/* Generated by Cython 3.0.2 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ "/Users/runner/work/pysam/pysam/htslib/htslib/bgzf.h", "/Users/runner/work/pysam/pysam/htslib/htslib/cram.h", "/Users/runner/work/pysam/pysam/htslib/htslib/faidx.h", "/Users/runner/work/pysam/pysam/htslib/htslib/hfile.h", "/Users/runner/work/pysam/pysam/htslib/htslib/hts.h", "/Users/runner/work/pysam/pysam/htslib/htslib/kstring.h", "/Users/runner/work/pysam/pysam/htslib/htslib/sam.h", "/Users/runner/work/pysam/pysam/htslib/htslib/tbx.h", "/Users/runner/work/pysam/pysam/htslib/htslib/vcf.h", "/Users/runner/work/pysam/pysam/htslib/htslib/vcfutils.h", "/Users/runner/work/pysam/pysam/pysam/htslib_util.h", "/Users/runner/work/pysam/pysam/pysam/pysam_stream.h" ], "extra_compile_args": [ "-Wno-unused", "-Wno-strict-prototypes", "-Wno-sign-compare", "-Wno-error=declaration-after-statement" ], "extra_link_args": [ "-dynamiclib", "-rpath", "@loader_path", "-Wl,-headerpad_max_install_names", "-Wl,-install_name,@rpath/libcalignmentfile.cpython-311-darwin.so", "-Wl,-x" ], "include_dirs": [ "pysam", "/Users/runner/work/pysam/pysam/pysam", "/Users/runner/work/pysam/pysam/htslib", "/Users/runner/work/pysam/pysam/samtools", "/Users/runner/work/pysam/pysam/samtools/lz4", "/Users/runner/work/pysam/pysam/bcftools", "/Users/runner/work/pysam/pysam" ], "language": "c", "libraries": [ "z", "lzma", "bz2", "z", "curl", "chtslib.cpython-311-darwin", "cutils.cpython-311-darwin" ], "library_dirs": [ "/Users/runner/work/pysam/pysam/pysam", "/Users/runner/work/pysam/pysam", "build/lib.macosx-10.9-x86_64-cpython-311/pysam", "build/lib.macosx-10.9-x86_64-cpython-311/pysam", "build/lib.macosx-10.9-x86_64-cpython-311/pysam", "build/lib.macosx-10.9-x86_64-cpython-311/pysam", "build/lib.macosx-10.9-x86_64-cpython-311/pysam" ], "name": "pysam.libcalignmentfile", "sources": [ "pysam/libcalignmentfile.pyx" ] }, "module_name": "pysam.libcalignmentfile" } 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 CYTHON_LIMITED_API #define __PYX_EXTRA_ABI_MODULE_NAME "limited" #else #define __PYX_EXTRA_ABI_MODULE_NAME "" #endif #define CYTHON_ABI "3_0_2" __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 0x030002F0 #define CYTHON_FUTURE_DIVISION 1 #include #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. 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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 #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 #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 #elif 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 #undef CYTHON_USE_PYTYPE_LOOKUP #define CYTHON_USE_PYTYPE_LOOKUP 0 #ifndef CYTHON_USE_ASYNC_SLOTS #define CYTHON_USE_ASYNC_SLOTS 1 #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 #undef CYTHON_USE_PYLONG_INTERNALS #define CYTHON_USE_PYLONG_INTERNALS 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_PYCALL #define CYTHON_FAST_PYCALL 0 #ifndef CYTHON_PEP489_MULTI_PHASE_INIT #define CYTHON_PEP489_MULTI_PHASE_INIT 1 #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 #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 #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 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 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 struct __PYX_IS_UNSIGNED_IMPL {static const bool value = T(0) < T(-1);}; #define __PYX_IS_UNSIGNED(type) (__PYX_IS_UNSIGNED_IMPL::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; PyObject *version_info; // borrowed PyObject *py_minor_version = NULL; long minor_version = 0; PyObject *type, *value, *traceback; PyErr_Fetch(&type, &value, &traceback); #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000 minor_version = 11; // we don't yet need to distinguish between versions > 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); 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); Py_XDECREF(py_minor_version); 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); // we don't have access to __pyx_empty_bytes here 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 #define __Pyx_PyCFunctionFast _PyCFunctionFast #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords #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 __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 >= 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 || 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 && 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(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 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 #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__libcalignmentfile #define __PYX_HAVE_API__pysam__libcalignmentfile /* Early includes */ #include #include #include #include #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 #include #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 "pysam_stream.h" #include #ifdef _OPENMP #include #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 #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 const char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) #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) #if CYTHON_COMPILING_IN_LIMITED_API static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const wchar_t *u) { const wchar_t *u_end = u; while (*u_end++) ; return (size_t)(u_end - u - 1); } #else static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { const Py_UNICODE *u_end = u; while (*u_end++) ; return (size_t)(u_end - u - 1); } #endif #define __Pyx_PyUnicode_FromOrdinal(o) PyUnicode_FromOrdinal((int)o) #define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) #define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode #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 // Py < 3.12 #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 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 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/libcalignmentfile.pyx", "contextvars.pxd", "array.pxd", "", "pysam/libcalignmentfile.pxd", "type.pxd", "bool.pxd", "complex.pxd", "pysam/libcfaidx.pxd", "pysam/libcalignedsegment.pxd", }; /* #### Code section: utility_code_proto_before_types ### */ /* 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() /* ForceInitThreads.proto */ #ifndef __PYX_FORCE_INIT_THREADS #define __PYX_FORCE_INIT_THREADS 0 #endif /* #### 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_9libcfaidx_FastaFile; struct __pyx_obj_5pysam_9libcfaidx_FastqProxy; struct __pyx_obj_5pysam_9libcfaidx_FastxRecord; struct __pyx_obj_5pysam_9libcfaidx_FastxFile; struct __pyx_obj_5pysam_9libcfaidx_FastqFile; struct __pyx_obj_5pysam_9libcfaidx_Fastafile; struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment; struct __pyx_obj_5pysam_18libcalignedsegment_PileupColumn; struct __pyx_obj_5pysam_18libcalignedsegment_PileupRead; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll; struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads; struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall; 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_9libcfaidx_10FastqProxy_get_quality_array; struct __pyx_opt_args_5pysam_9libcfaidx_11FastxRecord_get_quality_array; /* "pysam/libcfaidx.pxd":50 * cdef cython.str to_string(self) * cdef cython.str tostring(self) * cpdef array.array get_quality_array(self, int offset=*) # <<<<<<<<<<<<<< * * */ struct __pyx_opt_args_5pysam_9libcfaidx_10FastqProxy_get_quality_array { int __pyx_n; int offset; }; /* "pysam/libcfaidx.pxd":60 * cdef cython.str to_string(self) * cdef cython.str tostring(self) * cpdef array.array get_quality_array(self, int offset=*) # <<<<<<<<<<<<<< * * cdef class FastxFile: */ struct __pyx_opt_args_5pysam_9libcfaidx_11FastxRecord_get_quality_array { int __pyx_n; int offset; }; struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_set_tag; struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_get_tag; struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_tostring; /* "pysam/libcalignedsegment.pxd":31 * * from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader * ctypedef AlignmentFile AlignmentFile_t # <<<<<<<<<<<<<< * * */ typedef struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_t_5pysam_18libcalignedsegment_AlignmentFile_t; /* "pysam/libcalignedsegment.pxd":51 * # add an alignment tag with value to the AlignedSegment * # an existing tag of the same name will be replaced. * cpdef set_tag(self, tag, value, value_type=?, replace=?) # <<<<<<<<<<<<<< * * # get an alignment tag from the AlignedSegment */ struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_set_tag { int __pyx_n; PyObject *value_type; PyObject *replace; }; /* "pysam/libcalignedsegment.pxd":54 * * # get an alignment tag from the AlignedSegment * cpdef get_tag(self, tag, with_value_type=?) # <<<<<<<<<<<<<< * * # return true if tag exists */ struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_get_tag { int __pyx_n; PyObject *with_value_type; }; /* "pysam/libcalignedsegment.pxd":63 * * # returns a valid sam alignment string (deprecated) * cpdef tostring(self, htsfile=*) # <<<<<<<<<<<<<< * * */ struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_tostring { int __pyx_n; PyObject *htsfile; }; 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_t_5pysam_17libcalignmentfile___iterdata; typedef struct __pyx_t_5pysam_17libcalignmentfile___iterdata __pyx_t_5pysam_17libcalignmentfile___iterdata; struct __pyx_opt_args_5pysam_17libcalignmentfile_14IteratorColumn__setup_iterator; struct __pyx_opt_args_5pysam_17libcalignmentfile_fill_AlignmentHeader_from_list; /* "pysam/libcalignmentfile.pxd":25 * # Utility types * * ctypedef struct __iterdata: # <<<<<<<<<<<<<< * htsFile * htsfile * bam_hdr_t * header */ struct __pyx_t_5pysam_17libcalignmentfile___iterdata { htsFile *htsfile; bam_hdr_t *header; hts_itr_t *iter; faidx_t *fastafile; int tid; char *seq; int seq_len; int min_mapping_quality; int flag_require; int flag_filter; int compute_baq; int redo_baq; int ignore_orphans; int adjust_capq_threshold; }; /* "pysam/libcalignmentfile.pxd":121 * cdef int cnext(self) * cdef char * get_sequence(self) * cdef _setup_iterator(self, # <<<<<<<<<<<<<< * int tid, * int start, */ struct __pyx_opt_args_5pysam_17libcalignmentfile_14IteratorColumn__setup_iterator { int __pyx_n; int multiple_iterators; }; /* "pysam/libcalignmentfile.pyx":184 * # the following should be class-method for VariantHeader, but cdef @classmethods * # are not implemented in cython. * cdef int fill_AlignmentHeader_from_list(bam_hdr_t *dest, # <<<<<<<<<<<<<< * reference_names, * reference_lengths, */ struct __pyx_opt_args_5pysam_17libcalignmentfile_fill_AlignmentHeader_from_list { int __pyx_n; PyObject *add_sq_text; PyObject *text; }; /* "pysam/libchtslib.pxd":2700 * * * 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/libcfaidx.pxd":38 * int * dret) * * cdef class FastaFile: # <<<<<<<<<<<<<< * cdef bint is_remote * cdef object _filename, _references, _lengths, reference2length */ struct __pyx_obj_5pysam_9libcfaidx_FastaFile { PyObject_HEAD struct __pyx_vtabstruct_5pysam_9libcfaidx_FastaFile *__pyx_vtab; int is_remote; PyObject *_filename; PyObject *_references; PyObject *_lengths; PyObject *reference2length; faidx_t *fastafile; }; /* "pysam/libcfaidx.pxd":46 * * * cdef class FastqProxy: # <<<<<<<<<<<<<< * cdef kseq_t * _delegate * cdef cython.str to_string(self) */ struct __pyx_obj_5pysam_9libcfaidx_FastqProxy { PyObject_HEAD struct __pyx_vtabstruct_5pysam_9libcfaidx_FastqProxy *__pyx_vtab; kseq_t *_delegate; }; /* "pysam/libcfaidx.pxd":53 * * * cdef class FastxRecord: # <<<<<<<<<<<<<< * """ * Python container for pysam.libcfaidx.FastqProxy with persistence. */ struct __pyx_obj_5pysam_9libcfaidx_FastxRecord { PyObject_HEAD struct __pyx_vtabstruct_5pysam_9libcfaidx_FastxRecord *__pyx_vtab; PyObject *comment; PyObject *quality; PyObject *sequence; PyObject *name; }; /* "pysam/libcfaidx.pxd":62 * cpdef array.array get_quality_array(self, int offset=*) * * cdef class FastxFile: # <<<<<<<<<<<<<< * cdef object _filename * cdef BGZF * fastqfile */ struct __pyx_obj_5pysam_9libcfaidx_FastxFile { PyObject_HEAD struct __pyx_vtabstruct_5pysam_9libcfaidx_FastxFile *__pyx_vtab; PyObject *_filename; BGZF *fastqfile; kseq_t *entry; int persist; int is_remote; }; /* "pysam/libcfaidx.pxd":74 * * # Compatibility Layer for pysam 0.8.1 * cdef class FastqFile(FastxFile): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_9libcfaidx_FastqFile { struct __pyx_obj_5pysam_9libcfaidx_FastxFile __pyx_base; }; /* "pysam/libcfaidx.pxd":79 * * # Compatibility Layer for pysam < 0.8 * cdef class Fastafile(FastaFile): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_9libcfaidx_Fastafile { struct __pyx_obj_5pysam_9libcfaidx_FastaFile __pyx_base; }; /* "pysam/libcalignedsegment.pxd":35 * * # Note: need to declare all C fields and methods here * cdef class AlignedSegment: # <<<<<<<<<<<<<< * * # object that this AlignedSegment represents */ struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment { PyObject_HEAD struct __pyx_vtabstruct_5pysam_18libcalignedsegment_AlignedSegment *__pyx_vtab; bam1_t *_delegate; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *header; PyObject *cache_query_qualities; PyObject *cache_query_alignment_qualities; PyObject *cache_query_sequence; PyObject *cache_query_alignment_sequence; }; /* "pysam/libcalignedsegment.pxd":66 * * * cdef class PileupColumn: # <<<<<<<<<<<<<< * cdef const bam_pileup1_t ** plp * cdef int tid */ struct __pyx_obj_5pysam_18libcalignedsegment_PileupColumn { PyObject_HEAD bam_pileup1_t const **plp; int tid; int pos; int n_pu; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *header; uint32_t min_base_quality; kstring_t buf; char *reference_sequence; }; /* "pysam/libcalignedsegment.pxd":76 * cdef char * reference_sequence * * cdef class PileupRead: # <<<<<<<<<<<<<< * cdef int32_t _qpos * cdef AlignedSegment _alignment */ struct __pyx_obj_5pysam_18libcalignedsegment_PileupRead { PyObject_HEAD int32_t _qpos; struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment *_alignment; int _indel; int _level; uint32_t _is_del; uint32_t _is_head; uint32_t _is_tail; uint32_t _is_refskip; }; /* "pysam/libcalignmentfile.pxd":42 * * * cdef class AlignmentHeader(object): # <<<<<<<<<<<<<< * cdef bam_hdr_t *ptr * */ struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader { PyObject_HEAD bam_hdr_t *ptr; }; /* "pysam/libcalignmentfile.pxd":45 * cdef bam_hdr_t *ptr * * cdef class AlignmentFile(HTSFile): # <<<<<<<<<<<<<< * cdef readonly object reference_filename * cdef readonly AlignmentHeader header */ struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile { struct __pyx_obj_5pysam_10libchtslib_HTSFile __pyx_base; PyObject *reference_filename; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *header; hts_idx_t *index; bam1_t *b; }; /* "pysam/libcalignmentfile.pxd":62 * * * cdef class IteratorRow: # <<<<<<<<<<<<<< * cdef int retval * cdef bam1_t * b */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow { PyObject_HEAD int retval; bam1_t *b; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *samfile; htsFile *htsfile; hts_idx_t *index; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *header; int owns_samfile; }; /* "pysam/libcalignmentfile.pxd":72 * * * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<< * cdef hts_itr_t * iter * cdef bam1_t * getCurrent(self) */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow __pyx_base; struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_vtab; hts_itr_t *iter; }; /* "pysam/libcalignmentfile.pxd":78 * * * cdef class IteratorRowHead(IteratorRow): # <<<<<<<<<<<<<< * cdef int max_rows * cdef int current_row */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow __pyx_base; struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_vtab; int max_rows; int current_row; }; /* "pysam/libcalignmentfile.pxd":85 * * * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<< * cdef bam1_t * getCurrent(self) * cdef int cnext(self) */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow __pyx_base; struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_vtab; }; /* "pysam/libcalignmentfile.pxd":90 * * * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<< * cdef int tid * cdef IteratorRowRegion rowiter */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow __pyx_base; int tid; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *rowiter; }; /* "pysam/libcalignmentfile.pxd":95 * * * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<< * cdef int current_pos * cdef positions */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow __pyx_base; struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_vtab; int current_pos; PyObject *positions; }; /* "pysam/libcalignmentfile.pxd":102 * * * cdef class IteratorColumn: # <<<<<<<<<<<<<< * * # result of the last plbuf_push */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn { PyObject_HEAD struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumn *__pyx_vtab; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *iter; int tid; int pos; int n_plp; uint32_t min_base_quality; bam_pileup1_t const *plp; bam_mplp_t pileup_iter; __pyx_t_5pysam_17libcalignmentfile___iterdata iterdata; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *samfile; struct __pyx_obj_5pysam_9libcfaidx_FastaFile *fastafile; PyObject *stepper; int max_depth; int ignore_overlaps; }; /* "pysam/libcalignmentfile.pxd":134 * * * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<< * cdef int start * cdef int stop */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn __pyx_base; int start; int stop; int truncate; }; /* "pysam/libcalignmentfile.pxd":140 * * * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn __pyx_base; }; /* "pysam/libcalignmentfile.pxd":144 * * * cdef class IteratorColumnAll(IteratorColumn): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn __pyx_base; }; /* "pysam/libcalignmentfile.pxd":148 * * * cdef class IndexedReads: # <<<<<<<<<<<<<< * cdef AlignmentFile samfile * cdef htsFile * htsfile */ struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads { PyObject_HEAD struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *samfile; htsFile *htsfile; PyObject *index; int owns_samfile; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *header; }; /* "pysam/libcalignmentfile.pyx":2824 * * * cdef class SNPCall: # <<<<<<<<<<<<<< * '''the results of a SNP call.''' * cdef int _tid */ struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall { PyObject_HEAD int _tid; int _pos; char _reference_base; char _genotype; int _consensus_quality; int _snp_quality; int _rms_mapping_quality; int _coverage; }; /* "pysam/libchtslib.pxd":2700 * * * cdef class HTSFile(object): # <<<<<<<<<<<<<< * cdef htsFile *htsfile # pointer to htsFile structure * cdef int64_t start_offset # BGZF offset of first record */ 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/libcfaidx.pxd":38 * int * dret) * * cdef class FastaFile: # <<<<<<<<<<<<<< * cdef bint is_remote * cdef object _filename, _references, _lengths, reference2length */ struct __pyx_vtabstruct_5pysam_9libcfaidx_FastaFile { char *(*_fetch)(struct __pyx_obj_5pysam_9libcfaidx_FastaFile *, char *, int, int, int *); }; static struct __pyx_vtabstruct_5pysam_9libcfaidx_FastaFile *__pyx_vtabptr_5pysam_9libcfaidx_FastaFile; /* "pysam/libcfaidx.pxd":46 * * * cdef class FastqProxy: # <<<<<<<<<<<<<< * cdef kseq_t * _delegate * cdef cython.str to_string(self) */ struct __pyx_vtabstruct_5pysam_9libcfaidx_FastqProxy { PyObject *(*to_string)(struct __pyx_obj_5pysam_9libcfaidx_FastqProxy *); PyObject *(*tostring)(struct __pyx_obj_5pysam_9libcfaidx_FastqProxy *); arrayobject *(*get_quality_array)(struct __pyx_obj_5pysam_9libcfaidx_FastqProxy *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcfaidx_10FastqProxy_get_quality_array *__pyx_optional_args); }; static struct __pyx_vtabstruct_5pysam_9libcfaidx_FastqProxy *__pyx_vtabptr_5pysam_9libcfaidx_FastqProxy; /* "pysam/libcfaidx.pxd":53 * * * cdef class FastxRecord: # <<<<<<<<<<<<<< * """ * Python container for pysam.libcfaidx.FastqProxy with persistence. */ struct __pyx_vtabstruct_5pysam_9libcfaidx_FastxRecord { PyObject *(*to_string)(struct __pyx_obj_5pysam_9libcfaidx_FastxRecord *); PyObject *(*tostring)(struct __pyx_obj_5pysam_9libcfaidx_FastxRecord *); arrayobject *(*get_quality_array)(struct __pyx_obj_5pysam_9libcfaidx_FastxRecord *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcfaidx_11FastxRecord_get_quality_array *__pyx_optional_args); }; static struct __pyx_vtabstruct_5pysam_9libcfaidx_FastxRecord *__pyx_vtabptr_5pysam_9libcfaidx_FastxRecord; 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#define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw) #define __Pyx_Arg_NewRef_FASTCALL(arg) arg // no-op, __Pyx_Arg_FASTCALL is direct and this needs #define __Pyx_Arg_XDECREF_FASTCALL(arg) // no-op - arg was returned from array #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 /* 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); /* 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); /* 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 /* 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); PyList_SET_ITEM(list, len, x); __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 /* 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); /* PyObjectFormatAndDecref.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f); static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f); /* PyObject_Str.proto */ #define __Pyx_PyObject_Str(obj)\ (likely(PyString_CheckExact(obj)) ? __Pyx_NewRef(obj) : PyObject_Str(obj)) /* 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); /* PyObjectCallOneArg.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); /* 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 /* 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 /* 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)); } /* RaiseException.proto */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /* PyIntCompare.proto */ static CYTHON_INLINE int __Pyx_PyInt_BoolEqObjC(PyObject *op1, PyObject *op2, long intval, long inplace); /* KeywordStringCheck.proto */ static int __Pyx_CheckKeywordStrings(PyObject *kw, const char* function_name, int kw_allowed); /* PyObjectCallNoArg.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); /* ListCompAppend.proto */ #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); } #else #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) #endif /* SliceObject.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** py_start, PyObject** py_stop, PyObject** py_slice, int has_cstart, int has_cstop, int wraparound); /* DictGetItem.proto */ #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key); #define __Pyx_PyObject_Dict_GetItem(obj, name)\ (likely(PyDict_CheckExact(obj)) ?\ __Pyx_PyDict_GetItem(obj, name) : PyObject_GetItem(obj, name)) #else #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #define __Pyx_PyObject_Dict_GetItem(obj, name) PyObject_GetItem(obj, name) #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 /* 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 /* 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); /* UnicodeConcatInPlace.proto */ # if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_REFNANNY #define __Pyx_PyUnicode_ConcatInPlace(left, right) __Pyx_PyUnicode_ConcatInPlaceImpl(&left, right, __pyx_refnanny) #else #define __Pyx_PyUnicode_ConcatInPlace(left, right) __Pyx_PyUnicode_ConcatInPlaceImpl(&left, right) #endif static CYTHON_INLINE PyObject *__Pyx_PyUnicode_ConcatInPlaceImpl(PyObject **p_left, PyObject *right #if CYTHON_REFNANNY , void* __pyx_refnanny #endif ); #else #define __Pyx_PyUnicode_ConcatInPlace __Pyx_PyUnicode_Concat #endif #define __Pyx_PyUnicode_ConcatInPlaceSafe(left, right) ((unlikely((left) == Py_None) || unlikely((right) == Py_None)) ?\ PyNumber_InPlaceAdd(left, right) : __Pyx_PyUnicode_ConcatInPlace(left, right)) /* WriteUnraisableException.proto */ static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename, int full_traceback, int nogil); /* AssertionsEnabled.proto */ #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) #define __Pyx_init_assertions_enabled() (0) #define __pyx_assertions_enabled() (1) #elif CYTHON_COMPILING_IN_LIMITED_API || (CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030C0000) static int __pyx_assertions_enabled_flag; #define __pyx_assertions_enabled() (__pyx_assertions_enabled_flag) static int __Pyx_init_assertions_enabled(void) { PyObject *builtins, *debug, *debug_str; int flag; builtins = PyEval_GetBuiltins(); if (!builtins) goto bad; debug_str = PyUnicode_FromStringAndSize("__debug__", 9); if (!debug_str) goto bad; debug = PyObject_GetItem(builtins, debug_str); Py_DECREF(debug_str); if (!debug) goto bad; flag = PyObject_IsTrue(debug); Py_DECREF(debug); if (flag == -1) goto bad; __pyx_assertions_enabled_flag = flag; return 0; bad: __pyx_assertions_enabled_flag = 1; return -1; } #else #define __Pyx_init_assertions_enabled() (0) #define __pyx_assertions_enabled() (!Py_OptimizeFlag) #endif /* PyObjectCall2Args.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); /* 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); /* append.proto */ static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x); /* PyIntBinop.proto */ #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); #else #define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace, zerodivision_check)\ (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) #endif /* PyDictContains.proto */ static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) { int result = PyDict_Contains(dict, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } /* 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); /* GetAttr.proto */ static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); /* HasAttr.proto */ static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); /* ExtTypeTest.proto */ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /* PyIntCompare.proto */ static CYTHON_INLINE int __Pyx_PyInt_BoolNeObjC(PyObject *op1, PyObject *op2, long intval, long inplace); /* PyObjectCallMethod0.proto */ static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); /* RaiseNoneIterError.proto */ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); /* UnpackTupleError.proto */ static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /* UnpackTuple2.proto */ #define __Pyx_unpack_tuple2(tuple, value1, value2, is_tuple, has_known_size, decref_tuple)\ (likely(is_tuple || PyTuple_Check(tuple)) ?\ (likely(has_known_size || PyTuple_GET_SIZE(tuple) == 2) ?\ __Pyx_unpack_tuple2_exact(tuple, value1, value2, decref_tuple) :\ (__Pyx_UnpackTupleError(tuple, 2), -1)) :\ __Pyx_unpack_tuple2_generic(tuple, value1, value2, has_known_size, decref_tuple)) static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( PyObject* tuple, PyObject** value1, PyObject** value2, int decref_tuple); static int __Pyx_unpack_tuple2_generic( PyObject* tuple, PyObject** value1, PyObject** value2, int has_known_size, int decref_tuple); /* dict_iter.proto */ static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_is_dict); static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos, PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict); /* MergeKeywords.proto */ static int __Pyx_MergeKeywords(PyObject *kwdict, PyObject *source_mapping); /* PyIntBinop.proto */ #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_AndObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); #else #define __Pyx_PyInt_AndObjC(op1, op2, intval, inplace, zerodivision_check)\ (inplace ? PyNumber_InPlaceAnd(op1, op2) : PyNumber_And(op1, op2)) #endif /* RaiseUnexpectedTypeError.proto */ static int __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj); /* GetItemIntUnicode.proto */ #define __Pyx_GetItemInt_Unicode(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ __Pyx_GetItemInt_Unicode_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "string index out of range"), (Py_UCS4)-1)) static CYTHON_INLINE Py_UCS4 __Pyx_GetItemInt_Unicode_Fast(PyObject* ustring, Py_ssize_t i, int wraparound, int boundscheck); /* RaiseUnboundLocalError.proto */ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); /* pyfrozenset_new.proto */ static CYTHON_INLINE PyObject* __Pyx_PyFrozenSet_New(PyObject* it); /* PySetContains.proto */ static CYTHON_INLINE int __Pyx_PySet_ContainsTF(PyObject* key, PyObject* set, int eq); /* dict_getitem_default.proto */ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObject* default_value); /* UnpackUnboundCMethod.proto */ typedef struct { PyObject *type; PyObject **method_name; PyCFunction func; PyObject *method; int flag; } __Pyx_CachedCFunction; /* CallUnboundCMethod1.proto */ static PyObject* __Pyx__CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg); #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg); #else #define __Pyx_CallUnboundCMethod1(cfunc, self, arg) __Pyx__CallUnboundCMethod1(cfunc, self, arg) #endif /* CallUnboundCMethod2.proto */ static PyObject* __Pyx__CallUnboundCMethod2(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg1, PyObject* arg2); #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030600B1 static CYTHON_INLINE PyObject *__Pyx_CallUnboundCMethod2(__Pyx_CachedCFunction *cfunc, PyObject *self, PyObject *arg1, PyObject *arg2); #else #define __Pyx_CallUnboundCMethod2(cfunc, self, arg1, arg2) __Pyx__CallUnboundCMethod2(cfunc, self, arg1, arg2) #endif /* GetAttr3.proto */ static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); /* Import.proto */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /* ImportFrom.proto */ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); /* CallNextTpDealloc.proto */ static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc); /* CallNextTpTraverse.proto */ static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); /* CallNextTpClear.proto */ static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear); /* IncludeStructmemberH.proto */ #include /* FixUpExtensionType.proto */ #if CYTHON_USE_TYPE_SPECS static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject *type); #endif /* 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 /* 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_2 #define __PYX_HAVE_RT_ImportType_proto_3_0_2 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L #include #endif #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L #define __PYX_GET_STRUCT_ALIGNMENT_3_0_2(s) alignof(s) #else #define __PYX_GET_STRUCT_ALIGNMENT_3_0_2(s) sizeof(void*) #endif enum __Pyx_ImportType_CheckSize_3_0_2 { __Pyx_ImportType_CheckSize_Error_3_0_2 = 0, __Pyx_ImportType_CheckSize_Warn_3_0_2 = 1, __Pyx_ImportType_CheckSize_Ignore_3_0_2 = 2 }; static PyTypeObject *__Pyx_ImportType_3_0_2(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_2 check_size); #endif /* GetVTable.proto */ static void* __Pyx_GetVtable(PyTypeObject *type); /* SetVTable.proto */ static int __Pyx_SetVtable(PyTypeObject* typeptr , void* vtable); /* MergeVTables.proto */ #if !CYTHON_COMPILING_IN_LIMITED_API static int __Pyx_MergeVtables(PyTypeObject *type); #endif /* 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 /* 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; // used by FusedFunction for copying defaults int flags; PyObject *defaults_tuple; PyObject *defaults_kwdict; PyObject *(*defaults_getter)(PyObject *); PyObject *func_annotations; PyObject *func_is_coroutine; } __pyx_CyFunctionObject; #define __Pyx_CyFunction_Check(obj) __Pyx_TypeCheck(obj, __pyx_CyFunctionType) #define __Pyx_IsCyOrPyCFunction(obj) __Pyx_TypeCheck2(obj, __pyx_CyFunctionType, &PyCFunction_Type) #define __Pyx_CyFunction_CheckExact(obj) __Pyx_IS_TYPE(obj, __pyx_CyFunctionType) 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); /* ClassMethod.proto */ #include "descrobject.h" CYTHON_UNUSED static PyObject* __Pyx_Method_ClassMethod(PyObject *method); /* GetNameInClass.proto */ #define __Pyx_GetNameInClass(var, nmspace, name) (var) = __Pyx__GetNameInClass(nmspace, name) static PyObject *__Pyx__GetNameInClass(PyObject *nmspace, PyObject *name); /* 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); /* 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 /* GCCDiagnostics.proto */ #if !defined(__INTEL_COMPILER) && defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) #define __Pyx_HAS_GCC_DIAGNOSTIC #endif /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); /* CIntFromPy.proto */ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_char(char value); /* CIntFromPy.proto */ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); /* CIntFromPy.proto */ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); /* CIntFromPy.proto */ static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value); /* CIntFromPy.proto */ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *); /* CIntFromPy.proto */ static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value); /* CIntFromPy.proto */ static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *); /* 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 /* 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 int __Pyx_check_binary_version(void); /* FunctionImport.proto */ static int __Pyx_ImportFunction_3_0_2(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 int __pyx_f_5pysam_17libcalignmentfile_13AlignmentFile_write(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment *__pyx_v_read, int __pyx_skip_dispatch); /* proto*/ static bam1_t *__pyx_f_5pysam_17libcalignmentfile_13AlignmentFile_getCurrent(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto*/ static int __pyx_f_5pysam_17libcalignmentfile_13AlignmentFile_cnext(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto*/ static bam1_t *__pyx_f_5pysam_17libcalignmentfile_17IteratorRowRegion_getCurrent(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self); /* proto*/ static int __pyx_f_5pysam_17libcalignmentfile_17IteratorRowRegion_cnext(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self); /* proto*/ static bam1_t *__pyx_f_5pysam_17libcalignmentfile_15IteratorRowHead_getCurrent(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self); /* proto*/ static int __pyx_f_5pysam_17libcalignmentfile_15IteratorRowHead_cnext(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self); /* proto*/ static bam1_t *__pyx_f_5pysam_17libcalignmentfile_14IteratorRowAll_getCurrent(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self); /* proto*/ static int __pyx_f_5pysam_17libcalignmentfile_14IteratorRowAll_cnext(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self); /* proto*/ static bam1_t *__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_getCurrent(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self); /* proto*/ static int __pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self); /* proto*/ static int __pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto*/ static char *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_get_sequence(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto*/ static PyObject *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn__setup_iterator(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_stop, struct __pyx_opt_args_5pysam_17libcalignmentfile_14IteratorColumn__setup_iterator *__pyx_optional_args); /* proto*/ static PyObject *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn__setup_raw_rest_iterator(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto*/ static PyObject *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_reset(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_stop); /* proto*/ static PyObject *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn__free_pileup_iter(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto*/ static char *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_getSequence(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__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 "cython" */ /* 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 "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 "array" */ /* Module declarations from "cpython.array" */ static CYTHON_INLINE arrayobject *__pyx_f_7cpython_5array_clone(arrayobject *, Py_ssize_t, int); /*proto*/ static CYTHON_INLINE int __pyx_f_7cpython_5array_extend_buffer(arrayobject *, char *, Py_ssize_t); /*proto*/ /* Module declarations from "posix.types" */ /* Module declarations from "pysam.libchtslib" */ /* Module declarations from "pysam.libcfaidx" */ /* Module declarations from "pysam.libcalignedsegment" */ static struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment *(*__pyx_f_5pysam_18libcalignedsegment_makeAlignedSegment)(bam1_t *, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *); /*proto*/ static struct __pyx_obj_5pysam_18libcalignedsegment_PileupColumn *(*__pyx_f_5pysam_18libcalignedsegment_makePileupColumn)(bam_pileup1_t const **, int, int, int, uint32_t, char *, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *); /*proto*/ /* Module declarations from "libc.errno" */ /* Module declarations from "pysam.libcutils" */ 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_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.libcalignmentfile" */ static int __pyx_v_5pysam_17libcalignmentfile_MAX_POS; static struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_f_5pysam_17libcalignmentfile_makeAlignmentHeader(bam_hdr_t *); /*proto*/ static int __pyx_f_5pysam_17libcalignmentfile___advance_nofilter(void *, bam1_t *); /*proto*/ static int __pyx_f_5pysam_17libcalignmentfile___advance_raw_nofilter(void *, bam1_t *); /*proto*/ static int __pyx_f_5pysam_17libcalignmentfile___advance_all(void *, bam1_t *); /*proto*/ static int __pyx_f_5pysam_17libcalignmentfile___advance_raw_all(void *, bam1_t *); /*proto*/ static int __pyx_f_5pysam_17libcalignmentfile___advance_samtools(void *, bam1_t *); /*proto*/ static PyObject *__pyx_f_5pysam_17libcalignmentfile___pyx_unpickle_SNPCall__set_state(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *, PyObject *); /*proto*/ /* #### Code section: typeinfo ### */ /* #### Code section: before_global_var ### */ #define __Pyx_MODULE_NAME "pysam.libcalignmentfile" extern int __pyx_module_is_main_pysam__libcalignmentfile; int __pyx_module_is_main_pysam__libcalignmentfile = 0; /* Implementation of "pysam.libcalignmentfile" */ /* #### Code section: global_var ### */ static PyObject *__pyx_builtin_ImportError; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_MemoryError; static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_AssertionError; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_AttributeError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_OSError; /* #### Code section: string_decls ### */ static const char __pyx_k_L[] = "L"; static const char __pyx_k_N[] = "N"; static const char __pyx_k_b[] = "b"; static const char __pyx_k_c[] = "c"; static const char __pyx_k_h[] = "h"; static const char __pyx_k_n[] = "n"; static const char __pyx_k_r[] = "r"; static const char __pyx_k_s[] = "@%s"; static const char __pyx_k_t[] = "t"; static const char __pyx_k_w[] = "w"; static const char __pyx_k_x[] = "x"; static const char __pyx_k_y[] = "y"; static const char __pyx_k_AH[] = "AH"; static const char __pyx_k_AS[] = "AS"; static const char __pyx_k_CL[] = "CL"; static const char __pyx_k_CN[] = "CN"; static const char __pyx_k_CO[] = "CO"; static const char __pyx_k_DS[] = "DS"; static const char __pyx_k_DT[] = "DT"; static const char __pyx_k_FO[] = "FO"; static const char __pyx_k_GO[] = "GO"; static const char __pyx_k_HD[] = "HD"; static const char __pyx_k_ID[] = "ID"; static const char __pyx_k_KS[] = "KS"; static const char __pyx_k_LB[] = "LB"; static const char __pyx_k_LN[] = "LN"; static const char __pyx_k_M5[] = "M5"; static const char __pyx_k_PG[] = "PG"; static const char __pyx_k_PI[] = "PI"; static const char __pyx_k_PL[] = "PL"; static const char __pyx_k_PM[] = "PM"; static const char __pyx_k_PN[] = "PN"; static const char __pyx_k_PP[] = "PP"; static const char __pyx_k_PU[] = "PU"; static const char __pyx_k_RG[] = "RG"; static const char __pyx_k_SM[] = "SM"; static const char __pyx_k_SN[] = "SN"; static const char __pyx_k_SO[] = "SO"; static const char __pyx_k_SP[] = "SP"; static const char __pyx_k_SQ[] = "@SQ"; static const char __pyx_k_UR[] = "UR"; static const char __pyx_k_VN[] = "VN"; static const char __pyx_k__2[] = ":"; static const char __pyx_k__3[] = "\t"; static const char __pyx_k_gc[] = "gc"; static const char __pyx_k_io[] = "io"; static const char __pyx_k_nt[] = "nt"; static const char __pyx_k_op[] = "op"; static const char __pyx_k_os[] = "os"; static const char __pyx_k_rU[] = "rU"; static const char __pyx_k_rb[] = "rb"; static const char __pyx_k_rc[] = "rc"; static const char __pyx_k_re[] = "re"; static const char __pyx_k_sq[] = "sq"; static const char __pyx_k_wb[] = "wb"; static const char __pyx_k_wc[] = "wc"; static const char __pyx_k_wh[] = "wh"; static const char __pyx_k__12[] = "\n"; static const char __pyx_k__15[] = ""; static const char __pyx_k__19[] = " \000"; static const char __pyx_k__20[] = "@"; static const char __pyx_k__21[] = "': '"; static const char __pyx_k__22[] = "'"; static const char __pyx_k__46[] = "-"; static const char __pyx_k_all[] = "all"; static const char __pyx_k_beg[] = "beg"; static const char __pyx_k_cls[] = "cls"; static const char __pyx_k_end[] = "end"; static const char __pyx_k_get[] = "get"; static const char __pyx_k_hdr[] = "hdr"; static const char __pyx_k_idx[] = "idx"; static const char __pyx_k_key[] = "key"; static const char __pyx_k_len[] = "__len__"; static const char __pyx_k_map[] = "map"; static const char __pyx_k_new[] = "__new__"; static const char __pyx_k_pos[] = "pos"; static const char __pyx_k_ref[] = "ref"; static const char __pyx_k_res[] = "res"; static const char __pyx_k_ret[] = "ret"; static const char __pyx_k_seq[] = "seq"; static const char __pyx_k_str[] = "__str__"; static const char __pyx_k_sum[] = "sum"; static const char __pyx_k_tid[] = "tid"; static const char __pyx_k_wb0[] = "wb0"; static const char __pyx_k_wbu[] = "wbu"; static const char __pyx_k_zip[] = "zip"; static const char __pyx_k_SQ_2[] = "SQ"; static const char __pyx_k__124[] = "."; static const char __pyx_k__125[] = "*"; static const char __pyx_k__172[] = "?"; static const char __pyx_k_args[] = "args"; static const char __pyx_k_code[] = "code"; static const char __pyx_k_copy[] = "copy"; static const char __pyx_k_data[] = "data"; static const char __pyx_k_dict[] = "__dict__"; static const char __pyx_k_exit[] = "__exit__"; static const char __pyx_k_find[] = "find"; static const char __pyx_k_flag[] = "flag"; static const char __pyx_k_head[] = "head"; static const char __pyx_k_init[] = "__init__"; static const char __pyx_k_keys[] = "keys"; static const char __pyx_k_line[] = "line"; static const char __pyx_k_main[] = "__main__"; static const char __pyx_k_make[] = "_make"; static const char __pyx_k_mate[] = "mate"; static const char __pyx_k_mode[] = "mode"; static const char __pyx_k_name[] = "name"; static const char __pyx_k_open[] = "_open"; static const char __pyx_k_port[] = "port"; static const char __pyx_k_qpos[] = "qpos"; static const char __pyx_k_read[] = "read"; static const char __pyx_k_rtid[] = "rtid"; static const char __pyx_k_self[] = "self"; 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_text[] = "text"; static const char __pyx_k_warn[] = "warn"; static const char __pyx_k_all_2[] = "__all__"; static const char __pyx_k_array[] = "array"; static const char __pyx_k_btext[] = "btext"; static const char __pyx_k_build[] = "build"; static const char __pyx_k_cigar[] = "cigar"; static const char __pyx_k_close[] = "close"; static const char __pyx_k_cmode[] = "cmode"; static const char __pyx_k_count[] = "count"; static const char __pyx_k_ctext[] = "ctext"; static const char __pyx_k_enter[] = "__enter__"; static const char __pyx_k_fetch[] = "fetch"; static const char __pyx_k_field[] = "field"; static const char __pyx_k_items[] = "items"; static const char __pyx_k_lines[] = "lines"; static const char __pyx_k_qname[] = "qname"; static const char __pyx_k_range[] = "range"; 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_state[] = "state"; static const char __pyx_k_strip[] = "strip"; static const char __pyx_k_total[] = "total"; static const char __pyx_k_value[] = "value"; static const char __pyx_k_write[] = "write"; static const char __pyx_k_append[] = "append"; static const char __pyx_k_closed[] = "closed"; static const char __pyx_k_contig[] = "contig"; static const char __pyx_k_dict_2[] = "_dict"; static const char __pyx_k_enable[] = "enable"; static const char __pyx_k_fields[] = "fields"; static const char __pyx_k_fileno[] = "fileno"; static const char __pyx_k_format[] = "format"; static const char __pyx_k_gettid[] = "gettid"; static const char __pyx_k_header[] = "header"; static const char __pyx_k_import[] = "__import__"; static const char __pyx_k_is_bam[] = "is_bam"; static const char __pyx_k_kwargs[] = "kwargs"; static const char __pyx_k_l_text[] = "l_text"; static const char __pyx_k_length[] = "length"; static const char __pyx_k_mapped[] = "mapped"; static const char __pyx_k_name_2[] = "__name__"; static const char __pyx_k_pickle[] = "pickle"; static const char __pyx_k_pileup[] = "pileup"; static const char __pyx_k_record[] = "record"; static const char __pyx_k_reduce[] = "__reduce__"; static const char __pyx_k_refpos[] = "refpos"; static const char __pyx_k_region[] = "region"; static const char __pyx_k_result[] = "result"; static const char __pyx_k_rstart[] = "rstart"; static const char __pyx_k_stop_2[] = "_stop"; static const char __pyx_k_update[] = "update"; static const char __pyx_k_values[] = "values"; static const char __pyx_k_Counter[] = "Counter"; static const char __pyx_k_IOError[] = "IOError"; static const char __pyx_k_Mapping[] = "Mapping"; static const char __pyx_k_OSError[] = "OSError"; static const char __pyx_k_SNPCall[] = "SNPCall"; static const char __pyx_k_as_dict[] = "as_dict"; static const char __pyx_k_count_a[] = "count_a"; static const char __pyx_k_count_c[] = "count_c"; static const char __pyx_k_count_g[] = "count_g"; static const char __pyx_k_count_t[] = "count_t"; static const char __pyx_k_counter[] = "counter"; static const char __pyx_k_disable[] = "disable"; static const char __pyx_k_get_tid[] = "get_tid"; static const char __pyx_k_getitem[] = "__getitem__"; static const char __pyx_k_is_cram[] = "is_cram"; static const char __pyx_k_is_open[] = "is_open"; static const char __pyx_k_islower[] = "islower"; static const char __pyx_k_isupper[] = "isupper"; static const char __pyx_k_lengths[] = "lengths"; static const char __pyx_k_quality[] = "quality"; static const char __pyx_k_results[] = "results"; static const char __pyx_k_samfile[] = "samfile"; static const char __pyx_k_start_2[] = "_start"; static const char __pyx_k_stepper[] = "stepper"; static const char __pyx_k_threads[] = "threads"; static const char __pyx_k_to_dict[] = "to_dict"; static const char __pyx_k_KeyError[] = "KeyError"; static const char __pyx_k_SQ_SN_LN[] = "@SQ\tSN:{}\tLN:{}\n"; static const char __pyx_k_Sequence[] = "Sequence"; static const char __pyx_k_StringIO[] = "StringIO"; static const char __pyx_k_check_sq[] = "check_sq"; static const char __pyx_k_contains[] = "__contains__"; static const char __pyx_k_coverage[] = "coverage"; static const char __pyx_k_exc_type[] = "exc_type"; static const char __pyx_k_filename[] = "filename"; static const char __pyx_k_genotype[] = "genotype"; static const char __pyx_k_getrname[] = "getrname"; static const char __pyx_k_getstate[] = "__getstate__"; static const char __pyx_k_nextiter[] = "nextiter"; static const char __pyx_k_nofilter[] = "nofilter"; static const char __pyx_k_pyx_type[] = "__pyx_type"; static const char __pyx_k_read_loc[] = "read_loc"; static const char __pyx_k_redo_baq[] = "redo_baq"; static const char __pyx_k_samtools[] = "samtools"; static const char __pyx_k_setstate[] = "__setstate__"; static const char __pyx_k_template[] = "template"; static const char __pyx_k_truncate[] = "truncate"; static const char __pyx_k_unmapped[] = "unmapped"; static const char __pyx_k_warnings[] = "warnings"; static const char __pyx_k_TypeError[] = "TypeError"; static const char __pyx_k_cfilename[] = "cfilename"; static const char __pyx_k_enumerate[] = "enumerate"; static const char __pyx_k_exc_value[] = "exc_value"; static const char __pyx_k_fastafile[] = "fastafile"; static const char __pyx_k_from_dict[] = "from_dict"; static const char __pyx_k_from_text[] = "from_text"; static const char __pyx_k_has_coord[] = "has_coord"; static const char __pyx_k_has_index[] = "has_index"; static const char __pyx_k_isenabled[] = "isenabled"; static const char __pyx_k_iteritems[] = "iteritems"; static const char __pyx_k_max_depth[] = "max_depth"; static const char __pyx_k_positions[] = "positions"; static const char __pyx_k_pyx_state[] = "__pyx_state"; static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; static const char __pyx_k_reference[] = "reference"; static const char __pyx_k_threshold[] = "_threshold"; static const char __pyx_k_traceback[] = "traceback"; static const char __pyx_k_until_eof[] = "until_eof"; static const char __pyx_k_IndexStats[] = "IndexStats"; static const char __pyx_k_ValueError[] = "ValueError"; static const char __pyx_k_bfile_name[] = "bfile_name"; static const char __pyx_k_cindexname[] = "cindexname"; static const char __pyx_k_genome_loc[] = "genome_loc"; static const char __pyx_k_junc_start[] = "junc_start"; static const char __pyx_k_namedtuple[] = "namedtuple"; static const char __pyx_k_pyx_result[] = "__pyx_result"; static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; static const char __pyx_k_query_name[] = "query_name"; static const char __pyx_k_references[] = "references"; static const char __pyx_k_splitlines[] = "splitlines"; static const char __pyx_k_startswith[] = "startswith"; static const char __pyx_k_ImportError[] = "ImportError"; static const char __pyx_k_IteratorRow[] = "IteratorRow"; static const char __pyx_k_MemoryError[] = "MemoryError"; static const char __pyx_k_OrderedDict[] = "OrderedDict"; static const char __pyx_k_PickleError[] = "PickleError"; static const char __pyx_k_add_sq_text[] = "add_sq_text"; static const char __pyx_k_check_index[] = "check_index"; static const char __pyx_k_cigarstring[] = "cigarstring"; static const char __pyx_k_cigartuples[] = "cigartuples"; static const char __pyx_k_collections[] = "collections"; static const char __pyx_k_compute_baq[] = "compute_baq"; static const char __pyx_k_defaultdict[] = "defaultdict"; static const char __pyx_k_flag_filter[] = "flag_filter"; static const char __pyx_k_header_dict[] = "header_dict"; static const char __pyx_k_nreferences[] = "nreferences"; static const char __pyx_k_snp_quality[] = "snp_quality"; static const char __pyx_k_IndexedReads[] = "IndexedReads"; static const char __pyx_k_addReference[] = "addReference"; static const char __pyx_k_check_header[] = "check_header"; static const char __pyx_k_find_introns[] = "find_introns"; static const char __pyx_k_flag_require[] = "flag_require"; static const char __pyx_k_hasReference[] = "hasReference"; 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_pyx_checksum[] = "__pyx_checksum"; static const char __pyx_k_stringsource[] = ""; static const char __pyx_k_use_setstate[] = "use_setstate"; static const char __pyx_k_AlignmentFile[] = "AlignmentFile"; static const char __pyx_k_BAM_CREF_SKIP[] = "BAM_CREF_SKIP"; static const char __pyx_k_StopIteration[] = "StopIteration"; static const char __pyx_k_VALID_HEADERS[] = "VALID_HEADERS"; static const char __pyx_k_add_reference[] = "add_reference"; static const char __pyx_k_base_position[] = "base_position"; static const char __pyx_k_class_getitem[] = "__class_getitem__"; static const char __pyx_k_contig_length[] = "contig_length"; static const char __pyx_k_filter_method[] = "filter_method"; static const char __pyx_k_has_reference[] = "has_reference"; static const char __pyx_k_last_read_pos[] = "last_read_pos"; static const char __pyx_k_read_callback[] = "read_callback"; static const char __pyx_k_read_iterator[] = "read_iterator"; static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; static const char __pyx_k_require_index[] = "require_index"; static const char __pyx_k_AssertionError[] = "AssertionError"; static const char __pyx_k_AttributeError[] = "AttributeError"; static const char __pyx_k_IteratorColumn[] = "IteratorColumn"; static const char __pyx_k_IteratorRowAll[] = "IteratorRowAll"; static const char __pyx_k_add_sam_header[] = "add_sam_header"; static const char __pyx_k_count_coverage[] = "count_coverage"; static const char __pyx_k_filepath_index[] = "filepath_index"; static const char __pyx_k_format_options[] = "format_options"; static const char __pyx_k_ignore_orphans[] = "ignore_orphans"; static const char __pyx_k_index_filename[] = "index_filename"; static const char __pyx_k_mate_not_found[] = "mate not found"; static const char __pyx_k_reference_base[] = "reference_base"; static const char __pyx_k_referencenames[] = "referencenames"; static const char __pyx_k_truncated_file[] = "truncated file"; static const char __pyx_k_AlignmentHeader[] = "AlignmentHeader"; static const char __pyx_k_IteratorRowHead[] = "IteratorRowHead"; static const char __pyx_k_add_hts_options[] = "add_hts_options"; static const char __pyx_k_collections_abc[] = "collections.abc"; static const char __pyx_k_from_references[] = "from_references"; static const char __pyx_k_ignore_overlaps[] = "ignore_overlaps"; static const char __pyx_k_mapping_quality[] = "mapping_quality"; static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; static const char __pyx_k_query_qualities[] = "query_qualities"; static const char __pyx_k_reference_names[] = "reference_names"; static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; static const char __pyx_k_check_truncation[] = "check_truncation"; static const char __pyx_k_min_base_quality[] = "min_base_quality"; static const char __pyx_k_read_s_not_found[] = "read %s not found"; static const char __pyx_k_referencelengths[] = "referencelengths"; static const char __pyx_k_IndexedReads_find[] = "IndexedReads.find"; static const char __pyx_k_IteratorColumnAll[] = "IteratorColumnAll"; static const char __pyx_k_IteratorRowRegion[] = "IteratorRowRegion"; static const char __pyx_k_build_header_line[] = "build_header_line"; static const char __pyx_k_consensus_quality[] = "consensus_quality"; static const char __pyx_k_find_introns_slow[] = "find_introns_slow"; static const char __pyx_k_get_aligned_pairs[] = "get_aligned_pairs"; static const char __pyx_k_ignore_truncation[] = "ignore_truncation"; static const char __pyx_k_match_or_deletion[] = "match_or_deletion"; static const char __pyx_k_quality_threshold[] = "quality_threshold"; static const char __pyx_k_reference_lengths[] = "reference_lengths"; static const char __pyx_k_unknown_reference[] = "unknown reference {}"; static const char __pyx_k_AlignmentFile_head[] = "AlignmentFile.head"; static const char __pyx_k_AlignmentFile_mate[] = "AlignmentFile.mate"; static const char __pyx_k_IndexedReads_build[] = "IndexedReads.build"; static const char __pyx_k_IteratorRowAllRefs[] = "IteratorRowAllRefs"; static const char __pyx_k_VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER"; static const char __pyx_k_VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES"; 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_filepath_or_object[] = "filepath_or_object"; static const char __pyx_k_get_reference_name[] = "get_reference_name"; static const char __pyx_k_int_array_template[] = "int_array_template"; static const char __pyx_k_interval_of_size_0[] = "interval of size 0"; static const char __pyx_k_mate_s_is_unmapped[] = "mate %s: is unmapped"; static const char __pyx_k_multiple_iterators[] = "multiple_iterators"; static const char __pyx_k_read_s_is_unpaired[] = "read %s: is unpaired"; static const char __pyx_k_reference_filename[] = "reference_filename"; static const char __pyx_k_AlignmentFile__open[] = "AlignmentFile._open"; static const char __pyx_k_AlignmentFile_close[] = "AlignmentFile.close"; static const char __pyx_k_AlignmentFile_count[] = "AlignmentFile.count"; static const char __pyx_k_AlignmentFile_fetch[] = "AlignmentFile.fetch"; static const char __pyx_k_AlignmentFile_write[] = "AlignmentFile.write"; static const char __pyx_k_AlignmentHeader_get[] = "AlignmentHeader.get"; static const char __pyx_k_KNOWN_HEADER_FIELDS[] = "KNOWN_HEADER_FIELDS"; static const char __pyx_k_NotImplementedError[] = "NotImplementedError"; static const char __pyx_k_creference_filename[] = "creference_filename"; static const char __pyx_k_min_mapping_quality[] = "min_mapping_quality"; static const char __pyx_k_read_failure_reason[] = "read_failure_reason"; static const char __pyx_k_AlignmentFile___exit[] = "AlignmentFile.__exit__"; static const char __pyx_k_AlignmentFile_gettid[] = "AlignmentFile.gettid"; static const char __pyx_k_AlignmentFile_pileup[] = "AlignmentFile.pileup"; static const char __pyx_k_AlignmentHeader_copy[] = "AlignmentHeader.copy"; static const char __pyx_k_AlignmentHeader_keys[] = "AlignmentHeader.keys"; static const char __pyx_k_IteratorColumnRegion[] = "IteratorColumnRegion"; static const char __pyx_k_IteratorRowSelection[] = "IteratorRowSelection"; static const char __pyx_k_duplicate_filehandle[] = "duplicate_filehandle"; static const char __pyx_k_get_index_statistics[] = "get_index_statistics"; static const char __pyx_k_get_reference_length[] = "get_reference_length"; static const char __pyx_k_pyx_unpickle_SNPCall[] = "__pyx_unpickle_SNPCall"; static const char __pyx_k_AlignmentFile___enter[] = "AlignmentFile.__enter__"; static const char __pyx_k_AlignmentFile_get_tid[] = "AlignmentFile.get_tid"; static const char __pyx_k_AlignmentHeader_items[] = "AlignmentHeader.items"; static const char __pyx_k_IteratorColumnAllRefs[] = "IteratorColumnAllRefs"; static const char __pyx_k_adjust_capq_threshold[] = "adjust_capq_threshold"; static const char __pyx_k_from_text_and_lengths[] = "_from_text_and_lengths"; static const char __pyx_k_header_line_without_s[] = "header line without '@': '%s'"; static const char __pyx_k_AlignmentFile_getrname[] = "AlignmentFile.getrname"; static const char __pyx_k_AlignmentHeader_values[] = "AlignmentHeader.values"; static const char __pyx_k_build_sequence_section[] = "_build_sequence_section"; static const char __pyx_k_could_not_parse_header[] = "could not parse header"; static const char __pyx_k_error_during_iteration[] = "error during iteration"; static const char __pyx_k_AlignmentFile_has_index[] = "AlignmentFile.has_index"; static const char __pyx_k_AlignmentHeader_as_dict[] = "AlignmentHeader.as_dict"; static const char __pyx_k_AlignmentHeader_get_tid[] = "AlignmentHeader.get_tid"; static const char __pyx_k_AlignmentHeader_to_dict[] = "AlignmentHeader.to_dict"; static const char __pyx_k_SNPCall___reduce_cython[] = "SNPCall.__reduce_cython__"; static const char __pyx_k_could_not_create_header[] = "could not create header"; static const char __pyx_k_pysam_libcalignmentfile[] = "pysam.libcalignmentfile"; static const char __pyx_k_could_not_allocate_bytes[] = "could not allocate {} bytes"; static const char __pyx_k_error_while_reading_file[] = "error {} while reading file"; static const char __pyx_k_unable_to_reopen_htsfile[] = "unable to reopen htsfile"; static const char __pyx_k_AlignmentFile_check_index[] = "AlignmentFile.check_index"; static const char __pyx_k_AlignmentHeader_from_dict[] = "AlignmentHeader.from_dict"; static const char __pyx_k_AlignmentHeader_from_text[] = "AlignmentHeader.from_text"; static const char __pyx_k_AlignmentHeader_iteritems[] = "AlignmentHeader.iteritems"; static const char __pyx_k_SNPCall___setstate_cython[] = "SNPCall.__setstate_cython__"; static const char __pyx_k_unable_to_open_index_file[] = "unable to open index file"; static const char __pyx_k_AlignmentFile_find_introns[] = "AlignmentFile.find_introns"; static const char __pyx_k_AlignmentFile_is_valid_tid[] = "AlignmentFile.is_valid_tid"; static const char __pyx_k_error_while_reading_file_2[] = "error while reading file {}: {}"; static const char __pyx_k_IteratorColumn_addReference[] = "IteratorColumn.addReference"; static const char __pyx_k_IteratorColumn_hasReference[] = "IteratorColumn.hasReference"; static const char __pyx_k_IteratorRowAllRefs_nextiter[] = "IteratorRowAllRefs.nextiter"; static const char __pyx_k_IteratorRow___reduce_cython[] = "IteratorRow.__reduce_cython__"; static const char __pyx_k_invalid_file_opening_mode_s[] = "invalid file opening mode `%s`"; static const char __pyx_k_pysam_libcalignmentfile_pyx[] = "pysam/libcalignmentfile.pyx"; static const char __pyx_k_unable_to_open_index_file_s[] = "unable to open index file `%s`"; static const char __pyx_k_AlignmentFile_count_coverage[] = "AlignmentFile.count_coverage"; static const char __pyx_k_AlignmentHeader_is_valid_tid[] = "AlignmentHeader.is_valid_tid"; static const char __pyx_k_I_O_operation_on_closed_file[] = "I/O operation on closed file"; static const char __pyx_k_IndexedReads___reduce_cython[] = "IndexedReads.__reduce_cython__"; static const char __pyx_k_IteratorColumn_add_reference[] = "IteratorColumn.add_reference"; static const char __pyx_k_IteratorColumn_has_reference[] = "IteratorColumn.has_reference"; static const char __pyx_k_interval_of_size_less_than_0[] = "interval of size less than 0"; static const char __pyx_k_no_index_available_for_fetch[] = "no index available for fetch"; static const char __pyx_k_AlignmentFile___reduce_cython[] = "AlignmentFile.__reduce_cython__"; static const char __pyx_k_IteratorRow___setstate_cython[] = "IteratorRow.__setstate_cython__"; static const char __pyx_k_could_not_open_alignment_file[] = "could not open alignment file `{}`: {}"; static const char __pyx_k_header_line_with_invalid_type[] = "header line with invalid type '"; static const char __pyx_k_no_index_available_for_pileup[] = "no index available for pileup"; static const char __pyx_k_IndexedReads___setstate_cython[] = "IndexedReads.__setstate_cython__"; static const char __pyx_k_IteratorColumn___reduce_cython[] = "IteratorColumn.__reduce_cython__"; static const char __pyx_k_IteratorRowAll___reduce_cython[] = "IteratorRowAll.__reduce_cython__"; static const char __pyx_k_AlignmentFile___setstate_cython[] = "AlignmentFile.__setstate_cython__"; static const char __pyx_k_AlignmentFile_find_introns_slow[] = "AlignmentFile.find_introns_slow"; static const char __pyx_k_AlignmentHeader___reduce_cython[] = "AlignmentHeader.__reduce_cython__"; static const char __pyx_k_AlignmentHeader__build_sequence[] = "AlignmentHeader._build_sequence_section"; static const char __pyx_k_AlignmentHeader_from_references[] = "AlignmentHeader.from_references"; static const char __pyx_k_IteratorColumnRegion___setstate[] = "IteratorColumnRegion.__setstate_cython__"; static const char __pyx_k_IteratorRowHead___reduce_cython[] = "IteratorRowHead.__reduce_cython__"; static const char __pyx_k_IteratorRowSelection___setstate[] = "IteratorRowSelection.__setstate_cython__"; static const char __pyx_k_could_not_open_alignment_file_2[] = "could not open alignment file `{}`"; static const char __pyx_k_fetch_called_on_bamfile_without[] = "fetch called on bamfile without index"; static const char __pyx_k_file_does_not_contain_alignment[] = "file does not contain alignment data"; static const char __pyx_k_incomplete_sequence_information[] = "incomplete sequence information in '%s'"; static const char __pyx_k_malformatted_header_no_in_field[] = "malformatted header: no ':' in field"; static const char __pyx_k_wrong_sequence_information_in_s[] = "wrong sequence information in '%s'"; static const char __pyx_k_AlignedSegment_refers_to_referen[] = "AlignedSegment refers to reference number {} that is larger than the number of references ({}) in the header"; static const char __pyx_k_AlignmentFile_get_index_statisti[] = "AlignmentFile.get_index_statistics"; static const char __pyx_k_AlignmentFile_get_reference_leng[] = "AlignmentFile.get_reference_length"; static const char __pyx_k_AlignmentFile_get_reference_name[] = "AlignmentFile.get_reference_name"; static const char __pyx_k_AlignmentFile_mapped_only_availa[] = "AlignmentFile.mapped only available in bam files"; static const char __pyx_k_AlignmentHeader___setstate_cytho[] = "AlignmentHeader.__setstate_cython__"; static const char __pyx_k_AlignmentHeader__from_text_and_l[] = "AlignmentHeader._from_text_and_lengths"; static const char __pyx_k_AlignmentHeader_does_not_support[] = "AlignmentHeader does not support item assignment (use header.to_dict()"; static const char __pyx_k_AlignmentHeader_get_reference_le[] = "AlignmentHeader.get_reference_length"; static const char __pyx_k_AlignmentHeader_get_reference_na[] = "AlignmentHeader.get_reference_name"; static const char __pyx_k_Cannot_add_extra_threads_when_ig[] = "Cannot add extra threads when \"ignore_truncation\" is True"; static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0xe45c101, 0x1134a9c, 0x50b2281) = (_consensus_quality, _coverage, _genotype, _pos, _reference_base, _rms_mapping_quality, _snp_quality, _tid))"; static const char __pyx_k_IteratorColumnAllRefs___reduce_c[] = "IteratorColumnAllRefs.__reduce_cython__"; static const char __pyx_k_IteratorColumnAllRefs___setstate[] = "IteratorColumnAllRefs.__setstate_cython__"; static const char __pyx_k_IteratorColumnAll___reduce_cytho[] = "IteratorColumnAll.__reduce_cython__"; static const char __pyx_k_IteratorColumnAll___setstate_cyt[] = "IteratorColumnAll.__setstate_cython__"; static const char __pyx_k_IteratorColumnRegion___reduce_cy[] = "IteratorColumnRegion.__reduce_cython__"; static const char __pyx_k_IteratorColumn___setstate_cython[] = "IteratorColumn.__setstate_cython__"; static const char __pyx_k_IteratorRowAllRefs___reduce_cyth[] = "IteratorRowAllRefs.__reduce_cython__"; static const char __pyx_k_IteratorRowAllRefs___setstate_cy[] = "IteratorRowAllRefs.__setstate_cython__"; static const char __pyx_k_IteratorRowAll___setstate_cython[] = "IteratorRowAll.__setstate_cython__"; static const char __pyx_k_IteratorRowHead___setstate_cytho[] = "IteratorRowHead.__setstate_cython__"; static const char __pyx_k_IteratorRowRegion___reduce_cytho[] = "IteratorRowRegion.__reduce_cython__"; static const char __pyx_k_IteratorRowRegion___setstate_cyt[] = "IteratorRowRegion.__setstate_cython__"; static const char __pyx_k_IteratorRowSelection___reduce_cy[] = "IteratorRowSelection.__reduce_cython__"; static const char __pyx_k_Raw_iterator_set_up_without_regi[] = "Raw iterator set up without region cannot be reset"; static const char __pyx_k_SAM_file_does_not_have_a_valid_h[] = "SAM? file does not have a valid header (mode='%s'), please provide reference_names and reference_lengths"; static const char __pyx_k_access_from_StringIO_objects_not[] = "access from StringIO objects not supported"; static const char __pyx_k_can_not_iterate_over_samfile_wit[] = "can not iterate over samfile without header"; static const char __pyx_k_can_only_apply_IndexReads_on_bam[] = "can only apply IndexReads on bam files"; static const char __pyx_k_cannot_create_AlignmentHeader_re[] = "cannot create AlignmentHeader, received NULL pointer"; static const char __pyx_k_could_not_allocate_memory_of_siz[] = "could not allocate memory of size {}"; static const char __pyx_k_either_supply_options_template_h[] = "either supply options `template`, `header`, `text` or both `reference_names` and `reference_lengths` for writing"; static const char __pyx_k_failure_when_setting_reference_f[] = "failure when setting reference filename"; static const char __pyx_k_fetching_by_region_is_not_availa[] = "fetching by region is not available for SAM files"; static const char __pyx_k_file_does_not_have_a_valid_heade[] = "file does not have a valid header (mode='%s') - is it BAM/CRAM format?"; static const char __pyx_k_file_has_no_sequences_defined_mo[] = "file has no sequences defined (mode='%s') - is it SAM/BAM format? Consider opening with check_sq=False"; static const char __pyx_k_header_not_available_in_closed_f[] = "header not available in closed files"; static const char __pyx_k_invalid_type_for_record_s_s_expe[] = "invalid type for record %s: %s, expected %s"; static const char __pyx_k_mapping_information_not_recorded[] = "mapping information not recorded in index or index not available"; static const char __pyx_k_multiple_iterators_not_implement[] = "multiple iterators not implemented for SAM files"; static const char __pyx_k_multiple_s_lines_are_not_permitt[] = "multiple '%s' lines are not permitted"; static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__"; static const char __pyx_k_no_index_available_for_iteration[] = "no index available for iteration"; static const char __pyx_k_not_enough_information_to_constr[] = "not enough information to construct header. Please provide template, header, text or reference_names/reference_lengths"; static const char __pyx_k_number_of_reference_names_and_le[] = "number of reference names and lengths do not match"; static const char __pyx_k_reference_id_i_out_of_range_0_ti[] = "reference_id %i out of range 0<=tid<%i"; static const char __pyx_k_reference_sequence_for_tid_not_f[] = "reference sequence for '{}' (tid={}) not found"; static const char __pyx_k_sam_write1_failed_with_error_cod[] = "sam_write1 failed with error code {}"; static const char __pyx_k_self_b_self_htsfile_self_index_c[] = "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling"; static const char __pyx_k_self_b_self_htsfile_self_index_s[] = "self.b,self.htsfile,self.index,self.iter cannot be converted to a Python object for pickling"; static const char __pyx_k_self_htsfile_cannot_be_converted[] = "self.htsfile cannot be converted to a Python object for pickling"; static const char __pyx_k_unable_to_read_header_informatio[] = "unable to read header information"; static const char __pyx_k_unknown_stepper_option_s_in_Iter[] = "unknown stepper option `%s` in IteratorColumn"; static const char __pyx_k_multiple_iterators_not_implement_2[] = "multiple_iterators not implemented for CRAM"; /* #### 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_17libcalignmentfile_build_header_line(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_2read_failure_reason(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_code); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader___cinit__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_2__init__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_4_from_text_and_lengths(CYTHON_UNUSED PyTypeObject *__pyx_v_cls, PyObject *__pyx_v_text, PyObject *__pyx_v_reference_names, PyObject *__pyx_v_reference_lengths); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_6from_text(PyTypeObject *__pyx_v_cls, PyObject *__pyx_v_text); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_8from_dict(PyTypeObject *__pyx_v_cls, PyObject *__pyx_v_header_dict); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_10from_references(PyTypeObject *__pyx_v_cls, PyObject *__pyx_v_reference_names, PyObject *__pyx_v_reference_lengths, PyObject *__pyx_v_text, PyObject *__pyx_v_add_sq_text); /* proto */ static void __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_12__dealloc__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_14__bool__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_16copy(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_11nreferences___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_10references___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_7lengths___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_18_build_sequence_section(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_20to_dict(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_22as_dict(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_24get_reference_name(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_26get_reference_length(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_28is_valid_tid(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, int __pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_30get_tid(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_32__str__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_34__setitem__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_key, CYTHON_UNUSED PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_36__getitem__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_38items(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_40iteritems(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_42keys(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_44values(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_46get(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, PyObject *__pyx_v_args); /* proto */ static Py_ssize_t __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_48__len__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_50__contains__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_52__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15AlignmentHeader_54__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile___cinit__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_2has_index(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_4check_index(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_filepath_or_object, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_template, PyObject *__pyx_v_reference_names, PyObject *__pyx_v_reference_lengths, PyObject *__pyx_v_reference_filename, PyObject *__pyx_v_text, PyObject *__pyx_v_header, CYTHON_UNUSED PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_add_sam_header, CYTHON_UNUSED PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq, PyObject *__pyx_v_index_filename, PyObject *__pyx_v_filepath_index, PyObject *__pyx_v_require_index, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_duplicate_filehandle, PyObject *__pyx_v_ignore_truncation, PyObject *__pyx_v_format_options, PyObject *__pyx_v_threads); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_8fetch(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__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_until_eof, PyObject *__pyx_v_multiple_iterators, PyObject *__pyx_v_reference, PyObject *__pyx_v_end); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_10head(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_n, PyObject *__pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_12mate(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment *__pyx_v_read); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_14pileup(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_reference, PyObject *__pyx_v_end, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_16count(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof, PyObject *__pyx_v_read_callback, PyObject *__pyx_v_reference, PyObject *__pyx_v_end); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_18count_coverage(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_contig, PyObject *__pyx_v_start, PyObject *__pyx_v_stop, PyObject *__pyx_v_region, PyObject *__pyx_v_quality_threshold, PyObject *__pyx_v_read_callback, PyObject *__pyx_v_reference, PyObject *__pyx_v_end); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_20find_introns_slow(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_read_iterator); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_22find_introns(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_read_iterator); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_24close(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_26__dealloc__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_28write(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment *__pyx_v_read); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_30__enter__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_32__exit__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__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_17libcalignmentfile_13AlignmentFile_6mapped___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_8unmapped___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_12nocoordinate___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_34get_index_statistics(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_36__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_38__next__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_40is_valid_tid(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, int __pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_42get_tid(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_44get_reference_name(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_46get_reference_length(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_11nreferences___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_10references___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_7lengths___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_4text___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_48gettid(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_50getrname(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_18reference_filename___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6header___get__(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_52__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_54__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_11IteratorRow___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, int __pyx_v_multiple_iterators); /* proto */ static void __pyx_pf_5pysam_17libcalignmentfile_11IteratorRow_2__dealloc__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_11IteratorRow_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_11IteratorRow_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_17IteratorRowRegion___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_stop, int __pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_17libcalignmentfile_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorRowRegion_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorRowRegion_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_15IteratorRowHead___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, int __pyx_v_n, int __pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15IteratorRowHead_2__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15IteratorRowHead_4__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15IteratorRowHead_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_15IteratorRowHead_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_14IteratorRowAll___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, int __pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorRowAll_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorRowAll_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, PyObject *__pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_20IteratorRowSelection___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorRowSelection_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorRowSelection_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_4add_reference(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9libcfaidx_FastaFile *__pyx_v_fastafile); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_6has_reference(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_10hasReference(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_12addReference(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9libcfaidx_FastaFile *__pyx_v_fastafile); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_14__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_14IteratorColumn_16__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_stop, int __pyx_v_truncate, int __pyx_v_multiple_iterators, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorColumnRegion_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_20IteratorColumnRegion_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_17IteratorColumnAll___cinit__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorColumnAll_2__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorColumnAll_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_17IteratorColumnAll_6__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall___str__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_2__reduce_cython__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_7SNPCall_4__setstate_cython__(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ static int __pyx_pf_5pysam_17libcalignmentfile_12IndexedReads___init__(struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *__pyx_v_samfile, int __pyx_v_multiple_iterators); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_12IndexedReads_2build(struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_12IndexedReads_4find(struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *__pyx_v_self, PyObject *__pyx_v_query_name); /* proto */ static void __pyx_pf_5pysam_17libcalignmentfile_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_12IndexedReads_8__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_12IndexedReads_10__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_pf_5pysam_17libcalignmentfile_4__pyx_unpickle_SNPCall(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state); /* proto */ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_AlignmentHeader(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_AlignmentFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowHead(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnAll(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_get = {0, 0, 0, 0, 0}; /* #### 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 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 PyTypeObject *__pyx_ptype_7cpython_5array_array; #if CYTHON_USE_MODULE_STATE #endif #if CYTHON_USE_MODULE_STATE #endif PyTypeObject *__pyx_ptype_5pysam_10libchtslib_HTSFile; #if CYTHON_USE_MODULE_STATE #endif PyTypeObject *__pyx_ptype_5pysam_9libcfaidx_FastaFile; PyTypeObject *__pyx_ptype_5pysam_9libcfaidx_FastqProxy; PyTypeObject *__pyx_ptype_5pysam_9libcfaidx_FastxRecord; PyTypeObject *__pyx_ptype_5pysam_9libcfaidx_FastxFile; PyTypeObject *__pyx_ptype_5pysam_9libcfaidx_FastqFile; PyTypeObject *__pyx_ptype_5pysam_9libcfaidx_Fastafile; #if CYTHON_USE_MODULE_STATE #endif PyTypeObject *__pyx_ptype_5pysam_18libcalignedsegment_AlignedSegment; PyTypeObject *__pyx_ptype_5pysam_18libcalignedsegment_PileupColumn; PyTypeObject *__pyx_ptype_5pysam_18libcalignedsegment_PileupRead; #if CYTHON_USE_MODULE_STATE #endif #if CYTHON_USE_MODULE_STATE #endif #if CYTHON_USE_MODULE_STATE PyObject *__pyx_type_5pysam_17libcalignmentfile_AlignmentHeader; PyObject *__pyx_type_5pysam_17libcalignmentfile_AlignmentFile; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorRow; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorRowRegion; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorRowHead; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorRowAll; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorRowAllRefs; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorRowSelection; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorColumn; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorColumnRegion; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorColumnAllRefs; PyObject *__pyx_type_5pysam_17libcalignmentfile_IteratorColumnAll; PyObject *__pyx_type_5pysam_17libcalignmentfile_IndexedReads; PyObject *__pyx_type_5pysam_17libcalignmentfile_SNPCall; #endif PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_AlignmentHeader; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_AlignmentFile; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorRow; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowRegion; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowHead; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowAll; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowAllRefs; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowSelection; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumn; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnRegion; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnAllRefs; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnAll; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_IndexedReads; PyTypeObject *__pyx_ptype_5pysam_17libcalignmentfile_SNPCall; PyObject *__pyx_n_u_AH; PyObject *__pyx_n_u_AS; PyObject 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#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 #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 #endif #define __pyx_ptype_5pysam_10libchtslib_HTSFile __pyx_mstate_global->__pyx_ptype_5pysam_10libchtslib_HTSFile #if CYTHON_USE_MODULE_STATE #endif #define __pyx_ptype_5pysam_9libcfaidx_FastaFile __pyx_mstate_global->__pyx_ptype_5pysam_9libcfaidx_FastaFile #define __pyx_ptype_5pysam_9libcfaidx_FastqProxy __pyx_mstate_global->__pyx_ptype_5pysam_9libcfaidx_FastqProxy #define __pyx_ptype_5pysam_9libcfaidx_FastxRecord __pyx_mstate_global->__pyx_ptype_5pysam_9libcfaidx_FastxRecord #define __pyx_ptype_5pysam_9libcfaidx_FastxFile __pyx_mstate_global->__pyx_ptype_5pysam_9libcfaidx_FastxFile #define __pyx_ptype_5pysam_9libcfaidx_FastqFile __pyx_mstate_global->__pyx_ptype_5pysam_9libcfaidx_FastqFile #define __pyx_ptype_5pysam_9libcfaidx_Fastafile __pyx_mstate_global->__pyx_ptype_5pysam_9libcfaidx_Fastafile #if CYTHON_USE_MODULE_STATE #endif #define __pyx_ptype_5pysam_18libcalignedsegment_AlignedSegment __pyx_mstate_global->__pyx_ptype_5pysam_18libcalignedsegment_AlignedSegment #define __pyx_ptype_5pysam_18libcalignedsegment_PileupColumn __pyx_mstate_global->__pyx_ptype_5pysam_18libcalignedsegment_PileupColumn #define __pyx_ptype_5pysam_18libcalignedsegment_PileupRead __pyx_mstate_global->__pyx_ptype_5pysam_18libcalignedsegment_PileupRead #if CYTHON_USE_MODULE_STATE #endif #if CYTHON_USE_MODULE_STATE #endif #if CYTHON_USE_MODULE_STATE #define __pyx_type_5pysam_17libcalignmentfile_AlignmentHeader __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_AlignmentHeader #define __pyx_type_5pysam_17libcalignmentfile_AlignmentFile __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_AlignmentFile #define __pyx_type_5pysam_17libcalignmentfile_IteratorRow __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorRow #define __pyx_type_5pysam_17libcalignmentfile_IteratorRowRegion __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorRowRegion #define __pyx_type_5pysam_17libcalignmentfile_IteratorRowHead __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorRowHead #define __pyx_type_5pysam_17libcalignmentfile_IteratorRowAll __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorRowAll #define __pyx_type_5pysam_17libcalignmentfile_IteratorRowAllRefs __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorRowAllRefs #define __pyx_type_5pysam_17libcalignmentfile_IteratorRowSelection __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorRowSelection #define __pyx_type_5pysam_17libcalignmentfile_IteratorColumn __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorColumn #define __pyx_type_5pysam_17libcalignmentfile_IteratorColumnRegion __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorColumnRegion #define __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAllRefs __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorColumnAllRefs #define __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAll __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IteratorColumnAll #define __pyx_type_5pysam_17libcalignmentfile_IndexedReads __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_IndexedReads #define __pyx_type_5pysam_17libcalignmentfile_SNPCall __pyx_mstate_global->__pyx_type_5pysam_17libcalignmentfile_SNPCall #endif #define __pyx_ptype_5pysam_17libcalignmentfile_AlignmentHeader __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_AlignmentHeader #define __pyx_ptype_5pysam_17libcalignmentfile_AlignmentFile __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_AlignmentFile #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorRow __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorRow #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorRowRegion __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowRegion #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorRowHead __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowHead #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorRowAll __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowAll #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorRowAllRefs __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowAllRefs #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorRowSelection __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorRowSelection #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorColumn __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumn #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnRegion __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnRegion #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnAllRefs __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnAllRefs #define __pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnAll __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IteratorColumnAll #define __pyx_ptype_5pysam_17libcalignmentfile_IndexedReads __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_IndexedReads #define __pyx_ptype_5pysam_17libcalignmentfile_SNPCall __pyx_mstate_global->__pyx_ptype_5pysam_17libcalignmentfile_SNPCall #define __pyx_n_u_AH __pyx_mstate_global->__pyx_n_u_AH #define __pyx_n_u_AS __pyx_mstate_global->__pyx_n_u_AS #define __pyx_kp_u_AlignedSegment_refers_to_referen __pyx_mstate_global->__pyx_kp_u_AlignedSegment_refers_to_referen #define __pyx_n_s_AlignmentFile __pyx_mstate_global->__pyx_n_s_AlignmentFile #define __pyx_n_u_AlignmentFile __pyx_mstate_global->__pyx_n_u_AlignmentFile #define __pyx_n_s_AlignmentFile___enter __pyx_mstate_global->__pyx_n_s_AlignmentFile___enter #define __pyx_n_s_AlignmentFile___exit __pyx_mstate_global->__pyx_n_s_AlignmentFile___exit #define __pyx_n_s_AlignmentFile___reduce_cython __pyx_mstate_global->__pyx_n_s_AlignmentFile___reduce_cython #define __pyx_n_s_AlignmentFile___setstate_cython __pyx_mstate_global->__pyx_n_s_AlignmentFile___setstate_cython #define __pyx_n_s_AlignmentFile__open __pyx_mstate_global->__pyx_n_s_AlignmentFile__open #define __pyx_n_s_AlignmentFile_check_index __pyx_mstate_global->__pyx_n_s_AlignmentFile_check_index #define __pyx_n_s_AlignmentFile_close __pyx_mstate_global->__pyx_n_s_AlignmentFile_close #define __pyx_n_s_AlignmentFile_count __pyx_mstate_global->__pyx_n_s_AlignmentFile_count #define __pyx_n_s_AlignmentFile_count_coverage __pyx_mstate_global->__pyx_n_s_AlignmentFile_count_coverage #define __pyx_n_s_AlignmentFile_fetch __pyx_mstate_global->__pyx_n_s_AlignmentFile_fetch #define __pyx_n_s_AlignmentFile_find_introns __pyx_mstate_global->__pyx_n_s_AlignmentFile_find_introns #define __pyx_n_s_AlignmentFile_find_introns_slow __pyx_mstate_global->__pyx_n_s_AlignmentFile_find_introns_slow #define __pyx_n_s_AlignmentFile_get_index_statisti __pyx_mstate_global->__pyx_n_s_AlignmentFile_get_index_statisti #define __pyx_n_s_AlignmentFile_get_reference_leng __pyx_mstate_global->__pyx_n_s_AlignmentFile_get_reference_leng #define __pyx_n_s_AlignmentFile_get_reference_name __pyx_mstate_global->__pyx_n_s_AlignmentFile_get_reference_name #define __pyx_n_s_AlignmentFile_get_tid __pyx_mstate_global->__pyx_n_s_AlignmentFile_get_tid #define __pyx_n_s_AlignmentFile_getrname __pyx_mstate_global->__pyx_n_s_AlignmentFile_getrname #define __pyx_n_s_AlignmentFile_gettid __pyx_mstate_global->__pyx_n_s_AlignmentFile_gettid #define __pyx_n_s_AlignmentFile_has_index __pyx_mstate_global->__pyx_n_s_AlignmentFile_has_index #define __pyx_n_s_AlignmentFile_head __pyx_mstate_global->__pyx_n_s_AlignmentFile_head #define __pyx_n_s_AlignmentFile_is_valid_tid __pyx_mstate_global->__pyx_n_s_AlignmentFile_is_valid_tid #define __pyx_kp_u_AlignmentFile_mapped_only_availa __pyx_mstate_global->__pyx_kp_u_AlignmentFile_mapped_only_availa #define __pyx_n_s_AlignmentFile_mate __pyx_mstate_global->__pyx_n_s_AlignmentFile_mate #define __pyx_n_s_AlignmentFile_pileup __pyx_mstate_global->__pyx_n_s_AlignmentFile_pileup #define __pyx_n_s_AlignmentFile_write __pyx_mstate_global->__pyx_n_s_AlignmentFile_write #define __pyx_n_s_AlignmentHeader __pyx_mstate_global->__pyx_n_s_AlignmentHeader #define __pyx_n_u_AlignmentHeader __pyx_mstate_global->__pyx_n_u_AlignmentHeader #define __pyx_n_s_AlignmentHeader___reduce_cython __pyx_mstate_global->__pyx_n_s_AlignmentHeader___reduce_cython #define __pyx_n_s_AlignmentHeader___setstate_cytho __pyx_mstate_global->__pyx_n_s_AlignmentHeader___setstate_cytho #define __pyx_n_s_AlignmentHeader__build_sequence __pyx_mstate_global->__pyx_n_s_AlignmentHeader__build_sequence #define __pyx_n_s_AlignmentHeader__from_text_and_l __pyx_mstate_global->__pyx_n_s_AlignmentHeader__from_text_and_l #define __pyx_n_s_AlignmentHeader_as_dict __pyx_mstate_global->__pyx_n_s_AlignmentHeader_as_dict #define __pyx_n_s_AlignmentHeader_copy __pyx_mstate_global->__pyx_n_s_AlignmentHeader_copy #define __pyx_kp_u_AlignmentHeader_does_not_support __pyx_mstate_global->__pyx_kp_u_AlignmentHeader_does_not_support #define __pyx_n_s_AlignmentHeader_from_dict __pyx_mstate_global->__pyx_n_s_AlignmentHeader_from_dict #define __pyx_n_s_AlignmentHeader_from_references __pyx_mstate_global->__pyx_n_s_AlignmentHeader_from_references #define __pyx_n_s_AlignmentHeader_from_text __pyx_mstate_global->__pyx_n_s_AlignmentHeader_from_text #define __pyx_n_s_AlignmentHeader_get __pyx_mstate_global->__pyx_n_s_AlignmentHeader_get #define __pyx_n_s_AlignmentHeader_get_reference_le __pyx_mstate_global->__pyx_n_s_AlignmentHeader_get_reference_le #define __pyx_n_s_AlignmentHeader_get_reference_na __pyx_mstate_global->__pyx_n_s_AlignmentHeader_get_reference_na #define __pyx_n_s_AlignmentHeader_get_tid __pyx_mstate_global->__pyx_n_s_AlignmentHeader_get_tid #define __pyx_n_s_AlignmentHeader_is_valid_tid __pyx_mstate_global->__pyx_n_s_AlignmentHeader_is_valid_tid #define __pyx_n_s_AlignmentHeader_items __pyx_mstate_global->__pyx_n_s_AlignmentHeader_items #define __pyx_n_s_AlignmentHeader_iteritems __pyx_mstate_global->__pyx_n_s_AlignmentHeader_iteritems #define __pyx_n_s_AlignmentHeader_keys __pyx_mstate_global->__pyx_n_s_AlignmentHeader_keys #define __pyx_n_s_AlignmentHeader_to_dict __pyx_mstate_global->__pyx_n_s_AlignmentHeader_to_dict #define __pyx_n_s_AlignmentHeader_values __pyx_mstate_global->__pyx_n_s_AlignmentHeader_values #define __pyx_n_s_AssertionError __pyx_mstate_global->__pyx_n_s_AssertionError #define __pyx_n_s_AttributeError __pyx_mstate_global->__pyx_n_s_AttributeError #define __pyx_n_s_BAM_CREF_SKIP __pyx_mstate_global->__pyx_n_s_BAM_CREF_SKIP #define __pyx_n_u_CL __pyx_mstate_global->__pyx_n_u_CL #define __pyx_n_u_CN __pyx_mstate_global->__pyx_n_u_CN #define __pyx_n_u_CO __pyx_mstate_global->__pyx_n_u_CO #define __pyx_kp_u_Cannot_add_extra_threads_when_ig __pyx_mstate_global->__pyx_kp_u_Cannot_add_extra_threads_when_ig #define __pyx_n_s_Counter __pyx_mstate_global->__pyx_n_s_Counter #define __pyx_n_u_DS __pyx_mstate_global->__pyx_n_u_DS #define __pyx_n_u_DT __pyx_mstate_global->__pyx_n_u_DT #define __pyx_n_u_FO __pyx_mstate_global->__pyx_n_u_FO #define __pyx_n_u_GO __pyx_mstate_global->__pyx_n_u_GO #define __pyx_n_u_HD __pyx_mstate_global->__pyx_n_u_HD #define __pyx_n_u_ID __pyx_mstate_global->__pyx_n_u_ID #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_ImportError __pyx_mstate_global->__pyx_n_s_ImportError #define __pyx_kp_s_Incompatible_checksums_0x_x_vs_0 __pyx_mstate_global->__pyx_kp_s_Incompatible_checksums_0x_x_vs_0 #define __pyx_n_s_IndexStats __pyx_mstate_global->__pyx_n_s_IndexStats #define __pyx_n_u_IndexStats __pyx_mstate_global->__pyx_n_u_IndexStats #define __pyx_n_s_IndexedReads __pyx_mstate_global->__pyx_n_s_IndexedReads #define __pyx_n_u_IndexedReads __pyx_mstate_global->__pyx_n_u_IndexedReads #define __pyx_n_s_IndexedReads___reduce_cython __pyx_mstate_global->__pyx_n_s_IndexedReads___reduce_cython #define __pyx_n_s_IndexedReads___setstate_cython __pyx_mstate_global->__pyx_n_s_IndexedReads___setstate_cython #define __pyx_n_s_IndexedReads_build __pyx_mstate_global->__pyx_n_s_IndexedReads_build #define __pyx_n_s_IndexedReads_find __pyx_mstate_global->__pyx_n_s_IndexedReads_find #define __pyx_n_s_IteratorColumn __pyx_mstate_global->__pyx_n_s_IteratorColumn #define __pyx_n_u_IteratorColumn __pyx_mstate_global->__pyx_n_u_IteratorColumn #define __pyx_n_s_IteratorColumnAll __pyx_mstate_global->__pyx_n_s_IteratorColumnAll #define __pyx_n_s_IteratorColumnAllRefs __pyx_mstate_global->__pyx_n_s_IteratorColumnAllRefs #define __pyx_n_s_IteratorColumnAllRefs___reduce_c __pyx_mstate_global->__pyx_n_s_IteratorColumnAllRefs___reduce_c #define __pyx_n_s_IteratorColumnAllRefs___setstate __pyx_mstate_global->__pyx_n_s_IteratorColumnAllRefs___setstate #define __pyx_n_s_IteratorColumnAll___reduce_cytho __pyx_mstate_global->__pyx_n_s_IteratorColumnAll___reduce_cytho #define __pyx_n_s_IteratorColumnAll___setstate_cyt __pyx_mstate_global->__pyx_n_s_IteratorColumnAll___setstate_cyt #define __pyx_n_s_IteratorColumnRegion __pyx_mstate_global->__pyx_n_s_IteratorColumnRegion #define __pyx_n_s_IteratorColumnRegion___reduce_cy __pyx_mstate_global->__pyx_n_s_IteratorColumnRegion___reduce_cy #define __pyx_n_s_IteratorColumnRegion___setstate __pyx_mstate_global->__pyx_n_s_IteratorColumnRegion___setstate #define __pyx_n_s_IteratorColumn___reduce_cython __pyx_mstate_global->__pyx_n_s_IteratorColumn___reduce_cython #define __pyx_n_s_IteratorColumn___setstate_cython __pyx_mstate_global->__pyx_n_s_IteratorColumn___setstate_cython #define __pyx_n_s_IteratorColumn_addReference __pyx_mstate_global->__pyx_n_s_IteratorColumn_addReference #define __pyx_n_s_IteratorColumn_add_reference __pyx_mstate_global->__pyx_n_s_IteratorColumn_add_reference #define __pyx_n_s_IteratorColumn_hasReference __pyx_mstate_global->__pyx_n_s_IteratorColumn_hasReference #define __pyx_n_s_IteratorColumn_has_reference __pyx_mstate_global->__pyx_n_s_IteratorColumn_has_reference #define __pyx_n_s_IteratorRow __pyx_mstate_global->__pyx_n_s_IteratorRow #define __pyx_n_u_IteratorRow __pyx_mstate_global->__pyx_n_u_IteratorRow #define __pyx_n_s_IteratorRowAll __pyx_mstate_global->__pyx_n_s_IteratorRowAll #define __pyx_n_s_IteratorRowAllRefs __pyx_mstate_global->__pyx_n_s_IteratorRowAllRefs #define __pyx_n_s_IteratorRowAllRefs___reduce_cyth __pyx_mstate_global->__pyx_n_s_IteratorRowAllRefs___reduce_cyth #define __pyx_n_s_IteratorRowAllRefs___setstate_cy __pyx_mstate_global->__pyx_n_s_IteratorRowAllRefs___setstate_cy #define __pyx_n_s_IteratorRowAllRefs_nextiter __pyx_mstate_global->__pyx_n_s_IteratorRowAllRefs_nextiter #define __pyx_n_s_IteratorRowAll___reduce_cython __pyx_mstate_global->__pyx_n_s_IteratorRowAll___reduce_cython #define __pyx_n_s_IteratorRowAll___setstate_cython __pyx_mstate_global->__pyx_n_s_IteratorRowAll___setstate_cython #define __pyx_n_s_IteratorRowHead __pyx_mstate_global->__pyx_n_s_IteratorRowHead #define __pyx_n_s_IteratorRowHead___reduce_cython __pyx_mstate_global->__pyx_n_s_IteratorRowHead___reduce_cython #define __pyx_n_s_IteratorRowHead___setstate_cytho __pyx_mstate_global->__pyx_n_s_IteratorRowHead___setstate_cytho #define __pyx_n_s_IteratorRowRegion __pyx_mstate_global->__pyx_n_s_IteratorRowRegion #define __pyx_n_s_IteratorRowRegion___reduce_cytho __pyx_mstate_global->__pyx_n_s_IteratorRowRegion___reduce_cytho #define __pyx_n_s_IteratorRowRegion___setstate_cyt __pyx_mstate_global->__pyx_n_s_IteratorRowRegion___setstate_cyt #define __pyx_n_s_IteratorRowSelection __pyx_mstate_global->__pyx_n_s_IteratorRowSelection #define __pyx_n_s_IteratorRowSelection___reduce_cy __pyx_mstate_global->__pyx_n_s_IteratorRowSelection___reduce_cy #define __pyx_n_s_IteratorRowSelection___setstate __pyx_mstate_global->__pyx_n_s_IteratorRowSelection___setstate #define __pyx_n_s_IteratorRow___reduce_cython __pyx_mstate_global->__pyx_n_s_IteratorRow___reduce_cython #define __pyx_n_s_IteratorRow___setstate_cython __pyx_mstate_global->__pyx_n_s_IteratorRow___setstate_cython #define __pyx_n_s_KNOWN_HEADER_FIELDS __pyx_mstate_global->__pyx_n_s_KNOWN_HEADER_FIELDS #define __pyx_n_u_KS __pyx_mstate_global->__pyx_n_u_KS #define __pyx_n_s_KeyError __pyx_mstate_global->__pyx_n_s_KeyError #define __pyx_n_u_L __pyx_mstate_global->__pyx_n_u_L #define __pyx_n_u_LB __pyx_mstate_global->__pyx_n_u_LB #define __pyx_n_u_LN __pyx_mstate_global->__pyx_n_u_LN #define __pyx_n_u_M5 __pyx_mstate_global->__pyx_n_u_M5 #define __pyx_n_s_Mapping __pyx_mstate_global->__pyx_n_s_Mapping #define __pyx_n_s_MemoryError __pyx_mstate_global->__pyx_n_s_MemoryError #define __pyx_n_u_N __pyx_mstate_global->__pyx_n_u_N #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_OrderedDict __pyx_mstate_global->__pyx_n_s_OrderedDict #define __pyx_n_u_PG __pyx_mstate_global->__pyx_n_u_PG #define __pyx_n_u_PI __pyx_mstate_global->__pyx_n_u_PI #define __pyx_n_u_PL __pyx_mstate_global->__pyx_n_u_PL #define __pyx_n_u_PM __pyx_mstate_global->__pyx_n_u_PM #define __pyx_n_u_PN __pyx_mstate_global->__pyx_n_u_PN #define __pyx_n_u_PP __pyx_mstate_global->__pyx_n_u_PP #define __pyx_n_u_PU __pyx_mstate_global->__pyx_n_u_PU #define __pyx_n_s_PickleError __pyx_mstate_global->__pyx_n_s_PickleError #define __pyx_n_u_RG __pyx_mstate_global->__pyx_n_u_RG #define __pyx_kp_u_Raw_iterator_set_up_without_regi __pyx_mstate_global->__pyx_kp_u_Raw_iterator_set_up_without_regi #define __pyx_kp_u_SAM_file_does_not_have_a_valid_h __pyx_mstate_global->__pyx_kp_u_SAM_file_does_not_have_a_valid_h #define __pyx_n_u_SM __pyx_mstate_global->__pyx_n_u_SM #define __pyx_n_u_SN __pyx_mstate_global->__pyx_n_u_SN #define __pyx_n_s_SNPCall __pyx_mstate_global->__pyx_n_s_SNPCall #define __pyx_n_s_SNPCall___reduce_cython __pyx_mstate_global->__pyx_n_s_SNPCall___reduce_cython #define __pyx_n_s_SNPCall___setstate_cython __pyx_mstate_global->__pyx_n_s_SNPCall___setstate_cython #define __pyx_n_u_SO __pyx_mstate_global->__pyx_n_u_SO #define __pyx_n_u_SP __pyx_mstate_global->__pyx_n_u_SP #define __pyx_kp_u_SQ __pyx_mstate_global->__pyx_kp_u_SQ #define __pyx_n_u_SQ_2 __pyx_mstate_global->__pyx_n_u_SQ_2 #define __pyx_kp_u_SQ_SN_LN __pyx_mstate_global->__pyx_kp_u_SQ_SN_LN #define __pyx_n_s_Sequence __pyx_mstate_global->__pyx_n_s_Sequence #define __pyx_n_s_StopIteration __pyx_mstate_global->__pyx_n_s_StopIteration #define __pyx_n_s_StringIO __pyx_mstate_global->__pyx_n_s_StringIO #define __pyx_n_s_TypeError __pyx_mstate_global->__pyx_n_s_TypeError #define __pyx_n_u_UR __pyx_mstate_global->__pyx_n_u_UR #define __pyx_n_s_VALID_HEADERS __pyx_mstate_global->__pyx_n_s_VALID_HEADERS #define __pyx_n_s_VALID_HEADER_ORDER __pyx_mstate_global->__pyx_n_s_VALID_HEADER_ORDER #define __pyx_n_s_VALID_HEADER_TYPES __pyx_mstate_global->__pyx_n_s_VALID_HEADER_TYPES #define __pyx_n_u_VN __pyx_mstate_global->__pyx_n_u_VN #define __pyx_n_s_ValueError __pyx_mstate_global->__pyx_n_s_ValueError #define __pyx_kp_u__12 __pyx_mstate_global->__pyx_kp_u__12 #define __pyx_kp_u__124 __pyx_mstate_global->__pyx_kp_u__124 #define __pyx_n_s__125 __pyx_mstate_global->__pyx_n_s__125 #define __pyx_kp_u__15 __pyx_mstate_global->__pyx_kp_u__15 #define __pyx_n_s__172 __pyx_mstate_global->__pyx_n_s__172 #define __pyx_kp_u__19 __pyx_mstate_global->__pyx_kp_u__19 #define __pyx_kp_u__2 __pyx_mstate_global->__pyx_kp_u__2 #define __pyx_kp_u__20 __pyx_mstate_global->__pyx_kp_u__20 #define __pyx_kp_u__21 __pyx_mstate_global->__pyx_kp_u__21 #define __pyx_kp_u__22 __pyx_mstate_global->__pyx_kp_u__22 #define __pyx_kp_u__3 __pyx_mstate_global->__pyx_kp_u__3 #define __pyx_kp_b__46 __pyx_mstate_global->__pyx_kp_b__46 #define __pyx_kp_u_access_from_StringIO_objects_not __pyx_mstate_global->__pyx_kp_u_access_from_StringIO_objects_not #define __pyx_n_s_addReference __pyx_mstate_global->__pyx_n_s_addReference #define __pyx_n_s_add_hts_options __pyx_mstate_global->__pyx_n_s_add_hts_options #define __pyx_n_s_add_reference __pyx_mstate_global->__pyx_n_s_add_reference #define __pyx_n_s_add_sam_header __pyx_mstate_global->__pyx_n_s_add_sam_header #define __pyx_n_s_add_sq_text __pyx_mstate_global->__pyx_n_s_add_sq_text #define __pyx_n_u_adjust_capq_threshold __pyx_mstate_global->__pyx_n_u_adjust_capq_threshold #define __pyx_n_u_all __pyx_mstate_global->__pyx_n_u_all #define __pyx_n_s_all_2 __pyx_mstate_global->__pyx_n_s_all_2 #define __pyx_n_s_append __pyx_mstate_global->__pyx_n_s_append #define __pyx_n_s_args __pyx_mstate_global->__pyx_n_s_args #define __pyx_n_s_array __pyx_mstate_global->__pyx_n_s_array #define __pyx_n_s_as_dict __pyx_mstate_global->__pyx_n_s_as_dict #define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines #define __pyx_n_s_b __pyx_mstate_global->__pyx_n_s_b #define __pyx_n_u_b __pyx_mstate_global->__pyx_n_u_b #define __pyx_n_s_base_position __pyx_mstate_global->__pyx_n_s_base_position #define __pyx_n_s_beg __pyx_mstate_global->__pyx_n_s_beg #define __pyx_n_s_bfile_name __pyx_mstate_global->__pyx_n_s_bfile_name #define __pyx_n_s_btext __pyx_mstate_global->__pyx_n_s_btext #define __pyx_n_s_build __pyx_mstate_global->__pyx_n_s_build #define __pyx_n_s_build_header_line __pyx_mstate_global->__pyx_n_s_build_header_line #define __pyx_n_s_build_sequence_section __pyx_mstate_global->__pyx_n_s_build_sequence_section #define __pyx_n_s_c __pyx_mstate_global->__pyx_n_s_c #define __pyx_n_u_c __pyx_mstate_global->__pyx_n_u_c #define __pyx_kp_u_can_not_iterate_over_samfile_wit __pyx_mstate_global->__pyx_kp_u_can_not_iterate_over_samfile_wit #define __pyx_kp_u_can_only_apply_IndexReads_on_bam __pyx_mstate_global->__pyx_kp_u_can_only_apply_IndexReads_on_bam #define __pyx_kp_u_cannot_create_AlignmentHeader_re __pyx_mstate_global->__pyx_kp_u_cannot_create_AlignmentHeader_re #define __pyx_n_s_cfilename __pyx_mstate_global->__pyx_n_s_cfilename #define __pyx_n_s_check_header __pyx_mstate_global->__pyx_n_s_check_header #define __pyx_n_s_check_index __pyx_mstate_global->__pyx_n_s_check_index #define __pyx_n_s_check_sq __pyx_mstate_global->__pyx_n_s_check_sq #define __pyx_n_s_check_truncation __pyx_mstate_global->__pyx_n_s_check_truncation #define __pyx_n_s_cigar __pyx_mstate_global->__pyx_n_s_cigar #define __pyx_n_s_cigarstring __pyx_mstate_global->__pyx_n_s_cigarstring #define __pyx_n_s_cigartuples __pyx_mstate_global->__pyx_n_s_cigartuples #define __pyx_n_s_cindexname __pyx_mstate_global->__pyx_n_s_cindexname #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_closed __pyx_mstate_global->__pyx_n_s_closed #define __pyx_n_s_cls __pyx_mstate_global->__pyx_n_s_cls #define __pyx_n_s_cmode __pyx_mstate_global->__pyx_n_s_cmode #define __pyx_n_s_code __pyx_mstate_global->__pyx_n_s_code #define __pyx_n_s_collections __pyx_mstate_global->__pyx_n_s_collections #define __pyx_n_s_collections_abc __pyx_mstate_global->__pyx_n_s_collections_abc #define __pyx_n_u_compute_baq __pyx_mstate_global->__pyx_n_u_compute_baq #define __pyx_n_s_consensus_quality __pyx_mstate_global->__pyx_n_s_consensus_quality #define __pyx_n_s_contains __pyx_mstate_global->__pyx_n_s_contains #define __pyx_n_s_contig __pyx_mstate_global->__pyx_n_s_contig #define __pyx_n_u_contig __pyx_mstate_global->__pyx_n_u_contig #define __pyx_n_s_contig_length __pyx_mstate_global->__pyx_n_s_contig_length #define __pyx_n_s_copy __pyx_mstate_global->__pyx_n_s_copy #define __pyx_kp_u_could_not_allocate_bytes __pyx_mstate_global->__pyx_kp_u_could_not_allocate_bytes #define __pyx_kp_u_could_not_allocate_memory_of_siz __pyx_mstate_global->__pyx_kp_u_could_not_allocate_memory_of_siz #define __pyx_kp_u_could_not_create_header __pyx_mstate_global->__pyx_kp_u_could_not_create_header #define __pyx_kp_u_could_not_open_alignment_file __pyx_mstate_global->__pyx_kp_u_could_not_open_alignment_file #define __pyx_kp_u_could_not_open_alignment_file_2 __pyx_mstate_global->__pyx_kp_u_could_not_open_alignment_file_2 #define __pyx_kp_u_could_not_parse_header __pyx_mstate_global->__pyx_kp_u_could_not_parse_header #define __pyx_n_s_count __pyx_mstate_global->__pyx_n_s_count #define __pyx_n_s_count_a __pyx_mstate_global->__pyx_n_s_count_a #define __pyx_n_s_count_c __pyx_mstate_global->__pyx_n_s_count_c #define __pyx_n_s_count_coverage __pyx_mstate_global->__pyx_n_s_count_coverage #define __pyx_n_s_count_g __pyx_mstate_global->__pyx_n_s_count_g #define __pyx_n_s_count_t __pyx_mstate_global->__pyx_n_s_count_t #define __pyx_n_s_counter __pyx_mstate_global->__pyx_n_s_counter #define __pyx_n_s_coverage __pyx_mstate_global->__pyx_n_s_coverage #define __pyx_n_s_creference_filename __pyx_mstate_global->__pyx_n_s_creference_filename #define __pyx_n_s_ctext __pyx_mstate_global->__pyx_n_s_ctext #define __pyx_n_s_data __pyx_mstate_global->__pyx_n_s_data #define __pyx_n_s_defaultdict __pyx_mstate_global->__pyx_n_s_defaultdict #define __pyx_n_s_dict __pyx_mstate_global->__pyx_n_s_dict #define __pyx_n_s_dict_2 __pyx_mstate_global->__pyx_n_s_dict_2 #define __pyx_kp_u_disable __pyx_mstate_global->__pyx_kp_u_disable #define __pyx_n_s_duplicate_filehandle __pyx_mstate_global->__pyx_n_s_duplicate_filehandle #define __pyx_kp_u_either_supply_options_template_h __pyx_mstate_global->__pyx_kp_u_either_supply_options_template_h #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_enumerate __pyx_mstate_global->__pyx_n_s_enumerate #define __pyx_kp_u_error_during_iteration __pyx_mstate_global->__pyx_kp_u_error_during_iteration #define __pyx_kp_u_error_while_reading_file __pyx_mstate_global->__pyx_kp_u_error_while_reading_file #define __pyx_kp_u_error_while_reading_file_2 __pyx_mstate_global->__pyx_kp_u_error_while_reading_file_2 #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_failure_when_setting_reference_f __pyx_mstate_global->__pyx_kp_u_failure_when_setting_reference_f #define __pyx_n_s_fastafile __pyx_mstate_global->__pyx_n_s_fastafile #define __pyx_n_u_fastafile __pyx_mstate_global->__pyx_n_u_fastafile #define __pyx_n_s_fetch __pyx_mstate_global->__pyx_n_s_fetch #define __pyx_kp_u_fetch_called_on_bamfile_without __pyx_mstate_global->__pyx_kp_u_fetch_called_on_bamfile_without #define __pyx_kp_u_fetching_by_region_is_not_availa __pyx_mstate_global->__pyx_kp_u_fetching_by_region_is_not_availa #define __pyx_n_s_field __pyx_mstate_global->__pyx_n_s_field #define __pyx_n_s_fields __pyx_mstate_global->__pyx_n_s_fields #define __pyx_kp_u_file_does_not_contain_alignment __pyx_mstate_global->__pyx_kp_u_file_does_not_contain_alignment #define __pyx_kp_u_file_does_not_have_a_valid_heade __pyx_mstate_global->__pyx_kp_u_file_does_not_have_a_valid_heade #define __pyx_kp_u_file_has_no_sequences_defined_mo __pyx_mstate_global->__pyx_kp_u_file_has_no_sequences_defined_mo #define __pyx_n_s_filename __pyx_mstate_global->__pyx_n_s_filename #define __pyx_n_u_filename __pyx_mstate_global->__pyx_n_u_filename #define __pyx_n_u_fileno __pyx_mstate_global->__pyx_n_u_fileno #define __pyx_n_s_filepath_index __pyx_mstate_global->__pyx_n_s_filepath_index #define __pyx_n_s_filepath_or_object __pyx_mstate_global->__pyx_n_s_filepath_or_object #define __pyx_n_s_filter_method __pyx_mstate_global->__pyx_n_s_filter_method #define __pyx_n_s_find __pyx_mstate_global->__pyx_n_s_find #define __pyx_n_s_find_introns __pyx_mstate_global->__pyx_n_s_find_introns #define __pyx_n_s_find_introns_slow __pyx_mstate_global->__pyx_n_s_find_introns_slow #define __pyx_n_s_flag __pyx_mstate_global->__pyx_n_s_flag #define __pyx_n_u_flag_filter __pyx_mstate_global->__pyx_n_u_flag_filter #define __pyx_n_u_flag_require __pyx_mstate_global->__pyx_n_u_flag_require #define __pyx_n_s_format __pyx_mstate_global->__pyx_n_s_format #define __pyx_n_s_format_options __pyx_mstate_global->__pyx_n_s_format_options #define __pyx_n_s_from_dict __pyx_mstate_global->__pyx_n_s_from_dict #define __pyx_n_s_from_references __pyx_mstate_global->__pyx_n_s_from_references #define __pyx_n_s_from_text __pyx_mstate_global->__pyx_n_s_from_text #define __pyx_n_s_from_text_and_lengths __pyx_mstate_global->__pyx_n_s_from_text_and_lengths #define __pyx_kp_u_gc __pyx_mstate_global->__pyx_kp_u_gc #define __pyx_n_s_genome_loc __pyx_mstate_global->__pyx_n_s_genome_loc #define __pyx_n_s_genotype __pyx_mstate_global->__pyx_n_s_genotype #define __pyx_n_s_get __pyx_mstate_global->__pyx_n_s_get #define __pyx_n_s_get_aligned_pairs __pyx_mstate_global->__pyx_n_s_get_aligned_pairs #define __pyx_n_s_get_index_statistics __pyx_mstate_global->__pyx_n_s_get_index_statistics #define __pyx_n_s_get_reference_length __pyx_mstate_global->__pyx_n_s_get_reference_length #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_getitem __pyx_mstate_global->__pyx_n_s_getitem #define __pyx_n_s_getrname __pyx_mstate_global->__pyx_n_s_getrname #define __pyx_n_s_getstate __pyx_mstate_global->__pyx_n_s_getstate #define __pyx_n_s_gettid __pyx_mstate_global->__pyx_n_s_gettid #define __pyx_n_u_h __pyx_mstate_global->__pyx_n_u_h #define __pyx_n_s_hasReference __pyx_mstate_global->__pyx_n_s_hasReference #define __pyx_n_s_has_coord __pyx_mstate_global->__pyx_n_s_has_coord #define __pyx_n_s_has_index __pyx_mstate_global->__pyx_n_s_has_index #define __pyx_n_s_has_reference __pyx_mstate_global->__pyx_n_s_has_reference #define __pyx_n_s_hdr __pyx_mstate_global->__pyx_n_s_hdr #define __pyx_n_s_head __pyx_mstate_global->__pyx_n_s_head #define __pyx_n_s_header __pyx_mstate_global->__pyx_n_s_header #define __pyx_n_s_header_dict __pyx_mstate_global->__pyx_n_s_header_dict #define __pyx_kp_u_header_line_with_invalid_type __pyx_mstate_global->__pyx_kp_u_header_line_with_invalid_type #define __pyx_kp_u_header_line_without_s __pyx_mstate_global->__pyx_kp_u_header_line_without_s #define __pyx_kp_u_header_not_available_in_closed_f __pyx_mstate_global->__pyx_kp_u_header_not_available_in_closed_f #define __pyx_n_s_idx __pyx_mstate_global->__pyx_n_s_idx #define __pyx_n_u_ignore_orphans __pyx_mstate_global->__pyx_n_u_ignore_orphans #define __pyx_n_u_ignore_overlaps __pyx_mstate_global->__pyx_n_u_ignore_overlaps #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_kp_u_incomplete_sequence_information __pyx_mstate_global->__pyx_kp_u_incomplete_sequence_information #define __pyx_n_s_index_filename __pyx_mstate_global->__pyx_n_s_index_filename #define __pyx_n_s_init __pyx_mstate_global->__pyx_n_s_init #define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing #define __pyx_n_s_int_array_template __pyx_mstate_global->__pyx_n_s_int_array_template #define __pyx_kp_u_interval_of_size_0 __pyx_mstate_global->__pyx_kp_u_interval_of_size_0 #define __pyx_kp_u_interval_of_size_less_than_0 __pyx_mstate_global->__pyx_kp_u_interval_of_size_less_than_0 #define __pyx_kp_u_invalid_file_opening_mode_s __pyx_mstate_global->__pyx_kp_u_invalid_file_opening_mode_s #define __pyx_kp_u_invalid_type_for_record_s_s_expe __pyx_mstate_global->__pyx_kp_u_invalid_type_for_record_s_s_expe #define __pyx_n_s_io __pyx_mstate_global->__pyx_n_s_io #define __pyx_n_s_is_bam __pyx_mstate_global->__pyx_n_s_is_bam #define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine #define __pyx_n_s_is_cram __pyx_mstate_global->__pyx_n_s_is_cram #define __pyx_n_s_is_open __pyx_mstate_global->__pyx_n_s_is_open #define __pyx_n_s_is_valid_tid __pyx_mstate_global->__pyx_n_s_is_valid_tid #define __pyx_kp_u_isenabled __pyx_mstate_global->__pyx_kp_u_isenabled #define __pyx_n_s_islower __pyx_mstate_global->__pyx_n_s_islower #define __pyx_n_s_isupper __pyx_mstate_global->__pyx_n_s_isupper #define __pyx_n_s_items __pyx_mstate_global->__pyx_n_s_items #define __pyx_n_s_iteritems __pyx_mstate_global->__pyx_n_s_iteritems #define __pyx_n_s_junc_start __pyx_mstate_global->__pyx_n_s_junc_start #define __pyx_n_s_key __pyx_mstate_global->__pyx_n_s_key #define __pyx_n_s_keys __pyx_mstate_global->__pyx_n_s_keys #define __pyx_n_s_kwargs __pyx_mstate_global->__pyx_n_s_kwargs #define __pyx_n_s_l_text __pyx_mstate_global->__pyx_n_s_l_text #define __pyx_n_s_last_read_pos __pyx_mstate_global->__pyx_n_s_last_read_pos #define __pyx_n_s_len __pyx_mstate_global->__pyx_n_s_len #define __pyx_n_s_length __pyx_mstate_global->__pyx_n_s_length #define __pyx_n_s_lengths __pyx_mstate_global->__pyx_n_s_lengths #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_make __pyx_mstate_global->__pyx_n_s_make #define __pyx_kp_u_malformatted_header_no_in_field __pyx_mstate_global->__pyx_kp_u_malformatted_header_no_in_field #define __pyx_n_s_map __pyx_mstate_global->__pyx_n_s_map #define __pyx_n_s_mapped __pyx_mstate_global->__pyx_n_s_mapped #define __pyx_n_u_mapped __pyx_mstate_global->__pyx_n_u_mapped #define __pyx_kp_u_mapping_information_not_recorded __pyx_mstate_global->__pyx_kp_u_mapping_information_not_recorded #define __pyx_n_s_mapping_quality __pyx_mstate_global->__pyx_n_s_mapping_quality #define __pyx_n_s_match_or_deletion __pyx_mstate_global->__pyx_n_s_match_or_deletion #define __pyx_n_s_mate __pyx_mstate_global->__pyx_n_s_mate #define __pyx_kp_u_mate_not_found __pyx_mstate_global->__pyx_kp_u_mate_not_found #define __pyx_kp_u_mate_s_is_unmapped __pyx_mstate_global->__pyx_kp_u_mate_s_is_unmapped #define __pyx_n_u_max_depth __pyx_mstate_global->__pyx_n_u_max_depth #define __pyx_n_u_min_base_quality __pyx_mstate_global->__pyx_n_u_min_base_quality #define __pyx_n_u_min_mapping_quality __pyx_mstate_global->__pyx_n_u_min_mapping_quality #define __pyx_n_s_mode __pyx_mstate_global->__pyx_n_s_mode #define __pyx_n_s_multiple_iterators __pyx_mstate_global->__pyx_n_s_multiple_iterators #define __pyx_kp_u_multiple_iterators_not_implement __pyx_mstate_global->__pyx_kp_u_multiple_iterators_not_implement #define __pyx_kp_u_multiple_iterators_not_implement_2 __pyx_mstate_global->__pyx_kp_u_multiple_iterators_not_implement_2 #define __pyx_kp_u_multiple_s_lines_are_not_permitt __pyx_mstate_global->__pyx_kp_u_multiple_s_lines_are_not_permitt #define __pyx_n_s_n __pyx_mstate_global->__pyx_n_s_n #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_namedtuple __pyx_mstate_global->__pyx_n_s_namedtuple #define __pyx_n_s_new __pyx_mstate_global->__pyx_n_s_new #define __pyx_n_s_nextiter __pyx_mstate_global->__pyx_n_s_nextiter #define __pyx_kp_s_no_default___reduce___due_to_non __pyx_mstate_global->__pyx_kp_s_no_default___reduce___due_to_non #define __pyx_kp_u_no_index_available_for_fetch __pyx_mstate_global->__pyx_kp_u_no_index_available_for_fetch #define __pyx_kp_u_no_index_available_for_iteration __pyx_mstate_global->__pyx_kp_u_no_index_available_for_iteration #define __pyx_kp_u_no_index_available_for_pileup __pyx_mstate_global->__pyx_kp_u_no_index_available_for_pileup #define __pyx_n_u_nofilter __pyx_mstate_global->__pyx_n_u_nofilter #define __pyx_kp_u_not_enough_information_to_constr __pyx_mstate_global->__pyx_kp_u_not_enough_information_to_constr #define __pyx_n_s_nreferences __pyx_mstate_global->__pyx_n_s_nreferences #define __pyx_n_s_nt __pyx_mstate_global->__pyx_n_s_nt #define __pyx_kp_u_number_of_reference_names_and_le __pyx_mstate_global->__pyx_kp_u_number_of_reference_names_and_le #define __pyx_n_s_op __pyx_mstate_global->__pyx_n_s_op #define __pyx_n_s_open __pyx_mstate_global->__pyx_n_s_open #define __pyx_n_s_os __pyx_mstate_global->__pyx_n_s_os #define __pyx_n_s_parse_region __pyx_mstate_global->__pyx_n_s_parse_region #define __pyx_n_s_pickle __pyx_mstate_global->__pyx_n_s_pickle #define __pyx_n_s_pileup __pyx_mstate_global->__pyx_n_s_pileup #define __pyx_n_s_port __pyx_mstate_global->__pyx_n_s_port #define __pyx_n_s_pos __pyx_mstate_global->__pyx_n_s_pos #define __pyx_n_s_positions __pyx_mstate_global->__pyx_n_s_positions #define __pyx_n_s_pysam_libcalignmentfile __pyx_mstate_global->__pyx_n_s_pysam_libcalignmentfile #define __pyx_kp_s_pysam_libcalignmentfile_pyx __pyx_mstate_global->__pyx_kp_s_pysam_libcalignmentfile_pyx #define __pyx_n_s_pyx_PickleError __pyx_mstate_global->__pyx_n_s_pyx_PickleError #define __pyx_n_s_pyx_checksum __pyx_mstate_global->__pyx_n_s_pyx_checksum #define __pyx_n_s_pyx_result __pyx_mstate_global->__pyx_n_s_pyx_result #define __pyx_n_s_pyx_state __pyx_mstate_global->__pyx_n_s_pyx_state #define __pyx_n_s_pyx_type __pyx_mstate_global->__pyx_n_s_pyx_type #define __pyx_n_s_pyx_unpickle_SNPCall __pyx_mstate_global->__pyx_n_s_pyx_unpickle_SNPCall #define __pyx_n_s_pyx_vtable __pyx_mstate_global->__pyx_n_s_pyx_vtable #define __pyx_n_s_qname __pyx_mstate_global->__pyx_n_s_qname #define __pyx_n_s_qpos __pyx_mstate_global->__pyx_n_s_qpos #define __pyx_n_s_quality __pyx_mstate_global->__pyx_n_s_quality #define __pyx_n_s_quality_threshold __pyx_mstate_global->__pyx_n_s_quality_threshold #define __pyx_n_s_query_name __pyx_mstate_global->__pyx_n_s_query_name #define __pyx_n_s_query_qualities __pyx_mstate_global->__pyx_n_s_query_qualities #define __pyx_n_s_r __pyx_mstate_global->__pyx_n_s_r #define __pyx_n_u_r __pyx_mstate_global->__pyx_n_u_r #define __pyx_n_u_rU __pyx_mstate_global->__pyx_n_u_rU #define __pyx_n_s_range __pyx_mstate_global->__pyx_n_s_range #define __pyx_n_u_rb __pyx_mstate_global->__pyx_n_u_rb #define __pyx_n_u_rc __pyx_mstate_global->__pyx_n_u_rc #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_read_callback __pyx_mstate_global->__pyx_n_s_read_callback #define __pyx_n_s_read_failure_reason __pyx_mstate_global->__pyx_n_s_read_failure_reason #define __pyx_n_s_read_iterator __pyx_mstate_global->__pyx_n_s_read_iterator #define __pyx_n_s_read_loc __pyx_mstate_global->__pyx_n_s_read_loc #define __pyx_kp_u_read_s_is_unpaired __pyx_mstate_global->__pyx_kp_u_read_s_is_unpaired #define __pyx_kp_u_read_s_not_found __pyx_mstate_global->__pyx_kp_u_read_s_not_found #define __pyx_n_s_record __pyx_mstate_global->__pyx_n_s_record #define __pyx_n_u_redo_baq __pyx_mstate_global->__pyx_n_u_redo_baq #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_ref __pyx_mstate_global->__pyx_n_s_ref #define __pyx_n_s_reference __pyx_mstate_global->__pyx_n_s_reference #define __pyx_n_s_reference_base __pyx_mstate_global->__pyx_n_s_reference_base #define __pyx_n_s_reference_filename __pyx_mstate_global->__pyx_n_s_reference_filename #define __pyx_kp_u_reference_id_i_out_of_range_0_ti __pyx_mstate_global->__pyx_kp_u_reference_id_i_out_of_range_0_ti #define __pyx_n_s_reference_lengths __pyx_mstate_global->__pyx_n_s_reference_lengths #define __pyx_n_s_reference_names __pyx_mstate_global->__pyx_n_s_reference_names #define __pyx_kp_u_reference_sequence_for_tid_not_f __pyx_mstate_global->__pyx_kp_u_reference_sequence_for_tid_not_f #define __pyx_n_s_referencelengths __pyx_mstate_global->__pyx_n_s_referencelengths #define __pyx_n_s_referencenames __pyx_mstate_global->__pyx_n_s_referencenames #define __pyx_n_s_references __pyx_mstate_global->__pyx_n_s_references #define __pyx_n_s_refpos __pyx_mstate_global->__pyx_n_s_refpos #define __pyx_n_s_region __pyx_mstate_global->__pyx_n_s_region #define __pyx_n_s_require_index __pyx_mstate_global->__pyx_n_s_require_index #define __pyx_n_s_res __pyx_mstate_global->__pyx_n_s_res #define __pyx_n_s_result __pyx_mstate_global->__pyx_n_s_result #define __pyx_n_s_results __pyx_mstate_global->__pyx_n_s_results #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_kp_u_s __pyx_mstate_global->__pyx_kp_u_s #define __pyx_kp_u_sam_write1_failed_with_error_cod __pyx_mstate_global->__pyx_kp_u_sam_write1_failed_with_error_cod #define __pyx_n_s_samfile __pyx_mstate_global->__pyx_n_s_samfile #define __pyx_n_u_samtools __pyx_mstate_global->__pyx_n_u_samtools #define __pyx_n_s_self __pyx_mstate_global->__pyx_n_s_self #define __pyx_kp_s_self_b_self_htsfile_self_index_c __pyx_mstate_global->__pyx_kp_s_self_b_self_htsfile_self_index_c #define __pyx_kp_s_self_b_self_htsfile_self_index_s __pyx_mstate_global->__pyx_kp_s_self_b_self_htsfile_self_index_s #define __pyx_kp_s_self_htsfile_cannot_be_converted __pyx_mstate_global->__pyx_kp_s_self_htsfile_cannot_be_converted #define __pyx_n_s_seq __pyx_mstate_global->__pyx_n_s_seq #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_snp_quality __pyx_mstate_global->__pyx_n_s_snp_quality #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_splitlines __pyx_mstate_global->__pyx_n_s_splitlines #define __pyx_n_s_sq __pyx_mstate_global->__pyx_n_s_sq #define __pyx_n_s_start __pyx_mstate_global->__pyx_n_s_start #define __pyx_n_s_start_2 __pyx_mstate_global->__pyx_n_s_start_2 #define __pyx_n_s_startswith __pyx_mstate_global->__pyx_n_s_startswith #define __pyx_n_s_state __pyx_mstate_global->__pyx_n_s_state #define __pyx_n_u_stepper __pyx_mstate_global->__pyx_n_u_stepper #define __pyx_n_s_stop __pyx_mstate_global->__pyx_n_s_stop #define __pyx_n_s_stop_2 __pyx_mstate_global->__pyx_n_s_stop_2 #define __pyx_n_s_str __pyx_mstate_global->__pyx_n_s_str #define __pyx_kp_s_stringsource __pyx_mstate_global->__pyx_kp_s_stringsource #define __pyx_n_s_strip __pyx_mstate_global->__pyx_n_s_strip #define __pyx_n_s_sum __pyx_mstate_global->__pyx_n_s_sum #define __pyx_n_s_t __pyx_mstate_global->__pyx_n_s_t #define __pyx_n_s_tell __pyx_mstate_global->__pyx_n_s_tell #define __pyx_n_s_template __pyx_mstate_global->__pyx_n_s_template #define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test #define __pyx_n_s_text __pyx_mstate_global->__pyx_n_s_text #define __pyx_n_s_threads __pyx_mstate_global->__pyx_n_s_threads #define __pyx_n_s_threshold __pyx_mstate_global->__pyx_n_s_threshold #define __pyx_n_s_tid __pyx_mstate_global->__pyx_n_s_tid #define __pyx_n_s_to_dict __pyx_mstate_global->__pyx_n_s_to_dict #define __pyx_n_u_total __pyx_mstate_global->__pyx_n_u_total #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_kp_u_truncated_file __pyx_mstate_global->__pyx_kp_u_truncated_file #define __pyx_kp_u_unable_to_open_index_file __pyx_mstate_global->__pyx_kp_u_unable_to_open_index_file #define __pyx_kp_u_unable_to_open_index_file_s __pyx_mstate_global->__pyx_kp_u_unable_to_open_index_file_s #define __pyx_kp_u_unable_to_read_header_informatio __pyx_mstate_global->__pyx_kp_u_unable_to_read_header_informatio #define __pyx_kp_u_unable_to_reopen_htsfile __pyx_mstate_global->__pyx_kp_u_unable_to_reopen_htsfile #define __pyx_kp_u_unknown_reference __pyx_mstate_global->__pyx_kp_u_unknown_reference #define __pyx_kp_u_unknown_stepper_option_s_in_Iter __pyx_mstate_global->__pyx_kp_u_unknown_stepper_option_s_in_Iter #define __pyx_n_s_unmapped __pyx_mstate_global->__pyx_n_s_unmapped #define __pyx_n_u_unmapped __pyx_mstate_global->__pyx_n_u_unmapped #define __pyx_n_s_until_eof __pyx_mstate_global->__pyx_n_s_until_eof #define __pyx_n_s_update __pyx_mstate_global->__pyx_n_s_update #define __pyx_n_s_use_setstate __pyx_mstate_global->__pyx_n_s_use_setstate #define __pyx_n_s_value __pyx_mstate_global->__pyx_n_s_value #define __pyx_n_s_values __pyx_mstate_global->__pyx_n_s_values #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_u_wb __pyx_mstate_global->__pyx_n_u_wb #define __pyx_n_u_wb0 __pyx_mstate_global->__pyx_n_u_wb0 #define __pyx_n_u_wbu __pyx_mstate_global->__pyx_n_u_wbu #define __pyx_n_u_wc __pyx_mstate_global->__pyx_n_u_wc #define __pyx_n_u_wh __pyx_mstate_global->__pyx_n_u_wh #define __pyx_n_s_write __pyx_mstate_global->__pyx_n_s_write #define __pyx_kp_u_wrong_sequence_information_in_s __pyx_mstate_global->__pyx_kp_u_wrong_sequence_information_in_s #define __pyx_n_s_x __pyx_mstate_global->__pyx_n_s_x #define __pyx_n_s_y __pyx_mstate_global->__pyx_n_s_y #define __pyx_n_s_zip __pyx_mstate_global->__pyx_n_s_zip #define __pyx_int_0 __pyx_mstate_global->__pyx_int_0 #define __pyx_int_1 __pyx_mstate_global->__pyx_int_1 #define __pyx_int_2 __pyx_mstate_global->__pyx_int_2 #define __pyx_int_7 __pyx_mstate_global->__pyx_int_7 #define __pyx_int_8 __pyx_mstate_global->__pyx_int_8 #define __pyx_int_13 __pyx_mstate_global->__pyx_int_13 #define __pyx_int_15 __pyx_mstate_global->__pyx_int_15 #define __pyx_int_1796 __pyx_mstate_global->__pyx_int_1796 #define __pyx_int_8000 __pyx_mstate_global->__pyx_int_8000 #define __pyx_int_18041500 __pyx_mstate_global->__pyx_int_18041500 #define __pyx_int_84615809 __pyx_mstate_global->__pyx_int_84615809 #define __pyx_int_239452417 __pyx_mstate_global->__pyx_int_239452417 #define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1 #define __pyx_int_neg_2 __pyx_mstate_global->__pyx_int_neg_2 #define __pyx_k__107 __pyx_mstate_global->__pyx_k__107 #define __pyx_codeobj_ __pyx_mstate_global->__pyx_codeobj_ #define __pyx_slice__9 __pyx_mstate_global->__pyx_slice__9 #define __pyx_tuple__4 __pyx_mstate_global->__pyx_tuple__4 #define __pyx_tuple__6 __pyx_mstate_global->__pyx_tuple__6 #define __pyx_tuple__10 __pyx_mstate_global->__pyx_tuple__10 #define __pyx_tuple__14 __pyx_mstate_global->__pyx_tuple__14 #define __pyx_tuple__23 __pyx_mstate_global->__pyx_tuple__23 #define __pyx_tuple__29 __pyx_mstate_global->__pyx_tuple__29 #define __pyx_tuple__30 __pyx_mstate_global->__pyx_tuple__30 #define __pyx_tuple__40 __pyx_mstate_global->__pyx_tuple__40 #define __pyx_tuple__41 __pyx_mstate_global->__pyx_tuple__41 #define __pyx_tuple__42 __pyx_mstate_global->__pyx_tuple__42 #define __pyx_tuple__44 __pyx_mstate_global->__pyx_tuple__44 #define __pyx_tuple__45 __pyx_mstate_global->__pyx_tuple__45 #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__50 __pyx_mstate_global->__pyx_tuple__50 #define __pyx_tuple__51 __pyx_mstate_global->__pyx_tuple__51 #define __pyx_tuple__52 __pyx_mstate_global->__pyx_tuple__52 #define __pyx_tuple__54 __pyx_mstate_global->__pyx_tuple__54 #define __pyx_tuple__55 __pyx_mstate_global->__pyx_tuple__55 #define __pyx_tuple__56 __pyx_mstate_global->__pyx_tuple__56 #define __pyx_tuple__59 __pyx_mstate_global->__pyx_tuple__59 #define __pyx_tuple__61 __pyx_mstate_global->__pyx_tuple__61 #define __pyx_tuple__64 __pyx_mstate_global->__pyx_tuple__64 #define __pyx_tuple__65 __pyx_mstate_global->__pyx_tuple__65 #define __pyx_tuple__73 __pyx_mstate_global->__pyx_tuple__73 #define __pyx_tuple__75 __pyx_mstate_global->__pyx_tuple__75 #define __pyx_tuple__83 __pyx_mstate_global->__pyx_tuple__83 #define __pyx_tuple__86 __pyx_mstate_global->__pyx_tuple__86 #define __pyx_tuple__87 __pyx_mstate_global->__pyx_tuple__87 #define __pyx_tuple__94 __pyx_mstate_global->__pyx_tuple__94 #define __pyx_codeobj__5 __pyx_mstate_global->__pyx_codeobj__5 #define __pyx_codeobj__7 __pyx_mstate_global->__pyx_codeobj__7 #define __pyx_codeobj__8 __pyx_mstate_global->__pyx_codeobj__8 #define __pyx_tuple__102 __pyx_mstate_global->__pyx_tuple__102 #define __pyx_tuple__108 __pyx_mstate_global->__pyx_tuple__108 #define __pyx_tuple__117 __pyx_mstate_global->__pyx_tuple__117 #define __pyx_tuple__123 __pyx_mstate_global->__pyx_tuple__123 #define __pyx_tuple__126 __pyx_mstate_global->__pyx_tuple__126 #define __pyx_tuple__127 __pyx_mstate_global->__pyx_tuple__127 #define __pyx_tuple__128 __pyx_mstate_global->__pyx_tuple__128 #define __pyx_tuple__129 __pyx_mstate_global->__pyx_tuple__129 #define __pyx_tuple__130 __pyx_mstate_global->__pyx_tuple__130 #define __pyx_tuple__131 __pyx_mstate_global->__pyx_tuple__131 #define __pyx_tuple__132 __pyx_mstate_global->__pyx_tuple__132 #define __pyx_tuple__133 __pyx_mstate_global->__pyx_tuple__133 #define __pyx_tuple__134 __pyx_mstate_global->__pyx_tuple__134 #define __pyx_tuple__135 __pyx_mstate_global->__pyx_tuple__135 #define __pyx_tuple__136 __pyx_mstate_global->__pyx_tuple__136 #define __pyx_tuple__137 __pyx_mstate_global->__pyx_tuple__137 #define __pyx_tuple__138 __pyx_mstate_global->__pyx_tuple__138 #define __pyx_tuple__139 __pyx_mstate_global->__pyx_tuple__139 #define __pyx_tuple__140 __pyx_mstate_global->__pyx_tuple__140 #define __pyx_tuple__141 __pyx_mstate_global->__pyx_tuple__141 #define __pyx_tuple__142 __pyx_mstate_global->__pyx_tuple__142 #define __pyx_tuple__143 __pyx_mstate_global->__pyx_tuple__143 #define __pyx_tuple__144 __pyx_mstate_global->__pyx_tuple__144 #define __pyx_tuple__145 __pyx_mstate_global->__pyx_tuple__145 #define __pyx_tuple__146 __pyx_mstate_global->__pyx_tuple__146 #define __pyx_tuple__147 __pyx_mstate_global->__pyx_tuple__147 #define __pyx_tuple__148 __pyx_mstate_global->__pyx_tuple__148 #define __pyx_tuple__149 __pyx_mstate_global->__pyx_tuple__149 #define __pyx_tuple__150 __pyx_mstate_global->__pyx_tuple__150 #define __pyx_tuple__151 __pyx_mstate_global->__pyx_tuple__151 #define __pyx_tuple__152 __pyx_mstate_global->__pyx_tuple__152 #define __pyx_tuple__153 __pyx_mstate_global->__pyx_tuple__153 #define __pyx_tuple__154 __pyx_mstate_global->__pyx_tuple__154 #define __pyx_tuple__155 __pyx_mstate_global->__pyx_tuple__155 #define __pyx_tuple__156 __pyx_mstate_global->__pyx_tuple__156 #define __pyx_tuple__157 __pyx_mstate_global->__pyx_tuple__157 #define __pyx_tuple__158 __pyx_mstate_global->__pyx_tuple__158 #define __pyx_tuple__159 __pyx_mstate_global->__pyx_tuple__159 #define __pyx_tuple__160 __pyx_mstate_global->__pyx_tuple__160 #define __pyx_tuple__161 __pyx_mstate_global->__pyx_tuple__161 #define __pyx_tuple__162 __pyx_mstate_global->__pyx_tuple__162 #define __pyx_tuple__163 __pyx_mstate_global->__pyx_tuple__163 #define __pyx_tuple__164 __pyx_mstate_global->__pyx_tuple__164 #define __pyx_tuple__165 __pyx_mstate_global->__pyx_tuple__165 #define __pyx_tuple__166 __pyx_mstate_global->__pyx_tuple__166 #define __pyx_tuple__167 __pyx_mstate_global->__pyx_tuple__167 #define __pyx_tuple__168 __pyx_mstate_global->__pyx_tuple__168 #define __pyx_tuple__169 __pyx_mstate_global->__pyx_tuple__169 #define __pyx_tuple__170 __pyx_mstate_global->__pyx_tuple__170 #define __pyx_tuple__171 __pyx_mstate_global->__pyx_tuple__171 #define __pyx_codeobj__11 __pyx_mstate_global->__pyx_codeobj__11 #define __pyx_codeobj__13 __pyx_mstate_global->__pyx_codeobj__13 #define __pyx_codeobj__16 __pyx_mstate_global->__pyx_codeobj__16 #define __pyx_codeobj__17 __pyx_mstate_global->__pyx_codeobj__17 #define __pyx_codeobj__18 __pyx_mstate_global->__pyx_codeobj__18 #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__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__39 __pyx_mstate_global->__pyx_codeobj__39 #define __pyx_codeobj__43 __pyx_mstate_global->__pyx_codeobj__43 #define __pyx_codeobj__53 __pyx_mstate_global->__pyx_codeobj__53 #define __pyx_codeobj__57 __pyx_mstate_global->__pyx_codeobj__57 #define __pyx_codeobj__58 __pyx_mstate_global->__pyx_codeobj__58 #define __pyx_codeobj__60 __pyx_mstate_global->__pyx_codeobj__60 #define __pyx_codeobj__62 __pyx_mstate_global->__pyx_codeobj__62 #define __pyx_codeobj__63 __pyx_mstate_global->__pyx_codeobj__63 #define __pyx_codeobj__66 __pyx_mstate_global->__pyx_codeobj__66 #define __pyx_codeobj__67 __pyx_mstate_global->__pyx_codeobj__67 #define __pyx_codeobj__68 __pyx_mstate_global->__pyx_codeobj__68 #define __pyx_codeobj__69 __pyx_mstate_global->__pyx_codeobj__69 #define __pyx_codeobj__70 __pyx_mstate_global->__pyx_codeobj__70 #define __pyx_codeobj__71 __pyx_mstate_global->__pyx_codeobj__71 #define __pyx_codeobj__72 __pyx_mstate_global->__pyx_codeobj__72 #define __pyx_codeobj__74 __pyx_mstate_global->__pyx_codeobj__74 #define __pyx_codeobj__76 __pyx_mstate_global->__pyx_codeobj__76 #define __pyx_codeobj__77 __pyx_mstate_global->__pyx_codeobj__77 #define __pyx_codeobj__78 __pyx_mstate_global->__pyx_codeobj__78 #define __pyx_codeobj__79 __pyx_mstate_global->__pyx_codeobj__79 #define __pyx_codeobj__80 __pyx_mstate_global->__pyx_codeobj__80 #define __pyx_codeobj__81 __pyx_mstate_global->__pyx_codeobj__81 #define __pyx_codeobj__82 __pyx_mstate_global->__pyx_codeobj__82 #define __pyx_codeobj__84 __pyx_mstate_global->__pyx_codeobj__84 #define __pyx_codeobj__85 __pyx_mstate_global->__pyx_codeobj__85 #define __pyx_codeobj__88 __pyx_mstate_global->__pyx_codeobj__88 #define __pyx_codeobj__89 __pyx_mstate_global->__pyx_codeobj__89 #define __pyx_codeobj__90 __pyx_mstate_global->__pyx_codeobj__90 #define __pyx_codeobj__91 __pyx_mstate_global->__pyx_codeobj__91 #define __pyx_codeobj__92 __pyx_mstate_global->__pyx_codeobj__92 #define __pyx_codeobj__93 __pyx_mstate_global->__pyx_codeobj__93 #define __pyx_codeobj__95 __pyx_mstate_global->__pyx_codeobj__95 #define __pyx_codeobj__96 __pyx_mstate_global->__pyx_codeobj__96 #define __pyx_codeobj__97 __pyx_mstate_global->__pyx_codeobj__97 #define __pyx_codeobj__98 __pyx_mstate_global->__pyx_codeobj__98 #define __pyx_codeobj__99 __pyx_mstate_global->__pyx_codeobj__99 #define __pyx_codeobj__100 __pyx_mstate_global->__pyx_codeobj__100 #define __pyx_codeobj__101 __pyx_mstate_global->__pyx_codeobj__101 #define __pyx_codeobj__103 __pyx_mstate_global->__pyx_codeobj__103 #define __pyx_codeobj__104 __pyx_mstate_global->__pyx_codeobj__104 #define __pyx_codeobj__105 __pyx_mstate_global->__pyx_codeobj__105 #define __pyx_codeobj__106 __pyx_mstate_global->__pyx_codeobj__106 #define __pyx_codeobj__109 __pyx_mstate_global->__pyx_codeobj__109 #define __pyx_codeobj__110 __pyx_mstate_global->__pyx_codeobj__110 #define __pyx_codeobj__111 __pyx_mstate_global->__pyx_codeobj__111 #define __pyx_codeobj__112 __pyx_mstate_global->__pyx_codeobj__112 #define __pyx_codeobj__113 __pyx_mstate_global->__pyx_codeobj__113 #define __pyx_codeobj__114 __pyx_mstate_global->__pyx_codeobj__114 #define __pyx_codeobj__115 __pyx_mstate_global->__pyx_codeobj__115 #define __pyx_codeobj__116 __pyx_mstate_global->__pyx_codeobj__116 #define __pyx_codeobj__118 __pyx_mstate_global->__pyx_codeobj__118 #define __pyx_codeobj__119 __pyx_mstate_global->__pyx_codeobj__119 #define __pyx_codeobj__120 __pyx_mstate_global->__pyx_codeobj__120 #define __pyx_codeobj__121 __pyx_mstate_global->__pyx_codeobj__121 #define __pyx_codeobj__122 __pyx_mstate_global->__pyx_codeobj__122 /* #### Code section: module_code ### */ /* "cpython/complex.pxd":19 * * @property * cdef inline double real(self): # <<<<<<<<<<<<<< * return self.cval.real * */ static CYTHON_INLINE double __pyx_f_7cpython_7complex_7complex_4real_real(PyComplexObject *__pyx_v_self) { double __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("real", 0); /* "cpython/complex.pxd":20 * @property * cdef inline double real(self): * 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): # <<<<<<<<<<<<<< * return self.cval.real * */ /* function exit code */ __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* 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/*proto*/ PyDoc_STRVAR(__pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_14pileup, "AlignmentFile.pileup(self, contig=None, start=None, stop=None, region=None, reference=None, end=None, **kwargs)\nperform a :term:`pileup` within a :term:`region`. The region is\n specified by :term:`contig`, `start` and `stop` (using\n 0-based indexing). :term:`reference` and `end` are also accepted for\n backward compatibility as synonyms for :term:`contig` and `stop`,\n respectively. Alternatively, a samtools 'region' string\n can be supplied.\n\n Without 'contig' or 'region' all reads will be used for the\n pileup. The reads will be returned ordered by\n :term:`contig` sequence, which will not necessarily be the\n order within the file.\n\n Note that :term:`SAM` formatted files do not allow random\n access. In these files, if a 'region' or 'contig' are\n given an exception is raised.\n\n .. note::\n\n 'all' reads which overlap the region are returned. The\n first base returned will be the first base of the first\n read 'not' necessarily the first base of the region used\n in the query.\n\n Parameters\n ----------\n\n truncate : bool\n\n By default, the samtools pileup engine outputs all reads\n overlapping a region. 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This is the default.\n\n flag_filter : int\n\n ignore reads where any of the bits in the flag are set. The default is\n BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP.\n\n flag_require : int\n\n only use reads where certain flags are set. The default is 0.\n\n ignore_orphans: bool\n\n ignore orphans (paired reads that are not in a proper pair).\n The default is to ignore orphans.\n\n min_base_quality: int\n\n Minimum base quality. Bases below the minimum quality will\n not be output. The default is 13.\n\n adjust_capq_threshold: int\n\n adjust mapping quality. The default is 0 for no\n adjustment. The recommended value for adjustment is 50.\n\n min_mapping_quality : int\n\n only use reads above a minimum mapping quality. The default is 0.\n\n compute_baq: bool\n\n re-alignment computing per-Base Alignment Qualities (BAQ). The\n default is to do re-alignment. Realignment requires a reference\n sequence. 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__pyx_methods_5pysam_17libcalignmentfile_AlignmentHeader[] = { {"_from_text_and_lengths", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_5_from_text_and_lengths, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_4_from_text_and_lengths}, {"from_text", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_7from_text, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_6from_text}, {"from_dict", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_9from_dict, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_8from_dict}, {"from_references", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_11from_references, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_10from_references}, {"copy", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_17copy, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_16copy}, {"_build_sequence_section", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_19_build_sequence_section, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_18_build_sequence_section}, {"to_dict", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_21to_dict, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_20to_dict}, {"as_dict", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_23as_dict, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_22as_dict}, {"get_reference_name", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_25get_reference_name, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_24get_reference_name}, {"get_reference_length", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_27get_reference_length, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_26get_reference_length}, {"is_valid_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_29is_valid_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_28is_valid_tid}, {"get_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_31get_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_30get_tid}, {"items", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_39items, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_38items}, {"iteritems", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_41iteritems, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_40iteritems}, {"keys", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_43keys, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_42keys}, {"values", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_45values, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_44values}, {"get", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_47get, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_46get}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_53__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_52__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_55__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15AlignmentHeader_54__setstate_cython__}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_17libcalignmentfile_AlignmentHeader[] = { {(char *)"nreferences", __pyx_getprop_5pysam_17libcalignmentfile_15AlignmentHeader_nreferences, 0, (char *)PyDoc_STR("int with the number of :term:`reference` sequences in the file.\n\n This is a read-only attribute."), 0}, {(char *)"references", __pyx_getprop_5pysam_17libcalignmentfile_15AlignmentHeader_references, 0, (char *)PyDoc_STR("tuple with the names of :term:`reference` sequences. This is a\n read-only attribute"), 0}, {(char *)"lengths", __pyx_getprop_5pysam_17libcalignmentfile_15AlignmentHeader_lengths, 0, (char *)PyDoc_STR("tuple of the lengths of the :term:`reference` sequences. This is a\n read-only attribute. The lengths are in the same order as\n :attr:`pysam.AlignmentFile.references`\n "), 0}, {0, 0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_AlignmentHeader_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_AlignmentHeader}, {Py_nb_bool, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_15__bool__}, {Py_sq_length, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_49__len__}, {Py_sq_item, (void *)__pyx_sq_item_5pysam_17libcalignmentfile_AlignmentHeader}, {Py_sq_contains, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_51__contains__}, {Py_mp_length, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_49__len__}, {Py_mp_subscript, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_37__getitem__}, {Py_mp_ass_subscript, (void *)__pyx_mp_ass_subscript_5pysam_17libcalignmentfile_AlignmentHeader}, {Py_tp_str, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_33__str__}, {Py_tp_doc, (void *)PyDoc_STR("AlignmentHeader()\nheader information for a :class:`AlignmentFile` object\n\n Parameters\n ----------\n header_dict : dict\n build header from a multi-level dictionary. The\n first level are the four types ('HD', 'SQ', ...). The second\n level are a list of lines, with each line being a list of\n tag-value pairs. The header is constructed first from all the\n defined fields, followed by user tags in alphabetical\n order. Alternatively, an :class:`~pysam.AlignmentHeader`\n object can be passed directly.\n\n text : string\n use the string provided as the header\n\n reference_names : list\n see reference_lengths\n\n reference_lengths : list\n build header from list of chromosome names and lengths. By\n default, 'SQ' and 'LN' tags will be added to the header\n text. This option can be changed by unsetting the flag\n `add_sq_text`.\n\n add_sq_text : bool\n do not add 'SQ' and 'LN' tags to header. This option permits\n construction :term:`SAM` formatted files without a header.\n\n ")}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_AlignmentHeader}, {Py_tp_getset, (void *)__pyx_getsets_5pysam_17libcalignmentfile_AlignmentHeader}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_3__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_AlignmentHeader}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_AlignmentHeader_spec = { "pysam.libcalignmentfile.AlignmentHeader", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader), 0, Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, __pyx_type_5pysam_17libcalignmentfile_AlignmentHeader_slots, }; #else static PyNumberMethods __pyx_tp_as_number_AlignmentHeader = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ __pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_15__bool__, /*nb_bool*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 || (CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x03050000) 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ 0, /*nb_index*/ #if PY_VERSION_HEX >= 0x03050000 0, /*nb_matrix_multiply*/ #endif #if PY_VERSION_HEX >= 0x03050000 0, /*nb_inplace_matrix_multiply*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_AlignmentHeader = { __pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_49__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5pysam_17libcalignmentfile_AlignmentHeader, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ __pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_51__contains__, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_AlignmentHeader = { __pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_49__len__, /*mp_length*/ __pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_37__getitem__, /*mp_subscript*/ __pyx_mp_ass_subscript_5pysam_17libcalignmentfile_AlignmentHeader, /*mp_ass_subscript*/ }; static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_AlignmentHeader = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""AlignmentHeader", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_AlignmentHeader, /*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*/ &__pyx_tp_as_number_AlignmentHeader, /*tp_as_number*/ &__pyx_tp_as_sequence_AlignmentHeader, /*tp_as_sequence*/ &__pyx_tp_as_mapping_AlignmentHeader, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5pysam_17libcalignmentfile_15AlignmentHeader_33__str__, /*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, /*tp_flags*/ PyDoc_STR("AlignmentHeader()\nheader information for a :class:`AlignmentFile` object\n\n Parameters\n ----------\n header_dict : dict\n build header from a multi-level dictionary. The\n first level are the four types ('HD', 'SQ', ...). The second\n level are a list of lines, with each line being a list of\n tag-value pairs. The header is constructed first from all the\n defined fields, followed by user tags in alphabetical\n order. Alternatively, an :class:`~pysam.AlignmentHeader`\n object can be passed directly.\n\n text : string\n use the string provided as the header\n\n reference_names : list\n see reference_lengths\n\n reference_lengths : list\n build header from list of chromosome names and lengths. By\n default, 'SQ' and 'LN' tags will be added to the header\n text. This option can be changed by unsetting the flag\n `add_sq_text`.\n\n add_sq_text : bool\n do not add 'SQ' and 'LN' tags to header. This option permits\n construction :term:`SAM` formatted files without a header.\n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_AlignmentHeader, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_17libcalignmentfile_AlignmentHeader, /*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_17libcalignmentfile_15AlignmentHeader_3__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_AlignmentHeader, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_AlignmentFile __pyx_vtable_5pysam_17libcalignmentfile_AlignmentFile; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_AlignmentFile(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *p; PyObject *o = __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_10libchtslib_HTSFile, tp_new, newfunc)(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10libchtslib_HTSFile*)__pyx_vtabptr_5pysam_17libcalignmentfile_AlignmentFile; p->reference_filename = Py_None; Py_INCREF(Py_None); p->header = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *)Py_None); Py_INCREF(Py_None); if (unlikely(__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_1__cinit__(o, a, k) < 0)) goto bad; return o; bad: Py_DECREF(o); o = 0; return NULL; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_AlignmentFile(PyObject *o) { struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *p = (struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)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_17libcalignmentfile_AlignmentFile) { 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_17libcalignmentfile_13AlignmentFile_27__dealloc__(o); __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->reference_filename); Py_CLEAR(p->header); PyObject_GC_Track(o); if (likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) __Pyx_PyType_GetSlot(__pyx_ptype_5pysam_10libchtslib_HTSFile, tp_dealloc, destructor)(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_17libcalignmentfile_AlignmentFile); } static int __pyx_tp_traverse_5pysam_17libcalignmentfile_AlignmentFile(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *p = (struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)o; e = ((likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) ? ((__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_traverse) ? __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_17libcalignmentfile_AlignmentFile)); if (e) return e; if (p->reference_filename) { e = (*v)(p->reference_filename, a); if (e) return e; } if (p->header) { e = (*v)(((PyObject *)p->header), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_17libcalignmentfile_AlignmentFile(PyObject *o) { PyObject* tmp; struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *p = (struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)o; if (likely(__pyx_ptype_5pysam_10libchtslib_HTSFile)) { if (__pyx_ptype_5pysam_10libchtslib_HTSFile->tp_clear) __pyx_ptype_5pysam_10libchtslib_HTSFile->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_17libcalignmentfile_AlignmentFile); tmp = ((PyObject*)p->reference_filename); p->reference_filename = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->header); p->header = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_mapped(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_6mapped_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_unmapped(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_8unmapped_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_nocoordinate(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_12nocoordinate_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_nreferences(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_11nreferences_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_references(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_10references_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_lengths(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_7lengths_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_text(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_4text_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_reference_filename(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_18reference_filename_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_header(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_6header_1__get__(o); } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_39__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_39__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_AlignmentFile[] = { {"has_index", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_3has_index, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_2has_index}, {"check_index", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_5check_index, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_4check_index}, {"_open", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_7_open, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_6_open}, {"fetch", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_9fetch, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_8fetch}, {"head", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_11head, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_10head}, {"mate", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_13mate, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_12mate}, {"pileup", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_15pileup, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_14pileup}, {"count", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_17count, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_16count}, {"count_coverage", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_19count_coverage, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_18count_coverage}, {"find_introns_slow", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_21find_introns_slow, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_20find_introns_slow}, {"find_introns", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_23find_introns, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_22find_introns}, {"close", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_25close, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_24close}, {"__enter__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_31__enter__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_30__enter__}, {"__exit__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_33__exit__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_32__exit__}, {"get_index_statistics", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_35get_index_statistics, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_34get_index_statistics}, {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_39__next__, METH_NOARGS|METH_COEXIST, 0}, {"is_valid_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_41is_valid_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_40is_valid_tid}, {"get_tid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_43get_tid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_42get_tid}, {"get_reference_name", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_45get_reference_name, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_44get_reference_name}, {"get_reference_length", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_47get_reference_length, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_46get_reference_length}, {"gettid", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_49gettid, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_48gettid}, {"getrname", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_51getrname, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_50getrname}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_53__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_52__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_55__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_13AlignmentFile_54__setstate_cython__}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_17libcalignmentfile_AlignmentFile[] = { {(char *)"mapped", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_mapped, 0, (char *)PyDoc_STR("int with total number of mapped alignments according to the\n statistics recorded in the index. This is a read-only\n attribute.\n (This will be 0 for a CRAM file indexed by a .crai index, as that\n index format does not record these statistics.)\n "), 0}, {(char *)"unmapped", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_unmapped, 0, (char *)PyDoc_STR("int with total number of unmapped reads according to the statistics\n recorded in the index. This number of reads includes the number of reads\n without coordinates. This is a read-only attribute.\n (This will be 0 for a CRAM file indexed by a .crai index, as that\n index format does not record these statistics.)\n "), 0}, {(char *)"nocoordinate", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_nocoordinate, 0, (char *)PyDoc_STR("int with total number of reads without coordinates according to the\n statistics recorded in the index, i.e., the statistic printed for \"*\"\n by the ``samtools idxstats`` command. This is a read-only attribute.\n (This will be 0 for a CRAM file indexed by a .crai index, as that\n index format does not record these statistics.)\n "), 0}, {(char *)"nreferences", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_nreferences, 0, (char *)PyDoc_STR("int with the number of :term:`reference` sequences in the file.\n This is a read-only attribute."), 0}, {(char *)"references", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_references, 0, (char *)PyDoc_STR("tuple with the names of :term:`reference` sequences. This is a\n read-only attribute"), 0}, {(char *)"lengths", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_lengths, 0, (char *)PyDoc_STR("tuple of the lengths of the :term:`reference` sequences. This is a\n read-only attribute. The lengths are in the same order as\n :attr:`pysam.AlignmentFile.references`\n\n "), 0}, {(char *)"text", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_text, 0, (char *)PyDoc_STR("deprecated, use :attr:`references` and :attr:`lengths` instead"), 0}, {(char *)"reference_filename", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_reference_filename, 0, (char *)0, 0}, {(char *)"header", __pyx_getprop_5pysam_17libcalignmentfile_13AlignmentFile_header, 0, (char *)0, 0}, {0, 0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_AlignmentFile_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_AlignmentFile}, {Py_tp_doc, (void *)PyDoc_STR("AlignmentFile(filepath_or_object, mode=None, template=None,\n reference_names=None, reference_lengths=None, text=NULL,\n header=None, add_sq_text=False, check_header=True, check_sq=True,\n reference_filename=None, filename=None, index_filename=None,\n filepath_index=None, require_index=False, duplicate_filehandle=True,\n ignore_truncation=False, threads=1)\n\n A :term:`SAM`/:term:`BAM`/:term:`CRAM` formatted file.\n\n If `filepath_or_object` is a string, the file is automatically\n opened. If `filepath_or_object` is a python File object, the\n already opened file will be used.\n\n If the file is opened for reading and an index exists (if file is BAM, a\n .bai file or if CRAM a .crai file), it will be opened automatically.\n `index_filename` may be specified explicitly. If the index is not named\n in the standard manner, not located in the same directory as the\n BAM/CRAM file, or is remote. Without an index, random access via\n :meth:`~pysam.AlignmentFile.fetch` and :meth:`~pysam.AlignmentFile.pileup`\n is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can\n be constituted from several sources (see also the samtools format\n specification):\n\n 1. If `template` is given, the header is copied from another\n `AlignmentFile` (`template` must be a\n :class:`~pysam.AlignmentFile`).\n\n 2. If `header` is given, the header is built from a\n multi-level dictionary.\n\n 3. If `text` is given, new header text is copied from raw\n text.\n\n 4. The names (`reference_names`) and lengths\n (`reference_lengths`) are supplied directly as lists.\n\n When reading or writing a CRAM file, the filename of a FASTA-formatted\n reference can be specified with `reference_filename`.\n\n By default, if a file is opened in mode 'r', it is checked\n for a valid header (`check_header` = True) and a definition of\n chr""omosome names (`check_sq` = True).\n\n Parameters\n ----------\n mode : string\n `mode` should be ``r`` for reading or ``w`` for writing. The\n default is text mode (:term:`SAM`). For binary (:term:`BAM`)\n I/O you should append ``b`` for compressed or ``u`` for\n uncompressed :term:`BAM` output. Use ``h`` to output header\n information in text (:term:`TAM`) mode. Use ``c`` for\n :term:`CRAM` formatted files.\n\n If ``b`` is present, it must immediately follow ``r`` or\n ``w``. Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb``,\n ``wbu``, ``wb0``, ``rc`` and ``wc``. For instance, to open a\n :term:`BAM` formatted file for reading, type::\n\n f = pysam.AlignmentFile('ex1.bam','rb')\n\n If mode is not specified, the method will try to auto-detect\n in the order 'rb', 'r', thus both the following should work::\n\n f1 = pysam.AlignmentFile('ex1.bam')\n f2 = pysam.AlignmentFile('ex1.sam')\n\n template : AlignmentFile\n when writing, copy header from file `template`.\n\n header : dict or AlignmentHeader\n when writing, build header from a multi-level dictionary. The\n first level are the four types ('HD', 'SQ', ...). The second\n level are a list of lines, with each line being a list of\n tag-value pairs. The header is constructed first from all the\n defined fields, followed by user tags in alphabetical\n order. Alternatively, an :class:`~pysam.AlignmentHeader`\n object can be passed directly.\n\n text : string\n when writing, use the string provided as the header\n\n reference_names : list\n see reference_lengths\n\n reference_lengths : list\n when writing or opening a SAM file without header build header\n from list of chromosome names and lengths. By default, 'SQ'\n and 'LN' tags will be added to the header text. This option\n ""can be changed by unsetting the flag `add_sq_text`.\n\n add_sq_text : bool\n do not add 'SQ' and 'LN' tags to header. This option permits\n construction :term:`SAM` formatted files without a header.\n\n add_sam_header : bool\n when outputting SAM the default is to output a header. This is\n equivalent to opening the file in 'wh' mode. If this option is\n set to False, no header will be output. To read such a file,\n set `check_header=False`.\n\n check_header : bool\n obsolete: when reading a SAM file, check if header is present\n (default=True)\n\n check_sq : bool\n when reading, check if SQ entries are present in header\n (default=True)\n\n reference_filename : string\n Path to a FASTA-formatted reference file. Valid only for CRAM files.\n When reading a CRAM file, this overrides both ``$REF_PATH`` and the URL\n specified in the header (``UR`` tag), which are normally used to find\n the reference.\n\n index_filename : string\n Explicit path to the index file. Only needed if the index is not\n named in the standard manner, not located in the same directory as\n the BAM/CRAM file, or is remote. An IOError is raised if the index\n cannot be found or is invalid.\n\n filepath_index : string\n Alias for `index_filename`.\n\n require_index : bool\n When reading, require that an index file is present and is valid or\n raise an IOError. (default=False)\n\n filename : string\n Alternative to filepath_or_object. Filename of the file\n to be opened.\n\n duplicate_filehandle: bool\n By default, file handles passed either directly or through\n File-like objects will be duplicated before passing them to\n htslib. The duplication prevents issues where the same stream\n will be closed by htslib and through destruction of the\n high-level python object. Set ""to False to turn off\n duplication.\n\n ignore_truncation: bool\n Issue a warning, instead of raising an error if the current file\n appears to be truncated due to a missing EOF marker. Only applies\n to bgzipped formats. (Default=False)\n\n format_options: list\n A list of key=value strings, as accepted by --input-fmt-option and\n --output-fmt-option in samtools.\n threads: integer\n Number of threads to use for compressing/decompressing BAM/CRAM files.\n Setting threads to > 1 cannot be combined with `ignore_truncation`.\n (Default=1)\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_AlignmentFile}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_AlignmentFile}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_37__iter__}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_39__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_AlignmentFile}, {Py_tp_getset, (void *)__pyx_getsets_5pysam_17libcalignmentfile_AlignmentFile}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_AlignmentFile}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_AlignmentFile_spec = { "pysam.libcalignmentfile.AlignmentFile", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile), 0, Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC|Py_TPFLAGS_HAVE_FINALIZE, __pyx_type_5pysam_17libcalignmentfile_AlignmentFile_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_AlignmentFile = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""AlignmentFile", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_AlignmentFile, /*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|Py_TPFLAGS_HAVE_FINALIZE, /*tp_flags*/ PyDoc_STR("AlignmentFile(filepath_or_object, mode=None, template=None,\n reference_names=None, reference_lengths=None, text=NULL,\n header=None, add_sq_text=False, check_header=True, check_sq=True,\n reference_filename=None, filename=None, index_filename=None,\n filepath_index=None, require_index=False, duplicate_filehandle=True,\n ignore_truncation=False, threads=1)\n\n A :term:`SAM`/:term:`BAM`/:term:`CRAM` formatted file.\n\n If `filepath_or_object` is a string, the file is automatically\n opened. If `filepath_or_object` is a python File object, the\n already opened file will be used.\n\n If the file is opened for reading and an index exists (if file is BAM, a\n .bai file or if CRAM a .crai file), it will be opened automatically.\n `index_filename` may be specified explicitly. If the index is not named\n in the standard manner, not located in the same directory as the\n BAM/CRAM file, or is remote. Without an index, random access via\n :meth:`~pysam.AlignmentFile.fetch` and :meth:`~pysam.AlignmentFile.pileup`\n is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can\n be constituted from several sources (see also the samtools format\n specification):\n\n 1. If `template` is given, the header is copied from another\n `AlignmentFile` (`template` must be a\n :class:`~pysam.AlignmentFile`).\n\n 2. If `header` is given, the header is built from a\n multi-level dictionary.\n\n 3. If `text` is given, new header text is copied from raw\n text.\n\n 4. The names (`reference_names`) and lengths\n (`reference_lengths`) are supplied directly as lists.\n\n When reading or writing a CRAM file, the filename of a FASTA-formatted\n reference can be specified with `reference_filename`.\n\n By default, if a file is opened in mode 'r', it is checked\n for a valid header (`check_header` = True) and a definition of\n chr""omosome names (`check_sq` = True).\n\n Parameters\n ----------\n mode : string\n `mode` should be ``r`` for reading or ``w`` for writing. The\n default is text mode (:term:`SAM`). For binary (:term:`BAM`)\n I/O you should append ``b`` for compressed or ``u`` for\n uncompressed :term:`BAM` output. Use ``h`` to output header\n information in text (:term:`TAM`) mode. Use ``c`` for\n :term:`CRAM` formatted files.\n\n If ``b`` is present, it must immediately follow ``r`` or\n ``w``. Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb``,\n ``wbu``, ``wb0``, ``rc`` and ``wc``. For instance, to open a\n :term:`BAM` formatted file for reading, type::\n\n f = pysam.AlignmentFile('ex1.bam','rb')\n\n If mode is not specified, the method will try to auto-detect\n in the order 'rb', 'r', thus both the following should work::\n\n f1 = pysam.AlignmentFile('ex1.bam')\n f2 = pysam.AlignmentFile('ex1.sam')\n\n template : AlignmentFile\n when writing, copy header from file `template`.\n\n header : dict or AlignmentHeader\n when writing, build header from a multi-level dictionary. The\n first level are the four types ('HD', 'SQ', ...). The second\n level are a list of lines, with each line being a list of\n tag-value pairs. The header is constructed first from all the\n defined fields, followed by user tags in alphabetical\n order. Alternatively, an :class:`~pysam.AlignmentHeader`\n object can be passed directly.\n\n text : string\n when writing, use the string provided as the header\n\n reference_names : list\n see reference_lengths\n\n reference_lengths : list\n when writing or opening a SAM file without header build header\n from list of chromosome names and lengths. By default, 'SQ'\n and 'LN' tags will be added to the header text. This option\n ""can be changed by unsetting the flag `add_sq_text`.\n\n add_sq_text : bool\n do not add 'SQ' and 'LN' tags to header. This option permits\n construction :term:`SAM` formatted files without a header.\n\n add_sam_header : bool\n when outputting SAM the default is to output a header. This is\n equivalent to opening the file in 'wh' mode. If this option is\n set to False, no header will be output. To read such a file,\n set `check_header=False`.\n\n check_header : bool\n obsolete: when reading a SAM file, check if header is present\n (default=True)\n\n check_sq : bool\n when reading, check if SQ entries are present in header\n (default=True)\n\n reference_filename : string\n Path to a FASTA-formatted reference file. Valid only for CRAM files.\n When reading a CRAM file, this overrides both ``$REF_PATH`` and the URL\n specified in the header (``UR`` tag), which are normally used to find\n the reference.\n\n index_filename : string\n Explicit path to the index file. Only needed if the index is not\n named in the standard manner, not located in the same directory as\n the BAM/CRAM file, or is remote. An IOError is raised if the index\n cannot be found or is invalid.\n\n filepath_index : string\n Alias for `index_filename`.\n\n require_index : bool\n When reading, require that an index file is present and is valid or\n raise an IOError. (default=False)\n\n filename : string\n Alternative to filepath_or_object. Filename of the file\n to be opened.\n\n duplicate_filehandle: bool\n By default, file handles passed either directly or through\n File-like objects will be duplicated before passing them to\n htslib. The duplication prevents issues where the same stream\n will be closed by htslib and through destruction of the\n high-level python object. Set ""to False to turn off\n duplication.\n\n ignore_truncation: bool\n Issue a warning, instead of raising an error if the current file\n appears to be truncated due to a missing EOF marker. Only applies\n to bgzipped formats. (Default=False)\n\n format_options: list\n A list of key=value strings, as accepted by --input-fmt-option and\n --output-fmt-option in samtools.\n threads: integer\n Number of threads to use for compressing/decompressing BAM/CRAM files.\n Setting threads to > 1 cannot be combined with `ignore_truncation`.\n (Default=1)\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_AlignmentFile, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_AlignmentFile, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_37__iter__, /*tp_iter*/ __pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_39__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_AlignmentFile, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_17libcalignmentfile_AlignmentFile, /*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_17libcalignmentfile_AlignmentFile, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *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_17libcalignmentfile_IteratorRow *)o); p->samfile = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)Py_None); Py_INCREF(Py_None); p->header = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow(PyObject *o) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *)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_17libcalignmentfile_IteratorRow) { 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_17libcalignmentfile_11IteratorRow_3__dealloc__(o); __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->samfile); Py_CLEAR(p->header); #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_17libcalignmentfile_IteratorRow(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *)o; if (p->samfile) { e = (*v)(((PyObject *)p->samfile), a); if (e) return e; } if (p->header) { e = (*v)(((PyObject *)p->header), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow(PyObject *o) { PyObject* tmp; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow *)o; tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->header); p->header = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorRow[] = { {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_11IteratorRow_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_11IteratorRow_4__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_11IteratorRow_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_11IteratorRow_6__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorRow_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_doc, (void *)PyDoc_STR("IteratorRow(AlignmentFile samfile, int multiple_iterators=False)\nabstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n\n The method :meth:`AlignmentFile.fetch` returns an IteratorRow.\n\n .. note::\n\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_11IteratorRow_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorRow_spec = { "pysam.libcalignmentfile.IteratorRow", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow), 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_17libcalignmentfile_IteratorRow_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorRow = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorRow", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRow), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow, /*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("IteratorRow(AlignmentFile samfile, int multiple_iterators=False)\nabstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n\n The method :meth:`AlignmentFile.fetch` returns an IteratorRow.\n\n .. note::\n\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorRow, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_11IteratorRow_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowRegion __pyx_vtable_5pysam_17libcalignmentfile_IteratorRowRegion; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_17libcalignmentfile_IteratorRowRegion; return o; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowRegion(PyObject *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_17libcalignmentfile_IteratorRowRegion) { 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_17libcalignmentfile_17IteratorRowRegion_7__dealloc__(o); __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } PyObject_GC_Track(o); __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow(o); } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_5__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_5__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorRowRegion[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_17IteratorRowRegion_8__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_17IteratorRowRegion_10__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorRowRegion_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowRegion}, {Py_tp_doc, (void *)PyDoc_STR("IteratorRowRegion(AlignmentFile samfile, int tid, int beg, int stop, int multiple_iterators=False)\n*(AlignmentFile samfile, int tid, int beg, int stop,\n int multiple_iterators=False)*\n\n iterate over mapped reads in a region.\n\n .. note::\n\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_3__iter__}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_5__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorRowRegion}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowRegion}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorRowRegion_spec = { "pysam.libcalignmentfile.IteratorRowRegion", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion), 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_17libcalignmentfile_IteratorRowRegion_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorRowRegion = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorRowRegion", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowRegion, /*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("IteratorRowRegion(AlignmentFile samfile, int tid, int beg, int stop, int multiple_iterators=False)\n*(AlignmentFile samfile, int tid, int beg, int stop,\n int multiple_iterators=False)*\n\n iterate over mapped reads in a region.\n\n .. note::\n\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_17libcalignmentfile_17IteratorRowRegion_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorRowRegion, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_17IteratorRowRegion_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowRegion, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowHead __pyx_vtable_5pysam_17libcalignmentfile_IteratorRowHead; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowHead(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_17libcalignmentfile_IteratorRowHead; return o; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_5__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_5__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorRowHead[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_5__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_7__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15IteratorRowHead_6__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_9__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_15IteratorRowHead_8__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorRowHead_slots[] = { {Py_tp_doc, (void *)PyDoc_STR("IteratorRowHead(AlignmentFile samfile, int n, int multiple_iterators=False)\n*(AlignmentFile samfile, n, int multiple_iterators=False)*\n\n iterate over first n reads in `samfile`\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.head`.\n\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_3__iter__}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_5__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorRowHead}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowHead}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorRowHead_spec = { "pysam.libcalignmentfile.IteratorRowHead", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead), 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_17libcalignmentfile_IteratorRowHead_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorRowHead = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorRowHead", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowHead), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow, /*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("IteratorRowHead(AlignmentFile samfile, int n, int multiple_iterators=False)\n*(AlignmentFile samfile, n, int multiple_iterators=False)*\n\n iterate over first n reads in `samfile`\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.head`.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_17libcalignmentfile_15IteratorRowHead_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorRowHead, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_15IteratorRowHead_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowHead, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowAll __pyx_vtable_5pysam_17libcalignmentfile_IteratorRowAll; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_17libcalignmentfile_IteratorRowAll; return o; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_5__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_5__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorRowAll[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_7__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorRowAll_6__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_9__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorRowAll_8__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorRowAll_slots[] = { {Py_tp_doc, (void *)PyDoc_STR("IteratorRowAll(AlignmentFile samfile, int multiple_iterators=False)\n*(AlignmentFile samfile, int multiple_iterators=False)*\n\n iterate over all reads in `samfile`\n\n .. note::\n\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_3__iter__}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_5__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorRowAll}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAll}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorRowAll_spec = { "pysam.libcalignmentfile.IteratorRowAll", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll), 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_17libcalignmentfile_IteratorRowAll_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorRowAll = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorRowAll", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAll), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow, /*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("IteratorRowAll(AlignmentFile samfile, int multiple_iterators=False)\n*(AlignmentFile samfile, int multiple_iterators=False)*\n\n iterate over all reads in `samfile`\n\n .. note::\n\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_17libcalignmentfile_14IteratorRowAll_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorRowAll, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_14IteratorRowAll_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAll, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *)o); p->rowiter = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowAllRefs(PyObject *o) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *)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_17libcalignmentfile_IteratorRowAllRefs) { if (PyObject_CallFinalizerFromDealloc(o)) return; } } #endif PyObject_GC_UnTrack(o); Py_CLEAR(p->rowiter); PyObject_GC_Track(o); __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow(o); } static int __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *)o; e = __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow(o, v, a); if (e) return e; if (p->rowiter) { e = (*v)(((PyObject *)p->rowiter), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRowAllRefs(PyObject *o) { PyObject* tmp; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *)o; __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow(o); tmp = ((PyObject*)p->rowiter); p->rowiter = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_7__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorRowAllRefs[] = { {"nextiter", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_3nextiter, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_18IteratorRowAllRefs_2nextiter}, {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_18IteratorRowAllRefs_8__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_18IteratorRowAllRefs_10__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorRowAllRefs_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowAllRefs}, {Py_tp_doc, (void *)PyDoc_STR("IteratorRowAllRefs(AlignmentFile samfile, multiple_iterators=False)\niterates over all mapped reads by chaining iterators over each\n reference\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRowAllRefs}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRowAllRefs}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_5__iter__}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_7__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorRowAllRefs}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAllRefs}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorRowAllRefs_spec = { "pysam.libcalignmentfile.IteratorRowAllRefs", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs), 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_17libcalignmentfile_IteratorRowAllRefs_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorRowAllRefs = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorRowAllRefs", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowAllRefs, /*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("IteratorRowAllRefs(AlignmentFile samfile, multiple_iterators=False)\niterates over all mapped reads by chaining iterators over each\n reference\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a\n :meth:`AlignmentFile.fetch`.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRowAllRefs, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRowAllRefs, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_5__iter__, /*tp_iter*/ __pyx_pw_5pysam_17libcalignmentfile_18IteratorRowAllRefs_7__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorRowAllRefs, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_18IteratorRowAllRefs_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowAllRefs, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorRowSelection __pyx_vtable_5pysam_17libcalignmentfile_IteratorRowSelection; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRow(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_17libcalignmentfile_IteratorRowSelection; p->positions = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowSelection(PyObject *o) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *)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_17libcalignmentfile_IteratorRowSelection) { if (PyObject_CallFinalizerFromDealloc(o)) return; } } #endif PyObject_GC_UnTrack(o); Py_CLEAR(p->positions); PyObject_GC_Track(o); __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRow(o); } static int __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRowSelection(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *)o; e = __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRow(o, v, a); if (e) return e; if (p->positions) { e = (*v)(p->positions, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRowSelection(PyObject *o) { PyObject* tmp; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection *)o; __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRow(o); tmp = ((PyObject*)p->positions); p->positions = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_5__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_5__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorRowSelection[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_7__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_20IteratorRowSelection_6__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_9__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_20IteratorRowSelection_8__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorRowSelection_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowSelection}, {Py_tp_doc, (void *)PyDoc_STR("IteratorRowSelection(AlignmentFile samfile, positions, int multiple_iterators=True)\n*(AlignmentFile samfile)*\n\n iterate over reads in `samfile` at a given list of file positions.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRowSelection}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRowSelection}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_3__iter__}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_5__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorRowSelection}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowSelection}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorRowSelection_spec = { "pysam.libcalignmentfile.IteratorRowSelection", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection), 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_17libcalignmentfile_IteratorRowSelection_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorRowSelection = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorRowSelection", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowSelection), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorRowSelection, /*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("IteratorRowSelection(AlignmentFile samfile, positions, int multiple_iterators=True)\n*(AlignmentFile samfile)*\n\n iterate over reads in `samfile` at a given list of file positions.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorRowSelection, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorRowSelection, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_17libcalignmentfile_20IteratorRowSelection_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorRowSelection, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_20IteratorRowSelection_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IteratorRowSelection, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumn __pyx_vtable_5pysam_17libcalignmentfile_IteratorColumn; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *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_17libcalignmentfile_IteratorColumn *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_17libcalignmentfile_IteratorColumn; p->iter = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); p->samfile = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)Py_None); Py_INCREF(Py_None); p->fastafile = ((struct __pyx_obj_5pysam_9libcfaidx_FastaFile *)Py_None); Py_INCREF(Py_None); p->stepper = Py_None; Py_INCREF(Py_None); if (unlikely(__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_1__cinit__(o, a, k) < 0)) goto bad; return o; bad: Py_DECREF(o); o = 0; return NULL; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorColumn(PyObject *o) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *)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_17libcalignmentfile_IteratorColumn) { 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_17libcalignmentfile_14IteratorColumn_9__dealloc__(o); __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->iter); Py_CLEAR(p->samfile); Py_CLEAR(p->fastafile); Py_CLEAR(p->stepper); #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_17libcalignmentfile_IteratorColumn(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *)o; if (p->iter) { e = (*v)(((PyObject *)p->iter), a); if (e) return e; } if (p->samfile) { e = (*v)(((PyObject *)p->samfile), a); if (e) return e; } if (p->fastafile) { e = (*v)(((PyObject *)p->fastafile), a); if (e) return e; } if (p->stepper) { e = (*v)(p->stepper, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn(PyObject *o) { PyObject* tmp; struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *)o; tmp = ((PyObject*)p->iter); p->iter = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->fastafile); p->fastafile = ((struct __pyx_obj_5pysam_9libcfaidx_FastaFile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->stepper); p->stepper = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_14IteratorColumn_seq_len(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_7seq_len_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorColumn[] = { {"add_reference", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_5add_reference, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorColumn_4add_reference}, {"has_reference", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_7has_reference, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorColumn_6has_reference}, {"hasReference", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_11hasReference, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorColumn_10hasReference}, {"addReference", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_13addReference, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorColumn_12addReference}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_15__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorColumn_14__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_17__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_14IteratorColumn_16__setstate_cython__}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_17libcalignmentfile_IteratorColumn[] = { {(char *)"seq_len", __pyx_getprop_5pysam_17libcalignmentfile_14IteratorColumn_seq_len, 0, (char *)PyDoc_STR("current sequence length."), 0}, {0, 0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorColumn_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_doc, (void *)PyDoc_STR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behaviour. For example,\n consider the conversion to a list::\n\n f = AlignmentFile(\"file.bam\", \"rb\")\n result = list(f.pileup())\n\n Here, ``result`` will contain ``n`` objects of type\n :class:`~pysam.PileupColumn` for ``n`` columns, but each object in\n ``result`` will contain the same information.\n\n The desired behaviour can be achieved by list comprehension::\n\n result = [x.pileups() for x in f.pileup()]\n\n ``result`` will be a list of ``n`` lists of objects of type\n :class:`~pysam.PileupRead`.\n\n If the iterator is associated with a :class:`~pysam.Fastafile`\n using the :meth:`add_reference` method, then the iterator will\n export the current sequence via the methods :meth:`get_sequence`\n and :meth:`seq_len`.\n\n See :class:`~AlignmentFile.pileup` for kwargs to the iterator.\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_iter, (void *)__pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_3__iter__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_getset, (void *)__pyx_getsets_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumn}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorColumn_spec = { "pysam.libcalignmentfile.IteratorColumn", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn), 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_17libcalignmentfile_IteratorColumn_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorColumn = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorColumn", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorColumn, /*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("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behaviour. For example,\n consider the conversion to a list::\n\n f = AlignmentFile(\"file.bam\", \"rb\")\n result = list(f.pileup())\n\n Here, ``result`` will contain ``n`` objects of type\n :class:`~pysam.PileupColumn` for ``n`` columns, but each object in\n ``result`` will contain the same information.\n\n The desired behaviour can be achieved by list comprehension::\n\n result = [x.pileups() for x in f.pileup()]\n\n ``result`` will be a list of ``n`` lists of objects of type\n :class:`~pysam.PileupRead`.\n\n If the iterator is associated with a :class:`~pysam.Fastafile`\n using the :meth:`add_reference` method, then the iterator will\n export the current sequence via the methods :meth:`get_sequence`\n and :meth:`seq_len`.\n\n See :class:`~AlignmentFile.pileup` for kwargs to the iterator.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_3__iter__, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorColumn, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_17libcalignmentfile_IteratorColumn, /*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_17libcalignmentfile_IteratorColumn, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumnRegion __pyx_vtable_5pysam_17libcalignmentfile_IteratorColumnRegion; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumn(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumn*)__pyx_vtabptr_5pysam_17libcalignmentfile_IteratorColumnRegion; if (unlikely(__pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_1__cinit__(o, a, k) < 0)) goto bad; return o; bad: Py_DECREF(o); o = 0; return NULL; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_3__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorColumnRegion[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_20IteratorColumnRegion_4__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_20IteratorColumnRegion_6__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorColumnRegion_slots[] = { {Py_tp_doc, (void *)PyDoc_STR("iterates over a region only.\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_3__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorColumnRegion}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnRegion}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorColumnRegion_spec = { "pysam.libcalignmentfile.IteratorColumnRegion", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion), 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_17libcalignmentfile_IteratorColumnRegion_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorColumnRegion = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorColumnRegion", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnRegion), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorColumn, /*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("iterates over a region only.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ #if CYTHON_COMPILING_IN_PYPY || 0 __pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_3__iter__, /*tp_iter*/ #else 0, /*tp_iter*/ #endif __pyx_pw_5pysam_17libcalignmentfile_20IteratorColumnRegion_3__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorColumnRegion, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_IteratorColumnRegion, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumnAllRefs __pyx_vtable_5pysam_17libcalignmentfile_IteratorColumnAllRefs; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumn(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumn*)__pyx_vtabptr_5pysam_17libcalignmentfile_IteratorColumnAllRefs; if (unlikely(__pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0)) goto bad; return o; bad: Py_DECREF(o); o = 0; return NULL; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_3__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorColumnAllRefs[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_4__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_6__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAllRefs_slots[] = { {Py_tp_doc, (void *)PyDoc_STR("iterates over all columns by chaining iterators over each reference\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_3__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorColumnAllRefs}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnAllRefs}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAllRefs_spec = { "pysam.libcalignmentfile.IteratorColumnAllRefs", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs), 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_17libcalignmentfile_IteratorColumnAllRefs_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAllRefs = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorColumnAllRefs", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorColumn, /*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("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ #if CYTHON_COMPILING_IN_PYPY || 0 __pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_3__iter__, /*tp_iter*/ #else 0, /*tp_iter*/ #endif __pyx_pw_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorColumnAllRefs, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_IteratorColumnAllRefs, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumnAll __pyx_vtable_5pysam_17libcalignmentfile_IteratorColumnAll; static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnAll(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll *p; PyObject *o = __pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumn(t, a, k); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_17libcalignmentfile_IteratorColumn*)__pyx_vtabptr_5pysam_17libcalignmentfile_IteratorColumnAll; if (unlikely(__pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_1__cinit__(o, a, k) < 0)) goto bad; return o; bad: Py_DECREF(o); o = 0; return NULL; } static PyObject *__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_3__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) { PyObject *res = __pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_3__next__(self); if (!res && !PyErr_Occurred()) { PyErr_SetNone(PyExc_StopIteration); } return res; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IteratorColumnAll[] = { {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_3__next__, METH_NOARGS|METH_COEXIST, 0}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_5__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_17IteratorColumnAll_4__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_7__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_17IteratorColumnAll_6__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAll_slots[] = { {Py_tp_doc, (void *)PyDoc_STR("iterates over all columns, without using an index\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn}, {Py_tp_iternext, (void *)__pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_3__next__}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IteratorColumnAll}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnAll}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAll_spec = { "pysam.libcalignmentfile.IteratorColumnAll", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll), 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_17libcalignmentfile_IteratorColumnAll_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IteratorColumnAll = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IteratorColumnAll", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAll), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IteratorColumn, /*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("iterates over all columns, without using an index\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ #if CYTHON_COMPILING_IN_PYPY || 0 __pyx_pw_5pysam_17libcalignmentfile_14IteratorColumn_3__iter__, /*tp_iter*/ #else 0, /*tp_iter*/ #endif __pyx_pw_5pysam_17libcalignmentfile_17IteratorColumnAll_3__next__, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IteratorColumnAll, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_IteratorColumnAll, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IndexedReads(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *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_17libcalignmentfile_IndexedReads *)o); p->samfile = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)Py_None); Py_INCREF(Py_None); p->index = Py_None; Py_INCREF(Py_None); p->header = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_IndexedReads(PyObject *o) { struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *)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_17libcalignmentfile_IndexedReads) { 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_17libcalignmentfile_12IndexedReads_7__dealloc__(o); __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->samfile); Py_CLEAR(p->index); Py_CLEAR(p->header); #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_17libcalignmentfile_IndexedReads(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *)o; if (p->samfile) { e = (*v)(((PyObject *)p->samfile), a); if (e) return e; } if (p->index) { e = (*v)(p->index, a); if (e) return e; } if (p->header) { e = (*v)(((PyObject *)p->header), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_17libcalignmentfile_IndexedReads(PyObject *o) { PyObject* tmp; struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *p = (struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads *)o; tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentFile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->index); p->index = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->header); p->header = ((struct __pyx_obj_5pysam_17libcalignmentfile_AlignmentHeader *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_IndexedReads[] = { {"build", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_3build, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_12IndexedReads_2build}, {"find", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_5find, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_12IndexedReads_4find}, {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_9__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_12IndexedReads_8__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_11__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_12IndexedReads_10__setstate_cython__}, {0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_IndexedReads_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_IndexedReads}, {Py_tp_doc, (void *)PyDoc_STR("IndexedReads(AlignmentFile samfile, int multiple_iterators=True)\nIndex a Sam/BAM-file by query name while keeping the\n original sort order intact.\n\n The index is kept in memory and can be substantial.\n\n By default, the file is re-opened to avoid conflicts if multiple\n operators work on the same file. Set `multiple_iterators` = False\n to not re-open `samfile`.\n\n Parameters\n ----------\n\n samfile : AlignmentFile\n File to be indexed.\n\n multiple_iterators : bool\n Flag indicating whether the file should be reopened. Reopening prevents\n existing iterators being affected by the indexing.\n\n ")}, {Py_tp_traverse, (void *)__pyx_tp_traverse_5pysam_17libcalignmentfile_IndexedReads}, {Py_tp_clear, (void *)__pyx_tp_clear_5pysam_17libcalignmentfile_IndexedReads}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_IndexedReads}, {Py_tp_init, (void *)__pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_1__init__}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_IndexedReads}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_IndexedReads_spec = { "pysam.libcalignmentfile.IndexedReads", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads), 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_17libcalignmentfile_IndexedReads_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_IndexedReads = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""IndexedReads", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_IndexedReads), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_IndexedReads, /*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("IndexedReads(AlignmentFile samfile, int multiple_iterators=True)\nIndex a Sam/BAM-file by query name while keeping the\n original sort order intact.\n\n The index is kept in memory and can be substantial.\n\n By default, the file is re-opened to avoid conflicts if multiple\n operators work on the same file. Set `multiple_iterators` = False\n to not re-open `samfile`.\n\n Parameters\n ----------\n\n samfile : AlignmentFile\n File to be indexed.\n\n multiple_iterators : bool\n Flag indicating whether the file should be reopened. Reopening prevents\n existing iterators being affected by the indexing.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_17libcalignmentfile_IndexedReads, /*tp_traverse*/ __pyx_tp_clear_5pysam_17libcalignmentfile_IndexedReads, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_IndexedReads, /*tp_methods*/ 0, /*tp_members*/ 0, /*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_17libcalignmentfile_12IndexedReads_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_17libcalignmentfile_IndexedReads, /*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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 0, /*tp_pypy_flags*/ #endif }; #endif static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_SNPCall(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { 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 return o; } static void __pyx_tp_dealloc_5pysam_17libcalignmentfile_SNPCall(PyObject *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)) && (!PyType_IS_GC(Py_TYPE(o)) || !__Pyx_PyObject_GC_IsFinalized(o))) { if (__Pyx_PyObject_GetSlot(o, tp_dealloc, destructor) == __pyx_tp_dealloc_5pysam_17libcalignmentfile_SNPCall) { if (PyObject_CallFinalizerFromDealloc(o)) return; } } #endif #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 PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_tid(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_3tid_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_pos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_3pos_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_reference_base(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_14reference_base_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_genotype(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_8genotype_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_consensus_quality(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_17consensus_quality_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_snp_quality(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_11snp_quality_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_mapping_quality(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_15mapping_quality_1__get__(o); } static PyObject *__pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_coverage(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_8coverage_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_17libcalignmentfile_SNPCall[] = { {"__reduce_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_7SNPCall_3__reduce_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_7SNPCall_2__reduce_cython__}, {"__setstate_cython__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_5pysam_17libcalignmentfile_7SNPCall_5__setstate_cython__, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_5pysam_17libcalignmentfile_7SNPCall_4__setstate_cython__}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_17libcalignmentfile_SNPCall[] = { {(char *)"tid", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_tid, 0, (char *)PyDoc_STR("the chromosome ID as is defined in the header"), 0}, {(char *)"pos", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_pos, 0, (char *)PyDoc_STR("nucleotide position of SNP."), 0}, {(char *)"reference_base", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_reference_base, 0, (char *)PyDoc_STR("reference base at pos. ``N`` if no reference sequence supplied."), 0}, {(char *)"genotype", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_genotype, 0, (char *)PyDoc_STR("the genotype called."), 0}, {(char *)"consensus_quality", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_consensus_quality, 0, (char *)PyDoc_STR("the genotype quality (Phred-scaled)."), 0}, {(char *)"snp_quality", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_snp_quality, 0, (char *)PyDoc_STR("the snp quality (Phred scaled) - probability of consensus being\n identical to reference sequence."), 0}, {(char *)"mapping_quality", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_mapping_quality, 0, (char *)PyDoc_STR("the root mean square (rms) of the mapping quality of all reads\n involved in the call."), 0}, {(char *)"coverage", __pyx_getprop_5pysam_17libcalignmentfile_7SNPCall_coverage, 0, (char *)PyDoc_STR("coverage or read depth - the number of reads involved in the call."), 0}, {0, 0, 0, 0, 0} }; #if CYTHON_USE_TYPE_SPECS static PyType_Slot __pyx_type_5pysam_17libcalignmentfile_SNPCall_slots[] = { {Py_tp_dealloc, (void *)__pyx_tp_dealloc_5pysam_17libcalignmentfile_SNPCall}, {Py_tp_str, (void *)__pyx_pw_5pysam_17libcalignmentfile_7SNPCall_1__str__}, {Py_tp_doc, (void *)PyDoc_STR("the results of a SNP call.")}, {Py_tp_methods, (void *)__pyx_methods_5pysam_17libcalignmentfile_SNPCall}, {Py_tp_getset, (void *)__pyx_getsets_5pysam_17libcalignmentfile_SNPCall}, {Py_tp_new, (void *)__pyx_tp_new_5pysam_17libcalignmentfile_SNPCall}, {0, 0}, }; static PyType_Spec __pyx_type_5pysam_17libcalignmentfile_SNPCall_spec = { "pysam.libcalignmentfile.SNPCall", sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall), 0, Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, __pyx_type_5pysam_17libcalignmentfile_SNPCall_slots, }; #else static PyTypeObject __pyx_type_5pysam_17libcalignmentfile_SNPCall = { PyVarObject_HEAD_INIT(0, 0) "pysam.libcalignmentfile.""SNPCall", /*tp_name*/ sizeof(struct __pyx_obj_5pysam_17libcalignmentfile_SNPCall), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_17libcalignmentfile_SNPCall, /*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*/ __pyx_pw_5pysam_17libcalignmentfile_7SNPCall_1__str__, /*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, /*tp_flags*/ PyDoc_STR("the results of a SNP call."), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_17libcalignmentfile_SNPCall, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_17libcalignmentfile_SNPCall, /*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_17libcalignmentfile_SNPCall, /*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 || 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if (unlikely(!__pyx_codeobj__84)) __PYX_ERR(3, 1, __pyx_L1_error) /* "(tree fragment)":3 * def __reduce_cython__(self): * raise TypeError, "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling" * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< * raise TypeError, "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling" */ __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__146, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) __PYX_ERR(3, 3, __pyx_L1_error) /* "(tree fragment)":1 * def __reduce_cython__(self): # <<<<<<<<<<<<<< * raise TypeError, "self.b,self.htsfile,self.index,self.iter cannot be converted to a Python object for pickling" * def __setstate_cython__(self, __pyx_state): */ __pyx_codeobj__88 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__140, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__88)) __PYX_ERR(3, 1, __pyx_L1_error) /* "(tree fragment)":3 * def __reduce_cython__(self): * raise TypeError, "self.b,self.htsfile,self.index,self.iter cannot be converted to a Python object for pickling" * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< * raise TypeError, "self.b,self.htsfile,self.index,self.iter cannot be converted to a Python object for pickling" */ __pyx_codeobj__89 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__146, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__89)) __PYX_ERR(3, 3, __pyx_L1_error) /* "(tree fragment)":1 * def __reduce_cython__(self): # <<<<<<<<<<<<<< * raise TypeError, "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling" * def __setstate_cython__(self, __pyx_state): */ __pyx_codeobj__90 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__140, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); 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The file * # will not be re-opened. */ __pyx_codeobj__95 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__140, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcalignmentfile_pyx, __pyx_n_s_nextiter, 2237, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__95)) __PYX_ERR(0, 2237, __pyx_L1_error) /* "(tree fragment)":1 * def __reduce_cython__(self): # <<<<<<<<<<<<<< * raise TypeError, "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling" * def __setstate_cython__(self, __pyx_state): */ __pyx_codeobj__96 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__140, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_reduce_cython, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__96)) __PYX_ERR(3, 1, __pyx_L1_error) /* "(tree fragment)":3 * def __reduce_cython__(self): * raise TypeError, "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling" * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< * raise TypeError, "self.b,self.htsfile,self.index cannot be converted to a Python object for pickling" */ __pyx_codeobj__97 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__146, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_setstate_cython, 3, __pyx_empty_bytes); 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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 */ static void __Pyx_PyObject_GetAttrStr_ClearAttributeError(void) { __Pyx_PyThreadState_declare __Pyx_PyThreadState_assign if (likely(__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) __Pyx_PyErr_Clear(); } static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name) { PyObject *result; #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; } /* 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; // error return kwvalues[i]; } } return NULL; // not found (no exception set) } #endif /* 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); } /* 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); // transfer ownership of value to values 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; // ownership transferred to values #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; // ownership transferred to values #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; } /* 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 /* 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 (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) { return NULL; } 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 (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) return NULL; 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 = PyCFunction_GET_FUNCTION(func); self = PyCFunction_GET_SELF(func); if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) return NULL; 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 */ 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; } 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 defined(__Pyx_CyFunction_USED) && defined(NDEBUG) if (__Pyx_IsCyOrPyCFunction(func)) #else if (PyCFunction_Check(func)) #endif { if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { return __Pyx_PyObject_CallMethO(func, NULL); } } } else if (nargs == 1 && kwargs == NULL) { if (PyCFunction_Check(func)) { if (likely(PyCFunction_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 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, kwargs); } #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, kwargs); } #endif if (nargs == 0) { return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs); } return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs); } /* PyObjectFormatAndDecref */ static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f) { if (unlikely(!s)) return NULL; if (likely(PyUnicode_CheckExact(s))) return s; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(s))) { PyObject *result = PyUnicode_FromEncodedObject(s, NULL, "strict"); Py_DECREF(s); return result; } #endif return __Pyx_PyObject_FormatAndDecref(s, f); } static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatAndDecref(PyObject* s, PyObject* f) { PyObject *result = PyObject_Format(s, f); Py_DECREF(s); return result; } /* 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 || PySequence_Check(o)) { return PySequence_GetItem(o, i); } #endif return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } /* 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); } /* 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) { 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 /* 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 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); } /* 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 /* PyIntCompare */ static CYTHON_INLINE int __Pyx_PyInt_BoolEqObjC(PyObject *op1, PyObject *op2, long intval, long inplace) { CYTHON_MAYBE_UNUSED_VAR(intval); CYTHON_UNUSED_VAR(inplace); if (op1 == op2) { return 1; } #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(op1))) { const long b = intval; long a = PyInt_AS_LONG(op1); return (a == b); } #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) { return (__Pyx_PyLong_IsZero(op1) == 1); } else if (intval < 0) { if (__Pyx_PyLong_IsNonNeg(op1)) return 0; intval = -intval; } else { if (__Pyx_PyLong_IsNeg(op1)) return 0; } 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)); return (unequal == 0); } #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 return ((double)a == (double)b); } return __Pyx_PyObject_IsTrueAndDecref( PyObject_RichCompare(op1, op2, Py_EQ)); } /* 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; } /* PyObjectCallNoArg */ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { PyObject *arg = NULL; return __Pyx_PyObject_FastCall(func, (&arg)+1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); } /* SliceObject */ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, int wraparound) { __Pyx_TypeName obj_type_name; #if CYTHON_USE_TYPE_SLOTS PyMappingMethods* mp; #if PY_MAJOR_VERSION < 3 PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; if (likely(ms && ms->sq_slice)) { if (!has_cstart) { if (_py_start && (*_py_start != Py_None)) { cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; } else cstart = 0; } if (!has_cstop) { if (_py_stop && (*_py_stop != Py_None)) { cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; } else cstop = PY_SSIZE_T_MAX; } if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { Py_ssize_t l = ms->sq_length(obj); if (likely(l >= 0)) { if (cstop < 0) { cstop += l; if (cstop < 0) cstop = 0; } if (cstart < 0) { cstart += l; if (cstart < 0) cstart = 0; } } else { if (!PyErr_ExceptionMatches(PyExc_OverflowError)) goto bad; PyErr_Clear(); } } return ms->sq_slice(obj, cstart, cstop); } #else CYTHON_UNUSED_VAR(wraparound); #endif mp = Py_TYPE(obj)->tp_as_mapping; if (likely(mp && mp->mp_subscript)) #else CYTHON_UNUSED_VAR(wraparound); #endif { PyObject* result; PyObject *py_slice, *py_start, *py_stop; if (_py_slice) { py_slice = *_py_slice; } else { PyObject* owned_start = NULL; PyObject* owned_stop = NULL; if (_py_start) { py_start = *_py_start; } else { if (has_cstart) { owned_start = py_start = PyInt_FromSsize_t(cstart); if (unlikely(!py_start)) goto bad; } else py_start = Py_None; } if (_py_stop) { py_stop = *_py_stop; } else { if (has_cstop) { owned_stop = py_stop = PyInt_FromSsize_t(cstop); if (unlikely(!py_stop)) { Py_XDECREF(owned_start); goto bad; } } else py_stop = Py_None; } py_slice = PySlice_New(py_start, py_stop, Py_None); Py_XDECREF(owned_start); Py_XDECREF(owned_stop); if (unlikely(!py_slice)) goto bad; } #if CYTHON_USE_TYPE_SLOTS result = mp->mp_subscript(obj, py_slice); #else result = PyObject_GetItem(obj, py_slice); #endif if (!_py_slice) { Py_DECREF(py_slice); } return result; } obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); PyErr_Format(PyExc_TypeError, "'" __Pyx_FMT_TYPENAME "' object is unsliceable", obj_type_name); __Pyx_DECREF_TypeName(obj_type_name); bad: return NULL; } /* DictGetItem */ #if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) { if (unlikely(PyTuple_Check(key))) { PyObject* args = PyTuple_Pack(1, key); if (likely(args)) { PyErr_SetObject(PyExc_KeyError, args); Py_DECREF(args); } } else { PyErr_SetObject(PyExc_KeyError, key); } } return NULL; } Py_INCREF(value); return value; } #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 /* 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; } /* 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) { __Pyx_PyThreadState_declare __Pyx_PyThreadState_assign PyObject* 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(); } /* UnicodeConcatInPlace */ # if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 static int __Pyx_unicode_modifiable(PyObject *unicode) { if (Py_REFCNT(unicode) != 1) return 0; if (!PyUnicode_CheckExact(unicode)) return 0; if (PyUnicode_CHECK_INTERNED(unicode)) return 0; return 1; } static CYTHON_INLINE PyObject *__Pyx_PyUnicode_ConcatInPlaceImpl(PyObject **p_left, PyObject *right #if CYTHON_REFNANNY , void* __pyx_refnanny #endif ) { PyObject *left = *p_left; Py_ssize_t left_len, right_len, new_len; if (unlikely(__Pyx_PyUnicode_READY(left) == -1)) return NULL; if (unlikely(__Pyx_PyUnicode_READY(right) == -1)) return NULL; left_len = PyUnicode_GET_LENGTH(left); if (left_len == 0) { Py_INCREF(right); return right; } right_len = PyUnicode_GET_LENGTH(right); if (right_len == 0) { Py_INCREF(left); return left; } if (unlikely(left_len > PY_SSIZE_T_MAX - right_len)) { PyErr_SetString(PyExc_OverflowError, "strings are too large to concat"); return NULL; } new_len = left_len + right_len; if (__Pyx_unicode_modifiable(left) && PyUnicode_CheckExact(right) && PyUnicode_KIND(right) <= PyUnicode_KIND(left) && !(PyUnicode_IS_ASCII(left) && !PyUnicode_IS_ASCII(right))) { __Pyx_GIVEREF(*p_left); if (unlikely(PyUnicode_Resize(p_left, new_len) != 0)) { __Pyx_GOTREF(*p_left); return NULL; } __Pyx_INCREF(*p_left); #if PY_VERSION_HEX >= 0x030D0000 if (unlikely(PyUnicode_CopyCharacters(*p_left, left_len, right, 0, right_len) < 0)) return NULL; #else _PyUnicode_FastCopyCharacters(*p_left, left_len, right, 0, right_len); #endif return *p_left; } else { return __Pyx_PyUnicode_Concat(left, right); } } #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(1); } #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 } /* 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); } /* 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 */ static PyObject* __Pyx__PyObject_CallMethod1(PyObject* method, PyObject* arg) { PyObject *result = __Pyx_PyObject_CallOneArg(method, arg); Py_DECREF(method); return result; } static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { 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); } /* append */ static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1; } else { PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x); if (unlikely(!retval)) return -1; Py_DECREF(retval); } return 0; } /* PyIntBinop */ #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_AddObjC(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_add(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 __Pyx_NewRef(op2); } 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_add(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("add", return NULL) result = ((double)a) + (double)b; PyFPE_END_PROTECT(result) return PyFloat_FromDouble(result); } return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); } #endif /* 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; } /* GetAttr */ static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { #if CYTHON_USE_TYPE_SLOTS #if PY_MAJOR_VERSION >= 3 if (likely(PyUnicode_Check(n))) #else if (likely(PyString_Check(n))) #endif return __Pyx_PyObject_GetAttrStr(o, n); #endif return PyObject_GetAttr(o, n); } /* HasAttr */ static CYTHON_INLINE int __Pyx_HasAttr(PyObject *o, PyObject *n) { PyObject *r; if (unlikely(!__Pyx_PyBaseString_Check(n))) { PyErr_SetString(PyExc_TypeError, "hasattr(): attribute name must be string"); return -1; } r = __Pyx_GetAttr(o, n); if (!r) { PyErr_Clear(); return 0; } else { Py_DECREF(r); return 1; } } /* ExtTypeTest */ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { __Pyx_TypeName obj_type_name; __Pyx_TypeName type_name; if (unlikely(!type)) { PyErr_SetString(PyExc_SystemError, "Missing type object"); return 0; } if (likely(__Pyx_TypeCheck(obj, type))) return 1; obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); type_name = __Pyx_PyType_GetName(type); PyErr_Format(PyExc_TypeError, "Cannot convert " __Pyx_FMT_TYPENAME " to " __Pyx_FMT_TYPENAME, obj_type_name, type_name); __Pyx_DECREF_TypeName(obj_type_name); __Pyx_DECREF_TypeName(type_name); return 0; } /* PyIntCompare */ static CYTHON_INLINE int __Pyx_PyInt_BoolNeObjC(PyObject *op1, PyObject *op2, long intval, long inplace) { CYTHON_MAYBE_UNUSED_VAR(intval); CYTHON_UNUSED_VAR(inplace); if (op1 == op2) { return 0; } #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(op1))) { const long b = intval; long a = PyInt_AS_LONG(op1); return (a != b); } #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) { return (__Pyx_PyLong_IsZero(op1) != 1); } else if (intval < 0) { if (__Pyx_PyLong_IsNonNeg(op1)) return 1; intval = -intval; } else { if (__Pyx_PyLong_IsNeg(op1)) return 1; } 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)); return (unequal != 0); } #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 return ((double)a != (double)b); } return __Pyx_PyObject_IsTrueAndDecref( PyObject_RichCompare(op1, op2, Py_NE)); } /* 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; } /* RaiseNoneIterError */ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } /* UnpackTupleError */ static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { if (t == Py_None) { __Pyx_RaiseNoneNotIterableError(); } else if (PyTuple_GET_SIZE(t) < index) { __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); } else { __Pyx_RaiseTooManyValuesError(index); } } /* UnpackTuple2 */ static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int decref_tuple) { PyObject *value1 = NULL, *value2 = NULL; #if CYTHON_COMPILING_IN_PYPY value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad; value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad; #else value1 = PyTuple_GET_ITEM(tuple, 0); Py_INCREF(value1); value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value2); #endif if (decref_tuple) { Py_DECREF(tuple); } *pvalue1 = value1; *pvalue2 = value2; return 0; #if CYTHON_COMPILING_IN_PYPY bad: Py_XDECREF(value1); Py_XDECREF(value2); if (decref_tuple) { Py_XDECREF(tuple); } return -1; #endif } static int __Pyx_unpack_tuple2_generic(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int has_known_size, int decref_tuple) { Py_ssize_t index; PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; iternextfunc iternext; iter = PyObject_GetIter(tuple); if (unlikely(!iter)) goto bad; if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } iternext = __Pyx_PyObject_GetIterNextFunc(iter); value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; Py_DECREF(iter); *pvalue1 = value1; *pvalue2 = value2; return 0; unpacking_failed: if (!has_known_size && __Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); bad: Py_XDECREF(iter); Py_XDECREF(value1); Py_XDECREF(value2); if (decref_tuple) { Py_XDECREF(tuple); } return -1; } /* dict_iter */ static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_source_is_dict) { is_dict = is_dict || likely(PyDict_CheckExact(iterable)); *p_source_is_dict = is_dict; if (is_dict) { #if !CYTHON_COMPILING_IN_PYPY *p_orig_length = PyDict_Size(iterable); Py_INCREF(iterable); return iterable; #elif PY_MAJOR_VERSION >= 3 static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL; PyObject **pp = NULL; if (method_name) { const char *name = PyUnicode_AsUTF8(method_name); if (strcmp(name, "iteritems") == 0) pp = &py_items; else if (strcmp(name, "iterkeys") == 0) pp = &py_keys; else if (strcmp(name, "itervalues") == 0) pp = &py_values; if (pp) { if (!*pp) { *pp = PyUnicode_FromString(name + 4); if (!*pp) return NULL; } method_name = *pp; } } #endif } *p_orig_length = 0; if (method_name) { PyObject* iter; iterable = __Pyx_PyObject_CallMethod0(iterable, method_name); if (!iterable) return NULL; #if !CYTHON_COMPILING_IN_PYPY if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) return iterable; #endif iter = PyObject_GetIter(iterable); Py_DECREF(iterable); return iter; } return PyObject_GetIter(iterable); } static CYTHON_INLINE int __Pyx_dict_iter_next( PyObject* iter_obj, CYTHON_NCP_UNUSED Py_ssize_t orig_length, CYTHON_NCP_UNUSED Py_ssize_t* ppos, PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { PyObject* next_item; #if !CYTHON_COMPILING_IN_PYPY if (source_is_dict) { PyObject *key, *value; if (unlikely(orig_length != PyDict_Size(iter_obj))) { PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); return -1; } if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { return 0; } if (pitem) { PyObject* tuple = PyTuple_New(2); if (unlikely(!tuple)) { return -1; } Py_INCREF(key); Py_INCREF(value); PyTuple_SET_ITEM(tuple, 0, key); PyTuple_SET_ITEM(tuple, 1, value); *pitem = tuple; } else { if (pkey) { Py_INCREF(key); *pkey = key; } if (pvalue) { Py_INCREF(value); *pvalue = value; } } return 1; } else if (PyTuple_CheckExact(iter_obj)) { Py_ssize_t pos = *ppos; if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; *ppos = pos + 1; next_item = PyTuple_GET_ITEM(iter_obj, pos); Py_INCREF(next_item); } else if (PyList_CheckExact(iter_obj)) { Py_ssize_t pos = *ppos; if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; *ppos = pos + 1; next_item = PyList_GET_ITEM(iter_obj, pos); Py_INCREF(next_item); } else #endif { next_item = PyIter_Next(iter_obj); if (unlikely(!next_item)) { return __Pyx_IterFinish(); } } if (pitem) { *pitem = next_item; } else if (pkey && pvalue) { if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1)) return -1; } else if (pkey) { *pkey = next_item; } else { *pvalue = next_item; } return 1; } /* MergeKeywords */ static int __Pyx_MergeKeywords(PyObject *kwdict, PyObject *source_mapping) { PyObject *iter, *key = NULL, *value = NULL; int source_is_dict, result; Py_ssize_t orig_length, ppos = 0; iter = __Pyx_dict_iterator(source_mapping, 0, __pyx_n_s_items, &orig_length, &source_is_dict); if (unlikely(!iter)) { PyObject *args; if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError))) goto bad; PyErr_Clear(); args = PyTuple_Pack(1, source_mapping); if (likely(args)) { PyObject *fallback = PyObject_Call((PyObject*)&PyDict_Type, args, NULL); Py_DECREF(args); if (likely(fallback)) { iter = __Pyx_dict_iterator(fallback, 1, __pyx_n_s_items, &orig_length, &source_is_dict); Py_DECREF(fallback); } } if (unlikely(!iter)) goto bad; } while (1) { result = __Pyx_dict_iter_next(iter, orig_length, &ppos, &key, &value, NULL, source_is_dict); if (unlikely(result < 0)) goto bad; if (!result) break; if (unlikely(PyDict_Contains(kwdict, key))) { __Pyx_RaiseDoubleKeywordsError("function", key); result = -1; } else { result = PyDict_SetItem(kwdict, key, value); } Py_DECREF(key); Py_DECREF(value); if (unlikely(result < 0)) goto bad; } Py_XDECREF(iter); return 0; bad: Py_XDECREF(iter); return -1; } /* PyIntBinop */ #if !CYTHON_COMPILING_IN_PYPY static PyObject* __Pyx_PyInt_AndObjC(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 a = PyInt_AS_LONG(op1); return PyInt_FromLong(a & b); } #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 ((intval & PyLong_MASK) == intval) { long last_digit = (long) __Pyx_PyLong_Digits(op1)[0]; long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1)); return PyLong_FromLong(result); } if (unlikely(__Pyx_PyLong_IsZero(op1))) { return __Pyx_NewRef(op1); } 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_and(op1, op2); } } x = a & b; return PyLong_FromLong(x); #ifdef HAVE_LONG_LONG long_long: llx = lla & llb; return PyLong_FromLongLong(llx); #endif } #endif return (inplace ? PyNumber_InPlaceAnd : PyNumber_And)(op1, op2); } #endif /* RaiseUnexpectedTypeError */ static int __Pyx_RaiseUnexpectedTypeError(const char *expected, PyObject *obj) { __Pyx_TypeName obj_type_name = __Pyx_PyType_GetName(Py_TYPE(obj)); PyErr_Format(PyExc_TypeError, "Expected %s, got " __Pyx_FMT_TYPENAME, expected, obj_type_name); __Pyx_DECREF_TypeName(obj_type_name); return 0; } /* GetItemIntUnicode */ static CYTHON_INLINE Py_UCS4 __Pyx_GetItemInt_Unicode_Fast(PyObject* ustring, Py_ssize_t i, int wraparound, int boundscheck) { Py_ssize_t length; if (unlikely(__Pyx_PyUnicode_READY(ustring) < 0)) return (Py_UCS4)-1; if (wraparound | boundscheck) { length = __Pyx_PyUnicode_GET_LENGTH(ustring); if (wraparound & unlikely(i < 0)) i += length; if ((!boundscheck) || likely(__Pyx_is_valid_index(i, length))) { return __Pyx_PyUnicode_READ_CHAR(ustring, i); } else { PyErr_SetString(PyExc_IndexError, "string index out of range"); return (Py_UCS4)-1; } } else { return __Pyx_PyUnicode_READ_CHAR(ustring, i); } } /* RaiseUnboundLocalError */ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } /* pyfrozenset_new */ static CYTHON_INLINE PyObject* __Pyx_PyFrozenSet_New(PyObject* it) { if (it) { PyObject* result; #if CYTHON_COMPILING_IN_PYPY PyObject* args; args = PyTuple_Pack(1, it); if (unlikely(!args)) return NULL; result = PyObject_Call((PyObject*)&PyFrozenSet_Type, args, NULL); Py_DECREF(args); return result; #else if (PyFrozenSet_CheckExact(it)) { Py_INCREF(it); return it; } result = PyFrozenSet_New(it); if (unlikely(!result)) return NULL; if ((PY_VERSION_HEX >= 0x031000A1) || likely(PySet_GET_SIZE(result))) return result; Py_DECREF(result); #endif } #if CYTHON_USE_TYPE_SLOTS return PyFrozenSet_Type.tp_new(&PyFrozenSet_Type, __pyx_empty_tuple, NULL); #else return PyObject_Call((PyObject*)&PyFrozenSet_Type, __pyx_empty_tuple, NULL); #endif } /* PySetContains */ static int __Pyx_PySet_ContainsUnhashable(PyObject *set, PyObject *key) { int result = -1; if (PySet_Check(key) && PyErr_ExceptionMatches(PyExc_TypeError)) { PyObject *tmpkey; PyErr_Clear(); tmpkey = __Pyx_PyFrozenSet_New(key); if (tmpkey != NULL) { result = PySet_Contains(set, tmpkey); Py_DECREF(tmpkey); } } return result; } static CYTHON_INLINE int __Pyx_PySet_ContainsTF(PyObject* key, PyObject* set, int eq) { int result = PySet_Contains(set, key); if (unlikely(result < 0)) { result = __Pyx_PySet_ContainsUnhashable(set, key); } return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } /* UnpackUnboundCMethod */ static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) { PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args)); if (unlikely(!selfless_args)) return NULL; PyObject *result = PyObject_Call(method, selfless_args, kwargs); Py_DECREF(selfless_args); return result; } static PyMethodDef __Pyx_UnboundCMethod_Def = { "CythonUnboundCMethod", __PYX_REINTERPRET_FUNCION(PyCFunction, __Pyx_SelflessCall), METH_VARARGS | METH_KEYWORDS, NULL }; static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) { PyObject *method; method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name); if (unlikely(!method)) return -1; target->method = method; #if CYTHON_COMPILING_IN_CPYTHON #if PY_MAJOR_VERSION >= 3 if (likely(__Pyx_TypeCheck(method, &PyMethodDescr_Type))) #else if (likely(!PyCFunction_Check(method))) #endif { PyMethodDescrObject *descr = (PyMethodDescrObject*) method; target->func = descr->d_method->ml_meth; target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_STACKLESS); } else #endif #if defined(CYTHON_COMPILING_IN_PYPY) #elif PY_VERSION_HEX >= 0x03090000 if (PyCFunction_CheckExact(method)) #else if (PyCFunction_Check(method)) #endif { PyObject *self; int self_found; #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY self = PyObject_GetAttrString(method, "__self__"); if (!self) { PyErr_Clear(); } #else self = PyCFunction_GET_SELF(method); #endif self_found = (self && self != Py_None); #if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY Py_XDECREF(self); #endif if (self_found) { PyObject *unbound_method = PyCFunction_New(&__Pyx_UnboundCMethod_Def, method); if (unlikely(!unbound_method)) return -1; Py_DECREF(method); target->method = unbound_method; } } return 0; } /* CallUnboundCMethod1 */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg) { if (likely(cfunc->func)) { int flag = cfunc->flag; if (flag == METH_O) { return (*(cfunc->func))(self, arg); } else if ((PY_VERSION_HEX >= 0x030600B1) && flag == METH_FASTCALL) { #if PY_VERSION_HEX >= 0x030700A0 return (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)cfunc->func)(self, &arg, 1); #else return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); #endif } else if ((PY_VERSION_HEX >= 0x030700A0) && flag == (METH_FASTCALL | METH_KEYWORDS)) { return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); } } return __Pyx__CallUnboundCMethod1(cfunc, self, arg); } #endif static PyObject* __Pyx__CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg){ PyObject *args, *result = NULL; if (unlikely(!cfunc->func && !cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; #if CYTHON_COMPILING_IN_CPYTHON if (cfunc->func && (cfunc->flag & METH_VARARGS)) { args = PyTuple_New(1); if (unlikely(!args)) goto bad; Py_INCREF(arg); PyTuple_SET_ITEM(args, 0, arg); if (cfunc->flag & METH_KEYWORDS) result = (*(PyCFunctionWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, NULL); else result = (*cfunc->func)(self, args); } else { args = PyTuple_New(2); if (unlikely(!args)) goto bad; Py_INCREF(self); PyTuple_SET_ITEM(args, 0, self); Py_INCREF(arg); PyTuple_SET_ITEM(args, 1, arg); result = __Pyx_PyObject_Call(cfunc->method, args, NULL); } #else args = PyTuple_Pack(2, self, arg); if (unlikely(!args)) goto bad; result = __Pyx_PyObject_Call(cfunc->method, args, NULL); #endif bad: Py_XDECREF(args); return result; } /* CallUnboundCMethod2 */ #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030600B1 static CYTHON_INLINE PyObject *__Pyx_CallUnboundCMethod2(__Pyx_CachedCFunction *cfunc, PyObject *self, PyObject *arg1, PyObject *arg2) { if (likely(cfunc->func)) { PyObject *args[2] = {arg1, arg2}; if (cfunc->flag == METH_FASTCALL) { #if PY_VERSION_HEX >= 0x030700A0 return (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)cfunc->func)(self, args, 2); #else return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, 2, NULL); #endif } #if PY_VERSION_HEX >= 0x030700A0 if (cfunc->flag == (METH_FASTCALL | METH_KEYWORDS)) return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, 2, NULL); #endif } return __Pyx__CallUnboundCMethod2(cfunc, self, arg1, arg2); } #endif static PyObject* __Pyx__CallUnboundCMethod2(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg1, PyObject* arg2){ PyObject *args, *result = NULL; if (unlikely(!cfunc->func && !cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; #if CYTHON_COMPILING_IN_CPYTHON if (cfunc->func && (cfunc->flag & METH_VARARGS)) { args = PyTuple_New(2); if (unlikely(!args)) goto bad; Py_INCREF(arg1); PyTuple_SET_ITEM(args, 0, arg1); Py_INCREF(arg2); PyTuple_SET_ITEM(args, 1, arg2); if (cfunc->flag & METH_KEYWORDS) result = (*(PyCFunctionWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, NULL); else result = (*cfunc->func)(self, args); } else { args = PyTuple_New(3); if (unlikely(!args)) goto bad; Py_INCREF(self); PyTuple_SET_ITEM(args, 0, self); Py_INCREF(arg1); PyTuple_SET_ITEM(args, 1, arg1); Py_INCREF(arg2); PyTuple_SET_ITEM(args, 2, arg2); result = __Pyx_PyObject_Call(cfunc->method, args, NULL); } #else args = PyTuple_Pack(3, self, arg1, arg2); if (unlikely(!args)) goto bad; result = __Pyx_PyObject_Call(cfunc->method, args, NULL); #endif bad: Py_XDECREF(args); return result; } /* dict_getitem_default */ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObject* default_value) { PyObject* value; #if PY_MAJOR_VERSION >= 3 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07020000) value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (unlikely(PyErr_Occurred())) return NULL; value = default_value; } Py_INCREF(value); if ((1)); #else if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) { value = PyDict_GetItem(d, key); if (unlikely(!value)) { value = default_value; } Py_INCREF(value); } #endif else { if (default_value == Py_None) value = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PyDict_Type_get, d, key); else value = __Pyx_CallUnboundCMethod2(&__pyx_umethod_PyDict_Type_get, d, key, default_value); } return value; } /* GetAttr3 */ static PyObject *__Pyx_GetAttr3Default(PyObject *d) { __Pyx_PyThreadState_declare __Pyx_PyThreadState_assign if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) return NULL; __Pyx_PyErr_Clear(); Py_INCREF(d); return d; } static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { PyObject *r; #if CYTHON_USE_TYPE_SLOTS if (likely(PyString_Check(n))) { r = __Pyx_PyObject_GetAttrStrNoError(o, n); if (unlikely(!r) && likely(!PyErr_Occurred())) { r = __Pyx_NewRef(d); } return r; } #endif r = PyObject_GetAttr(o, n); return (likely(r)) ? r : __Pyx_GetAttr3Default(d); } /* 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 ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { 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; } /* 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__124); 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; } /* CallNextTpDealloc */ static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) { PyTypeObject* type = Py_TYPE(obj); destructor tp_dealloc = NULL; while (type && __Pyx_PyType_GetSlot(type, tp_dealloc, destructor) != current_tp_dealloc) type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); while (type && (tp_dealloc = __Pyx_PyType_GetSlot(type, tp_dealloc, destructor)) == current_tp_dealloc) type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); if (type) tp_dealloc(obj); } /* CallNextTpTraverse */ static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { PyTypeObject* type = Py_TYPE(obj); traverseproc tp_traverse = NULL; while (type && __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc) != current_tp_traverse) type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); while (type && (tp_traverse = __Pyx_PyType_GetSlot(type, tp_traverse, traverseproc)) == current_tp_traverse) type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); if (type && tp_traverse) return tp_traverse(obj, v, a); return 0; } /* CallNextTpClear */ static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { PyTypeObject* type = Py_TYPE(obj); inquiry tp_clear = NULL; while (type && __Pyx_PyType_GetSlot(type, tp_clear, inquiry) != current_tp_clear) type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); while (type && (tp_clear = __Pyx_PyType_GetSlot(type, tp_clear, inquiry)) == current_tp_clear) type = __Pyx_PyType_GetSlot(type, tp_base, PyTypeObject*); if (type && tp_clear) tp_clear(obj); } /* 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 /* 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 !CYTHON_USE_TYPE_SLOTS if (dictoffset == 0) { PyErr_Format(PyExc_TypeError, "extension type '%s.200s': " "unable to validate whether bases have a __dict__ " "when CYTHON_USE_TYPE_SLOTS is off " "(likely because you are building in the limited API). " "Therefore, all extension types with multiple bases " "must add 'cdef dict __dict__' in this compilation mode", type_name); #if CYTHON_AVOID_BORROWED_REFS Py_DECREF(b0); #endif return -1; } #else if (dictoffset == 0 && b->tp_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_AVOID_BORROWED_REFS Py_DECREF(b0); #endif return -1; } #endif #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 /* 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_2 #define __PYX_HAVE_RT_ImportType_3_0_2 static PyTypeObject *__Pyx_ImportType_3_0_2(PyObject *module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_0_2 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_2 && ((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_2 && (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 /* 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; } /* 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; } /* 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 /* 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__125; 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); } /* FetchSharedCythonModule */ static PyObject *__Pyx_FetchSharedCythonABIModule(void) { PyObject *abi_module = PyImport_AddModule((char*) __PYX_ABI_MODULE_NAME); if (unlikely(!abi_module)) return NULL; Py_INCREF(abi_module); return abi_module; } /* 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 */ 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("", op->func_qualname, (void *)op); #else return PyString_FromFormat("", 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 ((_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 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; } /* ClassMethod */ static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { #if CYTHON_COMPILING_IN_PYPY && PYPY_VERSION_NUM <= 0x05080000 if (PyObject_TypeCheck(method, &PyWrapperDescr_Type)) { return PyClassMethod_New(method); } #else #if CYTHON_COMPILING_IN_PYPY if (PyMethodDescr_Check(method)) #else #if PY_MAJOR_VERSION == 2 static PyTypeObject *methoddescr_type = NULL; if (unlikely(methoddescr_type == NULL)) { PyObject *meth = PyObject_GetAttrString((PyObject*)&PyList_Type, "append"); if (unlikely(!meth)) return NULL; methoddescr_type = Py_TYPE(meth); Py_DECREF(meth); } #else PyTypeObject *methoddescr_type = &PyMethodDescr_Type; #endif if (__Pyx_TypeCheck(method, methoddescr_type)) #endif { PyMethodDescrObject *descr = (PyMethodDescrObject *)method; #if PY_VERSION_HEX < 0x03020000 PyTypeObject *d_type = descr->d_type; #else PyTypeObject *d_type = descr->d_common.d_type; #endif return PyDescr_NewClassMethod(d_type, descr->d_method); } #endif else if (PyMethod_Check(method)) { return PyClassMethod_New(PyMethod_GET_FUNCTION(method)); } else { return PyClassMethod_New(method); } } /* GetNameInClass */ static PyObject *__Pyx__GetNameInClass(PyObject *nmspace, PyObject *name) { PyObject *result; PyObject *dict; assert(PyType_Check(nmspace)); #if CYTHON_USE_TYPE_SLOTS dict = ((PyTypeObject*)nmspace)->tp_dict; Py_XINCREF(dict); #else dict = PyObject_GetAttr(nmspace, __pyx_n_s_dict); #endif if (likely(dict)) { result = PyObject_GetItem(dict, name); Py_DECREF(dict); if (result) { return result; } } PyErr_Clear(); __Pyx_GetModuleGlobalNameUncached(result, name); 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; } #if __PYX_LIMITED_VERSION_HEX < 0x030780000 PyErr_Clear(); { 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", "", 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; } #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); // XDECREF since it's only set on Py3 if cline 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;\ } /* 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 } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; #if !CYTHON_COMPILING_IN_LIMITED_API return _PyLong_FromByteArray(bytes, sizeof(int), little, !is_unsigned); #else PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyInt_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; kwds = PyDict_New(); if (!kwds) goto limited_bad; if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(!is_unsigned ? Py_True : Py_False))) goto limited_bad; result = PyObject_Call(from_bytes, arg_tuple, kwds); limited_bad: Py_XDECREF(from_bytes); Py_XDECREF(py_bytes); Py_XDECREF(order_str); Py_XDECREF(arg_tuple); Py_XDECREF(kwds); return result; #endif } } /* 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; } } else #endif if (likely(PyLong_Check(x))) { 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; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (int) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (int) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (int) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (int) -1; } else { stepval = __Pyx_NewRef(v); } 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; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((int) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } 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 CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif 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 Py_DECREF(v); if (likely(!ret)) return val; } return (int) -1; } } else { int val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); if (!tmp) return (int) -1; val = __Pyx_PyInt_As_int(tmp); Py_DECREF(tmp); 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_char(char value) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic push #pragma GCC diagnostic ignored "-Wconversion" #endif const char neg_one = (char) -1, const_zero = (char) 0; #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic pop #endif const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(char) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(char) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); #ifdef HAVE_LONG_LONG } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); #endif } } else { if (sizeof(char) <= sizeof(long)) { return PyInt_FromLong((long) value); #ifdef HAVE_LONG_LONG } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { return PyLong_FromLongLong((PY_LONG_LONG) value); #endif } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; #if !CYTHON_COMPILING_IN_LIMITED_API return _PyLong_FromByteArray(bytes, sizeof(char), little, !is_unsigned); #else PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyInt_Type, "from_bytes"); if (!from_bytes) return NULL; py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(char)); 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; kwds = PyDict_New(); if (!kwds) goto limited_bad; if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(!is_unsigned ? Py_True : Py_False))) goto limited_bad; result = PyObject_Call(from_bytes, arg_tuple, kwds); limited_bad: Py_XDECREF(from_bytes); Py_XDECREF(py_bytes); Py_XDECREF(order_str); Py_XDECREF(arg_tuple); Py_XDECREF(kwds); return result; #endif } } /* CIntFromPy */ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic push #pragma GCC diagnostic ignored "-Wconversion" #endif const char neg_one = (char) -1, const_zero = (char) 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(char) < sizeof(long))) { __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } return (char) val; } } else #endif if (likely(PyLong_Check(x))) { 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(char, __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(char) > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) >= 2 * PyLong_SHIFT)) { return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } } break; case 3: if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) >= 3 * PyLong_SHIFT)) { return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } } break; case 4: if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) >= 4 * PyLong_SHIFT)) { return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)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 (char) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif if ((sizeof(char) <= sizeof(unsigned long))) { __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG } else if ((sizeof(char) <= sizeof(unsigned PY_LONG_LONG))) { __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS if (__Pyx_PyLong_IsCompact(x)) { __PYX_VERIFY_RETURN_INT(char, __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(char) - 1 > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case 2: if ((8 * sizeof(char) > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case -3: if ((8 * sizeof(char) - 1 > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case 3: if ((8 * sizeof(char) > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case -4: if ((8 * sizeof(char) - 1 > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) { return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case 4: if ((8 * sizeof(char) > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(char) - 1 > 4 * PyLong_SHIFT)) { return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; } } #endif if ((sizeof(char) <= sizeof(long))) { __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG } else if ((sizeof(char) <= sizeof(PY_LONG_LONG))) { __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } { char val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (char) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (char) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (char) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (char) -1; } else { stepval = __Pyx_NewRef(v); } val = (char) 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(char) * 8 - chunk_size; bits += chunk_size) { PyObject *tmp, *digit; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((char) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } idigit = PyLong_AsLong(stepval); if (unlikely(idigit < 0)) goto done; remaining_bits = ((int) sizeof(char) * 8) - bits - (is_unsigned ? 0 : 1); if (unlikely(idigit >= (1L << remaining_bits))) goto raise_overflow; val |= ((char) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif if (!is_unsigned) { if (unlikely(val & (((char) 1) << (sizeof(char) * 8 - 1)))) goto raise_overflow; if (is_negative) val = ~val; } ret = 0; done: Py_XDECREF(shift); Py_XDECREF(mask); Py_XDECREF(stepval); #endif Py_DECREF(v); if (likely(!ret)) return val; } return (char) -1; } } else { char val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); if (!tmp) return (char) -1; val = __Pyx_PyInt_As_char(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, "value too large to convert to char"); return (char) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, "can't convert negative value to char"); return (char) -1; } /* 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; } } else #endif if (likely(PyLong_Check(x))) { 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; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (long) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (long) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (long) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (long) -1; } else { stepval = __Pyx_NewRef(v); } 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; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((long) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } 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 CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif 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 Py_DECREF(v); if (likely(!ret)) return val; } return (long) -1; } } else { long val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); if (!tmp) return (long) -1; val = __Pyx_PyInt_As_long(tmp); Py_DECREF(tmp); 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; } /* 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 } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; #if !CYTHON_COMPILING_IN_LIMITED_API return _PyLong_FromByteArray(bytes, sizeof(long), little, !is_unsigned); #else PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyInt_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; kwds = PyDict_New(); if (!kwds) goto limited_bad; if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(!is_unsigned ? Py_True : Py_False))) goto limited_bad; result = PyObject_Call(from_bytes, arg_tuple, kwds); limited_bad: Py_XDECREF(from_bytes); Py_XDECREF(py_bytes); Py_XDECREF(order_str); Py_XDECREF(arg_tuple); Py_XDECREF(kwds); return result; #endif } } /* CIntFromPy */ static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *x) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic push #pragma GCC diagnostic ignored "-Wconversion" #endif const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_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(uint32_t) < sizeof(long))) { __PYX_VERIFY_RETURN_INT(uint32_t, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } return (uint32_t) val; } } else #endif if (likely(PyLong_Check(x))) { 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(uint32_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(uint32_t) > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(uint32_t) >= 2 * PyLong_SHIFT)) { return (uint32_t) (((((uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])); } } break; case 3: if ((8 * sizeof(uint32_t) > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(uint32_t) >= 3 * PyLong_SHIFT)) { return (uint32_t) (((((((uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0])); } } break; case 4: if ((8 * sizeof(uint32_t) > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_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(uint32_t) >= 4 * PyLong_SHIFT)) { return (uint32_t) (((((((((uint32_t)digits[3]) << PyLong_SHIFT) | (uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_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 (uint32_t) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif if ((sizeof(uint32_t) <= sizeof(unsigned long))) { __PYX_VERIFY_RETURN_INT_EXC(uint32_t, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG } else if ((sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG))) { __PYX_VERIFY_RETURN_INT_EXC(uint32_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS if (__Pyx_PyLong_IsCompact(x)) { __PYX_VERIFY_RETURN_INT(uint32_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(uint32_t) - 1 > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(uint32_t) - 1 > 2 * PyLong_SHIFT)) { return (uint32_t) (((uint32_t)-1)*(((((uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]))); } } break; case 2: if ((8 * sizeof(uint32_t) > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(uint32_t) - 1 > 2 * PyLong_SHIFT)) { return (uint32_t) ((((((uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]))); } } break; case -3: if ((8 * sizeof(uint32_t) - 1 > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(uint32_t) - 1 > 3 * PyLong_SHIFT)) { return (uint32_t) (((uint32_t)-1)*(((((((uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]))); } } break; case 3: if ((8 * sizeof(uint32_t) > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(uint32_t) - 1 > 3 * PyLong_SHIFT)) { return (uint32_t) ((((((((uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]))); } } break; case -4: if ((8 * sizeof(uint32_t) - 1 > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_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(uint32_t) - 1 > 4 * PyLong_SHIFT)) { return (uint32_t) (((uint32_t)-1)*(((((((((uint32_t)digits[3]) << PyLong_SHIFT) | (uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]))); } } break; case 4: if ((8 * sizeof(uint32_t) > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(uint32_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(uint32_t) - 1 > 4 * PyLong_SHIFT)) { return (uint32_t) ((((((((((uint32_t)digits[3]) << PyLong_SHIFT) | (uint32_t)digits[2]) << PyLong_SHIFT) | (uint32_t)digits[1]) << PyLong_SHIFT) | (uint32_t)digits[0]))); } } break; } } #endif if ((sizeof(uint32_t) <= sizeof(long))) { __PYX_VERIFY_RETURN_INT_EXC(uint32_t, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG } else if ((sizeof(uint32_t) <= sizeof(PY_LONG_LONG))) { __PYX_VERIFY_RETURN_INT_EXC(uint32_t, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } { uint32_t val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (uint32_t) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (uint32_t) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (uint32_t) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (uint32_t) -1; } else { stepval = __Pyx_NewRef(v); } val = (uint32_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(uint32_t) * 8 - chunk_size; bits += chunk_size) { PyObject *tmp, *digit; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((uint32_t) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } idigit = PyLong_AsLong(stepval); if (unlikely(idigit < 0)) goto done; remaining_bits = ((int) sizeof(uint32_t) * 8) - bits - (is_unsigned ? 0 : 1); if (unlikely(idigit >= (1L << remaining_bits))) goto raise_overflow; val |= ((uint32_t) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif if (!is_unsigned) { if (unlikely(val & (((uint32_t) 1) << (sizeof(uint32_t) * 8 - 1)))) goto raise_overflow; if (is_negative) val = ~val; } ret = 0; done: Py_XDECREF(shift); Py_XDECREF(mask); Py_XDECREF(stepval); #endif Py_DECREF(v); if (likely(!ret)) return val; } return (uint32_t) -1; } } else { uint32_t val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); if (!tmp) return (uint32_t) -1; val = __Pyx_PyInt_As_uint32_t(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, "value too large to convert to uint32_t"); return (uint32_t) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, "can't convert negative value to uint32_t"); return (uint32_t) -1; } /* 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 } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; #if !CYTHON_COMPILING_IN_LIMITED_API return _PyLong_FromByteArray(bytes, sizeof(int32_t), little, !is_unsigned); #else PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyInt_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; kwds = PyDict_New(); if (!kwds) goto limited_bad; if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(!is_unsigned ? Py_True : Py_False))) goto limited_bad; result = PyObject_Call(from_bytes, arg_tuple, kwds); limited_bad: Py_XDECREF(from_bytes); Py_XDECREF(py_bytes); Py_XDECREF(order_str); Py_XDECREF(arg_tuple); Py_XDECREF(kwds); return result; #endif } } /* CIntToPy */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC #pragma GCC diagnostic push #pragma GCC diagnostic ignored "-Wconversion" #endif const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_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(uint32_t) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(uint32_t) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); #ifdef HAVE_LONG_LONG } else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) { return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); #endif } } else { if (sizeof(uint32_t) <= sizeof(long)) { return PyInt_FromLong((long) value); #ifdef HAVE_LONG_LONG } else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) { return PyLong_FromLongLong((PY_LONG_LONG) value); #endif } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; #if !CYTHON_COMPILING_IN_LIMITED_API return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); #else PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyInt_Type, "from_bytes"); if (!from_bytes) return NULL; py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(uint32_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; kwds = PyDict_New(); if (!kwds) goto limited_bad; if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(!is_unsigned ? Py_True : Py_False))) goto limited_bad; result = PyObject_Call(from_bytes, arg_tuple, kwds); limited_bad: Py_XDECREF(from_bytes); Py_XDECREF(py_bytes); Py_XDECREF(order_str); Py_XDECREF(arg_tuple); Py_XDECREF(kwds); return result; #endif } } /* CIntFromPy */ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { #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 PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { if ((sizeof(int64_t) < sizeof(long))) { __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { goto raise_neg_overflow; } return (int64_t) val; } } else #endif if (likely(PyLong_Check(x))) { 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(int64_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(int64_t) > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) >= 2 * PyLong_SHIFT)) { return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); } } break; case 3: if ((8 * sizeof(int64_t) > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) >= 3 * PyLong_SHIFT)) { return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); } } break; case 4: if ((8 * sizeof(int64_t) > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) >= 4 * PyLong_SHIFT)) { return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); } } 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 (int64_t) -1; if (unlikely(result == 1)) goto raise_neg_overflow; } #endif if ((sizeof(int64_t) <= sizeof(unsigned long))) { __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x)) #ifdef HAVE_LONG_LONG } else if ((sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG))) { __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) #endif } } else { #if CYTHON_USE_PYLONG_INTERNALS if (__Pyx_PyLong_IsCompact(x)) { __PYX_VERIFY_RETURN_INT(int64_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(int64_t) - 1 > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) { return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case 2: if ((8 * sizeof(int64_t) > 1 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 2 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) { return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case -3: if ((8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) { return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case 3: if ((8 * sizeof(int64_t) > 2 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 3 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) { return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case -4: if ((8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT)) { return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case 4: if ((8 * sizeof(int64_t) > 3 * PyLong_SHIFT)) { if ((8 * sizeof(unsigned long) > 4 * PyLong_SHIFT)) { __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if ((8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT)) { return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; } } #endif if ((sizeof(int64_t) <= sizeof(long))) { __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x)) #ifdef HAVE_LONG_LONG } else if ((sizeof(int64_t) <= sizeof(PY_LONG_LONG))) { __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) #endif } } { int64_t val; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (int64_t) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (int64_t) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (int64_t) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (int64_t) -1; } else { stepval = __Pyx_NewRef(v); } val = (int64_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(int64_t) * 8 - chunk_size; bits += chunk_size) { PyObject *tmp, *digit; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((int64_t) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } idigit = PyLong_AsLong(stepval); if (unlikely(idigit < 0)) goto done; remaining_bits = ((int) sizeof(int64_t) * 8) - bits - (is_unsigned ? 0 : 1); if (unlikely(idigit >= (1L << remaining_bits))) goto raise_overflow; val |= ((int64_t) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif if (!is_unsigned) { if (unlikely(val & (((int64_t) 1) << (sizeof(int64_t) * 8 - 1)))) goto raise_overflow; if (is_negative) val = ~val; } ret = 0; done: Py_XDECREF(shift); Py_XDECREF(mask); Py_XDECREF(stepval); #endif Py_DECREF(v); if (likely(!ret)) return val; } return (int64_t) -1; } } else { int64_t val; PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); if (!tmp) return (int64_t) -1; val = __Pyx_PyInt_As_int64_t(tmp); Py_DECREF(tmp); return val; } raise_overflow: PyErr_SetString(PyExc_OverflowError, "value too large to convert to int64_t"); return (int64_t) -1; raise_neg_overflow: PyErr_SetString(PyExc_OverflowError, "can't convert negative value to int64_t"); return (int64_t) -1; } /* 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; } } else #endif if (likely(PyLong_Check(x))) { 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; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (int32_t) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (int32_t) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (int32_t) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (int32_t) -1; } else { stepval = __Pyx_NewRef(v); } 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; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((int32_t) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } 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 CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif 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 Py_DECREF(v); if (likely(!ret)) return val; } return (int32_t) -1; } } else { 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; } 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_uint64_t(uint64_t value) { #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 (is_unsigned) { if (sizeof(uint64_t) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(uint64_t) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); #ifdef HAVE_LONG_LONG } else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) { return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); #endif } } else { if (sizeof(uint64_t) <= sizeof(long)) { return PyInt_FromLong((long) value); #ifdef HAVE_LONG_LONG } else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) { return PyLong_FromLongLong((PY_LONG_LONG) value); #endif } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; #if !CYTHON_COMPILING_IN_LIMITED_API return _PyLong_FromByteArray(bytes, sizeof(uint64_t), little, !is_unsigned); #else PyObject *from_bytes, *result = NULL; PyObject *py_bytes = NULL, *arg_tuple = NULL, *kwds = NULL, *order_str = NULL; from_bytes = PyObject_GetAttrString((PyObject*)&PyInt_Type, "from_bytes"); if (!from_bytes) return NULL; py_bytes = PyBytes_FromStringAndSize((char*)bytes, sizeof(uint64_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; kwds = PyDict_New(); if (!kwds) goto limited_bad; if (PyDict_SetItemString(kwds, "signed", __Pyx_NewRef(!is_unsigned ? Py_True : Py_False))) goto limited_bad; result = PyObject_Call(from_bytes, arg_tuple, kwds); limited_bad: Py_XDECREF(from_bytes); Py_XDECREF(py_bytes); Py_XDECREF(order_str); Py_XDECREF(arg_tuple); Py_XDECREF(kwds); 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; } } else #endif if (likely(PyLong_Check(x))) { 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; PyObject *v = __Pyx_PyNumber_IntOrLong(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int ret = -1; #if !(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 *)v, bytes, sizeof(val), is_little, !is_unsigned); #else PyObject *stepval = NULL, *mask = NULL, *shift = NULL; int bits, remaining_bits, is_negative = 0; long idigit; int chunk_size = (sizeof(long) < 8) ? 30 : 62; if (unlikely(!PyLong_CheckExact(v))) { PyObject *tmp = v; v = PyNumber_Long(v); assert(PyLong_CheckExact(v)); Py_DECREF(tmp); if (unlikely(!v)) return (uint64_t) -1; } #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(x) == 0) return (uint64_t) 0; is_negative = Py_SIZE(x) < 0; #else { int result = PyObject_RichCompareBool(x, Py_False, Py_LT); if (unlikely(result < 0)) return (uint64_t) -1; is_negative = result == 1; } #endif if (is_unsigned && unlikely(is_negative)) { goto raise_neg_overflow; } else if (is_negative) { stepval = PyNumber_Invert(v); if (unlikely(!stepval)) return (uint64_t) -1; } else { stepval = __Pyx_NewRef(v); } 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; digit = PyNumber_And(stepval, mask); if (unlikely(!digit)) goto done; idigit = PyLong_AsLong(digit); Py_DECREF(digit); if (unlikely(idigit < 0)) goto done; tmp = PyNumber_Rshift(stepval, shift); if (unlikely(!tmp)) goto done; Py_DECREF(stepval); stepval = tmp; val |= ((uint64_t) idigit) << bits; #if CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 if (Py_SIZE(stepval) == 0) goto unpacking_done; #endif } 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 CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX < 0x030B0000 unpacking_done: #endif 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 Py_DECREF(v); if (likely(!ret)) return val; } return (uint64_t) -1; } } else { 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; } 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; } /* 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__172); } return name; } #endif /* 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 '9'); break; } if (rt_from_call[i] != ctversion[i]) { same = 0; break; } } if (!same) { char rtversion[5] = {'\0'}; char message[200]; for (i=0; i<4; ++i) { if (rt_from_call[i] == '.') { if (found_dot) break; found_dot = 1; } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') { break; } rtversion[i] = rt_from_call[i]; } PyOS_snprintf(message, sizeof(message), "compile time version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); return PyErr_WarnEx(NULL, message, 1); } return 0; } /* FunctionImport */ #ifndef __PYX_HAVE_RT_ImportFunction_3_0_2 #define __PYX_HAVE_RT_ImportFunction_3_0_2 static int __Pyx_ImportFunction_3_0_2(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; } static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); } 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 */