_2); + #if !CYTHON_ASSUME_SAFE_MACROS + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 582, __pyx_L1_error) + #endif + if (__pyx_t_3 >= __pyx_temp) break; + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 582, __pyx_L1_error) + #else + __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 582, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + #endif + } + } else { + __pyx_t_5 = __pyx_t_4(__pyx_t_2); + if (unlikely(!__pyx_t_5)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 582, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_5); + } + __Pyx_XDECREF_SET(__pyx_v_format_option, __pyx_t_5); + __pyx_t_5 = 0; + + /* "pysam/libchtslib.pyx":583 + * if format_options: + * for format_option in format_options: + * rval = hts_opt_add(&opts, format_option) # <<<<<<<<<<<<<< + * if rval != 0: + * if opts != NULL: + */ + __pyx_t_6 = __Pyx_PyObject_AsString(__pyx_v_format_option); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) __PYX_ERR(0, 583, __pyx_L1_error) + __pyx_v_rval = hts_opt_add((&__pyx_v_opts), __pyx_t_6); + + /* "pysam/libchtslib.pyx":584 + * for format_option in format_options: + * rval = hts_opt_add(&opts, format_option) + * if rval != 0: # <<<<<<<<<<<<<< + * if opts != NULL: + * hts_opt_free(opts) + */ + __pyx_t_1 = (__pyx_v_rval != 0); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":585 + * rval = hts_opt_add(&opts, format_option) + * if rval != 0: + * if opts != NULL: # <<<<<<<<<<<<<< + * hts_opt_free(opts) + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) + */ + __pyx_t_1 = (__pyx_v_opts != NULL); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":586 + * if rval != 0: + * if opts != NULL: + * hts_opt_free(opts) # <<<<<<<<<<<<<< + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) + * if opts != NULL: + */ + hts_opt_free(__pyx_v_opts); + + /* "pysam/libchtslib.pyx":585 + * rval = hts_opt_add(&opts, format_option) + * if rval != 0: + * if opts != NULL: # <<<<<<<<<<<<<< + * hts_opt_free(opts) + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) + */ + } + + /* "pysam/libchtslib.pyx":587 + * if opts != NULL: + * hts_opt_free(opts) + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) # <<<<<<<<<<<<<< + * if opts != NULL: + * rval = hts_opt_apply(self.htsfile, opts) + */ + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_kp_u_Invalid_format_option_specified, __pyx_n_s_format); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 587, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_8 = NULL; + __pyx_t_9 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_7))) { + __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_7); + if (likely(__pyx_t_8)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7); + __Pyx_INCREF(__pyx_t_8); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_7, function); + __pyx_t_9 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_v_format_option}; + __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_7, __pyx_callargs+1-__pyx_t_9, 1+__pyx_t_9); + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 587, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + } + __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_builtin_RuntimeError, __pyx_t_5); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 587, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_Raise(__pyx_t_7, 0, 0, 0); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __PYX_ERR(0, 587, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":584 + * for format_option in format_options: + * rval = hts_opt_add(&opts, format_option) + * if rval != 0: # <<<<<<<<<<<<<< + * if opts != NULL: + * hts_opt_free(opts) + */ + } + + /* "pysam/libchtslib.pyx":582 + * + * if format_options: + * for format_option in format_options: # <<<<<<<<<<<<<< + * rval = hts_opt_add(&opts, format_option) + * if rval != 0: + */ + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":588 + * hts_opt_free(opts) + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) + * if opts != NULL: # <<<<<<<<<<<<<< + * rval = hts_opt_apply(self.htsfile, opts) + * if rval != 0: + */ + __pyx_t_1 = (__pyx_v_opts != NULL); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":589 + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) + * if opts != NULL: + * rval = hts_opt_apply(self.htsfile, opts) # <<<<<<<<<<<<<< + * if rval != 0: + * hts_opt_free(opts) + */ + __pyx_v_rval = hts_opt_apply(__pyx_v_self->htsfile, __pyx_v_opts); + + /* "pysam/libchtslib.pyx":590 + * if opts != NULL: + * rval = hts_opt_apply(self.htsfile, opts) + * if rval != 0: # <<<<<<<<<<<<<< + * hts_opt_free(opts) + * raise RuntimeError('An error occurred while applying the requested format options') + */ + __pyx_t_1 = (__pyx_v_rval != 0); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":591 + * rval = hts_opt_apply(self.htsfile, opts) + * if rval != 0: + * hts_opt_free(opts) # <<<<<<<<<<<<<< + * raise RuntimeError('An error occurred while applying the requested format options') + * hts_opt_free(opts) + */ + hts_opt_free(__pyx_v_opts); + + /* "pysam/libchtslib.pyx":592 + * if rval != 0: + * hts_opt_free(opts) + * raise RuntimeError('An error occurred while applying the requested format options') # <<<<<<<<<<<<<< + * hts_opt_free(opts) + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__51, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 592, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 592, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":590 + * if opts != NULL: + * rval = hts_opt_apply(self.htsfile, opts) + * if rval != 0: # <<<<<<<<<<<<<< + * hts_opt_free(opts) + * raise RuntimeError('An error occurred while applying the requested format options') + */ + } + + /* "pysam/libchtslib.pyx":593 + * hts_opt_free(opts) + * raise RuntimeError('An error occurred while applying the requested format options') + * hts_opt_free(opts) # <<<<<<<<<<<<<< + * + * def parse_region(self, contig=None, start=None, stop=None, + */ + hts_opt_free(__pyx_v_opts); + + /* "pysam/libchtslib.pyx":588 + * hts_opt_free(opts) + * raise RuntimeError('Invalid format option ({}) specified'.format(format_option)) + * if opts != NULL: # <<<<<<<<<<<<<< + * rval = hts_opt_apply(self.htsfile, opts) + * if rval != 0: + */ + } + + /* "pysam/libchtslib.pyx":581 + * cdef hts_opt *opts = NULL + * + * if format_options: # <<<<<<<<<<<<<< + * for format_option in format_options: + * rval = hts_opt_add(&opts, format_option) + */ + } + + /* "pysam/libchtslib.pyx":575 + * return htsfile + * + * def add_hts_options(self, format_options=None): # <<<<<<<<<<<<<< + * """Given a list of key=value format option strings, add them to an open htsFile + * """ + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.add_hts_options", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_format_option); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":595 + * hts_opt_free(opts) + * + * def parse_region(self, contig=None, start=None, stop=None, # <<<<<<<<<<<<<< + * region=None, tid=None, + * reference=None, end=None): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_23parse_region(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_22parse_region, "HTSFile.parse_region(self, contig=None, start=None, stop=None, region=None, tid=None, reference=None, end=None)\nparse alternative ways to specify a genomic region. A region can\n either be specified by :term:`contig`, `start` and\n `stop`. `start` and `stop` denote 0-based, half-open\n intervals. :term:`reference` and `end` are also accepted for\n backward compatibility as synonyms for :term:`contig` and\n `stop`, respectively.\n\n Alternatively, a samtools :term:`region` string can be\n supplied.\n\n If any of the coordinates are missing they will be replaced by\n the minimum (`start`) or maximum (`stop`) coordinate.\n\n Note that region strings are 1-based inclusive, while `start`\n and `stop` denote an interval in 0-based, half-open\n coordinates (like BED files and Python slices).\n\n If `contig` or `region` or are ``*``, unmapped reads at the end\n of a BAM file will be returned. Setting either to ``.`` will\n iterate from the beginning of the file.\n\n Returns\n -------\n\n tuple :\n a tuple of `flag`, :term:`tid`, `start` and\n `stop`. The flag indicates whether no coordinates were\n supplied and the genomic region is the complete genomic space.\n\n Raises\n ------\n\n ValueError\n for invalid or out of bounds regions.\n\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_23parse_region = {"parse_region", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_23parse_region, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_22parse_region}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_23parse_region(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_contig = 0; + PyObject *__pyx_v_start = 0; + PyObject *__pyx_v_stop = 0; + PyObject *__pyx_v_region = 0; + PyObject *__pyx_v_tid = 0; + PyObject *__pyx_v_reference = 0; + PyObject *__pyx_v_end = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[7] = {0,0,0,0,0,0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("parse_region (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_contig,&__pyx_n_s_start,&__pyx_n_s_stop,&__pyx_n_s_region,&__pyx_n_s_tid,&__pyx_n_s_reference,&__pyx_n_s_end,0}; + values[0] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + values[1] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + values[2] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + + /* "pysam/libchtslib.pyx":596 + * + * def parse_region(self, contig=None, start=None, stop=None, + * region=None, tid=None, # <<<<<<<<<<<<<< + * reference=None, end=None): + * """parse alternative ways to specify a genomic region. A region can + */ + values[3] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + values[4] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + + /* "pysam/libchtslib.pyx":597 + * def parse_region(self, contig=None, start=None, stop=None, + * region=None, tid=None, + * reference=None, end=None): # <<<<<<<<<<<<<< + * """parse alternative ways to specify a genomic region. A region can + * either be specified by :term:`contig`, `start` and + */ + values[5] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + values[6] = __Pyx_Arg_NewRef_FASTCALL(((PyObject *)Py_None)); + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6); + CYTHON_FALLTHROUGH; + case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5); + CYTHON_FALLTHROUGH; + case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4); + CYTHON_FALLTHROUGH; + case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); + CYTHON_FALLTHROUGH; + case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_contig); + if (value) { values[0] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_start); + if (value) { values[1] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_stop); + if (value) { values[2] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 3: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_region); + if (value) { values[3] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 4: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_tid); + if (value) { values[4] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 5: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_reference); + if (value) { values[5] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 6: + if (kw_args > 0) { + PyObject* value = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_end); + if (value) { values[6] = __Pyx_Arg_NewRef_FASTCALL(value); kw_args--; } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 595, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "parse_region") < 0)) __PYX_ERR(0, 595, __pyx_L3_error) + } + } else { + switch (__pyx_nargs) { + case 7: values[6] = __Pyx_Arg_FASTCALL(__pyx_args, 6); + CYTHON_FALLTHROUGH; + case 6: values[5] = __Pyx_Arg_FASTCALL(__pyx_args, 5); + CYTHON_FALLTHROUGH; + case 5: values[4] = __Pyx_Arg_FASTCALL(__pyx_args, 4); + CYTHON_FALLTHROUGH; + case 4: values[3] = __Pyx_Arg_FASTCALL(__pyx_args, 3); + CYTHON_FALLTHROUGH; + case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_contig = values[0]; + __pyx_v_start = values[1]; + __pyx_v_stop = values[2]; + __pyx_v_region = values[3]; + __pyx_v_tid = values[4]; + __pyx_v_reference = values[5]; + __pyx_v_end = values[6]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("parse_region", 0, 0, 7, __pyx_nargs); __PYX_ERR(0, 595, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_22parse_region(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_contig, __pyx_v_start, __pyx_v_stop, __pyx_v_region, __pyx_v_tid, __pyx_v_reference, __pyx_v_end); + + /* "pysam/libchtslib.pyx":595 + * hts_opt_free(opts) + * + * def parse_region(self, contig=None, start=None, stop=None, # <<<<<<<<<<<<<< + * region=None, tid=None, + * reference=None, end=None): + */ + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_22parse_region(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_tid, PyObject *__pyx_v_reference, PyObject *__pyx_v_end) { + int __pyx_v_rtid; + int32_t __pyx_v_rstart; + int32_t __pyx_v_rstop; + PyObject *__pyx_v_coord = NULL; + PyObject *__pyx_v_parts = NULL; + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + int32_t __pyx_t_8; + int __pyx_t_9; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + PyObject *__pyx_t_12 = NULL; + unsigned int __pyx_t_13; + PyObject *(*__pyx_t_14)(PyObject *); + Py_ssize_t __pyx_t_15; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__52) + __Pyx_RefNannySetupContext("parse_region", 0); + __Pyx_TraceCall("parse_region", __pyx_f[0], 595, 0, __PYX_ERR(0, 595, __pyx_L1_error)); + __Pyx_INCREF(__pyx_v_contig); + __Pyx_INCREF(__pyx_v_stop); + __Pyx_INCREF(__pyx_v_region); + + /* "pysam/libchtslib.pyx":638 + * cdef int32_t rstop + * + * if reference is not None: # <<<<<<<<<<<<<< + * if contig is not None: + * raise ValueError('contig and reference should not both be specified') + */ + __pyx_t_1 = (__pyx_v_reference != Py_None); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":639 + * + * if reference is not None: + * if contig is not None: # <<<<<<<<<<<<<< + * raise ValueError('contig and reference should not both be specified') + * contig = reference + */ + __pyx_t_1 = (__pyx_v_contig != Py_None); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":640 + * if reference is not None: + * if contig is not None: + * raise ValueError('contig and reference should not both be specified') # <<<<<<<<<<<<<< + * contig = reference + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__53, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 640, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 640, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":639 + * + * if reference is not None: + * if contig is not None: # <<<<<<<<<<<<<< + * raise ValueError('contig and reference should not both be specified') + * contig = reference + */ + } + + /* "pysam/libchtslib.pyx":641 + * if contig is not None: + * raise ValueError('contig and reference should not both be specified') + * contig = reference # <<<<<<<<<<<<<< + * + * if end is not None: + */ + __Pyx_INCREF(__pyx_v_reference); + __Pyx_DECREF_SET(__pyx_v_contig, __pyx_v_reference); + + /* "pysam/libchtslib.pyx":638 + * cdef int32_t rstop + * + * if reference is not None: # <<<<<<<<<<<<<< + * if contig is not None: + * raise ValueError('contig and reference should not both be specified') + */ + } + + /* "pysam/libchtslib.pyx":643 + * contig = reference + * + * if end is not None: # <<<<<<<<<<<<<< + * if stop is not None: + * raise ValueError('stop and end should not both be specified') + */ + __pyx_t_1 = (__pyx_v_end != Py_None); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":644 + * + * if end is not None: + * if stop is not None: # <<<<<<<<<<<<<< + * raise ValueError('stop and end should not both be specified') + * stop = end + */ + __pyx_t_1 = (__pyx_v_stop != Py_None); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":645 + * if end is not None: + * if stop is not None: + * raise ValueError('stop and end should not both be specified') # <<<<<<<<<<<<<< + * stop = end + * + */ + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__54, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 645, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 645, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":644 + * + * if end is not None: + * if stop is not None: # <<<<<<<<<<<<<< + * raise ValueError('stop and end should not both be specified') + * stop = end + */ + } + + /* "pysam/libchtslib.pyx":646 + * if stop is not None: + * raise ValueError('stop and end should not both be specified') + * stop = end # <<<<<<<<<<<<<< + * + * if contig is None and tid is None and region is None: + */ + __Pyx_INCREF(__pyx_v_end); + __Pyx_DECREF_SET(__pyx_v_stop, __pyx_v_end); + + /* "pysam/libchtslib.pyx":643 + * contig = reference + * + * if end is not None: # <<<<<<<<<<<<<< + * if stop is not None: + * raise ValueError('stop and end should not both be specified') + */ + } + + /* "pysam/libchtslib.pyx":648 + * stop = end + * + * if contig is None and tid is None and region is None: # <<<<<<<<<<<<<< + * return 0, 0, 0, MAX_POS + * + */ + __pyx_t_3 = (__pyx_v_contig == Py_None); + if (__pyx_t_3) { + } else { + __pyx_t_1 = __pyx_t_3; + goto __pyx_L8_bool_binop_done; + } + __pyx_t_3 = (__pyx_v_tid == Py_None); + if (__pyx_t_3) { + } else { + __pyx_t_1 = __pyx_t_3; + goto __pyx_L8_bool_binop_done; + } + __pyx_t_3 = (__pyx_v_region == Py_None); + __pyx_t_1 = __pyx_t_3; + __pyx_L8_bool_binop_done:; + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":649 + * + * if contig is None and tid is None and region is None: + * return 0, 0, 0, MAX_POS # <<<<<<<<<<<<<< + * + * rtid = -1 + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_5pysam_10libchtslib_MAX_POS); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 649, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyTuple_New(4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 649, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_INCREF(__pyx_int_0); + __Pyx_GIVEREF(__pyx_int_0); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_int_0)) __PYX_ERR(0, 649, __pyx_L1_error); + __Pyx_INCREF(__pyx_int_0); + __Pyx_GIVEREF(__pyx_int_0); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_int_0)) __PYX_ERR(0, 649, __pyx_L1_error); + __Pyx_INCREF(__pyx_int_0); + __Pyx_GIVEREF(__pyx_int_0); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_int_0)) __PYX_ERR(0, 649, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_4, 3, __pyx_t_2)) __PYX_ERR(0, 649, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_r = __pyx_t_4; + __pyx_t_4 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":648 + * stop = end + * + * if contig is None and tid is None and region is None: # <<<<<<<<<<<<<< + * return 0, 0, 0, MAX_POS + * + */ + } + + /* "pysam/libchtslib.pyx":651 + * return 0, 0, 0, MAX_POS + * + * rtid = -1 # <<<<<<<<<<<<<< + * rstart = 0 + * rstop = MAX_POS + */ + __pyx_v_rtid = -1; + + /* "pysam/libchtslib.pyx":652 + * + * rtid = -1 + * rstart = 0 # <<<<<<<<<<<<<< + * rstop = MAX_POS + * if start is not None: + */ + __pyx_v_rstart = 0; + + /* "pysam/libchtslib.pyx":653 + * rtid = -1 + * rstart = 0 + * rstop = MAX_POS # <<<<<<<<<<<<<< + * if start is not None: + * try: + */ + __pyx_v_rstop = __pyx_v_5pysam_10libchtslib_MAX_POS; + + /* "pysam/libchtslib.pyx":654 + * rstart = 0 + * rstop = MAX_POS + * if start is not None: # <<<<<<<<<<<<<< + * try: + * rstart = start + */ + __pyx_t_1 = (__pyx_v_start != Py_None); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":655 + * rstop = MAX_POS + * if start is not None: + * try: # <<<<<<<<<<<<<< + * rstart = start + * except OverflowError: + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7); + __Pyx_XGOTREF(__pyx_t_5); + __Pyx_XGOTREF(__pyx_t_6); + __Pyx_XGOTREF(__pyx_t_7); + /*try:*/ { + + /* "pysam/libchtslib.pyx":656 + * if start is not None: + * try: + * rstart = start # <<<<<<<<<<<<<< + * except OverflowError: + * raise ValueError('start out of range (%i)' % start) + */ + __pyx_t_8 = __Pyx_PyInt_As_int32_t(__pyx_v_start); if (unlikely((__pyx_t_8 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 656, __pyx_L12_error) + __pyx_v_rstart = __pyx_t_8; + + /* "pysam/libchtslib.pyx":655 + * rstop = MAX_POS + * if start is not None: + * try: # <<<<<<<<<<<<<< + * rstart = start + * except OverflowError: + */ + } + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + goto __pyx_L17_try_end; + __pyx_L12_error:; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "pysam/libchtslib.pyx":657 + * try: + * rstart = start + * except OverflowError: # <<<<<<<<<<<<<< + * raise ValueError('start out of range (%i)' % start) + * + */ + __pyx_t_9 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_OverflowError); + if (__pyx_t_9) { + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_2, &__pyx_t_10) < 0) __PYX_ERR(0, 657, __pyx_L14_except_error) + __Pyx_XGOTREF(__pyx_t_4); + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_10); + + /* "pysam/libchtslib.pyx":658 + * rstart = start + * except OverflowError: + * raise ValueError('start out of range (%i)' % start) # <<<<<<<<<<<<<< + * + * if stop is not None: + */ + __pyx_t_11 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_start_out_of_range_i, __pyx_v_start); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 658, __pyx_L14_except_error) + __Pyx_GOTREF(__pyx_t_11); + __pyx_t_12 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_11); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 658, __pyx_L14_except_error) + __Pyx_GOTREF(__pyx_t_12); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __Pyx_Raise(__pyx_t_12, 0, 0, 0); + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __PYX_ERR(0, 658, __pyx_L14_except_error) + } + goto __pyx_L14_except_error; + + /* "pysam/libchtslib.pyx":655 + * rstop = MAX_POS + * if start is not None: + * try: # <<<<<<<<<<<<<< + * rstart = start + * except OverflowError: + */ + __pyx_L14_except_error:; + __Pyx_XGIVEREF(__pyx_t_5); + __Pyx_XGIVEREF(__pyx_t_6); + __Pyx_XGIVEREF(__pyx_t_7); + __Pyx_ExceptionReset(__pyx_t_5, __pyx_t_6, __pyx_t_7); + goto __pyx_L1_error; + __pyx_L17_try_end:; + } + + /* "pysam/libchtslib.pyx":654 + * rstart = 0 + * rstop = MAX_POS + * if start is not None: # <<<<<<<<<<<<<< + * try: + * rstart = start + */ + } + + /* "pysam/libchtslib.pyx":660 + * raise ValueError('start out of range (%i)' % start) + * + * if stop is not None: # <<<<<<<<<<<<<< + * try: + * rstop = stop + */ + __pyx_t_1 = (__pyx_v_stop != Py_None); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":661 + * + * if stop is not None: + * try: # <<<<<<<<<<<<<< + * rstop = stop + * except OverflowError: + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_7, &__pyx_t_6, &__pyx_t_5); + __Pyx_XGOTREF(__pyx_t_7); + __Pyx_XGOTREF(__pyx_t_6); + __Pyx_XGOTREF(__pyx_t_5); + /*try:*/ { + + /* "pysam/libchtslib.pyx":662 + * if stop is not None: + * try: + * rstop = stop # <<<<<<<<<<<<<< + * except OverflowError: + * raise ValueError('stop out of range (%i)' % stop) + */ + __pyx_t_8 = __Pyx_PyInt_As_int32_t(__pyx_v_stop); if (unlikely((__pyx_t_8 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 662, __pyx_L21_error) + __pyx_v_rstop = __pyx_t_8; + + /* "pysam/libchtslib.pyx":661 + * + * if stop is not None: + * try: # <<<<<<<<<<<<<< + * rstop = stop + * except OverflowError: + */ + } + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + goto __pyx_L26_try_end; + __pyx_L21_error:; + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0; + __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "pysam/libchtslib.pyx":663 + * try: + * rstop = stop + * except OverflowError: # <<<<<<<<<<<<<< + * raise ValueError('stop out of range (%i)' % stop) + * + */ + __pyx_t_9 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_OverflowError); + if (__pyx_t_9) { + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_2, &__pyx_t_4) < 0) __PYX_ERR(0, 663, __pyx_L23_except_error) + __Pyx_XGOTREF(__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_4); + + /* "pysam/libchtslib.pyx":664 + * rstop = stop + * except OverflowError: + * raise ValueError('stop out of range (%i)' % stop) # <<<<<<<<<<<<<< + * + * if region: + */ + __pyx_t_12 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_stop_out_of_range_i, __pyx_v_stop); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 664, __pyx_L23_except_error) + __Pyx_GOTREF(__pyx_t_12); + __pyx_t_11 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_12); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 664, __pyx_L23_except_error) + __Pyx_GOTREF(__pyx_t_11); + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __Pyx_Raise(__pyx_t_11, 0, 0, 0); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __PYX_ERR(0, 664, __pyx_L23_except_error) + } + goto __pyx_L23_except_error; + + /* "pysam/libchtslib.pyx":661 + * + * if stop is not None: + * try: # <<<<<<<<<<<<<< + * rstop = stop + * except OverflowError: + */ + __pyx_L23_except_error:; + __Pyx_XGIVEREF(__pyx_t_7); + __Pyx_XGIVEREF(__pyx_t_6); + __Pyx_XGIVEREF(__pyx_t_5); + __Pyx_ExceptionReset(__pyx_t_7, __pyx_t_6, __pyx_t_5); + goto __pyx_L1_error; + __pyx_L26_try_end:; + } + + /* "pysam/libchtslib.pyx":660 + * raise ValueError('start out of range (%i)' % start) + * + * if stop is not None: # <<<<<<<<<<<<<< + * try: + * rstop = stop + */ + } + + /* "pysam/libchtslib.pyx":666 + * raise ValueError('stop out of range (%i)' % stop) + * + * if region: # <<<<<<<<<<<<<< + * region = force_str(region) + * if ":" in region: + */ + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 666, __pyx_L1_error) + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":667 + * + * if region: + * region = force_str(region) # <<<<<<<<<<<<<< + * if ":" in region: + * contig, coord = region.split(":") + */ + __pyx_t_4 = __pyx_f_5pysam_9libcutils_force_str(__pyx_v_region, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 667, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF_SET(__pyx_v_region, __pyx_t_4); + __pyx_t_4 = 0; + + /* "pysam/libchtslib.pyx":668 + * if region: + * region = force_str(region) + * if ":" in region: # <<<<<<<<<<<<<< + * contig, coord = region.split(":") + * parts = coord.split("-") + */ + __pyx_t_1 = (__Pyx_PySequence_ContainsTF(__pyx_kp_u__55, __pyx_v_region, Py_EQ)); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 668, __pyx_L1_error) + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":669 + * region = force_str(region) + * if ":" in region: + * contig, coord = region.split(":") # <<<<<<<<<<<<<< + * parts = coord.split("-") + * rstart = int(parts[0]) - 1 + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_region, __pyx_n_s_split); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 669, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = NULL; + __pyx_t_13 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_10)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_10); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_13 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_10, __pyx_kp_u__55}; + __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 669, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) { + PyObject* sequence = __pyx_t_4; + Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + __PYX_ERR(0, 669, __pyx_L1_error) + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + if (likely(PyTuple_CheckExact(sequence))) { + __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1); + } else { + __pyx_t_2 = PyList_GET_ITEM(sequence, 0); + __pyx_t_10 = PyList_GET_ITEM(sequence, 1); + } + __Pyx_INCREF(__pyx_t_2); + __Pyx_INCREF(__pyx_t_10); + #else + __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 669, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 669, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + #endif + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } else { + Py_ssize_t index = -1; + __pyx_t_11 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 669, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_11); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_14 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_11); + index = 0; __pyx_t_2 = __pyx_t_14(__pyx_t_11); if (unlikely(!__pyx_t_2)) goto __pyx_L31_unpacking_failed; + __Pyx_GOTREF(__pyx_t_2); + index = 1; __pyx_t_10 = __pyx_t_14(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L31_unpacking_failed; + __Pyx_GOTREF(__pyx_t_10); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_11), 2) < 0) __PYX_ERR(0, 669, __pyx_L1_error) + __pyx_t_14 = NULL; + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + goto __pyx_L32_unpacking_done; + __pyx_L31_unpacking_failed:; + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __pyx_t_14 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); + __PYX_ERR(0, 669, __pyx_L1_error) + __pyx_L32_unpacking_done:; + } + __Pyx_DECREF_SET(__pyx_v_contig, __pyx_t_2); + __pyx_t_2 = 0; + __pyx_v_coord = __pyx_t_10; + __pyx_t_10 = 0; + + /* "pysam/libchtslib.pyx":670 + * if ":" in region: + * contig, coord = region.split(":") + * parts = coord.split("-") # <<<<<<<<<<<<<< + * rstart = int(parts[0]) - 1 + * if len(parts) >= 1: + */ + __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_v_coord, __pyx_n_s_split); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 670, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_2 = NULL; + __pyx_t_13 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_10))) { + __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_10); + if (likely(__pyx_t_2)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10); + __Pyx_INCREF(__pyx_t_2); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_10, function); + __pyx_t_13 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_kp_u__56}; + __pyx_t_4 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 670, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + } + __pyx_v_parts = __pyx_t_4; + __pyx_t_4 = 0; + + /* "pysam/libchtslib.pyx":671 + * contig, coord = region.split(":") + * parts = coord.split("-") + * rstart = int(parts[0]) - 1 # <<<<<<<<<<<<<< + * if len(parts) >= 1: + * rstop = int(parts[1]) + */ + __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_parts, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 671, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_10 = __Pyx_PyNumber_Int(__pyx_t_4); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 671, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = __Pyx_PyInt_SubtractObjC(__pyx_t_10, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 671, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_8 = __Pyx_PyInt_As_int32_t(__pyx_t_4); if (unlikely((__pyx_t_8 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 671, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_v_rstart = __pyx_t_8; + + /* "pysam/libchtslib.pyx":672 + * parts = coord.split("-") + * rstart = int(parts[0]) - 1 + * if len(parts) >= 1: # <<<<<<<<<<<<<< + * rstop = int(parts[1]) + * else: + */ + __pyx_t_15 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 672, __pyx_L1_error) + __pyx_t_1 = (__pyx_t_15 >= 1); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":673 + * rstart = int(parts[0]) - 1 + * if len(parts) >= 1: + * rstop = int(parts[1]) # <<<<<<<<<<<<<< + * else: + * contig = region + */ + __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_parts, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_10 = __Pyx_PyNumber_Int(__pyx_t_4); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_8 = __Pyx_PyInt_As_int32_t(__pyx_t_10); if (unlikely((__pyx_t_8 == ((int32_t)-1)) && PyErr_Occurred())) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_v_rstop = __pyx_t_8; + + /* "pysam/libchtslib.pyx":672 + * parts = coord.split("-") + * rstart = int(parts[0]) - 1 + * if len(parts) >= 1: # <<<<<<<<<<<<<< + * rstop = int(parts[1]) + * else: + */ + } + + /* "pysam/libchtslib.pyx":668 + * if region: + * region = force_str(region) + * if ":" in region: # <<<<<<<<<<<<<< + * contig, coord = region.split(":") + * parts = coord.split("-") + */ + goto __pyx_L30; + } + + /* "pysam/libchtslib.pyx":675 + * rstop = int(parts[1]) + * else: + * contig = region # <<<<<<<<<<<<<< + * + * if tid is not None: + */ + /*else*/ { + __Pyx_INCREF(__pyx_v_region); + __Pyx_DECREF_SET(__pyx_v_contig, __pyx_v_region); + } + __pyx_L30:; + + /* "pysam/libchtslib.pyx":666 + * raise ValueError('stop out of range (%i)' % stop) + * + * if region: # <<<<<<<<<<<<<< + * region = force_str(region) + * if ":" in region: + */ + } + + /* "pysam/libchtslib.pyx":677 + * contig = region + * + * if tid is not None: # <<<<<<<<<<<<<< + * if not self.is_valid_tid(tid): + * raise IndexError('invalid tid') + */ + __pyx_t_1 = (__pyx_v_tid != Py_None); + if (__pyx_t_1) { + + /* "pysam/libchtslib.pyx":678 + * + * if tid is not None: + * if not self.is_valid_tid(tid): # <<<<<<<<<<<<<< + * raise IndexError('invalid tid') + * rtid = tid + */ + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_is_valid_tid); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 678, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_2 = NULL; + __pyx_t_13 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_2)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_2); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + __pyx_t_13 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_v_tid}; + __pyx_t_10 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 678, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_1 < 0))) __PYX_ERR(0, 678, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_3 = (!__pyx_t_1); + if (unlikely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":679 + * if tid is not None: + * if not self.is_valid_tid(tid): + * raise IndexError('invalid tid') # <<<<<<<<<<<<<< + * rtid = tid + * else: + */ + __pyx_t_10 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_tuple__57, NULL); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 679, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_Raise(__pyx_t_10, 0, 0, 0); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __PYX_ERR(0, 679, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":678 + * + * if tid is not None: + * if not self.is_valid_tid(tid): # <<<<<<<<<<<<<< + * raise IndexError('invalid tid') + * rtid = tid + */ + } + + /* "pysam/libchtslib.pyx":680 + * if not self.is_valid_tid(tid): + * raise IndexError('invalid tid') + * rtid = tid # <<<<<<<<<<<<<< + * else: + * if contig == "*": + */ + __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_v_tid); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 680, __pyx_L1_error) + __pyx_v_rtid = __pyx_t_9; + + /* "pysam/libchtslib.pyx":677 + * contig = region + * + * if tid is not None: # <<<<<<<<<<<<<< + * if not self.is_valid_tid(tid): + * raise IndexError('invalid tid') + */ + goto __pyx_L34; + } + + /* "pysam/libchtslib.pyx":682 + * rtid = tid + * else: + * if contig == "*": # <<<<<<<<<<<<<< + * rtid = HTS_IDX_NOCOOR + * elif contig == ".": + */ + /*else*/ { + __pyx_t_3 = (__Pyx_PyUnicode_Equals(__pyx_v_contig, __pyx_kp_u__58, Py_EQ)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 682, __pyx_L1_error) + if (__pyx_t_3) { + + /* "pysam/libchtslib.pyx":683 + * else: + * if contig == "*": + * rtid = HTS_IDX_NOCOOR # <<<<<<<<<<<<<< + * elif contig == ".": + * rtid = HTS_IDX_START + */ + __pyx_v_rtid = HTS_IDX_NOCOOR; + + /* "pysam/libchtslib.pyx":682 + * rtid = tid + * else: + * if contig == "*": # <<<<<<<<<<<<<< + * rtid = HTS_IDX_NOCOOR + * elif contig == ".": + */ + goto __pyx_L36; + } + + /* "pysam/libchtslib.pyx":684 + * if contig == "*": + * rtid = HTS_IDX_NOCOOR + * elif contig == ".": # <<<<<<<<<<<<<< + * rtid = HTS_IDX_START + * else: + */ + __pyx_t_3 = (__Pyx_PyUnicode_Equals(__pyx_v_contig, __pyx_kp_u__59, Py_EQ)); if (unlikely((__pyx_t_3 < 0))) __PYX_ERR(0, 684, __pyx_L1_error) + if (__pyx_t_3) { + + /* "pysam/libchtslib.pyx":685 + * rtid = HTS_IDX_NOCOOR + * elif contig == ".": + * rtid = HTS_IDX_START # <<<<<<<<<<<<<< + * else: + * rtid = self.get_tid(contig) + */ + __pyx_v_rtid = HTS_IDX_START; + + /* "pysam/libchtslib.pyx":684 + * if contig == "*": + * rtid = HTS_IDX_NOCOOR + * elif contig == ".": # <<<<<<<<<<<<<< + * rtid = HTS_IDX_START + * else: + */ + goto __pyx_L36; + } + + /* "pysam/libchtslib.pyx":687 + * rtid = HTS_IDX_START + * else: + * rtid = self.get_tid(contig) # <<<<<<<<<<<<<< + * if rtid < 0: + * raise ValueError('invalid contig `%s`' % contig) + */ + /*else*/ { + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_get_tid); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 687, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_2 = NULL; + __pyx_t_13 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_2)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_2); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + __pyx_t_13 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_2, __pyx_v_contig}; + __pyx_t_10 = __Pyx_PyObject_FastCall(__pyx_t_4, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 687, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } + __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 687, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_v_rtid = __pyx_t_9; + + /* "pysam/libchtslib.pyx":688 + * else: + * rtid = self.get_tid(contig) + * if rtid < 0: # <<<<<<<<<<<<<< + * raise ValueError('invalid contig `%s`' % contig) + * + */ + __pyx_t_3 = (__pyx_v_rtid < 0); + if (unlikely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":689 + * rtid = self.get_tid(contig) + * if rtid < 0: + * raise ValueError('invalid contig `%s`' % contig) # <<<<<<<<<<<<<< + * + * if rstart > rstop: + */ + __pyx_t_10 = __Pyx_PyUnicode_FormatSafe(__pyx_kp_u_invalid_contig_s, __pyx_v_contig); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_10); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __PYX_ERR(0, 689, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":688 + * else: + * rtid = self.get_tid(contig) + * if rtid < 0: # <<<<<<<<<<<<<< + * raise ValueError('invalid contig `%s`' % contig) + * + */ + } + } + __pyx_L36:; + } + __pyx_L34:; + + /* "pysam/libchtslib.pyx":691 + * raise ValueError('invalid contig `%s`' % contig) + * + * if rstart > rstop: # <<<<<<<<<<<<<< + * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) + * if not 0 <= rstart < MAX_POS: + */ + __pyx_t_3 = (__pyx_v_rstart > __pyx_v_rstop); + if (unlikely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":692 + * + * if rstart > rstop: + * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) # <<<<<<<<<<<<<< + * if not 0 <= rstart < MAX_POS: + * raise ValueError('start out of range (%i)' % rstart) + */ + __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_rstart); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_10 = __Pyx_PyInt_From_int32_t(__pyx_v_rstop); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_GIVEREF(__pyx_t_4); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4)) __PYX_ERR(0, 692, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_10); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_10)) __PYX_ERR(0, 692, __pyx_L1_error); + __pyx_t_4 = 0; + __pyx_t_10 = 0; + __pyx_t_10 = PyUnicode_Format(__pyx_kp_u_invalid_coordinates_start_i_stop, __pyx_t_2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 692, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":691 + * raise ValueError('invalid contig `%s`' % contig) + * + * if rstart > rstop: # <<<<<<<<<<<<<< + * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) + * if not 0 <= rstart < MAX_POS: + */ + } + + /* "pysam/libchtslib.pyx":693 + * if rstart > rstop: + * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) + * if not 0 <= rstart < MAX_POS: # <<<<<<<<<<<<<< + * raise ValueError('start out of range (%i)' % rstart) + * if not 0 <= rstop <= MAX_POS: + */ + __pyx_t_3 = (0 <= __pyx_v_rstart); + if (__pyx_t_3) { + __pyx_t_3 = (__pyx_v_rstart < __pyx_v_5pysam_10libchtslib_MAX_POS); + } + __pyx_t_1 = (!__pyx_t_3); + if (unlikely(__pyx_t_1)) { + + /* "pysam/libchtslib.pyx":694 + * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) + * if not 0 <= rstart < MAX_POS: + * raise ValueError('start out of range (%i)' % rstart) # <<<<<<<<<<<<<< + * if not 0 <= rstop <= MAX_POS: + * raise ValueError('stop out of range (%i)' % rstop) + */ + __pyx_t_2 = __Pyx_PyInt_From_int32_t(__pyx_v_rstart); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 694, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = PyUnicode_Format(__pyx_kp_u_start_out_of_range_i, __pyx_t_2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 694, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 694, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 694, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":693 + * if rstart > rstop: + * raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop)) + * if not 0 <= rstart < MAX_POS: # <<<<<<<<<<<<<< + * raise ValueError('start out of range (%i)' % rstart) + * if not 0 <= rstop <= MAX_POS: + */ + } + + /* "pysam/libchtslib.pyx":695 + * if not 0 <= rstart < MAX_POS: + * raise ValueError('start out of range (%i)' % rstart) + * if not 0 <= rstop <= MAX_POS: # <<<<<<<<<<<<<< + * raise ValueError('stop out of range (%i)' % rstop) + * + */ + __pyx_t_1 = (0 <= __pyx_v_rstop); + if (__pyx_t_1) { + __pyx_t_1 = (__pyx_v_rstop <= __pyx_v_5pysam_10libchtslib_MAX_POS); + } + __pyx_t_3 = (!__pyx_t_1); + if (unlikely(__pyx_t_3)) { + + /* "pysam/libchtslib.pyx":696 + * raise ValueError('start out of range (%i)' % rstart) + * if not 0 <= rstop <= MAX_POS: + * raise ValueError('stop out of range (%i)' % rstop) # <<<<<<<<<<<<<< + * + * return 1, rtid, rstart, rstop + */ + __pyx_t_2 = __Pyx_PyInt_From_int32_t(__pyx_v_rstop); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 696, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = PyUnicode_Format(__pyx_kp_u_stop_out_of_range_i, __pyx_t_2); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 696, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 696, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 696, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":695 + * if not 0 <= rstart < MAX_POS: + * raise ValueError('start out of range (%i)' % rstart) + * if not 0 <= rstop <= MAX_POS: # <<<<<<<<<<<<<< + * raise ValueError('stop out of range (%i)' % rstop) + * + */ + } + + /* "pysam/libchtslib.pyx":698 + * raise ValueError('stop out of range (%i)' % rstop) + * + * return 1, rtid, rstart, rstop # <<<<<<<<<<<<<< + * + * def is_valid_tid(self, tid): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_rtid); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = __Pyx_PyInt_From_int32_t(__pyx_v_rstart); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_rstop); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_11 = PyTuple_New(4); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_11); + __Pyx_INCREF(__pyx_int_1); + __Pyx_GIVEREF(__pyx_int_1); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_int_1)) __PYX_ERR(0, 698, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_2); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_t_2)) __PYX_ERR(0, 698, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_10); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 2, __pyx_t_10)) __PYX_ERR(0, 698, __pyx_L1_error); + __Pyx_GIVEREF(__pyx_t_4); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_11, 3, __pyx_t_4)) __PYX_ERR(0, 698, __pyx_L1_error); + __pyx_t_2 = 0; + __pyx_t_10 = 0; + __pyx_t_4 = 0; + __pyx_r = __pyx_t_11; + __pyx_t_11 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":595 + * hts_opt_free(opts) + * + * def parse_region(self, contig=None, start=None, stop=None, # <<<<<<<<<<<<<< + * region=None, tid=None, + * reference=None, end=None): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_10); + __Pyx_XDECREF(__pyx_t_11); + __Pyx_XDECREF(__pyx_t_12); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.parse_region", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_coord); + __Pyx_XDECREF(__pyx_v_parts); + __Pyx_XDECREF(__pyx_v_contig); + __Pyx_XDECREF(__pyx_v_stop); + __Pyx_XDECREF(__pyx_v_region); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":700 + * return 1, rtid, rstart, rstop + * + * def is_valid_tid(self, tid): # <<<<<<<<<<<<<< + * """ + * return True if the numerical :term:`tid` is valid; False otherwise. + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_25is_valid_tid(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_24is_valid_tid, "HTSFile.is_valid_tid(self, tid)\n\n return True if the numerical :term:`tid` is valid; False otherwise.\n\n returns -1 if contig is not known.\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_25is_valid_tid = {"is_valid_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_25is_valid_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_24is_valid_tid}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_25is_valid_tid(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v_tid = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("is_valid_tid (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_tid,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_tid)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 700, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "is_valid_tid") < 0)) __PYX_ERR(0, 700, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_tid = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("is_valid_tid", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 700, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_valid_tid", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_24is_valid_tid(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_tid); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_24is_valid_tid(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_tid) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__60) + __Pyx_RefNannySetupContext("is_valid_tid", 1); + __Pyx_TraceCall("is_valid_tid", __pyx_f[0], 700, 0, __PYX_ERR(0, 700, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":706 + * returns -1 if contig is not known. + * """ + * raise NotImplementedError() # <<<<<<<<<<<<<< + * + * def is_valid_reference_name(self, contig): + */ + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_builtin_NotImplementedError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 706, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 706, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":700 + * return 1, rtid, rstart, rstop + * + * def is_valid_tid(self, tid): # <<<<<<<<<<<<<< + * """ + * return True if the numerical :term:`tid` is valid; False otherwise. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_valid_tid", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":708 + * raise NotImplementedError() + * + * def is_valid_reference_name(self, contig): # <<<<<<<<<<<<<< + * """ + * return True if the contig name :term:`contig` is valid; False otherwise. + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_27is_valid_reference_name(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_26is_valid_reference_name, "HTSFile.is_valid_reference_name(self, contig)\n\n return True if the contig name :term:`contig` is valid; False otherwise.\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_27is_valid_reference_name = {"is_valid_reference_name", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_27is_valid_reference_name, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_26is_valid_reference_name}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_27is_valid_reference_name(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_contig = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("is_valid_reference_name (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_contig,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_contig)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 708, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "is_valid_reference_name") < 0)) __PYX_ERR(0, 708, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_contig = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("is_valid_reference_name", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 708, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_valid_reference_name", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_26is_valid_reference_name(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_contig); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_26is_valid_reference_name(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, PyObject *__pyx_v_contig) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + unsigned int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__61) + __Pyx_RefNannySetupContext("is_valid_reference_name", 1); + __Pyx_TraceCall("is_valid_reference_name", __pyx_f[0], 708, 0, __PYX_ERR(0, 708, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":712 + * return True if the contig name :term:`contig` is valid; False otherwise. + * """ + * return self.get_tid(contig) != -1 # <<<<<<<<<<<<<< + * + * def get_tid(self, contig): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_get_tid); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 712, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + __pyx_t_4 = 0; + #if CYTHON_UNPACK_METHODS + if (likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + __pyx_t_4 = 1; + } + } + #endif + { + PyObject *__pyx_callargs[2] = {__pyx_t_3, __pyx_v_contig}; + __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_2, __pyx_callargs+1-__pyx_t_4, 1+__pyx_t_4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 712, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __pyx_t_2 = __Pyx_PyInt_NeObjC(__pyx_t_1, __pyx_int_neg_1, -1L, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 712, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pysam/libchtslib.pyx":708 + * raise NotImplementedError() + * + * def is_valid_reference_name(self, contig): # <<<<<<<<<<<<<< + * """ + * return True if the contig name :term:`contig` is valid; False otherwise. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_valid_reference_name", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":714 + * return self.get_tid(contig) != -1 + * + * def get_tid(self, contig): # <<<<<<<<<<<<<< + * """ + * return the numerical :term:`tid` corresponding to + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_29get_tid(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_28get_tid, "HTSFile.get_tid(self, contig)\n\n return the numerical :term:`tid` corresponding to\n :term:`contig`\n\n returns -1 if contig is not known.\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_29get_tid = {"get_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_29get_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_28get_tid}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_29get_tid(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v_contig = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("get_tid (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_contig,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_contig)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 714, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "get_tid") < 0)) __PYX_ERR(0, 714, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_contig = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("get_tid", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 714, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.get_tid", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_28get_tid(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_contig); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_28get_tid(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_contig) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__62) + __Pyx_RefNannySetupContext("get_tid", 1); + __Pyx_TraceCall("get_tid", __pyx_f[0], 714, 0, __PYX_ERR(0, 714, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":721 + * returns -1 if contig is not known. + * """ + * raise NotImplementedError() # <<<<<<<<<<<<<< + * + * def get_reference_name(self, tid): + */ + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_builtin_NotImplementedError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 721, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 721, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":714 + * return self.get_tid(contig) != -1 + * + * def get_tid(self, contig): # <<<<<<<<<<<<<< + * """ + * return the numerical :term:`tid` corresponding to + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.get_tid", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pyx":723 + * raise NotImplementedError() + * + * def get_reference_name(self, tid): # <<<<<<<<<<<<<< + * """ + * return :term:`contig` name corresponding to numerical :term:`tid` + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_31get_reference_name(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_30get_reference_name, "HTSFile.get_reference_name(self, tid)\n\n return :term:`contig` name corresponding to numerical :term:`tid`\n "); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_31get_reference_name = {"get_reference_name", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_31get_reference_name, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_30get_reference_name}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_31get_reference_name(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v_tid = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("get_reference_name (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_tid,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_tid)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 723, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "get_reference_name") < 0)) __PYX_ERR(0, 723, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v_tid = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("get_reference_name", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 723, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.get_reference_name", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_30get_reference_name(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v_tid); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_30get_reference_name(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_tid) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__63) + __Pyx_RefNannySetupContext("get_reference_name", 1); + __Pyx_TraceCall("get_reference_name", __pyx_f[0], 723, 0, __PYX_ERR(0, 723, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":727 + * return :term:`contig` name corresponding to numerical :term:`tid` + * """ + * raise NotImplementedError() # <<<<<<<<<<<<<< + */ + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_builtin_NotImplementedError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 727, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 727, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":723 + * raise NotImplementedError() + * + * def get_reference_name(self, tid): # <<<<<<<<<<<<<< + * """ + * return :term:`contig` name corresponding to numerical :term:`tid` + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.get_reference_name", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2710 + * cdef int64_t start_offset # BGZF offset of first record + * + * cdef readonly object filename # filename as supplied by user # <<<<<<<<<<<<<< + * cdef readonly object mode # file opening mode + * cdef readonly object threads # number of threads to use + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_8filename_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_8filename___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_8filename___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2710, 0, __PYX_ERR(4, 2710, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->filename); + __pyx_r = __pyx_v_self->filename; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2711 + * + * cdef readonly object filename # filename as supplied by user + * cdef readonly object mode # file opening mode # <<<<<<<<<<<<<< + * cdef readonly object threads # number of threads to use + * cdef readonly object index_filename # filename of index, if supplied by user + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_4mode_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_4mode_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_4mode___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_4mode___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2711, 0, __PYX_ERR(4, 2711, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->mode); + __pyx_r = __pyx_v_self->mode; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.mode.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2712 + * cdef readonly object filename # filename as supplied by user + * cdef readonly object mode # file opening mode + * cdef readonly object threads # number of threads to use # <<<<<<<<<<<<<< + * cdef readonly object index_filename # filename of index, if supplied by user + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7threads_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_7threads_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_7threads___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_7threads___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2712, 0, __PYX_ERR(4, 2712, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->threads); + __pyx_r = __pyx_v_self->threads; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.threads.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2713 + * cdef readonly object mode # file opening mode + * cdef readonly object threads # number of threads to use + * cdef readonly object index_filename # filename of index, if supplied by user # <<<<<<<<<<<<<< + * + * cdef readonly bint is_stream # Is htsfile a non-seekable stream + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_14index_filename_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_14index_filename_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_14index_filename___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_14index_filename___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2713, 0, __PYX_ERR(4, 2713, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->index_filename); + __pyx_r = __pyx_v_self->index_filename; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.index_filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2715 + * cdef readonly object index_filename # filename of index, if supplied by user + * + * cdef readonly bint is_stream # Is htsfile a non-seekable stream # <<<<<<<<<<<<<< + * cdef readonly bint is_remote # Is htsfile a remote stream + * cdef readonly bint duplicate_filehandle # Duplicate filehandle when opening via fh + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9is_stream_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9is_stream_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_9is_stream___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_stream___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2715, 0, __PYX_ERR(4, 2715, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->is_stream); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 2715, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_stream.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2716 + * + * cdef readonly bint is_stream # Is htsfile a non-seekable stream + * cdef readonly bint is_remote # Is htsfile a remote stream # <<<<<<<<<<<<<< + * cdef readonly bint duplicate_filehandle # Duplicate filehandle when opening via fh + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9is_remote_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_9is_remote_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_9is_remote___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_remote___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2716, 0, __PYX_ERR(4, 2716, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->is_remote); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 2716, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.is_remote.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pysam/libchtslib.pxd":2717 + * cdef readonly bint is_stream # Is htsfile a non-seekable stream + * cdef readonly bint is_remote # Is htsfile a remote stream + * cdef readonly bint duplicate_filehandle # Duplicate filehandle when opening via fh # <<<<<<<<<<<<<< + * + * cdef htsFile *_open_htsfile(self) except? NULL + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle_1__get__(PyObject *__pyx_v_self) { + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_kwvalues = __Pyx_KwValues_VARARGS(__pyx_args, __pyx_nargs); + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle___get__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle___get__(struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 1); + __Pyx_TraceCall("__get__", __pyx_f[4], 2717, 0, __PYX_ERR(4, 2717, __pyx_L1_error)); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->duplicate_filehandle); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 2717, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.duplicate_filehandle.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_33__reduce_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_32__reduce_cython__, "HTSFile.__reduce_cython__(self)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_33__reduce_cython__ = {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_33__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_32__reduce_cython__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_33__reduce_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + if (unlikely(__pyx_nargs > 0)) { + __Pyx_RaiseArgtupleInvalid("__reduce_cython__", 1, 0, 0, __pyx_nargs); return NULL;} + if (unlikely(__pyx_kwds) && __Pyx_NumKwargs_FASTCALL(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__reduce_cython__", 0))) return NULL; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_32__reduce_cython__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_32__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__64) + __Pyx_RefNannySetupContext("__reduce_cython__", 1); + __Pyx_TraceCall("__reduce_cython__", __pyx_f[1], 1, 0, __PYX_ERR(1, 1, __pyx_L1_error)); + + /* "(tree fragment)":2 + * def __reduce_cython__(self): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + */ + __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); + __PYX_ERR(1, 2, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_35__setstate_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +PyDoc_STRVAR(__pyx_doc_5pysam_10libchtslib_7HTSFile_34__setstate_cython__, "HTSFile.__setstate_cython__(self, __pyx_state)"); +static PyMethodDef __pyx_mdef_5pysam_10libchtslib_7HTSFile_35__setstate_cython__ = {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_35__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_34__setstate_cython__}; +static PyObject *__pyx_pw_5pysam_10libchtslib_7HTSFile_35__setstate_cython__(PyObject *__pyx_v_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + CYTHON_UNUSED PyObject *__pyx_v___pyx_state = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[1] = {0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_state,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_pyx_state)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 3, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + 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) + } + } else if (unlikely(__pyx_nargs != 1)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + } + __pyx_v___pyx_state = values[0]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, __pyx_nargs); __PYX_ERR(1, 3, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_5pysam_10libchtslib_7HTSFile_34__setstate_cython__(((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)__pyx_v_self), __pyx_v___pyx_state); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_5pysam_10libchtslib_7HTSFile_34__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_10libchtslib_HTSFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = NULL; + __Pyx_TraceDeclarations + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_TraceFrameInit(__pyx_codeobj__65) + __Pyx_RefNannySetupContext("__setstate_cython__", 1); + __Pyx_TraceCall("__setstate_cython__", __pyx_f[1], 3, 0, __PYX_ERR(1, 3, __pyx_L1_error)); + + /* "(tree fragment)":4 + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" # <<<<<<<<<<<<<< + */ + __Pyx_Raise(__pyx_builtin_TypeError, __pyx_kp_s_no_default___reduce___due_to_non, 0, 0); + __PYX_ERR(1, 4, __pyx_L1_error) + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("pysam.libchtslib.HTSFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_TraceReturn(__pyx_r, 0); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} +static struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile __pyx_vtable_5pysam_10libchtslib_HTSFile; + +static PyObject *__pyx_tp_new_5pysam_10libchtslib_HTSFile(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_5pysam_10libchtslib_HTSFile *p; + PyObject *o; + #if CYTHON_COMPILING_IN_LIMITED_API + allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc); + o = alloc_func(t, 0); + #else + if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + #endif + p = ((struct __pyx_obj_5pysam_10libchtslib_HTSFile *)o); + p->__pyx_vtab = __pyx_vtabptr_5pysam_10libchtslib_HTSFile; + p->filename = Py_None; Py_INCREF(Py_None); + p->mode = Py_None; Py_INCREF(Py_None); + p->threads = Py_None; Py_INCREF(Py_None); + p->index_filename = Py_None; Py_INCREF(Py_None); + if (unlikely(__pyx_pw_5pysam_10libchtslib_7HTSFile_1__cinit__(o, a, k) < 0)) goto bad; + return o; + bad: + Py_DECREF(o); o = 0; + return NULL; +} + +static void __pyx_tp_dealloc_5pysam_10libchtslib_HTSFile(PyObject *o) { + struct __pyx_obj_5pysam_10libchtslib_HTSFile *p = (struct __pyx_obj_5pysam_10libchtslib_HTSFile *)o; + #if CYTHON_USE_TP_FINALIZE + 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)) { + if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_10libchtslib_HTSFile) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); + __pyx_pw_5pysam_10libchtslib_7HTSFile_5__dealloc__(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->filename); + Py_CLEAR(p->mode); + Py_CLEAR(p->threads); + Py_CLEAR(p->index_filename); + #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY + (*Py_TYPE(o)->tp_free)(o); + #else + { + freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free); + if (tp_free) tp_free(o); + } + #endif +} + +static int __pyx_tp_traverse_5pysam_10libchtslib_HTSFile(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_5pysam_10libchtslib_HTSFile *p = (struct __pyx_obj_5pysam_10libchtslib_HTSFile *)o; + if (p->filename) { + e = (*v)(p->filename, a); if (e) return e; + } + if (p->mode) { + e = (*v)(p->mode, a); if (e) return e; + } + if (p->threads) { + e = (*v)(p->threads, a); if (e) return e; + } + if (p->index_filename) { + e = (*v)(p->index_filename, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_5pysam_10libchtslib_HTSFile(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_5pysam_10libchtslib_HTSFile *p = (struct __pyx_obj_5pysam_10libchtslib_HTSFile *)o; + tmp = ((PyObject*)p->filename); + p->filename = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->mode); + p->mode = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->threads); + p->threads = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->index_filename); + p->index_filename = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_category(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_8category_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_format(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_6format_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_version(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_7version_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_compression(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_11compression_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_description(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_11description_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_open(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_7is_open_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_closed(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_9is_closed_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_closed(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_6closed_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_write(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_8is_write_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_read(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_7is_read_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_sam(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_6is_sam_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_bam(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_6is_bam_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_cram(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_7is_cram_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_vcf(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_6is_vcf_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_bcf(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_6is_bcf_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_filename(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_8filename_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_mode(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_4mode_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_threads(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_7threads_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_index_filename(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_14index_filename_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_stream(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_9is_stream_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_is_remote(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_9is_remote_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_7HTSFile_duplicate_filehandle(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle_1__get__(o); +} + +static PyMethodDef __pyx_methods_5pysam_10libchtslib_HTSFile[] = { + {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_3close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_2close}, + {"flush", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_7flush, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_6flush}, + {"check_truncation", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_9check_truncation, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_8check_truncation}, + {"__enter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_11__enter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_10__enter__}, + {"__exit__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_13__exit__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_12__exit__}, + {"reset", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_15reset, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_14reset}, + {"seek", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_17seek, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_16seek}, + {"tell", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_19tell, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_18tell}, + {"add_hts_options", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_21add_hts_options, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_20add_hts_options}, + {"parse_region", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_23parse_region, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_22parse_region}, + {"is_valid_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_25is_valid_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_24is_valid_tid}, + {"is_valid_reference_name", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_27is_valid_reference_name, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_26is_valid_reference_name}, + {"get_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_29get_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_28get_tid}, + {"get_reference_name", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_31get_reference_name, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_30get_reference_name}, + {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_33__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_32__reduce_cython__}, + {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_7HTSFile_35__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_7HTSFile_34__setstate_cython__}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_5pysam_10libchtslib_HTSFile[] = { + {(char *)"category", __pyx_getprop_5pysam_10libchtslib_7HTSFile_category, 0, (char *)PyDoc_STR("General file format category. One of UNKNOWN, ALIGNMENTS,\n VARIANTS, INDEX, REGIONS"), 0}, + {(char *)"format", __pyx_getprop_5pysam_10libchtslib_7HTSFile_format, 0, (char *)PyDoc_STR("File format.\n\n One of UNKNOWN, BINARY_FORMAT, TEXT_FORMAT, SAM, BAM,\n BAI, CRAM, CRAI, VCF, BCF, CSI, GZI, TBI, BED.\n "), 0}, + {(char *)"version", __pyx_getprop_5pysam_10libchtslib_7HTSFile_version, 0, (char *)PyDoc_STR("Tuple of file format version numbers (major, minor)"), 0}, + {(char *)"compression", __pyx_getprop_5pysam_10libchtslib_7HTSFile_compression, 0, (char *)PyDoc_STR("File compression.\n\n One of NONE, GZIP, BGZF, CUSTOM."), 0}, + {(char *)"description", __pyx_getprop_5pysam_10libchtslib_7HTSFile_description, 0, (char *)PyDoc_STR("Vaguely human readable description of the file format"), 0}, + {(char *)"is_open", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_open, 0, (char *)PyDoc_STR("return True if HTSFile is open and in a valid state."), 0}, + {(char *)"is_closed", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_closed, 0, (char *)PyDoc_STR("return True if HTSFile is closed."), 0}, + {(char *)"closed", __pyx_getprop_5pysam_10libchtslib_7HTSFile_closed, 0, (char *)PyDoc_STR("return True if HTSFile is closed."), 0}, + {(char *)"is_write", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_write, 0, (char *)PyDoc_STR("return True if HTSFile is open for writing"), 0}, + {(char *)"is_read", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_read, 0, (char *)PyDoc_STR("return True if HTSFile is open for reading"), 0}, + {(char *)"is_sam", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_sam, 0, (char *)PyDoc_STR("return True if HTSFile is reading or writing a SAM alignment file"), 0}, + {(char *)"is_bam", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_bam, 0, (char *)PyDoc_STR("return True if HTSFile is reading or writing a BAM alignment file"), 0}, + {(char *)"is_cram", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_cram, 0, (char *)PyDoc_STR("return True if HTSFile is reading or writing a BAM alignment file"), 0}, + {(char *)"is_vcf", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_vcf, 0, (char *)PyDoc_STR("return True if HTSFile is reading or writing a VCF variant file"), 0}, + {(char *)"is_bcf", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_bcf, 0, (char *)PyDoc_STR("return True if HTSFile is reading or writing a BCF variant file"), 0}, + {(char *)"filename", __pyx_getprop_5pysam_10libchtslib_7HTSFile_filename, 0, (char *)0, 0}, + {(char *)"mode", __pyx_getprop_5pysam_10libchtslib_7HTSFile_mode, 0, (char *)0, 0}, + {(char *)"threads", __pyx_getprop_5pysam_10libchtslib_7HTSFile_threads, 0, (char *)0, 0}, + {(char *)"index_filename", __pyx_getprop_5pysam_10libchtslib_7HTSFile_index_filename, 0, (char *)0, 0}, + {(char *)"is_stream", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_stream, 0, (char *)0, 0}, + {(char *)"is_remote", __pyx_getprop_5pysam_10libchtslib_7HTSFile_is_remote, 0, (char *)0, 0}, + {(char *)"duplicate_filehandle", __pyx_getprop_5pysam_10libchtslib_7HTSFile_duplicate_filehandle, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; +#if CYTHON_USE_TYPE_SPECS +static PyType_Slot __pyx_type_5pysam_10libchtslib_HTSFile_slots[] = { + {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_10libchtslib_HTSFile}, + {Py_tp_doc, (void *)PyDoc_STR("\n Base class for HTS file types\n ")}, + {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_10libchtslib_HTSFile}, + {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_10libchtslib_HTSFile}, + {Py_tp_methods, (void *)__pyx_methods_5pysam_10libchtslib_HTSFile}, + {Py_tp_getset, (void *)__pyx_getsets_5pysam_10libchtslib_HTSFile}, + {Py_tp_new, (void *)__pyx_tp_new_5pysam_10libchtslib_HTSFile}, + {0, 0}, +}; +static PyType_Spec __pyx_type_5pysam_10libchtslib_HTSFile_spec = { + "pysam.libchtslib.HTSFile", + sizeof(struct __pyx_obj_5pysam_10libchtslib_HTSFile), + 0, + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, + __pyx_type_5pysam_10libchtslib_HTSFile_slots, +}; +#else + +static PyTypeObject __pyx_type_5pysam_10libchtslib_HTSFile = { + PyVarObject_HEAD_INIT(0, 0) + "pysam.libchtslib.""HTSFile", /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_10libchtslib_HTSFile), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_5pysam_10libchtslib_HTSFile, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 + 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + PyDoc_STR("\n Base class for HTS file types\n "), /*tp_doc*/ + __pyx_tp_traverse_5pysam_10libchtslib_HTSFile, /*tp_traverse*/ + __pyx_tp_clear_5pysam_10libchtslib_HTSFile, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_5pysam_10libchtslib_HTSFile, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_5pysam_10libchtslib_HTSFile, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + #if !CYTHON_USE_TYPE_SPECS + 0, /*tp_dictoffset*/ + #endif + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_5pysam_10libchtslib_HTSFile, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + #if CYTHON_USE_TP_FINALIZE + 0, /*tp_finalize*/ + #else + NULL, /*tp_finalize*/ + #endif + #endif + #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) + 0, /*tp_vectorcall*/ + #endif + #if __PYX_NEED_TP_PRINT_SLOT == 1 + 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030C0000 + 0, /*tp_watched*/ + #endif + #if PY_VERSION_HEX >= 0x030d00A4 + 0, /*tp_versions_used*/ + #endif + #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, /*tp_pypy_flags*/ + #endif +}; +#endif +static struct __pyx_vtabstruct_5pysam_10libchtslib_HFile __pyx_vtable_5pysam_10libchtslib_HFile; + +static PyObject *__pyx_tp_new_5pysam_10libchtslib_HFile(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_5pysam_10libchtslib_HFile *p; + PyObject *o; + #if CYTHON_COMPILING_IN_LIMITED_API + allocfunc alloc_func = (allocfunc)PyType_GetSlot(t, Py_tp_alloc); + o = alloc_func(t, 0); + #else + if (likely(!__Pyx_PyType_HasFeature(t, Py_TPFLAGS_IS_ABSTRACT))) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + #endif + p = ((struct __pyx_obj_5pysam_10libchtslib_HFile *)o); + p->__pyx_vtab = __pyx_vtabptr_5pysam_10libchtslib_HFile; + p->name = Py_None; Py_INCREF(Py_None); + p->mode = Py_None; Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_5pysam_10libchtslib_HFile(PyObject *o) { + struct __pyx_obj_5pysam_10libchtslib_HFile *p = (struct __pyx_obj_5pysam_10libchtslib_HFile *)o; + #if CYTHON_USE_TP_FINALIZE + 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)) { + if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_10libchtslib_HFile) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); + __pyx_pw_5pysam_10libchtslib_5HFile_3__dealloc__(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->name); + Py_CLEAR(p->mode); + #if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY + (*Py_TYPE(o)->tp_free)(o); + #else + { + freefunc tp_free = (freefunc)PyType_GetSlot(Py_TYPE(o), Py_tp_free); + if (tp_free) tp_free(o); + } + #endif +} + +static int __pyx_tp_traverse_5pysam_10libchtslib_HFile(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_5pysam_10libchtslib_HFile *p = (struct __pyx_obj_5pysam_10libchtslib_HFile *)o; + if (p->name) { + e = (*v)(p->name, a); if (e) return e; + } + if (p->mode) { + e = (*v)(p->mode, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_5pysam_10libchtslib_HFile(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_5pysam_10libchtslib_HFile *p = (struct __pyx_obj_5pysam_10libchtslib_HFile *)o; + tmp = ((PyObject*)p->name); + p->name = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->mode); + p->mode = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_5HFile_closed(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_5HFile_6closed_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_5HFile_name(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_5HFile_4name_1__get__(o); +} + +static PyObject *__pyx_getprop_5pysam_10libchtslib_5HFile_mode(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_10libchtslib_5HFile_4mode_1__get__(o); +} + +static PyObject *__pyx_specialmethod___pyx_pw_5pysam_10libchtslib_5HFile_15__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { + PyObject *res = __pyx_pw_5pysam_10libchtslib_5HFile_15__next__(self); + if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } + return res; +} + +static PyMethodDef __pyx_methods_5pysam_10libchtslib_HFile[] = { + {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_5close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_4close}, + {"fileno", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_7fileno, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_6fileno}, + {"__enter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_9__enter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_8__enter__}, + {"__exit__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_11__exit__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_10__exit__}, + {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_10libchtslib_5HFile_15__next__, METH_NOARGS|METH_COEXIST, 0}, + {"flush", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_17flush, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_16flush}, + {"isatty", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_19isatty, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_18isatty}, + {"readable", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_21readable, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_20readable}, + {"read", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_23read, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_22read}, + {"readall", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_25readall, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_24readall}, + {"readinto", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_27readinto, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_26readinto}, + {"readline", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_29readline, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_28readline}, + {"readlines", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_31readlines, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_30readlines}, + {"seek", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_33seek, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_32seek}, + {"tell", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_35tell, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_34tell}, + {"seekable", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_37seekable, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_36seekable}, + {"truncate", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_39truncate, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_38truncate}, + {"writable", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_41writable, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_40writable}, + {"write", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_43write, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_42write}, + {"writelines", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_45writelines, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_44writelines}, + {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_47__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_46__reduce_cython__}, + {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_10libchtslib_5HFile_49__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_10libchtslib_5HFile_48__setstate_cython__}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_5pysam_10libchtslib_HFile[] = { + {(char *)"closed", __pyx_getprop_5pysam_10libchtslib_5HFile_closed, 0, (char *)0, 0}, + {(char *)"name", __pyx_getprop_5pysam_10libchtslib_5HFile_name, 0, (char *)0, 0}, + {(char *)"mode", __pyx_getprop_5pysam_10libchtslib_5HFile_mode, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; +#if CYTHON_USE_TYPE_SPECS +static PyType_Slot __pyx_type_5pysam_10libchtslib_HFile_slots[] = { + {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_10libchtslib_HFile}, + {Py_tp_doc, (void *)PyDoc_STR("HFile(name, mode=u'r', closefd=True)")}, + {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_10libchtslib_HFile}, + {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_10libchtslib_HFile}, + {Py_tp_iter, (void *)__pyx_pw_5pysam_10libchtslib_5HFile_13__iter__}, + {Py_tp_iternext, (void *)__pyx_pw_5pysam_10libchtslib_5HFile_15__next__}, + {Py_tp_methods, (void *)__pyx_methods_5pysam_10libchtslib_HFile}, + {Py_tp_getset, (void *)__pyx_getsets_5pysam_10libchtslib_HFile}, + {Py_tp_init, (void *)__pyx_pw_5pysam_10libchtslib_5HFile_1__init__}, + {Py_tp_new, (void *)__pyx_tp_new_5pysam_10libchtslib_HFile}, + {0, 0}, +}; +static PyType_Spec __pyx_type_5pysam_10libchtslib_HFile_spec = { + "pysam.libchtslib.HFile", + sizeof(struct __pyx_obj_5pysam_10libchtslib_HFile), + 0, + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, + __pyx_type_5pysam_10libchtslib_HFile_slots, +}; +#else + +static PyTypeObject __pyx_type_5pysam_10libchtslib_HFile = { + PyVarObject_HEAD_INIT(0, 0) + "pysam.libchtslib.""HFile", /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_10libchtslib_HFile), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_5pysam_10libchtslib_HFile, /*tp_dealloc*/ + #if PY_VERSION_HEX < 0x030800b4 + 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 + 0, /*tp_vectorcall_offset*/ + #endif + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + PyDoc_STR("HFile(name, mode=u'r', closefd=True)"), /*tp_doc*/ + __pyx_tp_traverse_5pysam_10libchtslib_HFile, /*tp_traverse*/ + __pyx_tp_clear_5pysam_10libchtslib_HFile, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pw_5pysam_10libchtslib_5HFile_13__iter__, /*tp_iter*/ + __pyx_pw_5pysam_10libchtslib_5HFile_15__next__, /*tp_iternext*/ + __pyx_methods_5pysam_10libchtslib_HFile, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_5pysam_10libchtslib_HFile, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + #if !CYTHON_USE_TYPE_SPECS + 0, /*tp_dictoffset*/ + #endif + __pyx_pw_5pysam_10libchtslib_5HFile_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_5pysam_10libchtslib_HFile, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + #if CYTHON_USE_TP_FINALIZE + 0, /*tp_finalize*/ + #else + NULL, /*tp_finalize*/ + #endif + #endif + #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) + 0, /*tp_vectorcall*/ + #endif + #if __PYX_NEED_TP_PRINT_SLOT == 1 + 0, /*tp_print*/ + #endif + #if PY_VERSION_HEX >= 0x030C0000 + 0, /*tp_watched*/ + #endif + #if PY_VERSION_HEX >= 0x030d00A4 + 0, /*tp_versions_used*/ + #endif + #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, /*tp_pypy_flags*/ + #endif +}; +#endif + +static PyMethodDef __pyx_methods[] = { + {0, 0, 0, 0} +}; +#ifndef CYTHON_SMALL_CODE +#if defined(__clang__) + #define CYTHON_SMALL_CODE +#elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)) + #define CYTHON_SMALL_CODE __attribute__((cold)) +#else + #define CYTHON_SMALL_CODE +#endif +#endif +/* #### Code section: pystring_table ### */ + +static int __Pyx_CreateStringTabAndInitStrings(void) { + __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_n_u_ALIGNMENTS, __pyx_k_ALIGNMENTS, sizeof(__pyx_k_ALIGNMENTS), 0, 1, 0, 1}, + {&__pyx_kp_u_An_error_occurred_while_applying, __pyx_k_An_error_occurred_while_applying, sizeof(__pyx_k_An_error_occurred_while_applying), 0, 1, 0, 0}, + {&__pyx_n_s_AttributeError, __pyx_k_AttributeError, sizeof(__pyx_k_AttributeError), 0, 0, 1, 1}, + {&__pyx_n_u_BAI, __pyx_k_BAI, sizeof(__pyx_k_BAI), 0, 1, 0, 1}, + {&__pyx_n_u_BAM, __pyx_k_BAM, sizeof(__pyx_k_BAM), 0, 1, 0, 1}, + {&__pyx_n_u_BCF, __pyx_k_BCF, sizeof(__pyx_k_BCF), 0, 1, 0, 1}, + {&__pyx_n_u_BED, __pyx_k_BED, sizeof(__pyx_k_BED), 0, 1, 0, 1}, + {&__pyx_n_u_BGZF, __pyx_k_BGZF, sizeof(__pyx_k_BGZF), 0, 1, 0, 1}, + {&__pyx_n_u_BINARY_FORMAT, __pyx_k_BINARY_FORMAT, sizeof(__pyx_k_BINARY_FORMAT), 0, 1, 0, 1}, + {&__pyx_n_s_CFalse, __pyx_k_CFalse, sizeof(__pyx_k_CFalse), 0, 0, 1, 1}, + {&__pyx_n_u_CRAI, __pyx_k_CRAI, sizeof(__pyx_k_CRAI), 0, 1, 0, 1}, + {&__pyx_n_u_CRAM, __pyx_k_CRAM, sizeof(__pyx_k_CRAM), 0, 1, 0, 1}, + {&__pyx_n_u_CSI, __pyx_k_CSI, sizeof(__pyx_k_CSI), 0, 1, 0, 1}, + {&__pyx_n_s_CTrue, __pyx_k_CTrue, sizeof(__pyx_k_CTrue), 0, 0, 1, 1}, + {&__pyx_n_u_CUSTOM, __pyx_k_CUSTOM, sizeof(__pyx_k_CUSTOM), 0, 1, 0, 1}, + {&__pyx_n_s_CallableValue, __pyx_k_CallableValue, sizeof(__pyx_k_CallableValue), 0, 0, 1, 1}, + {&__pyx_n_s_CallableValue___bool, __pyx_k_CallableValue___bool, sizeof(__pyx_k_CallableValue___bool), 0, 0, 1, 1}, + {&__pyx_n_s_CallableValue___call, __pyx_k_CallableValue___call, sizeof(__pyx_k_CallableValue___call), 0, 0, 1, 1}, + {&__pyx_n_s_CallableValue___eq, __pyx_k_CallableValue___eq, sizeof(__pyx_k_CallableValue___eq), 0, 0, 1, 1}, + {&__pyx_n_s_CallableValue___init, __pyx_k_CallableValue___init, sizeof(__pyx_k_CallableValue___init), 0, 0, 1, 1}, + {&__pyx_n_s_CallableValue___ne, __pyx_k_CallableValue___ne, sizeof(__pyx_k_CallableValue___ne), 0, 0, 1, 1}, + {&__pyx_n_s_CallableValue___nonzero, __pyx_k_CallableValue___nonzero, sizeof(__pyx_k_CallableValue___nonzero), 0, 0, 1, 1}, + {&__pyx_kp_u_Cannot_create_hfile, __pyx_k_Cannot_create_hfile, sizeof(__pyx_k_Cannot_create_hfile), 0, 1, 0, 0}, + {&__pyx_kp_u_Flushing, __pyx_k_Flushing, sizeof(__pyx_k_Flushing), 0, 1, 0, 0}, + {&__pyx_n_u_GZI, __pyx_k_GZI, sizeof(__pyx_k_GZI), 0, 1, 0, 1}, + {&__pyx_n_u_GZIP, __pyx_k_GZIP, sizeof(__pyx_k_GZIP), 0, 1, 0, 1}, + {&__pyx_n_s_HFile, __pyx_k_HFile, sizeof(__pyx_k_HFile), 0, 0, 1, 1}, + {&__pyx_n_u_HFile, __pyx_k_HFile, sizeof(__pyx_k_HFile), 0, 1, 0, 1}, + {&__pyx_n_s_HFile___enter, __pyx_k_HFile___enter, sizeof(__pyx_k_HFile___enter), 0, 0, 1, 1}, + {&__pyx_n_s_HFile___exit, __pyx_k_HFile___exit, sizeof(__pyx_k_HFile___exit), 0, 0, 1, 1}, + {&__pyx_n_s_HFile___reduce_cython, __pyx_k_HFile___reduce_cython, sizeof(__pyx_k_HFile___reduce_cython), 0, 0, 1, 1}, + {&__pyx_n_s_HFile___setstate_cython, __pyx_k_HFile___setstate_cython, sizeof(__pyx_k_HFile___setstate_cython), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_close, __pyx_k_HFile_close, sizeof(__pyx_k_HFile_close), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_fileno, __pyx_k_HFile_fileno, sizeof(__pyx_k_HFile_fileno), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_flush, __pyx_k_HFile_flush, sizeof(__pyx_k_HFile_flush), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_isatty, __pyx_k_HFile_isatty, sizeof(__pyx_k_HFile_isatty), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_read, __pyx_k_HFile_read, sizeof(__pyx_k_HFile_read), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_readable, __pyx_k_HFile_readable, sizeof(__pyx_k_HFile_readable), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_readall, __pyx_k_HFile_readall, sizeof(__pyx_k_HFile_readall), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_readinto, __pyx_k_HFile_readinto, sizeof(__pyx_k_HFile_readinto), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_readline, __pyx_k_HFile_readline, sizeof(__pyx_k_HFile_readline), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_readlines, __pyx_k_HFile_readlines, sizeof(__pyx_k_HFile_readlines), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_seek, __pyx_k_HFile_seek, sizeof(__pyx_k_HFile_seek), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_seekable, __pyx_k_HFile_seekable, sizeof(__pyx_k_HFile_seekable), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_tell, __pyx_k_HFile_tell, sizeof(__pyx_k_HFile_tell), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_truncate, __pyx_k_HFile_truncate, sizeof(__pyx_k_HFile_truncate), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_writable, __pyx_k_HFile_writable, sizeof(__pyx_k_HFile_writable), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_write, __pyx_k_HFile_write, sizeof(__pyx_k_HFile_write), 0, 0, 1, 1}, + {&__pyx_n_s_HFile_writelines, __pyx_k_HFile_writelines, sizeof(__pyx_k_HFile_writelines), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile, __pyx_k_HTSFile, sizeof(__pyx_k_HTSFile), 0, 0, 1, 1}, + {&__pyx_n_u_HTSFile, __pyx_k_HTSFile, sizeof(__pyx_k_HTSFile), 0, 1, 0, 1}, + {&__pyx_n_s_HTSFile___enter, __pyx_k_HTSFile___enter, sizeof(__pyx_k_HTSFile___enter), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile___exit, __pyx_k_HTSFile___exit, sizeof(__pyx_k_HTSFile___exit), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile___reduce_cython, __pyx_k_HTSFile___reduce_cython, sizeof(__pyx_k_HTSFile___reduce_cython), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile___setstate_cython, __pyx_k_HTSFile___setstate_cython, sizeof(__pyx_k_HTSFile___setstate_cython), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_add_hts_options, __pyx_k_HTSFile_add_hts_options, sizeof(__pyx_k_HTSFile_add_hts_options), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_check_truncation, __pyx_k_HTSFile_check_truncation, sizeof(__pyx_k_HTSFile_check_truncation), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_close, __pyx_k_HTSFile_close, sizeof(__pyx_k_HTSFile_close), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_flush, __pyx_k_HTSFile_flush, sizeof(__pyx_k_HTSFile_flush), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_get_reference_name, __pyx_k_HTSFile_get_reference_name, sizeof(__pyx_k_HTSFile_get_reference_name), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_get_tid, __pyx_k_HTSFile_get_tid, sizeof(__pyx_k_HTSFile_get_tid), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_is_valid_reference_name, __pyx_k_HTSFile_is_valid_reference_name, sizeof(__pyx_k_HTSFile_is_valid_reference_name), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_is_valid_tid, __pyx_k_HTSFile_is_valid_tid, sizeof(__pyx_k_HTSFile_is_valid_tid), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_parse_region, __pyx_k_HTSFile_parse_region, sizeof(__pyx_k_HTSFile_parse_region), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_reset, __pyx_k_HTSFile_reset, sizeof(__pyx_k_HTSFile_reset), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_seek, __pyx_k_HTSFile_seek, sizeof(__pyx_k_HTSFile_seek), 0, 0, 1, 1}, + {&__pyx_n_s_HTSFile_tell, __pyx_k_HTSFile_tell, sizeof(__pyx_k_HTSFile_tell), 0, 0, 1, 1}, + {&__pyx_n_u_INDEX, __pyx_k_INDEX, sizeof(__pyx_k_INDEX), 0, 1, 0, 1}, + {&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1}, + {&__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}, + {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, + {&__pyx_kp_u_Invalid_format_option_specified, __pyx_k_Invalid_format_option_specified, sizeof(__pyx_k_Invalid_format_option_specified), 0, 1, 0, 0}, + {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1}, + {&__pyx_n_u_NONE, __pyx_k_NONE, sizeof(__pyx_k_NONE), 0, 1, 0, 1}, + {&__pyx_n_s_NotImplementedError, __pyx_k_NotImplementedError, sizeof(__pyx_k_NotImplementedError), 0, 0, 1, 1}, + {&__pyx_n_s_OSError, __pyx_k_OSError, sizeof(__pyx_k_OSError), 0, 0, 1, 1}, + {&__pyx_n_s_OverflowError, __pyx_k_OverflowError, sizeof(__pyx_k_OverflowError), 0, 0, 1, 1}, + {&__pyx_n_u_REGIONS, __pyx_k_REGIONS, sizeof(__pyx_k_REGIONS), 0, 1, 0, 1}, + {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, + {&__pyx_n_u_SAM, __pyx_k_SAM, sizeof(__pyx_k_SAM), 0, 1, 0, 1}, + {&__pyx_n_s_SEEK_SET, __pyx_k_SEEK_SET, sizeof(__pyx_k_SEEK_SET), 0, 0, 1, 1}, + {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1}, + {&__pyx_n_u_TBI, __pyx_k_TBI, sizeof(__pyx_k_TBI), 0, 1, 0, 1}, + {&__pyx_n_u_TEXT_FORMAT, __pyx_k_TEXT_FORMAT, sizeof(__pyx_k_TEXT_FORMAT), 0, 1, 0, 1}, + {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, + {&__pyx_n_u_UNKNOWN, __pyx_k_UNKNOWN, sizeof(__pyx_k_UNKNOWN), 0, 1, 0, 1}, + {&__pyx_n_u_VARIANTS, __pyx_k_VARIANTS, sizeof(__pyx_k_VARIANTS), 0, 1, 0, 1}, + {&__pyx_n_u_VCF, __pyx_k_VCF, sizeof(__pyx_k_VCF), 0, 1, 0, 1}, + {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, + {&__pyx_kp_b__13, __pyx_k__13, sizeof(__pyx_k__13), 0, 0, 0, 0}, + {&__pyx_kp_u__55, __pyx_k__55, sizeof(__pyx_k__55), 0, 1, 0, 0}, + {&__pyx_kp_u__56, __pyx_k__56, sizeof(__pyx_k__56), 0, 1, 0, 0}, + {&__pyx_n_s__58, __pyx_k__58, sizeof(__pyx_k__58), 0, 0, 1, 1}, + {&__pyx_kp_u__58, __pyx_k__58, sizeof(__pyx_k__58), 0, 1, 0, 0}, + {&__pyx_kp_u__59, __pyx_k__59, sizeof(__pyx_k__59), 0, 1, 0, 0}, + {&__pyx_n_s__97, __pyx_k__97, sizeof(__pyx_k__97), 0, 0, 1, 1}, + {&__pyx_n_s_add_hts_options, __pyx_k_add_hts_options, sizeof(__pyx_k_add_hts_options), 0, 0, 1, 1}, + {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1}, + {&__pyx_n_s_asyncio_coroutines, __pyx_k_asyncio_coroutines, sizeof(__pyx_k_asyncio_coroutines), 0, 0, 1, 1}, + {&__pyx_n_b_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 0, 1}, + {&__pyx_n_s_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 1, 1}, + {&__pyx_n_s_bgzfp, __pyx_k_bgzfp, sizeof(__pyx_k_bgzfp), 0, 0, 1, 1}, + {&__pyx_n_s_bool, __pyx_k_bool, sizeof(__pyx_k_bool), 0, 0, 1, 1}, + {&__pyx_n_s_buf, __pyx_k_buf, sizeof(__pyx_k_buf), 0, 0, 1, 1}, + {&__pyx_n_s_bytes_read, __pyx_k_bytes_read, sizeof(__pyx_k_bytes_read), 0, 0, 1, 1}, + {&__pyx_n_b_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 0, 1}, + {&__pyx_n_s_call, __pyx_k_call, sizeof(__pyx_k_call), 0, 0, 1, 1}, + {&__pyx_n_s_check_truncation, __pyx_k_check_truncation, sizeof(__pyx_k_check_truncation), 0, 0, 1, 1}, + {&__pyx_n_s_chunk_size, __pyx_k_chunk_size, sizeof(__pyx_k_chunk_size), 0, 0, 1, 1}, + {&__pyx_n_s_class_getitem, __pyx_k_class_getitem, sizeof(__pyx_k_class_getitem), 0, 0, 1, 1}, + {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, + {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1}, + {&__pyx_n_s_closefd, __pyx_k_closefd, sizeof(__pyx_k_closefd), 0, 0, 1, 1}, + {&__pyx_n_s_contig, __pyx_k_contig, sizeof(__pyx_k_contig), 0, 0, 1, 1}, + {&__pyx_kp_u_contig_and_reference_should_not, __pyx_k_contig_and_reference_should_not, sizeof(__pyx_k_contig_and_reference_should_not), 0, 1, 0, 0}, + {&__pyx_n_s_coord, __pyx_k_coord, sizeof(__pyx_k_coord), 0, 0, 1, 1}, + {&__pyx_n_s_cpart, __pyx_k_cpart, sizeof(__pyx_k_cpart), 0, 0, 1, 1}, + {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1}, + {&__pyx_kp_u_disable, __pyx_k_disable, sizeof(__pyx_k_disable), 0, 1, 0, 0}, + {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1}, + {&__pyx_kp_u_enable, __pyx_k_enable, sizeof(__pyx_k_enable), 0, 1, 0, 0}, + {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, + {&__pyx_n_s_enter, __pyx_k_enter, sizeof(__pyx_k_enter), 0, 0, 1, 1}, + {&__pyx_n_s_eq, __pyx_k_eq, sizeof(__pyx_k_eq), 0, 0, 1, 1}, + {&__pyx_kp_u_error_checking_for_EOF_marker, __pyx_k_error_checking_for_EOF_marker, sizeof(__pyx_k_error_checking_for_EOF_marker), 0, 1, 0, 0}, + {&__pyx_n_s_exc_type, __pyx_k_exc_type, sizeof(__pyx_k_exc_type), 0, 0, 1, 1}, + {&__pyx_n_s_exc_value, __pyx_k_exc_value, sizeof(__pyx_k_exc_value), 0, 0, 1, 1}, + {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1}, + {&__pyx_kp_u_failed, __pyx_k_failed, sizeof(__pyx_k_failed), 0, 1, 0, 0}, + {&__pyx_kp_u_failed_to_close_HFile, __pyx_k_failed_to_close_HFile, sizeof(__pyx_k_failed_to_close_HFile), 0, 1, 0, 0}, + {&__pyx_kp_u_failed_to_flush_HFile, __pyx_k_failed_to_flush_HFile, sizeof(__pyx_k_failed_to_flush_HFile), 0, 1, 0, 0}, + {&__pyx_kp_u_failed_to_open_HFile, __pyx_k_failed_to_open_HFile, sizeof(__pyx_k_failed_to_open_HFile), 0, 1, 0, 0}, + {&__pyx_kp_u_failed_to_read_HFile, __pyx_k_failed_to_read_HFile, sizeof(__pyx_k_failed_to_read_HFile), 0, 1, 0, 0}, + {&__pyx_kp_u_fd, __pyx_k_fd, sizeof(__pyx_k_fd), 0, 1, 0, 0}, + {&__pyx_n_s_fileno, __pyx_k_fileno, sizeof(__pyx_k_fileno), 0, 0, 1, 1}, + {&__pyx_kp_u_fileno_not_available, __pyx_k_fileno_not_available, sizeof(__pyx_k_fileno_not_available), 0, 1, 0, 0}, + {&__pyx_n_s_flush, __pyx_k_flush, sizeof(__pyx_k_flush), 0, 0, 1, 1}, + {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1}, + {&__pyx_n_s_format_option, __pyx_k_format_option, sizeof(__pyx_k_format_option), 0, 0, 1, 1}, + {&__pyx_n_s_format_options, __pyx_k_format_options, sizeof(__pyx_k_format_options), 0, 0, 1, 1}, + {&__pyx_n_s_fp, __pyx_k_fp, sizeof(__pyx_k_fp), 0, 0, 1, 1}, + {&__pyx_kp_u_gc, __pyx_k_gc, sizeof(__pyx_k_gc), 0, 1, 0, 0}, + {&__pyx_n_s_get_reference_name, __pyx_k_get_reference_name, sizeof(__pyx_k_get_reference_name), 0, 0, 1, 1}, + {&__pyx_n_s_get_tid, __pyx_k_get_tid, sizeof(__pyx_k_get_tid), 0, 0, 1, 1}, + {&__pyx_n_s_get_verbosity, __pyx_k_get_verbosity, sizeof(__pyx_k_get_verbosity), 0, 0, 1, 1}, + {&__pyx_n_u_get_verbosity, __pyx_k_get_verbosity, sizeof(__pyx_k_get_verbosity), 0, 1, 0, 1}, + {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1}, + {&__pyx_n_s_got, __pyx_k_got, sizeof(__pyx_k_got), 0, 0, 1, 1}, + {&__pyx_n_s_ignore_truncation, __pyx_k_ignore_truncation, sizeof(__pyx_k_ignore_truncation), 0, 0, 1, 1}, + {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, + {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1}, + {&__pyx_n_s_init_subclass, __pyx_k_init_subclass, sizeof(__pyx_k_init_subclass), 0, 0, 1, 1}, + {&__pyx_n_s_initializing, __pyx_k_initializing, sizeof(__pyx_k_initializing), 0, 0, 1, 1}, + {&__pyx_kp_u_invalid_contig_s, __pyx_k_invalid_contig_s, sizeof(__pyx_k_invalid_contig_s), 0, 1, 0, 0}, + {&__pyx_kp_u_invalid_coordinates_start_i_stop, __pyx_k_invalid_coordinates_start_i_stop, sizeof(__pyx_k_invalid_coordinates_start_i_stop), 0, 1, 0, 0}, + {&__pyx_kp_u_invalid_tid, __pyx_k_invalid_tid, sizeof(__pyx_k_invalid_tid), 0, 1, 0, 0}, + {&__pyx_n_s_io, __pyx_k_io, sizeof(__pyx_k_io), 0, 0, 1, 1}, + {&__pyx_n_s_is_coroutine, __pyx_k_is_coroutine, sizeof(__pyx_k_is_coroutine), 0, 0, 1, 1}, + {&__pyx_n_s_is_open, __pyx_k_is_open, sizeof(__pyx_k_is_open), 0, 0, 1, 1}, + {&__pyx_n_s_is_valid_reference_name, __pyx_k_is_valid_reference_name, sizeof(__pyx_k_is_valid_reference_name), 0, 0, 1, 1}, + {&__pyx_n_s_is_valid_tid, __pyx_k_is_valid_tid, sizeof(__pyx_k_is_valid_tid), 0, 0, 1, 1}, + {&__pyx_n_s_isatty, __pyx_k_isatty, sizeof(__pyx_k_isatty), 0, 0, 1, 1}, + {&__pyx_kp_u_isenabled, __pyx_k_isenabled, sizeof(__pyx_k_isenabled), 0, 1, 0, 0}, + {&__pyx_n_s_join, __pyx_k_join, sizeof(__pyx_k_join), 0, 0, 1, 1}, + {&__pyx_n_s_line, __pyx_k_line, sizeof(__pyx_k_line), 0, 0, 1, 1}, + {&__pyx_n_s_lines, __pyx_k_lines, sizeof(__pyx_k_lines), 0, 0, 1, 1}, + {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, + {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1}, + {&__pyx_kp_u_metadata_not_available_on_closed, __pyx_k_metadata_not_available_on_closed, sizeof(__pyx_k_metadata_not_available_on_closed), 0, 1, 0, 0}, + {&__pyx_n_s_mode, __pyx_k_mode, sizeof(__pyx_k_mode), 0, 0, 1, 1}, + {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1}, + {&__pyx_n_s_mro_entries, __pyx_k_mro_entries, sizeof(__pyx_k_mro_entries), 0, 0, 1, 1}, + {&__pyx_n_s_msg, __pyx_k_msg, sizeof(__pyx_k_msg), 0, 0, 1, 1}, + {&__pyx_n_s_mv, __pyx_k_mv, sizeof(__pyx_k_mv), 0, 0, 1, 1}, + {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1}, + {&__pyx_n_s_name_2, __pyx_k_name_2, sizeof(__pyx_k_name_2), 0, 0, 1, 1}, + {&__pyx_n_s_ne, __pyx_k_ne, sizeof(__pyx_k_ne), 0, 0, 1, 1}, + {&__pyx_kp_u_no_BGZF_EOF_marker_file_may_be_t, __pyx_k_no_BGZF_EOF_marker_file_may_be_t, sizeof(__pyx_k_no_BGZF_EOF_marker_file_may_be_t), 0, 1, 0, 0}, + {&__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}, + {&__pyx_n_s_nonzero, __pyx_k_nonzero, sizeof(__pyx_k_nonzero), 0, 0, 1, 1}, + {&__pyx_n_s_object, __pyx_k_object, sizeof(__pyx_k_object), 0, 0, 1, 1}, + {&__pyx_n_s_off, __pyx_k_off, sizeof(__pyx_k_off), 0, 0, 1, 1}, + {&__pyx_n_s_offset, __pyx_k_offset, sizeof(__pyx_k_offset), 0, 0, 1, 1}, + {&__pyx_kp_u_operation_on_closed_HFile, __pyx_k_operation_on_closed_HFile, sizeof(__pyx_k_operation_on_closed_HFile), 0, 1, 0, 0}, + {&__pyx_n_s_opts, __pyx_k_opts, sizeof(__pyx_k_opts), 0, 0, 1, 1}, + {&__pyx_n_s_os, __pyx_k_os, sizeof(__pyx_k_os), 0, 0, 1, 1}, + {&__pyx_n_s_other, __pyx_k_other, sizeof(__pyx_k_other), 0, 0, 1, 1}, + {&__pyx_n_s_parse_region, __pyx_k_parse_region, sizeof(__pyx_k_parse_region), 0, 0, 1, 1}, + {&__pyx_n_s_part, __pyx_k_part, sizeof(__pyx_k_part), 0, 0, 1, 1}, + {&__pyx_n_s_parts, __pyx_k_parts, sizeof(__pyx_k_parts), 0, 0, 1, 1}, + {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1}, + {&__pyx_n_s_pysam_libchtslib, __pyx_k_pysam_libchtslib, sizeof(__pyx_k_pysam_libchtslib), 0, 0, 1, 1}, + {&__pyx_kp_s_pysam_libchtslib_pyx, __pyx_k_pysam_libchtslib_pyx, sizeof(__pyx_k_pysam_libchtslib_pyx), 0, 0, 1, 0}, + {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1}, + {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1}, + {&__pyx_n_u_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 1, 0, 1}, + {&__pyx_n_s_re, __pyx_k_re, sizeof(__pyx_k_re), 0, 0, 1, 1}, + {&__pyx_n_s_read, __pyx_k_read, sizeof(__pyx_k_read), 0, 0, 1, 1}, + {&__pyx_n_s_readable, __pyx_k_readable, sizeof(__pyx_k_readable), 0, 0, 1, 1}, + {&__pyx_n_s_readall, __pyx_k_readall, sizeof(__pyx_k_readall), 0, 0, 1, 1}, + {&__pyx_n_s_readinto, __pyx_k_readinto, sizeof(__pyx_k_readinto), 0, 0, 1, 1}, + {&__pyx_n_s_readline, __pyx_k_readline, sizeof(__pyx_k_readline), 0, 0, 1, 1}, + {&__pyx_n_s_readlines, __pyx_k_readlines, sizeof(__pyx_k_readlines), 0, 0, 1, 1}, + {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1}, + {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1}, + {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 0, 0, 1, 1}, + {&__pyx_n_s_reference, __pyx_k_reference, sizeof(__pyx_k_reference), 0, 0, 1, 1}, + {&__pyx_n_s_region, __pyx_k_region, sizeof(__pyx_k_region), 0, 0, 1, 1}, + {&__pyx_n_s_replace, __pyx_k_replace, sizeof(__pyx_k_replace), 0, 0, 1, 1}, + {&__pyx_n_s_reset, __pyx_k_reset, sizeof(__pyx_k_reset), 0, 0, 1, 1}, + {&__pyx_n_s_ret, __pyx_k_ret, sizeof(__pyx_k_ret), 0, 0, 1, 1}, + {&__pyx_n_s_rstart, __pyx_k_rstart, sizeof(__pyx_k_rstart), 0, 0, 1, 1}, + {&__pyx_n_s_rstop, __pyx_k_rstop, sizeof(__pyx_k_rstop), 0, 0, 1, 1}, + {&__pyx_n_s_rtid, __pyx_k_rtid, sizeof(__pyx_k_rtid), 0, 0, 1, 1}, + {&__pyx_n_s_rval, __pyx_k_rval, sizeof(__pyx_k_rval), 0, 0, 1, 1}, + {&__pyx_n_s_seek, __pyx_k_seek, sizeof(__pyx_k_seek), 0, 0, 1, 1}, + {&__pyx_kp_u_seek_failed_on_HFile, __pyx_k_seek_failed_on_HFile, sizeof(__pyx_k_seek_failed_on_HFile), 0, 1, 0, 0}, + {&__pyx_kp_u_seek_not_available_in_streams, __pyx_k_seek_not_available_in_streams, sizeof(__pyx_k_seek_not_available_in_streams), 0, 1, 0, 0}, + {&__pyx_kp_u_seek_not_implemented_in_files_co, __pyx_k_seek_not_implemented_in_files_co, sizeof(__pyx_k_seek_not_implemented_in_files_co), 0, 1, 0, 0}, + {&__pyx_n_s_seekable, __pyx_k_seekable, sizeof(__pyx_k_seekable), 0, 0, 1, 1}, + {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1}, + {&__pyx_kp_s_self_fp_cannot_be_converted_to_a, __pyx_k_self_fp_cannot_be_converted_to_a, sizeof(__pyx_k_self_fp_cannot_be_converted_to_a), 0, 0, 1, 0}, + {&__pyx_n_s_set_name, __pyx_k_set_name, sizeof(__pyx_k_set_name), 0, 0, 1, 1}, + {&__pyx_n_s_set_verbosity, __pyx_k_set_verbosity, sizeof(__pyx_k_set_verbosity), 0, 0, 1, 1}, + {&__pyx_n_u_set_verbosity, __pyx_k_set_verbosity, sizeof(__pyx_k_set_verbosity), 0, 1, 0, 1}, + {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1}, + {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, + {&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1}, + {&__pyx_n_s_spec, __pyx_k_spec, sizeof(__pyx_k_spec), 0, 0, 1, 1}, + {&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1}, + {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1}, + {&__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}, + {&__pyx_n_s_stop, __pyx_k_stop, sizeof(__pyx_k_stop), 0, 0, 1, 1}, + {&__pyx_kp_u_stop_and_end_should_not_both_be, __pyx_k_stop_and_end_should_not_both_be, sizeof(__pyx_k_stop_and_end_should_not_both_be), 0, 1, 0, 0}, + {&__pyx_kp_u_stop_out_of_range_i, __pyx_k_stop_out_of_range_i, sizeof(__pyx_k_stop_out_of_range_i), 0, 1, 0, 0}, + {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0}, + {&__pyx_n_s_super, __pyx_k_super, sizeof(__pyx_k_super), 0, 0, 1, 1}, + {&__pyx_n_s_tb, __pyx_k_tb, sizeof(__pyx_k_tb), 0, 0, 1, 1}, + {&__pyx_n_s_tell, __pyx_k_tell, sizeof(__pyx_k_tell), 0, 0, 1, 1}, + {&__pyx_kp_u_tell_failed_on_HFile, __pyx_k_tell_failed_on_HFile, sizeof(__pyx_k_tell_failed_on_HFile), 0, 1, 0, 0}, + {&__pyx_kp_u_tell_not_available_in_streams, __pyx_k_tell_not_available_in_streams, sizeof(__pyx_k_tell_not_available_in_streams), 0, 1, 0, 0}, + {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, + {&__pyx_n_s_tid, __pyx_k_tid, sizeof(__pyx_k_tid), 0, 0, 1, 1}, + {&__pyx_n_s_traceback, __pyx_k_traceback, sizeof(__pyx_k_traceback), 0, 0, 1, 1}, + {&__pyx_n_s_truncate, __pyx_k_truncate, sizeof(__pyx_k_truncate), 0, 0, 1, 1}, + {&__pyx_n_s_type, __pyx_k_type, sizeof(__pyx_k_type), 0, 0, 1, 1}, + {&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1}, + {&__pyx_n_s_verbosity, __pyx_k_verbosity, sizeof(__pyx_k_verbosity), 0, 0, 1, 1}, + {&__pyx_n_u_w, __pyx_k_w, sizeof(__pyx_k_w), 0, 1, 0, 1}, + {&__pyx_n_s_warn, __pyx_k_warn, sizeof(__pyx_k_warn), 0, 0, 1, 1}, + {&__pyx_n_s_warnings, __pyx_k_warnings, sizeof(__pyx_k_warnings), 0, 0, 1, 1}, + {&__pyx_n_s_whence, __pyx_k_whence, sizeof(__pyx_k_whence), 0, 0, 1, 1}, + {&__pyx_n_s_writable, __pyx_k_writable, sizeof(__pyx_k_writable), 0, 0, 1, 1}, + {&__pyx_n_s_write, __pyx_k_write, sizeof(__pyx_k_write), 0, 0, 1, 1}, + {&__pyx_kp_u_write_failed_on_HFile, __pyx_k_write_failed_on_HFile, sizeof(__pyx_k_write_failed_on_HFile), 0, 1, 0, 0}, + {&__pyx_n_s_writelines, __pyx_k_writelines, sizeof(__pyx_k_writelines), 0, 0, 1, 1}, + {0, 0, 0, 0, 0, 0, 0} + }; + return __Pyx_InitStrings(__pyx_string_tab); +} +/* #### Code section: cached_builtins ### */ +static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) { + __pyx_builtin_object = __Pyx_GetBuiltinName(__pyx_n_s_object); if (!__pyx_builtin_object) __PYX_ERR(0, 297, __pyx_L1_error) + __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) __PYX_ERR(0, 96, __pyx_L1_error) + __pyx_builtin_AttributeError = __Pyx_GetBuiltinName(__pyx_n_s_AttributeError); if (!__pyx_builtin_AttributeError) __PYX_ERR(0, 114, __pyx_L1_error) + __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) __PYX_ERR(0, 128, __pyx_L1_error) + __pyx_builtin_NotImplementedError = __Pyx_GetBuiltinName(__pyx_n_s_NotImplementedError); if (!__pyx_builtin_NotImplementedError) __PYX_ERR(0, 270, __pyx_L1_error) + __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error) + __pyx_builtin_OSError = __Pyx_GetBuiltinName(__pyx_n_s_OSError); if (!__pyx_builtin_OSError) __PYX_ERR(0, 345, __pyx_L1_error) + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 381, __pyx_L1_error) + __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) __PYX_ERR(0, 587, __pyx_L1_error) + __pyx_builtin_OverflowError = __Pyx_GetBuiltinName(__pyx_n_s_OverflowError); if (!__pyx_builtin_OverflowError) __PYX_ERR(0, 657, __pyx_L1_error) + __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) __PYX_ERR(0, 679, __pyx_L1_error) + __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) __PYX_ERR(3, 120, __pyx_L1_error) + return 0; + __pyx_L1_error:; + return -1; +} +/* #### Code section: cached_constants ### */ + +static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); + + /* "pysam/libchtslib.pyx":110 + * def fileno(self): + * if self.fp == NULL: + * raise IOError('operation on closed HFile') # <<<<<<<<<<<<<< + * if isinstance(self.name, int): + * return self.name + */ + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_operation_on_closed_HFile); if (unlikely(!__pyx_tuple__5)) __PYX_ERR(0, 110, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__5); + __Pyx_GIVEREF(__pyx_tuple__5); + + /* "pysam/libchtslib.pyx":114 + * return self.name + * else: + * raise AttributeError('fileno not available') # <<<<<<<<<<<<<< + * + * def __enter__(self): + */ + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_fileno_not_available); if (unlikely(!__pyx_tuple__6)) __PYX_ERR(0, 114, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__6); + __Pyx_GIVEREF(__pyx_tuple__6); + + /* "pysam/libchtslib.pyx":381 + * VARIANTS, INDEX, REGIONS""" + * if not self.htsfile: + * raise ValueError('metadata not available on closed file') # <<<<<<<<<<<<<< + * return FORMAT_CATEGORIES[self.htsfile.format.category] + * + */ + __pyx_tuple__39 = PyTuple_Pack(1, __pyx_kp_u_metadata_not_available_on_closed); if (unlikely(!__pyx_tuple__39)) __PYX_ERR(0, 381, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__39); + __Pyx_GIVEREF(__pyx_tuple__39); + + /* "pysam/libchtslib.pyx":486 + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: + * raise ValueError('I/O operation on closed file') # <<<<<<<<<<<<<< + * if self.is_stream: + * raise IOError('seek not available in streams') + */ + __pyx_tuple__43 = PyTuple_Pack(1, __pyx_kp_u_I_O_operation_on_closed_file); if (unlikely(!__pyx_tuple__43)) __PYX_ERR(0, 486, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__43); + __Pyx_GIVEREF(__pyx_tuple__43); + + /* "pysam/libchtslib.pyx":488 + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + * raise IOError('seek not available in streams') # <<<<<<<<<<<<<< + * + * whence = libc_whence_from_io(whence) + */ + __pyx_tuple__44 = PyTuple_Pack(1, __pyx_kp_u_seek_not_available_in_streams); if (unlikely(!__pyx_tuple__44)) __PYX_ERR(0, 488, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__44); + __Pyx_GIVEREF(__pyx_tuple__44); + + /* "pysam/libchtslib.pyx":508 + * raise ValueError('I/O operation on closed file') + * if self.is_stream: + * raise IOError('tell not available in streams') # <<<<<<<<<<<<<< + * + * cdef int64_t ret + */ + __pyx_tuple__46 = PyTuple_Pack(1, __pyx_kp_u_tell_not_available_in_streams); if (unlikely(!__pyx_tuple__46)) __PYX_ERR(0, 508, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__46); + __Pyx_GIVEREF(__pyx_tuple__46); + + /* "pysam/libchtslib.pyx":550 + * + * # Replicate mode normalization done in hts_open_format + * smode = self.mode.replace(b'b', b'').replace(b'c', b'') # <<<<<<<<<<<<<< + * if b'b' in self.mode: + * smode += b'b' + */ + __pyx_tuple__47 = PyTuple_Pack(2, __pyx_n_b_b, __pyx_kp_b__13); if (unlikely(!__pyx_tuple__47)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__47); + __Pyx_GIVEREF(__pyx_tuple__47); + __pyx_tuple__48 = PyTuple_Pack(2, __pyx_n_b_c, __pyx_kp_b__13); if (unlikely(!__pyx_tuple__48)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__48); + __Pyx_GIVEREF(__pyx_tuple__48); + + /* "pysam/libchtslib.pyx":559 + * hfile = hdopen(dup_fd, cmode) + * if hfile == NULL: + * raise IOError('Cannot create hfile') # <<<<<<<<<<<<<< + * + * try: + */ + __pyx_tuple__49 = PyTuple_Pack(1, __pyx_kp_u_Cannot_create_hfile); if (unlikely(!__pyx_tuple__49)) __PYX_ERR(0, 559, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__49); + __Pyx_GIVEREF(__pyx_tuple__49); + + /* "pysam/libchtslib.pyx":592 + * if rval != 0: + * hts_opt_free(opts) + * raise RuntimeError('An error occurred while applying the requested format options') # <<<<<<<<<<<<<< + * hts_opt_free(opts) + * + */ + __pyx_tuple__51 = PyTuple_Pack(1, __pyx_kp_u_An_error_occurred_while_applying); if (unlikely(!__pyx_tuple__51)) __PYX_ERR(0, 592, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__51); + __Pyx_GIVEREF(__pyx_tuple__51); + + /* "pysam/libchtslib.pyx":640 + * if reference is not None: + * if contig is not None: + * raise ValueError('contig and reference should not both be specified') # <<<<<<<<<<<<<< + * contig = reference + * + */ + __pyx_tuple__53 = PyTuple_Pack(1, __pyx_kp_u_contig_and_reference_should_not); if (unlikely(!__pyx_tuple__53)) __PYX_ERR(0, 640, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__53); + __Pyx_GIVEREF(__pyx_tuple__53); + + /* "pysam/libchtslib.pyx":645 + * if end is not None: + * if stop is not None: + * raise ValueError('stop and end should not both be specified') # <<<<<<<<<<<<<< + * stop = end + * + */ + __pyx_tuple__54 = PyTuple_Pack(1, __pyx_kp_u_stop_and_end_should_not_both_be); if (unlikely(!__pyx_tuple__54)) __PYX_ERR(0, 645, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__54); + __Pyx_GIVEREF(__pyx_tuple__54); + + /* "pysam/libchtslib.pyx":679 + * if tid is not None: + * if not self.is_valid_tid(tid): + * raise IndexError('invalid tid') # <<<<<<<<<<<<<< + * rtid = tid + * else: + */ + __pyx_tuple__57 = PyTuple_Pack(1, __pyx_kp_u_invalid_tid); if (unlikely(!__pyx_tuple__57)) __PYX_ERR(0, 679, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__57); + __Pyx_GIVEREF(__pyx_tuple__57); + + /* "pysam/libchtslib.pyx":41 + * cdef int MAX_POS = (1 << 31) - 1 + * + * cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS') # <<<<<<<<<<<<<< + * cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', + * 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') + */ + __pyx_tuple__66 = PyTuple_Pack(5, __pyx_n_u_UNKNOWN, __pyx_n_u_ALIGNMENTS, __pyx_n_u_VARIANTS, __pyx_n_u_INDEX, __pyx_n_u_REGIONS); if (unlikely(!__pyx_tuple__66)) __PYX_ERR(0, 41, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__66); + __Pyx_GIVEREF(__pyx_tuple__66); + + /* "pysam/libchtslib.pyx":42 + * + * cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS') + * cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', # <<<<<<<<<<<<<< + * 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') + * cdef tuple COMPRESSION = ('NONE', 'GZIP', 'BGZF', 'CUSTOM') + */ + __pyx_tuple__67 = PyTuple_Pack(14, __pyx_n_u_UNKNOWN, __pyx_n_u_BINARY_FORMAT, __pyx_n_u_TEXT_FORMAT, __pyx_n_u_SAM, __pyx_n_u_BAM, __pyx_n_u_BAI, __pyx_n_u_CRAM, __pyx_n_u_CRAI, __pyx_n_u_VCF, __pyx_n_u_BCF, __pyx_n_u_CSI, __pyx_n_u_GZI, __pyx_n_u_TBI, __pyx_n_u_BED); if (unlikely(!__pyx_tuple__67)) __PYX_ERR(0, 42, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__67); + __Pyx_GIVEREF(__pyx_tuple__67); + + /* "pysam/libchtslib.pyx":44 + * cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', + * 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') + * cdef tuple COMPRESSION = ('NONE', 'GZIP', 'BGZF', 'CUSTOM') # <<<<<<<<<<<<<< + * + * + */ + __pyx_tuple__68 = PyTuple_Pack(4, __pyx_n_u_NONE, __pyx_n_u_GZIP, __pyx_n_u_BGZF, __pyx_n_u_CUSTOM); if (unlikely(!__pyx_tuple__68)) __PYX_ERR(0, 44, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__68); + __Pyx_GIVEREF(__pyx_tuple__68); + + /* "pysam/libchtslib.pyx":53 + * + * + * cpdef set_verbosity(int verbosity): # <<<<<<<<<<<<<< + * """Set htslib's hts_verbose global variable to the specified value.""" + * return hts_set_verbosity(verbosity) + */ + __pyx_tuple__69 = PyTuple_Pack(1, __pyx_n_s_verbosity); if (unlikely(!__pyx_tuple__69)) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__69); + __Pyx_GIVEREF(__pyx_tuple__69); + __pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_set_verbosity, 53, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 53, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":57 + * return hts_set_verbosity(verbosity) + * + * cpdef get_verbosity(): # <<<<<<<<<<<<<< + * """Return the value of htslib's hts_verbose global variable.""" + * return hts_get_verbosity() + */ + __pyx_codeobj__2 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_get_verbosity, 57, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__2)) __PYX_ERR(0, 57, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":98 + * raise IOError(errno, 'failed to open HFile', self.name) + * + * def close(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * return + */ + __pyx_tuple__70 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_fp); if (unlikely(!__pyx_tuple__70)) __PYX_ERR(0, 98, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__70); + __Pyx_GIVEREF(__pyx_tuple__70); + __pyx_codeobj__3 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_close, 98, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__3)) __PYX_ERR(0, 98, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":108 + * raise IOError(errno, 'failed to close HFile', self.name) + * + * def fileno(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_tuple__71 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__71)) __PYX_ERR(0, 108, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__71); + __Pyx_GIVEREF(__pyx_tuple__71); + __pyx_codeobj__4 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_fileno, 108, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__4)) __PYX_ERR(0, 108, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":116 + * raise AttributeError('fileno not available') + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + __pyx_codeobj__7 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_enter, 116, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__7)) __PYX_ERR(0, 116, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":119 + * return self + * + * def __exit__(self, type, value, tb): # <<<<<<<<<<<<<< + * self.close() + * + */ + __pyx_tuple__72 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_type, __pyx_n_s_value, __pyx_n_s_tb); if (unlikely(!__pyx_tuple__72)) __PYX_ERR(0, 119, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__72); + __Pyx_GIVEREF(__pyx_tuple__72); + __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_exit, 119, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 119, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":131 + * return line + * + * def flush(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_flush, 131, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) __PYX_ERR(0, 131, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":137 + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + * + * def isatty(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_isatty, 137, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 137, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":142 + * return False + * + * def readable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'r' in self.mode + * + */ + __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_readable, 142, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) __PYX_ERR(0, 142, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":145 + * return self.fp != NULL and 'r' in self.mode + * + * def read(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_tuple__73 = PyTuple_Pack(8, __pyx_n_s_self, __pyx_n_s_size, __pyx_n_s_parts, __pyx_n_s_part, __pyx_n_s_chunk_size, __pyx_n_s_ret, __pyx_n_s_bytes_read, __pyx_n_s_cpart); if (unlikely(!__pyx_tuple__73)) __PYX_ERR(0, 145, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__73); + __Pyx_GIVEREF(__pyx_tuple__73); + __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 8, 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_libchtslib_pyx, __pyx_n_s_read, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(0, 145, __pyx_L1_error) + __pyx_tuple__74 = PyTuple_Pack(1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__74)) __PYX_ERR(0, 145, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__74); + __Pyx_GIVEREF(__pyx_tuple__74); + + /* "pysam/libchtslib.pyx":180 + * return b''.join(parts) + * + * def readall(self): # <<<<<<<<<<<<<< + * return self.read() + * + */ + __pyx_codeobj__14 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_readall, 180, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__14)) __PYX_ERR(0, 180, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":183 + * return self.read() + * + * def readinto(self, buf): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_tuple__75 = PyTuple_Pack(5, __pyx_n_s_self, __pyx_n_s_buf, __pyx_n_s_size, __pyx_n_s_mv, __pyx_n_s_ret); if (unlikely(!__pyx_tuple__75)) __PYX_ERR(0, 183, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__75); + __Pyx_GIVEREF(__pyx_tuple__75); + __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 5, 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_libchtslib_pyx, __pyx_n_s_readinto, 183, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) __PYX_ERR(0, 183, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":200 + * return ret + * + * def readline(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_codeobj__16 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 8, 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_libchtslib_pyx, __pyx_n_s_readline, 200, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__16)) __PYX_ERR(0, 200, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":241 + * return b''.join(parts) + * + * def readlines(self): # <<<<<<<<<<<<<< + * return list(self) + * + */ + __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__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_readlines, 241, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) __PYX_ERR(0, 241, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":244 + * return list(self) + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_tuple__76 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_offset, __pyx_n_s_whence, __pyx_n_s_off); if (unlikely(!__pyx_tuple__76)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__76); + __Pyx_GIVEREF(__pyx_tuple__76); + __pyx_codeobj__19 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 4, 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_libchtslib_pyx, __pyx_n_s_seek, 244, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__19)) __PYX_ERR(0, 244, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":255 + * return off + * + * def tell(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_tuple__77 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_ret); if (unlikely(!__pyx_tuple__77)) __PYX_ERR(0, 255, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__77); + __Pyx_GIVEREF(__pyx_tuple__77); + __pyx_codeobj__20 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 2, 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_pysam_libchtslib_pyx, __pyx_n_s_tell, 255, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__20)) __PYX_ERR(0, 255, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":266 + * return ret + * + * def seekable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL + * + */ + __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__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_seekable, 266, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__21)) __PYX_ERR(0, 266, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":269 + * return self.fp != NULL + * + * def truncate(self, size=None): # <<<<<<<<<<<<<< + * raise NotImplementedError() + * + */ + __pyx_tuple__78 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_size); if (unlikely(!__pyx_tuple__78)) __PYX_ERR(0, 269, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__78); + __Pyx_GIVEREF(__pyx_tuple__78); + __pyx_codeobj__22 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_truncate, 269, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__22)) __PYX_ERR(0, 269, __pyx_L1_error) + __pyx_tuple__79 = PyTuple_Pack(1, Py_None); if (unlikely(!__pyx_tuple__79)) __PYX_ERR(0, 269, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__79); + __Pyx_GIVEREF(__pyx_tuple__79); + + /* "pysam/libchtslib.pyx":272 + * raise NotImplementedError() + * + * def writable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'w' in self.mode + * + */ + __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_writable, 272, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) __PYX_ERR(0, 272, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":275 + * return self.fp != NULL and 'w' in self.mode + * + * def write(self, bytes b): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_tuple__80 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_b, __pyx_n_s_got); if (unlikely(!__pyx_tuple__80)) __PYX_ERR(0, 275, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__80); + __Pyx_GIVEREF(__pyx_tuple__80); + __pyx_codeobj__24 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__80, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_write, 275, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__24)) __PYX_ERR(0, 275, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":286 + * return got + * + * def writelines(self, lines): # <<<<<<<<<<<<<< + * for line in lines: + * self.write(line) + */ + __pyx_tuple__81 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_lines, __pyx_n_s_line); if (unlikely(!__pyx_tuple__81)) __PYX_ERR(0, 286, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__81); + __Pyx_GIVEREF(__pyx_tuple__81); + __pyx_codeobj__25 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_writelines, 286, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__25)) __PYX_ERR(0, 286, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): + */ + __pyx_codeobj__26 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__26)) __PYX_ERR(1, 1, __pyx_L1_error) + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + */ + __pyx_tuple__82 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_pyx_state); if (unlikely(!__pyx_tuple__82)) __PYX_ERR(1, 3, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__82); + __Pyx_GIVEREF(__pyx_tuple__82); + __pyx_codeobj__27 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__27)) __PYX_ERR(1, 3, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":297 + * ######################################################################## + * + * class CallableValue(object): # <<<<<<<<<<<<<< + * def __init__(self, value): + * self.value = value + */ + __pyx_tuple__83 = PyTuple_Pack(1, __pyx_builtin_object); if (unlikely(!__pyx_tuple__83)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__83); + __Pyx_GIVEREF(__pyx_tuple__83); + __pyx_tuple__84 = PyTuple_Pack(1, __pyx_builtin_object); if (unlikely(!__pyx_tuple__84)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__84); + __Pyx_GIVEREF(__pyx_tuple__84); + + /* "pysam/libchtslib.pyx":298 + * + * class CallableValue(object): + * def __init__(self, value): # <<<<<<<<<<<<<< + * self.value = value + * def __call__(self): + */ + __pyx_tuple__85 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_value); if (unlikely(!__pyx_tuple__85)) __PYX_ERR(0, 298, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__85); + __Pyx_GIVEREF(__pyx_tuple__85); + __pyx_codeobj__28 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__85, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_init, 298, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__28)) __PYX_ERR(0, 298, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":300 + * def __init__(self, value): + * self.value = value + * def __call__(self): # <<<<<<<<<<<<<< + * return self.value + * def __bool__(self): + */ + __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__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_call, 300, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__29)) __PYX_ERR(0, 300, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":302 + * def __call__(self): + * return self.value + * def __bool__(self): # <<<<<<<<<<<<<< + * return self.value + * def __nonzero__(self): + */ + __pyx_codeobj__30 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_bool, 302, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__30)) __PYX_ERR(0, 302, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":304 + * def __bool__(self): + * return self.value + * def __nonzero__(self): # <<<<<<<<<<<<<< + * return self.value + * def __eq__(self, other): + */ + __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__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_nonzero, 304, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__31)) __PYX_ERR(0, 304, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":306 + * def __nonzero__(self): + * return self.value + * def __eq__(self, other): # <<<<<<<<<<<<<< + * return self.value == other + * def __ne__(self, other): + */ + __pyx_tuple__86 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_other); if (unlikely(!__pyx_tuple__86)) __PYX_ERR(0, 306, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__86); + __Pyx_GIVEREF(__pyx_tuple__86); + __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__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_eq, 306, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__32)) __PYX_ERR(0, 306, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":308 + * def __eq__(self, other): + * return self.value == other + * def __ne__(self, other): # <<<<<<<<<<<<<< + * return self.value != other + * + */ + __pyx_codeobj__33 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_ne, 308, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__33)) __PYX_ERR(0, 308, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":312 + * + * + * CTrue = CallableValue(True) # <<<<<<<<<<<<<< + * CFalse = CallableValue(False) + * + */ + __pyx_tuple__87 = PyTuple_Pack(1, Py_True); if (unlikely(!__pyx_tuple__87)) __PYX_ERR(0, 312, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__87); + __Pyx_GIVEREF(__pyx_tuple__87); + + /* "pysam/libchtslib.pyx":313 + * + * CTrue = CallableValue(True) + * CFalse = CallableValue(False) # <<<<<<<<<<<<<< + * + * + */ + __pyx_tuple__88 = PyTuple_Pack(1, Py_False); if (unlikely(!__pyx_tuple__88)) __PYX_ERR(0, 313, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__88); + __Pyx_GIVEREF(__pyx_tuple__88); + + /* "pysam/libchtslib.pyx":331 + * self.duplicate_filehandle = True + * + * def close(self): # <<<<<<<<<<<<<< + * if self.htsfile: + * hts_close(self.htsfile) + */ + __pyx_codeobj__34 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_close, 331, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__34)) __PYX_ERR(0, 331, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":341 + * self.htsfile = NULL + * + * def flush(self): # <<<<<<<<<<<<<< + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: + */ + __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__71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_flush, 341, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__35)) __PYX_ERR(0, 341, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":347 + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + * + * def check_truncation(self, ignore_truncation=False): # <<<<<<<<<<<<<< + * """Check if file is truncated.""" + * if not self.htsfile: + */ + __pyx_tuple__89 = PyTuple_Pack(5, __pyx_n_s_self, __pyx_n_s_ignore_truncation, __pyx_n_s_bgzfp, __pyx_n_s_ret, __pyx_n_s_msg); if (unlikely(!__pyx_tuple__89)) __PYX_ERR(0, 347, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__89); + __Pyx_GIVEREF(__pyx_tuple__89); + __pyx_codeobj__36 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__89, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_check_truncation, 347, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__36)) __PYX_ERR(0, 347, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":369 + * raise IOError(msg) + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + __pyx_codeobj__37 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_enter, 369, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__37)) __PYX_ERR(0, 369, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":372 + * return self + * + * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<< + * self.close() + * return False + */ + __pyx_tuple__90 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_exc_type, __pyx_n_s_exc_value, __pyx_n_s_traceback); if (unlikely(!__pyx_tuple__90)) __PYX_ERR(0, 372, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__90); + __Pyx_GIVEREF(__pyx_tuple__90); + __pyx_codeobj__38 = (PyObject*)__Pyx_PyCode_New(4, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__90, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_exit, 372, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__38)) __PYX_ERR(0, 372, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":472 + * return self.htsfile != NULL and self.htsfile.format.format == bcf + * + * def reset(self): # <<<<<<<<<<<<<< + * """reset file position to beginning of file just after the header. + * + */ + __pyx_codeobj__40 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_libchtslib_pyx, __pyx_n_s_reset, 472, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__40)) __PYX_ERR(0, 472, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":483 + * return self.seek(self.start_offset) + * + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: + */ + __pyx_tuple__91 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_offset, __pyx_n_s_whence, __pyx_n_s_ret); if (unlikely(!__pyx_tuple__91)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__91); + __Pyx_GIVEREF(__pyx_tuple__91); + __pyx_codeobj__42 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__91, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_seek, 483, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__42)) __PYX_ERR(0, 483, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":503 + * return ret + * + * def tell(self): # <<<<<<<<<<<<<< + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: + */ + __pyx_codeobj__45 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 2, 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_pysam_libchtslib_pyx, __pyx_n_s_tell, 503, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__45)) __PYX_ERR(0, 503, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":575 + * return htsfile + * + * def add_hts_options(self, format_options=None): # <<<<<<<<<<<<<< + * """Given a list of key=value format option strings, add them to an open htsFile + * """ + */ + __pyx_tuple__92 = PyTuple_Pack(5, __pyx_n_s_self, __pyx_n_s_format_options, __pyx_n_s_rval, __pyx_n_s_opts, __pyx_n_s_format_option); if (unlikely(!__pyx_tuple__92)) __PYX_ERR(0, 575, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__92); + __Pyx_GIVEREF(__pyx_tuple__92); + __pyx_codeobj__50 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__92, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_add_hts_options, 575, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__50)) __PYX_ERR(0, 575, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":595 + * hts_opt_free(opts) + * + * def parse_region(self, contig=None, start=None, stop=None, # <<<<<<<<<<<<<< + * region=None, tid=None, + * reference=None, end=None): + */ + __pyx_tuple__93 = PyTuple_Pack(13, __pyx_n_s_self, __pyx_n_s_contig, __pyx_n_s_start, __pyx_n_s_stop, __pyx_n_s_region, __pyx_n_s_tid, __pyx_n_s_reference, __pyx_n_s_end, __pyx_n_s_rtid, __pyx_n_s_rstart, __pyx_n_s_rstop, __pyx_n_s_coord, __pyx_n_s_parts); if (unlikely(!__pyx_tuple__93)) __PYX_ERR(0, 595, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__93); + __Pyx_GIVEREF(__pyx_tuple__93); + __pyx_codeobj__52 = (PyObject*)__Pyx_PyCode_New(8, 0, 0, 13, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__93, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_parse_region, 595, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__52)) __PYX_ERR(0, 595, __pyx_L1_error) + __pyx_tuple__94 = PyTuple_Pack(7, Py_None, Py_None, Py_None, Py_None, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__94)) __PYX_ERR(0, 595, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__94); + __Pyx_GIVEREF(__pyx_tuple__94); + + /* "pysam/libchtslib.pyx":700 + * return 1, rtid, rstart, rstop + * + * def is_valid_tid(self, tid): # <<<<<<<<<<<<<< + * """ + * return True if the numerical :term:`tid` is valid; False otherwise. + */ + __pyx_tuple__95 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_tid); if (unlikely(!__pyx_tuple__95)) __PYX_ERR(0, 700, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__95); + __Pyx_GIVEREF(__pyx_tuple__95); + __pyx_codeobj__60 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__95, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_is_valid_tid, 700, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__60)) __PYX_ERR(0, 700, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":708 + * raise NotImplementedError() + * + * def is_valid_reference_name(self, contig): # <<<<<<<<<<<<<< + * """ + * return True if the contig name :term:`contig` is valid; False otherwise. + */ + __pyx_tuple__96 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_contig); if (unlikely(!__pyx_tuple__96)) __PYX_ERR(0, 708, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__96); + __Pyx_GIVEREF(__pyx_tuple__96); + __pyx_codeobj__61 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__96, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_is_valid_reference_name, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__61)) __PYX_ERR(0, 708, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":714 + * return self.get_tid(contig) != -1 + * + * def get_tid(self, contig): # <<<<<<<<<<<<<< + * """ + * return the numerical :term:`tid` corresponding to + */ + __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__96, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_get_tid, 714, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) __PYX_ERR(0, 714, __pyx_L1_error) + + /* "pysam/libchtslib.pyx":723 + * raise NotImplementedError() + * + * def get_reference_name(self, tid): # <<<<<<<<<<<<<< + * """ + * return :term:`contig` name corresponding to numerical :term:`tid` + */ + __pyx_codeobj__63 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__95, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_get_reference_name, 723, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__63)) __PYX_ERR(0, 723, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): + */ + __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 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_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) __PYX_ERR(1, 1, __pyx_L1_error) + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + */ + __pyx_codeobj__65 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__65)) __PYX_ERR(1, 3, __pyx_L1_error) + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_RefNannyFinishContext(); + return -1; +} +/* #### Code section: init_constants ### */ + +static CYTHON_SMALL_CODE int __Pyx_InitConstants(void) { + if (__Pyx_CreateStringTabAndInitStrings() < 0) __PYX_ERR(0, 1, __pyx_L1_error); + __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) __PYX_ERR(0, 1, __pyx_L1_error) + return 0; + __pyx_L1_error:; + return -1; +} +/* #### Code section: init_globals ### */ + +static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) { + return 0; +} +/* #### Code section: init_module ### */ + +static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/ + +static int __Pyx_modinit_global_init_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0); + /*--- Global init code ---*/ + __pyx_v_5pysam_10libchtslib_FORMAT_CATEGORIES = ((PyObject*)Py_None); Py_INCREF(Py_None); + __pyx_v_5pysam_10libchtslib_FORMATS = ((PyObject*)Py_None); Py_INCREF(Py_None); + __pyx_v_5pysam_10libchtslib_COMPRESSION = ((PyObject*)Py_None); Py_INCREF(Py_None); + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_variable_export_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0); + /*--- Variable export code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_function_export_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0); + /*--- Function export code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_type_init_code(void) { + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0); + /*--- Type init code ---*/ + __pyx_vtabptr_5pysam_10libchtslib_HTSFile = &__pyx_vtable_5pysam_10libchtslib_HTSFile; + __pyx_vtable_5pysam_10libchtslib_HTSFile._open_htsfile = (htsFile *(*)(struct __pyx_obj_5pysam_10libchtslib_HTSFile *))__pyx_f_5pysam_10libchtslib_7HTSFile__open_htsfile; + #if CYTHON_USE_TYPE_SPECS + __pyx_ptype_5pysam_10libchtslib_HTSFile = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_10libchtslib_HTSFile_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_10libchtslib_HTSFile)) __PYX_ERR(0, 321, __pyx_L1_error) + if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_10libchtslib_HTSFile_spec, __pyx_ptype_5pysam_10libchtslib_HTSFile) < 0) __PYX_ERR(0, 321, __pyx_L1_error) + #else + __pyx_ptype_5pysam_10libchtslib_HTSFile = &__pyx_type_5pysam_10libchtslib_HTSFile; + #endif + #if !CYTHON_COMPILING_IN_LIMITED_API + #endif + #if !CYTHON_USE_TYPE_SPECS + if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_10libchtslib_HTSFile) < 0) __PYX_ERR(0, 321, __pyx_L1_error) + #endif + #if PY_MAJOR_VERSION < 3 + __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_print = 0; + #endif + #if !CYTHON_COMPILING_IN_LIMITED_API + if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_dictoffset && __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_getattro == PyObject_GenericGetAttr)) { + __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_getattro = __Pyx_PyObject_GenericGetAttr; + } + #endif + if (__Pyx_SetVtable(__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_vtabptr_5pysam_10libchtslib_HTSFile) < 0) __PYX_ERR(0, 321, __pyx_L1_error) + #if !CYTHON_COMPILING_IN_LIMITED_API + if (__Pyx_MergeVtables(__pyx_ptype_5pysam_10libchtslib_HTSFile) < 0) __PYX_ERR(0, 321, __pyx_L1_error) + #endif + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_HTSFile, (PyObject *) __pyx_ptype_5pysam_10libchtslib_HTSFile) < 0) __PYX_ERR(0, 321, __pyx_L1_error) + #if !CYTHON_COMPILING_IN_LIMITED_API + if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_10libchtslib_HTSFile) < 0) __PYX_ERR(0, 321, __pyx_L1_error) + #endif + __pyx_vtabptr_5pysam_10libchtslib_HFile = &__pyx_vtable_5pysam_10libchtslib_HFile; + __pyx_vtable_5pysam_10libchtslib_HFile._open = (PyObject *(*)(struct __pyx_obj_5pysam_10libchtslib_HFile *, PyObject *, PyObject *, struct __pyx_opt_args_5pysam_10libchtslib_5HFile__open *__pyx_optional_args))__pyx_f_5pysam_10libchtslib_5HFile__open; + #if CYTHON_USE_TYPE_SPECS + __pyx_ptype_5pysam_10libchtslib_HFile = (PyTypeObject *) __Pyx_PyType_FromModuleAndSpec(__pyx_m, &__pyx_type_5pysam_10libchtslib_HFile_spec, NULL); if (unlikely(!__pyx_ptype_5pysam_10libchtslib_HFile)) __PYX_ERR(0, 67, __pyx_L1_error) + if (__Pyx_fix_up_extension_type_from_spec(&__pyx_type_5pysam_10libchtslib_HFile_spec, __pyx_ptype_5pysam_10libchtslib_HFile) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + #else + __pyx_ptype_5pysam_10libchtslib_HFile = &__pyx_type_5pysam_10libchtslib_HFile; + #endif + #if !CYTHON_COMPILING_IN_LIMITED_API + #endif + #if !CYTHON_USE_TYPE_SPECS + if (__Pyx_PyType_Ready(__pyx_ptype_5pysam_10libchtslib_HFile) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + #endif + #if PY_MAJOR_VERSION < 3 + __pyx_ptype_5pysam_10libchtslib_HFile->tp_print = 0; + #endif + #if !CYTHON_COMPILING_IN_LIMITED_API + if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_ptype_5pysam_10libchtslib_HFile->tp_dictoffset && __pyx_ptype_5pysam_10libchtslib_HFile->tp_getattro == PyObject_GenericGetAttr)) { + __pyx_ptype_5pysam_10libchtslib_HFile->tp_getattro = __Pyx_PyObject_GenericGetAttr; + } + #endif + if (__Pyx_SetVtable(__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_vtabptr_5pysam_10libchtslib_HFile) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + #if !CYTHON_COMPILING_IN_LIMITED_API + if (__Pyx_MergeVtables(__pyx_ptype_5pysam_10libchtslib_HFile) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + #endif + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_HFile, (PyObject *) __pyx_ptype_5pysam_10libchtslib_HFile) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + #if !CYTHON_COMPILING_IN_LIMITED_API + if (__Pyx_setup_reduce((PyObject *) __pyx_ptype_5pysam_10libchtslib_HFile) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + #endif + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_RefNannyFinishContext(); + return -1; +} + +static int __Pyx_modinit_type_import_code(void) { + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0); + /*--- Type import code ---*/ + __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(5, 9, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", + #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000 + sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject), + #elif CYTHON_COMPILING_IN_LIMITED_API + sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject), + #else + sizeof(PyHeapTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyHeapTypeObject), + #endif + __Pyx_ImportType_CheckSize_Warn_3_0_11); if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(5, 9, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(6, 8, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __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) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(7, 15, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __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) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyImport_ImportModule("array"); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 69, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __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) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_RefNannyFinishContext(); + return -1; +} + +static int __Pyx_modinit_variable_import_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0); + /*--- Variable import code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_function_import_code(void) { + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0); + /*--- Function import code ---*/ + __pyx_t_1 = PyImport_ImportModule("pysam.libcutils"); if (!__pyx_t_1) __PYX_ERR(0, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "libc_whence_from_io", (void (**)(void))&__pyx_f_5pysam_9libcutils_libc_whence_from_io, "int (int)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) + 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) + if (__Pyx_ImportFunction_3_0_11(__pyx_t_1, "charptr_to_str_w_len", (void (**)(void))&__pyx_f_5pysam_9libcutils_charptr_to_str_w_len, "PyObject *(char const *, size_t, struct __pyx_opt_args_5pysam_9libcutils_charptr_to_str_w_len *__pyx_optional_args)") < 0) __PYX_ERR(0, 1, __pyx_L1_error) + 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) + 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) + 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) + 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) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_RefNannyFinishContext(); + return -1; +} + + +#if PY_MAJOR_VERSION >= 3 +#if CYTHON_PEP489_MULTI_PHASE_INIT +static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/ +static int __pyx_pymod_exec_libchtslib(PyObject* module); /*proto*/ +static PyModuleDef_Slot __pyx_moduledef_slots[] = { + {Py_mod_create, (void*)__pyx_pymod_create}, + {Py_mod_exec, (void*)__pyx_pymod_exec_libchtslib}, + {0, NULL} +}; +#endif + +#ifdef __cplusplus +namespace { + struct PyModuleDef __pyx_moduledef = + #else + static struct PyModuleDef __pyx_moduledef = + #endif + { + PyModuleDef_HEAD_INIT, + "libchtslib", + 0, /* m_doc */ + #if CYTHON_PEP489_MULTI_PHASE_INIT + 0, /* m_size */ + #elif CYTHON_USE_MODULE_STATE + sizeof(__pyx_mstate), /* m_size */ + #else + -1, /* m_size */ + #endif + __pyx_methods /* m_methods */, + #if CYTHON_PEP489_MULTI_PHASE_INIT + __pyx_moduledef_slots, /* m_slots */ + #else + NULL, /* m_reload */ + #endif + #if CYTHON_USE_MODULE_STATE + __pyx_m_traverse, /* m_traverse */ + __pyx_m_clear, /* m_clear */ + NULL /* m_free */ + #else + NULL, /* m_traverse */ + NULL, /* m_clear */ + NULL /* m_free */ + #endif + }; + #ifdef __cplusplus +} /* anonymous namespace */ +#endif +#endif + +#ifndef CYTHON_NO_PYINIT_EXPORT +#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC +#elif PY_MAJOR_VERSION < 3 +#ifdef __cplusplus +#define __Pyx_PyMODINIT_FUNC extern "C" void +#else +#define __Pyx_PyMODINIT_FUNC void +#endif +#else +#ifdef __cplusplus +#define __Pyx_PyMODINIT_FUNC extern "C" PyObject * +#else +#define __Pyx_PyMODINIT_FUNC PyObject * +#endif +#endif + + +#if PY_MAJOR_VERSION < 3 +__Pyx_PyMODINIT_FUNC initlibchtslib(void) CYTHON_SMALL_CODE; /*proto*/ +__Pyx_PyMODINIT_FUNC initlibchtslib(void) +#else +__Pyx_PyMODINIT_FUNC PyInit_libchtslib(void) CYTHON_SMALL_CODE; /*proto*/ +__Pyx_PyMODINIT_FUNC PyInit_libchtslib(void) +#if CYTHON_PEP489_MULTI_PHASE_INIT +{ + return PyModuleDef_Init(&__pyx_moduledef); +} +static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) { + #if PY_VERSION_HEX >= 0x030700A1 + static PY_INT64_T main_interpreter_id = -1; + PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp); + if (main_interpreter_id == -1) { + main_interpreter_id = current_id; + return (unlikely(current_id == -1)) ? -1 : 0; + } else if (unlikely(main_interpreter_id != current_id)) + #else + static PyInterpreterState *main_interpreter = NULL; + PyInterpreterState *current_interpreter = PyThreadState_Get()->interp; + if (!main_interpreter) { + main_interpreter = current_interpreter; + } else if (unlikely(main_interpreter != current_interpreter)) + #endif + { + PyErr_SetString( + PyExc_ImportError, + "Interpreter change detected - this module can only be loaded into one interpreter per process."); + return -1; + } + return 0; +} +#if CYTHON_COMPILING_IN_LIMITED_API +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) +#else +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) +#endif +{ + PyObject *value = PyObject_GetAttrString(spec, from_name); + int result = 0; + if (likely(value)) { + if (allow_none || value != Py_None) { +#if CYTHON_COMPILING_IN_LIMITED_API + result = PyModule_AddObject(module, to_name, value); +#else + result = PyDict_SetItemString(moddict, to_name, value); +#endif + } + Py_DECREF(value); + } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Clear(); + } else { + result = -1; + } + return result; +} +static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def) { + PyObject *module = NULL, *moddict, *modname; + CYTHON_UNUSED_VAR(def); + if (__Pyx_check_single_interpreter()) + return NULL; + if (__pyx_m) + return __Pyx_NewRef(__pyx_m); + modname = PyObject_GetAttrString(spec, "name"); + if (unlikely(!modname)) goto bad; + module = PyModule_NewObject(modname); + Py_DECREF(modname); + if (unlikely(!module)) goto bad; +#if CYTHON_COMPILING_IN_LIMITED_API + moddict = module; +#else + moddict = PyModule_GetDict(module); + if (unlikely(!moddict)) goto bad; +#endif + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad; + return module; +bad: + Py_XDECREF(module); + return NULL; +} + + +static CYTHON_SMALL_CODE int __pyx_pymod_exec_libchtslib(PyObject *__pyx_pyinit_module) +#endif +#endif +{ + int stringtab_initialized = 0; + #if CYTHON_USE_MODULE_STATE + int pystate_addmodule_run = 0; + #endif + __Pyx_TraceDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannyDeclarations + #if CYTHON_PEP489_MULTI_PHASE_INIT + if (__pyx_m) { + if (__pyx_m == __pyx_pyinit_module) return 0; + PyErr_SetString(PyExc_RuntimeError, "Module 'libchtslib' has already been imported. Re-initialisation is not supported."); + return -1; + } + #elif PY_MAJOR_VERSION >= 3 + if (__pyx_m) return __Pyx_NewRef(__pyx_m); + #endif + /*--- Module creation code ---*/ + #if CYTHON_PEP489_MULTI_PHASE_INIT + __pyx_m = __pyx_pyinit_module; + Py_INCREF(__pyx_m); + #else + #if PY_MAJOR_VERSION < 3 + __pyx_m = Py_InitModule4("libchtslib", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); + if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error) + #elif CYTHON_USE_MODULE_STATE + __pyx_t_1 = PyModule_Create(&__pyx_moduledef); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error) + { + int add_module_result = PyState_AddModule(__pyx_t_1, &__pyx_moduledef); + __pyx_t_1 = 0; /* transfer ownership from __pyx_t_1 to "libchtslib" pseudovariable */ + if (unlikely((add_module_result < 0))) __PYX_ERR(0, 1, __pyx_L1_error) + pystate_addmodule_run = 1; + } + #else + __pyx_m = PyModule_Create(&__pyx_moduledef); + if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #endif + CYTHON_UNUSED_VAR(__pyx_t_1); + __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error) + Py_INCREF(__pyx_d); + __pyx_b = __Pyx_PyImport_AddModuleRef(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_cython_runtime = __Pyx_PyImport_AddModuleRef((const char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error) + if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #if CYTHON_REFNANNY +__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); +if (!__Pyx_RefNanny) { + PyErr_Clear(); + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); + if (!__Pyx_RefNanny) + Py_FatalError("failed to import 'refnanny' module"); +} +#endif + __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_libchtslib(void)", 0); + 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) + #ifdef __Pxy_PyFrame_Initialize_Offsets + __Pxy_PyFrame_Initialize_Offsets(); + #endif + __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error) + #ifdef __Pyx_CyFunction_USED + if (__pyx_CyFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_FusedFunction_USED + if (__pyx_FusedFunction_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_Coroutine_USED + if (__pyx_Coroutine_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_Generator_USED + if (__pyx_Generator_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_AsyncGen_USED + if (__pyx_AsyncGen_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_StopAsyncIteration_USED + if (__pyx_StopAsyncIteration_init(__pyx_m) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + /*--- Library function declarations ---*/ + /*--- Threads initialization code ---*/ + #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + PyEval_InitThreads(); + #endif + /*--- Initialize various global constants etc. ---*/ + if (__Pyx_InitConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + stringtab_initialized = 1; + if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + if (__pyx_module_is_main_pysam__libchtslib) { + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name_2, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + } + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error) + if (!PyDict_GetItemString(modules, "pysam.libchtslib")) { + if (unlikely((PyDict_SetItemString(modules, "pysam.libchtslib", __pyx_m) < 0))) __PYX_ERR(0, 1, __pyx_L1_error) + } + } + #endif + /*--- Builtin init code ---*/ + if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + /*--- Constants init code ---*/ + if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + /*--- Global type/function init code ---*/ + (void)__Pyx_modinit_global_init_code(); + (void)__Pyx_modinit_variable_export_code(); + (void)__Pyx_modinit_function_export_code(); + if (unlikely((__Pyx_modinit_type_init_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error) + if (unlikely((__Pyx_modinit_type_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error) + (void)__Pyx_modinit_variable_import_code(); + if (unlikely((__Pyx_modinit_function_import_code() < 0))) __PYX_ERR(0, 1, __pyx_L1_error) + /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + __Pyx_TraceCall("__Pyx_PyMODINIT_FUNC PyInit_libchtslib(void)", __pyx_f[0], 1, 0, __PYX_ERR(0, 1, __pyx_L1_error)); + + /* "pysam/libchtslib.pyx":25 + * ######################################################################## + * + * import os # <<<<<<<<<<<<<< + * import io + * import re + */ + __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_os, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 25, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_os, __pyx_t_2) < 0) __PYX_ERR(0, 25, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":26 + * + * import os + * import io # <<<<<<<<<<<<<< + * import re + * from warnings import warn + */ + __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_io, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 26, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_io, __pyx_t_2) < 0) __PYX_ERR(0, 26, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":27 + * import os + * import io + * import re # <<<<<<<<<<<<<< + * from warnings import warn + * + */ + __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_re, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 27, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_re, __pyx_t_2) < 0) __PYX_ERR(0, 27, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":28 + * import io + * import re + * from warnings import warn # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 28, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(__pyx_n_s_warn); + __Pyx_GIVEREF(__pyx_n_s_warn); + if (__Pyx_PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_warn)) __PYX_ERR(0, 28, __pyx_L1_error); + __pyx_t_3 = __Pyx_Import(__pyx_n_s_warnings, __pyx_t_2, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 28, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_warn); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 28, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_warn, __pyx_t_2) < 0) __PYX_ERR(0, 28, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":36 + * ######################################################################## + * + * __all__ = ['get_verbosity', 'set_verbosity', 'HFile', 'HTSFile'] # <<<<<<<<<<<<<< + * + * # maximum genomic coordinace + */ + __pyx_t_3 = PyList_New(4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 36, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_INCREF(__pyx_n_u_get_verbosity); + __Pyx_GIVEREF(__pyx_n_u_get_verbosity); + if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_u_get_verbosity)) __PYX_ERR(0, 36, __pyx_L1_error); + __Pyx_INCREF(__pyx_n_u_set_verbosity); + __Pyx_GIVEREF(__pyx_n_u_set_verbosity); + if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 1, __pyx_n_u_set_verbosity)) __PYX_ERR(0, 36, __pyx_L1_error); + __Pyx_INCREF(__pyx_n_u_HFile); + __Pyx_GIVEREF(__pyx_n_u_HFile); + if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 2, __pyx_n_u_HFile)) __PYX_ERR(0, 36, __pyx_L1_error); + __Pyx_INCREF(__pyx_n_u_HTSFile); + __Pyx_GIVEREF(__pyx_n_u_HTSFile); + if (__Pyx_PyList_SET_ITEM(__pyx_t_3, 3, __pyx_n_u_HTSFile)) __PYX_ERR(0, 36, __pyx_L1_error); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_all, __pyx_t_3) < 0) __PYX_ERR(0, 36, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":39 + * + * # maximum genomic coordinace + * cdef int MAX_POS = (1 << 31) - 1 # <<<<<<<<<<<<<< + * + * cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS') + */ + __pyx_v_5pysam_10libchtslib_MAX_POS = 0x7fffffff; + + /* "pysam/libchtslib.pyx":41 + * cdef int MAX_POS = (1 << 31) - 1 + * + * cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS') # <<<<<<<<<<<<<< + * cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', + * 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') + */ + __Pyx_INCREF(__pyx_tuple__66); + __Pyx_XGOTREF(__pyx_v_5pysam_10libchtslib_FORMAT_CATEGORIES); + __Pyx_DECREF_SET(__pyx_v_5pysam_10libchtslib_FORMAT_CATEGORIES, __pyx_tuple__66); + __Pyx_GIVEREF(__pyx_tuple__66); + + /* "pysam/libchtslib.pyx":42 + * + * cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS') + * cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', # <<<<<<<<<<<<<< + * 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') + * cdef tuple COMPRESSION = ('NONE', 'GZIP', 'BGZF', 'CUSTOM') + */ + __Pyx_INCREF(__pyx_tuple__67); + __Pyx_XGOTREF(__pyx_v_5pysam_10libchtslib_FORMATS); + __Pyx_DECREF_SET(__pyx_v_5pysam_10libchtslib_FORMATS, __pyx_tuple__67); + __Pyx_GIVEREF(__pyx_tuple__67); + + /* "pysam/libchtslib.pyx":44 + * cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI', + * 'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED') + * cdef tuple COMPRESSION = ('NONE', 'GZIP', 'BGZF', 'CUSTOM') # <<<<<<<<<<<<<< + * + * + */ + __Pyx_INCREF(__pyx_tuple__68); + __Pyx_XGOTREF(__pyx_v_5pysam_10libchtslib_COMPRESSION); + __Pyx_DECREF_SET(__pyx_v_5pysam_10libchtslib_COMPRESSION, __pyx_tuple__68); + __Pyx_GIVEREF(__pyx_tuple__68); + + /* "pysam/libchtslib.pyx":53 + * + * + * cpdef set_verbosity(int verbosity): # <<<<<<<<<<<<<< + * """Set htslib's hts_verbose global variable to the specified value.""" + * return hts_set_verbosity(verbosity) + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_1set_verbosity, 0, __pyx_n_s_set_verbosity, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj_)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_set_verbosity, __pyx_t_3) < 0) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":57 + * return hts_set_verbosity(verbosity) + * + * cpdef get_verbosity(): # <<<<<<<<<<<<<< + * """Return the value of htslib's hts_verbose global variable.""" + * return hts_get_verbosity() + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_3get_verbosity, 0, __pyx_n_s_get_verbosity, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__2)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_get_verbosity, __pyx_t_3) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":98 + * raise IOError(errno, 'failed to open HFile', self.name) + * + * def close(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * return + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_5close, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_close, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__3)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 98, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_close, __pyx_t_3) < 0) __PYX_ERR(0, 98, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":108 + * raise IOError(errno, 'failed to close HFile', self.name) + * + * def fileno(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_7fileno, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_fileno, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__4)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 108, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_fileno, __pyx_t_3) < 0) __PYX_ERR(0, 108, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":116 + * raise AttributeError('fileno not available') + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_9__enter__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile___enter, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__7)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 116, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_enter, __pyx_t_3) < 0) __PYX_ERR(0, 116, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":119 + * return self + * + * def __exit__(self, type, value, tb): # <<<<<<<<<<<<<< + * self.close() + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_11__exit__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile___exit, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__8)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 119, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_exit, __pyx_t_3) < 0) __PYX_ERR(0, 119, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":131 + * return line + * + * def flush(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_17flush, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_flush, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__9)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 131, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_flush, __pyx_t_3) < 0) __PYX_ERR(0, 131, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":137 + * raise IOError(herrno(self.fp), 'failed to flush HFile', self.name) + * + * def isatty(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_19isatty, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_isatty, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_isatty, __pyx_t_3) < 0) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":142 + * return False + * + * def readable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'r' in self.mode + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_21readable, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_readable, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__11)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 142, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_readable, __pyx_t_3) < 0) __PYX_ERR(0, 142, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":145 + * return self.fp != NULL and 'r' in self.mode + * + * def read(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_23read, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_read, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__12)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 145, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__74); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_read, __pyx_t_3) < 0) __PYX_ERR(0, 145, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":180 + * return b''.join(parts) + * + * def readall(self): # <<<<<<<<<<<<<< + * return self.read() + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_25readall, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_readall, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__14)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_readall, __pyx_t_3) < 0) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":183 + * return self.read() + * + * def readinto(self, buf): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_27readinto, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_readinto, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__15)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 183, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_readinto, __pyx_t_3) < 0) __PYX_ERR(0, 183, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":200 + * return ret + * + * def readline(self, Py_ssize_t size=-1): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_29readline, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_readline, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__16)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 200, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__74); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_readline, __pyx_t_3) < 0) __PYX_ERR(0, 200, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":241 + * return b''.join(parts) + * + * def readlines(self): # <<<<<<<<<<<<<< + * return list(self) + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_31readlines, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_readlines, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__17)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 241, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_readlines, __pyx_t_3) < 0) __PYX_ERR(0, 241, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":244 + * return list(self) + * + * def seek(self, Py_ssize_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_io); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_SEEK_SET); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_k__18 = __pyx_t_4; + __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_io); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_SEEK_SET); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_GIVEREF(__pyx_t_3); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3)) __PYX_ERR(0, 244, __pyx_L1_error); + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_33seek, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_seek, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__19)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_seek, __pyx_t_3) < 0) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":255 + * return off + * + * def tell(self): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_35tell, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_tell, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__20)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 255, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_tell, __pyx_t_3) < 0) __PYX_ERR(0, 255, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":266 + * return ret + * + * def seekable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_37seekable, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_seekable, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__21)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 266, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_seekable, __pyx_t_3) < 0) __PYX_ERR(0, 266, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":269 + * return self.fp != NULL + * + * def truncate(self, size=None): # <<<<<<<<<<<<<< + * raise NotImplementedError() + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_39truncate, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_truncate, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__22)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 269, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__79); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_truncate, __pyx_t_3) < 0) __PYX_ERR(0, 269, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":272 + * raise NotImplementedError() + * + * def writable(self): # <<<<<<<<<<<<<< + * return self.fp != NULL and 'w' in self.mode + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_41writable, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_writable, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__23)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 272, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_writable, __pyx_t_3) < 0) __PYX_ERR(0, 272, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":275 + * return self.fp != NULL and 'w' in self.mode + * + * def write(self, bytes b): # <<<<<<<<<<<<<< + * if self.fp == NULL: + * raise IOError('operation on closed HFile') + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_43write, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_write, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__24)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 275, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_write, __pyx_t_3) < 0) __PYX_ERR(0, 275, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "pysam/libchtslib.pyx":286 + * return got + * + * def writelines(self, lines): # <<<<<<<<<<<<<< + * for line in lines: + * self.write(line) + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_45writelines, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile_writelines, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__25)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 286, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HFile, __pyx_n_s_writelines, __pyx_t_3) < 0) __PYX_ERR(0, 286, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HFile); + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_47__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile___reduce_cython, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__26)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "self.fp cannot be converted to a Python object for pickling" + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_5HFile_49__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HFile___setstate_cython, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__27)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":297 + * ######################################################################## + * + * class CallableValue(object): # <<<<<<<<<<<<<< + * def __init__(self, value): + * self.value = value + */ + __pyx_t_3 = __Pyx_PEP560_update_bases(__pyx_tuple__84); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = __Pyx_CalculateMetaclass(NULL, __pyx_t_3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_5 = __Pyx_Py3MetaclassPrepare(__pyx_t_2, __pyx_t_3, __pyx_n_s_CallableValue, __pyx_n_s_CallableValue, (PyObject *) NULL, __pyx_n_s_pysam_libchtslib, (PyObject *) NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (__pyx_t_3 != __pyx_tuple__84) { + if (unlikely((PyDict_SetItemString(__pyx_t_5, "__orig_bases__", __pyx_tuple__84) < 0))) __PYX_ERR(0, 297, __pyx_L1_error) + } + + /* "pysam/libchtslib.pyx":298 + * + * class CallableValue(object): + * def __init__(self, value): # <<<<<<<<<<<<<< + * self.value = value + * def __call__(self): + */ + __pyx_t_6 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_13CallableValue_1__init__, 0, __pyx_n_s_CallableValue___init, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__28)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 298, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_init, __pyx_t_6) < 0) __PYX_ERR(0, 298, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":300 + * def __init__(self, value): + * self.value = value + * def __call__(self): # <<<<<<<<<<<<<< + * return self.value + * def __bool__(self): + */ + __pyx_t_6 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_13CallableValue_3__call__, 0, __pyx_n_s_CallableValue___call, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__29)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 300, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_call, __pyx_t_6) < 0) __PYX_ERR(0, 300, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":302 + * def __call__(self): + * return self.value + * def __bool__(self): # <<<<<<<<<<<<<< + * return self.value + * def __nonzero__(self): + */ + __pyx_t_6 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_13CallableValue_5__bool__, 0, __pyx_n_s_CallableValue___bool, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__30)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 302, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_bool, __pyx_t_6) < 0) __PYX_ERR(0, 302, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":304 + * def __bool__(self): + * return self.value + * def __nonzero__(self): # <<<<<<<<<<<<<< + * return self.value + * def __eq__(self, other): + */ + __pyx_t_6 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_13CallableValue_7__nonzero__, 0, __pyx_n_s_CallableValue___nonzero, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__31)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 304, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_nonzero, __pyx_t_6) < 0) __PYX_ERR(0, 304, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":306 + * def __nonzero__(self): + * return self.value + * def __eq__(self, other): # <<<<<<<<<<<<<< + * return self.value == other + * def __ne__(self, other): + */ + __pyx_t_6 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_13CallableValue_9__eq__, 0, __pyx_n_s_CallableValue___eq, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__32)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 306, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_eq, __pyx_t_6) < 0) __PYX_ERR(0, 306, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":308 + * def __eq__(self, other): + * return self.value == other + * def __ne__(self, other): # <<<<<<<<<<<<<< + * return self.value != other + * + */ + __pyx_t_6 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_13CallableValue_11__ne__, 0, __pyx_n_s_CallableValue___ne, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__33)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 308, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_ne, __pyx_t_6) < 0) __PYX_ERR(0, 308, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pysam/libchtslib.pyx":297 + * ######################################################################## + * + * class CallableValue(object): # <<<<<<<<<<<<<< + * def __init__(self, value): + * self.value = value + */ + __pyx_t_6 = __Pyx_Py3ClassCreate(__pyx_t_2, __pyx_n_s_CallableValue, __pyx_t_3, __pyx_t_5, NULL, 0, 0); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_CallableValue, __pyx_t_6) < 0) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":312 + * + * + * CTrue = CallableValue(True) # <<<<<<<<<<<<<< + * CFalse = CallableValue(False) + * + */ + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_CallableValue); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 312, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__87, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 312, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PyDict_SetItem(__pyx_d, __pyx_n_s_CTrue, __pyx_t_2) < 0) __PYX_ERR(0, 312, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pysam/libchtslib.pyx":313 + * + * CTrue = CallableValue(True) + * CFalse = CallableValue(False) # <<<<<<<<<<<<<< + * + * + */ + __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_CallableValue); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 313, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__88, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 313, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (PyDict_SetItem(__pyx_d, __pyx_n_s_CFalse, __pyx_t_3) < 0) __PYX_ERR(0, 313, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":331 + * self.duplicate_filehandle = True + * + * def close(self): # <<<<<<<<<<<<<< + * if self.htsfile: + * hts_close(self.htsfile) + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_3close, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_close, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__34)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 331, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_close, __pyx_t_3) < 0) __PYX_ERR(0, 331, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":341 + * self.htsfile = NULL + * + * def flush(self): # <<<<<<<<<<<<<< + * """Flush any buffered data to the underlying output stream.""" + * if self.htsfile: + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_7flush, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_flush, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__35)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 341, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_flush, __pyx_t_3) < 0) __PYX_ERR(0, 341, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":347 + * raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename)) + * + * def check_truncation(self, ignore_truncation=False): # <<<<<<<<<<<<<< + * """Check if file is truncated.""" + * if not self.htsfile: + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_9check_truncation, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_check_truncation, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__36)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 347, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__88); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_check_truncation, __pyx_t_3) < 0) __PYX_ERR(0, 347, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":369 + * raise IOError(msg) + * + * def __enter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_11__enter__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile___enter, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__37)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 369, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_enter, __pyx_t_3) < 0) __PYX_ERR(0, 369, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":372 + * return self + * + * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<< + * self.close() + * return False + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_13__exit__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile___exit, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__38)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 372, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_exit, __pyx_t_3) < 0) __PYX_ERR(0, 372, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":472 + * return self.htsfile != NULL and self.htsfile.format.format == bcf + * + * def reset(self): # <<<<<<<<<<<<<< + * """reset file position to beginning of file just after the header. + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_15reset, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_reset, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__40)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 472, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_reset, __pyx_t_3) < 0) __PYX_ERR(0, 472, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":483 + * return self.seek(self.start_offset) + * + * def seek(self, uint64_t offset, int whence=io.SEEK_SET): # <<<<<<<<<<<<<< + * """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`.""" + * if not self.is_open: + */ + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_io); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_SEEK_SET); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_k__41 = __pyx_t_4; + __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_io); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_SEEK_SET); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_GIVEREF(__pyx_t_3); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3)) __PYX_ERR(0, 483, __pyx_L1_error); + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_17seek, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_seek, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__42)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_t_2); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_seek, __pyx_t_3) < 0) __PYX_ERR(0, 483, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":503 + * return ret + * + * def tell(self): # <<<<<<<<<<<<<< + * """return current file position, see :meth:`pysam.HTSFile.seek`.""" + * if not self.is_open: + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_19tell, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_tell, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__45)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 503, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_tell, __pyx_t_3) < 0) __PYX_ERR(0, 503, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":575 + * return htsfile + * + * def add_hts_options(self, format_options=None): # <<<<<<<<<<<<<< + * """Given a list of key=value format option strings, add them to an open htsFile + * """ + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_21add_hts_options, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_add_hts_options, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__50)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 575, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__79); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_add_hts_options, __pyx_t_3) < 0) __PYX_ERR(0, 575, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":595 + * hts_opt_free(opts) + * + * def parse_region(self, contig=None, start=None, stop=None, # <<<<<<<<<<<<<< + * region=None, tid=None, + * reference=None, end=None): + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_23parse_region, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_parse_region, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__52)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 595, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_3, __pyx_tuple__94); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_parse_region, __pyx_t_3) < 0) __PYX_ERR(0, 595, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":700 + * return 1, rtid, rstart, rstop + * + * def is_valid_tid(self, tid): # <<<<<<<<<<<<<< + * """ + * return True if the numerical :term:`tid` is valid; False otherwise. + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_25is_valid_tid, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_is_valid_tid, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__60)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 700, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_is_valid_tid, __pyx_t_3) < 0) __PYX_ERR(0, 700, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":708 + * raise NotImplementedError() + * + * def is_valid_reference_name(self, contig): # <<<<<<<<<<<<<< + * """ + * return True if the contig name :term:`contig` is valid; False otherwise. + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_27is_valid_reference_name, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_is_valid_reference_name, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__61)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 708, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_is_valid_reference_name, __pyx_t_3) < 0) __PYX_ERR(0, 708, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":714 + * return self.get_tid(contig) != -1 + * + * def get_tid(self, contig): # <<<<<<<<<<<<<< + * """ + * return the numerical :term:`tid` corresponding to + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_29get_tid, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_get_tid, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__62)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 714, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_get_tid, __pyx_t_3) < 0) __PYX_ERR(0, 714, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "pysam/libchtslib.pyx":723 + * raise NotImplementedError() + * + * def get_reference_name(self, tid): # <<<<<<<<<<<<<< + * """ + * return :term:`contig` name corresponding to numerical :term:`tid` + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_31get_reference_name, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile_get_reference_name, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__63)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 723, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetItemOnTypeDict((PyObject *)__pyx_ptype_5pysam_10libchtslib_HTSFile, __pyx_n_s_get_reference_name, __pyx_t_3) < 0) __PYX_ERR(0, 723, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + PyType_Modified(__pyx_ptype_5pysam_10libchtslib_HTSFile); + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_33__reduce_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile___reduce_cython, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__64)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_reduce_cython, __pyx_t_3) < 0) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError, "no default __reduce__ due to non-trivial __cinit__" + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_5pysam_10libchtslib_7HTSFile_35__setstate_cython__, __Pyx_CYFUNCTION_CCLASS, __pyx_n_s_HTSFile___setstate_cython, NULL, __pyx_n_s_pysam_libchtslib, __pyx_d, ((PyObject *)__pyx_codeobj__65)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 3, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_setstate_cython, __pyx_t_3) < 0) __PYX_ERR(1, 3, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pysam/libchtslib.pyx":1 + * # cython: language_level=3 # <<<<<<<<<<<<<< + * # cython: embedsignature=True + * # cython: profile=True + */ + __pyx_t_3 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_3) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_TraceReturn(Py_None, 0); + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + if (__pyx_m) { + if (__pyx_d && stringtab_initialized) { + __Pyx_AddTraceback("init pysam.libchtslib", __pyx_clineno, __pyx_lineno, __pyx_filename); + } + #if !CYTHON_USE_MODULE_STATE + Py_CLEAR(__pyx_m); + #else + Py_DECREF(__pyx_m); + if (pystate_addmodule_run) { + PyObject *tp, *value, *tb; + PyErr_Fetch(&tp, &value, &tb); + PyState_RemoveModule(&__pyx_moduledef); + PyErr_Restore(tp, value, tb); + } + #endif + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init pysam.libchtslib"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if CYTHON_PEP489_MULTI_PHASE_INIT + return (__pyx_m != NULL) ? 0 : -1; + #elif PY_MAJOR_VERSION >= 3 + return __pyx_m; + #else + return; + #endif +} +/* #### Code section: cleanup_globals ### */ +/* #### Code section: cleanup_module ### */ +/* #### Code section: main_method ### */ +/* #### Code section: utility_code_pragmas ### */ +#ifdef _MSC_VER +#pragma warning( push ) +/* Warning 4127: conditional expression is constant + * Cython uses constant conditional expressions to allow in inline functions to be optimized at + * compile-time, so this warning is not useful + */ +#pragma warning( disable : 4127 ) +#endif + + + +/* #### Code section: utility_code_def ### */ + +/* --- Runtime support code --- */ +/* Refnanny */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule(modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, "RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +/* PyErrExceptionMatches */ +#if CYTHON_FAST_THREAD_STATE +static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i<n; i++) { + if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1; + } +#endif + for (i=0; i<n; i++) { + if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1; + } + return 0; +} +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) { + int result; + PyObject *exc_type; +#if PY_VERSION_HEX >= 0x030C00A6 + PyObject *current_exception = tstate->current_exception; + if (unlikely(!current_exception)) return 0; + exc_type = (PyObject*) Py_TYPE(current_exception); + if (exc_type == err) return 1; +#else + exc_type = tstate->curexc_type; + if (exc_type == err) return 1; + if (unlikely(!exc_type)) return 0; +#endif + #if CYTHON_AVOID_BORROWED_REFS + Py_INCREF(exc_type); + #endif + if (unlikely(PyTuple_Check(err))) { + result = __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); + } else { + result = __Pyx_PyErr_GivenExceptionMatches(exc_type, err); + } + #if CYTHON_AVOID_BORROWED_REFS + Py_DECREF(exc_type); + #endif + return result; +} +#endif + +/* PyErrFetchRestore */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { +#if PY_VERSION_HEX >= 0x030C00A6 + PyObject *tmp_value; + assert(type == NULL || (value != NULL && type == (PyObject*) Py_TYPE(value))); + if (value) { + #if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(((PyBaseExceptionObject*) value)->traceback != tb)) + #endif + PyException_SetTraceback(value, tb); + } + tmp_value = tstate->current_exception; + tstate->current_exception = value; + Py_XDECREF(tmp_value); + Py_XDECREF(type); + Py_XDECREF(tb); +#else + PyObject *tmp_type, *tmp_value, *tmp_tb; + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { +#if PY_VERSION_HEX >= 0x030C00A6 + PyObject* exc_value; + exc_value = tstate->current_exception; + tstate->current_exception = 0; + *value = exc_value; + *type = NULL; + *tb = NULL; + if (exc_value) { + *type = (PyObject*) Py_TYPE(exc_value); + Py_INCREF(*type); + #if CYTHON_COMPILING_IN_CPYTHON + *tb = ((PyBaseExceptionObject*) exc_value)->traceback; + Py_XINCREF(*tb); + #else + *tb = PyException_GetTraceback(exc_value); + #endif + } +#else + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#endif +} +#endif + +/* PyObjectGetAttrStr */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#endif + +/* PyObjectGetAttrStrNoError */ +#if __PYX_LIMITED_VERSION_HEX < 0x030d00A1 +static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + __Pyx_PyErr_Clear(); +} +#endif +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { + PyObject *result; +#if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1 + (void) PyObject_GetOptionalAttr(obj, attr_name, &result); + return result; +#else +#if CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_TYPE_SLOTS && PY_VERSION_HEX >= 0x030700B1 + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro == PyObject_GenericGetAttr)) { + return _PyObject_GenericGetAttrWithDict(obj, attr_name, NULL, 1); + } +#endif + result = __Pyx_PyObject_GetAttrStr(obj, attr_name); + if (unlikely(!result)) { + __Pyx_PyObject_GetAttrStr_ClearAttributeError(); + } + return result; +#endif +} + +/* GetBuiltinName */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStrNoError(__pyx_b, name); + if (unlikely(!result) && !PyErr_Occurred()) { + PyErr_Format(PyExc_NameError, +#if PY_MAJOR_VERSION >= 3 + "name '%U' is not defined", name); +#else + "name '%.200s' is not defined", PyString_AS_STRING(name)); +#endif + } + return result; +} + +/* TupleAndListFromArray */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE void __Pyx_copy_object_array(PyObject *const *CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) { + PyObject *v; + Py_ssize_t i; + for (i = 0; i < length; i++) { + v = dest[i] = src[i]; + Py_INCREF(v); + } +} +static CYTHON_INLINE PyObject * +__Pyx_PyTuple_FromArray(PyObject *const *src, Py_ssize_t n) +{ + PyObject *res; + if (n <= 0) { + Py_INCREF(__pyx_empty_tuple); + return __pyx_empty_tuple; + } + res = PyTuple_New(n); + if (unlikely(res == NULL)) return NULL; + __Pyx_copy_object_array(src, ((PyTupleObject*)res)->ob_item, n); + return res; +} +static CYTHON_INLINE PyObject * +__Pyx_PyList_FromArray(PyObject *const *src, Py_ssize_t n) +{ + PyObject *res; + if (n <= 0) { + return PyList_New(0); + } + res = PyList_New(n); + if (unlikely(res == NULL)) return NULL; + __Pyx_copy_object_array(src, ((PyListObject*)res)->ob_item, n); + return res; +} +#endif + +/* BytesEquals */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result; +#if CYTHON_USE_UNICODE_INTERNALS && (PY_VERSION_HEX < 0x030B0000) + Py_hash_t hash1, hash2; + hash1 = ((PyBytesObject*)s1)->ob_shash; + hash2 = ((PyBytesObject*)s2)->ob_shash; + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + return (equals == Py_NE); + } +#endif + result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +/* UnicodeEquals */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; + #else + hash1 = ((PyUnicodeObject*)s1)->hash; + hash2 = ((PyUnicodeObject*)s2)->hash; + #endif + if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { + goto return_ne; + } + } +#endif + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +/* fastcall */ +#if CYTHON_METH_FASTCALL +static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues, PyObject *s) +{ + Py_ssize_t i, n = PyTuple_GET_SIZE(kwnames); + for (i = 0; i < n; i++) + { + if (s == PyTuple_GET_ITEM(kwnames, i)) return kwvalues[i]; + } + for (i = 0; i < n; i++) + { + int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ); + if (unlikely(eq != 0)) { + if (unlikely(eq < 0)) return NULL; + return kwvalues[i]; + } + } + return NULL; +} +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000 +CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) { + Py_ssize_t i, nkwargs = PyTuple_GET_SIZE(kwnames); + PyObject *dict; + dict = PyDict_New(); + if (unlikely(!dict)) + return NULL; + for (i=0; i<nkwargs; i++) { + PyObject *key = PyTuple_GET_ITEM(kwnames, i); + if (unlikely(PyDict_SetItem(dict, key, kwvalues[i]) < 0)) + goto bad; + } + return dict; +bad: + Py_DECREF(dict); + return NULL; +} +#endif +#endif + +/* Profile */ +#if CYTHON_PROFILE +static int __Pyx_TraceSetupAndCall(PyCodeObject** code, + PyFrameObject** frame, + PyThreadState* tstate, + const char *funcname, + const char *srcfile, + int firstlineno) { + PyObject *type, *value, *traceback; + int retval; + if (*frame == NULL || !CYTHON_PROFILE_REUSE_FRAME) { + if (*code == NULL) { + *code = __Pyx_createFrameCodeObject(funcname, srcfile, firstlineno); + if (*code == NULL) return 0; + } + *frame = PyFrame_New( + tstate, /*PyThreadState *tstate*/ + *code, /*PyCodeObject *code*/ + __pyx_d, /*PyObject *globals*/ + 0 /*PyObject *locals*/ + ); + if (*frame == NULL) return 0; + if (CYTHON_TRACE && (*frame)->f_trace == NULL) { + Py_INCREF(Py_None); + (*frame)->f_trace = Py_None; + } +#if PY_VERSION_HEX < 0x030400B1 + } else { + (*frame)->f_tstate = tstate; +#endif + } + __Pyx_PyFrame_SetLineNumber(*frame, firstlineno); + retval = 1; + __Pyx_EnterTracing(tstate); + __Pyx_ErrFetchInState(tstate, &type, &value, &traceback); + #if CYTHON_TRACE + if (tstate->c_tracefunc) + retval = tstate->c_tracefunc(tstate->c_traceobj, *frame, PyTrace_CALL, NULL) == 0; + if (retval && tstate->c_profilefunc) + #endif + retval = tstate->c_profilefunc(tstate->c_profileobj, *frame, PyTrace_CALL, NULL) == 0; + __Pyx_LeaveTracing(tstate); + if (retval) { + __Pyx_ErrRestoreInState(tstate, type, value, traceback); + return __Pyx_IsTracing(tstate, 0, 0) && retval; + } else { + Py_XDECREF(type); + Py_XDECREF(value); + Py_XDECREF(traceback); + return -1; + } +} +static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) { + PyCodeObject *py_code = 0; +#if PY_MAJOR_VERSION >= 3 + py_code = PyCode_NewEmpty(srcfile, funcname, firstlineno); + if (likely(py_code)) { + py_code->co_flags |= CO_OPTIMIZED | CO_NEWLOCALS; + } +#else + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + py_funcname = PyString_FromString(funcname); + if (unlikely(!py_funcname)) goto bad; + py_srcfile = PyString_FromString(srcfile); + if (unlikely(!py_srcfile)) goto bad; + py_code = PyCode_New( + 0, + 0, + 0, + CO_OPTIMIZED | CO_NEWLOCALS, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + firstlineno, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); +#endif + return py_code; +} +#endif + +/* RaiseDoubleKeywords */ +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +/* ParseKeywords */ +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject *const *kwvalues, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + int kwds_is_tuple = CYTHON_METH_FASTCALL && likely(PyTuple_Check(kwds)); + while (1) { + Py_XDECREF(key); key = NULL; + Py_XDECREF(value); value = NULL; + if (kwds_is_tuple) { + Py_ssize_t size; +#if CYTHON_ASSUME_SAFE_MACROS + size = PyTuple_GET_SIZE(kwds); +#else + size = PyTuple_Size(kwds); + if (size < 0) goto bad; +#endif + if (pos >= size) break; +#if CYTHON_AVOID_BORROWED_REFS + key = __Pyx_PySequence_ITEM(kwds, pos); + if (!key) goto bad; +#elif CYTHON_ASSUME_SAFE_MACROS + key = PyTuple_GET_ITEM(kwds, pos); +#else + key = PyTuple_GetItem(kwds, pos); + if (!key) goto bad; +#endif + value = kwvalues[pos]; + pos++; + } + else + { + if (!PyDict_Next(kwds, &pos, &key, &value)) break; +#if CYTHON_AVOID_BORROWED_REFS + Py_INCREF(key); +#endif + } + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; +#if CYTHON_AVOID_BORROWED_REFS + Py_INCREF(value); + Py_DECREF(key); +#endif + key = NULL; + value = NULL; + continue; + } +#if !CYTHON_AVOID_BORROWED_REFS + Py_INCREF(key); +#endif + Py_INCREF(value); + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; +#if CYTHON_AVOID_BORROWED_REFS + value = NULL; +#endif + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = ( + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key) + ); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; +#if CYTHON_AVOID_BORROWED_REFS + value = NULL; +#endif + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + Py_XDECREF(key); + Py_XDECREF(value); + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + #if PY_MAJOR_VERSION < 3 + PyErr_Format(PyExc_TypeError, + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + PyErr_Format(PyExc_TypeError, + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + Py_XDECREF(key); + Py_XDECREF(value); + return -1; +} + +/* RaiseArgTupleInvalid */ +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +/* PyFunctionFastCall */ +#if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL +static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, + PyObject *globals) { + PyFrameObject *f; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject **fastlocals; + Py_ssize_t i; + PyObject *result; + assert(globals != NULL); + /* XXX Perhaps we should create a specialized + PyFrame_New() that doesn't take locals, but does + take builtins without sanity checking them. + */ + assert(tstate != NULL); + f = PyFrame_New(tstate, co, globals, NULL); + if (f == NULL) { + return NULL; + } + fastlocals = __Pyx_PyFrame_GetLocalsplus(f); + for (i = 0; i < na; i++) { + Py_INCREF(*args); + fastlocals[i] = *args++; + } + result = PyEval_EvalFrameEx(f,0); + ++tstate->recursion_depth; + Py_DECREF(f); + --tstate->recursion_depth; + return result; +} +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { + PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); + PyObject *globals = PyFunction_GET_GLOBALS(func); + PyObject *argdefs = PyFunction_GET_DEFAULTS(func); + PyObject *closure; +#if PY_MAJOR_VERSION >= 3 + PyObject *kwdefs; +#endif + PyObject *kwtuple, **k; + PyObject **d; + Py_ssize_t nd; + Py_ssize_t nk; + PyObject *result; + assert(kwargs == NULL || PyDict_Check(kwargs)); + nk = kwargs ? PyDict_Size(kwargs) : 0; + #if PY_MAJOR_VERSION < 3 + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) { + return NULL; + } + #else + if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) { + return NULL; + } + #endif + if ( +#if PY_MAJOR_VERSION >= 3 + co->co_kwonlyargcount == 0 && +#endif + likely(kwargs == NULL || nk == 0) && + co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { + if (argdefs == NULL && co->co_argcount == nargs) { + result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); + goto done; + } + else if (nargs == 0 && argdefs != NULL + && co->co_argcount == Py_SIZE(argdefs)) { + /* function called with no arguments, but all parameters have + a default value: use default values as arguments .*/ + args = &PyTuple_GET_ITEM(argdefs, 0); + result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); + goto done; + } + } + if (kwargs != NULL) { + Py_ssize_t pos, i; + kwtuple = PyTuple_New(2 * nk); + if (kwtuple == NULL) { + result = NULL; + goto done; + } + k = &PyTuple_GET_ITEM(kwtuple, 0); + pos = i = 0; + while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { + Py_INCREF(k[i]); + Py_INCREF(k[i+1]); + i += 2; + } + nk = i / 2; + } + else { + kwtuple = NULL; + k = NULL; + } + closure = PyFunction_GET_CLOSURE(func); +#if PY_MAJOR_VERSION >= 3 + kwdefs = PyFunction_GET_KW_DEFAULTS(func); +#endif + if (argdefs != NULL) { + d = &PyTuple_GET_ITEM(argdefs, 0); + nd = Py_SIZE(argdefs); + } + else { + d = NULL; + nd = 0; + } +#if PY_MAJOR_VERSION >= 3 + result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, + args, (int)nargs, + k, (int)nk, + d, (int)nd, kwdefs, closure); +#else + result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, + args, (int)nargs, + k, (int)nk, + d, (int)nd, closure); +#endif + Py_XDECREF(kwtuple); +done: + Py_LeaveRecursiveCall(); + return result; +} +#endif + +/* PyObjectCall */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = Py_TYPE(func)->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + #if PY_MAJOR_VERSION < 3 + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + #else + if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) + return NULL; + #endif + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectCallMethO */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func); + self = __Pyx_CyOrPyCFunction_GET_SELF(func); + #if PY_MAJOR_VERSION < 3 + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + #else + if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) + return NULL; + #endif + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +/* PyObjectFastCall */ +#if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API +static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) { + PyObject *argstuple; + PyObject *result = 0; + size_t i; + argstuple = PyTuple_New((Py_ssize_t)nargs); + if (unlikely(!argstuple)) return NULL; + for (i = 0; i < nargs; i++) { + Py_INCREF(args[i]); + if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad; + } + result = __Pyx_PyObject_Call(func, argstuple, kwargs); + bad: + Py_DECREF(argstuple); + return result; +} +#endif +static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) { + Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs); +#if CYTHON_COMPILING_IN_CPYTHON + if (nargs == 0 && kwargs == NULL) { + if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS)) + return __Pyx_PyObject_CallMethO(func, NULL); + } + else if (nargs == 1 && kwargs == NULL) { + if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O)) + return __Pyx_PyObject_CallMethO(func, args[0]); + } +#endif + #if PY_VERSION_HEX < 0x030800B1 + #if CYTHON_FAST_PYCCALL + if (PyCFunction_Check(func)) { + if (kwargs) { + return _PyCFunction_FastCallDict(func, args, nargs, kwargs); + } else { + return _PyCFunction_FastCallKeywords(func, args, nargs, NULL); + } + } + #if PY_VERSION_HEX >= 0x030700A1 + if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) { + return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL); + } + #endif + #endif + #if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs); + } + #endif + #endif + if (kwargs == NULL) { + #if CYTHON_VECTORCALL + #if PY_VERSION_HEX < 0x03090000 + vectorcallfunc f = _PyVectorcall_Function(func); + #else + vectorcallfunc f = PyVectorcall_Function(func); + #endif + if (f) { + return f(func, args, (size_t)nargs, NULL); + } + #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL + if (__Pyx_CyFunction_CheckExact(func)) { + __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func); + if (f) return f(func, args, (size_t)nargs, NULL); + } + #endif + } + if (nargs == 0) { + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs); + } + #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API + return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs); + #else + return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs); + #endif +} + +/* WriteUnraisableException */ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback, int nogil) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_PyThreadState_declare +#ifdef WITH_THREAD + PyGILState_STATE state; + if (nogil) + state = PyGILState_Ensure(); + else state = (PyGILState_STATE)0; +#endif + CYTHON_UNUSED_VAR(clineno); + CYTHON_UNUSED_VAR(lineno); + CYTHON_UNUSED_VAR(filename); + CYTHON_MAYBE_UNUSED_VAR(nogil); + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(0); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +#ifdef WITH_THREAD + if (nogil) + PyGILState_Release(state); +#endif +} + +/* RaiseException */ +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + __Pyx_PyThreadState_declare + CYTHON_UNUSED_VAR(cause); + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_PyThreadState_assign + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { + instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } + if (cause) { + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { + #if PY_VERSION_HEX >= 0x030C00A6 + PyException_SetTraceback(value, tb); + #elif CYTHON_FAST_THREAD_STATE + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#else + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +/* KeywordStringCheck */ +static int __Pyx_CheckKeywordStrings( + PyObject *kw, + const char* function_name, + int kw_allowed) +{ + PyObject* key = 0; + Py_ssize_t pos = 0; +#if CYTHON_COMPILING_IN_PYPY + if (!kw_allowed && PyDict_Next(kw, &pos, &key, 0)) + goto invalid_keyword; + return 1; +#else + if (CYTHON_METH_FASTCALL && likely(PyTuple_Check(kw))) { + Py_ssize_t kwsize; +#if CYTHON_ASSUME_SAFE_MACROS + kwsize = PyTuple_GET_SIZE(kw); +#else + kwsize = PyTuple_Size(kw); + if (kwsize < 0) return 0; +#endif + if (unlikely(kwsize == 0)) + return 1; + if (!kw_allowed) { +#if CYTHON_ASSUME_SAFE_MACROS + key = PyTuple_GET_ITEM(kw, 0); +#else + key = PyTuple_GetItem(kw, pos); + if (!key) return 0; +#endif + goto invalid_keyword; + } +#if PY_VERSION_HEX < 0x03090000 + for (pos = 0; pos < kwsize; pos++) { +#if CYTHON_ASSUME_SAFE_MACROS + key = PyTuple_GET_ITEM(kw, pos); +#else + key = PyTuple_GetItem(kw, pos); + if (!key) return 0; +#endif + if (unlikely(!PyUnicode_Check(key))) + goto invalid_keyword_type; + } +#endif + return 1; + } + while (PyDict_Next(kw, &pos, &key, 0)) { + #if PY_MAJOR_VERSION < 3 + if (unlikely(!PyString_Check(key))) + #endif + if (unlikely(!PyUnicode_Check(key))) + goto invalid_keyword_type; + } + if (!kw_allowed && unlikely(key)) + goto invalid_keyword; + return 1; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + return 0; +#endif +invalid_keyword: + #if PY_MAJOR_VERSION < 3 + PyErr_Format(PyExc_TypeError, + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + PyErr_Format(PyExc_TypeError, + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif + return 0; +} + +/* PyObjectCall2Args */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { + PyObject *args[3] = {NULL, arg1, arg2}; + return __Pyx_PyObject_FastCall(function, args+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +} + +/* PyObjectCallOneArg */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *args[2] = {NULL, arg}; + return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +} + +/* PyObjectGetMethod */ +static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) { + PyObject *attr; +#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP + __Pyx_TypeName type_name; + PyTypeObject *tp = Py_TYPE(obj); + PyObject *descr; + descrgetfunc f = NULL; + PyObject **dictptr, *dict; + int meth_found = 0; + assert (*method == NULL); + if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) { + attr = __Pyx_PyObject_GetAttrStr(obj, name); + goto try_unpack; + } + if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) { + return 0; + } + descr = _PyType_Lookup(tp, name); + if (likely(descr != NULL)) { + Py_INCREF(descr); +#if defined(Py_TPFLAGS_METHOD_DESCRIPTOR) && Py_TPFLAGS_METHOD_DESCRIPTOR + if (__Pyx_PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_METHOD_DESCRIPTOR)) +#elif PY_MAJOR_VERSION >= 3 + #ifdef __Pyx_CyFunction_USED + if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr))) + #else + if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type))) + #endif +#else + #ifdef __Pyx_CyFunction_USED + if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr))) + #else + if (likely(PyFunction_Check(descr))) + #endif +#endif + { + meth_found = 1; + } else { + f = Py_TYPE(descr)->tp_descr_get; + if (f != NULL && PyDescr_IsData(descr)) { + attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); + Py_DECREF(descr); + goto try_unpack; + } + } + } + dictptr = _PyObject_GetDictPtr(obj); + if (dictptr != NULL && (dict = *dictptr) != NULL) { + Py_INCREF(dict); + attr = __Pyx_PyDict_GetItemStr(dict, name); + if (attr != NULL) { + Py_INCREF(attr); + Py_DECREF(dict); + Py_XDECREF(descr); + goto try_unpack; + } + Py_DECREF(dict); + } + if (meth_found) { + *method = descr; + return 1; + } + if (f != NULL) { + attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); + Py_DECREF(descr); + goto try_unpack; + } + if (likely(descr != NULL)) { + *method = descr; + return 0; + } + type_name = __Pyx_PyType_GetName(tp); + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'", + type_name, name); +#else + "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'", + type_name, PyString_AS_STRING(name)); +#endif + __Pyx_DECREF_TypeName(type_name); + return 0; +#else + attr = __Pyx_PyObject_GetAttrStr(obj, name); + goto try_unpack; +#endif +try_unpack: +#if CYTHON_UNPACK_METHODS + if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) { + PyObject *function = PyMethod_GET_FUNCTION(attr); + Py_INCREF(function); + Py_DECREF(attr); + *method = function; + return 1; + } +#endif + *method = attr; + return 0; +} + +/* PyObjectCallMethod1 */ +#if !(CYTHON_VECTORCALL && __PYX_LIMITED_VERSION_HEX >= 0x030C00A2) +static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) { + PyObject *result = __Pyx_PyObject_CallOneArg(method, arg); + Py_DECREF(method); + return result; +} +#endif +static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { +#if CYTHON_VECTORCALL && __PYX_LIMITED_VERSION_HEX >= 0x030C00A2 + PyObject *args[2] = {obj, arg}; + (void) __Pyx_PyObject_GetMethod; + (void) __Pyx_PyObject_CallOneArg; + (void) __Pyx_PyObject_Call2Args; + return PyObject_VectorcallMethod(method_name, args, 2 | PY_VECTORCALL_ARGUMENTS_OFFSET, NULL); +#else + PyObject *method = NULL, *result; + int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); + if (likely(is_method)) { + result = __Pyx_PyObject_Call2Args(method, obj, arg); + Py_DECREF(method); + return result; + } + if (unlikely(!method)) return NULL; + return __Pyx__PyObject_CallMethod1(method, arg); +#endif +} + +/* StringJoin */ +static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) { + (void) __Pyx_PyObject_CallMethod1; +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION < 3 + return _PyString_Join(sep, values); +#elif CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030d0000 + return _PyBytes_Join(sep, values); +#else + return __Pyx_PyObject_CallMethod1(sep, __pyx_n_s_join, values); +#endif +} + +/* PyObjectCallNoArg */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { + PyObject *arg[2] = {NULL, NULL}; + return __Pyx_PyObject_FastCall(func, arg + 1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +} + +/* ArgTypeTest */ +static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) +{ + __Pyx_TypeName type_name; + __Pyx_TypeName obj_type_name; + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + else if (exact) { + #if PY_MAJOR_VERSION == 2 + if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(__Pyx_TypeCheck(obj, type))) return 1; + } + type_name = __Pyx_PyType_GetName(type); + obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected " __Pyx_FMT_TYPENAME + ", got " __Pyx_FMT_TYPENAME ")", name, type_name, obj_type_name); + __Pyx_DECREF_TypeName(type_name); + __Pyx_DECREF_TypeName(obj_type_name); + return 0; +} + +/* PyObjectSetAttrStr */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_setattro)) + return tp->tp_setattro(obj, attr_name, value); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_setattr)) + return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); +#endif + return PyObject_SetAttr(obj, attr_name, value); +} +#endif + +/* JoinPyUnicode */ +static PyObject* __Pyx_PyUnicode_Join(PyObject* value_tuple, Py_ssize_t value_count, Py_ssize_t result_ulength, + Py_UCS4 max_char) { +#if CYTHON_USE_UNICODE_INTERNALS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + PyObject *result_uval; + int result_ukind, kind_shift; + Py_ssize_t i, char_pos; + void *result_udata; + CYTHON_MAYBE_UNUSED_VAR(max_char); +#if CYTHON_PEP393_ENABLED + result_uval = PyUnicode_New(result_ulength, max_char); + if (unlikely(!result_uval)) return NULL; + result_ukind = (max_char <= 255) ? PyUnicode_1BYTE_KIND : (max_char <= 65535) ? PyUnicode_2BYTE_KIND : PyUnicode_4BYTE_KIND; + kind_shift = (result_ukind == PyUnicode_4BYTE_KIND) ? 2 : result_ukind - 1; + result_udata = PyUnicode_DATA(result_uval); +#else + result_uval = PyUnicode_FromUnicode(NULL, result_ulength); + if (unlikely(!result_uval)) return NULL; + result_ukind = sizeof(Py_UNICODE); + kind_shift = (result_ukind == 4) ? 2 : result_ukind - 1; + result_udata = PyUnicode_AS_UNICODE(result_uval); +#endif + assert(kind_shift == 2 || kind_shift == 1 || kind_shift == 0); + char_pos = 0; + for (i=0; i < value_count; i++) { + int ukind; + Py_ssize_t ulength; + void *udata; + PyObject *uval = PyTuple_GET_ITEM(value_tuple, i); + if (unlikely(__Pyx_PyUnicode_READY(uval))) + goto bad; + ulength = __Pyx_PyUnicode_GET_LENGTH(uval); + if (unlikely(!ulength)) + continue; + if (unlikely((PY_SSIZE_T_MAX >> kind_shift) - ulength < char_pos)) + goto overflow; + ukind = __Pyx_PyUnicode_KIND(uval); + udata = __Pyx_PyUnicode_DATA(uval); + if (!CYTHON_PEP393_ENABLED || ukind == result_ukind) { + memcpy((char *)result_udata + (char_pos << kind_shift), udata, (size_t) (ulength << kind_shift)); + } else { + #if PY_VERSION_HEX >= 0x030d0000 + if (unlikely(PyUnicode_CopyCharacters(result_uval, char_pos, uval, 0, ulength) < 0)) goto bad; + #elif CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030300F0 || defined(_PyUnicode_FastCopyCharacters) + _PyUnicode_FastCopyCharacters(result_uval, char_pos, uval, 0, ulength); + #else + Py_ssize_t j; + for (j=0; j < ulength; j++) { + Py_UCS4 uchar = __Pyx_PyUnicode_READ(ukind, udata, j); + __Pyx_PyUnicode_WRITE(result_ukind, result_udata, char_pos+j, uchar); + } + #endif + } + char_pos += ulength; + } + return result_uval; +overflow: + PyErr_SetString(PyExc_OverflowError, "join() result is too long for a Python string"); +bad: + Py_DECREF(result_uval); + return NULL; +#else + CYTHON_UNUSED_VAR(max_char); + CYTHON_UNUSED_VAR(result_ulength); + CYTHON_UNUSED_VAR(value_count); + return PyUnicode_Join(__pyx_empty_unicode, value_tuple); +#endif +} + +/* PyDictVersioning */ +#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { + PyObject *dict = Py_TYPE(obj)->tp_dict; + return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; +} +static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { + PyObject **dictptr = NULL; + Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; + if (offset) { +#if CYTHON_COMPILING_IN_CPYTHON + dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); +#else + dictptr = _PyObject_GetDictPtr(obj); +#endif + } + return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; +} +static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { + PyObject *dict = Py_TYPE(obj)->tp_dict; + if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) + return 0; + return obj_dict_version == __Pyx_get_object_dict_version(obj); +} +#endif + +/* GetModuleGlobalName */ +#if CYTHON_USE_DICT_VERSIONS +static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) +#else +static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) +#endif +{ + PyObject *result; +#if !CYTHON_AVOID_BORROWED_REFS +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000 + result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); + __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) + if (likely(result)) { + return __Pyx_NewRef(result); + } else if (unlikely(PyErr_Occurred())) { + return NULL; + } +#elif CYTHON_COMPILING_IN_LIMITED_API + if (unlikely(!__pyx_m)) { + return NULL; + } + result = PyObject_GetAttr(__pyx_m, name); + if (likely(result)) { + return result; + } +#else + result = PyDict_GetItem(__pyx_d, name); + __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) + if (likely(result)) { + return __Pyx_NewRef(result); + } +#endif +#else + result = PyObject_GetItem(__pyx_d, name); + __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) + if (likely(result)) { + return __Pyx_NewRef(result); + } + PyErr_Clear(); +#endif + return __Pyx_GetBuiltinName(name); +} + +/* GetItemInt */ +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (unlikely(!j)) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); + } + if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); + } + if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping; + PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence; + if (mm && mm->mp_subscript) { + PyObject *r, *key = PyInt_FromSsize_t(i); + if (unlikely(!key)) return NULL; + r = mm->mp_subscript(o, key); + Py_DECREF(key); + return r; + } + if (likely(sm && sm->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) { + Py_ssize_t l = sm->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return NULL; + PyErr_Clear(); + } + } + return sm->sq_item(o, i); + } + } +#else + if (is_list || !PyMapping_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +/* ObjectGetItem */ +#if CYTHON_USE_TYPE_SLOTS +static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject *index) { + PyObject *runerr = NULL; + Py_ssize_t key_value; + key_value = __Pyx_PyIndex_AsSsize_t(index); + if (likely(key_value != -1 || !(runerr = PyErr_Occurred()))) { + return __Pyx_GetItemInt_Fast(obj, key_value, 0, 1, 1); + } + if (PyErr_GivenExceptionMatches(runerr, PyExc_OverflowError)) { + __Pyx_TypeName index_type_name = __Pyx_PyType_GetName(Py_TYPE(index)); + PyErr_Clear(); + PyErr_Format(PyExc_IndexError, + "cannot fit '" __Pyx_FMT_TYPENAME "' into an index-sized integer", index_type_name); + __Pyx_DECREF_TypeName(index_type_name); + } + return NULL; +} +static PyObject *__Pyx_PyObject_GetItem_Slow(PyObject *obj, PyObject *key) { + __Pyx_TypeName obj_type_name; + if (likely(PyType_Check(obj))) { + PyObject *meth = __Pyx_PyObject_GetAttrStrNoError(obj, __pyx_n_s_class_getitem); + if (!meth) { + PyErr_Clear(); + } else { + PyObject *result = __Pyx_PyObject_CallOneArg(meth, key); + Py_DECREF(meth); + return result; + } + } + obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); + PyErr_Format(PyExc_TypeError, + "'" __Pyx_FMT_TYPENAME "' object is not subscriptable", obj_type_name); + __Pyx_DECREF_TypeName(obj_type_name); + return NULL; +} +static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject *key) { + PyTypeObject *tp = Py_TYPE(obj); + PyMappingMethods *mm = tp->tp_as_mapping; + PySequenceMethods *sm = tp->tp_as_sequence; + if (likely(mm && mm->mp_subscript)) { + return mm->mp_subscript(obj, key); + } + if (likely(sm && sm->sq_item)) { + return __Pyx_PyObject_GetIndex(obj, key); + } + return __Pyx_PyObject_GetItem_Slow(obj, key); +} +#endif + +/* GetException */ +#if CYTHON_FAST_THREAD_STATE +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) +#endif +{ + PyObject *local_type = NULL, *local_value, *local_tb = NULL; +#if CYTHON_FAST_THREAD_STATE + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if PY_VERSION_HEX >= 0x030C00A6 + local_value = tstate->current_exception; + tstate->current_exception = 0; + if (likely(local_value)) { + local_type = (PyObject*) Py_TYPE(local_value); + Py_INCREF(local_type); + local_tb = PyException_GetTraceback(local_value); + } + #else + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; + #endif +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_FAST_THREAD_STATE && PY_VERSION_HEX >= 0x030C00A6 + if (unlikely(tstate->current_exception)) +#elif CYTHON_FAST_THREAD_STATE + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_FAST_THREAD_STATE + #if CYTHON_USE_EXC_INFO_STACK + { + _PyErr_StackItem *exc_info = tstate->exc_info; + #if PY_VERSION_HEX >= 0x030B00a4 + tmp_value = exc_info->exc_value; + exc_info->exc_value = local_value; + tmp_type = NULL; + tmp_tb = NULL; + Py_XDECREF(local_type); + Py_XDECREF(local_tb); + #else + tmp_type = exc_info->exc_type; + tmp_value = exc_info->exc_value; + tmp_tb = exc_info->exc_traceback; + exc_info->exc_type = local_type; + exc_info->exc_value = local_value; + exc_info->exc_traceback = local_tb; + #endif + } + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +/* SwapException */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4 + _PyErr_StackItem *exc_info = tstate->exc_info; + tmp_value = exc_info->exc_value; + exc_info->exc_value = *value; + if (tmp_value == NULL || tmp_value == Py_None) { + Py_XDECREF(tmp_value); + tmp_value = NULL; + tmp_type = NULL; + tmp_tb = NULL; + } else { + tmp_type = (PyObject*) Py_TYPE(tmp_value); + Py_INCREF(tmp_type); + #if CYTHON_COMPILING_IN_CPYTHON + tmp_tb = ((PyBaseExceptionObject*) tmp_value)->traceback; + Py_XINCREF(tmp_tb); + #else + tmp_tb = PyException_GetTraceback(tmp_value); + #endif + } + #elif CYTHON_USE_EXC_INFO_STACK + _PyErr_StackItem *exc_info = tstate->exc_info; + tmp_type = exc_info->exc_type; + tmp_value = exc_info->exc_value; + tmp_tb = exc_info->exc_traceback; + exc_info->exc_type = *type; + exc_info->exc_value = *value; + exc_info->exc_traceback = *tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; + #endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#endif + +/* GetTopmostException */ +#if CYTHON_USE_EXC_INFO_STACK && CYTHON_FAST_THREAD_STATE +static _PyErr_StackItem * +__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) +{ + _PyErr_StackItem *exc_info = tstate->exc_info; + while ((exc_info->exc_value == NULL || exc_info->exc_value == Py_None) && + exc_info->previous_item != NULL) + { + exc_info = exc_info->previous_item; + } + return exc_info; +} +#endif + +/* SaveResetException */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4 + _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); + PyObject *exc_value = exc_info->exc_value; + if (exc_value == NULL || exc_value == Py_None) { + *value = NULL; + *type = NULL; + *tb = NULL; + } else { + *value = exc_value; + Py_INCREF(*value); + *type = (PyObject*) Py_TYPE(exc_value); + Py_INCREF(*type); + *tb = PyException_GetTraceback(exc_value); + } + #elif CYTHON_USE_EXC_INFO_STACK + _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); + *type = exc_info->exc_type; + *value = exc_info->exc_value; + *tb = exc_info->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); + #else + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); + #endif +} +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + #if CYTHON_USE_EXC_INFO_STACK && PY_VERSION_HEX >= 0x030B00a4 + _PyErr_StackItem *exc_info = tstate->exc_info; + PyObject *tmp_value = exc_info->exc_value; + exc_info->exc_value = value; + Py_XDECREF(tmp_value); + Py_XDECREF(type); + Py_XDECREF(tb); + #else + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if CYTHON_USE_EXC_INFO_STACK + _PyErr_StackItem *exc_info = tstate->exc_info; + tmp_type = exc_info->exc_type; + tmp_value = exc_info->exc_value; + tmp_tb = exc_info->exc_traceback; + exc_info->exc_type = type; + exc_info->exc_value = value; + exc_info->exc_traceback = tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); + #endif +} +#endif + +/* PyIntBinop */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check) { + CYTHON_MAYBE_UNUSED_VAR(intval); + CYTHON_MAYBE_UNUSED_VAR(inplace); + CYTHON_UNUSED_VAR(zerodivision_check); + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long x; + long a = PyInt_AS_LONG(op1); + + x = (long)((unsigned long)a - (unsigned long)b); + if (likely((x^a) >= 0 || (x^~b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_subtract(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; +#ifdef HAVE_LONG_LONG + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; +#endif + if (unlikely(__Pyx_PyLong_IsZero(op1))) { + return PyLong_FromLong(-intval); + } + if (likely(__Pyx_PyLong_IsCompact(op1))) { + a = __Pyx_PyLong_CompactValue(op1); + } else { + const digit* digits = __Pyx_PyLong_Digits(op1); + const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(op1); + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + #ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + #endif + } + CYTHON_FALLTHROUGH; + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + #ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; + #endif + } + CYTHON_FALLTHROUGH; + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + #ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + 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])); + goto long_long; + #endif + } + CYTHON_FALLTHROUGH; + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + #ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + 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])); + goto long_long; + #endif + } + CYTHON_FALLTHROUGH; + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + #ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + 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])); + goto long_long; + #endif + } + CYTHON_FALLTHROUGH; + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; + #ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + 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])); + goto long_long; + #endif + } + CYTHON_FALLTHROUGH; + default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2); + } + } + x = a - b; + return PyLong_FromLong(x); +#ifdef HAVE_LONG_LONG + long_long: + llx = lla - llb; + return PyLong_FromLongLong(llx); +#endif + + + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; +#if CYTHON_COMPILING_IN_LIMITED_API + double a = __pyx_PyFloat_AsDouble(op1); +#else + double a = PyFloat_AS_DOUBLE(op1); +#endif + double result; + + PyFPE_START_PROTECT("subtract", return NULL) + result = ((double)a) - (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2); +} +#endif + +/* RaiseTooManyValuesToUnpack */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +/* RaiseNeedMoreValuesToUnpack */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +/* IterFinish */ +static CYTHON_INLINE int __Pyx_IterFinish(void) { + PyObject* exc_type; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + exc_type = __Pyx_PyErr_CurrentExceptionType(); + if (unlikely(exc_type)) { + if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) + return -1; + __Pyx_PyErr_Clear(); + return 0; + } + return 0; +} + +/* UnpackItemEndCheck */ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); + __Pyx_RaiseTooManyValuesError(expected); + return -1; + } + return __Pyx_IterFinish(); +} + +/* PyIntCompare */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_NeObjC(PyObject *op1, PyObject *op2, long intval, long inplace) { + CYTHON_MAYBE_UNUSED_VAR(intval); + CYTHON_UNUSED_VAR(inplace); + if (op1 == op2) { + Py_RETURN_FALSE; + } + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long a = PyInt_AS_LONG(op1); + if (a != b) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + int unequal; + unsigned long uintval; + Py_ssize_t size = __Pyx_PyLong_DigitCount(op1); + const digit* digits = __Pyx_PyLong_Digits(op1); + if (intval == 0) { + if (__Pyx_PyLong_IsZero(op1) != 1) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } else if (intval < 0) { + if (__Pyx_PyLong_IsNonNeg(op1)) + Py_RETURN_TRUE; + intval = -intval; + } else { + if (__Pyx_PyLong_IsNeg(op1)) + Py_RETURN_TRUE; + } + uintval = (unsigned long) intval; +#if PyLong_SHIFT * 4 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 4)) { + unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif +#if PyLong_SHIFT * 3 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 3)) { + unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif +#if PyLong_SHIFT * 2 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 2)) { + unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif +#if PyLong_SHIFT * 1 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 1)) { + unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif + unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK)); + if (unequal != 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; +#if CYTHON_COMPILING_IN_LIMITED_API + double a = __pyx_PyFloat_AsDouble(op1); +#else + double a = PyFloat_AS_DOUBLE(op1); +#endif + if ((double)a != (double)b) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } + return ( + PyObject_RichCompare(op1, op2, Py_NE)); +} + +/* FixUpExtensionType */ +#if CYTHON_USE_TYPE_SPECS +static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type) { +#if PY_VERSION_HEX > 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API + CYTHON_UNUSED_VAR(spec); + CYTHON_UNUSED_VAR(type); +#else + const PyType_Slot *slot = spec->slots; + while (slot && slot->slot && slot->slot != Py_tp_members) + slot++; + if (slot && slot->slot == Py_tp_members) { + int changed = 0; +#if !(PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON) + const +#endif + PyMemberDef *memb = (PyMemberDef*) slot->pfunc; + while (memb && memb->name) { + if (memb->name[0] == '_' && memb->name[1] == '_') { +#if PY_VERSION_HEX < 0x030900b1 + if (strcmp(memb->name, "__weaklistoffset__") == 0) { + assert(memb->type == T_PYSSIZET); + assert(memb->flags == READONLY); + type->tp_weaklistoffset = memb->offset; + changed = 1; + } + else if (strcmp(memb->name, "__dictoffset__") == 0) { + assert(memb->type == T_PYSSIZET); + assert(memb->flags == READONLY); + type->tp_dictoffset = memb->offset; + changed = 1; + } +#if CYTHON_METH_FASTCALL + else if (strcmp(memb->name, "__vectorcalloffset__") == 0) { + assert(memb->type == T_PYSSIZET); + assert(memb->flags == READONLY); +#if PY_VERSION_HEX >= 0x030800b4 + type->tp_vectorcall_offset = memb->offset; +#else + type->tp_print = (printfunc) memb->offset; +#endif + changed = 1; + } +#endif +#else + if ((0)); +#endif +#if PY_VERSION_HEX <= 0x030900b1 && CYTHON_COMPILING_IN_CPYTHON + else if (strcmp(memb->name, "__module__") == 0) { + PyObject *descr; + assert(memb->type == T_OBJECT); + assert(memb->flags == 0 || memb->flags == READONLY); + descr = PyDescr_NewMember(type, memb); + if (unlikely(!descr)) + return -1; + if (unlikely(PyDict_SetItem(type->tp_dict, PyDescr_NAME(descr), descr) < 0)) { + Py_DECREF(descr); + return -1; + } + Py_DECREF(descr); + changed = 1; + } +#endif + } + memb++; + } + if (changed) + PyType_Modified(type); + } +#endif + return 0; +} +#endif + +/* PyObjectCallMethod0 */ +static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { + PyObject *method = NULL, *result = NULL; + int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); + if (likely(is_method)) { + result = __Pyx_PyObject_CallOneArg(method, obj); + Py_DECREF(method); + return result; + } + if (unlikely(!method)) goto bad; + result = __Pyx_PyObject_CallNoArg(method); + Py_DECREF(method); +bad: + return result; +} + +/* ValidateBasesTuple */ +#if CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API || CYTHON_USE_TYPE_SPECS +static int __Pyx_validate_bases_tuple(const char *type_name, Py_ssize_t dictoffset, PyObject *bases) { + Py_ssize_t i, n; +#if CYTHON_ASSUME_SAFE_MACROS + n = PyTuple_GET_SIZE(bases); +#else + n = PyTuple_Size(bases); + if (n < 0) return -1; +#endif + for (i = 1; i < n; i++) + { +#if CYTHON_AVOID_BORROWED_REFS + PyObject *b0 = PySequence_GetItem(bases, i); + if (!b0) return -1; +#elif CYTHON_ASSUME_SAFE_MACROS + PyObject *b0 = PyTuple_GET_ITEM(bases, i); +#else + PyObject *b0 = PyTuple_GetItem(bases, i); + if (!b0) return -1; +#endif + PyTypeObject *b; +#if PY_MAJOR_VERSION < 3 + if (PyClass_Check(b0)) + { + PyErr_Format(PyExc_TypeError, "base class '%.200s' is an old-style class", + PyString_AS_STRING(((PyClassObject*)b0)->cl_name)); +#if CYTHON_AVOID_BORROWED_REFS + Py_DECREF(b0); +#endif + return -1; + } +#endif + b = (PyTypeObject*) b0; + if (!__Pyx_PyType_HasFeature(b, Py_TPFLAGS_HEAPTYPE)) + { + __Pyx_TypeName b_name = __Pyx_PyType_GetName(b); + PyErr_Format(PyExc_TypeError, + "base class '" __Pyx_FMT_TYPENAME "' is not a heap type", b_name); + __Pyx_DECREF_TypeName(b_name); +#if CYTHON_AVOID_BORROWED_REFS + Py_DECREF(b0); +#endif + return -1; + } + if (dictoffset == 0) + { + Py_ssize_t b_dictoffset = 0; +#if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY + b_dictoffset = b->tp_dictoffset; +#else + PyObject *py_b_dictoffset = PyObject_GetAttrString((PyObject*)b, "__dictoffset__"); + if (!py_b_dictoffset) goto dictoffset_return; + b_dictoffset = PyLong_AsSsize_t(py_b_dictoffset); + Py_DECREF(py_b_dictoffset); + if (b_dictoffset == -1 && PyErr_Occurred()) goto dictoffset_return; +#endif + if (b_dictoffset) { + { + __Pyx_TypeName b_name = __Pyx_PyType_GetName(b); + PyErr_Format(PyExc_TypeError, + "extension type '%.200s' has no __dict__ slot, " + "but base type '" __Pyx_FMT_TYPENAME "' has: " + "either add 'cdef dict __dict__' to the extension type " + "or add '__slots__ = [...]' to the base type", + type_name, b_name); + __Pyx_DECREF_TypeName(b_name); + } +#if !(CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY) + dictoffset_return: +#endif +#if CYTHON_AVOID_BORROWED_REFS + Py_DECREF(b0); +#endif + return -1; + } + } +#if CYTHON_AVOID_BORROWED_REFS + Py_DECREF(b0); +#endif + } + return 0; +} +#endif + +/* PyType_Ready */ +static int __Pyx_PyType_Ready(PyTypeObject *t) { +#if CYTHON_USE_TYPE_SPECS || !(CYTHON_COMPILING_IN_CPYTHON || CYTHON_COMPILING_IN_LIMITED_API) || defined(PYSTON_MAJOR_VERSION) + (void)__Pyx_PyObject_CallMethod0; +#if CYTHON_USE_TYPE_SPECS + (void)__Pyx_validate_bases_tuple; +#endif + return PyType_Ready(t); +#else + int r; + PyObject *bases = __Pyx_PyType_GetSlot(t, tp_bases, PyObject*); + if (bases && unlikely(__Pyx_validate_bases_tuple(t->tp_name, t->tp_dictoffset, bases) == -1)) + return -1; +#if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION) + { + int gc_was_enabled; + #if PY_VERSION_HEX >= 0x030A00b1 + gc_was_enabled = PyGC_Disable(); + (void)__Pyx_PyObject_CallMethod0; + #else + PyObject *ret, *py_status; + PyObject *gc = NULL; + #if PY_VERSION_HEX >= 0x030700a1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM+0 >= 0x07030400) + gc = PyImport_GetModule(__pyx_kp_u_gc); + #endif + if (unlikely(!gc)) gc = PyImport_Import(__pyx_kp_u_gc); + if (unlikely(!gc)) return -1; + py_status = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_isenabled); + if (unlikely(!py_status)) { + Py_DECREF(gc); + return -1; + } + gc_was_enabled = __Pyx_PyObject_IsTrue(py_status); + Py_DECREF(py_status); + if (gc_was_enabled > 0) { + ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_disable); + if (unlikely(!ret)) { + Py_DECREF(gc); + return -1; + } + Py_DECREF(ret); + } else if (unlikely(gc_was_enabled == -1)) { + Py_DECREF(gc); + return -1; + } + #endif + t->tp_flags |= Py_TPFLAGS_HEAPTYPE; +#if PY_VERSION_HEX >= 0x030A0000 + t->tp_flags |= Py_TPFLAGS_IMMUTABLETYPE; +#endif +#else + (void)__Pyx_PyObject_CallMethod0; +#endif + r = PyType_Ready(t); +#if PY_VERSION_HEX >= 0x03050000 && !defined(PYSTON_MAJOR_VERSION) + t->tp_flags &= ~Py_TPFLAGS_HEAPTYPE; + #if PY_VERSION_HEX >= 0x030A00b1 + if (gc_was_enabled) + PyGC_Enable(); + #else + if (gc_was_enabled) { + PyObject *tp, *v, *tb; + PyErr_Fetch(&tp, &v, &tb); + ret = __Pyx_PyObject_CallMethod0(gc, __pyx_kp_u_enable); + if (likely(ret || r == -1)) { + Py_XDECREF(ret); + PyErr_Restore(tp, v, tb); + } else { + Py_XDECREF(tp); + Py_XDECREF(v); + Py_XDECREF(tb); + r = -1; + } + } + Py_DECREF(gc); + #endif + } +#endif + return r; +#endif +} + +/* PyObject_GenericGetAttrNoDict */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { + __Pyx_TypeName type_name = __Pyx_PyType_GetName(tp); + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'", + type_name, attr_name); +#else + "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'", + type_name, PyString_AS_STRING(attr_name)); +#endif + __Pyx_DECREF_TypeName(type_name); + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { + PyObject *descr; + PyTypeObject *tp = Py_TYPE(obj); + if (unlikely(!PyString_Check(attr_name))) { + return PyObject_GenericGetAttr(obj, attr_name); + } + assert(!tp->tp_dictoffset); + descr = _PyType_Lookup(tp, attr_name); + if (unlikely(!descr)) { + return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); + } + Py_INCREF(descr); + #if PY_MAJOR_VERSION < 3 + if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) + #endif + { + descrgetfunc f = Py_TYPE(descr)->tp_descr_get; + if (unlikely(f)) { + PyObject *res = f(descr, obj, (PyObject *)tp); + Py_DECREF(descr); + return res; + } + } + return descr; +} +#endif + +/* PyObject_GenericGetAttr */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { + if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { + return PyObject_GenericGetAttr(obj, attr_name); + } + return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); +} +#endif + +/* SetVTable */ +static int __Pyx_SetVtable(PyTypeObject *type, void *vtable) { + PyObject *ob = PyCapsule_New(vtable, 0, 0); + if (unlikely(!ob)) + goto bad; +#if CYTHON_COMPILING_IN_LIMITED_API + if (unlikely(PyObject_SetAttr((PyObject *) type, __pyx_n_s_pyx_vtable, ob) < 0)) +#else + if (unlikely(PyDict_SetItem(type->tp_dict, __pyx_n_s_pyx_vtable, ob) < 0)) +#endif + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +/* GetVTable */ +static void* __Pyx_GetVtable(PyTypeObject *type) { + void* ptr; +#if CYTHON_COMPILING_IN_LIMITED_API + PyObject *ob = PyObject_GetAttr((PyObject *)type, __pyx_n_s_pyx_vtable); +#else + PyObject *ob = PyObject_GetItem(type->tp_dict, __pyx_n_s_pyx_vtable); +#endif + if (!ob) + goto bad; + ptr = PyCapsule_GetPointer(ob, 0); + if (!ptr && !PyErr_Occurred()) + PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type"); + Py_DECREF(ob); + return ptr; +bad: + Py_XDECREF(ob); + return NULL; +} + +/* MergeVTables */ +#if !CYTHON_COMPILING_IN_LIMITED_API +static int __Pyx_MergeVtables(PyTypeObject *type) { + int i; + void** base_vtables; + __Pyx_TypeName tp_base_name; + __Pyx_TypeName base_name; + void* unknown = (void*)-1; + PyObject* bases = type->tp_bases; + int base_depth = 0; + { + PyTypeObject* base = type->tp_base; + while (base) { + base_depth += 1; + base = base->tp_base; + } + } + base_vtables = (void**) malloc(sizeof(void*) * (size_t)(base_depth + 1)); + base_vtables[0] = unknown; + for (i = 1; i < PyTuple_GET_SIZE(bases); i++) { + void* base_vtable = __Pyx_GetVtable(((PyTypeObject*)PyTuple_GET_ITEM(bases, i))); + if (base_vtable != NULL) { + int j; + PyTypeObject* base = type->tp_base; + for (j = 0; j < base_depth; j++) { + if (base_vtables[j] == unknown) { + base_vtables[j] = __Pyx_GetVtable(base); + base_vtables[j + 1] = unknown; + } + if (base_vtables[j] == base_vtable) { + break; + } else if (base_vtables[j] == NULL) { + goto bad; + } + base = base->tp_base; + } + } + } + PyErr_Clear(); + free(base_vtables); + return 0; +bad: + tp_base_name = __Pyx_PyType_GetName(type->tp_base); + base_name = __Pyx_PyType_GetName((PyTypeObject*)PyTuple_GET_ITEM(bases, i)); + PyErr_Format(PyExc_TypeError, + "multiple bases have vtable conflict: '" __Pyx_FMT_TYPENAME "' and '" __Pyx_FMT_TYPENAME "'", tp_base_name, base_name); + __Pyx_DECREF_TypeName(tp_base_name); + __Pyx_DECREF_TypeName(base_name); + free(base_vtables); + return -1; +} +#endif + +/* SetupReduce */ +#if !CYTHON_COMPILING_IN_LIMITED_API +static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = __Pyx_PyObject_GetAttrStrNoError(meth, __pyx_n_s_name_2); + if (likely(name_attr)) { + ret = PyObject_RichCompareBool(name_attr, name, Py_EQ); + } else { + ret = -1; + } + if (unlikely(ret < 0)) { + PyErr_Clear(); + ret = 0; + } + Py_XDECREF(name_attr); + return ret; +} +static int __Pyx_setup_reduce(PyObject* type_obj) { + int ret = 0; + PyObject *object_reduce = NULL; + PyObject *object_getstate = NULL; + PyObject *object_reduce_ex = NULL; + PyObject *reduce = NULL; + PyObject *reduce_ex = NULL; + PyObject *reduce_cython = NULL; + PyObject *setstate = NULL; + PyObject *setstate_cython = NULL; + PyObject *getstate = NULL; +#if CYTHON_USE_PYTYPE_LOOKUP + getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate); +#else + getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate); + if (!getstate && PyErr_Occurred()) { + goto __PYX_BAD; + } +#endif + if (getstate) { +#if CYTHON_USE_PYTYPE_LOOKUP + object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate); +#else + object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate); + if (!object_getstate && PyErr_Occurred()) { + goto __PYX_BAD; + } +#endif + if (object_getstate != getstate) { + goto __PYX_GOOD; + } + } +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; +#else + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; +#endif + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; + if (reduce_ex == object_reduce_ex) { +#if CYTHON_USE_PYTYPE_LOOKUP + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; +#else + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; +#endif + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; + if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { + reduce_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_reduce_cython); + if (likely(reduce_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (reduce == object_reduce || PyErr_Occurred()) { + goto __PYX_BAD; + } + setstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate); + if (!setstate) PyErr_Clear(); + if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { + setstate_cython = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_setstate_cython); + if (likely(setstate_cython)) { + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + } else if (!setstate || PyErr_Occurred()) { + goto __PYX_BAD; + } + } + PyType_Modified((PyTypeObject*)type_obj); + } + } + goto __PYX_GOOD; +__PYX_BAD: + if (!PyErr_Occurred()) { + __Pyx_TypeName type_obj_name = + __Pyx_PyType_GetName((PyTypeObject*)type_obj); + PyErr_Format(PyExc_RuntimeError, + "Unable to initialize pickling for " __Pyx_FMT_TYPENAME, type_obj_name); + __Pyx_DECREF_TypeName(type_obj_name); + } + ret = -1; +__PYX_GOOD: +#if !CYTHON_USE_PYTYPE_LOOKUP + Py_XDECREF(object_reduce); + Py_XDECREF(object_reduce_ex); + Py_XDECREF(object_getstate); + Py_XDECREF(getstate); +#endif + Py_XDECREF(reduce); + Py_XDECREF(reduce_ex); + Py_XDECREF(reduce_cython); + Py_XDECREF(setstate); + Py_XDECREF(setstate_cython); + return ret; +} +#endif + +/* TypeImport */ +#ifndef __PYX_HAVE_RT_ImportType_3_0_11 +#define __PYX_HAVE_RT_ImportType_3_0_11 +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) +{ + PyObject *result = 0; + char warning[200]; + Py_ssize_t basicsize; + Py_ssize_t itemsize; +#if CYTHON_COMPILING_IN_LIMITED_API + PyObject *py_basicsize; + PyObject *py_itemsize; +#endif + result = PyObject_GetAttrString(module, class_name); + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#if !CYTHON_COMPILING_IN_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; + itemsize = ((PyTypeObject *)result)->tp_itemsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; + py_itemsize = PyObject_GetAttrString(result, "__itemsize__"); + if (!py_itemsize) + goto bad; + itemsize = PyLong_AsSsize_t(py_itemsize); + Py_DECREF(py_itemsize); + py_itemsize = 0; + if (itemsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (itemsize) { + if (size % alignment) { + alignment = size % alignment; + } + if (itemsize < (Py_ssize_t)alignment) + itemsize = (Py_ssize_t)alignment; + } + if ((size_t)(basicsize + itemsize) < size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s size changed, may indicate binary incompatibility. " + "Expected %zd from C header, got %zd from PyObject", + module_name, class_name, size, basicsize+itemsize); + goto bad; + } + if (check_size == __Pyx_ImportType_CheckSize_Error_3_0_11 && + ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s size changed, may indicate binary incompatibility. " + "Expected %zd from C header, got %zd-%zd from PyObject", + module_name, class_name, size, basicsize, basicsize+itemsize); + goto bad; + } + else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_0_11 && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility. " + "Expected %zd from C header, got %zd from PyObject", + module_name, class_name, size, basicsize); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(result); + return NULL; +} +#endif + +/* Import */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *module = 0; + PyObject *empty_dict = 0; + PyObject *empty_list = 0; + #if PY_MAJOR_VERSION < 3 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (unlikely(!py_import)) + goto bad; + if (!from_list) { + empty_list = PyList_New(0); + if (unlikely(!empty_list)) + goto bad; + from_list = empty_list; + } + #endif + empty_dict = PyDict_New(); + if (unlikely(!empty_dict)) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.') != NULL) { + module = PyImport_ImportModuleLevelObject( + name, __pyx_d, empty_dict, from_list, 1); + if (unlikely(!module)) { + if (unlikely(!PyErr_ExceptionMatches(PyExc_ImportError))) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_MAJOR_VERSION < 3 + PyObject *py_level = PyInt_FromLong(level); + if (unlikely(!py_level)) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, __pyx_d, empty_dict, from_list, py_level, (PyObject *)NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, __pyx_d, empty_dict, from_list, level); + #endif + } + } +bad: + Py_XDECREF(empty_dict); + Py_XDECREF(empty_list); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(py_import); + #endif + return module; +} + +/* ImportDottedModule */ +#if PY_MAJOR_VERSION >= 3 +static PyObject *__Pyx__ImportDottedModule_Error(PyObject *name, PyObject *parts_tuple, Py_ssize_t count) { + PyObject *partial_name = NULL, *slice = NULL, *sep = NULL; + if (unlikely(PyErr_Occurred())) { + PyErr_Clear(); + } + if (likely(PyTuple_GET_SIZE(parts_tuple) == count)) { + partial_name = name; + } else { + slice = PySequence_GetSlice(parts_tuple, 0, count); + if (unlikely(!slice)) + goto bad; + sep = PyUnicode_FromStringAndSize(".", 1); + if (unlikely(!sep)) + goto bad; + partial_name = PyUnicode_Join(sep, slice); + } + PyErr_Format( +#if PY_MAJOR_VERSION < 3 + PyExc_ImportError, + "No module named '%s'", PyString_AS_STRING(partial_name)); +#else +#if PY_VERSION_HEX >= 0x030600B1 + PyExc_ModuleNotFoundError, +#else + PyExc_ImportError, +#endif + "No module named '%U'", partial_name); +#endif +bad: + Py_XDECREF(sep); + Py_XDECREF(slice); + Py_XDECREF(partial_name); + return NULL; +} +#endif +#if PY_MAJOR_VERSION >= 3 +static PyObject *__Pyx__ImportDottedModule_Lookup(PyObject *name) { + PyObject *imported_module; +#if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400) + PyObject *modules = PyImport_GetModuleDict(); + if (unlikely(!modules)) + return NULL; + imported_module = __Pyx_PyDict_GetItemStr(modules, name); + Py_XINCREF(imported_module); +#else + imported_module = PyImport_GetModule(name); +#endif + return imported_module; +} +#endif +#if PY_MAJOR_VERSION >= 3 +static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple) { + Py_ssize_t i, nparts; + nparts = PyTuple_GET_SIZE(parts_tuple); + for (i=1; i < nparts && module; i++) { + PyObject *part, *submodule; +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + part = PyTuple_GET_ITEM(parts_tuple, i); +#else + part = PySequence_ITEM(parts_tuple, i); +#endif + submodule = __Pyx_PyObject_GetAttrStrNoError(module, part); +#if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) + Py_DECREF(part); +#endif + Py_DECREF(module); + module = submodule; + } + if (unlikely(!module)) { + return __Pyx__ImportDottedModule_Error(name, parts_tuple, i); + } + return module; +} +#endif +static PyObject *__Pyx__ImportDottedModule(PyObject *name, PyObject *parts_tuple) { +#if PY_MAJOR_VERSION < 3 + PyObject *module, *from_list, *star = __pyx_n_s__58; + CYTHON_UNUSED_VAR(parts_tuple); + from_list = PyList_New(1); + if (unlikely(!from_list)) + return NULL; + Py_INCREF(star); + PyList_SET_ITEM(from_list, 0, star); + module = __Pyx_Import(name, from_list, 0); + Py_DECREF(from_list); + return module; +#else + PyObject *imported_module; + PyObject *module = __Pyx_Import(name, NULL, 0); + if (!parts_tuple || unlikely(!module)) + return module; + imported_module = __Pyx__ImportDottedModule_Lookup(name); + if (likely(imported_module)) { + Py_DECREF(module); + return imported_module; + } + PyErr_Clear(); + return __Pyx_ImportDottedModule_WalkParts(module, name, parts_tuple); +#endif +} +static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030400B1 + PyObject *module = __Pyx__ImportDottedModule_Lookup(name); + if (likely(module)) { + PyObject *spec = __Pyx_PyObject_GetAttrStrNoError(module, __pyx_n_s_spec); + if (likely(spec)) { + PyObject *unsafe = __Pyx_PyObject_GetAttrStrNoError(spec, __pyx_n_s_initializing); + if (likely(!unsafe || !__Pyx_PyObject_IsTrue(unsafe))) { + Py_DECREF(spec); + spec = NULL; + } + Py_XDECREF(unsafe); + } + if (likely(!spec)) { + PyErr_Clear(); + return module; + } + Py_DECREF(spec); + Py_DECREF(module); + } else if (PyErr_Occurred()) { + PyErr_Clear(); + } +#endif + return __Pyx__ImportDottedModule(name, parts_tuple); +} + +/* ImportFrom */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { + PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); + if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { + const char* module_name_str = 0; + PyObject* module_name = 0; + PyObject* module_dot = 0; + PyObject* full_name = 0; + PyErr_Clear(); + module_name_str = PyModule_GetName(module); + if (unlikely(!module_name_str)) { goto modbad; } + module_name = PyUnicode_FromString(module_name_str); + if (unlikely(!module_name)) { goto modbad; } + module_dot = PyUnicode_Concat(module_name, __pyx_kp_u__59); + if (unlikely(!module_dot)) { goto modbad; } + full_name = PyUnicode_Concat(module_dot, name); + if (unlikely(!full_name)) { goto modbad; } + #if PY_VERSION_HEX < 0x030700A1 || (CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM < 0x07030400) + { + PyObject *modules = PyImport_GetModuleDict(); + if (unlikely(!modules)) + goto modbad; + value = PyObject_GetItem(modules, full_name); + } + #else + value = PyImport_GetModule(full_name); + #endif + modbad: + Py_XDECREF(full_name); + Py_XDECREF(module_dot); + Py_XDECREF(module_name); + } + if (unlikely(!value)) { + PyErr_Format(PyExc_ImportError, + #if PY_MAJOR_VERSION < 3 + "cannot import name %.230s", PyString_AS_STRING(name)); + #else + "cannot import name %S", name); + #endif + } + return value; +} + +/* FetchSharedCythonModule */ +static PyObject *__Pyx_FetchSharedCythonABIModule(void) { + return __Pyx_PyImport_AddModuleRef((char*) __PYX_ABI_MODULE_NAME); +} + +/* FetchCommonType */ +static int __Pyx_VerifyCachedType(PyObject *cached_type, + const char *name, + Py_ssize_t basicsize, + Py_ssize_t expected_basicsize) { + if (!PyType_Check(cached_type)) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s is not a type object", name); + return -1; + } + if (basicsize != expected_basicsize) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s has the wrong size, try recompiling", + name); + return -1; + } + return 0; +} +#if !CYTHON_USE_TYPE_SPECS +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { + PyObject* abi_module; + const char* object_name; + PyTypeObject *cached_type = NULL; + abi_module = __Pyx_FetchSharedCythonABIModule(); + if (!abi_module) return NULL; + object_name = strrchr(type->tp_name, '.'); + object_name = object_name ? object_name+1 : type->tp_name; + cached_type = (PyTypeObject*) PyObject_GetAttrString(abi_module, object_name); + if (cached_type) { + if (__Pyx_VerifyCachedType( + (PyObject *)cached_type, + object_name, + cached_type->tp_basicsize, + type->tp_basicsize) < 0) { + goto bad; + } + goto done; + } + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; + PyErr_Clear(); + if (PyType_Ready(type) < 0) goto bad; + if (PyObject_SetAttrString(abi_module, object_name, (PyObject *)type) < 0) + goto bad; + Py_INCREF(type); + cached_type = type; +done: + Py_DECREF(abi_module); + return cached_type; +bad: + Py_XDECREF(cached_type); + cached_type = NULL; + goto done; +} +#else +static PyTypeObject *__Pyx_FetchCommonTypeFromSpec(PyObject *module, PyType_Spec *spec, PyObject *bases) { + PyObject *abi_module, *cached_type = NULL; + const char* object_name = strrchr(spec->name, '.'); + object_name = object_name ? object_name+1 : spec->name; + abi_module = __Pyx_FetchSharedCythonABIModule(); + if (!abi_module) return NULL; + cached_type = PyObject_GetAttrString(abi_module, object_name); + if (cached_type) { + Py_ssize_t basicsize; +#if CYTHON_COMPILING_IN_LIMITED_API + PyObject *py_basicsize; + py_basicsize = PyObject_GetAttrString(cached_type, "__basicsize__"); + if (unlikely(!py_basicsize)) goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (unlikely(basicsize == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; +#else + basicsize = likely(PyType_Check(cached_type)) ? ((PyTypeObject*) cached_type)->tp_basicsize : -1; +#endif + if (__Pyx_VerifyCachedType( + cached_type, + object_name, + basicsize, + spec->basicsize) < 0) { + goto bad; + } + goto done; + } + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; + PyErr_Clear(); + CYTHON_UNUSED_VAR(module); + cached_type = __Pyx_PyType_FromModuleAndSpec(abi_module, spec, bases); + if (unlikely(!cached_type)) goto bad; + if (unlikely(__Pyx_fix_up_extension_type_from_spec(spec, (PyTypeObject *) cached_type) < 0)) goto bad; + if (PyObject_SetAttrString(abi_module, object_name, cached_type) < 0) goto bad; +done: + Py_DECREF(abi_module); + assert(cached_type == NULL || PyType_Check(cached_type)); + return (PyTypeObject *) cached_type; +bad: + Py_XDECREF(cached_type); + cached_type = NULL; + goto done; +} +#endif + +/* PyVectorcallFastCallDict */ +#if CYTHON_METH_FASTCALL +static PyObject *__Pyx_PyVectorcall_FastCallDict_kw(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw) +{ + PyObject *res = NULL; + PyObject *kwnames; + PyObject **newargs; + PyObject **kwvalues; + Py_ssize_t i, pos; + size_t j; + PyObject *key, *value; + unsigned long keys_are_strings; + Py_ssize_t nkw = PyDict_GET_SIZE(kw); + newargs = (PyObject **)PyMem_Malloc((nargs + (size_t)nkw) * sizeof(args[0])); + if (unlikely(newargs == NULL)) { + PyErr_NoMemory(); + return NULL; + } + for (j = 0; j < nargs; j++) newargs[j] = args[j]; + kwnames = PyTuple_New(nkw); + if (unlikely(kwnames == NULL)) { + PyMem_Free(newargs); + return NULL; + } + kwvalues = newargs + nargs; + pos = i = 0; + keys_are_strings = Py_TPFLAGS_UNICODE_SUBCLASS; + while (PyDict_Next(kw, &pos, &key, &value)) { + keys_are_strings &= Py_TYPE(key)->tp_flags; + Py_INCREF(key); + Py_INCREF(value); + PyTuple_SET_ITEM(kwnames, i, key); + kwvalues[i] = value; + i++; + } + if (unlikely(!keys_are_strings)) { + PyErr_SetString(PyExc_TypeError, "keywords must be strings"); + goto cleanup; + } + res = vc(func, newargs, nargs, kwnames); +cleanup: + Py_DECREF(kwnames); + for (i = 0; i < nkw; i++) + Py_DECREF(kwvalues[i]); + PyMem_Free(newargs); + return res; +} +static CYTHON_INLINE PyObject *__Pyx_PyVectorcall_FastCallDict(PyObject *func, __pyx_vectorcallfunc vc, PyObject *const *args, size_t nargs, PyObject *kw) +{ + if (likely(kw == NULL) || PyDict_GET_SIZE(kw) == 0) { + return vc(func, args, nargs, NULL); + } + return __Pyx_PyVectorcall_FastCallDict_kw(func, vc, args, nargs, kw); +} +#endif + +/* CythonFunctionShared */ +#if CYTHON_COMPILING_IN_LIMITED_API +static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) { + if (__Pyx_CyFunction_Check(func)) { + return PyCFunction_GetFunction(((__pyx_CyFunctionObject*)func)->func) == (PyCFunction) cfunc; + } else if (PyCFunction_Check(func)) { + return PyCFunction_GetFunction(func) == (PyCFunction) cfunc; + } + return 0; +} +#else +static CYTHON_INLINE int __Pyx__IsSameCyOrCFunction(PyObject *func, void *cfunc) { + return __Pyx_CyOrPyCFunction_Check(func) && __Pyx_CyOrPyCFunction_GET_FUNCTION(func) == (PyCFunction) cfunc; +} +#endif +static CYTHON_INLINE void __Pyx__CyFunction_SetClassObj(__pyx_CyFunctionObject* f, PyObject* classobj) { +#if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API + __Pyx_Py_XDECREF_SET( + __Pyx_CyFunction_GetClassObj(f), + ((classobj) ? __Pyx_NewRef(classobj) : NULL)); +#else + __Pyx_Py_XDECREF_SET( + ((PyCMethodObject *) (f))->mm_class, + (PyTypeObject*)((classobj) ? __Pyx_NewRef(classobj) : NULL)); +#endif +} +static PyObject * +__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, void *closure) +{ + CYTHON_UNUSED_VAR(closure); + if (unlikely(op->func_doc == NULL)) { +#if CYTHON_COMPILING_IN_LIMITED_API + op->func_doc = PyObject_GetAttrString(op->func, "__doc__"); + if (unlikely(!op->func_doc)) return NULL; +#else + if (((PyCFunctionObject*)op)->m_ml->ml_doc) { +#if PY_MAJOR_VERSION >= 3 + op->func_doc = PyUnicode_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc); +#else + op->func_doc = PyString_FromString(((PyCFunctionObject*)op)->m_ml->ml_doc); +#endif + if (unlikely(op->func_doc == NULL)) + return NULL; + } else { + Py_INCREF(Py_None); + return Py_None; + } +#endif + } + Py_INCREF(op->func_doc); + return op->func_doc; +} +static int +__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, void *context) +{ + CYTHON_UNUSED_VAR(context); + if (value == NULL) { + value = Py_None; + } + Py_INCREF(value); + __Pyx_Py_XDECREF_SET(op->func_doc, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, void *context) +{ + CYTHON_UNUSED_VAR(context); + if (unlikely(op->func_name == NULL)) { +#if CYTHON_COMPILING_IN_LIMITED_API + op->func_name = PyObject_GetAttrString(op->func, "__name__"); +#elif PY_MAJOR_VERSION >= 3 + op->func_name = PyUnicode_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name); +#else + op->func_name = PyString_InternFromString(((PyCFunctionObject*)op)->m_ml->ml_name); +#endif + if (unlikely(op->func_name == NULL)) + return NULL; + } + Py_INCREF(op->func_name); + return op->func_name; +} +static int +__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value, void *context) +{ + CYTHON_UNUSED_VAR(context); +#if PY_MAJOR_VERSION >= 3 + if (unlikely(value == NULL || !PyUnicode_Check(value))) +#else + if (unlikely(value == NULL || !PyString_Check(value))) +#endif + { + PyErr_SetString(PyExc_TypeError, + "__name__ must be set to a string object"); + return -1; + } + Py_INCREF(value); + __Pyx_Py_XDECREF_SET(op->func_name, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, void *context) +{ + CYTHON_UNUSED_VAR(context); + Py_INCREF(op->func_qualname); + return op->func_qualname; +} +static int +__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, void *context) +{ + CYTHON_UNUSED_VAR(context); +#if PY_MAJOR_VERSION >= 3 + if (unlikely(value == NULL || !PyUnicode_Check(value))) +#else + if (unlikely(value == NULL || !PyString_Check(value))) +#endif + { + PyErr_SetString(PyExc_TypeError, + "__qualname__ must be set to a string object"); + return -1; + } + Py_INCREF(value); + __Pyx_Py_XDECREF_SET(op->func_qualname, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, void *context) +{ + CYTHON_UNUSED_VAR(context); + if (unlikely(op->func_dict == NULL)) { + op->func_dict = PyDict_New(); + if (unlikely(op->func_dict == NULL)) + return NULL; + } + Py_INCREF(op->func_dict); + return op->func_dict; +} +static int +__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value, void *context) +{ + CYTHON_UNUSED_VAR(context); + if (unlikely(value == NULL)) { + PyErr_SetString(PyExc_TypeError, + "function's dictionary may not be deleted"); + return -1; + } + if (unlikely(!PyDict_Check(value))) { + PyErr_SetString(PyExc_TypeError, + "setting function's dictionary to a non-dict"); + return -1; + } + Py_INCREF(value); + __Pyx_Py_XDECREF_SET(op->func_dict, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op, void *context) +{ + CYTHON_UNUSED_VAR(context); + Py_INCREF(op->func_globals); + return op->func_globals; +} +static PyObject * +__Pyx_CyFunction_get_closure(__pyx_CyFunctionObject *op, void *context) +{ + CYTHON_UNUSED_VAR(op); + CYTHON_UNUSED_VAR(context); + Py_INCREF(Py_None); + return Py_None; +} +static PyObject * +__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op, void *context) +{ + PyObject* result = (op->func_code) ? op->func_code : Py_None; + CYTHON_UNUSED_VAR(context); + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) { + int result = 0; + PyObject *res = op->defaults_getter((PyObject *) op); + if (unlikely(!res)) + return -1; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + op->defaults_tuple = PyTuple_GET_ITEM(res, 0); + Py_INCREF(op->defaults_tuple); + op->defaults_kwdict = PyTuple_GET_ITEM(res, 1); + Py_INCREF(op->defaults_kwdict); + #else + op->defaults_tuple = __Pyx_PySequence_ITEM(res, 0); + if (unlikely(!op->defaults_tuple)) result = -1; + else { + op->defaults_kwdict = __Pyx_PySequence_ITEM(res, 1); + if (unlikely(!op->defaults_kwdict)) result = -1; + } + #endif + Py_DECREF(res); + return result; +} +static int +__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) { + CYTHON_UNUSED_VAR(context); + if (!value) { + value = Py_None; + } else if (unlikely(value != Py_None && !PyTuple_Check(value))) { + PyErr_SetString(PyExc_TypeError, + "__defaults__ must be set to a tuple object"); + return -1; + } + PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__defaults__ will not " + "currently affect the values used in function calls", 1); + Py_INCREF(value); + __Pyx_Py_XDECREF_SET(op->defaults_tuple, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op, void *context) { + PyObject* result = op->defaults_tuple; + CYTHON_UNUSED_VAR(context); + if (unlikely(!result)) { + if (op->defaults_getter) { + if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL; + result = op->defaults_tuple; + } else { + result = Py_None; + } + } + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value, void *context) { + CYTHON_UNUSED_VAR(context); + if (!value) { + value = Py_None; + } else if (unlikely(value != Py_None && !PyDict_Check(value))) { + PyErr_SetString(PyExc_TypeError, + "__kwdefaults__ must be set to a dict object"); + return -1; + } + PyErr_WarnEx(PyExc_RuntimeWarning, "changes to cyfunction.__kwdefaults__ will not " + "currently affect the values used in function calls", 1); + Py_INCREF(value); + __Pyx_Py_XDECREF_SET(op->defaults_kwdict, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op, void *context) { + PyObject* result = op->defaults_kwdict; + CYTHON_UNUSED_VAR(context); + if (unlikely(!result)) { + if (op->defaults_getter) { + if (unlikely(__Pyx_CyFunction_init_defaults(op) < 0)) return NULL; + result = op->defaults_kwdict; + } else { + result = Py_None; + } + } + Py_INCREF(result); + return result; +} +static int +__Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value, void *context) { + CYTHON_UNUSED_VAR(context); + if (!value || value == Py_None) { + value = NULL; + } else if (unlikely(!PyDict_Check(value))) { + PyErr_SetString(PyExc_TypeError, + "__annotations__ must be set to a dict object"); + return -1; + } + Py_XINCREF(value); + __Pyx_Py_XDECREF_SET(op->func_annotations, value); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op, void *context) { + PyObject* result = op->func_annotations; + CYTHON_UNUSED_VAR(context); + if (unlikely(!result)) { + result = PyDict_New(); + if (unlikely(!result)) return NULL; + op->func_annotations = result; + } + Py_INCREF(result); + return result; +} +static PyObject * +__Pyx_CyFunction_get_is_coroutine(__pyx_CyFunctionObject *op, void *context) { + int is_coroutine; + CYTHON_UNUSED_VAR(context); + if (op->func_is_coroutine) { + return __Pyx_NewRef(op->func_is_coroutine); + } + is_coroutine = op->flags & __Pyx_CYFUNCTION_COROUTINE; +#if PY_VERSION_HEX >= 0x03050000 + if (is_coroutine) { + PyObject *module, *fromlist, *marker = __pyx_n_s_is_coroutine; + fromlist = PyList_New(1); + if (unlikely(!fromlist)) return NULL; + Py_INCREF(marker); +#if CYTHON_ASSUME_SAFE_MACROS + PyList_SET_ITEM(fromlist, 0, marker); +#else + if (unlikely(PyList_SetItem(fromlist, 0, marker) < 0)) { + Py_DECREF(marker); + Py_DECREF(fromlist); + return NULL; + } +#endif + module = PyImport_ImportModuleLevelObject(__pyx_n_s_asyncio_coroutines, NULL, NULL, fromlist, 0); + Py_DECREF(fromlist); + if (unlikely(!module)) goto ignore; + op->func_is_coroutine = __Pyx_PyObject_GetAttrStr(module, marker); + Py_DECREF(module); + if (likely(op->func_is_coroutine)) { + return __Pyx_NewRef(op->func_is_coroutine); + } +ignore: + PyErr_Clear(); + } +#endif + op->func_is_coroutine = __Pyx_PyBool_FromLong(is_coroutine); + return __Pyx_NewRef(op->func_is_coroutine); +} +#if CYTHON_COMPILING_IN_LIMITED_API +static PyObject * +__Pyx_CyFunction_get_module(__pyx_CyFunctionObject *op, void *context) { + CYTHON_UNUSED_VAR(context); + return PyObject_GetAttrString(op->func, "__module__"); +} +static int +__Pyx_CyFunction_set_module(__pyx_CyFunctionObject *op, PyObject* value, void *context) { + CYTHON_UNUSED_VAR(context); + return PyObject_SetAttrString(op->func, "__module__", value); +} +#endif +static PyGetSetDef __pyx_CyFunction_getsets[] = { + {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, + {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, + {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0}, + {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0}, + {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0}, + {(char *) "_is_coroutine", (getter)__Pyx_CyFunction_get_is_coroutine, 0, 0, 0}, +#if CYTHON_COMPILING_IN_LIMITED_API + {"__module__", (getter)__Pyx_CyFunction_get_module, (setter)__Pyx_CyFunction_set_module, 0, 0}, +#endif + {0, 0, 0, 0, 0} +}; +static PyMemberDef __pyx_CyFunction_members[] = { +#if !CYTHON_COMPILING_IN_LIMITED_API + {(char *) "__module__", T_OBJECT, offsetof(PyCFunctionObject, m_module), 0, 0}, +#endif +#if CYTHON_USE_TYPE_SPECS + {(char *) "__dictoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_dict), READONLY, 0}, +#if CYTHON_METH_FASTCALL +#if CYTHON_BACKPORT_VECTORCALL + {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_vectorcall), READONLY, 0}, +#else +#if !CYTHON_COMPILING_IN_LIMITED_API + {(char *) "__vectorcalloffset__", T_PYSSIZET, offsetof(PyCFunctionObject, vectorcall), READONLY, 0}, +#endif +#endif +#endif +#if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API + {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(__pyx_CyFunctionObject, func_weakreflist), READONLY, 0}, +#else + {(char *) "__weaklistoffset__", T_PYSSIZET, offsetof(PyCFunctionObject, m_weakreflist), READONLY, 0}, +#endif +#endif + {0, 0, 0, 0, 0} +}; +static PyObject * +__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, PyObject *args) +{ + CYTHON_UNUSED_VAR(args); +#if PY_MAJOR_VERSION >= 3 + Py_INCREF(m->func_qualname); + return m->func_qualname; +#else + return PyString_FromString(((PyCFunctionObject*)m)->m_ml->ml_name); +#endif +} +static PyMethodDef __pyx_CyFunction_methods[] = { + {"__reduce__", (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, + {0, 0, 0, 0} +}; +#if PY_VERSION_HEX < 0x030500A0 || CYTHON_COMPILING_IN_LIMITED_API +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist) +#else +#define __Pyx_CyFunction_weakreflist(cyfunc) (((PyCFunctionObject*)cyfunc)->m_weakreflist) +#endif +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject *op, PyMethodDef *ml, int flags, PyObject* qualname, + PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { +#if !CYTHON_COMPILING_IN_LIMITED_API + PyCFunctionObject *cf = (PyCFunctionObject*) op; +#endif + if (unlikely(op == NULL)) + return NULL; +#if CYTHON_COMPILING_IN_LIMITED_API + op->func = PyCFunction_NewEx(ml, (PyObject*)op, module); + if (unlikely(!op->func)) return NULL; +#endif + op->flags = flags; + __Pyx_CyFunction_weakreflist(op) = NULL; +#if !CYTHON_COMPILING_IN_LIMITED_API + cf->m_ml = ml; + cf->m_self = (PyObject *) op; +#endif + Py_XINCREF(closure); + op->func_closure = closure; +#if !CYTHON_COMPILING_IN_LIMITED_API + Py_XINCREF(module); + cf->m_module = module; +#endif + op->func_dict = NULL; + op->func_name = NULL; + Py_INCREF(qualname); + op->func_qualname = qualname; + op->func_doc = NULL; +#if PY_VERSION_HEX < 0x030900B1 || CYTHON_COMPILING_IN_LIMITED_API + op->func_classobj = NULL; +#else + ((PyCMethodObject*)op)->mm_class = NULL; +#endif + op->func_globals = globals; + Py_INCREF(op->func_globals); + Py_XINCREF(code); + op->func_code = code; + op->defaults_pyobjects = 0; + op->defaults_size = 0; + op->defaults = NULL; + op->defaults_tuple = NULL; + op->defaults_kwdict = NULL; + op->defaults_getter = NULL; + op->func_annotations = NULL; + op->func_is_coroutine = NULL; +#if CYTHON_METH_FASTCALL + switch (ml->ml_flags & (METH_VARARGS | METH_FASTCALL | METH_NOARGS | METH_O | METH_KEYWORDS | METH_METHOD)) { + case METH_NOARGS: + __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_NOARGS; + break; + case METH_O: + __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_O; + break; + case METH_METHOD | METH_FASTCALL | METH_KEYWORDS: + __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD; + break; + case METH_FASTCALL | METH_KEYWORDS: + __Pyx_CyFunction_func_vectorcall(op) = __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS; + break; + case METH_VARARGS | METH_KEYWORDS: + __Pyx_CyFunction_func_vectorcall(op) = NULL; + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction"); + Py_DECREF(op); + return NULL; + } +#endif + return (PyObject *) op; +} +static int +__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) +{ + Py_CLEAR(m->func_closure); +#if CYTHON_COMPILING_IN_LIMITED_API + Py_CLEAR(m->func); +#else + Py_CLEAR(((PyCFunctionObject*)m)->m_module); +#endif + Py_CLEAR(m->func_dict); + Py_CLEAR(m->func_name); + Py_CLEAR(m->func_qualname); + Py_CLEAR(m->func_doc); + Py_CLEAR(m->func_globals); + Py_CLEAR(m->func_code); +#if !CYTHON_COMPILING_IN_LIMITED_API +#if PY_VERSION_HEX < 0x030900B1 + Py_CLEAR(__Pyx_CyFunction_GetClassObj(m)); +#else + { + PyObject *cls = (PyObject*) ((PyCMethodObject *) (m))->mm_class; + ((PyCMethodObject *) (m))->mm_class = NULL; + Py_XDECREF(cls); + } +#endif +#endif + Py_CLEAR(m->defaults_tuple); + Py_CLEAR(m->defaults_kwdict); + Py_CLEAR(m->func_annotations); + Py_CLEAR(m->func_is_coroutine); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_XDECREF(pydefaults[i]); + PyObject_Free(m->defaults); + m->defaults = NULL; + } + return 0; +} +static void __Pyx__CyFunction_dealloc(__pyx_CyFunctionObject *m) +{ + if (__Pyx_CyFunction_weakreflist(m) != NULL) + PyObject_ClearWeakRefs((PyObject *) m); + __Pyx_CyFunction_clear(m); + __Pyx_PyHeapTypeObject_GC_Del(m); +} +static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) +{ + PyObject_GC_UnTrack(m); + __Pyx__CyFunction_dealloc(m); +} +static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) +{ + Py_VISIT(m->func_closure); +#if CYTHON_COMPILING_IN_LIMITED_API + Py_VISIT(m->func); +#else + Py_VISIT(((PyCFunctionObject*)m)->m_module); +#endif + Py_VISIT(m->func_dict); + Py_VISIT(m->func_name); + Py_VISIT(m->func_qualname); + Py_VISIT(m->func_doc); + Py_VISIT(m->func_globals); + Py_VISIT(m->func_code); +#if !CYTHON_COMPILING_IN_LIMITED_API + Py_VISIT(__Pyx_CyFunction_GetClassObj(m)); +#endif + Py_VISIT(m->defaults_tuple); + Py_VISIT(m->defaults_kwdict); + Py_VISIT(m->func_is_coroutine); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_VISIT(pydefaults[i]); + } + return 0; +} +static PyObject* +__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromFormat("<cyfunction %U at %p>", + op->func_qualname, (void *)op); +#else + return PyString_FromFormat("<cyfunction %s at %p>", + PyString_AsString(op->func_qualname), (void *)op); +#endif +} +static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) { +#if CYTHON_COMPILING_IN_LIMITED_API + PyObject *f = ((__pyx_CyFunctionObject*)func)->func; + PyObject *py_name = NULL; + PyCFunction meth; + int flags; + meth = PyCFunction_GetFunction(f); + if (unlikely(!meth)) return NULL; + flags = PyCFunction_GetFlags(f); + if (unlikely(flags < 0)) return NULL; +#else + PyCFunctionObject* f = (PyCFunctionObject*)func; + PyCFunction meth = f->m_ml->ml_meth; + int flags = f->m_ml->ml_flags; +#endif + Py_ssize_t size; + switch (flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) { + case METH_VARARGS: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) + return (*meth)(self, arg); + break; + case METH_VARARGS | METH_KEYWORDS: + return (*(PyCFunctionWithKeywords)(void*)meth)(self, arg, kw); + case METH_NOARGS: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { +#if CYTHON_ASSUME_SAFE_MACROS + size = PyTuple_GET_SIZE(arg); +#else + size = PyTuple_Size(arg); + if (unlikely(size < 0)) return NULL; +#endif + if (likely(size == 0)) + return (*meth)(self, NULL); +#if CYTHON_COMPILING_IN_LIMITED_API + py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL); + if (!py_name) return NULL; + PyErr_Format(PyExc_TypeError, + "%.200S() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + py_name, size); + Py_DECREF(py_name); +#else + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); +#endif + return NULL; + } + break; + case METH_O: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { +#if CYTHON_ASSUME_SAFE_MACROS + size = PyTuple_GET_SIZE(arg); +#else + size = PyTuple_Size(arg); + if (unlikely(size < 0)) return NULL; +#endif + if (likely(size == 1)) { + PyObject *result, *arg0; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + arg0 = PyTuple_GET_ITEM(arg, 0); + #else + arg0 = __Pyx_PySequence_ITEM(arg, 0); if (unlikely(!arg0)) return NULL; + #endif + result = (*meth)(self, arg0); + #if !(CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS) + Py_DECREF(arg0); + #endif + return result; + } +#if CYTHON_COMPILING_IN_LIMITED_API + py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL); + if (!py_name) return NULL; + PyErr_Format(PyExc_TypeError, + "%.200S() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + py_name, size); + Py_DECREF(py_name); +#else + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); +#endif + return NULL; + } + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags for CyFunction"); + return NULL; + } +#if CYTHON_COMPILING_IN_LIMITED_API + py_name = __Pyx_CyFunction_get_name((__pyx_CyFunctionObject*)func, NULL); + if (!py_name) return NULL; + PyErr_Format(PyExc_TypeError, "%.200S() takes no keyword arguments", + py_name); + Py_DECREF(py_name); +#else + PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", + f->m_ml->ml_name); +#endif + return NULL; +} +static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *self, *result; +#if CYTHON_COMPILING_IN_LIMITED_API + self = PyCFunction_GetSelf(((__pyx_CyFunctionObject*)func)->func); + if (unlikely(!self) && PyErr_Occurred()) return NULL; +#else + self = ((PyCFunctionObject*)func)->m_self; +#endif + result = __Pyx_CyFunction_CallMethod(func, self, arg, kw); + return result; +} +static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) { + PyObject *result; + __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func; +#if CYTHON_METH_FASTCALL + __pyx_vectorcallfunc vc = __Pyx_CyFunction_func_vectorcall(cyfunc); + if (vc) { +#if CYTHON_ASSUME_SAFE_MACROS + return __Pyx_PyVectorcall_FastCallDict(func, vc, &PyTuple_GET_ITEM(args, 0), (size_t)PyTuple_GET_SIZE(args), kw); +#else + (void) &__Pyx_PyVectorcall_FastCallDict; + return PyVectorcall_Call(func, args, kw); +#endif + } +#endif + if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) { + Py_ssize_t argc; + PyObject *new_args; + PyObject *self; +#if CYTHON_ASSUME_SAFE_MACROS + argc = PyTuple_GET_SIZE(args); +#else + argc = PyTuple_Size(args); + if (unlikely(!argc) < 0) return NULL; +#endif + new_args = PyTuple_GetSlice(args, 1, argc); + if (unlikely(!new_args)) + return NULL; + self = PyTuple_GetItem(args, 0); + if (unlikely(!self)) { + Py_DECREF(new_args); +#if PY_MAJOR_VERSION > 2 + PyErr_Format(PyExc_TypeError, + "unbound method %.200S() needs an argument", + cyfunc->func_qualname); +#else + PyErr_SetString(PyExc_TypeError, + "unbound method needs an argument"); +#endif + return NULL; + } + result = __Pyx_CyFunction_CallMethod(func, self, new_args, kw); + Py_DECREF(new_args); + } else { + result = __Pyx_CyFunction_Call(func, args, kw); + } + return result; +} +#if CYTHON_METH_FASTCALL +static CYTHON_INLINE int __Pyx_CyFunction_Vectorcall_CheckArgs(__pyx_CyFunctionObject *cyfunc, Py_ssize_t nargs, PyObject *kwnames) +{ + int ret = 0; + if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) { + if (unlikely(nargs < 1)) { + PyErr_Format(PyExc_TypeError, "%.200s() needs an argument", + ((PyCFunctionObject*)cyfunc)->m_ml->ml_name); + return -1; + } + ret = 1; + } + if (unlikely(kwnames) && unlikely(PyTuple_GET_SIZE(kwnames))) { + PyErr_Format(PyExc_TypeError, + "%.200s() takes no keyword arguments", ((PyCFunctionObject*)cyfunc)->m_ml->ml_name); + return -1; + } + return ret; +} +static PyObject * __Pyx_CyFunction_Vectorcall_NOARGS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) +{ + __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; + PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; +#if CYTHON_BACKPORT_VECTORCALL + Py_ssize_t nargs = (Py_ssize_t)nargsf; +#else + Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); +#endif + PyObject *self; + switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) { + case 1: + self = args[0]; + args += 1; + nargs -= 1; + break; + case 0: + self = ((PyCFunctionObject*)cyfunc)->m_self; + break; + default: + return NULL; + } + if (unlikely(nargs != 0)) { + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + def->ml_name, nargs); + return NULL; + } + return def->ml_meth(self, NULL); +} +static PyObject * __Pyx_CyFunction_Vectorcall_O(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) +{ + __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; + PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; +#if CYTHON_BACKPORT_VECTORCALL + Py_ssize_t nargs = (Py_ssize_t)nargsf; +#else + Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); +#endif + PyObject *self; + switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, kwnames)) { + case 1: + self = args[0]; + args += 1; + nargs -= 1; + break; + case 0: + self = ((PyCFunctionObject*)cyfunc)->m_self; + break; + default: + return NULL; + } + if (unlikely(nargs != 1)) { + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + def->ml_name, nargs); + return NULL; + } + return def->ml_meth(self, args[0]); +} +static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) +{ + __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; + PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; +#if CYTHON_BACKPORT_VECTORCALL + Py_ssize_t nargs = (Py_ssize_t)nargsf; +#else + Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); +#endif + PyObject *self; + switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) { + case 1: + self = args[0]; + args += 1; + nargs -= 1; + break; + case 0: + self = ((PyCFunctionObject*)cyfunc)->m_self; + break; + default: + return NULL; + } + return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames); +} +static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames) +{ + __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *)func; + PyMethodDef* def = ((PyCFunctionObject*)cyfunc)->m_ml; + PyTypeObject *cls = (PyTypeObject *) __Pyx_CyFunction_GetClassObj(cyfunc); +#if CYTHON_BACKPORT_VECTORCALL + Py_ssize_t nargs = (Py_ssize_t)nargsf; +#else + Py_ssize_t nargs = PyVectorcall_NARGS(nargsf); +#endif + PyObject *self; + switch (__Pyx_CyFunction_Vectorcall_CheckArgs(cyfunc, nargs, NULL)) { + case 1: + self = args[0]; + args += 1; + nargs -= 1; + break; + case 0: + self = ((PyCFunctionObject*)cyfunc)->m_self; + break; + default: + return NULL; + } + return ((__Pyx_PyCMethod)(void(*)(void))def->ml_meth)(self, cls, args, (size_t)nargs, kwnames); +} +#endif +#if CYTHON_USE_TYPE_SPECS +static PyType_Slot __pyx_CyFunctionType_slots[] = { + {Py_tp_dealloc, (void *)__Pyx_CyFunction_dealloc}, + {Py_tp_repr, (void *)__Pyx_CyFunction_repr}, + {Py_tp_call, (void *)__Pyx_CyFunction_CallAsMethod}, + {Py_tp_traverse, (void *)__Pyx_CyFunction_traverse}, + {Py_tp_clear, (void *)__Pyx_CyFunction_clear}, + {Py_tp_methods, (void *)__pyx_CyFunction_methods}, + {Py_tp_members, (void *)__pyx_CyFunction_members}, + {Py_tp_getset, (void *)__pyx_CyFunction_getsets}, + {Py_tp_descr_get, (void *)__Pyx_PyMethod_New}, + {0, 0}, +}; +static PyType_Spec __pyx_CyFunctionType_spec = { + __PYX_TYPE_MODULE_PREFIX "cython_function_or_method", + sizeof(__pyx_CyFunctionObject), + 0, +#ifdef Py_TPFLAGS_METHOD_DESCRIPTOR + Py_TPFLAGS_METHOD_DESCRIPTOR | +#endif +#if (defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL) + _Py_TPFLAGS_HAVE_VECTORCALL | +#endif + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE, + __pyx_CyFunctionType_slots +}; +#else +static PyTypeObject __pyx_CyFunctionType_type = { + PyVarObject_HEAD_INIT(0, 0) + __PYX_TYPE_MODULE_PREFIX "cython_function_or_method", + sizeof(__pyx_CyFunctionObject), + 0, + (destructor) __Pyx_CyFunction_dealloc, +#if !CYTHON_METH_FASTCALL + 0, +#elif CYTHON_BACKPORT_VECTORCALL + (printfunc)offsetof(__pyx_CyFunctionObject, func_vectorcall), +#else + offsetof(PyCFunctionObject, vectorcall), +#endif + 0, + 0, +#if PY_MAJOR_VERSION < 3 + 0, +#else + 0, +#endif + (reprfunc) __Pyx_CyFunction_repr, + 0, + 0, + 0, + 0, + __Pyx_CyFunction_CallAsMethod, + 0, + 0, + 0, + 0, +#ifdef Py_TPFLAGS_METHOD_DESCRIPTOR + Py_TPFLAGS_METHOD_DESCRIPTOR | +#endif +#if defined(_Py_TPFLAGS_HAVE_VECTORCALL) && CYTHON_METH_FASTCALL + _Py_TPFLAGS_HAVE_VECTORCALL | +#endif + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_BASETYPE, + 0, + (traverseproc) __Pyx_CyFunction_traverse, + (inquiry) __Pyx_CyFunction_clear, + 0, +#if PY_VERSION_HEX < 0x030500A0 + offsetof(__pyx_CyFunctionObject, func_weakreflist), +#else + offsetof(PyCFunctionObject, m_weakreflist), +#endif + 0, + 0, + __pyx_CyFunction_methods, + __pyx_CyFunction_members, + __pyx_CyFunction_getsets, + 0, + 0, + __Pyx_PyMethod_New, + 0, + offsetof(__pyx_CyFunctionObject, func_dict), + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, +#if PY_VERSION_HEX >= 0x030400a1 + 0, +#endif +#if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) + 0, +#endif +#if __PYX_NEED_TP_PRINT_SLOT + 0, +#endif +#if PY_VERSION_HEX >= 0x030C0000 + 0, +#endif +#if PY_VERSION_HEX >= 0x030d00A4 + 0, +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, +#endif +}; +#endif +static int __pyx_CyFunction_init(PyObject *module) { +#if CYTHON_USE_TYPE_SPECS + __pyx_CyFunctionType = __Pyx_FetchCommonTypeFromSpec(module, &__pyx_CyFunctionType_spec, NULL); +#else + CYTHON_UNUSED_VAR(module); + __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); +#endif + if (unlikely(__pyx_CyFunctionType == NULL)) { + return -1; + } + return 0; +} +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults = PyObject_Malloc(size); + if (unlikely(!m->defaults)) + return PyErr_NoMemory(); + memset(m->defaults, 0, size); + m->defaults_pyobjects = pyobjects; + m->defaults_size = size; + return m->defaults; +} +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_tuple = tuple; + Py_INCREF(tuple); +} +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_kwdict = dict; + Py_INCREF(dict); +} +static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) { + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->func_annotations = dict; + Py_INCREF(dict); +} + +/* CythonFunction */ +static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, int flags, PyObject* qualname, + PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) { + PyObject *op = __Pyx_CyFunction_Init( + PyObject_GC_New(__pyx_CyFunctionObject, __pyx_CyFunctionType), + ml, flags, qualname, closure, module, globals, code + ); + if (likely(op)) { + PyObject_GC_Track(op); + } + return op; +} + +/* Py3UpdateBases */ +static PyObject* +__Pyx_PEP560_update_bases(PyObject *bases) +{ + Py_ssize_t i, j, size_bases; + PyObject *base, *meth, *new_base, *result, *new_bases = NULL; + size_bases = PyTuple_GET_SIZE(bases); + for (i = 0; i < size_bases; i++) { + base = PyTuple_GET_ITEM(bases, i); + if (PyType_Check(base)) { + if (new_bases) { + if (PyList_Append(new_bases, base) < 0) { + goto error; + } + } + continue; + } + meth = __Pyx_PyObject_GetAttrStrNoError(base, __pyx_n_s_mro_entries); + if (!meth && PyErr_Occurred()) { + goto error; + } + if (!meth) { + if (new_bases) { + if (PyList_Append(new_bases, base) < 0) { + goto error; + } + } + continue; + } + new_base = __Pyx_PyObject_CallOneArg(meth, bases); + Py_DECREF(meth); + if (!new_base) { + goto error; + } + if (!PyTuple_Check(new_base)) { + PyErr_SetString(PyExc_TypeError, + "__mro_entries__ must return a tuple"); + Py_DECREF(new_base); + goto error; + } + if (!new_bases) { + if (!(new_bases = PyList_New(i))) { + goto error; + } + for (j = 0; j < i; j++) { + base = PyTuple_GET_ITEM(bases, j); + PyList_SET_ITEM(new_bases, j, base); + Py_INCREF(base); + } + } + j = PyList_GET_SIZE(new_bases); + if (PyList_SetSlice(new_bases, j, j, new_base) < 0) { + goto error; + } + Py_DECREF(new_base); + } + if (!new_bases) { + Py_INCREF(bases); + return bases; + } + result = PyList_AsTuple(new_bases); + Py_DECREF(new_bases); + return result; +error: + Py_XDECREF(new_bases); + return NULL; +} + +/* CalculateMetaclass */ +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { + Py_ssize_t i, nbases; +#if CYTHON_ASSUME_SAFE_MACROS + nbases = PyTuple_GET_SIZE(bases); +#else + nbases = PyTuple_Size(bases); + if (nbases < 0) return NULL; +#endif + for (i=0; i < nbases; i++) { + PyTypeObject *tmptype; +#if CYTHON_ASSUME_SAFE_MACROS + PyObject *tmp = PyTuple_GET_ITEM(bases, i); +#else + PyObject *tmp = PyTuple_GetItem(bases, i); + if (!tmp) return NULL; +#endif + tmptype = Py_TYPE(tmp); +#if PY_MAJOR_VERSION < 3 + if (tmptype == &PyClass_Type) + continue; +#endif + if (!metaclass) { + metaclass = tmptype; + continue; + } + if (PyType_IsSubtype(metaclass, tmptype)) + continue; + if (PyType_IsSubtype(tmptype, metaclass)) { + metaclass = tmptype; + continue; + } + PyErr_SetString(PyExc_TypeError, + "metaclass conflict: " + "the metaclass of a derived class " + "must be a (non-strict) subclass " + "of the metaclasses of all its bases"); + return NULL; + } + if (!metaclass) { +#if PY_MAJOR_VERSION < 3 + metaclass = &PyClass_Type; +#else + metaclass = &PyType_Type; +#endif + } + Py_INCREF((PyObject*) metaclass); + return (PyObject*) metaclass; +} + +/* PyObjectLookupSpecial */ +#if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error) { + PyObject *res; + PyTypeObject *tp = Py_TYPE(obj); +#if PY_MAJOR_VERSION < 3 + if (unlikely(PyInstance_Check(obj))) + return with_error ? __Pyx_PyObject_GetAttrStr(obj, attr_name) : __Pyx_PyObject_GetAttrStrNoError(obj, attr_name); +#endif + res = _PyType_Lookup(tp, attr_name); + if (likely(res)) { + descrgetfunc f = Py_TYPE(res)->tp_descr_get; + if (!f) { + Py_INCREF(res); + } else { + res = f(res, obj, (PyObject *)tp); + } + } else if (with_error) { + PyErr_SetObject(PyExc_AttributeError, attr_name); + } + return res; +} +#endif + +/* Py3ClassCreate */ +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, + PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { + PyObject *ns; + if (metaclass) { + PyObject *prep = __Pyx_PyObject_GetAttrStrNoError(metaclass, __pyx_n_s_prepare); + if (prep) { + PyObject *pargs[3] = {NULL, name, bases}; + ns = __Pyx_PyObject_FastCallDict(prep, pargs+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, mkw); + Py_DECREF(prep); + } else { + if (unlikely(PyErr_Occurred())) + return NULL; + ns = PyDict_New(); + } + } else { + ns = PyDict_New(); + } + if (unlikely(!ns)) + return NULL; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad; +#if PY_VERSION_HEX >= 0x03030000 + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad; +#else + CYTHON_MAYBE_UNUSED_VAR(qualname); +#endif + if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad; + return ns; +bad: + Py_DECREF(ns); + return NULL; +} +#if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS +static int __Pyx_SetNamesPEP487(PyObject *type_obj) { + PyTypeObject *type = (PyTypeObject*) type_obj; + PyObject *names_to_set, *key, *value, *set_name, *tmp; + Py_ssize_t i = 0; +#if CYTHON_USE_TYPE_SLOTS + names_to_set = PyDict_Copy(type->tp_dict); +#else + { + PyObject *d = PyObject_GetAttr(type_obj, __pyx_n_s_dict); + names_to_set = NULL; + if (likely(d)) { + PyObject *names_to_set = PyDict_New(); + int ret = likely(names_to_set) ? PyDict_Update(names_to_set, d) : -1; + Py_DECREF(d); + if (unlikely(ret < 0)) + Py_CLEAR(names_to_set); + } + } +#endif + if (unlikely(names_to_set == NULL)) + goto bad; + while (PyDict_Next(names_to_set, &i, &key, &value)) { + set_name = __Pyx_PyObject_LookupSpecialNoError(value, __pyx_n_s_set_name); + if (unlikely(set_name != NULL)) { + tmp = __Pyx_PyObject_Call2Args(set_name, type_obj, key); + Py_DECREF(set_name); + if (unlikely(tmp == NULL)) { + __Pyx_TypeName value_type_name = + __Pyx_PyType_GetName(Py_TYPE(value)); + __Pyx_TypeName type_name = __Pyx_PyType_GetName(type); + PyErr_Format(PyExc_RuntimeError, +#if PY_MAJOR_VERSION >= 3 + "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %R " "in '" __Pyx_FMT_TYPENAME "'", + value_type_name, key, type_name); +#else + "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %.100s in '" __Pyx_FMT_TYPENAME "'", + value_type_name, + PyString_Check(key) ? PyString_AS_STRING(key) : "?", + type_name); +#endif + goto bad; + } else { + Py_DECREF(tmp); + } + } + else if (unlikely(PyErr_Occurred())) { + goto bad; + } + } + Py_DECREF(names_to_set); + return 0; +bad: + Py_XDECREF(names_to_set); + return -1; +} +static PyObject *__Pyx_InitSubclassPEP487(PyObject *type_obj, PyObject *mkw) { +#if CYTHON_USE_TYPE_SLOTS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + PyTypeObject *type = (PyTypeObject*) type_obj; + PyObject *mro = type->tp_mro; + Py_ssize_t i, nbases; + if (unlikely(!mro)) goto done; + (void) &__Pyx_GetBuiltinName; + Py_INCREF(mro); + nbases = PyTuple_GET_SIZE(mro); + assert(PyTuple_GET_ITEM(mro, 0) == type_obj); + for (i = 1; i < nbases-1; i++) { + PyObject *base, *dict, *meth; + base = PyTuple_GET_ITEM(mro, i); + dict = ((PyTypeObject *)base)->tp_dict; + meth = __Pyx_PyDict_GetItemStrWithError(dict, __pyx_n_s_init_subclass); + if (unlikely(meth)) { + descrgetfunc f = Py_TYPE(meth)->tp_descr_get; + PyObject *res; + Py_INCREF(meth); + if (likely(f)) { + res = f(meth, NULL, type_obj); + Py_DECREF(meth); + if (unlikely(!res)) goto bad; + meth = res; + } + res = __Pyx_PyObject_FastCallDict(meth, NULL, 0, mkw); + Py_DECREF(meth); + if (unlikely(!res)) goto bad; + Py_DECREF(res); + goto done; + } else if (unlikely(PyErr_Occurred())) { + goto bad; + } + } +done: + Py_XDECREF(mro); + return type_obj; +bad: + Py_XDECREF(mro); + Py_DECREF(type_obj); + return NULL; +#else + PyObject *super_type, *super, *func, *res; +#if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type) + super_type = __Pyx_GetBuiltinName(__pyx_n_s_super); +#else + super_type = (PyObject*) &PySuper_Type; + (void) &__Pyx_GetBuiltinName; +#endif + super = likely(super_type) ? __Pyx_PyObject_Call2Args(super_type, type_obj, type_obj) : NULL; +#if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type) + Py_XDECREF(super_type); +#endif + if (unlikely(!super)) { + Py_CLEAR(type_obj); + goto done; + } + func = __Pyx_PyObject_GetAttrStrNoError(super, __pyx_n_s_init_subclass); + Py_DECREF(super); + if (likely(!func)) { + if (unlikely(PyErr_Occurred())) + Py_CLEAR(type_obj); + goto done; + } + res = __Pyx_PyObject_FastCallDict(func, NULL, 0, mkw); + Py_DECREF(func); + if (unlikely(!res)) + Py_CLEAR(type_obj); + Py_XDECREF(res); +done: + return type_obj; +#endif +} +#endif +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, + PyObject *dict, PyObject *mkw, + int calculate_metaclass, int allow_py2_metaclass) { + PyObject *result; + PyObject *owned_metaclass = NULL; + PyObject *margs[4] = {NULL, name, bases, dict}; + if (allow_py2_metaclass) { + owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass); + if (owned_metaclass) { + metaclass = owned_metaclass; + } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) { + PyErr_Clear(); + } else { + return NULL; + } + } + if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) { + metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases); + Py_XDECREF(owned_metaclass); + if (unlikely(!metaclass)) + return NULL; + owned_metaclass = metaclass; + } + result = __Pyx_PyObject_FastCallDict(metaclass, margs+1, 3 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, +#if PY_VERSION_HEX < 0x030600A4 + (metaclass == (PyObject*)&PyType_Type) ? NULL : mkw +#else + mkw +#endif + ); + Py_XDECREF(owned_metaclass); +#if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS + if (likely(result) && likely(PyType_Check(result))) { + if (unlikely(__Pyx_SetNamesPEP487(result) < 0)) { + Py_CLEAR(result); + } else { + result = __Pyx_InitSubclassPEP487(result, mkw); + } + } +#else + (void) &__Pyx_GetBuiltinName; +#endif + return result; +} + +/* CLineInTraceback */ +#ifndef CYTHON_CLINE_IN_TRACEBACK +static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) { + PyObject *use_cline; + PyObject *ptype, *pvalue, *ptraceback; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject **cython_runtime_dict; +#endif + CYTHON_MAYBE_UNUSED_VAR(tstate); + if (unlikely(!__pyx_cython_runtime)) { + return c_line; + } + __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); +#if CYTHON_COMPILING_IN_CPYTHON + cython_runtime_dict = _PyObject_GetDictPtr(__pyx_cython_runtime); + if (likely(cython_runtime_dict)) { + __PYX_PY_DICT_LOOKUP_IF_MODIFIED( + use_cline, *cython_runtime_dict, + __Pyx_PyDict_GetItemStr(*cython_runtime_dict, __pyx_n_s_cline_in_traceback)) + } else +#endif + { + PyObject *use_cline_obj = __Pyx_PyObject_GetAttrStrNoError(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback); + if (use_cline_obj) { + use_cline = PyObject_Not(use_cline_obj) ? Py_False : Py_True; + Py_DECREF(use_cline_obj); + } else { + PyErr_Clear(); + use_cline = NULL; + } + } + if (!use_cline) { + c_line = 0; + (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False); + } + else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) { + c_line = 0; + } + __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); + return c_line; +} +#endif + +/* CodeObjectCache */ +#if !CYTHON_COMPILING_IN_LIMITED_API +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = start + (end - start) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, ((size_t)new_max) * sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} +#endif + +/* AddTraceback */ +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +#if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API + #ifndef Py_BUILD_CORE + #define Py_BUILD_CORE 1 + #endif + #include "internal/pycore_frame.h" +#endif +#if CYTHON_COMPILING_IN_LIMITED_API +static PyObject *__Pyx_PyCode_Replace_For_AddTraceback(PyObject *code, PyObject *scratch_dict, + PyObject *firstlineno, PyObject *name) { + PyObject *replace = NULL; + if (unlikely(PyDict_SetItemString(scratch_dict, "co_firstlineno", firstlineno))) return NULL; + if (unlikely(PyDict_SetItemString(scratch_dict, "co_name", name))) return NULL; + replace = PyObject_GetAttrString(code, "replace"); + if (likely(replace)) { + PyObject *result; + result = PyObject_Call(replace, __pyx_empty_tuple, scratch_dict); + Py_DECREF(replace); + return result; + } + PyErr_Clear(); + #if __PYX_LIMITED_VERSION_HEX < 0x030780000 + { + PyObject *compiled = NULL, *result = NULL; + if (unlikely(PyDict_SetItemString(scratch_dict, "code", code))) return NULL; + if (unlikely(PyDict_SetItemString(scratch_dict, "type", (PyObject*)(&PyType_Type)))) return NULL; + compiled = Py_CompileString( + "out = type(code)(\n" + " code.co_argcount, code.co_kwonlyargcount, code.co_nlocals, code.co_stacksize,\n" + " code.co_flags, code.co_code, code.co_consts, code.co_names,\n" + " code.co_varnames, code.co_filename, co_name, co_firstlineno,\n" + " code.co_lnotab)\n", "<dummy>", Py_file_input); + if (!compiled) return NULL; + result = PyEval_EvalCode(compiled, scratch_dict, scratch_dict); + Py_DECREF(compiled); + if (!result) PyErr_Print(); + Py_DECREF(result); + result = PyDict_GetItemString(scratch_dict, "out"); + if (result) Py_INCREF(result); + return result; + } + #else + return NULL; + #endif +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyObject *code_object = NULL, *py_py_line = NULL, *py_funcname = NULL, *dict = NULL; + PyObject *replace = NULL, *getframe = NULL, *frame = NULL; + PyObject *exc_type, *exc_value, *exc_traceback; + int success = 0; + if (c_line) { + (void) __pyx_cfilenm; + (void) __Pyx_CLineForTraceback(__Pyx_PyThreadState_Current, c_line); + } + PyErr_Fetch(&exc_type, &exc_value, &exc_traceback); + code_object = Py_CompileString("_getframe()", filename, Py_eval_input); + if (unlikely(!code_object)) goto bad; + py_py_line = PyLong_FromLong(py_line); + if (unlikely(!py_py_line)) goto bad; + py_funcname = PyUnicode_FromString(funcname); + if (unlikely(!py_funcname)) goto bad; + dict = PyDict_New(); + if (unlikely(!dict)) goto bad; + { + PyObject *old_code_object = code_object; + code_object = __Pyx_PyCode_Replace_For_AddTraceback(code_object, dict, py_py_line, py_funcname); + Py_DECREF(old_code_object); + } + if (unlikely(!code_object)) goto bad; + getframe = PySys_GetObject("_getframe"); + if (unlikely(!getframe)) goto bad; + if (unlikely(PyDict_SetItemString(dict, "_getframe", getframe))) goto bad; + frame = PyEval_EvalCode(code_object, dict, dict); + if (unlikely(!frame) || frame == Py_None) goto bad; + success = 1; + bad: + PyErr_Restore(exc_type, exc_value, exc_traceback); + Py_XDECREF(code_object); + Py_XDECREF(py_py_line); + Py_XDECREF(py_funcname); + Py_XDECREF(dict); + Py_XDECREF(replace); + if (success) { + PyTraceBack_Here( + (struct _frame*)frame); + } + Py_XDECREF(frame); +} +#else +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = NULL; + PyObject *py_funcname = NULL; + #if PY_MAJOR_VERSION < 3 + PyObject *py_srcfile = NULL; + py_srcfile = PyString_FromString(filename); + if (!py_srcfile) goto bad; + #endif + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + if (!py_funcname) goto bad; + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + if (!py_funcname) goto bad; + funcname = PyUnicode_AsUTF8(py_funcname); + if (!funcname) goto bad; + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + if (!py_funcname) goto bad; + #endif + } + #if PY_MAJOR_VERSION < 3 + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + #else + py_code = PyCode_NewEmpty(filename, funcname, py_line); + #endif + Py_XDECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_funcname); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(py_srcfile); + #endif + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject *ptype, *pvalue, *ptraceback; + if (c_line) { + c_line = __Pyx_CLineForTraceback(tstate, c_line); + } + py_code = __pyx_find_code_object(c_line ? -c_line : py_line); + if (!py_code) { + __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback); + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) { + /* If the code object creation fails, then we should clear the + fetched exception references and propagate the new exception */ + Py_XDECREF(ptype); + Py_XDECREF(pvalue); + Py_XDECREF(ptraceback); + goto bad; + } + __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback); + __pyx_insert_code_object(c_line ? -c_line : py_line, py_code); + } + py_frame = PyFrame_New( + tstate, /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + __Pyx_PyFrame_SetLineNumber(py_frame, py_line); + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} +#endif + +/* CIntFromPyVerify */ +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ + } + +/* CIntFromPy */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const int neg_one = (int) -1, const_zero = (int) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if ((sizeof(int) < sizeof(long))) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } +#endif + if (unlikely(!PyLong_Check(x))) { + int val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 2 * PyLong_SHIFT)) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 3: + if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) >= 3 * PyLong_SHIFT)) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + case 4: + if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(int) >= 4 * PyLong_SHIFT)) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + } + } + break; + } + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if ((sizeof(int) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(int) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(int) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 2: + if ((8 * sizeof(int) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -3: + if ((8 * sizeof(int) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 3: + if ((8 * sizeof(int) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case -4: + if ((8 * sizeof(int) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + case 4: + if ((8 * sizeof(int) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(int) - 1 > 4 * PyLong_SHIFT)) { + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + } + } + break; + } + } +#endif + if ((sizeof(int) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(int) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { + int val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (int) -1; + assert(PyLong_CheckExact(v)); + } + { + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { + Py_DECREF(v); + return (int) -1; + } + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (int) -1; + } else { + stepval = v; + } + v = NULL; + val = (int) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(int) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((int) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(int) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((int) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((int) 1) << (sizeof(int) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (int) -1; + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const int neg_one = (int) -1, const_zero = (int) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntFromPy */ +static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if ((sizeof(uint64_t) < sizeof(long))) { + __PYX_VERIFY_RETURN_INT(uint64_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (uint64_t) val; + } + } +#endif + if (unlikely(!PyLong_Check(x))) { + uint64_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (uint64_t) -1; + val = __Pyx_PyInt_As_uint64_t(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(uint64_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(uint64_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(uint64_t) >= 2 * PyLong_SHIFT)) { + return (uint64_t) (((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])); + } + } + break; + case 3: + if ((8 * sizeof(uint64_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(uint64_t) >= 3 * PyLong_SHIFT)) { + return (uint64_t) (((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])); + } + } + break; + case 4: + if ((8 * sizeof(uint64_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_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]))) + } else if ((8 * sizeof(uint64_t) >= 4 * PyLong_SHIFT)) { + return (uint64_t) (((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0])); + } + } + break; + } + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (uint64_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if ((sizeof(uint64_t) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(uint64_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(uint64_t) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT)) { + return (uint64_t) (((uint64_t)-1)*(((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); + } + } + break; + case 2: + if ((8 * sizeof(uint64_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT)) { + return (uint64_t) ((((((uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); + } + } + break; + case -3: + if ((8 * sizeof(uint64_t) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT)) { + return (uint64_t) (((uint64_t)-1)*(((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); + } + } + break; + case 3: + if ((8 * sizeof(uint64_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT)) { + return (uint64_t) ((((((((uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); + } + } + break; + case -4: + if ((8 * sizeof(uint64_t) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_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]))) + } else if ((8 * sizeof(uint64_t) - 1 > 4 * PyLong_SHIFT)) { + return (uint64_t) (((uint64_t)-1)*(((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); + } + } + break; + case 4: + if ((8 * sizeof(uint64_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(uint64_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]))) + } else if ((8 * sizeof(uint64_t) - 1 > 4 * PyLong_SHIFT)) { + return (uint64_t) ((((((((((uint64_t)digits[3]) << PyLong_SHIFT) | (uint64_t)digits[2]) << PyLong_SHIFT) | (uint64_t)digits[1]) << PyLong_SHIFT) | (uint64_t)digits[0]))); + } + } + break; + } + } +#endif + if ((sizeof(uint64_t) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(uint64_t, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(uint64_t) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(uint64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { + uint64_t val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (uint64_t) -1; + assert(PyLong_CheckExact(v)); + } + { + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { + Py_DECREF(v); + return (uint64_t) -1; + } + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (uint64_t) -1; + } else { + stepval = v; + } + v = NULL; + val = (uint64_t) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(uint64_t) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((uint64_t) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(uint64_t) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((uint64_t) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((uint64_t) 1) << (sizeof(uint64_t) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (uint64_t) -1; + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to uint64_t"); + return (uint64_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to uint64_t"); + return (uint64_t) -1; +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_off_t(off_t value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const off_t neg_one = (off_t) -1, const_zero = (off_t) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(off_t) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(off_t) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(off_t) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(off_t) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(off_t) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(off_t), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(off_t)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__htsFormatCategory(enum htsFormatCategory value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const enum htsFormatCategory neg_one = (enum htsFormatCategory) -1, const_zero = (enum htsFormatCategory) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum htsFormatCategory) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum htsFormatCategory) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum htsFormatCategory) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum htsFormatCategory) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum htsFormatCategory) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(enum htsFormatCategory), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(enum htsFormatCategory)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__htsExactFormat(enum htsExactFormat value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const enum htsExactFormat neg_one = (enum htsExactFormat) -1, const_zero = (enum htsExactFormat) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum htsExactFormat) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum htsExactFormat) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum htsExactFormat) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum htsExactFormat) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum htsExactFormat) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(enum htsExactFormat), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(enum htsExactFormat)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const short neg_one = (short) -1, const_zero = (short) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(short) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(short) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(short) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(short) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(short) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(short), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(short)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__htsCompression(enum htsCompression value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const enum htsCompression neg_one = (enum htsCompression) -1, const_zero = (enum htsCompression) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum htsCompression) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum htsCompression) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum htsCompression) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(enum htsCompression) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(enum htsCompression) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(enum htsCompression), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(enum htsCompression)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int64_t) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int64_t) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int64_t) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(int64_t), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int64_t)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntFromPy */ +static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if ((sizeof(int32_t) < sizeof(long))) { + __PYX_VERIFY_RETURN_INT(int32_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int32_t) val; + } + } +#endif + if (unlikely(!PyLong_Check(x))) { + int32_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (int32_t) -1; + val = __Pyx_PyInt_As_int32_t(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int32_t) >= 2 * PyLong_SHIFT)) { + return (int32_t) (((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])); + } + } + break; + case 3: + if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int32_t) >= 3 * PyLong_SHIFT)) { + return (int32_t) (((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0])); + } + } + break; + case 4: + if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(int32_t) >= 4 * PyLong_SHIFT)) { + 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])); + } + } + break; + } + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int32_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if ((sizeof(int32_t) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(int32_t, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(int32_t) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) { + return (int32_t) (((int32_t)-1)*(((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); + } + } + break; + case 2: + if ((8 * sizeof(int32_t) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) { + return (int32_t) ((((((int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); + } + } + break; + case -3: + if ((8 * sizeof(int32_t) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int32_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) { + return (int32_t) (((int32_t)-1)*(((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); + } + } + break; + case 3: + if ((8 * sizeof(int32_t) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) { + return (int32_t) ((((((((int32_t)digits[2]) << PyLong_SHIFT) | (int32_t)digits[1]) << PyLong_SHIFT) | (int32_t)digits[0]))); + } + } + break; + case -4: + if ((8 * sizeof(int32_t) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) { + 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]))); + } + } + break; + case 4: + if ((8 * sizeof(int32_t) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(int32_t) - 1 > 4 * PyLong_SHIFT)) { + 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]))); + } + } + break; + } + } +#endif + if ((sizeof(int32_t) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(int32_t, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(int32_t) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(int32_t, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { + int32_t val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (int32_t) -1; + assert(PyLong_CheckExact(v)); + } + { + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { + Py_DECREF(v); + return (int32_t) -1; + } + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (int32_t) -1; + } else { + stepval = v; + } + v = NULL; + val = (int32_t) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(int32_t) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((int32_t) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(int32_t) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((int32_t) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((int32_t) 1) << (sizeof(int32_t) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (int32_t) -1; + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int32_t"); + return (int32_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int32_t"); + return (int32_t) -1; +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const long neg_one = (long) -1, const_zero = (long) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(long)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const int32_t neg_one = (int32_t) -1, const_zero = (int32_t) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int32_t) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int32_t) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int32_t) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(int32_t) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(int32_t) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + unsigned char *bytes = (unsigned char *)&value; +#if !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4 + if (is_unsigned) { + return PyLong_FromUnsignedNativeBytes(bytes, sizeof(value), -1); + } else { + return PyLong_FromNativeBytes(bytes, sizeof(value), -1); + } +#elif !CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030d0000 + int one = 1; int little = (int)*(unsigned char *)&one; + return _PyLong_FromByteArray(bytes, sizeof(int32_t), + little, !is_unsigned); +#else + int one = 1; int little = (int)*(unsigned char *)&one; + PyObject *from_bytes, *result = NULL; + PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; + from_bytes = PyObject_GetAttrString((PyObject*)&PyLong_Type, "from_bytes"); + if (!from_bytes) return NULL; + py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(int32_t)); + if (!py_bytes) goto limited_bad; + order_str = PyUnicode_FromString(little ? "little" : "big"); + if (!order_str) goto limited_bad; + arg_tuple = PyTuple_Pack(2, py_bytes, order_str); + if (!arg_tuple) goto limited_bad; + if (!is_unsigned) { + kwds = PyDict_New(); + if (!kwds) goto limited_bad; + if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(Py_True))) goto limited_bad; + } + result = PyObject_Call(from_bytes, arg_tuple, kwds); + limited_bad: + Py_XDECREF(kwds); + Py_XDECREF(arg_tuple); + Py_XDECREF(order_str); + Py_XDECREF(py_bytes); + Py_XDECREF(from_bytes); + return result; +#endif + } +} + +/* FormatTypeName */ +#if CYTHON_COMPILING_IN_LIMITED_API +static __Pyx_TypeName +__Pyx_PyType_GetName(PyTypeObject* tp) +{ + PyObject *name = __Pyx_PyObject_GetAttrStr((PyObject *)tp, + __pyx_n_s_name_2); + if (unlikely(name == NULL) || unlikely(!PyUnicode_Check(name))) { + PyErr_Clear(); + Py_XDECREF(name); + name = __Pyx_NewRef(__pyx_n_s__97); + } + return name; +} +#endif + +/* CIntFromPy */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const long neg_one = (long) -1, const_zero = (long) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if ((sizeof(long) < sizeof(long))) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } +#endif + if (unlikely(!PyLong_Check(x))) { + long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + if (unlikely(__Pyx_PyLong_IsNeg(x))) { + goto raise_neg_overflow; + } else if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_upylong, __Pyx_PyLong_CompactValueUnsigned(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_DigitCount(x)) { + case 2: + if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 2 * PyLong_SHIFT)) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 3: + if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) >= 3 * PyLong_SHIFT)) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + case 4: + if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(long) >= 4 * PyLong_SHIFT)) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + } + } + break; + } + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX < 0x030C00A7 + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if ((sizeof(long) <= sizeof(unsigned long))) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(long) <= sizeof(unsigned PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + if (__Pyx_PyLong_IsCompact(x)) { + __PYX_VERIFY_RETURN_INT(long, __Pyx_compact_pylong, __Pyx_PyLong_CompactValue(x)) + } else { + const digit* digits = __Pyx_PyLong_Digits(x); + assert(__Pyx_PyLong_DigitCount(x) > 1); + switch (__Pyx_PyLong_SignedDigitCount(x)) { + case -2: + if ((8 * sizeof(long) - 1 > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 2: + if ((8 * sizeof(long) > 1 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -3: + if ((8 * sizeof(long) - 1 > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 3: + if ((8 * sizeof(long) > 2 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case -4: + if ((8 * sizeof(long) - 1 > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + case 4: + if ((8 * sizeof(long) > 3 * PyLong_SHIFT)) { + if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { + __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]))) + } else if ((8 * sizeof(long) - 1 > 4 * PyLong_SHIFT)) { + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + } + } + break; + } + } +#endif + if ((sizeof(long) <= sizeof(long))) { + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if ((sizeof(long) <= sizeof(PY_LONG_LONG))) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { + long val; + int ret = -1; +#if PY_VERSION_HEX >= 0x030d00A6 && !CYTHON_COMPILING_IN_LIMITED_API + Py_ssize_t bytes_copied = PyLong_AsNativeBytes( + x, &val, sizeof(val), Py_ASNATIVEBYTES_NATIVE_ENDIAN | (is_unsigned ? Py_ASNATIVEBYTES_UNSIGNED_BUFFER | Py_ASNATIVEBYTES_REJECT_NEGATIVE : 0)); + if (unlikely(bytes_copied == -1)) { + } else if (unlikely(bytes_copied > (Py_ssize_t) sizeof(val))) { + goto raise_overflow; + } else { + ret = 0; + } +#elif PY_VERSION_HEX < 0x030d0000 && !(CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_LIMITED_API) || defined(_PyLong_AsByteArray) + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + ret = _PyLong_AsByteArray((PyLongObject *)x, + bytes, sizeof(val), + is_little, !is_unsigned); +#else + PyObject *v; + PyObject *stepval = NULL, *mask = NULL, *shift = NULL; + int bits, remaining_bits, is_negative = 0; + int chunk_size = (sizeof(long) < 8) ? 30 : 62; + if (likely(PyLong_CheckExact(x))) { + v = __Pyx_NewRef(x); + } else { + v = PyNumber_Long(x); + if (unlikely(!v)) return (long) -1; + assert(PyLong_CheckExact(v)); + } + { + int result = PyObject_RichCompareBool(v, Py_False, Py_LT); + if (unlikely(result < 0)) { + Py_DECREF(v); + return (long) -1; + } + is_negative = result == 1; + } + if (is_unsigned && unlikely(is_negative)) { + Py_DECREF(v); + goto raise_neg_overflow; + } else if (is_negative) { + stepval = PyNumber_Invert(v); + Py_DECREF(v); + if (unlikely(!stepval)) + return (long) -1; + } else { + stepval = v; + } + v = NULL; + val = (long) 0; + mask = PyLong_FromLong((1L << chunk_size) - 1); if (unlikely(!mask)) goto done; + shift = PyLong_FromLong(chunk_size); if (unlikely(!shift)) goto done; + for (bits = 0; bits < (int) sizeof(long) * 8 - chunk_size; bits += chunk_size) { + PyObject *tmp, *digit; + long idigit; + digit = PyNumber_And(stepval, mask); + if (unlikely(!digit)) goto done; + idigit = PyLong_AsLong(digit); + Py_DECREF(digit); + if (unlikely(idigit < 0)) goto done; + val |= ((long) idigit) << bits; + tmp = PyNumber_Rshift(stepval, shift); + if (unlikely(!tmp)) goto done; + Py_DECREF(stepval); stepval = tmp; + } + Py_DECREF(shift); shift = NULL; + Py_DECREF(mask); mask = NULL; + { + long idigit = PyLong_AsLong(stepval); + if (unlikely(idigit < 0)) goto done; + remaining_bits = ((int) sizeof(long) * 8) - bits - (is_unsigned ? 0 : 1); + if (unlikely(idigit >= (1L << remaining_bits))) + goto raise_overflow; + val |= ((long) idigit) << bits; + } + if (!is_unsigned) { + if (unlikely(val & (((long) 1) << (sizeof(long) * 8 - 1)))) + goto raise_overflow; + if (is_negative) + val = ~val; + } + ret = 0; + done: + Py_XDECREF(shift); + Py_XDECREF(mask); + Py_XDECREF(stepval); +#endif + if (unlikely(ret)) + return (long) -1; + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +/* FastTypeChecks */ +#if CYTHON_COMPILING_IN_CPYTHON +static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { + while (a) { + a = __Pyx_PyType_GetSlot(a, tp_base, PyTypeObject*); + if (a == b) + return 1; + } + return b == &PyBaseObject_Type; +} +static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b) { + PyObject *mro; + if (a == b) return 1; + mro = a->tp_mro; + if (likely(mro)) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(mro); + for (i = 0; i < n; i++) { + if (PyTuple_GET_ITEM(mro, i) == (PyObject *)b) + return 1; + } + return 0; + } + return __Pyx_InBases(a, b); +} +static CYTHON_INLINE int __Pyx_IsAnySubtype2(PyTypeObject *cls, PyTypeObject *a, PyTypeObject *b) { + PyObject *mro; + if (cls == a || cls == b) return 1; + mro = cls->tp_mro; + if (likely(mro)) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(mro); + for (i = 0; i < n; i++) { + PyObject *base = PyTuple_GET_ITEM(mro, i); + if (base == (PyObject *)a || base == (PyObject *)b) + return 1; + } + return 0; + } + return __Pyx_InBases(cls, a) || __Pyx_InBases(cls, b); +} +#if PY_MAJOR_VERSION == 2 +static int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject* exc_type2) { + PyObject *exception, *value, *tb; + int res; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ErrFetch(&exception, &value, &tb); + res = exc_type1 ? PyObject_IsSubclass(err, exc_type1) : 0; + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + if (!res) { + res = PyObject_IsSubclass(err, exc_type2); + if (unlikely(res == -1)) { + PyErr_WriteUnraisable(err); + res = 0; + } + } + __Pyx_ErrRestore(exception, value, tb); + return res; +} +#else +static CYTHON_INLINE int __Pyx_inner_PyErr_GivenExceptionMatches2(PyObject *err, PyObject* exc_type1, PyObject *exc_type2) { + if (exc_type1) { + return __Pyx_IsAnySubtype2((PyTypeObject*)err, (PyTypeObject*)exc_type1, (PyTypeObject*)exc_type2); + } else { + return __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); + } +} +#endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i<n; i++) { + if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1; + } +#endif + for (i=0; i<n; i++) { + PyObject *t = PyTuple_GET_ITEM(tuple, i); + #if PY_MAJOR_VERSION < 3 + if (likely(exc_type == t)) return 1; + #endif + if (likely(PyExceptionClass_Check(t))) { + if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1; + } else { + } + } + return 0; +} +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) { + if (likely(err == exc_type)) return 1; + if (likely(PyExceptionClass_Check(err))) { + if (likely(PyExceptionClass_Check(exc_type))) { + return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type); + } else if (likely(PyTuple_Check(exc_type))) { + return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type); + } else { + } + } + return PyErr_GivenExceptionMatches(err, exc_type); +} +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) { + assert(PyExceptionClass_Check(exc_type1)); + assert(PyExceptionClass_Check(exc_type2)); + if (likely(err == exc_type1 || err == exc_type2)) return 1; + if (likely(PyExceptionClass_Check(err))) { + return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2); + } + return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2)); +} +#endif + +/* CheckBinaryVersion */ +static unsigned long __Pyx_get_runtime_version(void) { +#if __PYX_LIMITED_VERSION_HEX >= 0x030B00A4 + return Py_Version & ~0xFFUL; +#else + const char* rt_version = Py_GetVersion(); + unsigned long version = 0; + unsigned long factor = 0x01000000UL; + unsigned int digit = 0; + int i = 0; + while (factor) { + while ('0' <= rt_version[i] && rt_version[i] <= '9') { + digit = digit * 10 + (unsigned int) (rt_version[i] - '0'); + ++i; + } + version += factor * digit; + if (rt_version[i] != '.') + break; + digit = 0; + factor >>= 8; + ++i; + } + return version; +#endif +} +static int __Pyx_check_binary_version(unsigned long ct_version, unsigned long rt_version, int allow_newer) { + const unsigned long MAJOR_MINOR = 0xFFFF0000UL; + if ((rt_version & MAJOR_MINOR) == (ct_version & MAJOR_MINOR)) + return 0; + if (likely(allow_newer && (rt_version & MAJOR_MINOR) > (ct_version & MAJOR_MINOR))) + return 1; + { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compile time Python version %d.%d " + "of module '%.100s' " + "%s " + "runtime version %d.%d", + (int) (ct_version >> 24), (int) ((ct_version >> 16) & 0xFF), + __Pyx_MODULE_NAME, + (allow_newer) ? "was newer than" : "does not match", + (int) (rt_version >> 24), (int) ((rt_version >> 16) & 0xFF) + ); + return PyErr_WarnEx(NULL, message, 1); + } +} + +/* FunctionImport */ +#ifndef __PYX_HAVE_RT_ImportFunction_3_0_11 +#define __PYX_HAVE_RT_ImportFunction_3_0_11 +static int __Pyx_ImportFunction_3_0_11(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { + PyObject *d = 0; + PyObject *cobj = 0; + union { + void (*fp)(void); + void *p; + } tmp; + d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); + if (!d) + goto bad; + cobj = PyDict_GetItemString(d, funcname); + if (!cobj) { + PyErr_Format(PyExc_ImportError, + "%.200s does not export expected C function %.200s", + PyModule_GetName(module), funcname); + goto bad; + } + if (!PyCapsule_IsValid(cobj, sig)) { + PyErr_Format(PyExc_TypeError, + "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", + PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); + goto bad; + } + tmp.p = PyCapsule_GetPointer(cobj, sig); + *f = tmp.fp; + if (!(*f)) + goto bad; + Py_DECREF(d); + return 0; +bad: + Py_XDECREF(d); + return -1; +} +#endif + +/* InitStrings */ +#if PY_MAJOR_VERSION >= 3 +static int __Pyx_InitString(__Pyx_StringTabEntry t, PyObject **str) { + if (t.is_unicode | t.is_str) { + if (t.intern) { + *str = PyUnicode_InternFromString(t.s); + } else if (t.encoding) { + *str = PyUnicode_Decode(t.s, t.n - 1, t.encoding, NULL); + } else { + *str = PyUnicode_FromStringAndSize(t.s, t.n - 1); + } + } else { + *str = PyBytes_FromStringAndSize(t.s, t.n - 1); + } + if (!*str) + return -1; + if (PyObject_Hash(*str) == -1) + return -1; + return 0; +} +#endif +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION >= 3 + __Pyx_InitString(*t, t->p); + #else + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + if (!*t->p) + return -1; + if (PyObject_Hash(*t->p) == -1) + return -1; + #endif + ++t; + } + return 0; +} + +#include <string.h> +static CYTHON_INLINE Py_ssize_t __Pyx_ssize_strlen(const char *s) { + size_t len = strlen(s); + if (unlikely(len > (size_t) PY_SSIZE_T_MAX)) { + PyErr_SetString(PyExc_OverflowError, "byte string is too long"); + return -1; + } + return (Py_ssize_t) len; +} +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + Py_ssize_t len = __Pyx_ssize_strlen(c_str); + if (unlikely(len < 0)) return NULL; + return __Pyx_PyUnicode_FromStringAndSize(c_str, len); +} +static CYTHON_INLINE PyObject* __Pyx_PyByteArray_FromString(const char* c_str) { + Py_ssize_t len = __Pyx_ssize_strlen(c_str); + if (unlikely(len < 0)) return NULL; + return PyByteArray_FromStringAndSize(c_str, len); +} +static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +#if !CYTHON_PEP393_ENABLED +static const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +} +#else +static CYTHON_INLINE const char* __Pyx_PyUnicode_AsStringAndSize(PyObject* o, Py_ssize_t *length) { + if (unlikely(__Pyx_PyUnicode_READY(o) == -1)) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (likely(PyUnicode_IS_ASCII(o))) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +} +#endif +#endif +static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { + return __Pyx_PyUnicode_AsStringAndSize(o, length); + } else +#endif +#if (!CYTHON_COMPILING_IN_PYPY && !CYTHON_COMPILING_IN_LIMITED_API) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject* x) { + int retval; + if (unlikely(!x)) return -1; + retval = __Pyx_PyObject_IsTrue(x); + Py_DECREF(x); + return retval; +} +static PyObject* __Pyx_PyNumber_IntOrLongWrongResultType(PyObject* result, const char* type_name) { + __Pyx_TypeName result_type_name = __Pyx_PyType_GetName(Py_TYPE(result)); +#if PY_MAJOR_VERSION >= 3 + if (PyLong_Check(result)) { + if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, + "__int__ returned non-int (type " __Pyx_FMT_TYPENAME "). " + "The ability to return an instance of a strict subclass of int is deprecated, " + "and may be removed in a future version of Python.", + result_type_name)) { + __Pyx_DECREF_TypeName(result_type_name); + Py_DECREF(result); + return NULL; + } + __Pyx_DECREF_TypeName(result_type_name); + return result; + } +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type " __Pyx_FMT_TYPENAME ")", + type_name, type_name, result_type_name); + __Pyx_DECREF_TypeName(result_type_name); + Py_DECREF(result); + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { +#if CYTHON_USE_TYPE_SLOTS + PyNumberMethods *m; +#endif + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x) || PyLong_Check(x))) +#else + if (likely(PyLong_Check(x))) +#endif + return __Pyx_NewRef(x); +#if CYTHON_USE_TYPE_SLOTS + m = Py_TYPE(x)->tp_as_number; + #if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = m->nb_int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = m->nb_long(x); + } + #else + if (likely(m && m->nb_int)) { + name = "int"; + res = m->nb_int(x); + } + #endif +#else + if (!PyBytes_CheckExact(x) && !PyUnicode_CheckExact(x)) { + res = PyNumber_Int(x); + } +#endif + if (likely(res)) { +#if PY_MAJOR_VERSION < 3 + if (unlikely(!PyInt_Check(res) && !PyLong_Check(res))) { +#else + if (unlikely(!PyLong_CheckExact(res))) { +#endif + return __Pyx_PyNumber_IntOrLongWrongResultType(res, name); + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(b); + } +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(__Pyx_PyLong_IsCompact(b))) { + return __Pyx_PyLong_CompactValue(b); + } else { + const digit* digits = __Pyx_PyLong_Digits(b); + const Py_ssize_t size = __Pyx_PyLong_SignedDigitCount(b); + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + 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])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + 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])); + } + break; + } + } + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) { + if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) { + return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o); +#if PY_MAJOR_VERSION < 3 + } else if (likely(PyInt_CheckExact(o))) { + return PyInt_AS_LONG(o); +#endif + } else { + Py_ssize_t ival; + PyObject *x; + x = PyNumber_Index(o); + if (!x) return -1; + ival = PyInt_AsLong(x); + Py_DECREF(x); + return ival; + } +} +static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { + return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False); +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +/* #### Code section: utility_code_pragmas_end ### */ +#ifdef _MSC_VER +#pragma warning( pop ) +#endif + + + +/* #### Code section: end ### */ +#endif /* Py_PYTHON_H */