Mercurial > repos > rliterman > csp2
diff CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/cbedtools.cpp @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/cbedtools.cpp Tue Mar 18 16:23:26 2025 -0400 @@ -0,0 +1,23055 @@ +/* Generated by Cython 0.29.37 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "depends": [ + "pybedtools/include/bedFile.h", + "pybedtools/include/fileType.h", + "pybedtools/include/gzstream.h", + "pybedtools/include/lineFileUtilities.h" + ], + "include_dirs": [ + "pybedtools/include/" + ], + "language": "c++", + "libraries": [ + "stdc++", + "z" + ], + "name": "pybedtools.cbedtools", + "sources": [ + "pybedtools/cbedtools.pyx", + "pybedtools/include/bedFile.cpp", + "pybedtools/include/fileType.cpp", + "pybedtools/include/gzstream.cpp" + ] + }, + "module_name": "pybedtools.cbedtools" +} +END: Cython Metadata */ + +#ifndef PY_SSIZE_T_CLEAN +#define PY_SSIZE_T_CLEAN +#endif /* PY_SSIZE_T_CLEAN */ +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) + #error Cython requires Python 2.6+ or Python 3.3+. +#else +#define CYTHON_ABI "0_29_37" +#define CYTHON_HEX_VERSION 0x001D25F0 +#define CYTHON_FUTURE_DIVISION 0 +#include <stddef.h> +#ifndef offsetof + #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !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 + #if PY_VERSION_HEX >= 0x02070000 + #define HAVE_LONG_LONG + #endif +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION + #define CYTHON_COMPILING_IN_PYPY 1 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_NOGIL 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 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_PYCALL + #define CYTHON_FAST_PYCALL 0 + #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_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(PYSTON_VERSION) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 1 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_NOGIL 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #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 + #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 + #undef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT 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(PY_NOGIL) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 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_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 1 + #define CYTHON_COMPILING_IN_NOGIL 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYTYPE_LOOKUP + #define CYTHON_USE_PYTYPE_LOOKUP 0 + #elif !defined(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 + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #elif !defined(CYTHON_USE_PYLONG_INTERNALS) + #define CYTHON_USE_PYLONG_INTERNALS (PY_VERSION_HEX < 0x030C00A5) + #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 + #if PY_VERSION_HEX >= 0x030B00A4 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #elif !defined(CYTHON_FAST_THREAD_STATE) + #define CYTHON_FAST_THREAD_STATE 1 + #endif + #ifndef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000) + #endif + #ifndef CYTHON_PEP489_MULTI_PHASE_INIT + #define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000) + #endif + #ifndef CYTHON_USE_TP_FINALIZE + #define CYTHON_USE_TP_FINALIZE (PY_VERSION_HEX >= 0x030400a1) + #endif + #ifndef CYTHON_USE_DICT_VERSIONS + #define CYTHON_USE_DICT_VERSIONS ((PY_VERSION_HEX >= 0x030600B1) && (PY_VERSION_HEX < 0x030C00A5)) + #endif + #if PY_VERSION_HEX >= 0x030B00A4 + #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 (PY_VERSION_HEX >= 0x030700A3) + #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 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(__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_MAYBE_UNUSED_VAR +# if defined(__cplusplus) + template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } +# else +# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# 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 int uint32_t; + #else + typedef unsigned __int8 uint8_t; + typedef unsigned __int32 uint32_t; + #endif + #endif +#else + #include <stdint.h> +#endif +#ifndef CYTHON_FALLTHROUGH + #if defined(__cplusplus) && __cplusplus >= 201103L + #if __has_cpp_attribute(fallthrough) + #define CYTHON_FALLTHROUGH [[fallthrough]] + #elif __has_cpp_attribute(clang::fallthrough) + #define CYTHON_FALLTHROUGH [[clang::fallthrough]] + #elif __has_cpp_attribute(gnu::fallthrough) + #define CYTHON_FALLTHROUGH [[gnu::fallthrough]] + #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 + +#ifndef __cplusplus + #error "Cython files generated with the C++ option must be compiled with a C++ compiler." +#endif +#ifndef CYTHON_INLINE + #if defined(__clang__) + #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) + #else + #define CYTHON_INLINE inline + #endif +#endif +template<typename T> +void __Pyx_call_destructor(T& x) { + x.~T(); +} +template<typename T> +class __Pyx_FakeReference { + public: + __Pyx_FakeReference() : ptr(NULL) { } + __Pyx_FakeReference(const T& ref) : ptr(const_cast<T*>(&ref)) { } + T *operator->() { return ptr; } + T *operator&() { return ptr; } + operator T&() { return *ptr; } + template<typename U> bool operator ==(U other) { return *ptr == other; } + template<typename U> bool operator !=(U other) { return *ptr != other; } + private: + T *ptr; +}; + +#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_PyCode_New(a, 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) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_DefaultClassType PyType_Type +#if PY_VERSION_HEX >= 0x030B00A1 + static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, 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 *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL; + PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL; + const char *fn_cstr=NULL; + const char *name_cstr=NULL; + PyCodeObject* co=NULL; + PyObject *type, *value, *traceback; + PyErr_Fetch(&type, &value, &traceback); + if (!(kwds=PyDict_New())) goto end; + if (!(argcount=PyLong_FromLong(a))) goto end; + if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end; + if (!(posonlyargcount=PyLong_FromLong(0))) goto end; + if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end; + if (!(kwonlyargcount=PyLong_FromLong(k))) goto end; + if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end; + if (!(nlocals=PyLong_FromLong(l))) goto end; + if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end; + if (!(stacksize=PyLong_FromLong(s))) goto end; + if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end; + if (!(flags=PyLong_FromLong(f))) goto end; + if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end; + if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end; + if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end; + if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end; + if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end; + if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too; + if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here + if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too; + Py_XDECREF((PyObject*)co); + co = (PyCodeObject*)call_result; + call_result = NULL; + if (0) { + cleanup_code_too: + Py_XDECREF((PyObject*)co); + co = NULL; + } + end: + Py_XDECREF(kwds); + Py_XDECREF(argcount); + Py_XDECREF(posonlyargcount); + Py_XDECREF(kwonlyargcount); + Py_XDECREF(nlocals); + Py_XDECREF(stacksize); + Py_XDECREF(replace); + Py_XDECREF(call_result); + Py_XDECREF(empty); + if (type) { + PyErr_Restore(type, value, traceback); + } + return co; + } +#else + #define __Pyx_PyCode_New(a, 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 + #define __Pyx_DefaultClassType PyType_Type +#endif +#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 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 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_FAST_PYCCALL +#define __Pyx_PyFastCFunction_Check(func)\ + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))))) +#else +#define __Pyx_PyFastCFunction_Check(func) 0 +#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_CPYTHON && PY_VERSION_HEX < 0x030400A1 + #define PyMem_RawMalloc(n) PyMem_Malloc(n) + #define PyMem_RawRealloc(p, n) PyMem_Realloc(p, n) + #define PyMem_RawFree(p) PyMem_Free(p) +#endif +#if CYTHON_COMPILING_IN_PYSTON + #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) 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_FAST_THREAD_STATE || PY_VERSION_HEX < 0x02070000 + #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 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 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 >= 0x030500A1 && CYTHON_USE_UNICODE_INTERNALS +#define __Pyx_PyDict_GetItemStr(dict, name) _PyDict_GetItem_KnownHash(dict, name, ((PyASCIIObject *) name)->hash) +#else +#define __Pyx_PyDict_GetItemStr(dict, name) PyDict_GetItem(dict, name) +#endif +#if 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) 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, 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) ? 65535 : 1114111) + #define __Pyx_PyUnicode_KIND(u) (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] = 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 && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) + #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) + #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) +#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 +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_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_SIZE(seq) Py_SIZE(seq) +#else + #define __Pyx_PySequence_SIZE(seq) PySequence_Size(seq) +#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 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 +#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 PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#if CYTHON_USE_ASYNC_SLOTS + #if PY_VERSION_HEX >= 0x030500B1 + #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods + #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) + #else + #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) + #endif +#else + #define __Pyx_PyType_AsAsync(obj) NULL +#endif +#ifndef __Pyx_PyAsyncMethodsStruct + typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; + } __Pyx_PyAsyncMethodsStruct; +#endif + +#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS) + #if !defined(_USE_MATH_DEFINES) + #define _USE_MATH_DEFINES + #endif +#endif +#include <math.h> +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) +#define __Pyx_truncl trunc +#else +#define __Pyx_truncl truncl +#endif + +#define __PYX_MARK_ERR_POS(f_index, lineno) \ + { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; } +#define __PYX_ERR(f_index, lineno, Ln_error) \ + { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; } + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#define __PYX_HAVE__pybedtools__cbedtools +#define __PYX_HAVE_API__pybedtools__cbedtools +/* Early includes */ +#include <string.h> +#include <stdio.h> +#include "pythread.h" +#include "ios" +#include "new" +#include "stdexcept" +#include "typeinfo" +#include <vector> +#include <string> +#include "bedFile.h" +#ifdef _OPENMP +#include <omp.h> +#endif /* _OPENMP */ + +#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS) +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT (PY_MAJOR_VERSION >= 3 && __PYX_DEFAULT_STRING_ENCODING_IS_UTF8) +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE int __Pyx_is_valid_index(Py_ssize_t i, Py_ssize_t limit) { + return (size_t) i < (size_t) limit; +} +#if defined (__cplusplus) && __cplusplus >= 201103L + #include <cstdlib> + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) + #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value)) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif +static CYTHON_INLINE 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_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __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) +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); +} +#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 +#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) +#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] = 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; } + +static PyObject *__pyx_m = NULL; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_cython_runtime = NULL; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static PyObject *__pyx_empty_unicode; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + + +static const char *__pyx_f[] = { + "pybedtools/cbedtools.pyx", + "stringsource", + "env39/lib/python3.9/site-packages/Cython/Includes/cpython/type.pxd", + "env39/lib/python3.9/site-packages/Cython/Includes/cpython/bool.pxd", + "env39/lib/python3.9/site-packages/Cython/Includes/cpython/complex.pxd", +}; + +/*--- Type declarations ---*/ +struct __pyx_obj_10pybedtools_9cbedtools_Interval; +struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator; +struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile; + +/* "pybedtools/cbedtools.pxd":84 + * + * + * cdef class Interval: # <<<<<<<<<<<<<< + * cdef BED *_bed + * cdef object _attrs + */ +struct __pyx_obj_10pybedtools_9cbedtools_Interval { + PyObject_HEAD + struct __pyx_vtabstruct_10pybedtools_9cbedtools_Interval *__pyx_vtab; + BED *_bed; + PyObject *_attrs; +}; + + +/* "pybedtools/cbedtools.pyx":729 + * + * + * cdef class IntervalIterator: # <<<<<<<<<<<<<< + * cdef object stream + * cdef int _itemtype + */ +struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator { + PyObject_HEAD + PyObject *stream; + int _itemtype; +}; + + +/* "pybedtools/cbedtools.pyx":794 + * + * + * cdef class IntervalFile: # <<<<<<<<<<<<<< + * cdef BedFile *intervalFile_ptr + * cdef bint _loaded + */ +struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile { + PyObject_HEAD + BedFile *intervalFile_ptr; + int _loaded; + int _open; + std::string _fn; +}; + + + +/* "pybedtools/cbedtools.pyx":201 + * return self.sep.join(pairs) + self.sep + * + * cdef class Interval: # <<<<<<<<<<<<<< + * """ + * Class to represent a genomic interval. + */ + +struct __pyx_vtabstruct_10pybedtools_9cbedtools_Interval { + PyObject *(*append)(struct __pyx_obj_10pybedtools_9cbedtools_Interval *, PyObject *, int __pyx_skip_dispatch); + PyObject *(*deparse_attrs)(struct __pyx_obj_10pybedtools_9cbedtools_Interval *, int __pyx_skip_dispatch); +}; +static struct __pyx_vtabstruct_10pybedtools_9cbedtools_Interval *__pyx_vtabptr_10pybedtools_9cbedtools_Interval; + +/* --- Runtime support code (head) --- */ +/* Refnanny.proto */ +#ifndef CYTHON_REFNANNY + #define CYTHON_REFNANNY 0 +#endif +#if CYTHON_REFNANNY + typedef struct { + void (*INCREF)(void*, PyObject*, int); + void (*DECREF)(void*, PyObject*, int); + void (*GOTREF)(void*, PyObject*, int); + void (*GIVEREF)(void*, PyObject*, int); + void* (*SetupContext)(const char*, int, const char*); + void (*FinishContext)(void**); + } __Pyx_RefNannyAPIStruct; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); + #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; +#ifdef WITH_THREAD + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + } +#else + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) +#endif + #define __Pyx_RefNannyFinishContext()\ + __Pyx_RefNanny->FinishContext(&__pyx_refnanny) + #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0) + #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0) + #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0) + #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) +#else + #define __Pyx_RefNannyDeclarations + #define __Pyx_RefNannySetupContext(name, acquire_gil) + #define __Pyx_RefNannyFinishContext() + #define __Pyx_INCREF(r) Py_INCREF(r) + #define __Pyx_DECREF(r) Py_DECREF(r) + #define __Pyx_GOTREF(r) + #define __Pyx_GIVEREF(r) + #define __Pyx_XINCREF(r) Py_XINCREF(r) + #define __Pyx_XDECREF(r) Py_XDECREF(r) + #define __Pyx_XGOTREF(r) + #define __Pyx_XGIVEREF(r) +#endif +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ + } while (0) +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ + } while (0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) + +/* PyObjectGetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +/* GetBuiltinName.proto */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +/* 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 + +/* PyCFunctionFastCall.proto */ +#if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); +#else +#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) +#endif + +/* PyFunctionFastCall.proto */ +#if CYTHON_FAST_PYCALL +#define __Pyx_PyFunction_FastCall(func, args, nargs)\ + __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); +#else +#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, 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_FAST_PYCALL + static size_t __pyx_pyframe_localsplus_offset = 0; + #include "frameobject.h" +#if PY_VERSION_HEX >= 0x030b00a6 + #ifndef Py_BUILD_CORE + #define Py_BUILD_CORE 1 + #endif + #include "internal/pycore_frame.h" +#endif + #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 // CYTHON_FAST_PYCALL +#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 + +/* PyObjectCallOneArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +/* PyObjectCall2Args.proto */ +static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); + +/* IncludeCppStringH.proto */ +#include <string> + +/* decode_c_string_utf16.proto */ +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 0; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16LE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = -1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} +static CYTHON_INLINE PyObject *__Pyx_PyUnicode_DecodeUTF16BE(const char *s, Py_ssize_t size, const char *errors) { + int byteorder = 1; + return PyUnicode_DecodeUTF16(s, size, errors, &byteorder); +} + +/* decode_c_bytes.proto */ +static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( + const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +/* decode_cpp_string.proto */ +static CYTHON_INLINE PyObject* __Pyx_decode_cpp_string( + std::string cppstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + return __Pyx_decode_c_bytes( + cppstring.data(), cppstring.size(), start, stop, encoding, errors, decode_func); +} + +/* RaiseDoubleKeywords.proto */ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +/* ParseKeywords.proto */ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ + const char* function_name); + +/* RaiseArgTupleInvalid.proto */ +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +/* PyObjectSetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS +#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o, n, NULL) +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value); +#else +#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) +#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) +#endif + +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace, int zerodivision_check); +#else +#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace, zerodivision_check)\ + (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) +#endif + +/* IncludeStringH.proto */ +#include <string.h> + +/* BytesEquals.proto */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); + +/* UnicodeEquals.proto */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); + +/* StrEquals.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + +/* PyObjectCallNoArg.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); +#else +#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) +#endif + +/* 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 + +/* RaiseTooManyValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +/* RaiseNeedMoreValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +/* IterFinish.proto */ +static CYTHON_INLINE int __Pyx_IterFinish(void); + +/* UnpackItemEndCheck.proto */ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); + +/* PyIntCompare.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, long inplace); + +/* py_dict_iteritems.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyDict_IterItems(PyObject* d); + +/* UnpackUnboundCMethod.proto */ +typedef struct { + PyObject *type; + PyObject **method_name; + PyCFunction func; + PyObject *method; + int flag; +} __Pyx_CachedCFunction; + +/* CallUnboundCMethod0.proto */ +static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self); +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_CallUnboundCMethod0(cfunc, self)\ + (likely((cfunc)->func) ?\ + (likely((cfunc)->flag == METH_NOARGS) ? (*((cfunc)->func))(self, NULL) :\ + (PY_VERSION_HEX >= 0x030600B1 && likely((cfunc)->flag == METH_FASTCALL) ?\ + (PY_VERSION_HEX >= 0x030700A0 ?\ + (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0) :\ + (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0, NULL)) :\ + (PY_VERSION_HEX >= 0x030700A0 && (cfunc)->flag == (METH_FASTCALL | METH_KEYWORDS) ?\ + (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, &__pyx_empty_tuple, 0, NULL) :\ + (likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ? ((*(PyCFunctionWithKeywords)(void*)(PyCFunction)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\ + ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) :\ + __Pyx__CallUnboundCMethod0(cfunc, self)))))) :\ + __Pyx__CallUnboundCMethod0(cfunc, self)) +#else +#define __Pyx_CallUnboundCMethod0(cfunc, self) __Pyx__CallUnboundCMethod0(cfunc, self) +#endif + +/* GetItemInt.proto */ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +/* ObjectGetItem.proto */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key); +#else +#define __Pyx_PyObject_GetItem(obj, key) PyObject_GetItem(obj, key) +#endif + +/* GetTopmostException.proto */ +#if CYTHON_USE_EXC_INFO_STACK +static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); +#endif + +/* PyThreadStateGet.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; +#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current; +#define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type +#else +#define __Pyx_PyThreadState_declare +#define __Pyx_PyThreadState_assign +#define __Pyx_PyErr_Occurred() PyErr_Occurred() +#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 + +/* PyErrExceptionMatches.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); +#else +#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) +#endif + +/* PyErrFetchRestore.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL) +#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL)) +#else +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#endif +#else +#define __Pyx_PyErr_Clear() PyErr_Clear() +#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc) +#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) +#endif + +/* 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 + +/* ListExtend.proto */ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +/* StringJoin.proto */ +#if PY_MAJOR_VERSION < 3 +#define __Pyx_PyString_Join __Pyx_PyBytes_Join +#define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v)) +#else +#define __Pyx_PyString_Join PyUnicode_Join +#define __Pyx_PyBaseString_Join PyUnicode_Join +#endif +#if CYTHON_COMPILING_IN_CPYTHON + #if PY_MAJOR_VERSION < 3 + #define __Pyx_PyBytes_Join _PyString_Join + #else + #define __Pyx_PyBytes_Join _PyBytes_Join + #endif +#else +static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values); +#endif + +/* 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 + +/* FetchCommonType.proto */ +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); + +/* CythonFunctionShared.proto */ +#define __Pyx_CyFunction_USED 1 +#define __Pyx_CYFUNCTION_STATICMETHOD 0x01 +#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 +#define __Pyx_CYFUNCTION_CCLASS 0x04 +#define __Pyx_CyFunction_GetClosure(f)\ + (((__pyx_CyFunctionObject *) (f))->func_closure) +#define __Pyx_CyFunction_GetClassObj(f)\ + (((__pyx_CyFunctionObject *) (f))->func_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 { + PyCFunctionObject func; +#if PY_VERSION_HEX < 0x030500A0 + 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; + PyObject *func_classobj; + 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; +} __pyx_CyFunctionObject; +static PyTypeObject *__pyx_CyFunctionType = 0; +#define __Pyx_CyFunction_Check(obj) (__Pyx_TypeCheck(obj, __pyx_CyFunctionType)) +static PyObject *__Pyx_CyFunction_Init(__pyx_CyFunctionObject* op, PyMethodDef *ml, + int flags, PyObject* qualname, + PyObject *self, + PyObject *module, PyObject *globals, + PyObject* code); +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(void); + +/* CythonFunction.proto */ +static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, + int flags, PyObject* qualname, + PyObject *closure, + PyObject *module, PyObject *globals, + PyObject* code); + +/* RaiseException.proto */ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +/* 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)); +} + +/* 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 + +/* GetAttr.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +/* SliceTupleAndList.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop); +static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop); +#else +#define __Pyx_PyList_GetSlice(seq, start, stop) PySequence_GetSlice(seq, start, stop) +#define __Pyx_PyTuple_GetSlice(seq, start, stop) PySequence_GetSlice(seq, start, stop) +#endif + +/* 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 + +/* 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 + +/* SetItemInt.proto */ +#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\ + __Pyx_SetItemInt_Generic(o, to_py_func(i), v))) +static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v); +static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, + int is_list, int wraparound, int boundscheck); + +/* ArgTypeTest.proto */ +#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\ + ((likely((Py_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); + +/* WriteUnraisableException.proto */ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback, int nogil); + +/* HasAttr.proto */ +static CYTHON_INLINE int __Pyx_HasAttr(PyObject *, PyObject *); + +/* IterNext.proto */ +#define __Pyx_PyIter_Next(obj) __Pyx_PyIter_Next2(obj, NULL) +static CYTHON_INLINE PyObject *__Pyx_PyIter_Next2(PyObject *, PyObject *); + +/* None.proto */ +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +/* GetAttr3.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); + +/* FastTypeChecks.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type) +static CYTHON_INLINE int __Pyx_IsSubtype(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_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_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) + +/* PyObjectLookupSpecial.proto */ +#if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name) { + PyObject *res; + PyTypeObject *tp = Py_TYPE(obj); +#if PY_MAJOR_VERSION < 3 + if (unlikely(PyInstance_Check(obj))) + return __Pyx_PyObject_GetAttrStr(obj, attr_name); +#endif + res = _PyType_Lookup(tp, attr_name); + if (likely(res)) { + descrgetfunc f = Py_TYPE(res)->tp_descr_get; + if (!f) { + Py_INCREF(res); + } else { + res = f(res, obj, (PyObject *)tp); + } + } else { + PyErr_SetObject(PyExc_AttributeError, attr_name); + } + return res; +} +#else +#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) +#endif + +/* SwapException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); +#endif + +/* Import.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +/* ImportFrom.proto */ +static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); + +/* PyObject_GenericGetAttrNoDict.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttrNoDict PyObject_GenericGetAttr +#endif + +/* PyObject_GenericGetAttr.proto */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name); +#else +#define __Pyx_PyObject_GenericGetAttr PyObject_GenericGetAttr +#endif + +/* SetVTable.proto */ +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +/* PyObjectGetAttrStrNoError.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, PyObject* attr_name); + +/* SetupReduce.proto */ +static int __Pyx_setup_reduce(PyObject* type_obj); + +/* TypeImport.proto */ +#ifndef __PYX_HAVE_RT_ImportType_proto_0_29_37 +#define __PYX_HAVE_RT_ImportType_proto_0_29_37 +#if __STDC_VERSION__ >= 201112L +#include <stdalign.h> +#endif +#if __STDC_VERSION__ >= 201112L || __cplusplus >= 201103L +#define __PYX_GET_STRUCT_ALIGNMENT_0_29_37(s) alignof(s) +#else +#define __PYX_GET_STRUCT_ALIGNMENT_0_29_37(s) sizeof(void*) +#endif +enum __Pyx_ImportType_CheckSize_0_29_37 { + __Pyx_ImportType_CheckSize_Error_0_29_37 = 0, + __Pyx_ImportType_CheckSize_Warn_0_29_37 = 1, + __Pyx_ImportType_CheckSize_Ignore_0_29_37 = 2 +}; +static PyTypeObject *__Pyx_ImportType_0_29_37(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_0_29_37 check_size); +#endif + +/* py_dict_items.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyDict_Items(PyObject* d); + +/* CalculateMetaclass.proto */ +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); + +/* Py3ClassCreate.proto */ +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, + PyObject *mkw, PyObject *modname, PyObject *doc); +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, + PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); + +/* SetNameInClass.proto */ +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 +#define __Pyx_SetNameInClass(ns, name, value)\ + (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value)) +#elif CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_SetNameInClass(ns, name, value)\ + (likely(PyDict_CheckExact(ns)) ? PyDict_SetItem(ns, name, value) : PyObject_SetItem(ns, name, value)) +#else +#define __Pyx_SetNameInClass(ns, name, value) PyObject_SetItem(ns, name, value) +#endif + +/* 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 */ +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); + +/* AddTraceback.proto */ +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +/* None.proto */ +#include <new> + +/* GCCDiagnostics.proto */ +#if defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6)) +#define __Pyx_HAS_GCC_DIAGNOSTIC +#endif + +/* CppExceptionConversion.proto */ +#ifndef __Pyx_CppExn2PyErr +#include <new> +#include <typeinfo> +#include <stdexcept> +#include <ios> +static void __Pyx_CppExn2PyErr() { + try { + if (PyErr_Occurred()) + ; // let the latest Python exn pass through and ignore the current one + else + throw; + } catch (const std::bad_alloc& exn) { + PyErr_SetString(PyExc_MemoryError, exn.what()); + } catch (const std::bad_cast& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::bad_typeid& exn) { + PyErr_SetString(PyExc_TypeError, exn.what()); + } catch (const std::domain_error& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::invalid_argument& exn) { + PyErr_SetString(PyExc_ValueError, exn.what()); + } catch (const std::ios_base::failure& exn) { + PyErr_SetString(PyExc_IOError, exn.what()); + } catch (const std::out_of_range& exn) { + PyErr_SetString(PyExc_IndexError, exn.what()); + } catch (const std::overflow_error& exn) { + PyErr_SetString(PyExc_OverflowError, exn.what()); + } catch (const std::range_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::underflow_error& exn) { + PyErr_SetString(PyExc_ArithmeticError, exn.what()); + } catch (const std::exception& exn) { + PyErr_SetString(PyExc_RuntimeError, exn.what()); + } + catch (...) + { + PyErr_SetString(PyExc_RuntimeError, "Unknown exception"); + } +} +#endif + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +/* CIntFromPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE CHRPOS __Pyx_PyInt_As_CHRPOS(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_CHRPOS(CHRPOS value); + +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +/* CIntFromPy.proto */ +static CYTHON_INLINE unsigned long __Pyx_PyInt_As_unsigned_long(PyObject *); + +/* CheckBinaryVersion.proto */ +static int __Pyx_check_binary_version(void); + +/* InitStrings.proto */ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static PyObject *__pyx_f_10pybedtools_9cbedtools_8Interval_deparse_attrs(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools_8Interval_append(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value, int __pyx_skip_dispatch); /* proto*/ + +/* Module declarations from 'cpython.version' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* 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' */ +static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0; + +/* Module declarations from 'cpython.long' */ + +/* Module declarations from 'cpython.float' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.complex' */ +static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; + +/* Module declarations from 'cpython.string' */ + +/* Module declarations from 'cpython.unicode' */ + +/* 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' */ + +/* Module declarations from 'libcpp.vector' */ + +/* Module declarations from 'libcpp.string' */ + +/* Module declarations from 'pybedtools.cbedtools' */ +static PyTypeObject *__pyx_ptype_10pybedtools_9cbedtools_Interval = 0; +static PyTypeObject *__pyx_ptype_10pybedtools_9cbedtools_IntervalIterator = 0; +static PyTypeObject *__pyx_ptype_10pybedtools_9cbedtools_IntervalFile = 0; +static PyObject *__pyx_v_10pybedtools_9cbedtools_LOOKUPS = 0; +static PyObject *__pyx_f_10pybedtools_9cbedtools__cppstr(PyObject *); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools__pystr(std::string); /*proto*/ +static struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_f_10pybedtools_9cbedtools_create_interval(BED); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools_isdigit(PyObject *); /*proto*/ +static struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_f_10pybedtools_9cbedtools_create_interval_from_list(PyObject *, int __pyx_skip_dispatch); /*proto*/ +static std::vector<std::string> __pyx_f_10pybedtools_9cbedtools_list_to_vector(PyObject *); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools_string_vec2list(std::vector<std::string> ); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools_bed_vec2list(std::vector<BED> ); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools___pyx_unpickle_IntervalIterator__set_state(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *, PyObject *); /*proto*/ +static std::string __pyx_convert_string_from_py_std__in_string(PyObject *); /*proto*/ +static CYTHON_INLINE PyObject *__pyx_convert_PyObject_string_to_py_std__in_string(std::string const &); /*proto*/ +static CYTHON_INLINE PyObject *__pyx_convert_PyUnicode_string_to_py_std__in_string(std::string const &); /*proto*/ +static CYTHON_INLINE PyObject *__pyx_convert_PyStr_string_to_py_std__in_string(std::string const &); /*proto*/ +static CYTHON_INLINE PyObject *__pyx_convert_PyBytes_string_to_py_std__in_string(std::string const &); /*proto*/ +static CYTHON_INLINE PyObject *__pyx_convert_PyByteArray_string_to_py_std__in_string(std::string const &); /*proto*/ +static std::vector<std::string> __pyx_convert_vector_from_py_std_3a__3a_string(PyObject *); /*proto*/ +#define __Pyx_MODULE_NAME "pybedtools.cbedtools" +extern int __pyx_module_is_main_pybedtools__cbedtools; +int __pyx_module_is_main_pybedtools__cbedtools = 0; + +/* Implementation of 'pybedtools.cbedtools' */ +static PyObject *__pyx_builtin_map; +static PyObject *__pyx_builtin_KeyError; +static PyObject *__pyx_builtin_NotImplementedError; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_AttributeError; +static PyObject *__pyx_builtin_StopIteration; +static PyObject *__pyx_builtin_open; +static const char __pyx_k_[] = ""; +static const char __pyx_k_k[] = "k"; +static const char __pyx_k_v[] = "v"; +static const char __pyx_k_x[] = "x"; +static const char __pyx_k_y[] = "y"; +static const char __pyx_k_ID[] = "ID"; +static const char __pyx_k__2[] = ";"; +static const char __pyx_k__3[] = "="; +static const char __pyx_k__4[] = "\""; +static const char __pyx_k__5[] = " "; +static const char __pyx_k__7[] = "."; +static const char __pyx_k__8[] = "\t"; +static const char __pyx_k_e1[] = "e1"; +static const char __pyx_k_e2[] = "e2"; +static const char __pyx_k_fn[] = "fn"; +static const char __pyx_k_kv[] = "kv"; +static const char __pyx_k_np[] = "np"; +static const char __pyx_k_s1[] = "s1"; +static const char __pyx_k_s2[] = "s2"; +static const char __pyx_k__15[] = "\n"; +static const char __pyx_k__19[] = "+"; +static const char __pyx_k__20[] = "-"; +static const char __pyx_k__21[] = "*"; +static const char __pyx_k__22[] = "@"; +static const char __pyx_k__23[] = "#"; +static const char __pyx_k__25[] = "\r\n"; +static const char __pyx_k_bed[] = "bed"; +static const char __pyx_k_cmp[] = "cmp"; +static const char __pyx_k_doc[] = "__doc__"; +static const char __pyx_k_end[] = "end"; +static const char __pyx_k_gff[] = "gff"; +static const char __pyx_k_kvs[] = "kvs"; +static const char __pyx_k_map[] = "map"; +static const char __pyx_k_new[] = "__new__"; +static const char __pyx_k_s_i[] = "%s:%i"; +static const char __pyx_k_sam[] = "sam"; +static const char __pyx_k_sep[] = "sep"; +static const char __pyx_k_str[] = "__str__"; +static const char __pyx_k_sys[] = "sys"; +static const char __pyx_k_val[] = "val"; +static const char __pyx_k_vcf[] = "vcf"; +static const char __pyx_k_Name[] = "Name"; +static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_exit[] = "__exit__"; +static const char __pyx_k_init[] = "__init__"; +static const char __pyx_k_join[] = "join"; +static const char __pyx_k_main[] = "__main__"; +static const char __pyx_k_n_eq[] = "n_eq"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_open[] = "open"; +static const char __pyx_k_self[] = "self"; +static const char __pyx_k_stop[] = "stop"; +static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_UTF_8[] = "UTF-8"; +static const char __pyx_k_attrs[] = "attrs"; +static const char __pyx_k_chrom[] = "chrom"; +static const char __pyx_k_close[] = "close"; +static const char __pyx_k_count[] = "count"; +static const char __pyx_k_enter[] = "__enter__"; +static const char __pyx_k_field[] = "field"; +static const char __pyx_k_int64[] = "int64"; +static const char __pyx_k_items[] = "items"; +static const char __pyx_k_kdict[] = "kdict"; +static const char __pyx_k_ktype[] = "ktype"; +static const char __pyx_k_numpy[] = "numpy"; +static const char __pyx_k_pairs[] = "pairs"; +static const char __pyx_k_range[] = "range"; +static const char __pyx_k_score[] = "score"; +static const char __pyx_k_split[] = "split"; +static const char __pyx_k_start[] = "start"; +static const char __pyx_k_strip[] = "strip"; +static const char __pyx_k_track[] = "track"; +static const char __pyx_k_value[] = "value"; +static const char __pyx_k_Parent[] = "Parent"; +static const char __pyx_k_append[] = "append"; +static const char __pyx_k_closed[] = "closed"; +static const char __pyx_k_encode[] = "encode"; +static const char __pyx_k_fields[] = "fields"; +static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_module[] = "__module__"; +static const char __pyx_k_n_semi[] = "n_semi"; +static const char __pyx_k_name_2[] = "__name__"; +static const char __pyx_k_pickle[] = "pickle"; +static const char __pyx_k_quoted[] = "_quoted"; +static const char __pyx_k_reduce[] = "__reduce__"; +static const char __pyx_k_rstrip[] = "rstrip"; +static const char __pyx_k_search[] = "search"; +static const char __pyx_k_strand[] = "strand"; +static const char __pyx_k_stream[] = "stream"; +static const char __pyx_k_update[] = "update"; +static const char __pyx_k_browser[] = "browser"; +static const char __pyx_k_gene_id[] = "gene_id"; +static const char __pyx_k_indices[] = "indices"; +static const char __pyx_k_isdigit[] = "isdigit"; +static const char __pyx_k_overlap[] = "overlap"; +static const char __pyx_k_prepare[] = "__prepare__"; +static const char __pyx_k_replace[] = "replace"; +static const char __pyx_k_Interval[] = "Interval"; +static const char __pyx_k_KeyError[] = "KeyError"; +static const char __pyx_k_all_hits[] = "all_hits"; +static const char __pyx_k_attr_str[] = "attr_str"; +static const char __pyx_k_getstate[] = "__getstate__"; +static const char __pyx_k_interval[] = "interval"; +static const char __pyx_k_n_quotes[] = "n_quotes"; +static const char __pyx_k_pyx_type[] = "__pyx_type"; +static const char __pyx_k_qualname[] = "__qualname__"; +static const char __pyx_k_readline[] = "readline"; +static const char __pyx_k_setstate[] = "__setstate__"; +static const char __pyx_k_TypeError[] = "TypeError"; +static const char __pyx_k_field_sep[] = "field_sep"; +static const char __pyx_k_file_type[] = "file_type"; +static const char __pyx_k_gene_name[] = "gene_name"; +static const char __pyx_k_iteritems[] = "iteritems"; +static const char __pyx_k_metaclass[] = "__metaclass__"; +static const char __pyx_k_pyx_state[] = "__pyx_state"; +static const char __pyx_k_reduce_ex[] = "__reduce_ex__"; +static const char __pyx_k_sort_keys[] = "sort_keys"; +static const char __pyx_k_Attributes[] = "Attributes"; +static const char __pyx_k_IndexError[] = "IndexError"; +static const char __pyx_k_ValueError[] = "ValueError"; +static const char __pyx_k_attr_str_2[] = "_attr_str"; +static const char __pyx_k_pyx_result[] = "__pyx_result"; +static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static const char __pyx_k_startswith[] = "startswith"; +static const char __pyx_k_subprocess[] = "subprocess"; +static const char __pyx_k_PickleError[] = "PickleError"; +static const char __pyx_k_collections[] = "collections"; +static const char __pyx_k_defaultdict[] = "defaultdict"; +static const char __pyx_k_loadIntoMap[] = "loadIntoMap"; +static const char __pyx_k_otherfields[] = "otherfields"; +static const char __pyx_k_same_strand[] = "same_strand"; +static const char __pyx_k_IntervalFile[] = "IntervalFile"; +static const char __pyx_k_intervalFile[] = "intervalFile"; +static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; +static const char __pyx_k_stringsource[] = "stringsource"; +static const char __pyx_k_PROFILES_TRUE[] = "PROFILES_TRUE"; +static const char __pyx_k_StopIteration[] = "StopIteration"; +static const char __pyx_k_deparse_attrs[] = "deparse_attrs"; +static const char __pyx_k_integer_types[] = "integer_types"; +static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; +static const char __pyx_k_transcript_id[] = "transcript_id"; +static const char __pyx_k_AttributeError[] = "AttributeError"; +static const char __pyx_k_Interval_s_i_i[] = "Interval(%s:%i-%i)"; +static const char __pyx_k_pyx_PickleError[] = "__pyx_PickleError"; +static const char __pyx_k_setstate_cython[] = "__setstate_cython__"; +static const char __pyx_k_Attributes___str[] = "Attributes.__str__"; +static const char __pyx_k_IntervalIterator[] = "IntervalIterator"; +static const char __pyx_k_malformed_line_s[] = "malformed line: %s"; +static const char __pyx_k_Attributes___init[] = "Attributes.__init__"; +static const char __pyx_k_BedToolsFileError[] = "BedToolsFileError"; +static const char __pyx_k_Error_opening_file[] = "Error opening file"; +static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; +static const char __pyx_k_NotImplementedError[] = "NotImplementedError"; +static const char __pyx_k_pybedtools_cbedtools[] = "pybedtools.cbedtools"; +static const char __pyx_k_richcmp___locals_cmp[] = "__richcmp__.<locals>.cmp"; +static const char __pyx_k_MalformedBedLineError[] = "MalformedBedLineError"; +static const char __pyx_k_field_index_out_of_range[] = "field index out of range"; +static const char __pyx_k_pybedtools_cbedtools_pyx[] = "pybedtools/cbedtools.pyx"; +static const char __pyx_k_Start_is_greater_than_stop[] = "Start is greater than stop"; +static const char __pyx_k_pyx_unpickle_IntervalIterator[] = "__pyx_unpickle_IntervalIterator"; +static const char __pyx_k_Class_to_map_between_a_dict_of[] = "\n Class to map between a dict of attrs and fields[8] of a GFF Interval obj.\n "; +static const char __pyx_k_Create_an_Interval_object_from[] = "\n Create an Interval object from a list of strings.\n\n Constructor::\n\n create_interval_from_list(fields)\n\n Given the list of strings, `fields`, automatically detects the format (BED,\n GFF, VCF, SAM) and creates a new Interval object.\n\n `fields` is a list with an arbitrary number of items (it can be quite long,\n say after a -wao intersection of a BED12 and a GFF), however, the first\n fields must conform to one of the supported formats. For example, if you\n want the resulting Interval to be considered a GFF feature, then the first\n 9 fields must conform to the GFF format. Similarly, if you want the\n resulting Interval to be considered a BED feature, then the first three\n fields must be chrom, start, stop.\n\n Example usage:\n\n >>> # Creates a BED3 feature\n >>> feature = create_interval_from_list(['chr1', '1', '100'])\n\n "; +static const char __pyx_k_IntervalFile_all_hits_line_888[] = "IntervalFile.all_hits (line 888)"; +static const char __pyx_k_IntervalFile_any_hits_line_934[] = "IntervalFile.any_hits (line 934)"; +static const char __pyx_k_Unable_to_detect_format_from_s[] = "Unable to detect format from %s"; +static const char __pyx_k_IntervalFile_objects_do_not_yet[] = "IntervalFile objects do not yet natively support SAM. Please convert to BED/GFF/VCF first if you want to use the low-level API of IntervalFile"; +static const char __pyx_k_Interval_attrs_was_not_None_but[] = "Interval.attrs was not None, but this was a non-GFF Interval"; +static const char __pyx_k_Signature_IntervalFile_all_hits[] = "\n :Signature: `IntervalFile.all_hits(interval, same_strand=False, overlap=0.0)`\n\n Search for the Interval `interval` this file and return **all**\n overlaps as a list.\n\n `same_strand`, if True, will only consider hits on the same strand as `interval`.\n\n `overlap` can be used to specify the fraction of overlap between\n `interval` and each feature in the IntervalFile.\n\n Example usage:\n\n >>> fn = pybedtools.example_filename('a.bed')\n\n >>> # create an Interval to query with\n >>> i = pybedtools.Interval('chr1', 1, 10000, strand='+')\n\n >>> # Create an IntervalFile out of a.bed\n >>> intervalfile = pybedtools.IntervalFile(fn)\n\n >>> # get stranded hits\n >>> intervalfile.all_hits(i, same_strand=True)\n [Interval(chr1:1-100), Interval(chr1:100-200), Interval(chr1:900-950)]\n\n "; +static const char __pyx_k_Signature_IntervalFile_any_hits[] = "\n :Signature: `IntervalFile.any_hits(interval, same_strand=False, overlap=0.0)`\n\n Return 1 if the Interval `interval` had >=1 hit in this IntervalFile, 0 otherwise.\n\n `same_strand`, if True, will only consider hits on the same strand as `interval`.\n\n `overlap` can be used to specify the fraction of overlap between\n `interval` and each feature in the IntervalFile.\n\n Example usage:\n\n >>> fn = pybedtools.example_filename('a.bed')\n\n >>> # create an Interval to query with\n >>> i = pybedtools.Interval('chr1', 1, 10000, strand='+')\n\n >>> # Create an IntervalFile out of a.bed\n >>> intervalfile = pybedtools.IntervalFile(fn)\n\n >>> # any stranded hits?\n >>> intervalfile.any_hits(i, same_strand=True)\n 1\n\n "; +static const char __pyx_k_Signature_IntervalFile_count_hi[] = "\n :Signature: `IntervalFile.count_hits(interval, same_strand=False, overlap=0.0)`\n\n Return the number of overlaps of the Interval `interval` had with this\n IntervalFile.\n\n `same_strand`, if True, will only consider hits on the same strand as\n `interval`.\n\n `overlap` can be used to specify the fraction of overlap between\n `interval` and each feature in the IntervalFile.\n\n Example usage:\n\n >>> fn = pybedtools.example_filename('a.bed')\n\n >>> # create an Interval to query with\n >>> i = pybedtools.Interval('chr1', 1, 10000, strand='+')\n\n >>> # Create an IntervalFile out of a.bed\n >>> intervalfile = pybedtools.IntervalFile(fn)\n\n >>> # get number of stranded hits\n >>> intervalfile.count_hits(i, same_strand=True)\n 3\n\n "; +static const char __pyx_k_self_intervalFile_ptr_cannot_be[] = "self.intervalFile_ptr cannot be converted to a Python object for pickling"; +static const char __pyx_k_Currently_unsupported_comparison[] = "Currently unsupported comparison -- please submit a bug report"; +static const char __pyx_k_Features_are_nested_comparison_u[] = "Features are nested -- comparison undefined"; +static const char __pyx_k_Incompatible_checksums_0x_x_vs_0[] = "Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))"; +static const char __pyx_k_IntervalFile_count_hits_line_970[] = "IntervalFile.count_hits (line 970)"; +static const char __pyx_k_create_interval_from_list_line_5[] = "create_interval_from_list (line 579)"; +static const char __pyx_k_self__bed_cannot_be_converted_to[] = "self._bed cannot be converted to a Python object for pickling"; +static PyObject *__pyx_kp_s_; +static PyObject *__pyx_n_s_AttributeError; +static PyObject *__pyx_n_s_Attributes; +static PyObject *__pyx_n_s_Attributes___init; +static PyObject *__pyx_n_s_Attributes___str; +static PyObject *__pyx_n_s_BedToolsFileError; +static PyObject *__pyx_kp_s_Class_to_map_between_a_dict_of; +static PyObject *__pyx_kp_u_Create_an_Interval_object_from; +static PyObject *__pyx_kp_s_Currently_unsupported_comparison; +static PyObject *__pyx_kp_s_Error_opening_file; +static PyObject *__pyx_kp_s_Features_are_nested_comparison_u; +static PyObject *__pyx_n_s_ID; +static PyObject *__pyx_kp_s_Incompatible_checksums_0x_x_vs_0; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_n_s_Interval; +static PyObject *__pyx_n_s_IntervalFile; +static PyObject *__pyx_kp_u_IntervalFile_all_hits_line_888; +static PyObject *__pyx_kp_u_IntervalFile_any_hits_line_934; +static PyObject *__pyx_kp_u_IntervalFile_count_hits_line_970; +static PyObject *__pyx_kp_s_IntervalFile_objects_do_not_yet; +static PyObject *__pyx_n_s_IntervalIterator; +static PyObject *__pyx_kp_s_Interval_attrs_was_not_None_but; +static PyObject *__pyx_kp_s_Interval_s_i_i; +static PyObject *__pyx_n_s_KeyError; +static PyObject *__pyx_n_s_MalformedBedLineError; +static PyObject *__pyx_n_s_Name; +static PyObject *__pyx_n_s_NotImplementedError; +static PyObject *__pyx_n_s_PROFILES_TRUE; +static PyObject *__pyx_n_s_Parent; +static PyObject *__pyx_n_s_PickleError; +static PyObject *__pyx_kp_u_Signature_IntervalFile_all_hits; +static PyObject *__pyx_kp_u_Signature_IntervalFile_any_hits; +static PyObject *__pyx_kp_u_Signature_IntervalFile_count_hi; +static PyObject *__pyx_kp_s_Start_is_greater_than_stop; +static PyObject *__pyx_n_s_StopIteration; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_UTF_8; +static PyObject *__pyx_kp_s_Unable_to_detect_format_from_s; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_kp_s__15; +static PyObject *__pyx_kp_s__19; +static PyObject *__pyx_kp_s__2; +static PyObject *__pyx_kp_s__20; +static PyObject *__pyx_kp_s__21; +static PyObject *__pyx_kp_s__22; +static PyObject *__pyx_kp_s__23; +static PyObject *__pyx_kp_s__25; +static PyObject *__pyx_kp_s__3; +static PyObject *__pyx_kp_s__4; +static PyObject *__pyx_kp_s__5; +static PyObject *__pyx_kp_s__7; +static PyObject *__pyx_kp_s__8; +static PyObject *__pyx_n_s_all_hits; +static PyObject *__pyx_n_s_append; +static PyObject *__pyx_n_s_attr_str; +static PyObject *__pyx_n_s_attr_str_2; +static PyObject *__pyx_n_s_attrs; +static PyObject *__pyx_n_b_bed; +static PyObject *__pyx_n_s_bed; +static PyObject *__pyx_n_s_browser; +static PyObject *__pyx_n_s_chrom; +static PyObject *__pyx_n_s_cline_in_traceback; +static PyObject *__pyx_n_s_close; +static PyObject *__pyx_n_s_closed; +static PyObject *__pyx_n_s_cmp; +static PyObject *__pyx_n_s_collections; +static PyObject *__pyx_n_s_count; +static PyObject *__pyx_kp_u_create_interval_from_list_line_5; +static PyObject *__pyx_n_s_defaultdict; +static PyObject *__pyx_n_s_deparse_attrs; +static PyObject *__pyx_n_s_dict; +static PyObject *__pyx_n_s_doc; +static PyObject *__pyx_n_s_e1; +static PyObject *__pyx_n_s_e2; +static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_end; +static PyObject *__pyx_n_s_enter; +static PyObject *__pyx_n_s_exit; +static PyObject *__pyx_n_s_field; +static PyObject *__pyx_kp_s_field_index_out_of_range; +static PyObject *__pyx_n_s_field_sep; +static PyObject *__pyx_n_s_fields; +static PyObject *__pyx_n_s_file_type; +static PyObject *__pyx_n_s_fn; +static PyObject *__pyx_n_s_gene_id; +static PyObject *__pyx_n_s_gene_name; +static PyObject *__pyx_n_s_getstate; +static PyObject *__pyx_n_b_gff; +static PyObject *__pyx_n_s_gff; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_indices; +static PyObject *__pyx_n_s_init; +static PyObject *__pyx_n_s_int64; +static PyObject *__pyx_n_s_integer_types; +static PyObject *__pyx_n_s_interval; +static PyObject *__pyx_n_s_intervalFile; +static PyObject *__pyx_n_s_isdigit; +static PyObject *__pyx_n_s_items; +static PyObject *__pyx_n_s_iteritems; +static PyObject *__pyx_n_s_join; +static PyObject *__pyx_n_s_k; +static PyObject *__pyx_n_s_kdict; +static PyObject *__pyx_n_s_ktype; +static PyObject *__pyx_n_s_kv; +static PyObject *__pyx_n_s_kvs; +static PyObject *__pyx_n_s_loadIntoMap; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_kp_s_malformed_line_s; +static PyObject *__pyx_n_s_map; +static PyObject *__pyx_n_s_metaclass; +static PyObject *__pyx_n_s_module; +static PyObject *__pyx_n_s_n_eq; +static PyObject *__pyx_n_s_n_quotes; +static PyObject *__pyx_n_s_n_semi; +static PyObject *__pyx_n_s_name; +static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_n_s_new; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_open; +static PyObject *__pyx_n_s_otherfields; +static PyObject *__pyx_n_s_overlap; +static PyObject *__pyx_n_s_pairs; +static PyObject *__pyx_n_s_pickle; +static PyObject *__pyx_n_s_prepare; +static PyObject *__pyx_n_s_pybedtools_cbedtools; +static PyObject *__pyx_kp_s_pybedtools_cbedtools_pyx; +static PyObject *__pyx_n_s_pyx_PickleError; +static PyObject *__pyx_n_s_pyx_checksum; +static PyObject *__pyx_n_s_pyx_result; +static PyObject *__pyx_n_s_pyx_state; +static PyObject *__pyx_n_s_pyx_type; +static PyObject *__pyx_n_s_pyx_unpickle_IntervalIterator; +static PyObject *__pyx_n_s_pyx_vtable; +static PyObject *__pyx_n_s_qualname; +static PyObject *__pyx_n_s_quoted; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_readline; +static PyObject *__pyx_n_s_reduce; +static PyObject *__pyx_n_s_reduce_cython; +static PyObject *__pyx_n_s_reduce_ex; +static PyObject *__pyx_n_s_replace; +static PyObject *__pyx_n_s_richcmp___locals_cmp; +static PyObject *__pyx_n_s_rstrip; +static PyObject *__pyx_n_s_s1; +static PyObject *__pyx_n_s_s2; +static PyObject *__pyx_kp_s_s_i; +static PyObject *__pyx_n_s_sam; +static PyObject *__pyx_n_s_same_strand; +static PyObject *__pyx_n_s_score; +static PyObject *__pyx_n_s_search; +static PyObject *__pyx_n_s_self; +static PyObject *__pyx_kp_s_self__bed_cannot_be_converted_to; +static PyObject *__pyx_kp_s_self_intervalFile_ptr_cannot_be; +static PyObject *__pyx_n_s_sep; +static PyObject *__pyx_n_s_setstate; +static PyObject *__pyx_n_s_setstate_cython; +static PyObject *__pyx_n_s_sort_keys; +static PyObject *__pyx_n_s_split; +static PyObject *__pyx_n_s_start; +static PyObject *__pyx_n_s_startswith; +static PyObject *__pyx_n_s_stop; +static PyObject *__pyx_n_s_str; +static PyObject *__pyx_n_s_strand; +static PyObject *__pyx_n_s_stream; +static PyObject *__pyx_kp_s_stringsource; +static PyObject *__pyx_n_s_strip; +static PyObject *__pyx_n_s_subprocess; +static PyObject *__pyx_n_s_sys; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_track; +static PyObject *__pyx_n_s_transcript_id; +static PyObject *__pyx_n_s_update; +static PyObject *__pyx_n_s_v; +static PyObject *__pyx_n_s_val; +static PyObject *__pyx_n_s_value; +static PyObject *__pyx_n_b_vcf; +static PyObject *__pyx_n_s_vcf; +static PyObject *__pyx_n_s_x; +static PyObject *__pyx_n_s_y; +static PyObject *__pyx_pf_10pybedtools_9cbedtools_10Attributes___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_attr_str); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_10Attributes_2__str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval___init__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_name, PyObject *__pyx_v_score, PyObject *__pyx_v_strand, PyObject *__pyx_v_otherfields); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_2__copy__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static Py_hash_t __pyx_pf_10pybedtools_9cbedtools_8Interval_4__hash__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5chrom___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5chrom_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_chrom); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, PyObject *__pyx_v_y); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6__richcmp__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_other, int __pyx_v_op); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5start___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5start_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_v_start); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_3end___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_3end_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_v_end); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_4stop___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_4stop_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_v_end); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6strand___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_6strand_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_strand); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6length___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_8deparse_attrs(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6fields___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_attrs); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5count___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_4name___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_4name_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5score___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5score_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_9file_type___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_9file_type_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_7o_start___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5o_end___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5o_amt___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_10__str__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_12__repr__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static void __pyx_pf_10pybedtools_9cbedtools_8Interval_14__dealloc__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_pf_10pybedtools_9cbedtools_8Interval_16__len__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_18__getitem__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_20__setitem__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_22append(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_24__nonzero__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_26__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_28__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_create_interval_from_list(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fields); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_2overlap(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_s1, int __pyx_v_s2, int __pyx_v_e1, int __pyx_v_e2); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator___init__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static void __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_2__dealloc__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_4__iter__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_6__next__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_8__reduce_cython__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_10__setstate_cython__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self, PyObject *__pyx_v___pyx_state); /* proto */ +static int __pyx_pf_10pybedtools_9cbedtools_12IntervalFile___init__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, PyObject *__pyx_v_intervalFile); /* proto */ +static void __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_2__dealloc__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_4__iter__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_6__next__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_2fn___get__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_9file_type___get__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_8loadIntoMap(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_10rewind(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_12seek(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, PyObject *__pyx_v_offset); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_14all_hits(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval, PyBoolObject *__pyx_v_same_strand, float __pyx_v_overlap); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_16any_hits(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval, PyBoolObject *__pyx_v_same_strand, float __pyx_v_overlap); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_18count_hits(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval, PyBoolObject *__pyx_v_same_strand, float __pyx_v_overlap); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_20__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_22__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */ +static PyObject *__pyx_pf_10pybedtools_9cbedtools_4__pyx_unpickle_IntervalIterator(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_10pybedtools_9cbedtools_Interval(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_10pybedtools_9cbedtools_IntervalIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_10pybedtools_9cbedtools_IntervalFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_items = {0, &__pyx_n_s_items, 0, 0, 0}; +static __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_iteritems = {0, &__pyx_n_s_iteritems, 0, 0, 0}; +static PyObject *__pyx_int_0; +static PyObject *__pyx_int_1; +static PyObject *__pyx_int_2; +static PyObject *__pyx_int_3; +static PyObject *__pyx_int_4; +static PyObject *__pyx_int_5; +static PyObject *__pyx_int_6; +static PyObject *__pyx_int_16; +static PyObject *__pyx_int_22915542; +static PyObject *__pyx_int_26969663; +static PyObject *__pyx_int_172054328; +static PyObject *__pyx_int_neg_1; +static PyObject *__pyx_tuple__6; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_tuple__12; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__14; +static PyObject *__pyx_tuple__16; +static PyObject *__pyx_tuple__17; +static PyObject *__pyx_tuple__18; +static PyObject *__pyx_tuple__24; +static PyObject *__pyx_tuple__26; +static PyObject *__pyx_tuple__27; +static PyObject *__pyx_tuple__28; +static PyObject *__pyx_tuple__29; +static PyObject *__pyx_tuple__30; +static PyObject *__pyx_tuple__31; +static PyObject *__pyx_tuple__32; +static PyObject *__pyx_tuple__33; +static PyObject *__pyx_tuple__34; +static PyObject *__pyx_tuple__35; +static PyObject *__pyx_tuple__36; +static PyObject *__pyx_tuple__37; +static PyObject *__pyx_tuple__38; +static PyObject *__pyx_tuple__39; +static PyObject *__pyx_tuple__40; +static PyObject *__pyx_tuple__41; +static PyObject *__pyx_tuple__42; +static PyObject *__pyx_tuple__43; +static PyObject *__pyx_tuple__44; +static PyObject *__pyx_tuple__45; +static PyObject *__pyx_tuple__46; +static PyObject *__pyx_tuple__47; +static PyObject *__pyx_tuple__48; +static PyObject *__pyx_tuple__49; +static PyObject *__pyx_tuple__50; +static PyObject *__pyx_tuple__51; +static PyObject *__pyx_tuple__52; +static PyObject *__pyx_tuple__53; +static PyObject *__pyx_tuple__55; +static PyObject *__pyx_tuple__56; +static PyObject *__pyx_tuple__58; +static PyObject *__pyx_tuple__60; +static PyObject *__pyx_codeobj__10; +static PyObject *__pyx_codeobj__54; +static PyObject *__pyx_codeobj__57; +static PyObject *__pyx_codeobj__59; +static PyObject *__pyx_codeobj__61; +/* Late includes */ + +/* "pybedtools/cbedtools.pyx":21 + * # Python byte strings automatically coerce to/from C++ strings. + * + * cdef _cppstr(s): # <<<<<<<<<<<<<< + * # Use this to handle incoming strings from Python. + * # + */ + +static PyObject *__pyx_f_10pybedtools_9cbedtools__cppstr(PyObject *__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + std::string __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_cppstr", 0); + __Pyx_INCREF(__pyx_v_s); + + /* "pybedtools/cbedtools.pyx":26 + * # C++ uses bytestrings. PY2 strings need no conversion; bare PY3 strings + * # are unicode and so must be encoded to bytestring. + * if isinstance(s, integer_types): # <<<<<<<<<<<<<< + * s = str(s) + * if isinstance(s, unicode): + */ + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_integer_types); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 26, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_IsInstance(__pyx_v_s, __pyx_t_1); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 26, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":27 + * # are unicode and so must be encoded to bytestring. + * if isinstance(s, integer_types): + * s = str(s) # <<<<<<<<<<<<<< + * if isinstance(s, unicode): + * s = s.encode('UTF-8') + */ + __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_s); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 27, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_s, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":26 + * # C++ uses bytestrings. PY2 strings need no conversion; bare PY3 strings + * # are unicode and so must be encoded to bytestring. + * if isinstance(s, integer_types): # <<<<<<<<<<<<<< + * s = str(s) + * if isinstance(s, unicode): + */ + } + + /* "pybedtools/cbedtools.pyx":28 + * if isinstance(s, integer_types): + * s = str(s) + * if isinstance(s, unicode): # <<<<<<<<<<<<<< + * s = s.encode('UTF-8') + * return <string> s + */ + __pyx_t_3 = PyUnicode_Check(__pyx_v_s); + __pyx_t_2 = (__pyx_t_3 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":29 + * s = str(s) + * if isinstance(s, unicode): + * s = s.encode('UTF-8') # <<<<<<<<<<<<<< + * return <string> s + * + */ + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_s, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 29, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + __pyx_t_1 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_5, __pyx_kp_s_UTF_8) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_kp_s_UTF_8); + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 29, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF_SET(__pyx_v_s, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":28 + * if isinstance(s, integer_types): + * s = str(s) + * if isinstance(s, unicode): # <<<<<<<<<<<<<< + * s = s.encode('UTF-8') + * return <string> s + */ + } + + /* "pybedtools/cbedtools.pyx":30 + * if isinstance(s, unicode): + * s = s.encode('UTF-8') + * return <string> s # <<<<<<<<<<<<<< + * + * cdef _pystr(string s): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_6 = __pyx_convert_string_from_py_std__in_string(__pyx_v_s); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 30, __pyx_L1_error) + __pyx_t_1 = __pyx_convert_PyBytes_string_to_py_std__in_string(((std::string)__pyx_t_6)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 30, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":21 + * # Python byte strings automatically coerce to/from C++ strings. + * + * cdef _cppstr(s): # <<<<<<<<<<<<<< + * # Use this to handle incoming strings from Python. + * # + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pybedtools.cbedtools._cppstr", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_s); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":32 + * return <string> s + * + * cdef _pystr(string s): # <<<<<<<<<<<<<< + * # Use this to prepare a string for sending to Python. + * # + */ + +static PyObject *__pyx_f_10pybedtools_9cbedtools__pystr(std::string __pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_pystr", 0); + + /* "pybedtools/cbedtools.pyx":36 + * # + * # Always returns unicode. + * return s.decode('UTF-8', 'strict') # <<<<<<<<<<<<<< + * + * integer_types = (int, long, np.int64) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_decode_cpp_string(__pyx_v_s, 0, PY_SSIZE_T_MAX, NULL, NULL, PyUnicode_DecodeUTF8); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 36, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":32 + * return <string> s + * + * cdef _pystr(string s): # <<<<<<<<<<<<<< + * # Use this to prepare a string for sending to Python. + * # + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools._pystr", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":146 + * """ + * + * def __init__(self, attr_str=""): # <<<<<<<<<<<<<< + * attr_str = str(attr_str) + * self._attr_str = attr_str + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_10Attributes_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_10pybedtools_9cbedtools_10Attributes_1__init__ = {"__init__", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_10Attributes_1__init__, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_10Attributes_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_attr_str = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_attr_str,0}; + PyObject* values[2] = {0,0}; + values[1] = ((PyObject *)((PyObject*)__pyx_kp_s_)); + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_self)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_attr_str); + if (value) { values[1] = value; kw_args--; } + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 146, __pyx_L3_error) + } + } else { + switch (PyTuple_GET_SIZE(__pyx_args)) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_self = values[0]; + __pyx_v_attr_str = values[1]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 146, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.Attributes.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_10Attributes___init__(__pyx_self, __pyx_v_self, __pyx_v_attr_str); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_10Attributes___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_attr_str) { + PyObject *__pyx_v_n_semi = NULL; + PyObject *__pyx_v_n_eq = NULL; + CYTHON_UNUSED PyObject *__pyx_v_n_quotes = NULL; + PyObject *__pyx_v_kvs = NULL; + PyObject *__pyx_v_field = NULL; + PyObject *__pyx_v_value = NULL; + PyObject *__pyx_v_kv = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + Py_ssize_t __pyx_t_7; + PyObject *(*__pyx_t_8)(PyObject *); + PyObject *__pyx_t_9 = NULL; + int __pyx_t_10; + PyObject *__pyx_t_11 = NULL; + PyObject *(*__pyx_t_12)(PyObject *); + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 0); + __Pyx_INCREF(__pyx_v_attr_str); + + /* "pybedtools/cbedtools.pyx":147 + * + * def __init__(self, attr_str=""): + * attr_str = str(attr_str) # <<<<<<<<<<<<<< + * self._attr_str = attr_str + * self.sort_keys = False + */ + __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_attr_str); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 147, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_attr_str, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":148 + * def __init__(self, attr_str=""): + * attr_str = str(attr_str) + * self._attr_str = attr_str # <<<<<<<<<<<<<< + * self.sort_keys = False + * + */ + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_attr_str_2, __pyx_v_attr_str) < 0) __PYX_ERR(0, 148, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":149 + * attr_str = str(attr_str) + * self._attr_str = attr_str + * self.sort_keys = False # <<<<<<<<<<<<<< + * + * # in general, GFF files will have either as many '=' as ';' + */ + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_sort_keys, Py_False) < 0) __PYX_ERR(0, 149, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":153 + * # in general, GFF files will have either as many '=' as ';' + * # (or ';'-1 if there's no trailing ';') + * n_semi = attr_str.count(';') # <<<<<<<<<<<<<< + * n_eq = attr_str.count('=') + * n_quotes = attr_str.count('"') + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_attr_str, __pyx_n_s_count); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 153, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_3, __pyx_kp_s__2) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_kp_s__2); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 153, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_n_semi = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":154 + * # (or ';'-1 if there's no trailing ';') + * n_semi = attr_str.count(';') + * n_eq = attr_str.count('=') # <<<<<<<<<<<<<< + * n_quotes = attr_str.count('"') + * + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_attr_str, __pyx_n_s_count); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 154, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_3, __pyx_kp_s__3) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_kp_s__3); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 154, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_n_eq = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":155 + * n_semi = attr_str.count(';') + * n_eq = attr_str.count('=') + * n_quotes = attr_str.count('"') # <<<<<<<<<<<<<< + * + * if n_eq > n_semi - 1: + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_attr_str, __pyx_n_s_count); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 155, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_3, __pyx_kp_s__4) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_kp_s__4); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 155, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_n_quotes = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":157 + * n_quotes = attr_str.count('"') + * + * if n_eq > n_semi - 1: # <<<<<<<<<<<<<< + * self.sep, self.field_sep = (';', '=') + * else: + */ + __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_v_n_semi, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 157, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_n_eq, __pyx_t_1, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 157, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 157, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__pyx_t_4) { + + /* "pybedtools/cbedtools.pyx":158 + * + * if n_eq > n_semi - 1: + * self.sep, self.field_sep = (';', '=') # <<<<<<<<<<<<<< + * else: + * self.sep, self.field_sep = (';', ' ') + */ + __pyx_t_2 = __pyx_kp_s__2; + __Pyx_INCREF(__pyx_t_2); + __pyx_t_1 = __pyx_kp_s__3; + __Pyx_INCREF(__pyx_t_1); + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_sep, __pyx_t_2) < 0) __PYX_ERR(0, 158, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_field_sep, __pyx_t_1) < 0) __PYX_ERR(0, 158, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":157 + * n_quotes = attr_str.count('"') + * + * if n_eq > n_semi - 1: # <<<<<<<<<<<<<< + * self.sep, self.field_sep = (';', '=') + * else: + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":160 + * self.sep, self.field_sep = (';', '=') + * else: + * self.sep, self.field_sep = (';', ' ') # <<<<<<<<<<<<<< + * + * self._quoted = {} + */ + /*else*/ { + __pyx_t_1 = __pyx_kp_s__2; + __Pyx_INCREF(__pyx_t_1); + __pyx_t_2 = __pyx_kp_s__5; + __Pyx_INCREF(__pyx_t_2); + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_sep, __pyx_t_1) < 0) __PYX_ERR(0, 160, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_field_sep, __pyx_t_2) < 0) __PYX_ERR(0, 160, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + __pyx_L3:; + + /* "pybedtools/cbedtools.pyx":162 + * self.sep, self.field_sep = (';', ' ') + * + * self._quoted = {} # <<<<<<<<<<<<<< + * + * # TODO: pathological case . . . detect this as GFF: + */ + __pyx_t_2 = __Pyx_PyDict_NewPresized(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 162, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_quoted, __pyx_t_2) < 0) __PYX_ERR(0, 162, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":173 + * + * # quick exit + * if attr_str == "": # <<<<<<<<<<<<<< + * return + * + */ + __pyx_t_4 = (__Pyx_PyString_Equals(__pyx_v_attr_str, __pyx_kp_s_, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 173, __pyx_L1_error) + if (__pyx_t_4) { + + /* "pybedtools/cbedtools.pyx":174 + * # quick exit + * if attr_str == "": + * return # <<<<<<<<<<<<<< + * + * kvs = map(str.strip, attr_str.strip().split(self.sep)) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":173 + * + * # quick exit + * if attr_str == "": # <<<<<<<<<<<<<< + * return + * + */ + } + + /* "pybedtools/cbedtools.pyx":176 + * return + * + * kvs = map(str.strip, attr_str.strip().split(self.sep)) # <<<<<<<<<<<<<< + * for field, value in [kv.split(self.field_sep, 1) for kv in kvs if kv]: + * if value.count('"') == 2: + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)(&PyString_Type)), __pyx_n_s_strip); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_attr_str, __pyx_n_s_strip); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_5))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_5, function); + } + } + __pyx_t_3 = (__pyx_t_6) ? __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6) : __Pyx_PyObject_CallNoArg(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_split); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_sep); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_6 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_5))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_5, function); + } + } + __pyx_t_1 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_5, __pyx_t_6, __pyx_t_3) : __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_3); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1); + __pyx_t_2 = 0; + __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 176, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_v_kvs = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":177 + * + * kvs = map(str.strip, attr_str.strip().split(self.sep)) + * for field, value in [kv.split(self.field_sep, 1) for kv in kvs if kv]: # <<<<<<<<<<<<<< + * if value.count('"') == 2: + * self._quoted[field] = True + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (likely(PyList_CheckExact(__pyx_v_kvs)) || PyTuple_CheckExact(__pyx_v_kvs)) { + __pyx_t_5 = __pyx_v_kvs; __Pyx_INCREF(__pyx_t_5); __pyx_t_7 = 0; + __pyx_t_8 = NULL; + } else { + __pyx_t_7 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_v_kvs); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_8 = Py_TYPE(__pyx_t_5)->tp_iternext; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 177, __pyx_L1_error) + } + for (;;) { + if (likely(!__pyx_t_8)) { + if (likely(PyList_CheckExact(__pyx_t_5))) { + if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_5)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) __PYX_ERR(0, 177, __pyx_L1_error) + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + #endif + } else { + if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_5)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) __PYX_ERR(0, 177, __pyx_L1_error) + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + #endif + } + } else { + __pyx_t_2 = __pyx_t_8(__pyx_t_5); + if (unlikely(!__pyx_t_2)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 177, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_2); + } + __Pyx_XDECREF_SET(__pyx_v_kv, __pyx_t_2); + __pyx_t_2 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_kv); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 177, __pyx_L1_error) + if (__pyx_t_4) { + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_kv, __pyx_n_s_split); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_field_sep); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __pyx_t_9 = NULL; + __pyx_t_10 = 0; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_9)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_9); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + __pyx_t_10 = 1; + } + } + #if CYTHON_FAST_PYCALL + if (PyFunction_Check(__pyx_t_3)) { + PyObject *__pyx_temp[3] = {__pyx_t_9, __pyx_t_6, __pyx_int_1}; + __pyx_t_2 = __Pyx_PyFunction_FastCall(__pyx_t_3, __pyx_temp+1-__pyx_t_10, 2+__pyx_t_10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + } else + #endif + #if CYTHON_FAST_PYCCALL + if (__Pyx_PyFastCFunction_Check(__pyx_t_3)) { + PyObject *__pyx_temp[3] = {__pyx_t_9, __pyx_t_6, __pyx_int_1}; + __pyx_t_2 = __Pyx_PyCFunction_FastCall(__pyx_t_3, __pyx_temp+1-__pyx_t_10, 2+__pyx_t_10); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + } else + #endif + { + __pyx_t_11 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_11); + if (__pyx_t_9) { + __Pyx_GIVEREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9); __pyx_t_9 = NULL; + } + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_11, 0+__pyx_t_10, __pyx_t_6); + __Pyx_INCREF(__pyx_int_1); + __Pyx_GIVEREF(__pyx_int_1); + PyTuple_SET_ITEM(__pyx_t_11, 1+__pyx_t_10, __pyx_int_1); + __pyx_t_6 = 0; + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_11, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + } + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_2))) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + } + } + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = __pyx_t_1; __Pyx_INCREF(__pyx_t_5); __pyx_t_7 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + for (;;) { + if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_5)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) __PYX_ERR(0, 177, __pyx_L1_error) + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_5, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + #endif + if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) { + PyObject* sequence = __pyx_t_1; + Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + __PYX_ERR(0, 177, __pyx_L1_error) + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + if (likely(PyTuple_CheckExact(sequence))) { + __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_3 = PyTuple_GET_ITEM(sequence, 1); + } else { + __pyx_t_2 = PyList_GET_ITEM(sequence, 0); + __pyx_t_3 = PyList_GET_ITEM(sequence, 1); + } + __Pyx_INCREF(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + #else + __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + #endif + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } else { + Py_ssize_t index = -1; + __pyx_t_11 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 177, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_11); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext; + index = 0; __pyx_t_2 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_2)) goto __pyx_L10_unpacking_failed; + __Pyx_GOTREF(__pyx_t_2); + index = 1; __pyx_t_3 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_3)) goto __pyx_L10_unpacking_failed; + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) __PYX_ERR(0, 177, __pyx_L1_error) + __pyx_t_12 = NULL; + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + goto __pyx_L11_unpacking_done; + __pyx_L10_unpacking_failed:; + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __pyx_t_12 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); + __PYX_ERR(0, 177, __pyx_L1_error) + __pyx_L11_unpacking_done:; + } + __Pyx_XDECREF_SET(__pyx_v_field, __pyx_t_2); + __pyx_t_2 = 0; + __Pyx_XDECREF_SET(__pyx_v_value, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":178 + * kvs = map(str.strip, attr_str.strip().split(self.sep)) + * for field, value in [kv.split(self.field_sep, 1) for kv in kvs if kv]: + * if value.count('"') == 2: # <<<<<<<<<<<<<< + * self._quoted[field] = True + * self[field] = value.replace('"', '') + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_value, __pyx_n_s_count); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 178, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_2)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_2); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + } + } + __pyx_t_1 = (__pyx_t_2) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_2, __pyx_kp_s__4) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_kp_s__4); + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 178, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyInt_EqObjC(__pyx_t_1, __pyx_int_2, 2, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 178, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 178, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (__pyx_t_4) { + + /* "pybedtools/cbedtools.pyx":179 + * for field, value in [kv.split(self.field_sep, 1) for kv in kvs if kv]: + * if value.count('"') == 2: + * self._quoted[field] = True # <<<<<<<<<<<<<< + * self[field] = value.replace('"', '') + * + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_quoted); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 179, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (unlikely(PyObject_SetItem(__pyx_t_3, __pyx_v_field, Py_True) < 0)) __PYX_ERR(0, 179, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":178 + * kvs = map(str.strip, attr_str.strip().split(self.sep)) + * for field, value in [kv.split(self.field_sep, 1) for kv in kvs if kv]: + * if value.count('"') == 2: # <<<<<<<<<<<<<< + * self._quoted[field] = True + * self[field] = value.replace('"', '') + */ + } + + /* "pybedtools/cbedtools.pyx":180 + * if value.count('"') == 2: + * self._quoted[field] = True + * self[field] = value.replace('"', '') # <<<<<<<<<<<<<< + * + * def __str__(self): + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_value, __pyx_n_s_replace); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(PyObject_SetItem(__pyx_v_self, __pyx_v_field, __pyx_t_1) < 0)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":177 + * + * kvs = map(str.strip, attr_str.strip().split(self.sep)) + * for field, value in [kv.split(self.field_sep, 1) for kv in kvs if kv]: # <<<<<<<<<<<<<< + * if value.count('"') == 2: + * self._quoted[field] = True + */ + } + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":146 + * """ + * + * def __init__(self, attr_str=""): # <<<<<<<<<<<<<< + * attr_str = str(attr_str) + * self._attr_str = attr_str + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_XDECREF(__pyx_t_11); + __Pyx_AddTraceback("pybedtools.cbedtools.Attributes.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_n_semi); + __Pyx_XDECREF(__pyx_v_n_eq); + __Pyx_XDECREF(__pyx_v_n_quotes); + __Pyx_XDECREF(__pyx_v_kvs); + __Pyx_XDECREF(__pyx_v_field); + __Pyx_XDECREF(__pyx_v_value); + __Pyx_XDECREF(__pyx_v_kv); + __Pyx_XDECREF(__pyx_v_attr_str); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":182 + * self[field] = value.replace('"', '') + * + * def __str__(self): # <<<<<<<<<<<<<< + * # stringify all items first + * items = [] + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_10Attributes_3__str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static PyMethodDef __pyx_mdef_10pybedtools_9cbedtools_10Attributes_3__str__ = {"__str__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_10Attributes_3__str__, METH_O, 0}; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_10Attributes_3__str__(PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__str__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_10Attributes_2__str__(__pyx_self, ((PyObject *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_10Attributes_2__str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { + PyObject *__pyx_v_items = NULL; + PyObject *__pyx_v_field = NULL; + PyObject *__pyx_v_val = NULL; + PyObject *__pyx_v_pairs = NULL; + PyObject *__pyx_v_k = NULL; + PyObject *__pyx_v_v = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + Py_ssize_t __pyx_t_3; + PyObject *(*__pyx_t_4)(PyObject *); + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *(*__pyx_t_8)(PyObject *); + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + int __pyx_t_12; + int __pyx_t_13; + int __pyx_t_14; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__str__", 0); + + /* "pybedtools/cbedtools.pyx":184 + * def __str__(self): + * # stringify all items first + * items = [] # <<<<<<<<<<<<<< + * for field, val in dict.iteritems(self): + * try: + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 184, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_items = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":185 + * # stringify all items first + * items = [] + * for field, val in dict.iteritems(self): # <<<<<<<<<<<<<< + * try: + * if self._quoted[field]: + */ + if (unlikely(__pyx_v_self == Py_None)) { + PyErr_Format(PyExc_TypeError, "descriptor '%s' requires a '%s' object but received a 'NoneType'", "iteritems", "dict"); + __PYX_ERR(0, 185, __pyx_L1_error) + } + if (!(likely(PyDict_Check(__pyx_v_self))||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "dict", Py_TYPE(__pyx_v_self)->tp_name), 0))) __PYX_ERR(0, 185, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyDict_IterItems(((PyObject*)__pyx_v_self)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) { + __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; + __pyx_t_4 = NULL; + } else { + __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 185, __pyx_L1_error) + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + for (;;) { + if (likely(!__pyx_t_4)) { + if (likely(PyList_CheckExact(__pyx_t_2))) { + if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 185, __pyx_L1_error) + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + #endif + } else { + if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 185, __pyx_L1_error) + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + #endif + } + } else { + __pyx_t_1 = __pyx_t_4(__pyx_t_2); + if (unlikely(!__pyx_t_1)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 185, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_1); + } + if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) { + PyObject* sequence = __pyx_t_1; + Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + __PYX_ERR(0, 185, __pyx_L1_error) + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + if (likely(PyTuple_CheckExact(sequence))) { + __pyx_t_5 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_6 = PyTuple_GET_ITEM(sequence, 1); + } else { + __pyx_t_5 = PyList_GET_ITEM(sequence, 0); + __pyx_t_6 = PyList_GET_ITEM(sequence, 1); + } + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + #else + __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + #endif + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } else { + Py_ssize_t index = -1; + __pyx_t_7 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 185, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext; + index = 0; __pyx_t_5 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_5)) goto __pyx_L5_unpacking_failed; + __Pyx_GOTREF(__pyx_t_5); + index = 1; __pyx_t_6 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_6)) goto __pyx_L5_unpacking_failed; + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) __PYX_ERR(0, 185, __pyx_L1_error) + __pyx_t_8 = NULL; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + goto __pyx_L6_unpacking_done; + __pyx_L5_unpacking_failed:; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_8 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); + __PYX_ERR(0, 185, __pyx_L1_error) + __pyx_L6_unpacking_done:; + } + __Pyx_XDECREF_SET(__pyx_v_field, __pyx_t_5); + __pyx_t_5 = 0; + __Pyx_XDECREF_SET(__pyx_v_val, __pyx_t_6); + __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":186 + * items = [] + * for field, val in dict.iteritems(self): + * try: # <<<<<<<<<<<<<< + * if self._quoted[field]: + * val = '"' + str(val) + '"' + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11); + __Pyx_XGOTREF(__pyx_t_9); + __Pyx_XGOTREF(__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_11); + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":187 + * for field, val in dict.iteritems(self): + * try: + * if self._quoted[field]: # <<<<<<<<<<<<<< + * val = '"' + str(val) + '"' + * except KeyError: + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_quoted); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 187, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_6 = __Pyx_PyObject_GetItem(__pyx_t_1, __pyx_v_field); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 187, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_12 < 0)) __PYX_ERR(0, 187, __pyx_L7_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + if (__pyx_t_12) { + + /* "pybedtools/cbedtools.pyx":188 + * try: + * if self._quoted[field]: + * val = '"' + str(val) + '"' # <<<<<<<<<<<<<< + * except KeyError: + * pass + */ + __pyx_t_6 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_val); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 188, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_6); + __pyx_t_1 = PyNumber_Add(__pyx_kp_s__4, __pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 188, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_6 = PyNumber_Add(__pyx_t_1, __pyx_kp_s__4); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 188, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF_SET(__pyx_v_val, __pyx_t_6); + __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":187 + * for field, val in dict.iteritems(self): + * try: + * if self._quoted[field]: # <<<<<<<<<<<<<< + * val = '"' + str(val) + '"' + * except KeyError: + */ + } + + /* "pybedtools/cbedtools.pyx":186 + * items = [] + * for field, val in dict.iteritems(self): + * try: # <<<<<<<<<<<<<< + * if self._quoted[field]: + * val = '"' + str(val) + '"' + */ + } + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0; + goto __pyx_L14_try_end; + __pyx_L7_error:; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":189 + * if self._quoted[field]: + * val = '"' + str(val) + '"' + * except KeyError: # <<<<<<<<<<<<<< + * pass + * items.append((field, val)) + */ + __pyx_t_13 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError); + if (__pyx_t_13) { + __Pyx_ErrRestore(0,0,0); + goto __pyx_L8_exception_handled; + } + goto __pyx_L9_except_error; + __pyx_L9_except_error:; + + /* "pybedtools/cbedtools.pyx":186 + * items = [] + * for field, val in dict.iteritems(self): + * try: # <<<<<<<<<<<<<< + * if self._quoted[field]: + * val = '"' + str(val) + '"' + */ + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11); + goto __pyx_L1_error; + __pyx_L8_exception_handled:; + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11); + __pyx_L14_try_end:; + } + + /* "pybedtools/cbedtools.pyx":191 + * except KeyError: + * pass + * items.append((field, val)) # <<<<<<<<<<<<<< + * + * pairs = [] + */ + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 191, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_INCREF(__pyx_v_field); + __Pyx_GIVEREF(__pyx_v_field); + PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_field); + __Pyx_INCREF(__pyx_v_val); + __Pyx_GIVEREF(__pyx_v_val); + PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_val); + __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_items, __pyx_t_6); if (unlikely(__pyx_t_14 == ((int)-1))) __PYX_ERR(0, 191, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":185 + * # stringify all items first + * items = [] + * for field, val in dict.iteritems(self): # <<<<<<<<<<<<<< + * try: + * if self._quoted[field]: + */ + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":193 + * items.append((field, val)) + * + * pairs = [] # <<<<<<<<<<<<<< + * if self.sort_keys: + * items.sort() + */ + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 193, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_pairs = ((PyObject*)__pyx_t_2); + __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":194 + * + * pairs = [] + * if self.sort_keys: # <<<<<<<<<<<<<< + * items.sort() + * for k, v in items: + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_sort_keys); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 194, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) __PYX_ERR(0, 194, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__pyx_t_12) { + + /* "pybedtools/cbedtools.pyx":195 + * pairs = [] + * if self.sort_keys: + * items.sort() # <<<<<<<<<<<<<< + * for k, v in items: + * pairs.append(self.field_sep.join([k, v])) + */ + __pyx_t_14 = PyList_Sort(__pyx_v_items); if (unlikely(__pyx_t_14 == ((int)-1))) __PYX_ERR(0, 195, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":194 + * + * pairs = [] + * if self.sort_keys: # <<<<<<<<<<<<<< + * items.sort() + * for k, v in items: + */ + } + + /* "pybedtools/cbedtools.pyx":196 + * if self.sort_keys: + * items.sort() + * for k, v in items: # <<<<<<<<<<<<<< + * pairs.append(self.field_sep.join([k, v])) + * + */ + __pyx_t_2 = __pyx_v_items; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; + for (;;) { + if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 196, __pyx_L1_error) + #else + __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + #endif + if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { + PyObject* sequence = __pyx_t_6; + Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + __PYX_ERR(0, 196, __pyx_L1_error) + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + if (likely(PyTuple_CheckExact(sequence))) { + __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_5 = PyTuple_GET_ITEM(sequence, 1); + } else { + __pyx_t_1 = PyList_GET_ITEM(sequence, 0); + __pyx_t_5 = PyList_GET_ITEM(sequence, 1); + } + __Pyx_INCREF(__pyx_t_1); + __Pyx_INCREF(__pyx_t_5); + #else + __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + #endif + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + } else { + Py_ssize_t index = -1; + __pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 196, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext; + index = 0; __pyx_t_1 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L19_unpacking_failed; + __Pyx_GOTREF(__pyx_t_1); + index = 1; __pyx_t_5 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_5)) goto __pyx_L19_unpacking_failed; + __Pyx_GOTREF(__pyx_t_5); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) __PYX_ERR(0, 196, __pyx_L1_error) + __pyx_t_8 = NULL; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + goto __pyx_L20_unpacking_done; + __pyx_L19_unpacking_failed:; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_8 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); + __PYX_ERR(0, 196, __pyx_L1_error) + __pyx_L20_unpacking_done:; + } + __Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_1); + __pyx_t_1 = 0; + __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_5); + __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":197 + * items.sort() + * for k, v in items: + * pairs.append(self.field_sep.join([k, v])) # <<<<<<<<<<<<<< + * + * return self.sep.join(pairs) + self.sep + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_field_sep); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 197, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_join); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 197, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = PyList_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 197, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_INCREF(__pyx_v_k); + __Pyx_GIVEREF(__pyx_v_k); + PyList_SET_ITEM(__pyx_t_5, 0, __pyx_v_k); + __Pyx_INCREF(__pyx_v_v); + __Pyx_GIVEREF(__pyx_v_v); + PyList_SET_ITEM(__pyx_t_5, 1, __pyx_v_v); + __pyx_t_7 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_7)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_7); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_6 = (__pyx_t_7) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_7, __pyx_t_5) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_5); + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 197, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_pairs, __pyx_t_6); if (unlikely(__pyx_t_14 == ((int)-1))) __PYX_ERR(0, 197, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":196 + * if self.sort_keys: + * items.sort() + * for k, v in items: # <<<<<<<<<<<<<< + * pairs.append(self.field_sep.join([k, v])) + * + */ + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":199 + * pairs.append(self.field_sep.join([k, v])) + * + * return self.sep.join(pairs) + self.sep # <<<<<<<<<<<<<< + * + * cdef class Interval: + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_sep); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 199, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_join); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 199, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_6 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_2 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_6, __pyx_v_pairs) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_v_pairs); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 199, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_sep); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 199, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 199, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_r = __pyx_t_6; + __pyx_t_6 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":182 + * self[field] = value.replace('"', '') + * + * def __str__(self): # <<<<<<<<<<<<<< + * # stringify all items first + * items = [] + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_AddTraceback("pybedtools.cbedtools.Attributes.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_items); + __Pyx_XDECREF(__pyx_v_field); + __Pyx_XDECREF(__pyx_v_val); + __Pyx_XDECREF(__pyx_v_pairs); + __Pyx_XDECREF(__pyx_v_k); + __Pyx_XDECREF(__pyx_v_v); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":242 + * + * """ + * def __init__(self, chrom, start, end, name=".", score=".", strand=".", otherfields=None): # <<<<<<<<<<<<<< + * if otherfields is None: + * otherfields = [] + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_chrom = 0; + PyObject *__pyx_v_start = 0; + PyObject *__pyx_v_end = 0; + PyObject *__pyx_v_name = 0; + PyObject *__pyx_v_score = 0; + PyObject *__pyx_v_strand = 0; + PyObject *__pyx_v_otherfields = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_chrom,&__pyx_n_s_start,&__pyx_n_s_end,&__pyx_n_s_name,&__pyx_n_s_score,&__pyx_n_s_strand,&__pyx_n_s_otherfields,0}; + PyObject* values[7] = {0,0,0,0,0,0,0}; + values[3] = ((PyObject *)__pyx_kp_s__7); + values[4] = ((PyObject *)__pyx_kp_s__7); + values[5] = ((PyObject *)__pyx_kp_s__7); + values[6] = ((PyObject *)Py_None); + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6); + CYTHON_FALLTHROUGH; + case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); + CYTHON_FALLTHROUGH; + case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; + case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_chrom)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_start)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 7, 1); __PYX_ERR(0, 242, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_end)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 7, 2); __PYX_ERR(0, 242, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 3: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_name); + if (value) { values[3] = value; kw_args--; } + } + CYTHON_FALLTHROUGH; + case 4: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_score); + if (value) { values[4] = value; kw_args--; } + } + CYTHON_FALLTHROUGH; + case 5: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_strand); + if (value) { values[5] = value; kw_args--; } + } + CYTHON_FALLTHROUGH; + case 6: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_otherfields); + if (value) { values[6] = value; kw_args--; } + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 242, __pyx_L3_error) + } + } else { + switch (PyTuple_GET_SIZE(__pyx_args)) { + case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6); + CYTHON_FALLTHROUGH; + case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); + CYTHON_FALLTHROUGH; + case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + CYTHON_FALLTHROUGH; + case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_chrom = values[0]; + __pyx_v_start = values[1]; + __pyx_v_end = values[2]; + __pyx_v_name = values[3]; + __pyx_v_score = values[4]; + __pyx_v_strand = values[5]; + __pyx_v_otherfields = values[6]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 0, 3, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 242, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval___init__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), __pyx_v_chrom, __pyx_v_start, __pyx_v_end, __pyx_v_name, __pyx_v_score, __pyx_v_strand, __pyx_v_otherfields); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval___init__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_name, PyObject *__pyx_v_score, PyObject *__pyx_v_strand, PyObject *__pyx_v_otherfields) { + PyObject *__pyx_v_fields = NULL; + PyObject *__pyx_v_i = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + Py_ssize_t __pyx_t_5; + PyObject *(*__pyx_t_6)(PyObject *); + PyObject *__pyx_t_7 = NULL; + std::string __pyx_t_8; + CHRPOS __pyx_t_9; + CHRPOS __pyx_t_10; + std::string __pyx_t_11; + std::string __pyx_t_12; + std::string __pyx_t_13; + std::vector<std::string> __pyx_t_14; + PyObject *__pyx_t_15 = NULL; + PyObject *__pyx_t_16 = NULL; + PyObject *__pyx_t_17 = NULL; + PyObject *__pyx_t_18 = NULL; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 0); + __Pyx_INCREF(__pyx_v_otherfields); + + /* "pybedtools/cbedtools.pyx":243 + * """ + * def __init__(self, chrom, start, end, name=".", score=".", strand=".", otherfields=None): + * if otherfields is None: # <<<<<<<<<<<<<< + * otherfields = [] + * otherfields = [_cppstr(i) for i in otherfields] + */ + __pyx_t_1 = (__pyx_v_otherfields == Py_None); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":244 + * def __init__(self, chrom, start, end, name=".", score=".", strand=".", otherfields=None): + * if otherfields is None: + * otherfields = [] # <<<<<<<<<<<<<< + * otherfields = [_cppstr(i) for i in otherfields] + * self._bed = new BED( + */ + __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 244, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF_SET(__pyx_v_otherfields, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":243 + * """ + * def __init__(self, chrom, start, end, name=".", score=".", strand=".", otherfields=None): + * if otherfields is None: # <<<<<<<<<<<<<< + * otherfields = [] + * otherfields = [_cppstr(i) for i in otherfields] + */ + } + + /* "pybedtools/cbedtools.pyx":245 + * if otherfields is None: + * otherfields = [] + * otherfields = [_cppstr(i) for i in otherfields] # <<<<<<<<<<<<<< + * self._bed = new BED( + * _cppstr(chrom), start, end, _cppstr(name), _cppstr(score), + */ + __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 245, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (likely(PyList_CheckExact(__pyx_v_otherfields)) || PyTuple_CheckExact(__pyx_v_otherfields)) { + __pyx_t_4 = __pyx_v_otherfields; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0; + __pyx_t_6 = NULL; + } else { + __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_otherfields); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 245, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 245, __pyx_L1_error) + } + for (;;) { + if (likely(!__pyx_t_6)) { + if (likely(PyList_CheckExact(__pyx_t_4))) { + if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(0, 245, __pyx_L1_error) + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 245, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + #endif + } else { + if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) __PYX_ERR(0, 245, __pyx_L1_error) + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 245, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + #endif + } + } else { + __pyx_t_7 = __pyx_t_6(__pyx_t_4); + if (unlikely(!__pyx_t_7)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 245, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_7); + } + __Pyx_XDECREF_SET(__pyx_v_i, __pyx_t_7); + __pyx_t_7 = 0; + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_i); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 245, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) __PYX_ERR(0, 245, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + } + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF_SET(__pyx_v_otherfields, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":247 + * otherfields = [_cppstr(i) for i in otherfields] + * self._bed = new BED( + * _cppstr(chrom), start, end, _cppstr(name), _cppstr(score), # <<<<<<<<<<<<<< + * _cppstr(strand), otherfields) + * + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_chrom); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 247, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_8 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 247, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_9 = __Pyx_PyInt_As_CHRPOS(__pyx_v_start); if (unlikely((__pyx_t_9 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 247, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyInt_As_CHRPOS(__pyx_v_end); if (unlikely((__pyx_t_10 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 247, __pyx_L1_error) + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_name); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 247, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_11 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 247, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_score); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 247, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_12 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 247, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":248 + * self._bed = new BED( + * _cppstr(chrom), start, end, _cppstr(name), _cppstr(score), + * _cppstr(strand), otherfields) # <<<<<<<<<<<<<< + * + * #self._bed.chrom = _cppstr(chrom) + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_strand); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 248, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_13 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 248, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_14 = __pyx_convert_vector_from_py_std_3a__3a_string(__pyx_v_otherfields); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 248, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":246 + * otherfields = [] + * otherfields = [_cppstr(i) for i in otherfields] + * self._bed = new BED( # <<<<<<<<<<<<<< + * _cppstr(chrom), start, end, _cppstr(name), _cppstr(score), + * _cppstr(strand), otherfields) + */ + __pyx_v_self->_bed = new BED(__pyx_t_8, __pyx_t_9, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_t_14); + + /* "pybedtools/cbedtools.pyx":256 + * #self._bed.score = _cppstr(score) + * #self._bed.strand = _cppstr(strand) + * fields = [_cppstr(chrom), _cppstr(str(start)), _cppstr(str(end)), _cppstr(name), _cppstr(score), _cppstr(strand)] # <<<<<<<<<<<<<< + * fields.extend(otherfields) + * self._bed.fields = fields + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_chrom); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_start); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_4); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_end); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_15 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_4); if (unlikely(!__pyx_t_15)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_15); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_name); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_16 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_score); if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_16); + __pyx_t_17 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_strand); if (unlikely(!__pyx_t_17)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_17); + __pyx_t_18 = PyList_New(6); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 256, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_18); + __Pyx_GIVEREF(__pyx_t_3); + PyList_SET_ITEM(__pyx_t_18, 0, __pyx_t_3); + __Pyx_GIVEREF(__pyx_t_7); + PyList_SET_ITEM(__pyx_t_18, 1, __pyx_t_7); + __Pyx_GIVEREF(__pyx_t_15); + PyList_SET_ITEM(__pyx_t_18, 2, __pyx_t_15); + __Pyx_GIVEREF(__pyx_t_4); + PyList_SET_ITEM(__pyx_t_18, 3, __pyx_t_4); + __Pyx_GIVEREF(__pyx_t_16); + PyList_SET_ITEM(__pyx_t_18, 4, __pyx_t_16); + __Pyx_GIVEREF(__pyx_t_17); + PyList_SET_ITEM(__pyx_t_18, 5, __pyx_t_17); + __pyx_t_3 = 0; + __pyx_t_7 = 0; + __pyx_t_15 = 0; + __pyx_t_4 = 0; + __pyx_t_16 = 0; + __pyx_t_17 = 0; + __pyx_v_fields = ((PyObject*)__pyx_t_18); + __pyx_t_18 = 0; + + /* "pybedtools/cbedtools.pyx":257 + * #self._bed.strand = _cppstr(strand) + * fields = [_cppstr(chrom), _cppstr(str(start)), _cppstr(str(end)), _cppstr(name), _cppstr(score), _cppstr(strand)] + * fields.extend(otherfields) # <<<<<<<<<<<<<< + * self._bed.fields = fields + * self._attrs = None + */ + __pyx_t_19 = __Pyx_PyList_Extend(__pyx_v_fields, __pyx_v_otherfields); if (unlikely(__pyx_t_19 == ((int)-1))) __PYX_ERR(0, 257, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":258 + * fields = [_cppstr(chrom), _cppstr(str(start)), _cppstr(str(end)), _cppstr(name), _cppstr(score), _cppstr(strand)] + * fields.extend(otherfields) + * self._bed.fields = fields # <<<<<<<<<<<<<< + * self._attrs = None + * + */ + __pyx_t_14 = __pyx_convert_vector_from_py_std_3a__3a_string(__pyx_v_fields); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 258, __pyx_L1_error) + __pyx_v_self->_bed->fields = __pyx_t_14; + + /* "pybedtools/cbedtools.pyx":259 + * fields.extend(otherfields) + * self._bed.fields = fields + * self._attrs = None # <<<<<<<<<<<<<< + * + * def __copy__(self): + */ + __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(Py_None); + __Pyx_GOTREF(__pyx_v_self->_attrs); + __Pyx_DECREF(__pyx_v_self->_attrs); + __pyx_v_self->_attrs = Py_None; + + /* "pybedtools/cbedtools.pyx":242 + * + * """ + * def __init__(self, chrom, start, end, name=".", score=".", strand=".", otherfields=None): # <<<<<<<<<<<<<< + * if otherfields is None: + * otherfields = [] + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_15); + __Pyx_XDECREF(__pyx_t_16); + __Pyx_XDECREF(__pyx_t_17); + __Pyx_XDECREF(__pyx_t_18); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_fields); + __Pyx_XDECREF(__pyx_v_i); + __Pyx_XDECREF(__pyx_v_otherfields); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":261 + * self._attrs = None + * + * def __copy__(self): # <<<<<<<<<<<<<< + * return create_interval_from_list(self.fields) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_3__copy__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_3__copy__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__copy__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_2__copy__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_2__copy__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__copy__", 0); + + /* "pybedtools/cbedtools.pyx":262 + * + * def __copy__(self): + * return create_interval_from_list(self.fields) # <<<<<<<<<<<<<< + * + * def __hash__(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fields); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 262, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (!(likely(PyList_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_1)->tp_name), 0))) __PYX_ERR(0, 262, __pyx_L1_error) + __pyx_t_2 = ((PyObject *)__pyx_f_10pybedtools_9cbedtools_create_interval_from_list(((PyObject*)__pyx_t_1), 0)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 262, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":261 + * self._attrs = None + * + * def __copy__(self): # <<<<<<<<<<<<<< + * return create_interval_from_list(self.fields) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__copy__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":264 + * return create_interval_from_list(self.fields) + * + * def __hash__(self): # <<<<<<<<<<<<<< + * return hash("\t".join(self.fields)) + * + */ + +/* Python wrapper */ +static Py_hash_t __pyx_pw_10pybedtools_9cbedtools_8Interval_5__hash__(PyObject *__pyx_v_self); /*proto*/ +static Py_hash_t __pyx_pw_10pybedtools_9cbedtools_8Interval_5__hash__(PyObject *__pyx_v_self) { + Py_hash_t __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_4__hash__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static Py_hash_t __pyx_pf_10pybedtools_9cbedtools_8Interval_4__hash__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + Py_hash_t __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + Py_hash_t __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__hash__", 0); + + /* "pybedtools/cbedtools.pyx":265 + * + * def __hash__(self): + * return hash("\t".join(self.fields)) # <<<<<<<<<<<<<< + * + * property chrom: + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fields); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 265, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyString_Join(__pyx_kp_s__8, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 265, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = PyObject_Hash(__pyx_t_2); if (unlikely(__pyx_t_3 == ((Py_hash_t)-1))) __PYX_ERR(0, 265, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_3; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":264 + * return create_interval_from_list(self.fields) + * + * def __hash__(self): # <<<<<<<<<<<<<< + * return hash("\t".join(self.fields)) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__hash__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + if (unlikely(__pyx_r == -1) && !PyErr_Occurred()) __pyx_r = -2; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":269 + * property chrom: + * """ the chromosome of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.chrom) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5chrom_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5chrom_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5chrom___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5chrom___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":270 + * """ the chromosome of the feature""" + * def __get__(self): + * return _pystr(self._bed.chrom) # <<<<<<<<<<<<<< + * + * def __set__(self, chrom): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->chrom); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 270, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":269 + * property chrom: + * """ the chromosome of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.chrom) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.chrom.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":272 + * return _pystr(self._bed.chrom) + * + * def __set__(self, chrom): # <<<<<<<<<<<<<< + * chrom = _cppstr(chrom) + * self._bed.chrom = chrom + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5chrom_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_chrom); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5chrom_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_chrom) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5chrom_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_chrom)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5chrom_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_chrom) { + PyObject *__pyx_v_idx = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + std::string __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + std::vector<std::string> ::size_type __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_INCREF(__pyx_v_chrom); + + /* "pybedtools/cbedtools.pyx":273 + * + * def __set__(self, chrom): + * chrom = _cppstr(chrom) # <<<<<<<<<<<<<< + * self._bed.chrom = chrom + * idx = LOOKUPS[self.file_type]["chrom"] + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_chrom); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 273, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_chrom, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":274 + * def __set__(self, chrom): + * chrom = _cppstr(chrom) + * self._bed.chrom = chrom # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["chrom"] + * self._bed.fields[idx] = _cppstr(chrom) + */ + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_v_chrom); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 274, __pyx_L1_error) + __pyx_v_self->_bed->chrom = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":275 + * chrom = _cppstr(chrom) + * self._bed.chrom = chrom + * idx = LOOKUPS[self.file_type]["chrom"] # <<<<<<<<<<<<<< + * self._bed.fields[idx] = _cppstr(chrom) + * + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 275, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 275, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 275, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_t_3, __pyx_n_s_chrom); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 275, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_v_idx = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":276 + * self._bed.chrom = chrom + * idx = LOOKUPS[self.file_type]["chrom"] + * self._bed.fields[idx] = _cppstr(chrom) # <<<<<<<<<<<<<< + * + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_chrom); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 276, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyInt_As_size_t(__pyx_v_idx); if (unlikely((__pyx_t_4 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 276, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_4]) = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":272 + * return _pystr(self._bed.chrom) + * + * def __set__(self, chrom): # <<<<<<<<<<<<<< + * chrom = _cppstr(chrom) + * self._bed.chrom = chrom + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.chrom.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_idx); + __Pyx_XDECREF(__pyx_v_chrom); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":279 + * + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * def __richcmp__(self, other, int op): # <<<<<<<<<<<<<< + * if (self.chrom != other.chrom) or (self.strand != other.strand): + * if op == 3: return True + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_7__richcmp__(PyObject *__pyx_v_self, PyObject *__pyx_v_other, int __pyx_v_op); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_7__richcmp__(PyObject *__pyx_v_self, PyObject *__pyx_v_other, int __pyx_v_op) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__richcmp__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_6__richcmp__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_other), ((int)__pyx_v_op)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":284 + * return False + * + * def cmp(x, y): # <<<<<<<<<<<<<< + * if x < y: + * return -1 + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_11__richcmp___1cmp(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_10pybedtools_9cbedtools_8Interval_11__richcmp___1cmp = {"cmp", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_8Interval_11__richcmp___1cmp, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_11__richcmp___1cmp(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_x = 0; + PyObject *__pyx_v_y = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("cmp (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_x,&__pyx_n_s_y,0}; + PyObject* values[2] = {0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_x)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_y)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("cmp", 1, 2, 2, 1); __PYX_ERR(0, 284, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "cmp") < 0)) __PYX_ERR(0, 284, __pyx_L3_error) + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + } + __pyx_v_x = values[0]; + __pyx_v_y = values[1]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("cmp", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 284, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__richcmp__.cmp", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(__pyx_self, __pyx_v_x, __pyx_v_y); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x, PyObject *__pyx_v_y) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("cmp", 0); + + /* "pybedtools/cbedtools.pyx":285 + * + * def cmp(x, y): + * if x < y: # <<<<<<<<<<<<<< + * return -1 + * if x == y: + */ + __pyx_t_1 = PyObject_RichCompare(__pyx_v_x, __pyx_v_y, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 285, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 285, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":286 + * def cmp(x, y): + * if x < y: + * return -1 # <<<<<<<<<<<<<< + * if x == y: + * return 0 + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_int_neg_1); + __pyx_r = __pyx_int_neg_1; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":285 + * + * def cmp(x, y): + * if x < y: # <<<<<<<<<<<<<< + * return -1 + * if x == y: + */ + } + + /* "pybedtools/cbedtools.pyx":287 + * if x < y: + * return -1 + * if x == y: # <<<<<<<<<<<<<< + * return 0 + * if x > y: + */ + __pyx_t_1 = PyObject_RichCompare(__pyx_v_x, __pyx_v_y, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 287, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 287, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":288 + * return -1 + * if x == y: + * return 0 # <<<<<<<<<<<<<< + * if x > y: + * return 1 + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_int_0); + __pyx_r = __pyx_int_0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":287 + * if x < y: + * return -1 + * if x == y: # <<<<<<<<<<<<<< + * return 0 + * if x > y: + */ + } + + /* "pybedtools/cbedtools.pyx":289 + * if x == y: + * return 0 + * if x > y: # <<<<<<<<<<<<<< + * return 1 + * + */ + __pyx_t_1 = PyObject_RichCompare(__pyx_v_x, __pyx_v_y, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 289, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 289, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":290 + * return 0 + * if x > y: + * return 1 # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_int_1); + __pyx_r = __pyx_int_1; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":289 + * if x == y: + * return 0 + * if x > y: # <<<<<<<<<<<<<< + * return 1 + * + */ + } + + /* "pybedtools/cbedtools.pyx":284 + * return False + * + * def cmp(x, y): # <<<<<<<<<<<<<< + * if x < y: + * return -1 + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__richcmp__.cmp", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":279 + * + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * def __richcmp__(self, other, int op): # <<<<<<<<<<<<<< + * if (self.chrom != other.chrom) or (self.strand != other.strand): + * if op == 3: return True + */ + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6__richcmp__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_other, int __pyx_v_op) { + PyObject *__pyx_v_cmp = 0; + PyObject *__pyx_v_profile = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_t_5; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + int __pyx_t_12; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__richcmp__", 0); + + /* "pybedtools/cbedtools.pyx":280 + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * def __richcmp__(self, other, int op): + * if (self.chrom != other.chrom) or (self.strand != other.strand): # <<<<<<<<<<<<<< + * if op == 3: return True + * return False + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_chrom); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_other, __pyx_n_s_chrom); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_NE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (!__pyx_t_5) { + } else { + __pyx_t_1 = __pyx_t_5; + goto __pyx_L4_bool_binop_done; + } + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_strand); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_other, __pyx_n_s_strand); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_4, __pyx_t_3, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 280, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = __pyx_t_5; + __pyx_L4_bool_binop_done:; + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":281 + * def __richcmp__(self, other, int op): + * if (self.chrom != other.chrom) or (self.strand != other.strand): + * if op == 3: return True # <<<<<<<<<<<<<< + * return False + * + */ + __pyx_t_1 = ((__pyx_v_op == 3) != 0); + if (__pyx_t_1) { + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_True); + __pyx_r = Py_True; + goto __pyx_L0; + } + + /* "pybedtools/cbedtools.pyx":282 + * if (self.chrom != other.chrom) or (self.strand != other.strand): + * if op == 3: return True + * return False # <<<<<<<<<<<<<< + * + * def cmp(x, y): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_False); + __pyx_r = Py_False; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":280 + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * def __richcmp__(self, other, int op): + * if (self.chrom != other.chrom) or (self.strand != other.strand): # <<<<<<<<<<<<<< + * if op == 3: return True + * return False + */ + } + + /* "pybedtools/cbedtools.pyx":284 + * return False + * + * def cmp(x, y): # <<<<<<<<<<<<<< + * if x < y: + * return -1 + */ + __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_10pybedtools_9cbedtools_8Interval_11__richcmp___1cmp, 0, __pyx_n_s_richcmp___locals_cmp, NULL, __pyx_n_s_pybedtools_cbedtools, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 284, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_cmp = __pyx_t_2; + __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":294 + * + * # check all 4 so that we can handle nesting and partial overlaps. + * profile = (cmp(self.start, other.start), # <<<<<<<<<<<<<< + * cmp(self.stop, other.stop), + * cmp(self.start, other.stop), + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_start); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 294, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_other, __pyx_n_s_start); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 294, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = __pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(__pyx_v_cmp, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 294, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":295 + * # check all 4 so that we can handle nesting and partial overlaps. + * profile = (cmp(self.start, other.start), + * cmp(self.stop, other.stop), # <<<<<<<<<<<<<< + * cmp(self.start, other.stop), + * cmp(self.stop, other.start)) + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_stop); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 295, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_other, __pyx_n_s_stop); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 295, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_6 = __pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(__pyx_v_cmp, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 295, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":296 + * profile = (cmp(self.start, other.start), + * cmp(self.stop, other.stop), + * cmp(self.start, other.stop), # <<<<<<<<<<<<<< + * cmp(self.stop, other.start)) + * + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_start); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 296, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_other, __pyx_n_s_stop); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 296, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_7 = __pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(__pyx_v_cmp, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 296, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":297 + * cmp(self.stop, other.stop), + * cmp(self.start, other.stop), + * cmp(self.stop, other.start)) # <<<<<<<<<<<<<< + * + * try: + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_stop); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_other, __pyx_n_s_start); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_8 = __pyx_pf_10pybedtools_9cbedtools_8Interval_11__richcmp___cmp(__pyx_v_cmp, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 297, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":294 + * + * # check all 4 so that we can handle nesting and partial overlaps. + * profile = (cmp(self.start, other.start), # <<<<<<<<<<<<<< + * cmp(self.stop, other.stop), + * cmp(self.start, other.stop), + */ + __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 294, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_6); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7); + __Pyx_GIVEREF(__pyx_t_8); + PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8); + __pyx_t_4 = 0; + __pyx_t_6 = 0; + __pyx_t_7 = 0; + __pyx_t_8 = 0; + __pyx_v_profile = ((PyObject*)__pyx_t_2); + __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":299 + * cmp(self.stop, other.start)) + * + * try: # <<<<<<<<<<<<<< + * if PROFILES_TRUE[profile] == tuple(): + * raise NotImplementedError('Features are nested -- comparison undefined') + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11); + __Pyx_XGOTREF(__pyx_t_9); + __Pyx_XGOTREF(__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_11); + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":300 + * + * try: + * if PROFILES_TRUE[profile] == tuple(): # <<<<<<<<<<<<<< + * raise NotImplementedError('Features are nested -- comparison undefined') + * + */ + __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 300, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_8 = __Pyx_PyObject_GetItem(__pyx_t_2, __pyx_v_profile); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 300, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __Pyx_PyObject_CallNoArg(((PyObject *)(&PyTuple_Type))); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 300, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_8, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 300, __pyx_L7_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 300, __pyx_L7_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(__pyx_t_1)) { + + /* "pybedtools/cbedtools.pyx":301 + * try: + * if PROFILES_TRUE[profile] == tuple(): + * raise NotImplementedError('Features are nested -- comparison undefined') # <<<<<<<<<<<<<< + * + * if op != 3: + */ + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 301, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_Raise(__pyx_t_7, 0, 0, 0); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __PYX_ERR(0, 301, __pyx_L7_error) + + /* "pybedtools/cbedtools.pyx":300 + * + * try: + * if PROFILES_TRUE[profile] == tuple(): # <<<<<<<<<<<<<< + * raise NotImplementedError('Features are nested -- comparison undefined') + * + */ + } + + /* "pybedtools/cbedtools.pyx":303 + * raise NotImplementedError('Features are nested -- comparison undefined') + * + * if op != 3: # <<<<<<<<<<<<<< + * if op in PROFILES_TRUE[profile]: + * return True + */ + __pyx_t_1 = ((__pyx_v_op != 3) != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":304 + * + * if op != 3: + * if op in PROFILES_TRUE[profile]: # <<<<<<<<<<<<<< + * return True + * return False + */ + __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_op); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 304, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 304, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_8 = __Pyx_PyObject_GetItem(__pyx_t_2, __pyx_v_profile); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 304, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = (__Pyx_PySequence_ContainsTF(__pyx_t_7, __pyx_t_8, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 304, __pyx_L7_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_5 = (__pyx_t_1 != 0); + if (__pyx_t_5) { + + /* "pybedtools/cbedtools.pyx":305 + * if op != 3: + * if op in PROFILES_TRUE[profile]: + * return True # <<<<<<<<<<<<<< + * return False + * else: + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_True); + __pyx_r = Py_True; + goto __pyx_L11_try_return; + + /* "pybedtools/cbedtools.pyx":304 + * + * if op != 3: + * if op in PROFILES_TRUE[profile]: # <<<<<<<<<<<<<< + * return True + * return False + */ + } + + /* "pybedtools/cbedtools.pyx":306 + * if op in PROFILES_TRUE[profile]: + * return True + * return False # <<<<<<<<<<<<<< + * else: + * if 2 in PROFILES_TRUE[profile]: + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_False); + __pyx_r = Py_False; + goto __pyx_L11_try_return; + + /* "pybedtools/cbedtools.pyx":303 + * raise NotImplementedError('Features are nested -- comparison undefined') + * + * if op != 3: # <<<<<<<<<<<<<< + * if op in PROFILES_TRUE[profile]: + * return True + */ + } + + /* "pybedtools/cbedtools.pyx":308 + * return False + * else: + * if 2 in PROFILES_TRUE[profile]: # <<<<<<<<<<<<<< + * return False + * return True + */ + /*else*/ { + __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 308, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_8, __pyx_v_profile); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 308, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_5 = (__Pyx_PySequence_ContainsTF(__pyx_int_2, __pyx_t_7, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 308, __pyx_L7_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_1 = (__pyx_t_5 != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":309 + * else: + * if 2 in PROFILES_TRUE[profile]: + * return False # <<<<<<<<<<<<<< + * return True + * except KeyError: + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_False); + __pyx_r = Py_False; + goto __pyx_L11_try_return; + + /* "pybedtools/cbedtools.pyx":308 + * return False + * else: + * if 2 in PROFILES_TRUE[profile]: # <<<<<<<<<<<<<< + * return False + * return True + */ + } + + /* "pybedtools/cbedtools.pyx":310 + * if 2 in PROFILES_TRUE[profile]: + * return False + * return True # <<<<<<<<<<<<<< + * except KeyError: + * raise ValueError('Currently unsupported comparison -- please ' + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_True); + __pyx_r = Py_True; + goto __pyx_L11_try_return; + } + + /* "pybedtools/cbedtools.pyx":299 + * cmp(self.stop, other.start)) + * + * try: # <<<<<<<<<<<<<< + * if PROFILES_TRUE[profile] == tuple(): + * raise NotImplementedError('Features are nested -- comparison undefined') + */ + } + __pyx_L7_error:; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + + /* "pybedtools/cbedtools.pyx":311 + * return False + * return True + * except KeyError: # <<<<<<<<<<<<<< + * raise ValueError('Currently unsupported comparison -- please ' + * 'submit a bug report') + */ + __pyx_t_12 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError); + if (__pyx_t_12) { + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__richcmp__", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_8, &__pyx_t_2) < 0) __PYX_ERR(0, 311, __pyx_L9_except_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(__pyx_t_2); + + /* "pybedtools/cbedtools.pyx":312 + * return True + * except KeyError: + * raise ValueError('Currently unsupported comparison -- please ' # <<<<<<<<<<<<<< + * 'submit a bug report') + * + */ + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 312, __pyx_L9_except_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_Raise(__pyx_t_6, 0, 0, 0); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __PYX_ERR(0, 312, __pyx_L9_except_error) + } + goto __pyx_L9_except_error; + __pyx_L9_except_error:; + + /* "pybedtools/cbedtools.pyx":299 + * cmp(self.stop, other.start)) + * + * try: # <<<<<<<<<<<<<< + * if PROFILES_TRUE[profile] == tuple(): + * raise NotImplementedError('Features are nested -- comparison undefined') + */ + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11); + goto __pyx_L1_error; + __pyx_L11_try_return:; + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11); + goto __pyx_L0; + } + + /* "pybedtools/cbedtools.pyx":279 + * + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * def __richcmp__(self, other, int op): # <<<<<<<<<<<<<< + * if (self.chrom != other.chrom) or (self.strand != other.strand): + * if op == 3: return True + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__richcmp__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_cmp); + __Pyx_XDECREF(__pyx_v_profile); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":317 + * property start: + * """The 0-based start of the feature.""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.start + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5start_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5start_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5start___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5start___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":318 + * """The 0-based start of the feature.""" + * def __get__(self): + * return self._bed.start # <<<<<<<<<<<<<< + * + * def __set__(self, int start): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS(__pyx_v_self->_bed->start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 318, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":317 + * property start: + * """The 0-based start of the feature.""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.start + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.start.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":320 + * return self._bed.start + * + * def __set__(self, int start): # <<<<<<<<<<<<<< + * self._bed.start = start + * idx = LOOKUPS[self.file_type]["start"] + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5start_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_arg_start); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5start_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_arg_start) { + int __pyx_v_start; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + assert(__pyx_arg_start); { + __pyx_v_start = __Pyx_PyInt_As_int(__pyx_arg_start); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 320, __pyx_L3_error) + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.start.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5start_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((int)__pyx_v_start)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5start_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_v_start) { + PyObject *__pyx_v_idx = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + std::string __pyx_t_4; + std::vector<std::string> ::size_type __pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":321 + * + * def __set__(self, int start): + * self._bed.start = start # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["start"] + * + */ + __pyx_v_self->_bed->start = __pyx_v_start; + + /* "pybedtools/cbedtools.pyx":322 + * def __set__(self, int start): + * self._bed.start = start + * idx = LOOKUPS[self.file_type]["start"] # <<<<<<<<<<<<<< + * + * # Non-BED files should have 1-based coords in fields + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 322, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 322, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 322, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_t_2, __pyx_n_s_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 322, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_idx = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":325 + * + * # Non-BED files should have 1-based coords in fields + * if self.file_type != 'bed': # <<<<<<<<<<<<<< + * start += 1 + * self._bed.fields[idx] = _cppstr(str(start)) + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 325, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = (__Pyx_PyString_Equals(__pyx_t_1, __pyx_n_s_bed, Py_NE)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 325, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":326 + * # Non-BED files should have 1-based coords in fields + * if self.file_type != 'bed': + * start += 1 # <<<<<<<<<<<<<< + * self._bed.fields[idx] = _cppstr(str(start)) + * + */ + __pyx_v_start = (__pyx_v_start + 1); + + /* "pybedtools/cbedtools.pyx":325 + * + * # Non-BED files should have 1-based coords in fields + * if self.file_type != 'bed': # <<<<<<<<<<<<<< + * start += 1 + * self._bed.fields[idx] = _cppstr(str(start)) + */ + } + + /* "pybedtools/cbedtools.pyx":327 + * if self.file_type != 'bed': + * start += 1 + * self._bed.fields[idx] = _cppstr(str(start)) # <<<<<<<<<<<<<< + * + * property end: + */ + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 327, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 327, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 327, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_4 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 327, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_5 = __Pyx_PyInt_As_size_t(__pyx_v_idx); if (unlikely((__pyx_t_5 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 327, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_5]) = __pyx_t_4; + + /* "pybedtools/cbedtools.pyx":320 + * return self._bed.start + * + * def __set__(self, int start): # <<<<<<<<<<<<<< + * self._bed.start = start + * idx = LOOKUPS[self.file_type]["start"] + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.start.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_idx); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":331 + * property end: + * """The end of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.end + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_3end_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_3end_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_3end___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_3end___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":332 + * """The end of the feature""" + * def __get__(self): + * return self._bed.end # <<<<<<<<<<<<<< + * + * def __set__(self, int end): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS(__pyx_v_self->_bed->end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 332, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":331 + * property end: + * """The end of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.end + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.end.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":334 + * return self._bed.end + * + * def __set__(self, int end): # <<<<<<<<<<<<<< + * self._bed.end = end + * idx = LOOKUPS[self.file_type]["stop"] + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_3end_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_arg_end); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_3end_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_arg_end) { + int __pyx_v_end; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + assert(__pyx_arg_end); { + __pyx_v_end = __Pyx_PyInt_As_int(__pyx_arg_end); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 334, __pyx_L3_error) + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.end.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_3end_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((int)__pyx_v_end)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_3end_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_v_end) { + PyObject *__pyx_v_idx = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + std::string __pyx_t_3; + std::vector<std::string> ::size_type __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":335 + * + * def __set__(self, int end): + * self._bed.end = end # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["stop"] + * self._bed.fields[idx] = _cppstr(str(end)) + */ + __pyx_v_self->_bed->end = __pyx_v_end; + + /* "pybedtools/cbedtools.pyx":336 + * def __set__(self, int end): + * self._bed.end = end + * idx = LOOKUPS[self.file_type]["stop"] # <<<<<<<<<<<<<< + * self._bed.fields[idx] = _cppstr(str(end)) + * + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 336, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 336, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 336, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_t_2, __pyx_n_s_stop); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 336, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_idx = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":337 + * self._bed.end = end + * idx = LOOKUPS[self.file_type]["stop"] + * self._bed.fields[idx] = _cppstr(str(end)) # <<<<<<<<<<<<<< + * + * property stop: + */ + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 337, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 337, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 337, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_3 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 337, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyInt_As_size_t(__pyx_v_idx); if (unlikely((__pyx_t_4 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 337, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_4]) = __pyx_t_3; + + /* "pybedtools/cbedtools.pyx":334 + * return self._bed.end + * + * def __set__(self, int end): # <<<<<<<<<<<<<< + * self._bed.end = end + * idx = LOOKUPS[self.file_type]["stop"] + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.end.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_idx); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":341 + * property stop: + * """ the end of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.end + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_4stop_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_4stop_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_4stop___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_4stop___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":342 + * """ the end of the feature""" + * def __get__(self): + * return self._bed.end # <<<<<<<<<<<<<< + * + * def __set__(self, int end): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS(__pyx_v_self->_bed->end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 342, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":341 + * property stop: + * """ the end of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.end + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.stop.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":344 + * return self._bed.end + * + * def __set__(self, int end): # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["stop"] + * self._bed.fields[idx] = _cppstr(str(end)) + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_4stop_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_arg_end); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_4stop_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_arg_end) { + int __pyx_v_end; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + assert(__pyx_arg_end); { + __pyx_v_end = __Pyx_PyInt_As_int(__pyx_arg_end); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 344, __pyx_L3_error) + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.stop.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_4stop_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((int)__pyx_v_end)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_4stop_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_v_end) { + PyObject *__pyx_v_idx = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + std::string __pyx_t_3; + std::vector<std::string> ::size_type __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":345 + * + * def __set__(self, int end): + * idx = LOOKUPS[self.file_type]["stop"] # <<<<<<<<<<<<<< + * self._bed.fields[idx] = _cppstr(str(end)) + * self._bed.end = end + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 345, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_t_2, __pyx_n_s_stop); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 345, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_idx = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":346 + * def __set__(self, int end): + * idx = LOOKUPS[self.file_type]["stop"] + * self._bed.fields[idx] = _cppstr(str(end)) # <<<<<<<<<<<<<< + * self._bed.end = end + * + */ + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 346, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 346, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 346, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_3 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 346, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyInt_As_size_t(__pyx_v_idx); if (unlikely((__pyx_t_4 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 346, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_4]) = __pyx_t_3; + + /* "pybedtools/cbedtools.pyx":347 + * idx = LOOKUPS[self.file_type]["stop"] + * self._bed.fields[idx] = _cppstr(str(end)) + * self._bed.end = end # <<<<<<<<<<<<<< + * + * property strand: + */ + __pyx_v_self->_bed->end = __pyx_v_end; + + /* "pybedtools/cbedtools.pyx":344 + * return self._bed.end + * + * def __set__(self, int end): # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["stop"] + * self._bed.fields[idx] = _cppstr(str(end)) + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.stop.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_idx); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":351 + * property strand: + * """ the strand of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.strand) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_6strand_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_6strand_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_6strand___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6strand___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":352 + * """ the strand of the feature""" + * def __get__(self): + * return _pystr(self._bed.strand) # <<<<<<<<<<<<<< + * + * def __set__(self, strand): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 352, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":351 + * property strand: + * """ the strand of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.strand) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.strand.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":354 + * return _pystr(self._bed.strand) + * + * def __set__(self, strand): # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["strand"] + * self._bed.fields[idx] = _cppstr(strand) + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_6strand_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_strand); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_6strand_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_strand) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_6strand_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_strand)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_6strand_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_strand) { + PyObject *__pyx_v_idx = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + std::string __pyx_t_3; + std::vector<std::string> ::size_type __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":355 + * + * def __set__(self, strand): + * idx = LOOKUPS[self.file_type]["strand"] # <<<<<<<<<<<<<< + * self._bed.fields[idx] = _cppstr(strand) + * self._bed.strand = _cppstr(strand) + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 355, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 355, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 355, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_t_2, __pyx_n_s_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 355, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_idx = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":356 + * def __set__(self, strand): + * idx = LOOKUPS[self.file_type]["strand"] + * self._bed.fields[idx] = _cppstr(strand) # <<<<<<<<<<<<<< + * self._bed.strand = _cppstr(strand) + * + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 356, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 356, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyInt_As_size_t(__pyx_v_idx); if (unlikely((__pyx_t_4 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 356, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_4]) = __pyx_t_3; + + /* "pybedtools/cbedtools.pyx":357 + * idx = LOOKUPS[self.file_type]["strand"] + * self._bed.fields[idx] = _cppstr(strand) + * self._bed.strand = _cppstr(strand) # <<<<<<<<<<<<<< + * + * property length: + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_strand); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 357, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 357, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v_self->_bed->strand = __pyx_t_3; + + /* "pybedtools/cbedtools.pyx":354 + * return _pystr(self._bed.strand) + * + * def __set__(self, strand): # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["strand"] + * self._bed.fields[idx] = _cppstr(strand) + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.strand.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_idx); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":361 + * property length: + * """ the length of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.end - self._bed.start + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_6length_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_6length_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_6length___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6length___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":362 + * """ the length of the feature""" + * def __get__(self): + * return self._bed.end - self._bed.start # <<<<<<<<<<<<<< + * + * cpdef deparse_attrs(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS((__pyx_v_self->_bed->end - __pyx_v_self->_bed->start)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 362, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":361 + * property length: + * """ the length of the feature""" + * def __get__(self): # <<<<<<<<<<<<<< + * return self._bed.end - self._bed.start + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.length.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":364 + * return self._bed.end - self._bed.start + * + * cpdef deparse_attrs(self): # <<<<<<<<<<<<<< + * + * if not self._attrs: return + */ + +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_9deparse_attrs(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools_8Interval_deparse_attrs(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, int __pyx_skip_dispatch) { + PyObject *__pyx_v_s = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_t_5; + int __pyx_t_6; + std::string __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("deparse_attrs", 0); + /* Check if called by wrapper */ + if (unlikely(__pyx_skip_dispatch)) ; + /* Check if overridden in Python */ + else if (unlikely((Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0) || (Py_TYPE(((PyObject *)__pyx_v_self))->tp_flags & (Py_TPFLAGS_IS_ABSTRACT | Py_TPFLAGS_HEAPTYPE)))) { + #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS + static PY_UINT64_T __pyx_tp_dict_version = __PYX_DICT_VERSION_INIT, __pyx_obj_dict_version = __PYX_DICT_VERSION_INIT; + if (unlikely(!__Pyx_object_dict_version_matches(((PyObject *)__pyx_v_self), __pyx_tp_dict_version, __pyx_obj_dict_version))) { + PY_UINT64_T __pyx_type_dict_guard = __Pyx_get_tp_dict_version(((PyObject *)__pyx_v_self)); + #endif + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_deparse_attrs); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 364, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)(void*)__pyx_pw_10pybedtools_9cbedtools_8Interval_9deparse_attrs)) { + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_t_1); + __pyx_t_3 = __pyx_t_1; __pyx_t_4 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + } + } + __pyx_t_2 = (__pyx_t_4) ? __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4) : __Pyx_PyObject_CallNoArg(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 364, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + goto __pyx_L0; + } + #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS + __pyx_tp_dict_version = __Pyx_get_tp_dict_version(((PyObject *)__pyx_v_self)); + __pyx_obj_dict_version = __Pyx_get_object_dict_version(((PyObject *)__pyx_v_self)); + if (unlikely(__pyx_type_dict_guard != __pyx_tp_dict_version)) { + __pyx_tp_dict_version = __pyx_obj_dict_version = __PYX_DICT_VERSION_INIT; + } + #endif + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS + } + #endif + } + + /* "pybedtools/cbedtools.pyx":366 + * cpdef deparse_attrs(self): + * + * if not self._attrs: return # <<<<<<<<<<<<<< + * + * if self.file_type != "gff": + */ + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_self->_attrs); if (unlikely(__pyx_t_5 < 0)) __PYX_ERR(0, 366, __pyx_L1_error) + __pyx_t_6 = ((!__pyx_t_5) != 0); + if (__pyx_t_6) { + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + } + + /* "pybedtools/cbedtools.pyx":368 + * if not self._attrs: return + * + * if self.file_type != "gff": # <<<<<<<<<<<<<< + * raise ValueError('Interval.attrs was not None, but this was a non-GFF Interval') + * + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 368, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_6 = (__Pyx_PyString_Equals(__pyx_t_1, __pyx_n_s_gff, Py_NE)); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 368, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(__pyx_t_6)) { + + /* "pybedtools/cbedtools.pyx":369 + * + * if self.file_type != "gff": + * raise ValueError('Interval.attrs was not None, but this was a non-GFF Interval') # <<<<<<<<<<<<<< + * + * s = self._attrs.__str__() + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 369, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 369, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":368 + * if not self._attrs: return + * + * if self.file_type != "gff": # <<<<<<<<<<<<<< + * raise ValueError('Interval.attrs was not None, but this was a non-GFF Interval') + * + */ + } + + /* "pybedtools/cbedtools.pyx":371 + * raise ValueError('Interval.attrs was not None, but this was a non-GFF Interval') + * + * s = self._attrs.__str__() # <<<<<<<<<<<<<< + * self._bed.fields[8] = _cppstr(s) + * + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->_attrs, __pyx_n_s_str); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 371, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 371, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_s = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":372 + * + * s = self._attrs.__str__() + * self._bed.fields[8] = _cppstr(s) # <<<<<<<<<<<<<< + * + * property fields: + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_s); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 372, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 372, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + (__pyx_v_self->_bed->fields[8]) = __pyx_t_7; + + /* "pybedtools/cbedtools.pyx":364 + * return self._bed.end - self._bed.start + * + * cpdef deparse_attrs(self): # <<<<<<<<<<<<<< + * + * if not self._attrs: return + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.deparse_attrs", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_s); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_9deparse_attrs(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_9deparse_attrs(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("deparse_attrs (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_8deparse_attrs(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_8deparse_attrs(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("deparse_attrs", 0); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_8Interval_deparse_attrs(__pyx_v_self, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 364, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.deparse_attrs", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":375 + * + * property fields: + * def __get__(self): # <<<<<<<<<<<<<< + * self.deparse_attrs() + * items = [] + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_6fields_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_6fields_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_6fields___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_6fields___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_v_items = NULL; + std::string __pyx_v_i; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + std::vector<std::string> ::iterator __pyx_t_2; + std::vector<std::string> *__pyx_t_3; + std::string __pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + int __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":376 + * property fields: + * def __get__(self): + * self.deparse_attrs() # <<<<<<<<<<<<<< + * items = [] + * for i in self._bed.fields: + */ + __pyx_t_1 = ((struct __pyx_vtabstruct_10pybedtools_9cbedtools_Interval *)__pyx_v_self->__pyx_vtab)->deparse_attrs(__pyx_v_self, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 376, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":377 + * def __get__(self): + * self.deparse_attrs() + * items = [] # <<<<<<<<<<<<<< + * for i in self._bed.fields: + * if isinstance(i, int): + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 377, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_items = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":378 + * self.deparse_attrs() + * items = [] + * for i in self._bed.fields: # <<<<<<<<<<<<<< + * if isinstance(i, int): + * items.append(i) + */ + __pyx_t_3 = &__pyx_v_self->_bed->fields; + __pyx_t_2 = __pyx_t_3->begin(); + for (;;) { + if (!(__pyx_t_2 != __pyx_t_3->end())) break; + __pyx_t_4 = *__pyx_t_2; + ++__pyx_t_2; + __pyx_v_i = __pyx_t_4; + + /* "pybedtools/cbedtools.pyx":379 + * items = [] + * for i in self._bed.fields: + * if isinstance(i, int): # <<<<<<<<<<<<<< + * items.append(i) + * else: + */ + __pyx_t_1 = __pyx_convert_PyBytes_string_to_py_std__in_string(__pyx_v_i); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 379, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = PyInt_Check(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_6 = (__pyx_t_5 != 0); + if (__pyx_t_6) { + + /* "pybedtools/cbedtools.pyx":380 + * for i in self._bed.fields: + * if isinstance(i, int): + * items.append(i) # <<<<<<<<<<<<<< + * else: + * items.append(_pystr(i)) + */ + __pyx_t_1 = __pyx_convert_PyBytes_string_to_py_std__in_string(__pyx_v_i); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 380, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_items, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 380, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":379 + * items = [] + * for i in self._bed.fields: + * if isinstance(i, int): # <<<<<<<<<<<<<< + * items.append(i) + * else: + */ + goto __pyx_L5; + } + + /* "pybedtools/cbedtools.pyx":382 + * items.append(i) + * else: + * items.append(_pystr(i)) # <<<<<<<<<<<<<< + * return items + * + */ + /*else*/ { + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_i); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 382, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_items, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 382, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } + __pyx_L5:; + + /* "pybedtools/cbedtools.pyx":378 + * self.deparse_attrs() + * items = [] + * for i in self._bed.fields: # <<<<<<<<<<<<<< + * if isinstance(i, int): + * items.append(i) + */ + } + + /* "pybedtools/cbedtools.pyx":383 + * else: + * items.append(_pystr(i)) + * return items # <<<<<<<<<<<<<< + * + * property attrs: + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_items); + __pyx_r = __pyx_v_items; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":375 + * + * property fields: + * def __get__(self): # <<<<<<<<<<<<<< + * self.deparse_attrs() + * items = [] + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.fields.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_items); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":386 + * + * property attrs: + * def __get__(self): # <<<<<<<<<<<<<< + * if self._attrs is None: + * ft = _pystr(self._bed.file_type) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5attrs_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5attrs_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_v_ft = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":387 + * property attrs: + * def __get__(self): + * if self._attrs is None: # <<<<<<<<<<<<<< + * ft = _pystr(self._bed.file_type) + * if ft == 'gff': + */ + __pyx_t_1 = (__pyx_v_self->_attrs == Py_None); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":388 + * def __get__(self): + * if self._attrs is None: + * ft = _pystr(self._bed.file_type) # <<<<<<<<<<<<<< + * if ft == 'gff': + * self._attrs = Attributes(_pystr(self._bed.fields[8])) + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->file_type); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 388, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_v_ft = __pyx_t_3; + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":389 + * if self._attrs is None: + * ft = _pystr(self._bed.file_type) + * if ft == 'gff': # <<<<<<<<<<<<<< + * self._attrs = Attributes(_pystr(self._bed.fields[8])) + * else: + */ + __pyx_t_2 = (__Pyx_PyString_Equals(__pyx_v_ft, __pyx_n_s_gff, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 389, __pyx_L1_error) + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":390 + * ft = _pystr(self._bed.file_type) + * if ft == 'gff': + * self._attrs = Attributes(_pystr(self._bed.fields[8])) # <<<<<<<<<<<<<< + * else: + * self._attrs = Attributes("") + */ + __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 390, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __pyx_f_10pybedtools_9cbedtools__pystr((__pyx_v_self->_bed->fields[8])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 390, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + __pyx_t_3 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_6, __pyx_t_5) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 390, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_GIVEREF(__pyx_t_3); + __Pyx_GOTREF(__pyx_v_self->_attrs); + __Pyx_DECREF(__pyx_v_self->_attrs); + __pyx_v_self->_attrs = __pyx_t_3; + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":389 + * if self._attrs is None: + * ft = _pystr(self._bed.file_type) + * if ft == 'gff': # <<<<<<<<<<<<<< + * self._attrs = Attributes(_pystr(self._bed.fields[8])) + * else: + */ + goto __pyx_L4; + } + + /* "pybedtools/cbedtools.pyx":392 + * self._attrs = Attributes(_pystr(self._bed.fields[8])) + * else: + * self._attrs = Attributes("") # <<<<<<<<<<<<<< + * return self._attrs + * + */ + /*else*/ { + __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 392, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + __pyx_t_3 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_4, __pyx_t_5, __pyx_kp_s_) : __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_kp_s_); + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 392, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_GIVEREF(__pyx_t_3); + __Pyx_GOTREF(__pyx_v_self->_attrs); + __Pyx_DECREF(__pyx_v_self->_attrs); + __pyx_v_self->_attrs = __pyx_t_3; + __pyx_t_3 = 0; + } + __pyx_L4:; + + /* "pybedtools/cbedtools.pyx":387 + * property attrs: + * def __get__(self): + * if self._attrs is None: # <<<<<<<<<<<<<< + * ft = _pystr(self._bed.file_type) + * if ft == 'gff': + */ + } + + /* "pybedtools/cbedtools.pyx":393 + * else: + * self._attrs = Attributes("") + * return self._attrs # <<<<<<<<<<<<<< + * + * def __set__(self, attrs): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_self->_attrs); + __pyx_r = __pyx_v_self->_attrs; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":386 + * + * property attrs: + * def __get__(self): # <<<<<<<<<<<<<< + * if self._attrs is None: + * ft = _pystr(self._bed.file_type) + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.attrs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_ft); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":395 + * return self._attrs + * + * def __set__(self, attrs): # <<<<<<<<<<<<<< + * self._attrs = attrs + * + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5attrs_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_attrs); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5attrs_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_attrs) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_attrs)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_attrs) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":396 + * + * def __set__(self, attrs): + * self._attrs = attrs # <<<<<<<<<<<<<< + * + * # TODO: make this more robust. + */ + __Pyx_INCREF(__pyx_v_attrs); + __Pyx_GIVEREF(__pyx_v_attrs); + __Pyx_GOTREF(__pyx_v_self->_attrs); + __Pyx_DECREF(__pyx_v_self->_attrs); + __pyx_v_self->_attrs = __pyx_v_attrs; + + /* "pybedtools/cbedtools.pyx":395 + * return self._attrs + * + * def __set__(self, attrs): # <<<<<<<<<<<<<< + * self._attrs = attrs + * + */ + + /* function exit code */ + __pyx_r = 0; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":400 + * # TODO: make this more robust. + * @property + * def count(self): # <<<<<<<<<<<<<< + * return int(self.fields[-1]) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5count_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5count_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5count___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5count___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":401 + * @property + * def count(self): + * return int(self.fields[-1]) # <<<<<<<<<<<<<< + * + * property name: + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fields); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 401, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, -1L, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 401, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 401, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":400 + * # TODO: make this more robust. + * @property + * def count(self): # <<<<<<<<<<<<<< + * return int(self.fields[-1]) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.count.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":411 + * + * """ + * def __get__(self): # <<<<<<<<<<<<<< + * cdef string ftype = self._bed.file_type + * value = None + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_4name_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_4name_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_4name___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_4name___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + std::string __pyx_v_ftype; + PyObject *__pyx_v_value = NULL; + PyObject *__pyx_v_key = NULL; + PyObject *__pyx_v_s = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + std::string __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + Py_ssize_t __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + int __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":412 + * """ + * def __get__(self): + * cdef string ftype = self._bed.file_type # <<<<<<<<<<<<<< + * value = None + * if ftype == <string>"gff": + */ + __pyx_t_1 = __pyx_v_self->_bed->file_type; + __pyx_v_ftype = __pyx_t_1; + + /* "pybedtools/cbedtools.pyx":413 + * def __get__(self): + * cdef string ftype = self._bed.file_type + * value = None # <<<<<<<<<<<<<< + * if ftype == <string>"gff": + * """ + */ + __Pyx_INCREF(Py_None); + __pyx_v_value = Py_None; + + /* "pybedtools/cbedtools.pyx":414 + * cdef string ftype = self._bed.file_type + * value = None + * if ftype == <string>"gff": # <<<<<<<<<<<<<< + * """ + * # TODO. allow setting a name_key in the BedTool constructor? + */ + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_n_b_gff); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 414, __pyx_L1_error) + __pyx_t_2 = ((__pyx_v_ftype == ((std::string)__pyx_t_1)) != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":420 + * return attrs[self.name_key] + * """ + * for key in ("ID", "Name", "gene_name", "transcript_id", \ # <<<<<<<<<<<<<< + * "gene_id", "Parent"): + * if key in self.attrs: + */ + __pyx_t_3 = __pyx_tuple__14; __Pyx_INCREF(__pyx_t_3); __pyx_t_4 = 0; + for (;;) { + if (__pyx_t_4 >= 6) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_5); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(0, 420, __pyx_L1_error) + #else + __pyx_t_5 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 420, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + #endif + __Pyx_XDECREF_SET(__pyx_v_key, __pyx_t_5); + __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":422 + * for key in ("ID", "Name", "gene_name", "transcript_id", \ + * "gene_id", "Parent"): + * if key in self.attrs: # <<<<<<<<<<<<<< + * value = self.attrs[key] + * break + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_attrs); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 422, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_key, __pyx_t_5, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 422, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_6 = (__pyx_t_2 != 0); + if (__pyx_t_6) { + + /* "pybedtools/cbedtools.pyx":423 + * "gene_id", "Parent"): + * if key in self.attrs: + * value = self.attrs[key] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_attrs); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 423, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_5, __pyx_v_key); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 423, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF_SET(__pyx_v_value, __pyx_t_7); + __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":424 + * if key in self.attrs: + * value = self.attrs[key] + * break # <<<<<<<<<<<<<< + * + * elif ftype == <string>"vcf": + */ + goto __pyx_L5_break; + + /* "pybedtools/cbedtools.pyx":422 + * for key in ("ID", "Name", "gene_name", "transcript_id", \ + * "gene_id", "Parent"): + * if key in self.attrs: # <<<<<<<<<<<<<< + * value = self.attrs[key] + * break + */ + } + + /* "pybedtools/cbedtools.pyx":420 + * return attrs[self.name_key] + * """ + * for key in ("ID", "Name", "gene_name", "transcript_id", \ # <<<<<<<<<<<<<< + * "gene_id", "Parent"): + * if key in self.attrs: + */ + } + __pyx_L5_break:; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":414 + * cdef string ftype = self._bed.file_type + * value = None + * if ftype == <string>"gff": # <<<<<<<<<<<<<< + * """ + * # TODO. allow setting a name_key in the BedTool constructor? + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":426 + * break + * + * elif ftype == <string>"vcf": # <<<<<<<<<<<<<< + * s = self.fields[2] + * if s in ("", "."): + */ + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_n_b_vcf); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 426, __pyx_L1_error) + __pyx_t_6 = ((__pyx_v_ftype == ((std::string)__pyx_t_1)) != 0); + if (__pyx_t_6) { + + /* "pybedtools/cbedtools.pyx":427 + * + * elif ftype == <string>"vcf": + * s = self.fields[2] # <<<<<<<<<<<<<< + * if s in ("", "."): + * value = "%s:%i" % (self.chrom, self.start) + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fields); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 427, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_3, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 427, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_v_s = __pyx_t_7; + __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":428 + * elif ftype == <string>"vcf": + * s = self.fields[2] + * if s in ("", "."): # <<<<<<<<<<<<<< + * value = "%s:%i" % (self.chrom, self.start) + * else: + */ + __Pyx_INCREF(__pyx_v_s); + __pyx_t_7 = __pyx_v_s; + __pyx_t_2 = (__Pyx_PyString_Equals(__pyx_t_7, __pyx_kp_s_, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 428, __pyx_L1_error) + if (!__pyx_t_2) { + } else { + __pyx_t_6 = __pyx_t_2; + goto __pyx_L8_bool_binop_done; + } + __pyx_t_2 = (__Pyx_PyString_Equals(__pyx_t_7, __pyx_kp_s__7, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 428, __pyx_L1_error) + __pyx_t_6 = __pyx_t_2; + __pyx_L8_bool_binop_done:; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_2 = (__pyx_t_6 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":429 + * s = self.fields[2] + * if s in ("", "."): + * value = "%s:%i" % (self.chrom, self.start) # <<<<<<<<<<<<<< + * else: + * value = _pystr(s) + */ + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_chrom); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 429, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_start); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 429, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 429, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7); + __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3); + __pyx_t_7 = 0; + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_s_i, __pyx_t_5); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 429, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF_SET(__pyx_v_value, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":428 + * elif ftype == <string>"vcf": + * s = self.fields[2] + * if s in ("", "."): # <<<<<<<<<<<<<< + * value = "%s:%i" % (self.chrom, self.start) + * else: + */ + goto __pyx_L7; + } + + /* "pybedtools/cbedtools.pyx":431 + * value = "%s:%i" % (self.chrom, self.start) + * else: + * value = _pystr(s) # <<<<<<<<<<<<<< + * elif ftype == <string>"bed": + * value = _pystr(self._bed.name) + */ + /*else*/ { + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_v_s); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 431, __pyx_L1_error) + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 431, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF_SET(__pyx_v_value, __pyx_t_3); + __pyx_t_3 = 0; + } + __pyx_L7:; + + /* "pybedtools/cbedtools.pyx":426 + * break + * + * elif ftype == <string>"vcf": # <<<<<<<<<<<<<< + * s = self.fields[2] + * if s in ("", "."): + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":432 + * else: + * value = _pystr(s) + * elif ftype == <string>"bed": # <<<<<<<<<<<<<< + * value = _pystr(self._bed.name) + * + */ + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_n_b_bed); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 432, __pyx_L1_error) + __pyx_t_2 = ((__pyx_v_ftype == ((std::string)__pyx_t_1)) != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":433 + * value = _pystr(s) + * elif ftype == <string>"bed": + * value = _pystr(self._bed.name) # <<<<<<<<<<<<<< + * + * return value + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->name); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 433, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF_SET(__pyx_v_value, __pyx_t_3); + __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":432 + * else: + * value = _pystr(s) + * elif ftype == <string>"bed": # <<<<<<<<<<<<<< + * value = _pystr(self._bed.name) + * + */ + } + __pyx_L3:; + + /* "pybedtools/cbedtools.pyx":435 + * value = _pystr(self._bed.name) + * + * return value # <<<<<<<<<<<<<< + * + * def __set__(self, value): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_value); + __pyx_r = __pyx_v_value; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":411 + * + * """ + * def __get__(self): # <<<<<<<<<<<<<< + * cdef string ftype = self._bed.file_type + * value = None + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.name.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_value); + __Pyx_XDECREF(__pyx_v_key); + __Pyx_XDECREF(__pyx_v_s); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":437 + * return value + * + * def __set__(self, value): # <<<<<<<<<<<<<< + * cdef string ftype = self._bed.file_type + * + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_4name_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_4name_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_4name_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_value)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_4name_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value) { + std::string __pyx_v_ftype; + PyObject *__pyx_v_key = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + std::string __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + Py_ssize_t __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":438 + * + * def __set__(self, value): + * cdef string ftype = self._bed.file_type # <<<<<<<<<<<<<< + * + * if ftype == <string>"gff": + */ + __pyx_t_1 = __pyx_v_self->_bed->file_type; + __pyx_v_ftype = __pyx_t_1; + + /* "pybedtools/cbedtools.pyx":440 + * cdef string ftype = self._bed.file_type + * + * if ftype == <string>"gff": # <<<<<<<<<<<<<< + * for key in ("ID", "Name", "gene_name", "transcript_id", \ + * "gene_id", "Parent"): + */ + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_n_b_gff); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 440, __pyx_L1_error) + __pyx_t_2 = ((__pyx_v_ftype == ((std::string)__pyx_t_1)) != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":441 + * + * if ftype == <string>"gff": + * for key in ("ID", "Name", "gene_name", "transcript_id", \ # <<<<<<<<<<<<<< + * "gene_id", "Parent"): + * if not key in self.attrs: + */ + __pyx_t_3 = __pyx_tuple__14; __Pyx_INCREF(__pyx_t_3); __pyx_t_4 = 0; + for (;;) { + if (__pyx_t_4 >= 6) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_5); __pyx_t_4++; if (unlikely(0 < 0)) __PYX_ERR(0, 441, __pyx_L1_error) + #else + __pyx_t_5 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 441, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + #endif + __Pyx_XDECREF_SET(__pyx_v_key, __pyx_t_5); + __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":443 + * for key in ("ID", "Name", "gene_name", "transcript_id", \ + * "gene_id", "Parent"): + * if not key in self.attrs: # <<<<<<<<<<<<<< + * continue + * + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_attrs); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 443, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_key, __pyx_t_5, Py_NE)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 443, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_6 = (__pyx_t_2 != 0); + if (__pyx_t_6) { + + /* "pybedtools/cbedtools.pyx":444 + * "gene_id", "Parent"): + * if not key in self.attrs: + * continue # <<<<<<<<<<<<<< + * + * # If it's incoming from Python it's unicode, so store that directly + */ + goto __pyx_L4_continue; + + /* "pybedtools/cbedtools.pyx":443 + * for key in ("ID", "Name", "gene_name", "transcript_id", \ + * "gene_id", "Parent"): + * if not key in self.attrs: # <<<<<<<<<<<<<< + * continue + * + */ + } + + /* "pybedtools/cbedtools.pyx":449 + * # in the attributes (since an Attribute object works on + * # unicode)... + * self.attrs[key] = value # <<<<<<<<<<<<<< + * break + * + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_attrs); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 449, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (unlikely(PyObject_SetItem(__pyx_t_5, __pyx_v_key, __pyx_v_value) < 0)) __PYX_ERR(0, 449, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":450 + * # unicode)... + * self.attrs[key] = value + * break # <<<<<<<<<<<<<< + * + * # Otherwise use _cppstr() because we're storing it in _bed.fields. + */ + goto __pyx_L5_break; + + /* "pybedtools/cbedtools.pyx":441 + * + * if ftype == <string>"gff": + * for key in ("ID", "Name", "gene_name", "transcript_id", \ # <<<<<<<<<<<<<< + * "gene_id", "Parent"): + * if not key in self.attrs: + */ + __pyx_L4_continue:; + } + __pyx_L5_break:; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "pybedtools/cbedtools.pyx":440 + * cdef string ftype = self._bed.file_type + * + * if ftype == <string>"gff": # <<<<<<<<<<<<<< + * for key in ("ID", "Name", "gene_name", "transcript_id", \ + * "gene_id", "Parent"): + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":453 + * + * # Otherwise use _cppstr() because we're storing it in _bed.fields. + * elif ftype == <string>"vcf": # <<<<<<<<<<<<<< + * self._bed.fields[2] = _cppstr(value) + * else: + */ + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_n_b_vcf); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 453, __pyx_L1_error) + __pyx_t_6 = ((__pyx_v_ftype == ((std::string)__pyx_t_1)) != 0); + if (__pyx_t_6) { + + /* "pybedtools/cbedtools.pyx":454 + * # Otherwise use _cppstr() because we're storing it in _bed.fields. + * elif ftype == <string>"vcf": + * self._bed.fields[2] = _cppstr(value) # <<<<<<<<<<<<<< + * else: + * self._bed.name = _cppstr(value) + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 454, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 454, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + (__pyx_v_self->_bed->fields[2]) = __pyx_t_1; + + /* "pybedtools/cbedtools.pyx":453 + * + * # Otherwise use _cppstr() because we're storing it in _bed.fields. + * elif ftype == <string>"vcf": # <<<<<<<<<<<<<< + * self._bed.fields[2] = _cppstr(value) + * else: + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":456 + * self._bed.fields[2] = _cppstr(value) + * else: + * self._bed.name = _cppstr(value) # <<<<<<<<<<<<<< + * self._bed.fields[3] = _cppstr(value) + * + */ + /*else*/ { + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 456, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 456, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_v_self->_bed->name = __pyx_t_1; + + /* "pybedtools/cbedtools.pyx":457 + * else: + * self._bed.name = _cppstr(value) + * self._bed.fields[3] = _cppstr(value) # <<<<<<<<<<<<<< + * + * property score: + */ + __pyx_t_3 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 457, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_1 = __pyx_convert_string_from_py_std__in_string(__pyx_t_3); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 457, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + (__pyx_v_self->_bed->fields[3]) = __pyx_t_1; + } + __pyx_L3:; + + /* "pybedtools/cbedtools.pyx":437 + * return value + * + * def __set__(self, value): # <<<<<<<<<<<<<< + * cdef string ftype = self._bed.file_type + * + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.name.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_key); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":460 + * + * property score: + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.score) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5score_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5score_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5score___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5score___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":461 + * property score: + * def __get__(self): + * return _pystr(self._bed.score) # <<<<<<<<<<<<<< + * + * def __set__(self, value): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->score); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 461, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":460 + * + * property score: + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.score) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.score.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":463 + * return _pystr(self._bed.score) + * + * def __set__(self, value): # <<<<<<<<<<<<<< + * value = _cppstr(value) + * self._bed.score = value + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5score_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_5score_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5score_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_value)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_5score_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value) { + PyObject *__pyx_v_idx = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + std::string __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + std::vector<std::string> ::size_type __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_INCREF(__pyx_v_value); + + /* "pybedtools/cbedtools.pyx":464 + * + * def __set__(self, value): + * value = _cppstr(value) # <<<<<<<<<<<<<< + * self._bed.score = value + * idx = LOOKUPS[self.file_type]["score"] + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 464, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_value, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":465 + * def __set__(self, value): + * value = _cppstr(value) + * self._bed.score = value # <<<<<<<<<<<<<< + * idx = LOOKUPS[self.file_type]["score"] + * self._bed.fields[idx] = value + */ + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_v_value); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 465, __pyx_L1_error) + __pyx_v_self->_bed->score = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":466 + * value = _cppstr(value) + * self._bed.score = value + * idx = LOOKUPS[self.file_type]["score"] # <<<<<<<<<<<<<< + * self._bed.fields[idx] = value + * + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 466, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 466, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 466, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyObject_Dict_GetItem(__pyx_t_3, __pyx_n_s_score); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 466, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_v_idx = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":467 + * self._bed.score = value + * idx = LOOKUPS[self.file_type]["score"] + * self._bed.fields[idx] = value # <<<<<<<<<<<<<< + * + * property file_type: + */ + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_v_value); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyInt_As_size_t(__pyx_v_idx); if (unlikely((__pyx_t_4 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 467, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_4]) = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":463 + * return _pystr(self._bed.score) + * + * def __set__(self, value): # <<<<<<<<<<<<<< + * value = _cppstr(value) + * self._bed.score = value + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.score.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_idx); + __Pyx_XDECREF(__pyx_v_value); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":471 + * property file_type: + * "bed/vcf/gff" + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.file_type) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_9file_type_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_9file_type_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_9file_type___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_9file_type___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":472 + * "bed/vcf/gff" + * def __get__(self): + * return _pystr(self._bed.file_type) # <<<<<<<<<<<<<< + * + * def __set__(self, value): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 472, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":471 + * property file_type: + * "bed/vcf/gff" + * def __get__(self): # <<<<<<<<<<<<<< + * return _pystr(self._bed.file_type) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.file_type.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":474 + * return _pystr(self._bed.file_type) + * + * def __set__(self, value): # <<<<<<<<<<<<<< + * self._bed.file_type = _cppstr(value) + * + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_9file_type_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_9file_type_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_9file_type_2__set__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_value)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_9file_type_2__set__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value) { + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + std::string __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__set__", 0); + + /* "pybedtools/cbedtools.pyx":475 + * + * def __set__(self, value): + * self._bed.file_type = _cppstr(value) # <<<<<<<<<<<<<< + * + * # TODO: maybe bed.overlap_start or bed.overlap.start ?? + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 475, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 475, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v_self->_bed->file_type = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":474 + * return _pystr(self._bed.file_type) + * + * def __set__(self, value): # <<<<<<<<<<<<<< + * self._bed.file_type = _cppstr(value) + * + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.file_type.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":479 + * # TODO: maybe bed.overlap_start or bed.overlap.start ?? + * @property + * def o_start(self): # <<<<<<<<<<<<<< + * return self._bed.o_start + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_7o_start_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_7o_start_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_7o_start___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_7o_start___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":480 + * @property + * def o_start(self): + * return self._bed.o_start # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS(__pyx_v_self->_bed->o_start); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 480, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":479 + * # TODO: maybe bed.overlap_start or bed.overlap.start ?? + * @property + * def o_start(self): # <<<<<<<<<<<<<< + * return self._bed.o_start + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.o_start.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":483 + * + * @property + * def o_end(self): # <<<<<<<<<<<<<< + * return self._bed.o_end + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5o_end_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5o_end_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5o_end___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5o_end___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":484 + * @property + * def o_end(self): + * return self._bed.o_end # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS(__pyx_v_self->_bed->o_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 484, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":483 + * + * @property + * def o_end(self): # <<<<<<<<<<<<<< + * return self._bed.o_end + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.o_end.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":487 + * + * @property + * def o_amt(self): # <<<<<<<<<<<<<< + * return self._bed.o_end - self._bed.o_start + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5o_amt_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_5o_amt_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_5o_amt___get__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_5o_amt___get__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":488 + * @property + * def o_amt(self): + * return self._bed.o_end - self._bed.o_start # <<<<<<<<<<<<<< + * + * def __str__(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_CHRPOS((__pyx_v_self->_bed->o_end - __pyx_v_self->_bed->o_start)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 488, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":487 + * + * @property + * def o_amt(self): # <<<<<<<<<<<<<< + * return self._bed.o_end - self._bed.o_start + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.o_amt.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":490 + * return self._bed.o_end - self._bed.o_start + * + * def __str__(self): # <<<<<<<<<<<<<< + * """ + * Interval objects always print with a newline to mimic a line in a + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_11__str__(PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_8Interval_10__str__[] = "\n Interval objects always print with a newline to mimic a line in a\n BED/GFF/VCF file\n "; +#if CYTHON_UPDATE_DESCRIPTOR_DOC +struct wrapperbase __pyx_wrapperbase_10pybedtools_9cbedtools_8Interval_10__str__; +#endif +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_11__str__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__str__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_10__str__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_10__str__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_v_items = NULL; + PyObject *__pyx_v_i = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + Py_ssize_t __pyx_t_3; + PyObject *(*__pyx_t_4)(PyObject *); + int __pyx_t_5; + int __pyx_t_6; + int __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__str__", 0); + + /* "pybedtools/cbedtools.pyx":495 + * BED/GFF/VCF file + * """ + * items = [] # <<<<<<<<<<<<<< + * for i in self.fields: + * if isinstance(i, int): + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 495, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_items = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":496 + * """ + * items = [] + * for i in self.fields: # <<<<<<<<<<<<<< + * if isinstance(i, int): + * i = str(i) + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fields); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 496, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) { + __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; + __pyx_t_4 = NULL; + } else { + __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 496, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 496, __pyx_L1_error) + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + for (;;) { + if (likely(!__pyx_t_4)) { + if (likely(PyList_CheckExact(__pyx_t_2))) { + if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 496, __pyx_L1_error) + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 496, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + #endif + } else { + if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 496, __pyx_L1_error) + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 496, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + #endif + } + } else { + __pyx_t_1 = __pyx_t_4(__pyx_t_2); + if (unlikely(!__pyx_t_1)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 496, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_1); + } + __Pyx_XDECREF_SET(__pyx_v_i, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":497 + * items = [] + * for i in self.fields: + * if isinstance(i, int): # <<<<<<<<<<<<<< + * i = str(i) + * items.append(i) + */ + __pyx_t_5 = PyInt_Check(__pyx_v_i); + __pyx_t_6 = (__pyx_t_5 != 0); + if (__pyx_t_6) { + + /* "pybedtools/cbedtools.pyx":498 + * for i in self.fields: + * if isinstance(i, int): + * i = str(i) # <<<<<<<<<<<<<< + * items.append(i) + * + */ + __pyx_t_1 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_v_i); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 498, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_i, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":497 + * items = [] + * for i in self.fields: + * if isinstance(i, int): # <<<<<<<<<<<<<< + * i = str(i) + * items.append(i) + */ + } + + /* "pybedtools/cbedtools.pyx":499 + * if isinstance(i, int): + * i = str(i) + * items.append(i) # <<<<<<<<<<<<<< + * + * return '\t'.join(items) + '\n' + */ + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_items, __pyx_v_i); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 499, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":496 + * """ + * items = [] + * for i in self.fields: # <<<<<<<<<<<<<< + * if isinstance(i, int): + * i = str(i) + */ + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":501 + * items.append(i) + * + * return '\t'.join(items) + '\n' # <<<<<<<<<<<<<< + * + * def __repr__(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyString_Join(__pyx_kp_s__8, __pyx_v_items); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 501, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyNumber_Add(__pyx_t_2, __pyx_kp_s__15); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 501, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":490 + * return self._bed.o_end - self._bed.o_start + * + * def __str__(self): # <<<<<<<<<<<<<< + * """ + * Interval objects always print with a newline to mimic a line in a + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_items); + __Pyx_XDECREF(__pyx_v_i); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":503 + * return '\t'.join(items) + '\n' + * + * def __repr__(self): # <<<<<<<<<<<<<< + * return "Interval(%s:%i-%i)" % (self.chrom, self.start, self.end) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_13__repr__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_13__repr__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__repr__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_12__repr__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_12__repr__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__repr__", 0); + + /* "pybedtools/cbedtools.pyx":504 + * + * def __repr__(self): + * return "Interval(%s:%i-%i)" % (self.chrom, self.start, self.end) # <<<<<<<<<<<<<< + * + * def __dealloc__(self): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_chrom); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 504, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_start); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 504, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_end); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 504, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 504, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); + __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_3); + __pyx_t_1 = 0; + __pyx_t_2 = 0; + __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_Interval_s_i_i, __pyx_t_4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 504, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_r = __pyx_t_3; + __pyx_t_3 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":503 + * return '\t'.join(items) + '\n' + * + * def __repr__(self): # <<<<<<<<<<<<<< + * return "Interval(%s:%i-%i)" % (self.chrom, self.start, self.end) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__repr__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":506 + * return "Interval(%s:%i-%i)" % (self.chrom, self.start, self.end) + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * del self._bed + * + */ + +/* Python wrapper */ +static void __pyx_pw_10pybedtools_9cbedtools_8Interval_15__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_10pybedtools_9cbedtools_8Interval_15__dealloc__(PyObject *__pyx_v_self) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); + __pyx_pf_10pybedtools_9cbedtools_8Interval_14__dealloc__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_10pybedtools_9cbedtools_8Interval_14__dealloc__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__", 0); + + /* "pybedtools/cbedtools.pyx":507 + * + * def __dealloc__(self): + * del self._bed # <<<<<<<<<<<<<< + * + * def __len__(self): + */ + delete __pyx_v_self->_bed; + + /* "pybedtools/cbedtools.pyx":506 + * return "Interval(%s:%i-%i)" % (self.chrom, self.start, self.end) + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * del self._bed + * + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +/* "pybedtools/cbedtools.pyx":509 + * del self._bed + * + * def __len__(self): # <<<<<<<<<<<<<< + * return self._bed.end - self._bed.start + * + */ + +/* Python wrapper */ +static Py_ssize_t __pyx_pw_10pybedtools_9cbedtools_8Interval_17__len__(PyObject *__pyx_v_self); /*proto*/ +static Py_ssize_t __pyx_pw_10pybedtools_9cbedtools_8Interval_17__len__(PyObject *__pyx_v_self) { + Py_ssize_t __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__len__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_16__len__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static Py_ssize_t __pyx_pf_10pybedtools_9cbedtools_8Interval_16__len__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + Py_ssize_t __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__len__", 0); + + /* "pybedtools/cbedtools.pyx":510 + * + * def __len__(self): + * return self._bed.end - self._bed.start # <<<<<<<<<<<<<< + * + * def __getitem__(self, object key): + */ + __pyx_r = (__pyx_v_self->_bed->end - __pyx_v_self->_bed->start); + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":509 + * del self._bed + * + * def __len__(self): # <<<<<<<<<<<<<< + * return self._bed.end - self._bed.start + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":512 + * return self._bed.end - self._bed.start + * + * def __getitem__(self, object key): # <<<<<<<<<<<<<< + * cdef int i + * ftype = _pystr(self._bed.file_type) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_19__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_19__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_18__getitem__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_key)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_18__getitem__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_key) { + int __pyx_v_i; + PyObject *__pyx_v_ftype = NULL; + PyObject *__pyx_v_nfields = NULL; + PyObject *__pyx_v_indices = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + std::vector<std::string> ::size_type __pyx_t_5; + __Pyx_FakeReference<std::string> __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + Py_ssize_t __pyx_t_10; + PyObject *(*__pyx_t_11)(PyObject *); + int __pyx_t_12; + __Pyx_FakeReference<std::string> __pyx_t_13; + PyObject *__pyx_t_14 = NULL; + PyObject *__pyx_t_15 = NULL; + PyObject *__pyx_t_16 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__getitem__", 0); + __Pyx_INCREF(__pyx_v_key); + + /* "pybedtools/cbedtools.pyx":514 + * def __getitem__(self, object key): + * cdef int i + * ftype = _pystr(self._bed.file_type) # <<<<<<<<<<<<<< + * + * self.deparse_attrs() + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->file_type); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 514, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_ftype = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":516 + * ftype = _pystr(self._bed.file_type) + * + * self.deparse_attrs() # <<<<<<<<<<<<<< + * + * if isinstance(key, (int, long)): + */ + __pyx_t_1 = ((struct __pyx_vtabstruct_10pybedtools_9cbedtools_Interval *)__pyx_v_self->__pyx_vtab)->deparse_attrs(__pyx_v_self, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 516, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":518 + * self.deparse_attrs() + * + * if isinstance(key, (int, long)): # <<<<<<<<<<<<<< + * nfields = self._bed.fields.size() + * if key >= nfields: + */ + __pyx_t_3 = PyInt_Check(__pyx_v_key); + __pyx_t_4 = (__pyx_t_3 != 0); + if (!__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L4_bool_binop_done; + } + __pyx_t_4 = PyLong_Check(__pyx_v_key); + __pyx_t_3 = (__pyx_t_4 != 0); + __pyx_t_2 = __pyx_t_3; + __pyx_L4_bool_binop_done:; + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":519 + * + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() # <<<<<<<<<<<<<< + * if key >= nfields: + * raise IndexError('field index out of range') + */ + __pyx_t_1 = __Pyx_PyInt_FromSize_t(__pyx_v_self->_bed->fields.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 519, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_nfields = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":520 + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() + * if key >= nfields: # <<<<<<<<<<<<<< + * raise IndexError('field index out of range') + * elif key < 0: + */ + __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, __pyx_v_nfields, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 520, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 520, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(__pyx_t_3)) { + + /* "pybedtools/cbedtools.pyx":521 + * nfields = self._bed.fields.size() + * if key >= nfields: + * raise IndexError('field index out of range') # <<<<<<<<<<<<<< + * elif key < 0: + * key = nfields + key + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 521, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(0, 521, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":520 + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() + * if key >= nfields: # <<<<<<<<<<<<<< + * raise IndexError('field index out of range') + * elif key < 0: + */ + } + + /* "pybedtools/cbedtools.pyx":522 + * if key >= nfields: + * raise IndexError('field index out of range') + * elif key < 0: # <<<<<<<<<<<<<< + * key = nfields + key + * return _pystr(self._bed.fields.at(key)) + */ + __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 522, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 522, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":523 + * raise IndexError('field index out of range') + * elif key < 0: + * key = nfields + key # <<<<<<<<<<<<<< + * return _pystr(self._bed.fields.at(key)) + * elif isinstance(key, slice): + */ + __pyx_t_1 = PyNumber_Add(__pyx_v_nfields, __pyx_v_key); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 523, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF_SET(__pyx_v_key, __pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":522 + * if key >= nfields: + * raise IndexError('field index out of range') + * elif key < 0: # <<<<<<<<<<<<<< + * key = nfields + key + * return _pystr(self._bed.fields.at(key)) + */ + } + + /* "pybedtools/cbedtools.pyx":524 + * elif key < 0: + * key = nfields + key + * return _pystr(self._bed.fields.at(key)) # <<<<<<<<<<<<<< + * elif isinstance(key, slice): + * indices = key.indices(self._bed.fields.size()) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_5 = __Pyx_PyInt_As_size_t(__pyx_v_key); if (unlikely((__pyx_t_5 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 524, __pyx_L1_error) + try { + __pyx_t_6 = __pyx_v_self->_bed->fields.at(__pyx_t_5); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 524, __pyx_L1_error) + } + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_t_6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 524, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":518 + * self.deparse_attrs() + * + * if isinstance(key, (int, long)): # <<<<<<<<<<<<<< + * nfields = self._bed.fields.size() + * if key >= nfields: + */ + } + + /* "pybedtools/cbedtools.pyx":525 + * key = nfields + key + * return _pystr(self._bed.fields.at(key)) + * elif isinstance(key, slice): # <<<<<<<<<<<<<< + * indices = key.indices(self._bed.fields.size()) + * return [_pystr(self._bed.fields.at(i)) for i in range(*indices)] + */ + __pyx_t_3 = PySlice_Check(__pyx_v_key); + __pyx_t_2 = (__pyx_t_3 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":526 + * return _pystr(self._bed.fields.at(key)) + * elif isinstance(key, slice): + * indices = key.indices(self._bed.fields.size()) # <<<<<<<<<<<<<< + * return [_pystr(self._bed.fields.at(i)) for i in range(*indices)] + * + */ + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_key, __pyx_n_s_indices); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 526, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_self->_bed->fields.size()); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 526, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_7))) { + __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_7); + if (likely(__pyx_t_9)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7); + __Pyx_INCREF(__pyx_t_9); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_7, function); + } + } + __pyx_t_1 = (__pyx_t_9) ? __Pyx_PyObject_Call2Args(__pyx_t_7, __pyx_t_9, __pyx_t_8) : __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_t_8); + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 526, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_v_indices = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":527 + * elif isinstance(key, slice): + * indices = key.indices(self._bed.fields.size()) + * return [_pystr(self._bed.fields.at(i)) for i in range(*indices)] # <<<<<<<<<<<<<< + * + * elif isinstance(key, str): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PySequence_Tuple(__pyx_v_indices); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_7, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (likely(PyList_CheckExact(__pyx_t_8)) || PyTuple_CheckExact(__pyx_t_8)) { + __pyx_t_7 = __pyx_t_8; __Pyx_INCREF(__pyx_t_7); __pyx_t_10 = 0; + __pyx_t_11 = NULL; + } else { + __pyx_t_10 = -1; __pyx_t_7 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_11 = Py_TYPE(__pyx_t_7)->tp_iternext; if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 527, __pyx_L1_error) + } + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + for (;;) { + if (likely(!__pyx_t_11)) { + if (likely(PyList_CheckExact(__pyx_t_7))) { + if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_7)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_7, __pyx_t_10); __Pyx_INCREF(__pyx_t_8); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 527, __pyx_L1_error) + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_7, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + #endif + } else { + if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_7)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_7, __pyx_t_10); __Pyx_INCREF(__pyx_t_8); __pyx_t_10++; if (unlikely(0 < 0)) __PYX_ERR(0, 527, __pyx_L1_error) + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_7, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + #endif + } + } else { + __pyx_t_8 = __pyx_t_11(__pyx_t_7); + if (unlikely(!__pyx_t_8)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(0, 527, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_8); + } + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_8); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_v_i = __pyx_t_12; + try { + __pyx_t_13 = __pyx_v_self->_bed->fields.at(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 527, __pyx_L1_error) + } + __pyx_t_8 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_t_13); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_8))) __PYX_ERR(0, 527, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + } + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":525 + * key = nfields + key + * return _pystr(self._bed.fields.at(key)) + * elif isinstance(key, slice): # <<<<<<<<<<<<<< + * indices = key.indices(self._bed.fields.size()) + * return [_pystr(self._bed.fields.at(i)) for i in range(*indices)] + */ + } + + /* "pybedtools/cbedtools.pyx":529 + * return [_pystr(self._bed.fields.at(i)) for i in range(*indices)] + * + * elif isinstance(key, str): # <<<<<<<<<<<<<< + * if ftype == "gff": + * try: + */ + __pyx_t_2 = PyString_Check(__pyx_v_key); + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":530 + * + * elif isinstance(key, str): + * if ftype == "gff": # <<<<<<<<<<<<<< + * try: + * return self.attrs[key] + */ + __pyx_t_3 = (__Pyx_PyString_Equals(__pyx_v_ftype, __pyx_n_s_gff, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 530, __pyx_L1_error) + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":531 + * elif isinstance(key, str): + * if ftype == "gff": + * try: # <<<<<<<<<<<<<< + * return self.attrs[key] + * except KeyError: + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_14, &__pyx_t_15, &__pyx_t_16); + __Pyx_XGOTREF(__pyx_t_14); + __Pyx_XGOTREF(__pyx_t_15); + __Pyx_XGOTREF(__pyx_t_16); + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":532 + * if ftype == "gff": + * try: + * return self.attrs[key] # <<<<<<<<<<<<<< + * except KeyError: + * pass + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_attrs); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 532, __pyx_L10_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 532, __pyx_L10_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_r = __pyx_t_7; + __pyx_t_7 = 0; + goto __pyx_L14_try_return; + + /* "pybedtools/cbedtools.pyx":531 + * elif isinstance(key, str): + * if ftype == "gff": + * try: # <<<<<<<<<<<<<< + * return self.attrs[key] + * except KeyError: + */ + } + __pyx_L10_error:; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + + /* "pybedtools/cbedtools.pyx":533 + * try: + * return self.attrs[key] + * except KeyError: # <<<<<<<<<<<<<< + * pass + * # We don't have to convert using _pystr() because the __get__ + */ + __pyx_t_12 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_KeyError); + if (__pyx_t_12) { + __Pyx_ErrRestore(0,0,0); + goto __pyx_L11_exception_handled; + } + goto __pyx_L12_except_error; + __pyx_L12_except_error:; + + /* "pybedtools/cbedtools.pyx":531 + * elif isinstance(key, str): + * if ftype == "gff": + * try: # <<<<<<<<<<<<<< + * return self.attrs[key] + * except KeyError: + */ + __Pyx_XGIVEREF(__pyx_t_14); + __Pyx_XGIVEREF(__pyx_t_15); + __Pyx_XGIVEREF(__pyx_t_16); + __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16); + goto __pyx_L1_error; + __pyx_L14_try_return:; + __Pyx_XGIVEREF(__pyx_t_14); + __Pyx_XGIVEREF(__pyx_t_15); + __Pyx_XGIVEREF(__pyx_t_16); + __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16); + goto __pyx_L0; + __pyx_L11_exception_handled:; + __Pyx_XGIVEREF(__pyx_t_14); + __Pyx_XGIVEREF(__pyx_t_15); + __Pyx_XGIVEREF(__pyx_t_16); + __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16); + } + + /* "pybedtools/cbedtools.pyx":530 + * + * elif isinstance(key, str): + * if ftype == "gff": # <<<<<<<<<<<<<< + * try: + * return self.attrs[key] + */ + } + + /* "pybedtools/cbedtools.pyx":537 + * # We don't have to convert using _pystr() because the __get__ + * # methods do that already. + * return getattr(self, key) # <<<<<<<<<<<<<< + * + * def __setitem__(self, object key, object value): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_7 = __Pyx_GetAttr(((PyObject *)__pyx_v_self), __pyx_v_key); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 537, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_r = __pyx_t_7; + __pyx_t_7 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":529 + * return [_pystr(self._bed.fields.at(i)) for i in range(*indices)] + * + * elif isinstance(key, str): # <<<<<<<<<<<<<< + * if ftype == "gff": + * try: + */ + } + + /* "pybedtools/cbedtools.pyx":512 + * return self._bed.end - self._bed.start + * + * def __getitem__(self, object key): # <<<<<<<<<<<<<< + * cdef int i + * ftype = _pystr(self._bed.file_type) + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_ftype); + __Pyx_XDECREF(__pyx_v_nfields); + __Pyx_XDECREF(__pyx_v_indices); + __Pyx_XDECREF(__pyx_v_key); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":539 + * return getattr(self, key) + * + * def __setitem__(self, object key, object value): # <<<<<<<<<<<<<< + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_21__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_21__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setitem__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_20__setitem__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_20__setitem__(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) { + PyObject *__pyx_v_nfields = NULL; + PyObject *__pyx_v_ft = NULL; + int __pyx_r; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + std::string __pyx_t_5; + std::vector<std::string> ::size_type __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + int __pyx_t_8; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__setitem__", 0); + __Pyx_INCREF(__pyx_v_key); + + /* "pybedtools/cbedtools.pyx":540 + * + * def __setitem__(self, object key, object value): + * if isinstance(key, (int, long)): # <<<<<<<<<<<<<< + * nfields = self._bed.fields.size() + * if key >= nfields: + */ + __pyx_t_2 = PyInt_Check(__pyx_v_key); + __pyx_t_3 = (__pyx_t_2 != 0); + if (!__pyx_t_3) { + } else { + __pyx_t_1 = __pyx_t_3; + goto __pyx_L4_bool_binop_done; + } + __pyx_t_3 = PyLong_Check(__pyx_v_key); + __pyx_t_2 = (__pyx_t_3 != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L4_bool_binop_done:; + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":541 + * def __setitem__(self, object key, object value): + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() # <<<<<<<<<<<<<< + * if key >= nfields: + * raise IndexError('field index out of range') + */ + __pyx_t_4 = __Pyx_PyInt_FromSize_t(__pyx_v_self->_bed->fields.size()); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 541, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_v_nfields = __pyx_t_4; + __pyx_t_4 = 0; + + /* "pybedtools/cbedtools.pyx":542 + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() + * if key >= nfields: # <<<<<<<<<<<<<< + * raise IndexError('field index out of range') + * elif key < 0: + */ + __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, __pyx_v_nfields, Py_GE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 542, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 542, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (unlikely(__pyx_t_2)) { + + /* "pybedtools/cbedtools.pyx":543 + * nfields = self._bed.fields.size() + * if key >= nfields: + * raise IndexError('field index out of range') # <<<<<<<<<<<<<< + * elif key < 0: + * key = nfields + key + */ + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 543, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __PYX_ERR(0, 543, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":542 + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() + * if key >= nfields: # <<<<<<<<<<<<<< + * raise IndexError('field index out of range') + * elif key < 0: + */ + } + + /* "pybedtools/cbedtools.pyx":544 + * if key >= nfields: + * raise IndexError('field index out of range') + * elif key < 0: # <<<<<<<<<<<<<< + * key = nfields + key + * self._bed.fields[key] = _cppstr(value) + */ + __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 544, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 544, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":545 + * raise IndexError('field index out of range') + * elif key < 0: + * key = nfields + key # <<<<<<<<<<<<<< + * self._bed.fields[key] = _cppstr(value) + * + */ + __pyx_t_4 = PyNumber_Add(__pyx_v_nfields, __pyx_v_key); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 545, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF_SET(__pyx_v_key, __pyx_t_4); + __pyx_t_4 = 0; + + /* "pybedtools/cbedtools.pyx":544 + * if key >= nfields: + * raise IndexError('field index out of range') + * elif key < 0: # <<<<<<<<<<<<<< + * key = nfields + key + * self._bed.fields[key] = _cppstr(value) + */ + } + + /* "pybedtools/cbedtools.pyx":546 + * elif key < 0: + * key = nfields + key + * self._bed.fields[key] = _cppstr(value) # <<<<<<<<<<<<<< + * + * ft = _pystr(self._bed.file_type) + */ + __pyx_t_4 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 546, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __pyx_convert_string_from_py_std__in_string(__pyx_t_4); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 546, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyInt_As_size_t(__pyx_v_key); if (unlikely((__pyx_t_6 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 546, __pyx_L1_error) + (__pyx_v_self->_bed->fields[__pyx_t_6]) = __pyx_t_5; + + /* "pybedtools/cbedtools.pyx":548 + * self._bed.fields[key] = _cppstr(value) + * + * ft = _pystr(self._bed.file_type) # <<<<<<<<<<<<<< + * if key in LOOKUPS[ft]: + * setattr(self, LOOKUPS[ft][key], value) + */ + __pyx_t_4 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_bed->file_type); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 548, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_v_ft = __pyx_t_4; + __pyx_t_4 = 0; + + /* "pybedtools/cbedtools.pyx":549 + * + * ft = _pystr(self._bed.file_type) + * if key in LOOKUPS[ft]: # <<<<<<<<<<<<<< + * setattr(self, LOOKUPS[ft][key], value) + * + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 549, __pyx_L1_error) + } + __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_v_ft); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 549, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_v_key, __pyx_t_4, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 549, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_1 = (__pyx_t_2 != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":550 + * ft = _pystr(self._bed.file_type) + * if key in LOOKUPS[ft]: + * setattr(self, LOOKUPS[ft][key], value) # <<<<<<<<<<<<<< + * + * elif isinstance(key, (basestring)): + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 550, __pyx_L1_error) + } + __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, __pyx_v_ft); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_7 = __Pyx_PyObject_GetItem(__pyx_t_4, __pyx_v_key); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_8 = PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_t_7, __pyx_v_value); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 550, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":549 + * + * ft = _pystr(self._bed.file_type) + * if key in LOOKUPS[ft]: # <<<<<<<<<<<<<< + * setattr(self, LOOKUPS[ft][key], value) + * + */ + } + + /* "pybedtools/cbedtools.pyx":540 + * + * def __setitem__(self, object key, object value): + * if isinstance(key, (int, long)): # <<<<<<<<<<<<<< + * nfields = self._bed.fields.size() + * if key >= nfields: + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":552 + * setattr(self, LOOKUPS[ft][key], value) + * + * elif isinstance(key, (basestring)): # <<<<<<<<<<<<<< + * setattr(self, key, value) + * + */ + __pyx_t_1 = __Pyx_PyBaseString_Check(__pyx_v_key); + __pyx_t_2 = (__pyx_t_1 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":553 + * + * elif isinstance(key, (basestring)): + * setattr(self, key, value) # <<<<<<<<<<<<<< + * + * cpdef append(self, object value): + */ + __pyx_t_8 = PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_v_key, __pyx_v_value); if (unlikely(__pyx_t_8 == ((int)-1))) __PYX_ERR(0, 553, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":552 + * setattr(self, LOOKUPS[ft][key], value) + * + * elif isinstance(key, (basestring)): # <<<<<<<<<<<<<< + * setattr(self, key, value) + * + */ + } + __pyx_L3:; + + /* "pybedtools/cbedtools.pyx":539 + * return getattr(self, key) + * + * def __setitem__(self, object key, object value): # <<<<<<<<<<<<<< + * if isinstance(key, (int, long)): + * nfields = self._bed.fields.size() + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__setitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_nfields); + __Pyx_XDECREF(__pyx_v_ft); + __Pyx_XDECREF(__pyx_v_key); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":555 + * setattr(self, key, value) + * + * cpdef append(self, object value): # <<<<<<<<<<<<<< + * self._bed.fields.push_back(_cppstr(value)) + * + */ + +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_23append(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/ +static PyObject *__pyx_f_10pybedtools_9cbedtools_8Interval_append(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value, int __pyx_skip_dispatch) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + std::string __pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("append", 0); + /* Check if called by wrapper */ + if (unlikely(__pyx_skip_dispatch)) ; + /* Check if overridden in Python */ + else if (unlikely((Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0) || (Py_TYPE(((PyObject *)__pyx_v_self))->tp_flags & (Py_TPFLAGS_IS_ABSTRACT | Py_TPFLAGS_HEAPTYPE)))) { + #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS + static PY_UINT64_T __pyx_tp_dict_version = __PYX_DICT_VERSION_INIT, __pyx_obj_dict_version = __PYX_DICT_VERSION_INIT; + if (unlikely(!__Pyx_object_dict_version_matches(((PyObject *)__pyx_v_self), __pyx_tp_dict_version, __pyx_obj_dict_version))) { + PY_UINT64_T __pyx_type_dict_guard = __Pyx_get_tp_dict_version(((PyObject *)__pyx_v_self)); + #endif + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_append); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 555, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)(void*)__pyx_pw_10pybedtools_9cbedtools_8Interval_23append)) { + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_t_1); + __pyx_t_3 = __pyx_t_1; __pyx_t_4 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + } + } + __pyx_t_2 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_4, __pyx_v_value) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_value); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 555, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + goto __pyx_L0; + } + #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS + __pyx_tp_dict_version = __Pyx_get_tp_dict_version(((PyObject *)__pyx_v_self)); + __pyx_obj_dict_version = __Pyx_get_object_dict_version(((PyObject *)__pyx_v_self)); + if (unlikely(__pyx_type_dict_guard != __pyx_tp_dict_version)) { + __pyx_tp_dict_version = __pyx_obj_dict_version = __PYX_DICT_VERSION_INIT; + } + #endif + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS + } + #endif + } + + /* "pybedtools/cbedtools.pyx":556 + * + * cpdef append(self, object value): + * self._bed.fields.push_back(_cppstr(value)) # <<<<<<<<<<<<<< + * + * def __nonzero__(self): + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_value); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 556, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 556, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + try { + __pyx_v_self->_bed->fields.push_back(__pyx_t_5); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 556, __pyx_L1_error) + } + + /* "pybedtools/cbedtools.pyx":555 + * setattr(self, key, value) + * + * cpdef append(self, object value): # <<<<<<<<<<<<<< + * self._bed.fields.push_back(_cppstr(value)) + * + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.append", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_23append(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_23append(PyObject *__pyx_v_self, PyObject *__pyx_v_value) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("append (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_22append(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v_value)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_22append(struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, PyObject *__pyx_v_value) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("append", 0); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_8Interval_append(__pyx_v_self, __pyx_v_value, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 555, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.append", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":558 + * self._bed.fields.push_back(_cppstr(value)) + * + * def __nonzero__(self): # <<<<<<<<<<<<<< + * return True + * + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_25__nonzero__(PyObject *__pyx_v_self); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_8Interval_25__nonzero__(PyObject *__pyx_v_self) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__nonzero__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_24__nonzero__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_8Interval_24__nonzero__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__nonzero__", 0); + + /* "pybedtools/cbedtools.pyx":559 + * + * def __nonzero__(self): + * return True # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = 1; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":558 + * self._bed.fields.push_back(_cppstr(value)) + * + * def __nonzero__(self): # <<<<<<<<<<<<<< + * return True + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_27__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_27__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_26__reduce_cython__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_26__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__reduce_cython__", 0); + + /* "(tree fragment)":2 + * def __reduce_cython__(self): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(1, 2, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_29__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_8Interval_29__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_8Interval_28__setstate_cython__(((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_8Interval_28__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__setstate_cython__", 0); + + /* "(tree fragment)":4 + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(1, 4, __pyx_L1_error) + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.Interval.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":562 + * + * + * cdef Interval create_interval(BED b): # <<<<<<<<<<<<<< + * cdef Interval pyb = Interval.__new__(Interval) + * pyb._bed = new BED(b.chrom, b.start, b.end, b.name, + */ + +static struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_f_10pybedtools_9cbedtools_create_interval(BED __pyx_v_b) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_pyb = 0; + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + std::vector<std::string> __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("create_interval", 0); + + /* "pybedtools/cbedtools.pyx":563 + * + * cdef Interval create_interval(BED b): + * cdef Interval pyb = Interval.__new__(Interval) # <<<<<<<<<<<<<< + * pyb._bed = new BED(b.chrom, b.start, b.end, b.name, + * b.score, b.strand, b.fields, + */ + __pyx_t_1 = ((PyObject *)__pyx_tp_new_10pybedtools_9cbedtools_Interval(((PyTypeObject *)__pyx_ptype_10pybedtools_9cbedtools_Interval), __pyx_empty_tuple, NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 563, __pyx_L1_error) + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __pyx_v_pyb = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":564 + * cdef Interval create_interval(BED b): + * cdef Interval pyb = Interval.__new__(Interval) + * pyb._bed = new BED(b.chrom, b.start, b.end, b.name, # <<<<<<<<<<<<<< + * b.score, b.strand, b.fields, + * b.o_start, b.o_end, b.bedType, b.file_type, b.status) + */ + __pyx_v_pyb->_bed = new BED(__pyx_v_b.chrom, __pyx_v_b.start, __pyx_v_b.end, __pyx_v_b.name, __pyx_v_b.score, __pyx_v_b.strand, __pyx_v_b.fields, __pyx_v_b.o_start, __pyx_v_b.o_end, __pyx_v_b.bedType, __pyx_v_b.file_type, __pyx_v_b.status); + + /* "pybedtools/cbedtools.pyx":567 + * b.score, b.strand, b.fields, + * b.o_start, b.o_end, b.bedType, b.file_type, b.status) + * pyb._bed.fields = b.fields # <<<<<<<<<<<<<< + * return pyb + * + */ + __pyx_t_2 = __pyx_v_b.fields; + __pyx_v_pyb->_bed->fields = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":568 + * b.o_start, b.o_end, b.bedType, b.file_type, b.status) + * pyb._bed.fields = b.fields + * return pyb # <<<<<<<<<<<<<< + * + * # TODO: optimization: Previously we had (fields[1] + fields[2]).isdigit() when + */ + __Pyx_XDECREF(((PyObject *)__pyx_r)); + __Pyx_INCREF(((PyObject *)__pyx_v_pyb)); + __pyx_r = __pyx_v_pyb; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":562 + * + * + * cdef Interval create_interval(BED b): # <<<<<<<<<<<<<< + * cdef Interval pyb = Interval.__new__(Interval) + * pyb._bed = new BED(b.chrom, b.start, b.end, b.name, + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.create_interval", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_pyb); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":573 + * # checking in create_interval_from_list for filetype heuruistics. Is there + * # a performance hit by checking instances? + * cdef isdigit(s): # <<<<<<<<<<<<<< + * if isinstance(s, integer_types): + * return True + */ + +static PyObject *__pyx_f_10pybedtools_9cbedtools_isdigit(PyObject *__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("isdigit", 0); + + /* "pybedtools/cbedtools.pyx":574 + * # a performance hit by checking instances? + * cdef isdigit(s): + * if isinstance(s, integer_types): # <<<<<<<<<<<<<< + * return True + * return s.isdigit() + */ + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_integer_types); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 574, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_IsInstance(__pyx_v_s, __pyx_t_1); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 574, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":575 + * cdef isdigit(s): + * if isinstance(s, integer_types): + * return True # <<<<<<<<<<<<<< + * return s.isdigit() + * + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(Py_True); + __pyx_r = Py_True; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":574 + * # a performance hit by checking instances? + * cdef isdigit(s): + * if isinstance(s, integer_types): # <<<<<<<<<<<<<< + * return True + * return s.isdigit() + */ + } + + /* "pybedtools/cbedtools.pyx":576 + * if isinstance(s, integer_types): + * return True + * return s.isdigit() # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_s, __pyx_n_s_isdigit); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 576, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + __pyx_t_1 = (__pyx_t_5) ? __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5) : __Pyx_PyObject_CallNoArg(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 576, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":573 + * # checking in create_interval_from_list for filetype heuruistics. Is there + * # a performance hit by checking instances? + * cdef isdigit(s): # <<<<<<<<<<<<<< + * if isinstance(s, integer_types): + * return True + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pybedtools.cbedtools.isdigit", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":579 + * + * + * cpdef Interval create_interval_from_list(list fields): # <<<<<<<<<<<<<< + * """ + * Create an Interval object from a list of strings. + */ + +static PyObject *__pyx_pw_10pybedtools_9cbedtools_1create_interval_from_list(PyObject *__pyx_self, PyObject *__pyx_v_fields); /*proto*/ +static struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_f_10pybedtools_9cbedtools_create_interval_from_list(PyObject *__pyx_v_fields, CYTHON_UNUSED int __pyx_skip_dispatch) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_pyb = 0; + PyObject *__pyx_v_orig_fields = NULL; + PyObject *__pyx_v_chrom = NULL; + PyObject *__pyx_v_start = NULL; + PyObject *__pyx_v_stop = NULL; + PyObject *__pyx_v_name = NULL; + PyObject *__pyx_v_score = NULL; + PyObject *__pyx_v_strand = NULL; + PyObject *__pyx_v_other_fields = NULL; + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + Py_ssize_t __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + int __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + std::string __pyx_t_8; + CHRPOS __pyx_t_9; + CHRPOS __pyx_t_10; + std::string __pyx_t_11; + std::string __pyx_t_12; + std::string __pyx_t_13; + int __pyx_t_14; + PyObject *__pyx_t_15 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("create_interval_from_list", 0); + + /* "pybedtools/cbedtools.pyx":608 + * # have an optimized version that is directly provided the filetype. + * + * cdef Interval pyb = Interval.__new__(Interval) # <<<<<<<<<<<<<< + * orig_fields = fields[:] + * # BED -- though a VCF will be detected as BED if its 2nd field, id, is a + */ + __pyx_t_1 = ((PyObject *)__pyx_tp_new_10pybedtools_9cbedtools_Interval(((PyTypeObject *)__pyx_ptype_10pybedtools_9cbedtools_Interval), __pyx_empty_tuple, NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 608, __pyx_L1_error) + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __pyx_v_pyb = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":609 + * + * cdef Interval pyb = Interval.__new__(Interval) + * orig_fields = fields[:] # <<<<<<<<<<<<<< + * # BED -- though a VCF will be detected as BED if its 2nd field, id, is a + * # digit + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 609, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyList_GetSlice(__pyx_v_fields, 0, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 609, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_orig_fields = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":615 + * # SAM + * if ( + * (len(fields) >= 11) # <<<<<<<<<<<<<< + * and isdigit(fields[1]) + * and isdigit(fields[3]) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 615, __pyx_L1_error) + } + __pyx_t_3 = PyList_GET_SIZE(__pyx_v_fields); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 615, __pyx_L1_error) + __pyx_t_4 = ((__pyx_t_3 >= 11) != 0); + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L4_bool_binop_done; + } + + /* "pybedtools/cbedtools.pyx":616 + * if ( + * (len(fields) >= 11) + * and isdigit(fields[1]) # <<<<<<<<<<<<<< + * and isdigit(fields[3]) + * and isdigit(fields[4]) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 616, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 616, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 616, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 616, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L4_bool_binop_done; + } + + /* "pybedtools/cbedtools.pyx":617 + * (len(fields) >= 11) + * and isdigit(fields[1]) + * and isdigit(fields[3]) # <<<<<<<<<<<<<< + * and isdigit(fields[4]) + * and (fields[5] not in ['.', '+', '-']) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 617, __pyx_L1_error) + } + __pyx_t_5 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 617, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 617, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 617, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L4_bool_binop_done; + } + + /* "pybedtools/cbedtools.pyx":618 + * and isdigit(fields[1]) + * and isdigit(fields[3]) + * and isdigit(fields[4]) # <<<<<<<<<<<<<< + * and (fields[5] not in ['.', '+', '-']) + * ): + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 618, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 4, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 618, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 618, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 618, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L4_bool_binop_done; + } + + /* "pybedtools/cbedtools.pyx":619 + * and isdigit(fields[3]) + * and isdigit(fields[4]) + * and (fields[5] not in ['.', '+', '-']) # <<<<<<<<<<<<<< + * ): + * # TODO: what should the stop position be? Here, it's just the start + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 619, __pyx_L1_error) + } + __pyx_t_5 = __Pyx_GetItemInt_List(__pyx_v_fields, 5, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 619, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = (__Pyx_PyString_Equals(__pyx_t_5, __pyx_kp_s__7, Py_NE)); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 619, __pyx_L1_error) + if (__pyx_t_6) { + } else { + __pyx_t_4 = __pyx_t_6; + goto __pyx_L9_bool_binop_done; + } + __pyx_t_6 = (__Pyx_PyString_Equals(__pyx_t_5, __pyx_kp_s__19, Py_NE)); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 619, __pyx_L1_error) + if (__pyx_t_6) { + } else { + __pyx_t_4 = __pyx_t_6; + goto __pyx_L9_bool_binop_done; + } + __pyx_t_6 = (__Pyx_PyString_Equals(__pyx_t_5, __pyx_kp_s__20, Py_NE)); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 619, __pyx_L1_error) + __pyx_t_4 = __pyx_t_6; + __pyx_L9_bool_binop_done:; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_6 = (__pyx_t_4 != 0); + __pyx_t_2 = __pyx_t_6; + __pyx_L4_bool_binop_done:; + + /* "pybedtools/cbedtools.pyx":614 + * + * # SAM + * if ( # <<<<<<<<<<<<<< + * (len(fields) >= 11) + * and isdigit(fields[1]) + */ + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":624 + * # plus the length of the sequence, but perhaps this should eventually + * # do CIGAR string parsing. + * if int(fields[1]) & 0x04: # <<<<<<<<<<<<<< + * # handle unmapped reads + * chrom = _cppstr("*") + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 624, __pyx_L1_error) + } + __pyx_t_5 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 624, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 624, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = __Pyx_PyInt_AndObjC(__pyx_t_1, __pyx_int_4, 0x04, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 624, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 624, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":626 + * if int(fields[1]) & 0x04: + * # handle unmapped reads + * chrom = _cppstr("*") # <<<<<<<<<<<<<< + * start = 0 + * stop = 0 + */ + __pyx_t_5 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_kp_s__21); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 626, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_v_chrom = __pyx_t_5; + __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":627 + * # handle unmapped reads + * chrom = _cppstr("*") + * start = 0 # <<<<<<<<<<<<<< + * stop = 0 + * else: + */ + __Pyx_INCREF(__pyx_int_0); + __pyx_v_start = __pyx_int_0; + + /* "pybedtools/cbedtools.pyx":628 + * chrom = _cppstr("*") + * start = 0 + * stop = 0 # <<<<<<<<<<<<<< + * else: + * chrom = _cppstr(fields[2]) + */ + __Pyx_INCREF(__pyx_int_0); + __pyx_v_stop = __pyx_int_0; + + /* "pybedtools/cbedtools.pyx":624 + * # plus the length of the sequence, but perhaps this should eventually + * # do CIGAR string parsing. + * if int(fields[1]) & 0x04: # <<<<<<<<<<<<<< + * # handle unmapped reads + * chrom = _cppstr("*") + */ + goto __pyx_L12; + } + + /* "pybedtools/cbedtools.pyx":630 + * stop = 0 + * else: + * chrom = _cppstr(fields[2]) # <<<<<<<<<<<<<< + * start = int(fields[3]) - 1 + * stop = int(fields[3]) + len(fields[9]) - 1 + */ + /*else*/ { + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 630, __pyx_L1_error) + } + __pyx_t_5 = __Pyx_GetItemInt_List(__pyx_v_fields, 2, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 630, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 630, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_v_chrom = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":631 + * else: + * chrom = _cppstr(fields[2]) + * start = int(fields[3]) - 1 # <<<<<<<<<<<<<< + * stop = int(fields[3]) + len(fields[9]) - 1 + * name = _cppstr(fields[0]) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 631, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 631, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __Pyx_PyNumber_Int(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 631, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_t_5, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 631, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_v_start = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":632 + * chrom = _cppstr(fields[2]) + * start = int(fields[3]) - 1 + * stop = int(fields[3]) + len(fields[9]) - 1 # <<<<<<<<<<<<<< + * name = _cppstr(fields[0]) + * score = _cppstr(fields[1]) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 632, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __Pyx_PyNumber_Int(__pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 632, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 9, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = PyNumber_Add(__pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyInt_SubtractObjC(__pyx_t_7, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 632, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_v_stop = __pyx_t_1; + __pyx_t_1 = 0; + } + __pyx_L12:; + + /* "pybedtools/cbedtools.pyx":633 + * start = int(fields[3]) - 1 + * stop = int(fields[3]) + len(fields[9]) - 1 + * name = _cppstr(fields[0]) # <<<<<<<<<<<<<< + * score = _cppstr(fields[1]) + * if int(fields[1]) & 0x10: + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 633, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 633, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 633, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v_name = __pyx_t_7; + __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":634 + * stop = int(fields[3]) + len(fields[9]) - 1 + * name = _cppstr(fields[0]) + * score = _cppstr(fields[1]) # <<<<<<<<<<<<<< + * if int(fields[1]) & 0x10: + * strand = _cppstr('-') + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 634, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 634, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 634, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_v_score = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":635 + * name = _cppstr(fields[0]) + * score = _cppstr(fields[1]) + * if int(fields[1]) & 0x10: # <<<<<<<<<<<<<< + * strand = _cppstr('-') + * else: + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 635, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 635, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyNumber_Int(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 635, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_PyInt_AndObjC(__pyx_t_7, __pyx_int_16, 0x10, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 635, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 635, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":636 + * score = _cppstr(fields[1]) + * if int(fields[1]) & 0x10: + * strand = _cppstr('-') # <<<<<<<<<<<<<< + * else: + * strand = _cppstr('+') + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_kp_s__20); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 636, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_strand = __pyx_t_1; + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":635 + * name = _cppstr(fields[0]) + * score = _cppstr(fields[1]) + * if int(fields[1]) & 0x10: # <<<<<<<<<<<<<< + * strand = _cppstr('-') + * else: + */ + goto __pyx_L13; + } + + /* "pybedtools/cbedtools.pyx":638 + * strand = _cppstr('-') + * else: + * strand = _cppstr('+') # <<<<<<<<<<<<<< + * + * # Fields is in SAM format + */ + /*else*/ { + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_kp_s__19); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 638, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_strand = __pyx_t_1; + __pyx_t_1 = 0; + } + __pyx_L13:; + + /* "pybedtools/cbedtools.pyx":641 + * + * # Fields is in SAM format + * fields[3] = str(start + 1) # <<<<<<<<<<<<<< + * + * pyb._bed = new BED( + */ + __pyx_t_1 = __Pyx_PyInt_AddObjC(__pyx_v_start, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 641, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyObject_CallOneArg(((PyObject *)(&PyString_Type)), __pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 641, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 641, __pyx_L1_error) + } + if (unlikely(__Pyx_SetItemInt(__pyx_v_fields, 3, __pyx_t_7, long, 1, __Pyx_PyInt_From_long, 1, 0, 1) < 0)) __PYX_ERR(0, 641, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":644 + * + * pyb._bed = new BED( + * chrom, # <<<<<<<<<<<<<< + * start, + * stop, + */ + __pyx_t_8 = __pyx_convert_string_from_py_std__in_string(__pyx_v_chrom); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 644, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":645 + * pyb._bed = new BED( + * chrom, + * start, # <<<<<<<<<<<<<< + * stop, + * strand, + */ + __pyx_t_9 = __Pyx_PyInt_As_CHRPOS(__pyx_v_start); if (unlikely((__pyx_t_9 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 645, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":646 + * chrom, + * start, + * stop, # <<<<<<<<<<<<<< + * strand, + * name, + */ + __pyx_t_10 = __Pyx_PyInt_As_CHRPOS(__pyx_v_stop); if (unlikely((__pyx_t_10 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 646, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":647 + * start, + * stop, + * strand, # <<<<<<<<<<<<<< + * name, + * score, + */ + __pyx_t_11 = __pyx_convert_string_from_py_std__in_string(__pyx_v_strand); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 647, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":648 + * stop, + * strand, + * name, # <<<<<<<<<<<<<< + * score, + * list_to_vector(fields)) + */ + __pyx_t_12 = __pyx_convert_string_from_py_std__in_string(__pyx_v_name); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 648, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":649 + * strand, + * name, + * score, # <<<<<<<<<<<<<< + * list_to_vector(fields)) + * pyb.file_type = _cppstr('sam') + */ + __pyx_t_13 = __pyx_convert_string_from_py_std__in_string(__pyx_v_score); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 649, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":643 + * fields[3] = str(start + 1) + * + * pyb._bed = new BED( # <<<<<<<<<<<<<< + * chrom, + * start, + */ + __pyx_v_pyb->_bed = new BED(__pyx_t_8, __pyx_t_9, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_f_10pybedtools_9cbedtools_list_to_vector(__pyx_v_fields)); + + /* "pybedtools/cbedtools.pyx":651 + * score, + * list_to_vector(fields)) + * pyb.file_type = _cppstr('sam') # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_n_s_sam); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 651, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_pyb), __pyx_n_s_file_type, __pyx_t_7) < 0) __PYX_ERR(0, 651, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":614 + * + * # SAM + * if ( # <<<<<<<<<<<<<< + * (len(fields) >= 11) + * and isdigit(fields[1]) + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":654 + * + * + * elif isdigit(fields[1]) and isdigit(fields[2]): # <<<<<<<<<<<<<< + * # if it's too short, just add some empty fields. + * if len(fields) < 7: + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 654, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 654, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 654, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 654, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_6) { + } else { + __pyx_t_2 = __pyx_t_6; + goto __pyx_L14_bool_binop_done; + } + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 654, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 2, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 654, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 654, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 654, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_2 = __pyx_t_6; + __pyx_L14_bool_binop_done:; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":656 + * elif isdigit(fields[1]) and isdigit(fields[2]): + * # if it's too short, just add some empty fields. + * if len(fields) < 7: # <<<<<<<<<<<<<< + * fields.extend([".".encode('UTF-8')] * (6 - len(fields))) + * other_fields = [] + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 656, __pyx_L1_error) + } + __pyx_t_3 = PyList_GET_SIZE(__pyx_v_fields); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 656, __pyx_L1_error) + __pyx_t_2 = ((__pyx_t_3 < 7) != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":657 + * # if it's too short, just add some empty fields. + * if len(fields) < 7: + * fields.extend([".".encode('UTF-8')] * (6 - len(fields))) # <<<<<<<<<<<<<< + * other_fields = [] + * else: + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "extend"); + __PYX_ERR(0, 657, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s__7, __pyx_n_s_encode); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 657, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_7 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_5, __pyx_kp_s_UTF_8) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_kp_s_UTF_8); + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 657, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 657, __pyx_L1_error) + } + __pyx_t_3 = PyList_GET_SIZE(__pyx_v_fields); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 657, __pyx_L1_error) + __pyx_t_1 = PyList_New(1 * (((6 - __pyx_t_3)<0) ? 0:(6 - __pyx_t_3))); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 657, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + { Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (6 - __pyx_t_3); __pyx_temp++) { + __Pyx_INCREF(__pyx_t_7); + __Pyx_GIVEREF(__pyx_t_7); + PyList_SET_ITEM(__pyx_t_1, __pyx_temp, __pyx_t_7); + } + } + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_14 = __Pyx_PyList_Extend(__pyx_v_fields, __pyx_t_1); if (unlikely(__pyx_t_14 == ((int)-1))) __PYX_ERR(0, 657, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":658 + * if len(fields) < 7: + * fields.extend([".".encode('UTF-8')] * (6 - len(fields))) + * other_fields = [] # <<<<<<<<<<<<<< + * else: + * other_fields = fields[6:] + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 658, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_other_fields = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":656 + * elif isdigit(fields[1]) and isdigit(fields[2]): + * # if it's too short, just add some empty fields. + * if len(fields) < 7: # <<<<<<<<<<<<<< + * fields.extend([".".encode('UTF-8')] * (6 - len(fields))) + * other_fields = [] + */ + goto __pyx_L16; + } + + /* "pybedtools/cbedtools.pyx":660 + * other_fields = [] + * else: + * other_fields = fields[6:] # <<<<<<<<<<<<<< + * + * pyb._bed = new BED( + */ + /*else*/ { + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 660, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_PyList_GetSlice(__pyx_v_fields, 6, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 660, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_other_fields = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + } + __pyx_L16:; + + /* "pybedtools/cbedtools.pyx":663 + * + * pyb._bed = new BED( + * _cppstr(fields[0]), # <<<<<<<<<<<<<< + * int(fields[1]), + * int(fields[2]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 663, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 663, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 663, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_13 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 663, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":664 + * pyb._bed = new BED( + * _cppstr(fields[0]), + * int(fields[1]), # <<<<<<<<<<<<<< + * int(fields[2]), + * _cppstr(fields[3]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 664, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 664, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 664, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_10 = __Pyx_PyInt_As_CHRPOS(__pyx_t_1); if (unlikely((__pyx_t_10 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 664, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":665 + * _cppstr(fields[0]), + * int(fields[1]), + * int(fields[2]), # <<<<<<<<<<<<<< + * _cppstr(fields[3]), + * _cppstr(fields[4]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 665, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 2, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 665, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyNumber_Int(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 665, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_9 = __Pyx_PyInt_As_CHRPOS(__pyx_t_7); if (unlikely((__pyx_t_9 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 665, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":666 + * int(fields[1]), + * int(fields[2]), + * _cppstr(fields[3]), # <<<<<<<<<<<<<< + * _cppstr(fields[4]), + * _cppstr(fields[5]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 666, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 666, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 666, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_12 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 666, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":667 + * int(fields[2]), + * _cppstr(fields[3]), + * _cppstr(fields[4]), # <<<<<<<<<<<<<< + * _cppstr(fields[5]), + * list_to_vector(other_fields)) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 667, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 4, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 667, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 667, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_11 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 667, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":668 + * _cppstr(fields[3]), + * _cppstr(fields[4]), + * _cppstr(fields[5]), # <<<<<<<<<<<<<< + * list_to_vector(other_fields)) + * pyb.file_type = _cppstr('bed') + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 668, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 5, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 668, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 668, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_8 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 668, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":662 + * other_fields = fields[6:] + * + * pyb._bed = new BED( # <<<<<<<<<<<<<< + * _cppstr(fields[0]), + * int(fields[1]), + */ + __pyx_v_pyb->_bed = new BED(__pyx_t_13, __pyx_t_10, __pyx_t_9, __pyx_t_12, __pyx_t_11, __pyx_t_8, __pyx_f_10pybedtools_9cbedtools_list_to_vector(__pyx_v_other_fields)); + + /* "pybedtools/cbedtools.pyx":670 + * _cppstr(fields[5]), + * list_to_vector(other_fields)) + * pyb.file_type = _cppstr('bed') # <<<<<<<<<<<<<< + * + * # VCF + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_n_s_bed); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 670, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_pyb), __pyx_n_s_file_type, __pyx_t_1) < 0) __PYX_ERR(0, 670, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":654 + * + * + * elif isdigit(fields[1]) and isdigit(fields[2]): # <<<<<<<<<<<<<< + * # if it's too short, just add some empty fields. + * if len(fields) < 7: + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":673 + * + * # VCF + * elif isdigit(fields[1]) and not isdigit(fields[3]) and len(fields) >= 8: # <<<<<<<<<<<<<< + * pyb._bed = new BED( + * _cppstr(fields[0]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 673, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (__pyx_t_6) { + } else { + __pyx_t_2 = __pyx_t_6; + goto __pyx_L17_bool_binop_done; + } + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 673, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) __PYX_ERR(0, 673, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = ((!__pyx_t_6) != 0); + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L17_bool_binop_done; + } + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 673, __pyx_L1_error) + } + __pyx_t_3 = PyList_GET_SIZE(__pyx_v_fields); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 673, __pyx_L1_error) + __pyx_t_4 = ((__pyx_t_3 >= 8) != 0); + __pyx_t_2 = __pyx_t_4; + __pyx_L17_bool_binop_done:; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":675 + * elif isdigit(fields[1]) and not isdigit(fields[3]) and len(fields) >= 8: + * pyb._bed = new BED( + * _cppstr(fields[0]), # <<<<<<<<<<<<<< + * int(fields[1]) - 1, + * int(fields[1]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 675, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 675, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 675, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_8 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 675, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":676 + * pyb._bed = new BED( + * _cppstr(fields[0]), + * int(fields[1]) - 1, # <<<<<<<<<<<<<< + * int(fields[1]), + * _cppstr(fields[2]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 676, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 676, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 676, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyInt_SubtractObjC(__pyx_t_1, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 676, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_9 = __Pyx_PyInt_As_CHRPOS(__pyx_t_7); if (unlikely((__pyx_t_9 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 676, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":677 + * _cppstr(fields[0]), + * int(fields[1]) - 1, + * int(fields[1]), # <<<<<<<<<<<<<< + * _cppstr(fields[2]), + * _cppstr(fields[5]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 677, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 1, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 677, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 677, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_10 = __Pyx_PyInt_As_CHRPOS(__pyx_t_1); if (unlikely((__pyx_t_10 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 677, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":678 + * int(fields[1]) - 1, + * int(fields[1]), + * _cppstr(fields[2]), # <<<<<<<<<<<<<< + * _cppstr(fields[5]), + * _cppstr('.'), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 678, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 2, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 678, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 678, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_11 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 678, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":679 + * int(fields[1]), + * _cppstr(fields[2]), + * _cppstr(fields[5]), # <<<<<<<<<<<<<< + * _cppstr('.'), + * list_to_vector(fields)) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 679, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 5, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 679, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 679, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_12 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 679, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":680 + * _cppstr(fields[2]), + * _cppstr(fields[5]), + * _cppstr('.'), # <<<<<<<<<<<<<< + * list_to_vector(fields)) + * pyb.file_type = b'vcf' + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_kp_s__7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 680, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_13 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 680, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":674 + * # VCF + * elif isdigit(fields[1]) and not isdigit(fields[3]) and len(fields) >= 8: + * pyb._bed = new BED( # <<<<<<<<<<<<<< + * _cppstr(fields[0]), + * int(fields[1]) - 1, + */ + __pyx_v_pyb->_bed = new BED(__pyx_t_8, __pyx_t_9, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_f_10pybedtools_9cbedtools_list_to_vector(__pyx_v_fields)); + + /* "pybedtools/cbedtools.pyx":682 + * _cppstr('.'), + * list_to_vector(fields)) + * pyb.file_type = b'vcf' # <<<<<<<<<<<<<< + * + * + */ + if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_pyb), __pyx_n_s_file_type, __pyx_n_b_vcf) < 0) __PYX_ERR(0, 682, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":673 + * + * # VCF + * elif isdigit(fields[1]) and not isdigit(fields[3]) and len(fields) >= 8: # <<<<<<<<<<<<<< + * pyb._bed = new BED( + * _cppstr(fields[0]), + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":686 + * + * # GFF + * elif len(fields) >= 9 and isdigit(fields[3]) and isdigit(fields[4]): # <<<<<<<<<<<<<< + * pyb._bed = new BED( + * _cppstr(fields[0]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 686, __pyx_L1_error) + } + __pyx_t_3 = PyList_GET_SIZE(__pyx_v_fields); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 686, __pyx_L1_error) + __pyx_t_4 = ((__pyx_t_3 >= 9) != 0); + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L20_bool_binop_done; + } + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 686, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 686, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 686, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 686, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (__pyx_t_4) { + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L20_bool_binop_done; + } + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 686, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 4, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 686, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_isdigit(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 686, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 686, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_2 = __pyx_t_4; + __pyx_L20_bool_binop_done:; + if (likely(__pyx_t_2)) { + + /* "pybedtools/cbedtools.pyx":688 + * elif len(fields) >= 9 and isdigit(fields[3]) and isdigit(fields[4]): + * pyb._bed = new BED( + * _cppstr(fields[0]), # <<<<<<<<<<<<<< + * int(fields[3])-1, int(fields[4]), + * _cppstr(fields[2]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 688, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 688, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 688, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_13 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 688, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":689 + * pyb._bed = new BED( + * _cppstr(fields[0]), + * int(fields[3])-1, int(fields[4]), # <<<<<<<<<<<<<< + * _cppstr(fields[2]), + * _cppstr(fields[5]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 689, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 3, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyInt_SubtractObjC(__pyx_t_1, __pyx_int_1, 1, 0, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_10 = __Pyx_PyInt_As_CHRPOS(__pyx_t_7); if (unlikely((__pyx_t_10 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 689, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 4, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __Pyx_PyNumber_Int(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = __Pyx_PyInt_As_CHRPOS(__pyx_t_1); if (unlikely((__pyx_t_9 == ((CHRPOS)-1)) && PyErr_Occurred())) __PYX_ERR(0, 689, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":690 + * _cppstr(fields[0]), + * int(fields[3])-1, int(fields[4]), + * _cppstr(fields[2]), # <<<<<<<<<<<<<< + * _cppstr(fields[5]), + * _cppstr(fields[6]), + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 690, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 2, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 690, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 690, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_12 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 690, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":691 + * int(fields[3])-1, int(fields[4]), + * _cppstr(fields[2]), + * _cppstr(fields[5]), # <<<<<<<<<<<<<< + * _cppstr(fields[6]), + * list_to_vector(fields[7:])) + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 691, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_fields, 5, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 691, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_7); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 691, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_11 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 691, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":692 + * _cppstr(fields[2]), + * _cppstr(fields[5]), + * _cppstr(fields[6]), # <<<<<<<<<<<<<< + * list_to_vector(fields[7:])) + * pyb.file_type = _cppstr('gff') + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 692, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_fields, 6, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_8 = __pyx_convert_string_from_py_std__in_string(__pyx_t_7); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 692, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":693 + * _cppstr(fields[5]), + * _cppstr(fields[6]), + * list_to_vector(fields[7:])) # <<<<<<<<<<<<<< + * pyb.file_type = _cppstr('gff') + * else: + */ + if (unlikely(__pyx_v_fields == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 693, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_PyList_GetSlice(__pyx_v_fields, 7, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 693, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + + /* "pybedtools/cbedtools.pyx":687 + * # GFF + * elif len(fields) >= 9 and isdigit(fields[3]) and isdigit(fields[4]): + * pyb._bed = new BED( # <<<<<<<<<<<<<< + * _cppstr(fields[0]), + * int(fields[3])-1, int(fields[4]), + */ + __pyx_v_pyb->_bed = new BED(__pyx_t_13, __pyx_t_10, __pyx_t_9, __pyx_t_12, __pyx_t_11, __pyx_t_8, __pyx_f_10pybedtools_9cbedtools_list_to_vector(((PyObject*)__pyx_t_7))); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":694 + * _cppstr(fields[6]), + * list_to_vector(fields[7:])) + * pyb.file_type = _cppstr('gff') # <<<<<<<<<<<<<< + * else: + * raise MalformedBedLineError('Unable to detect format from %s' % fields) + */ + __pyx_t_7 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_n_s_gff); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 694, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + if (__Pyx_PyObject_SetAttrStr(((PyObject *)__pyx_v_pyb), __pyx_n_s_file_type, __pyx_t_7) < 0) __PYX_ERR(0, 694, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":686 + * + * # GFF + * elif len(fields) >= 9 and isdigit(fields[3]) and isdigit(fields[4]): # <<<<<<<<<<<<<< + * pyb._bed = new BED( + * _cppstr(fields[0]), + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":696 + * pyb.file_type = _cppstr('gff') + * else: + * raise MalformedBedLineError('Unable to detect format from %s' % fields) # <<<<<<<<<<<<<< + * + * if pyb.start > pyb.end: + */ + /*else*/ { + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 696, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_Unable_to_detect_format_from_s, __pyx_v_fields); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 696, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_15 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_15 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_15)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_15); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_7 = (__pyx_t_15) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_15, __pyx_t_5) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_5); + __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 696, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_Raise(__pyx_t_7, 0, 0, 0); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __PYX_ERR(0, 696, __pyx_L1_error) + } + __pyx_L3:; + + /* "pybedtools/cbedtools.pyx":698 + * raise MalformedBedLineError('Unable to detect format from %s' % fields) + * + * if pyb.start > pyb.end: # <<<<<<<<<<<<<< + * raise MalformedBedLineError("Start is greater than stop") + * pyb._bed.fields = list_to_vector(orig_fields) + */ + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_pyb), __pyx_n_s_start); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_pyb), __pyx_n_s_end); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = PyObject_RichCompare(__pyx_t_7, __pyx_t_1, Py_GT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(0, 698, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(__pyx_t_2)) { + + /* "pybedtools/cbedtools.pyx":699 + * + * if pyb.start > pyb.end: + * raise MalformedBedLineError("Start is greater than stop") # <<<<<<<<<<<<<< + * pyb._bed.fields = list_to_vector(orig_fields) + * return pyb + */ + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 699, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_7)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_7); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_5 = (__pyx_t_7) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_7, __pyx_kp_s_Start_is_greater_than_stop) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_kp_s_Start_is_greater_than_stop); + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 699, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_Raise(__pyx_t_5, 0, 0, 0); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __PYX_ERR(0, 699, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":698 + * raise MalformedBedLineError('Unable to detect format from %s' % fields) + * + * if pyb.start > pyb.end: # <<<<<<<<<<<<<< + * raise MalformedBedLineError("Start is greater than stop") + * pyb._bed.fields = list_to_vector(orig_fields) + */ + } + + /* "pybedtools/cbedtools.pyx":700 + * if pyb.start > pyb.end: + * raise MalformedBedLineError("Start is greater than stop") + * pyb._bed.fields = list_to_vector(orig_fields) # <<<<<<<<<<<<<< + * return pyb + * + */ + __pyx_v_pyb->_bed->fields = __pyx_f_10pybedtools_9cbedtools_list_to_vector(__pyx_v_orig_fields); + + /* "pybedtools/cbedtools.pyx":701 + * raise MalformedBedLineError("Start is greater than stop") + * pyb._bed.fields = list_to_vector(orig_fields) + * return pyb # <<<<<<<<<<<<<< + * + * cdef vector[string] list_to_vector(list li): + */ + __Pyx_XDECREF(((PyObject *)__pyx_r)); + __Pyx_INCREF(((PyObject *)__pyx_v_pyb)); + __pyx_r = __pyx_v_pyb; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":579 + * + * + * cpdef Interval create_interval_from_list(list fields): # <<<<<<<<<<<<<< + * """ + * Create an Interval object from a list of strings. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_15); + __Pyx_AddTraceback("pybedtools.cbedtools.create_interval_from_list", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_pyb); + __Pyx_XDECREF(__pyx_v_orig_fields); + __Pyx_XDECREF(__pyx_v_chrom); + __Pyx_XDECREF(__pyx_v_start); + __Pyx_XDECREF(__pyx_v_stop); + __Pyx_XDECREF(__pyx_v_name); + __Pyx_XDECREF(__pyx_v_score); + __Pyx_XDECREF(__pyx_v_strand); + __Pyx_XDECREF(__pyx_v_other_fields); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_1create_interval_from_list(PyObject *__pyx_self, PyObject *__pyx_v_fields); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_create_interval_from_list[] = "\n Create an Interval object from a list of strings.\n\n Constructor::\n\n create_interval_from_list(fields)\n\n Given the list of strings, `fields`, automatically detects the format (BED,\n GFF, VCF, SAM) and creates a new Interval object.\n\n `fields` is a list with an arbitrary number of items (it can be quite long,\n say after a -wao intersection of a BED12 and a GFF), however, the first\n fields must conform to one of the supported formats. For example, if you\n want the resulting Interval to be considered a GFF feature, then the first\n 9 fields must conform to the GFF format. Similarly, if you want the\n resulting Interval to be considered a BED feature, then the first three\n fields must be chrom, start, stop.\n\n Example usage:\n\n >>> # Creates a BED3 feature\n >>> feature = create_interval_from_list(['chr1', '1', '100'])\n\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_1create_interval_from_list(PyObject *__pyx_self, PyObject *__pyx_v_fields) { + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("create_interval_from_list (wrapper)", 0); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fields), (&PyList_Type), 1, "fields", 1))) __PYX_ERR(0, 579, __pyx_L1_error) + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_create_interval_from_list(__pyx_self, ((PyObject*)__pyx_v_fields)); + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __pyx_r = NULL; + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_create_interval_from_list(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fields) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("create_interval_from_list", 0); + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = ((PyObject *)__pyx_f_10pybedtools_9cbedtools_create_interval_from_list(__pyx_v_fields, 0)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 579, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.create_interval_from_list", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":703 + * return pyb + * + * cdef vector[string] list_to_vector(list li): # <<<<<<<<<<<<<< + * cdef vector[string] s + * cdef int i + */ + +static std::vector<std::string> __pyx_f_10pybedtools_9cbedtools_list_to_vector(PyObject *__pyx_v_li) { + std::vector<std::string> __pyx_v_s; + int __pyx_v_i; + PyObject *__pyx_v__s = NULL; + std::vector<std::string> __pyx_r; + __Pyx_RefNannyDeclarations + Py_ssize_t __pyx_t_1; + Py_ssize_t __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + std::string __pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("list_to_vector", 0); + + /* "pybedtools/cbedtools.pyx":706 + * cdef vector[string] s + * cdef int i + * for i in range(len(li)): # <<<<<<<<<<<<<< + * _s = li[i] + * s.push_back(_cppstr(_s)) + */ + if (unlikely(__pyx_v_li == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(0, 706, __pyx_L1_error) + } + __pyx_t_1 = PyList_GET_SIZE(__pyx_v_li); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1))) __PYX_ERR(0, 706, __pyx_L1_error) + __pyx_t_2 = __pyx_t_1; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "pybedtools/cbedtools.pyx":707 + * cdef int i + * for i in range(len(li)): + * _s = li[i] # <<<<<<<<<<<<<< + * s.push_back(_cppstr(_s)) + * return s + */ + if (unlikely(__pyx_v_li == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(0, 707, __pyx_L1_error) + } + __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_v_li, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 707, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_XDECREF_SET(__pyx_v__s, __pyx_t_4); + __pyx_t_4 = 0; + + /* "pybedtools/cbedtools.pyx":708 + * for i in range(len(li)): + * _s = li[i] + * s.push_back(_cppstr(_s)) # <<<<<<<<<<<<<< + * return s + * + */ + __pyx_t_4 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v__s); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 708, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __pyx_convert_string_from_py_std__in_string(__pyx_t_4); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 708, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + try { + __pyx_v_s.push_back(__pyx_t_5); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 708, __pyx_L1_error) + } + } + + /* "pybedtools/cbedtools.pyx":709 + * _s = li[i] + * s.push_back(_cppstr(_s)) + * return s # <<<<<<<<<<<<<< + * + * cdef list string_vec2list(vector[string] sv): + */ + __pyx_r = __pyx_v_s; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":703 + * return pyb + * + * cdef vector[string] list_to_vector(list li): # <<<<<<<<<<<<<< + * cdef vector[string] s + * cdef int i + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_4); + __Pyx_WriteUnraisable("pybedtools.cbedtools.list_to_vector", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); + __Pyx_pretend_to_initialize(&__pyx_r); + __pyx_L0:; + __Pyx_XDECREF(__pyx_v__s); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":711 + * return s + * + * cdef list string_vec2list(vector[string] sv): # <<<<<<<<<<<<<< + * cdef size_t size = sv.size(), i + * return [_pystr(sv.at(i)) for i in range(size)] + */ + +static PyObject *__pyx_f_10pybedtools_9cbedtools_string_vec2list(std::vector<std::string> __pyx_v_sv) { + size_t __pyx_v_size; + size_t __pyx_v_i; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + size_t __pyx_t_2; + size_t __pyx_t_3; + size_t __pyx_t_4; + __Pyx_FakeReference<std::string> __pyx_t_5; + PyObject *__pyx_t_6 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("string_vec2list", 0); + + /* "pybedtools/cbedtools.pyx":712 + * + * cdef list string_vec2list(vector[string] sv): + * cdef size_t size = sv.size(), i # <<<<<<<<<<<<<< + * return [_pystr(sv.at(i)) for i in range(size)] + * + */ + __pyx_v_size = __pyx_v_sv.size(); + + /* "pybedtools/cbedtools.pyx":713 + * cdef list string_vec2list(vector[string] sv): + * cdef size_t size = sv.size(), i + * return [_pystr(sv.at(i)) for i in range(size)] # <<<<<<<<<<<<<< + * + * cdef list bed_vec2list(vector[BED] bv): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 713, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __pyx_v_size; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + try { + __pyx_t_5 = __pyx_v_sv.at(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 713, __pyx_L1_error) + } + __pyx_t_6 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_t_5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 713, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_t_6))) __PYX_ERR(0, 713, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + } + __pyx_r = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":711 + * return s + * + * cdef list string_vec2list(vector[string] sv): # <<<<<<<<<<<<<< + * cdef size_t size = sv.size(), i + * return [_pystr(sv.at(i)) for i in range(size)] + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("pybedtools.cbedtools.string_vec2list", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":715 + * return [_pystr(sv.at(i)) for i in range(size)] + * + * cdef list bed_vec2list(vector[BED] bv): # <<<<<<<<<<<<<< + * cdef size_t size = bv.size(), i + * cdef list l = [] + */ + +static PyObject *__pyx_f_10pybedtools_9cbedtools_bed_vec2list(std::vector<BED> __pyx_v_bv) { + size_t __pyx_v_size; + size_t __pyx_v_i; + PyObject *__pyx_v_l = 0; + BED __pyx_v_b; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + size_t __pyx_t_2; + size_t __pyx_t_3; + size_t __pyx_t_4; + __Pyx_FakeReference<BED> __pyx_t_5; + int __pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("bed_vec2list", 0); + + /* "pybedtools/cbedtools.pyx":716 + * + * cdef list bed_vec2list(vector[BED] bv): + * cdef size_t size = bv.size(), i # <<<<<<<<<<<<<< + * cdef list l = [] + * cdef BED b + */ + __pyx_v_size = __pyx_v_bv.size(); + + /* "pybedtools/cbedtools.pyx":717 + * cdef list bed_vec2list(vector[BED] bv): + * cdef size_t size = bv.size(), i + * cdef list l = [] # <<<<<<<<<<<<<< + * cdef BED b + * for i in range(size): + */ + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 717, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_v_l = ((PyObject*)__pyx_t_1); + __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":719 + * cdef list l = [] + * cdef BED b + * for i in range(size): # <<<<<<<<<<<<<< + * b = bv.at(i) + * l.append(create_interval(b)) + */ + __pyx_t_2 = __pyx_v_size; + __pyx_t_3 = __pyx_t_2; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "pybedtools/cbedtools.pyx":720 + * cdef BED b + * for i in range(size): + * b = bv.at(i) # <<<<<<<<<<<<<< + * l.append(create_interval(b)) + * return l + */ + try { + __pyx_t_5 = __pyx_v_bv.at(__pyx_v_i); + } catch(...) { + __Pyx_CppExn2PyErr(); + __PYX_ERR(0, 720, __pyx_L1_error) + } + __pyx_v_b = __pyx_t_5; + + /* "pybedtools/cbedtools.pyx":721 + * for i in range(size): + * b = bv.at(i) + * l.append(create_interval(b)) # <<<<<<<<<<<<<< + * return l + * + */ + __pyx_t_1 = ((PyObject *)__pyx_f_10pybedtools_9cbedtools_create_interval(__pyx_v_b)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 721, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_6 = __Pyx_PyList_Append(__pyx_v_l, __pyx_t_1); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(0, 721, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } + + /* "pybedtools/cbedtools.pyx":722 + * b = bv.at(i) + * l.append(create_interval(b)) + * return l # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_l); + __pyx_r = __pyx_v_l; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":715 + * return [_pystr(sv.at(i)) for i in range(size)] + * + * cdef list bed_vec2list(vector[BED] bv): # <<<<<<<<<<<<<< + * cdef size_t size = bv.size(), i + * cdef list l = [] + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.bed_vec2list", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_l); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":725 + * + * + * def overlap(int s1, int s2, int e1, int e2): # <<<<<<<<<<<<<< + * return min(e1, e2) - max(s1, s2) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_3overlap(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_10pybedtools_9cbedtools_3overlap = {"overlap", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_3overlap, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_3overlap(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + int __pyx_v_s1; + int __pyx_v_s2; + int __pyx_v_e1; + int __pyx_v_e2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("overlap (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_s1,&__pyx_n_s_s2,&__pyx_n_s_e1,&__pyx_n_s_e2,0}; + PyObject* values[4] = {0,0,0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + CYTHON_FALLTHROUGH; + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_s1)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_s2)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("overlap", 1, 4, 4, 1); __PYX_ERR(0, 725, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_e1)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("overlap", 1, 4, 4, 2); __PYX_ERR(0, 725, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 3: + if (likely((values[3] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_e2)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("overlap", 1, 4, 4, 3); __PYX_ERR(0, 725, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "overlap") < 0)) __PYX_ERR(0, 725, __pyx_L3_error) + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 4) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + } + __pyx_v_s1 = __Pyx_PyInt_As_int(values[0]); if (unlikely((__pyx_v_s1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 725, __pyx_L3_error) + __pyx_v_s2 = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_s2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 725, __pyx_L3_error) + __pyx_v_e1 = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_e1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 725, __pyx_L3_error) + __pyx_v_e2 = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_e2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 725, __pyx_L3_error) + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("overlap", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 725, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_2overlap(__pyx_self, __pyx_v_s1, __pyx_v_s2, __pyx_v_e1, __pyx_v_e2); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_2overlap(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_s1, int __pyx_v_s2, int __pyx_v_e1, int __pyx_v_e2) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("overlap", 0); + + /* "pybedtools/cbedtools.pyx":726 + * + * def overlap(int s1, int s2, int e1, int e2): + * return min(e1, e2) - max(s1, s2) # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_v_e2; + __pyx_t_2 = __pyx_v_e1; + if (((__pyx_t_1 < __pyx_t_2) != 0)) { + __pyx_t_3 = __pyx_t_1; + } else { + __pyx_t_3 = __pyx_t_2; + } + __pyx_t_1 = __pyx_v_s2; + __pyx_t_2 = __pyx_v_s1; + if (((__pyx_t_1 > __pyx_t_2) != 0)) { + __pyx_t_4 = __pyx_t_1; + } else { + __pyx_t_4 = __pyx_t_2; + } + __pyx_t_5 = __Pyx_PyInt_From_int((__pyx_t_3 - __pyx_t_4)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 726, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":725 + * + * + * def overlap(int s1, int s2, int e1, int e2): # <<<<<<<<<<<<<< + * return min(e1, e2) - max(s1, s2) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pybedtools.cbedtools.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":732 + * cdef object stream + * cdef int _itemtype + * def __init__(self, stream): # <<<<<<<<<<<<<< + * self.stream = stream + * + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_stream = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_stream,0}; + PyObject* values[1] = {0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_stream)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 732, __pyx_L3_error) + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 1) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + } + __pyx_v_stream = values[0]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 732, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalIterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator___init__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v_self), __pyx_v_stream); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator___init__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self, PyObject *__pyx_v_stream) { + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__", 0); + + /* "pybedtools/cbedtools.pyx":733 + * cdef int _itemtype + * def __init__(self, stream): + * self.stream = stream # <<<<<<<<<<<<<< + * + * # For speed, check int rather than call isinstance(). + */ + __Pyx_INCREF(__pyx_v_stream); + __Pyx_GIVEREF(__pyx_v_stream); + __Pyx_GOTREF(__pyx_v_self->stream); + __Pyx_DECREF(__pyx_v_self->stream); + __pyx_v_self->stream = __pyx_v_stream; + + /* "pybedtools/cbedtools.pyx":740 + * # Also assumes that all items in the iterable `stream` are the same + * # type...this seems like a reasonable assumption. + * self._itemtype = -1 # <<<<<<<<<<<<<< + * + * def __dealloc__(self): + */ + __pyx_v_self->_itemtype = -1; + + /* "pybedtools/cbedtools.pyx":732 + * cdef object stream + * cdef int _itemtype + * def __init__(self, stream): # <<<<<<<<<<<<<< + * self.stream = stream + * + */ + + /* function exit code */ + __pyx_r = 0; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":742 + * self._itemtype = -1 + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * try: + * self.stream.close() + */ + +/* Python wrapper */ +static void __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_3__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_3__dealloc__(PyObject *__pyx_v_self) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); + __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_2__dealloc__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_2__dealloc__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self) { + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + int __pyx_t_7; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__dealloc__", 0); + + /* "pybedtools/cbedtools.pyx":743 + * + * def __dealloc__(self): + * try: # <<<<<<<<<<<<<< + * self.stream.close() + * except AttributeError: + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_1, &__pyx_t_2, &__pyx_t_3); + __Pyx_XGOTREF(__pyx_t_1); + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_3); + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":744 + * def __dealloc__(self): + * try: + * self.stream.close() # <<<<<<<<<<<<<< + * except AttributeError: + * pass + */ + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->stream, __pyx_n_s_close); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 744, __pyx_L3_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_5))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_5); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_5, function); + } + } + __pyx_t_4 = (__pyx_t_6) ? __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6) : __Pyx_PyObject_CallNoArg(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 744, __pyx_L3_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "pybedtools/cbedtools.pyx":743 + * + * def __dealloc__(self): + * try: # <<<<<<<<<<<<<< + * self.stream.close() + * except AttributeError: + */ + } + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + goto __pyx_L8_try_end; + __pyx_L3_error:; + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":745 + * try: + * self.stream.close() + * except AttributeError: # <<<<<<<<<<<<<< + * pass + * + */ + __pyx_t_7 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_AttributeError); + if (__pyx_t_7) { + __Pyx_ErrRestore(0,0,0); + goto __pyx_L4_exception_handled; + } + goto __pyx_L5_except_error; + __pyx_L5_except_error:; + + /* "pybedtools/cbedtools.pyx":743 + * + * def __dealloc__(self): + * try: # <<<<<<<<<<<<<< + * self.stream.close() + * except AttributeError: + */ + __Pyx_XGIVEREF(__pyx_t_1); + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); + goto __pyx_L1_error; + __pyx_L4_exception_handled:; + __Pyx_XGIVEREF(__pyx_t_1); + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); + __pyx_L8_try_end:; + } + + /* "pybedtools/cbedtools.pyx":742 + * self._itemtype = -1 + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * try: + * self.stream.close() + */ + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_WriteUnraisable("pybedtools.cbedtools.IntervalIterator.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 0); + __pyx_L0:; + __Pyx_RefNannyFinishContext(); +} + +/* "pybedtools/cbedtools.pyx":748 + * pass + * + * def __iter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_5__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_5__iter__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_4__iter__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_4__iter__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__iter__", 0); + + /* "pybedtools/cbedtools.pyx":749 + * + * def __iter__(self): + * return self # <<<<<<<<<<<<<< + * + * def __next__(self): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(((PyObject *)__pyx_v_self)); + __pyx_r = ((PyObject *)__pyx_v_self); + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":748 + * pass + * + * def __iter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":751 + * return self + * + * def __next__(self): # <<<<<<<<<<<<<< + * while True: + * if hasattr(self.stream, 'closed'): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_7__next__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_7__next__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_6__next__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_6__next__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self) { + PyObject *__pyx_v_line = NULL; + PyObject *__pyx_v_fields = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + int __pyx_t_8; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + PyObject *__pyx_t_12 = NULL; + Py_ssize_t __pyx_t_13; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__next__", 0); + + /* "pybedtools/cbedtools.pyx":752 + * + * def __next__(self): + * while True: # <<<<<<<<<<<<<< + * if hasattr(self.stream, 'closed'): + * if self.stream.closed: + */ + while (1) { + + /* "pybedtools/cbedtools.pyx":753 + * def __next__(self): + * while True: + * if hasattr(self.stream, 'closed'): # <<<<<<<<<<<<<< + * if self.stream.closed: + * raise StopIteration + */ + __pyx_t_1 = __pyx_v_self->stream; + __Pyx_INCREF(__pyx_t_1); + __pyx_t_2 = __Pyx_HasAttr(__pyx_t_1, __pyx_n_s_closed); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 753, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":754 + * while True: + * if hasattr(self.stream, 'closed'): + * if self.stream.closed: # <<<<<<<<<<<<<< + * raise StopIteration + * try: + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->stream, __pyx_n_s_closed); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 754, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 754, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(__pyx_t_3)) { + + /* "pybedtools/cbedtools.pyx":755 + * if hasattr(self.stream, 'closed'): + * if self.stream.closed: + * raise StopIteration # <<<<<<<<<<<<<< + * try: + * line = next(self.stream) + */ + __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); + __PYX_ERR(0, 755, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":754 + * while True: + * if hasattr(self.stream, 'closed'): + * if self.stream.closed: # <<<<<<<<<<<<<< + * raise StopIteration + * try: + */ + } + + /* "pybedtools/cbedtools.pyx":753 + * def __next__(self): + * while True: + * if hasattr(self.stream, 'closed'): # <<<<<<<<<<<<<< + * if self.stream.closed: + * raise StopIteration + */ + } + + /* "pybedtools/cbedtools.pyx":756 + * if self.stream.closed: + * raise StopIteration + * try: # <<<<<<<<<<<<<< + * line = next(self.stream) + * except StopIteration: + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_4, &__pyx_t_5, &__pyx_t_6); + __Pyx_XGOTREF(__pyx_t_4); + __Pyx_XGOTREF(__pyx_t_5); + __Pyx_XGOTREF(__pyx_t_6); + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":757 + * raise StopIteration + * try: + * line = next(self.stream) # <<<<<<<<<<<<<< + * except StopIteration: + * if hasattr(self.stream, 'close'): + */ + __pyx_t_1 = __pyx_v_self->stream; + __Pyx_INCREF(__pyx_t_1); + __pyx_t_7 = __Pyx_PyIter_Next(__pyx_t_1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 757, __pyx_L7_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF_SET(__pyx_v_line, __pyx_t_7); + __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":756 + * if self.stream.closed: + * raise StopIteration + * try: # <<<<<<<<<<<<<< + * line = next(self.stream) + * except StopIteration: + */ + } + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + goto __pyx_L14_try_end; + __pyx_L7_error:; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + + /* "pybedtools/cbedtools.pyx":758 + * try: + * line = next(self.stream) + * except StopIteration: # <<<<<<<<<<<<<< + * if hasattr(self.stream, 'close'): + * self.stream.close() + */ + __pyx_t_8 = __Pyx_PyErr_ExceptionMatches(__pyx_builtin_StopIteration); + if (__pyx_t_8) { + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_1, &__pyx_t_9) < 0) __PYX_ERR(0, 758, __pyx_L9_except_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(__pyx_t_9); + + /* "pybedtools/cbedtools.pyx":759 + * line = next(self.stream) + * except StopIteration: + * if hasattr(self.stream, 'close'): # <<<<<<<<<<<<<< + * self.stream.close() + * raise StopIteration + */ + __pyx_t_10 = __pyx_v_self->stream; + __Pyx_INCREF(__pyx_t_10); + __pyx_t_3 = __Pyx_HasAttr(__pyx_t_10, __pyx_n_s_close); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 759, __pyx_L9_except_error) + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_2 = (__pyx_t_3 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":760 + * except StopIteration: + * if hasattr(self.stream, 'close'): + * self.stream.close() # <<<<<<<<<<<<<< + * raise StopIteration + * + */ + __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->stream, __pyx_n_s_close); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 760, __pyx_L9_except_error) + __Pyx_GOTREF(__pyx_t_11); + __pyx_t_12 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_11))) { + __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_11); + if (likely(__pyx_t_12)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11); + __Pyx_INCREF(__pyx_t_12); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_11, function); + } + } + __pyx_t_10 = (__pyx_t_12) ? __Pyx_PyObject_CallOneArg(__pyx_t_11, __pyx_t_12) : __Pyx_PyObject_CallNoArg(__pyx_t_11); + __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0; + if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 760, __pyx_L9_except_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + + /* "pybedtools/cbedtools.pyx":759 + * line = next(self.stream) + * except StopIteration: + * if hasattr(self.stream, 'close'): # <<<<<<<<<<<<<< + * self.stream.close() + * raise StopIteration + */ + } + + /* "pybedtools/cbedtools.pyx":761 + * if hasattr(self.stream, 'close'): + * self.stream.close() + * raise StopIteration # <<<<<<<<<<<<<< + * + * if self._itemtype < 0: + */ + __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); + __PYX_ERR(0, 761, __pyx_L9_except_error) + } + goto __pyx_L9_except_error; + __pyx_L9_except_error:; + + /* "pybedtools/cbedtools.pyx":756 + * if self.stream.closed: + * raise StopIteration + * try: # <<<<<<<<<<<<<< + * line = next(self.stream) + * except StopIteration: + */ + __Pyx_XGIVEREF(__pyx_t_4); + __Pyx_XGIVEREF(__pyx_t_5); + __Pyx_XGIVEREF(__pyx_t_6); + __Pyx_ExceptionReset(__pyx_t_4, __pyx_t_5, __pyx_t_6); + goto __pyx_L1_error; + __pyx_L14_try_end:; + } + + /* "pybedtools/cbedtools.pyx":763 + * raise StopIteration + * + * if self._itemtype < 0: # <<<<<<<<<<<<<< + * if isinstance(line, Interval): + * self._itemtype = 2 + */ + __pyx_t_2 = ((__pyx_v_self->_itemtype < 0) != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":764 + * + * if self._itemtype < 0: + * if isinstance(line, Interval): # <<<<<<<<<<<<<< + * self._itemtype = 2 + * elif isinstance(line, basestring): + */ + __pyx_t_2 = __Pyx_TypeCheck(__pyx_v_line, __pyx_ptype_10pybedtools_9cbedtools_Interval); + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "pybedtools/cbedtools.pyx":765 + * if self._itemtype < 0: + * if isinstance(line, Interval): + * self._itemtype = 2 # <<<<<<<<<<<<<< + * elif isinstance(line, basestring): + * self._itemtype = 1 + */ + __pyx_v_self->_itemtype = 2; + + /* "pybedtools/cbedtools.pyx":764 + * + * if self._itemtype < 0: + * if isinstance(line, Interval): # <<<<<<<<<<<<<< + * self._itemtype = 2 + * elif isinstance(line, basestring): + */ + goto __pyx_L19; + } + + /* "pybedtools/cbedtools.pyx":766 + * if isinstance(line, Interval): + * self._itemtype = 2 + * elif isinstance(line, basestring): # <<<<<<<<<<<<<< + * self._itemtype = 1 + * else: + */ + __pyx_t_3 = __Pyx_PyBaseString_Check(__pyx_v_line); + __pyx_t_2 = (__pyx_t_3 != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":767 + * self._itemtype = 2 + * elif isinstance(line, basestring): + * self._itemtype = 1 # <<<<<<<<<<<<<< + * else: + * self._itemtype = 0 + */ + __pyx_v_self->_itemtype = 1; + + /* "pybedtools/cbedtools.pyx":766 + * if isinstance(line, Interval): + * self._itemtype = 2 + * elif isinstance(line, basestring): # <<<<<<<<<<<<<< + * self._itemtype = 1 + * else: + */ + goto __pyx_L19; + } + + /* "pybedtools/cbedtools.pyx":769 + * self._itemtype = 1 + * else: + * self._itemtype = 0 # <<<<<<<<<<<<<< + * + * if self._itemtype == 1: + */ + /*else*/ { + __pyx_v_self->_itemtype = 0; + } + __pyx_L19:; + + /* "pybedtools/cbedtools.pyx":763 + * raise StopIteration + * + * if self._itemtype < 0: # <<<<<<<<<<<<<< + * if isinstance(line, Interval): + * self._itemtype = 2 + */ + } + + /* "pybedtools/cbedtools.pyx":771 + * self._itemtype = 0 + * + * if self._itemtype == 1: # <<<<<<<<<<<<<< + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: + * continue + */ + __pyx_t_2 = ((__pyx_v_self->_itemtype == 1) != 0); + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":772 + * + * if self._itemtype == 1: + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: # <<<<<<<<<<<<<< + * continue + * break + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_startswith); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_7)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_7); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_9 = (__pyx_t_7) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_7, __pyx_tuple__24) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_tuple__24); + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_3 < 0)) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + if (!__pyx_t_3) { + } else { + __pyx_t_2 = __pyx_t_3; + goto __pyx_L22_bool_binop_done; + } + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_strip); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_7 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_7)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_7); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_9 = (__pyx_t_7) ? __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_7) : __Pyx_PyObject_CallNoArg(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_13 = PyObject_Length(__pyx_t_9); if (unlikely(__pyx_t_13 == ((Py_ssize_t)-1))) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_3 = ((__pyx_t_13 == 0) != 0); + __pyx_t_2 = __pyx_t_3; + __pyx_L22_bool_binop_done:; + if (__pyx_t_2) { + + /* "pybedtools/cbedtools.pyx":773 + * if self._itemtype == 1: + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: + * continue # <<<<<<<<<<<<<< + * break + * + */ + goto __pyx_L3_continue; + + /* "pybedtools/cbedtools.pyx":772 + * + * if self._itemtype == 1: + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: # <<<<<<<<<<<<<< + * continue + * break + */ + } + + /* "pybedtools/cbedtools.pyx":771 + * self._itemtype = 0 + * + * if self._itemtype == 1: # <<<<<<<<<<<<<< + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: + * continue + */ + } + + /* "pybedtools/cbedtools.pyx":774 + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: + * continue + * break # <<<<<<<<<<<<<< + * + * # Iterable of Interval objects + */ + goto __pyx_L4_break; + __pyx_L3_continue:; + } + __pyx_L4_break:; + + /* "pybedtools/cbedtools.pyx":777 + * + * # Iterable of Interval objects + * if self._itemtype == 2: # <<<<<<<<<<<<<< + * return line + * + */ + switch (__pyx_v_self->_itemtype) { + case 2: + + /* "pybedtools/cbedtools.pyx":778 + * # Iterable of Interval objects + * if self._itemtype == 2: + * return line # <<<<<<<<<<<<<< + * + * # Iterable of strings, in which case we need to split + */ + __Pyx_XDECREF(__pyx_r); + if (unlikely(!__pyx_v_line)) { __Pyx_RaiseUnboundLocalError("line"); __PYX_ERR(0, 778, __pyx_L1_error) } + __Pyx_INCREF(__pyx_v_line); + __pyx_r = __pyx_v_line; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":777 + * + * # Iterable of Interval objects + * if self._itemtype == 2: # <<<<<<<<<<<<<< + * return line + * + */ + break; + case 1: + + /* "pybedtools/cbedtools.pyx":782 + * # Iterable of strings, in which case we need to split + * elif self._itemtype == 1: + * fields = line.rstrip('\r\n').split('\t') # <<<<<<<<<<<<<< + * + * # Otherwise assume list/tuple/iterable of fields + */ + if (unlikely(!__pyx_v_line)) { __Pyx_RaiseUnboundLocalError("line"); __PYX_ERR(0, 782, __pyx_L1_error) } + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_line, __pyx_n_s_rstrip); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 782, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_10 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_7))) { + __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_7); + if (likely(__pyx_t_10)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7); + __Pyx_INCREF(__pyx_t_10); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_7, function); + } + } + __pyx_t_1 = (__pyx_t_10) ? __Pyx_PyObject_Call2Args(__pyx_t_7, __pyx_t_10, __pyx_kp_s__25) : __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_kp_s__25); + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 782, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_split); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 782, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_7))) { + __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_7); + if (likely(__pyx_t_1)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7); + __Pyx_INCREF(__pyx_t_1); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_7, function); + } + } + __pyx_t_9 = (__pyx_t_1) ? __Pyx_PyObject_Call2Args(__pyx_t_7, __pyx_t_1, __pyx_kp_s__8) : __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_kp_s__8); + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 782, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_v_fields = __pyx_t_9; + __pyx_t_9 = 0; + + /* "pybedtools/cbedtools.pyx":781 + * + * # Iterable of strings, in which case we need to split + * elif self._itemtype == 1: # <<<<<<<<<<<<<< + * fields = line.rstrip('\r\n').split('\t') + * + */ + break; + default: + + /* "pybedtools/cbedtools.pyx":786 + * # Otherwise assume list/tuple/iterable of fields + * else: + * fields = list(line) # <<<<<<<<<<<<<< + * + * # TODO: optimization: create_interval_from_list should have a version + */ + if (unlikely(!__pyx_v_line)) { __Pyx_RaiseUnboundLocalError("line"); __PYX_ERR(0, 786, __pyx_L1_error) } + __pyx_t_9 = PySequence_List(__pyx_v_line); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 786, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __pyx_v_fields = __pyx_t_9; + __pyx_t_9 = 0; + break; + } + + /* "pybedtools/cbedtools.pyx":790 + * # TODO: optimization: create_interval_from_list should have a version + * # that accepts C++ string instances + * return create_interval_from_list(fields) # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + if (!(likely(PyList_CheckExact(__pyx_v_fields))||((__pyx_v_fields) == Py_None)||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_v_fields)->tp_name), 0))) __PYX_ERR(0, 790, __pyx_L1_error) + __pyx_t_9 = ((PyObject *)__pyx_f_10pybedtools_9cbedtools_create_interval_from_list(((PyObject*)__pyx_v_fields), 0)); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 790, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __pyx_r = __pyx_t_9; + __pyx_t_9 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":751 + * return self + * + * def __next__(self): # <<<<<<<<<<<<<< + * while True: + * if hasattr(self.stream, 'closed'): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_XDECREF(__pyx_t_10); + __Pyx_XDECREF(__pyx_t_11); + __Pyx_XDECREF(__pyx_t_12); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_line); + __Pyx_XDECREF(__pyx_v_fields); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * cdef tuple state + * cdef object _dict + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_9__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_9__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_8__reduce_cython__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_8__reduce_cython__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self) { + PyObject *__pyx_v_state = 0; + PyObject *__pyx_v__dict = 0; + int __pyx_v_use_setstate; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__reduce_cython__", 0); + + /* "(tree fragment)":5 + * cdef object _dict + * cdef bint use_setstate + * state = (self._itemtype, self.stream) # <<<<<<<<<<<<<< + * _dict = getattr(self, '__dict__', None) + * if _dict is not None: + */ + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->_itemtype); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 5, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1); + __Pyx_INCREF(__pyx_v_self->stream); + __Pyx_GIVEREF(__pyx_v_self->stream); + PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_self->stream); + __pyx_t_1 = 0; + __pyx_v_state = ((PyObject*)__pyx_t_2); + __pyx_t_2 = 0; + + /* "(tree fragment)":6 + * cdef bint use_setstate + * state = (self._itemtype, self.stream) + * _dict = getattr(self, '__dict__', None) # <<<<<<<<<<<<<< + * if _dict is not None: + * state += (_dict,) + */ + __pyx_t_2 = __Pyx_GetAttr3(((PyObject *)__pyx_v_self), __pyx_n_s_dict, Py_None); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 6, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_v__dict = __pyx_t_2; + __pyx_t_2 = 0; + + /* "(tree fragment)":7 + * state = (self._itemtype, self.stream) + * _dict = getattr(self, '__dict__', None) + * if _dict is not None: # <<<<<<<<<<<<<< + * state += (_dict,) + * use_setstate = True + */ + __pyx_t_3 = (__pyx_v__dict != Py_None); + __pyx_t_4 = (__pyx_t_3 != 0); + if (__pyx_t_4) { + + /* "(tree fragment)":8 + * _dict = getattr(self, '__dict__', None) + * if _dict is not None: + * state += (_dict,) # <<<<<<<<<<<<<< + * use_setstate = True + * else: + */ + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 8, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(__pyx_v__dict); + __Pyx_GIVEREF(__pyx_v__dict); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v__dict); + __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_state, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 8, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF_SET(__pyx_v_state, ((PyObject*)__pyx_t_1)); + __pyx_t_1 = 0; + + /* "(tree fragment)":9 + * if _dict is not None: + * state += (_dict,) + * use_setstate = True # <<<<<<<<<<<<<< + * else: + * use_setstate = self.stream is not None + */ + __pyx_v_use_setstate = 1; + + /* "(tree fragment)":7 + * state = (self._itemtype, self.stream) + * _dict = getattr(self, '__dict__', None) + * if _dict is not None: # <<<<<<<<<<<<<< + * state += (_dict,) + * use_setstate = True + */ + goto __pyx_L3; + } + + /* "(tree fragment)":11 + * use_setstate = True + * else: + * use_setstate = self.stream is not None # <<<<<<<<<<<<<< + * if use_setstate: + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, None), state + */ + /*else*/ { + __pyx_t_4 = (__pyx_v_self->stream != Py_None); + __pyx_v_use_setstate = __pyx_t_4; + } + __pyx_L3:; + + /* "(tree fragment)":12 + * else: + * use_setstate = self.stream is not None + * if use_setstate: # <<<<<<<<<<<<<< + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, None), state + * else: + */ + __pyx_t_4 = (__pyx_v_use_setstate != 0); + if (__pyx_t_4) { + + /* "(tree fragment)":13 + * use_setstate = self.stream is not None + * if use_setstate: + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, None), state # <<<<<<<<<<<<<< + * else: + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, state) + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 13, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); + __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); + __Pyx_INCREF(__pyx_int_22915542); + __Pyx_GIVEREF(__pyx_int_22915542); + PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_int_22915542); + __Pyx_INCREF(Py_None); + __Pyx_GIVEREF(Py_None); + PyTuple_SET_ITEM(__pyx_t_2, 2, Py_None); + __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 13, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1); + __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_2); + __Pyx_INCREF(__pyx_v_state); + __Pyx_GIVEREF(__pyx_v_state); + PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_v_state); + __pyx_t_1 = 0; + __pyx_t_2 = 0; + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L0; + + /* "(tree fragment)":12 + * else: + * use_setstate = self.stream is not None + * if use_setstate: # <<<<<<<<<<<<<< + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, None), state + * else: + */ + } + + /* "(tree fragment)":15 + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, None), state + * else: + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, state) # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * __pyx_unpickle_IntervalIterator__set_state(self, __pyx_state) + */ + /*else*/ { + __Pyx_XDECREF(__pyx_r); + __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 15, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 15, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); + __Pyx_GIVEREF(((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self)))); + __Pyx_INCREF(__pyx_int_22915542); + __Pyx_GIVEREF(__pyx_int_22915542); + PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_int_22915542); + __Pyx_INCREF(__pyx_v_state); + __Pyx_GIVEREF(__pyx_v_state); + PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_state); + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 15, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_5); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5); + __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2); + __pyx_t_5 = 0; + __pyx_t_2 = 0; + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + } + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * cdef tuple state + * cdef object _dict + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalIterator.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_state); + __Pyx_XDECREF(__pyx_v__dict); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":16 + * else: + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, state) + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * __pyx_unpickle_IntervalIterator__set_state(self, __pyx_state) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_11__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_11__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_10__setstate_cython__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_10__setstate_cython__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v_self, PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__setstate_cython__", 0); + + /* "(tree fragment)":17 + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, state) + * def __setstate_cython__(self, __pyx_state): + * __pyx_unpickle_IntervalIterator__set_state(self, __pyx_state) # <<<<<<<<<<<<<< + */ + if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None)||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_v___pyx_state)->tp_name), 0))) __PYX_ERR(1, 17, __pyx_L1_error) + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools___pyx_unpickle_IntervalIterator__set_state(__pyx_v_self, ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 17, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":16 + * else: + * return __pyx_unpickle_IntervalIterator, (type(self), 0x15da9d6, state) + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * __pyx_unpickle_IntervalIterator__set_state(self, __pyx_state) + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalIterator.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":806 + * + * """ + * def __init__(self, intervalFile): # <<<<<<<<<<<<<< + * self.intervalFile_ptr = new BedFile(_cppstr(intervalFile)) + * self._loaded = 0 + */ + +/* Python wrapper */ +static int __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_intervalFile = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + int __pyx_r; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_intervalFile,0}; + PyObject* values[1] = {0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_intervalFile)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 806, __pyx_L3_error) + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 1) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + } + __pyx_v_intervalFile = values[0]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 806, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return -1; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile___init__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self), __pyx_v_intervalFile); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static int __pyx_pf_10pybedtools_9cbedtools_12IntervalFile___init__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, PyObject *__pyx_v_intervalFile) { + int __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + std::string __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__init__", 0); + + /* "pybedtools/cbedtools.pyx":807 + * """ + * def __init__(self, intervalFile): + * self.intervalFile_ptr = new BedFile(_cppstr(intervalFile)) # <<<<<<<<<<<<<< + * self._loaded = 0 + * self._open = 0 + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_intervalFile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 807, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 807, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v_self->intervalFile_ptr = new BedFile(__pyx_t_2); + + /* "pybedtools/cbedtools.pyx":808 + * def __init__(self, intervalFile): + * self.intervalFile_ptr = new BedFile(_cppstr(intervalFile)) + * self._loaded = 0 # <<<<<<<<<<<<<< + * self._open = 0 + * self._fn = _cppstr(intervalFile) + */ + __pyx_v_self->_loaded = 0; + + /* "pybedtools/cbedtools.pyx":809 + * self.intervalFile_ptr = new BedFile(_cppstr(intervalFile)) + * self._loaded = 0 + * self._open = 0 # <<<<<<<<<<<<<< + * self._fn = _cppstr(intervalFile) + * + */ + __pyx_v_self->_open = 0; + + /* "pybedtools/cbedtools.pyx":810 + * self._loaded = 0 + * self._open = 0 + * self._fn = _cppstr(intervalFile) # <<<<<<<<<<<<<< + * + * def __dealloc__(self): + */ + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__cppstr(__pyx_v_intervalFile); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 810, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __pyx_convert_string_from_py_std__in_string(__pyx_t_1); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 810, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v_self->_fn = __pyx_t_2; + + /* "pybedtools/cbedtools.pyx":806 + * + * """ + * def __init__(self, intervalFile): # <<<<<<<<<<<<<< + * self.intervalFile_ptr = new BedFile(_cppstr(intervalFile)) + * self._loaded = 0 + */ + + /* function exit code */ + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":812 + * self._fn = _cppstr(intervalFile) + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * del self.intervalFile_ptr + * + */ + +/* Python wrapper */ +static void __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_3__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_3__dealloc__(PyObject *__pyx_v_self) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); + __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_2__dealloc__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +static void __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_2__dealloc__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__dealloc__", 0); + + /* "pybedtools/cbedtools.pyx":813 + * + * def __dealloc__(self): + * del self.intervalFile_ptr # <<<<<<<<<<<<<< + * + * def __iter__(self): + */ + delete __pyx_v_self->intervalFile_ptr; + + /* "pybedtools/cbedtools.pyx":812 + * self._fn = _cppstr(intervalFile) + * + * def __dealloc__(self): # <<<<<<<<<<<<<< + * del self.intervalFile_ptr + * + */ + + /* function exit code */ + __Pyx_RefNannyFinishContext(); +} + +/* "pybedtools/cbedtools.pyx":815 + * del self.intervalFile_ptr + * + * def __iter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_5__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_5__iter__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_4__iter__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_4__iter__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__iter__", 0); + + /* "pybedtools/cbedtools.pyx":816 + * + * def __iter__(self): + * return self # <<<<<<<<<<<<<< + * + * def __next__(self): + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(((PyObject *)__pyx_v_self)); + __pyx_r = ((PyObject *)__pyx_v_self); + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":815 + * del self.intervalFile_ptr + * + * def __iter__(self): # <<<<<<<<<<<<<< + * return self + * + */ + + /* function exit code */ + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":818 + * return self + * + * def __next__(self): # <<<<<<<<<<<<<< + * if not self._open: + * result = self.intervalFile_ptr.Open() + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_7__next__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_7__next__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_6__next__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_6__next__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + int __pyx_v_result; + BED __pyx_v_b; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__next__", 0); + + /* "pybedtools/cbedtools.pyx":819 + * + * def __next__(self): + * if not self._open: # <<<<<<<<<<<<<< + * result = self.intervalFile_ptr.Open() + * if result == -1: + */ + __pyx_t_1 = ((!(__pyx_v_self->_open != 0)) != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":820 + * def __next__(self): + * if not self._open: + * result = self.intervalFile_ptr.Open() # <<<<<<<<<<<<<< + * if result == -1: + * raise BedToolsFileError("Error opening file") + */ + __pyx_v_result = __pyx_v_self->intervalFile_ptr->Open(); + + /* "pybedtools/cbedtools.pyx":821 + * if not self._open: + * result = self.intervalFile_ptr.Open() + * if result == -1: # <<<<<<<<<<<<<< + * raise BedToolsFileError("Error opening file") + * self._open = 1 + */ + __pyx_t_1 = ((__pyx_v_result == -1L) != 0); + if (unlikely(__pyx_t_1)) { + + /* "pybedtools/cbedtools.pyx":822 + * result = self.intervalFile_ptr.Open() + * if result == -1: + * raise BedToolsFileError("Error opening file") # <<<<<<<<<<<<<< + * self._open = 1 + * cdef BED b = self.intervalFile_ptr.GetNextBed() + */ + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_BedToolsFileError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 822, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + } + } + __pyx_t_2 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_4, __pyx_kp_s_Error_opening_file) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_kp_s_Error_opening_file); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 822, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 822, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":821 + * if not self._open: + * result = self.intervalFile_ptr.Open() + * if result == -1: # <<<<<<<<<<<<<< + * raise BedToolsFileError("Error opening file") + * self._open = 1 + */ + } + + /* "pybedtools/cbedtools.pyx":823 + * if result == -1: + * raise BedToolsFileError("Error opening file") + * self._open = 1 # <<<<<<<<<<<<<< + * cdef BED b = self.intervalFile_ptr.GetNextBed() + * if b.status == BED_VALID: + */ + __pyx_v_self->_open = 1; + + /* "pybedtools/cbedtools.pyx":819 + * + * def __next__(self): + * if not self._open: # <<<<<<<<<<<<<< + * result = self.intervalFile_ptr.Open() + * if result == -1: + */ + } + + /* "pybedtools/cbedtools.pyx":824 + * raise BedToolsFileError("Error opening file") + * self._open = 1 + * cdef BED b = self.intervalFile_ptr.GetNextBed() # <<<<<<<<<<<<<< + * if b.status == BED_VALID: + * return create_interval(b) + */ + __pyx_v_b = __pyx_v_self->intervalFile_ptr->GetNextBed(); + + /* "pybedtools/cbedtools.pyx":825 + * self._open = 1 + * cdef BED b = self.intervalFile_ptr.GetNextBed() + * if b.status == BED_VALID: # <<<<<<<<<<<<<< + * return create_interval(b) + * elif b.status == BED_INVALID: + */ + switch (__pyx_v_b.status) { + case BED_VALID: + + /* "pybedtools/cbedtools.pyx":826 + * cdef BED b = self.intervalFile_ptr.GetNextBed() + * if b.status == BED_VALID: + * return create_interval(b) # <<<<<<<<<<<<<< + * elif b.status == BED_INVALID: + * self.intervalFile_ptr.Close() + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = ((PyObject *)__pyx_f_10pybedtools_9cbedtools_create_interval(__pyx_v_b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 826, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":825 + * self._open = 1 + * cdef BED b = self.intervalFile_ptr.GetNextBed() + * if b.status == BED_VALID: # <<<<<<<<<<<<<< + * return create_interval(b) + * elif b.status == BED_INVALID: + */ + break; + case BED_INVALID: + + /* "pybedtools/cbedtools.pyx":828 + * return create_interval(b) + * elif b.status == BED_INVALID: + * self.intervalFile_ptr.Close() # <<<<<<<<<<<<<< + * raise StopIteration + * elif b.status == BED_MALFORMED: + */ + __pyx_v_self->intervalFile_ptr->Close(); + + /* "pybedtools/cbedtools.pyx":829 + * elif b.status == BED_INVALID: + * self.intervalFile_ptr.Close() + * raise StopIteration # <<<<<<<<<<<<<< + * elif b.status == BED_MALFORMED: + * self.intervalFile_ptr.Close() + */ + __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); + __PYX_ERR(0, 829, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":827 + * if b.status == BED_VALID: + * return create_interval(b) + * elif b.status == BED_INVALID: # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Close() + * raise StopIteration + */ + break; + case BED_MALFORMED: + + /* "pybedtools/cbedtools.pyx":831 + * raise StopIteration + * elif b.status == BED_MALFORMED: + * self.intervalFile_ptr.Close() # <<<<<<<<<<<<<< + * raise MalformedBedLineError("malformed line: %s" % string_vec2list(b.fields)) + * else: + */ + __pyx_v_self->intervalFile_ptr->Close(); + + /* "pybedtools/cbedtools.pyx":832 + * elif b.status == BED_MALFORMED: + * self.intervalFile_ptr.Close() + * raise MalformedBedLineError("malformed line: %s" % string_vec2list(b.fields)) # <<<<<<<<<<<<<< + * else: + * return next(self) + */ + __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 832, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = __pyx_f_10pybedtools_9cbedtools_string_vec2list(__pyx_v_b.fields); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 832, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_malformed_line_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 832, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_3, function); + } + } + __pyx_t_2 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_4, __pyx_t_5) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_5); + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 832, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __PYX_ERR(0, 832, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":830 + * self.intervalFile_ptr.Close() + * raise StopIteration + * elif b.status == BED_MALFORMED: # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Close() + * raise MalformedBedLineError("malformed line: %s" % string_vec2list(b.fields)) + */ + break; + default: + + /* "pybedtools/cbedtools.pyx":834 + * raise MalformedBedLineError("malformed line: %s" % string_vec2list(b.fields)) + * else: + * return next(self) # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_2 = __Pyx_PyIter_Next(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 834, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_r = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L0; + break; + } + + /* "pybedtools/cbedtools.pyx":818 + * return self + * + * def __next__(self): # <<<<<<<<<<<<<< + * if not self._open: + * result = self.intervalFile_ptr.Open() + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":837 + * + * @property + * def fn(self): # <<<<<<<<<<<<<< + * return _pystr(self._fn) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_2fn_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_2fn_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_2fn___get__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_2fn___get__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":838 + * @property + * def fn(self): + * return _pystr(self._fn) # <<<<<<<<<<<<<< + * + * @property + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->_fn); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 838, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":837 + * + * @property + * def fn(self): # <<<<<<<<<<<<<< + * return _pystr(self._fn) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.fn.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":841 + * + * @property + * def file_type(self): # <<<<<<<<<<<<<< + * if not self.intervalFile_ptr._typeIsKnown: + * try: + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_9file_type_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_9file_type_1__get__(PyObject *__pyx_v_self) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_9file_type___get__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_9file_type___get__(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + CYTHON_UNUSED PyObject *__pyx_v_a = NULL; + PyObject *__pyx_v_file_type = NULL; + PyObject *__pyx_v_fn = NULL; + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval = NULL; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + int __pyx_t_9; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + PyObject *__pyx_t_12 = NULL; + PyObject *__pyx_t_13 = NULL; + PyObject *__pyx_t_14 = NULL; + PyObject *__pyx_t_15 = NULL; + PyObject *__pyx_t_16 = NULL; + PyObject *__pyx_t_17 = NULL; + PyObject *__pyx_t_18 = NULL; + int __pyx_t_19; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__get__", 0); + + /* "pybedtools/cbedtools.pyx":842 + * @property + * def file_type(self): + * if not self.intervalFile_ptr._typeIsKnown: # <<<<<<<<<<<<<< + * try: + * a = next(iter(self)) + */ + __pyx_t_1 = ((!(__pyx_v_self->intervalFile_ptr->_typeIsKnown != 0)) != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":843 + * def file_type(self): + * if not self.intervalFile_ptr._typeIsKnown: + * try: # <<<<<<<<<<<<<< + * a = next(iter(self)) + * file_type = _pystr(self.intervalFile_ptr.file_type) + */ + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_2, &__pyx_t_3, &__pyx_t_4); + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_3); + __Pyx_XGOTREF(__pyx_t_4); + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":844 + * if not self.intervalFile_ptr._typeIsKnown: + * try: + * a = next(iter(self)) # <<<<<<<<<<<<<< + * file_type = _pystr(self.intervalFile_ptr.file_type) + * self.intervalFile_ptr.Close() + */ + __pyx_t_5 = PyObject_GetIter(((PyObject *)__pyx_v_self)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 844, __pyx_L4_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = __Pyx_PyIter_Next(__pyx_t_5); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 844, __pyx_L4_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_v_a = __pyx_t_6; + __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":845 + * try: + * a = next(iter(self)) + * file_type = _pystr(self.intervalFile_ptr.file_type) # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Close() + * return file_type + */ + __pyx_t_6 = __pyx_f_10pybedtools_9cbedtools__pystr(__pyx_v_self->intervalFile_ptr->file_type); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 845, __pyx_L4_error) + __Pyx_GOTREF(__pyx_t_6); + __pyx_v_file_type = __pyx_t_6; + __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":846 + * a = next(iter(self)) + * file_type = _pystr(self.intervalFile_ptr.file_type) + * self.intervalFile_ptr.Close() # <<<<<<<<<<<<<< + * return file_type + * except MalformedBedLineError: + */ + __pyx_v_self->intervalFile_ptr->Close(); + + /* "pybedtools/cbedtools.pyx":847 + * file_type = _pystr(self.intervalFile_ptr.file_type) + * self.intervalFile_ptr.Close() + * return file_type # <<<<<<<<<<<<<< + * except MalformedBedLineError: + * # If it's a SAM, raise a meaningful exception. If not, fail. + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v_file_type); + __pyx_r = __pyx_v_file_type; + goto __pyx_L8_try_return; + + /* "pybedtools/cbedtools.pyx":843 + * def file_type(self): + * if not self.intervalFile_ptr._typeIsKnown: + * try: # <<<<<<<<<<<<<< + * a = next(iter(self)) + * file_type = _pystr(self.intervalFile_ptr.file_type) + */ + } + __pyx_L4_error:; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":848 + * self.intervalFile_ptr.Close() + * return file_type + * except MalformedBedLineError: # <<<<<<<<<<<<<< + * # If it's a SAM, raise a meaningful exception. If not, fail. + * with open(self.fn) as fn: + */ + __Pyx_ErrFetch(&__pyx_t_6, &__pyx_t_5, &__pyx_t_7); + __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 848, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = __Pyx_PyErr_GivenExceptionMatches(__pyx_t_6, __pyx_t_8); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_ErrRestore(__pyx_t_6, __pyx_t_5, __pyx_t_7); + __pyx_t_6 = 0; __pyx_t_5 = 0; __pyx_t_7 = 0; + if (__pyx_t_9) { + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.file_type.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_5, &__pyx_t_6) < 0) __PYX_ERR(0, 848, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(__pyx_t_6); + + /* "pybedtools/cbedtools.pyx":850 + * except MalformedBedLineError: + * # If it's a SAM, raise a meaningful exception. If not, fail. + * with open(self.fn) as fn: # <<<<<<<<<<<<<< + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': + */ + /*with:*/ { + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_fn); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 850, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_10 = __Pyx_PyObject_CallOneArg(__pyx_builtin_open, __pyx_t_8); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 850, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_11 = __Pyx_PyObject_LookupSpecial(__pyx_t_10, __pyx_n_s_exit); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 850, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_11); + __pyx_t_12 = __Pyx_PyObject_LookupSpecial(__pyx_t_10, __pyx_n_s_enter); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 850, __pyx_L12_error) + __Pyx_GOTREF(__pyx_t_12); + __pyx_t_13 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_12))) { + __pyx_t_13 = PyMethod_GET_SELF(__pyx_t_12); + if (likely(__pyx_t_13)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12); + __Pyx_INCREF(__pyx_t_13); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_12, function); + } + } + __pyx_t_8 = (__pyx_t_13) ? __Pyx_PyObject_CallOneArg(__pyx_t_12, __pyx_t_13) : __Pyx_PyObject_CallNoArg(__pyx_t_12); + __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 850, __pyx_L12_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __pyx_t_12 = __pyx_t_8; + __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + /*try:*/ { + { + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __Pyx_ExceptionSave(&__pyx_t_14, &__pyx_t_15, &__pyx_t_16); + __Pyx_XGOTREF(__pyx_t_14); + __Pyx_XGOTREF(__pyx_t_15); + __Pyx_XGOTREF(__pyx_t_16); + /*try:*/ { + __pyx_v_fn = __pyx_t_12; + __pyx_t_12 = 0; + + /* "pybedtools/cbedtools.pyx":851 + * # If it's a SAM, raise a meaningful exception. If not, fail. + * with open(self.fn) as fn: + * interval = create_interval_from_list(fn.readline().strip().split()) # <<<<<<<<<<<<<< + * if interval.file_type == 'sam': + * raise ValueError('IntervalFile objects do not yet natively support SAM. ' + */ + __pyx_t_13 = __Pyx_PyObject_GetAttrStr(__pyx_v_fn, __pyx_n_s_readline); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_13); + __pyx_t_17 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_13))) { + __pyx_t_17 = PyMethod_GET_SELF(__pyx_t_13); + if (likely(__pyx_t_17)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_13); + __Pyx_INCREF(__pyx_t_17); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_13, function); + } + } + __pyx_t_8 = (__pyx_t_17) ? __Pyx_PyObject_CallOneArg(__pyx_t_13, __pyx_t_17) : __Pyx_PyObject_CallNoArg(__pyx_t_13); + __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0; + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; + __pyx_t_13 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_strip); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_13); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_13))) { + __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_13); + if (likely(__pyx_t_8)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_13); + __Pyx_INCREF(__pyx_t_8); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_13, function); + } + } + __pyx_t_10 = (__pyx_t_8) ? __Pyx_PyObject_CallOneArg(__pyx_t_13, __pyx_t_8) : __Pyx_PyObject_CallNoArg(__pyx_t_13); + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; + __pyx_t_13 = __Pyx_PyObject_GetAttrStr(__pyx_t_10, __pyx_n_s_split); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_13); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_10 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_13))) { + __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_13); + if (likely(__pyx_t_10)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_13); + __Pyx_INCREF(__pyx_t_10); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_13, function); + } + } + __pyx_t_12 = (__pyx_t_10) ? __Pyx_PyObject_CallOneArg(__pyx_t_13, __pyx_t_10) : __Pyx_PyObject_CallNoArg(__pyx_t_13); + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_12); + __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; + if (!(likely(PyList_CheckExact(__pyx_t_12))||((__pyx_t_12) == Py_None)||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_12)->tp_name), 0))) __PYX_ERR(0, 851, __pyx_L18_error) + __pyx_t_13 = ((PyObject *)__pyx_f_10pybedtools_9cbedtools_create_interval_from_list(((PyObject*)__pyx_t_12), 0)); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 851, __pyx_L18_error) + __Pyx_GOTREF(__pyx_t_13); + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __pyx_v_interval = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)__pyx_t_13); + __pyx_t_13 = 0; + + /* "pybedtools/cbedtools.pyx":850 + * except MalformedBedLineError: + * # If it's a SAM, raise a meaningful exception. If not, fail. + * with open(self.fn) as fn: # <<<<<<<<<<<<<< + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': + */ + } + __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0; + __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0; + __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0; + goto __pyx_L25_try_end; + __pyx_L18_error:; + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0; + __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; + __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0; + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + /*except:*/ { + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.file_type.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_13, &__pyx_t_12, &__pyx_t_10) < 0) __PYX_ERR(0, 850, __pyx_L20_except_error) + __Pyx_GOTREF(__pyx_t_13); + __Pyx_GOTREF(__pyx_t_12); + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_8 = PyTuple_Pack(3, __pyx_t_13, __pyx_t_12, __pyx_t_10); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 850, __pyx_L20_except_error) + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_18 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_8, NULL); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 850, __pyx_L20_except_error) + __Pyx_GOTREF(__pyx_t_18); + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18); + __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; + if (__pyx_t_1 < 0) __PYX_ERR(0, 850, __pyx_L20_except_error) + __pyx_t_19 = ((!(__pyx_t_1 != 0)) != 0); + if (__pyx_t_19) { + __Pyx_GIVEREF(__pyx_t_13); + __Pyx_GIVEREF(__pyx_t_12); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_ErrRestoreWithState(__pyx_t_13, __pyx_t_12, __pyx_t_10); + __pyx_t_13 = 0; __pyx_t_12 = 0; __pyx_t_10 = 0; + __PYX_ERR(0, 850, __pyx_L20_except_error) + } + __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; + __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0; + __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; + goto __pyx_L19_exception_handled; + } + __pyx_L20_except_error:; + __Pyx_XGIVEREF(__pyx_t_14); + __Pyx_XGIVEREF(__pyx_t_15); + __Pyx_XGIVEREF(__pyx_t_16); + __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16); + goto __pyx_L6_except_error; + __pyx_L19_exception_handled:; + __Pyx_XGIVEREF(__pyx_t_14); + __Pyx_XGIVEREF(__pyx_t_15); + __Pyx_XGIVEREF(__pyx_t_16); + __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16); + __pyx_L25_try_end:; + } + } + /*finally:*/ { + /*normal exit:*/{ + if (__pyx_t_11) { + __pyx_t_16 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_tuple__26, NULL); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + if (unlikely(!__pyx_t_16)) __PYX_ERR(0, 850, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_16); + __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; + } + goto __pyx_L17; + } + __pyx_L17:; + } + goto __pyx_L29; + __pyx_L12_error:; + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + goto __pyx_L6_except_error; + __pyx_L29:; + } + + /* "pybedtools/cbedtools.pyx":852 + * with open(self.fn) as fn: + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': # <<<<<<<<<<<<<< + * raise ValueError('IntervalFile objects do not yet natively support SAM. ' + * 'Please convert to BED/GFF/VCF first if you want to ' + */ + if (unlikely(!__pyx_v_interval)) { __Pyx_RaiseUnboundLocalError("interval"); __PYX_ERR(0, 852, __pyx_L6_except_error) } + __pyx_t_10 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_interval), __pyx_n_s_file_type); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 852, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_19 = (__Pyx_PyString_Equals(__pyx_t_10, __pyx_n_s_sam, Py_EQ)); if (unlikely(__pyx_t_19 < 0)) __PYX_ERR(0, 852, __pyx_L6_except_error) + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + if (unlikely(__pyx_t_19)) { + + /* "pybedtools/cbedtools.pyx":853 + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': + * raise ValueError('IntervalFile objects do not yet natively support SAM. ' # <<<<<<<<<<<<<< + * 'Please convert to BED/GFF/VCF first if you want to ' + * 'use the low-level API of IntervalFile') + */ + __pyx_t_10 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__27, NULL); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 853, __pyx_L6_except_error) + __Pyx_GOTREF(__pyx_t_10); + __Pyx_Raise(__pyx_t_10, 0, 0, 0); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __PYX_ERR(0, 853, __pyx_L6_except_error) + + /* "pybedtools/cbedtools.pyx":852 + * with open(self.fn) as fn: + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': # <<<<<<<<<<<<<< + * raise ValueError('IntervalFile objects do not yet natively support SAM. ' + * 'Please convert to BED/GFF/VCF first if you want to ' + */ + } + + /* "pybedtools/cbedtools.pyx":857 + * 'use the low-level API of IntervalFile') + * else: + * raise # <<<<<<<<<<<<<< + * + * + */ + /*else*/ { + __Pyx_GIVEREF(__pyx_t_7); + __Pyx_GIVEREF(__pyx_t_5); + __Pyx_XGIVEREF(__pyx_t_6); + __Pyx_ErrRestoreWithState(__pyx_t_7, __pyx_t_5, __pyx_t_6); + __pyx_t_7 = 0; __pyx_t_5 = 0; __pyx_t_6 = 0; + __PYX_ERR(0, 857, __pyx_L6_except_error) + } + } + goto __pyx_L6_except_error; + __pyx_L6_except_error:; + + /* "pybedtools/cbedtools.pyx":843 + * def file_type(self): + * if not self.intervalFile_ptr._typeIsKnown: + * try: # <<<<<<<<<<<<<< + * a = next(iter(self)) + * file_type = _pystr(self.intervalFile_ptr.file_type) + */ + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_XGIVEREF(__pyx_t_4); + __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4); + goto __pyx_L1_error; + __pyx_L8_try_return:; + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_XGIVEREF(__pyx_t_4); + __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4); + goto __pyx_L0; + } + + /* "pybedtools/cbedtools.pyx":842 + * @property + * def file_type(self): + * if not self.intervalFile_ptr._typeIsKnown: # <<<<<<<<<<<<<< + * try: + * a = next(iter(self)) + */ + } + + /* "pybedtools/cbedtools.pyx":841 + * + * @property + * def file_type(self): # <<<<<<<<<<<<<< + * if not self.intervalFile_ptr._typeIsKnown: + * try: + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_10); + __Pyx_XDECREF(__pyx_t_12); + __Pyx_XDECREF(__pyx_t_13); + __Pyx_XDECREF(__pyx_t_17); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.file_type.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_a); + __Pyx_XDECREF(__pyx_v_file_type); + __Pyx_XDECREF(__pyx_v_fn); + __Pyx_XDECREF((PyObject *)__pyx_v_interval); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":860 + * + * + * def loadIntoMap(self): # <<<<<<<<<<<<<< + * """ + * Prepares file for checking intersections. Used by other methods like all_hits() + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_9loadIntoMap(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_8loadIntoMap[] = "\n Prepares file for checking intersections. Used by other methods like all_hits()\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_9loadIntoMap(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("loadIntoMap (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_8loadIntoMap(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_8loadIntoMap(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + __Pyx_RefNannySetupContext("loadIntoMap", 0); + + /* "pybedtools/cbedtools.pyx":864 + * Prepares file for checking intersections. Used by other methods like all_hits() + * """ + * if self._loaded: # <<<<<<<<<<<<<< + * return + * self.intervalFile_ptr.loadBedFileIntoMap() + */ + __pyx_t_1 = (__pyx_v_self->_loaded != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":865 + * """ + * if self._loaded: + * return # <<<<<<<<<<<<<< + * self.intervalFile_ptr.loadBedFileIntoMap() + * self._loaded = 1 + */ + __Pyx_XDECREF(__pyx_r); + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":864 + * Prepares file for checking intersections. Used by other methods like all_hits() + * """ + * if self._loaded: # <<<<<<<<<<<<<< + * return + * self.intervalFile_ptr.loadBedFileIntoMap() + */ + } + + /* "pybedtools/cbedtools.pyx":866 + * if self._loaded: + * return + * self.intervalFile_ptr.loadBedFileIntoMap() # <<<<<<<<<<<<<< + * self._loaded = 1 + * + */ + __pyx_v_self->intervalFile_ptr->loadBedFileIntoMap(); + + /* "pybedtools/cbedtools.pyx":867 + * return + * self.intervalFile_ptr.loadBedFileIntoMap() + * self._loaded = 1 # <<<<<<<<<<<<<< + * + * def rewind(self): + */ + __pyx_v_self->_loaded = 1; + + /* "pybedtools/cbedtools.pyx":860 + * + * + * def loadIntoMap(self): # <<<<<<<<<<<<<< + * """ + * Prepares file for checking intersections. Used by other methods like all_hits() + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":869 + * self._loaded = 1 + * + * def rewind(self): # <<<<<<<<<<<<<< + * """ + * Jump to the beginning of the file. + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_11rewind(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_10rewind[] = "\n Jump to the beginning of the file.\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_11rewind(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("rewind (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_10rewind(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_10rewind(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + __Pyx_RefNannySetupContext("rewind", 0); + + /* "pybedtools/cbedtools.pyx":873 + * Jump to the beginning of the file. + * """ + * if not self._open: # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Open() + * self._open = 1 + */ + __pyx_t_1 = ((!(__pyx_v_self->_open != 0)) != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":874 + * """ + * if not self._open: + * self.intervalFile_ptr.Open() # <<<<<<<<<<<<<< + * self._open = 1 + * self.intervalFile_ptr.Rewind() + */ + (void)(__pyx_v_self->intervalFile_ptr->Open()); + + /* "pybedtools/cbedtools.pyx":875 + * if not self._open: + * self.intervalFile_ptr.Open() + * self._open = 1 # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Rewind() + * + */ + __pyx_v_self->_open = 1; + + /* "pybedtools/cbedtools.pyx":873 + * Jump to the beginning of the file. + * """ + * if not self._open: # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Open() + * self._open = 1 + */ + } + + /* "pybedtools/cbedtools.pyx":876 + * self.intervalFile_ptr.Open() + * self._open = 1 + * self.intervalFile_ptr.Rewind() # <<<<<<<<<<<<<< + * + * def seek(self, offset): + */ + __pyx_v_self->intervalFile_ptr->Rewind(); + + /* "pybedtools/cbedtools.pyx":869 + * self._loaded = 1 + * + * def rewind(self): # <<<<<<<<<<<<<< + * """ + * Jump to the beginning of the file. + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":878 + * self.intervalFile_ptr.Rewind() + * + * def seek(self, offset): # <<<<<<<<<<<<<< + * """ + * Jump to a specific byte offset in the file + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_13seek(PyObject *__pyx_v_self, PyObject *__pyx_v_offset); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_12seek[] = "\n Jump to a specific byte offset in the file\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_13seek(PyObject *__pyx_v_self, PyObject *__pyx_v_offset) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("seek (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_12seek(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self), ((PyObject *)__pyx_v_offset)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_12seek(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, PyObject *__pyx_v_offset) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + unsigned long __pyx_t_2; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("seek", 0); + + /* "pybedtools/cbedtools.pyx":882 + * Jump to a specific byte offset in the file + * """ + * if not self._open: # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Open() + * self._open = 1 + */ + __pyx_t_1 = ((!(__pyx_v_self->_open != 0)) != 0); + if (__pyx_t_1) { + + /* "pybedtools/cbedtools.pyx":883 + * """ + * if not self._open: + * self.intervalFile_ptr.Open() # <<<<<<<<<<<<<< + * self._open = 1 + * self.intervalFile_ptr.Seek(offset) + */ + (void)(__pyx_v_self->intervalFile_ptr->Open()); + + /* "pybedtools/cbedtools.pyx":884 + * if not self._open: + * self.intervalFile_ptr.Open() + * self._open = 1 # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Seek(offset) + * + */ + __pyx_v_self->_open = 1; + + /* "pybedtools/cbedtools.pyx":882 + * Jump to a specific byte offset in the file + * """ + * if not self._open: # <<<<<<<<<<<<<< + * self.intervalFile_ptr.Open() + * self._open = 1 + */ + } + + /* "pybedtools/cbedtools.pyx":885 + * self.intervalFile_ptr.Open() + * self._open = 1 + * self.intervalFile_ptr.Seek(offset) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = __Pyx_PyInt_As_unsigned_long(__pyx_v_offset); if (unlikely((__pyx_t_2 == (unsigned long)-1) && PyErr_Occurred())) __PYX_ERR(0, 885, __pyx_L1_error) + __pyx_v_self->intervalFile_ptr->Seek(__pyx_t_2); + + /* "pybedtools/cbedtools.pyx":878 + * self.intervalFile_ptr.Rewind() + * + * def seek(self, offset): # <<<<<<<<<<<<<< + * """ + * Jump to a specific byte offset in the file + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":888 + * + * + * def all_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): # <<<<<<<<<<<<<< + * """ + * :Signature: `IntervalFile.all_hits(interval, same_strand=False, overlap=0.0)` + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_15all_hits(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_14all_hits[] = "\n :Signature: `IntervalFile.all_hits(interval, same_strand=False, overlap=0.0)`\n\n Search for the Interval `interval` this file and return **all**\n overlaps as a list.\n\n `same_strand`, if True, will only consider hits on the same strand as `interval`.\n\n `overlap` can be used to specify the fraction of overlap between\n `interval` and each feature in the IntervalFile.\n\n Example usage:\n\n >>> fn = pybedtools.example_filename('a.bed')\n\n >>> # create an Interval to query with\n >>> i = pybedtools.Interval('chr1', 1, 10000, strand='+')\n\n >>> # Create an IntervalFile out of a.bed\n >>> intervalfile = pybedtools.IntervalFile(fn)\n\n >>> # get stranded hits\n >>> intervalfile.all_hits(i, same_strand=True)\n [Interval(chr1:1-100), Interval(chr1:100-200), Interval(chr1:900-950)]\n\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_15all_hits(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval = 0; + PyBoolObject *__pyx_v_same_strand = 0; + float __pyx_v_overlap; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("all_hits (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_interval,&__pyx_n_s_same_strand,&__pyx_n_s_overlap,0}; + PyObject* values[3] = {0,0,0}; + values[1] = (PyObject *)((PyBoolObject *)Py_False); + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_interval)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_same_strand); + if (value) { values[1] = value; kw_args--; } + } + CYTHON_FALLTHROUGH; + case 2: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_overlap); + if (value) { values[2] = value; kw_args--; } + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "all_hits") < 0)) __PYX_ERR(0, 888, __pyx_L3_error) + } + } else { + switch (PyTuple_GET_SIZE(__pyx_args)) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_interval = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)values[0]); + __pyx_v_same_strand = ((PyBoolObject *)values[1]); + if (values[2]) { + __pyx_v_overlap = __pyx_PyFloat_AsFloat(values[2]); if (unlikely((__pyx_v_overlap == (float)-1) && PyErr_Occurred())) __PYX_ERR(0, 888, __pyx_L3_error) + } else { + __pyx_v_overlap = ((float)0.0); + } + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("all_hits", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 888, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.all_hits", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_interval), __pyx_ptype_10pybedtools_9cbedtools_Interval, 1, "interval", 0))) __PYX_ERR(0, 888, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_same_strand), __pyx_ptype_7cpython_4bool_bool, 1, "same_strand", 0))) __PYX_ERR(0, 888, __pyx_L1_error) + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_14all_hits(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self), __pyx_v_interval, __pyx_v_same_strand, __pyx_v_overlap); + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __pyx_r = NULL; + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_14all_hits(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval, PyBoolObject *__pyx_v_same_strand, float __pyx_v_overlap) { + std::vector<BED> __pyx_v_vec_b; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + char const *__pyx_t_7; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + PyObject *__pyx_t_12 = NULL; + PyObject *__pyx_t_13 = NULL; + char const *__pyx_t_14; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("all_hits", 0); + + /* "pybedtools/cbedtools.pyx":916 + * """ + * cdef vector[BED] vec_b + * self.loadIntoMap() # <<<<<<<<<<<<<< + * + * if same_strand == False: + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_loadIntoMap); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 916, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 916, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":918 + * self.loadIntoMap() + * + * if same_strand == False: # <<<<<<<<<<<<<< + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), overlap) + * try: + */ + __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_v_same_strand), Py_False, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 918, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 918, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_4) { + + /* "pybedtools/cbedtools.pyx":919 + * + * if same_strand == False: + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), overlap) # <<<<<<<<<<<<<< + * try: + * return bed_vec2list(vec_b) + */ + __pyx_v_vec_b = __pyx_v_self->intervalFile_ptr->FindOverlapsPerBin((*__pyx_v_interval->_bed), __pyx_v_overlap); + + /* "pybedtools/cbedtools.pyx":920 + * if same_strand == False: + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), overlap) + * try: # <<<<<<<<<<<<<< + * return bed_vec2list(vec_b) + * finally: + */ + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":921 + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), overlap) + * try: + * return bed_vec2list(vec_b) # <<<<<<<<<<<<<< + * finally: + * pass + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_bed_vec2list(__pyx_v_vec_b); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 921, __pyx_L5_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L4_return; + } + + /* "pybedtools/cbedtools.pyx":923 + * return bed_vec2list(vec_b) + * finally: + * pass # <<<<<<<<<<<<<< + * else: + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), same_strand, overlap) + */ + /*finally:*/ { + __pyx_L5_error:; + /*exception exit:*/{ + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __pyx_t_8 = 0; __pyx_t_9 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0; __pyx_t_12 = 0; __pyx_t_13 = 0; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PY_MAJOR_VERSION >= 3) __Pyx_ExceptionSwap(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13); + if ((PY_MAJOR_VERSION < 3) || unlikely(__Pyx_GetException(&__pyx_t_8, &__pyx_t_9, &__pyx_t_10) < 0)) __Pyx_ErrFetch(&__pyx_t_8, &__pyx_t_9, &__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_8); + __Pyx_XGOTREF(__pyx_t_9); + __Pyx_XGOTREF(__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_11); + __Pyx_XGOTREF(__pyx_t_12); + __Pyx_XGOTREF(__pyx_t_13); + __pyx_t_5 = __pyx_lineno; __pyx_t_6 = __pyx_clineno; __pyx_t_7 = __pyx_filename; + { + } + if (PY_MAJOR_VERSION >= 3) { + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_XGIVEREF(__pyx_t_12); + __Pyx_XGIVEREF(__pyx_t_13); + __Pyx_ExceptionReset(__pyx_t_11, __pyx_t_12, __pyx_t_13); + } + __Pyx_XGIVEREF(__pyx_t_8); + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_ErrRestore(__pyx_t_8, __pyx_t_9, __pyx_t_10); + __pyx_t_8 = 0; __pyx_t_9 = 0; __pyx_t_10 = 0; __pyx_t_11 = 0; __pyx_t_12 = 0; __pyx_t_13 = 0; + __pyx_lineno = __pyx_t_5; __pyx_clineno = __pyx_t_6; __pyx_filename = __pyx_t_7; + goto __pyx_L1_error; + } + __pyx_L4_return: { + __pyx_t_13 = __pyx_r; + __pyx_r = 0; + __pyx_r = __pyx_t_13; + __pyx_t_13 = 0; + goto __pyx_L0; + } + } + + /* "pybedtools/cbedtools.pyx":918 + * self.loadIntoMap() + * + * if same_strand == False: # <<<<<<<<<<<<<< + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), overlap) + * try: + */ + } + + /* "pybedtools/cbedtools.pyx":925 + * pass + * else: + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), same_strand, overlap) # <<<<<<<<<<<<<< + * try: + * return bed_vec2list(vec_b) + */ + /*else*/ { + __pyx_v_vec_b = __pyx_v_self->intervalFile_ptr->FindOverlapsPerBin((*__pyx_v_interval->_bed), __pyx_v_same_strand, __pyx_v_overlap); + + /* "pybedtools/cbedtools.pyx":926 + * else: + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), same_strand, overlap) + * try: # <<<<<<<<<<<<<< + * return bed_vec2list(vec_b) + * finally: + */ + /*try:*/ { + + /* "pybedtools/cbedtools.pyx":927 + * vec_b = self.intervalFile_ptr.FindOverlapsPerBin(deref(interval._bed), same_strand, overlap) + * try: + * return bed_vec2list(vec_b) # <<<<<<<<<<<<<< + * finally: + * pass + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __pyx_f_10pybedtools_9cbedtools_bed_vec2list(__pyx_v_vec_b); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 927, __pyx_L10_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L9_return; + } + + /* "pybedtools/cbedtools.pyx":929 + * return bed_vec2list(vec_b) + * finally: + * pass # <<<<<<<<<<<<<< + * + * # search() is an alias for all_hits + */ + /*finally:*/ { + __pyx_L10_error:; + /*exception exit:*/{ + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + __pyx_t_13 = 0; __pyx_t_12 = 0; __pyx_t_11 = 0; __pyx_t_10 = 0; __pyx_t_9 = 0; __pyx_t_8 = 0; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PY_MAJOR_VERSION >= 3) __Pyx_ExceptionSwap(&__pyx_t_10, &__pyx_t_9, &__pyx_t_8); + if ((PY_MAJOR_VERSION < 3) || unlikely(__Pyx_GetException(&__pyx_t_13, &__pyx_t_12, &__pyx_t_11) < 0)) __Pyx_ErrFetch(&__pyx_t_13, &__pyx_t_12, &__pyx_t_11); + __Pyx_XGOTREF(__pyx_t_13); + __Pyx_XGOTREF(__pyx_t_12); + __Pyx_XGOTREF(__pyx_t_11); + __Pyx_XGOTREF(__pyx_t_10); + __Pyx_XGOTREF(__pyx_t_9); + __Pyx_XGOTREF(__pyx_t_8); + __pyx_t_6 = __pyx_lineno; __pyx_t_5 = __pyx_clineno; __pyx_t_14 = __pyx_filename; + { + } + if (PY_MAJOR_VERSION >= 3) { + __Pyx_XGIVEREF(__pyx_t_10); + __Pyx_XGIVEREF(__pyx_t_9); + __Pyx_XGIVEREF(__pyx_t_8); + __Pyx_ExceptionReset(__pyx_t_10, __pyx_t_9, __pyx_t_8); + } + __Pyx_XGIVEREF(__pyx_t_13); + __Pyx_XGIVEREF(__pyx_t_12); + __Pyx_XGIVEREF(__pyx_t_11); + __Pyx_ErrRestore(__pyx_t_13, __pyx_t_12, __pyx_t_11); + __pyx_t_13 = 0; __pyx_t_12 = 0; __pyx_t_11 = 0; __pyx_t_10 = 0; __pyx_t_9 = 0; __pyx_t_8 = 0; + __pyx_lineno = __pyx_t_6; __pyx_clineno = __pyx_t_5; __pyx_filename = __pyx_t_14; + goto __pyx_L1_error; + } + __pyx_L9_return: { + __pyx_t_8 = __pyx_r; + __pyx_r = 0; + __pyx_r = __pyx_t_8; + __pyx_t_8 = 0; + goto __pyx_L0; + } + } + } + + /* "pybedtools/cbedtools.pyx":888 + * + * + * def all_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): # <<<<<<<<<<<<<< + * """ + * :Signature: `IntervalFile.all_hits(interval, same_strand=False, overlap=0.0)` + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.all_hits", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":934 + * search = all_hits + * + * def any_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): # <<<<<<<<<<<<<< + * """ + * :Signature: `IntervalFile.any_hits(interval, same_strand=False, overlap=0.0)` + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_17any_hits(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_16any_hits[] = "\n :Signature: `IntervalFile.any_hits(interval, same_strand=False, overlap=0.0)`\n\n Return 1 if the Interval `interval` had >=1 hit in this IntervalFile, 0 otherwise.\n\n `same_strand`, if True, will only consider hits on the same strand as `interval`.\n\n `overlap` can be used to specify the fraction of overlap between\n `interval` and each feature in the IntervalFile.\n\n Example usage:\n\n >>> fn = pybedtools.example_filename('a.bed')\n\n >>> # create an Interval to query with\n >>> i = pybedtools.Interval('chr1', 1, 10000, strand='+')\n\n >>> # Create an IntervalFile out of a.bed\n >>> intervalfile = pybedtools.IntervalFile(fn)\n\n >>> # any stranded hits?\n >>> intervalfile.any_hits(i, same_strand=True)\n 1\n\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_17any_hits(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval = 0; + PyBoolObject *__pyx_v_same_strand = 0; + float __pyx_v_overlap; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("any_hits (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_interval,&__pyx_n_s_same_strand,&__pyx_n_s_overlap,0}; + PyObject* values[3] = {0,0,0}; + values[1] = (PyObject *)((PyBoolObject *)Py_False); + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_interval)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_same_strand); + if (value) { values[1] = value; kw_args--; } + } + CYTHON_FALLTHROUGH; + case 2: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_overlap); + if (value) { values[2] = value; kw_args--; } + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "any_hits") < 0)) __PYX_ERR(0, 934, __pyx_L3_error) + } + } else { + switch (PyTuple_GET_SIZE(__pyx_args)) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_interval = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)values[0]); + __pyx_v_same_strand = ((PyBoolObject *)values[1]); + if (values[2]) { + __pyx_v_overlap = __pyx_PyFloat_AsFloat(values[2]); if (unlikely((__pyx_v_overlap == (float)-1) && PyErr_Occurred())) __PYX_ERR(0, 934, __pyx_L3_error) + } else { + __pyx_v_overlap = ((float)0.0); + } + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("any_hits", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 934, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.any_hits", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_interval), __pyx_ptype_10pybedtools_9cbedtools_Interval, 1, "interval", 0))) __PYX_ERR(0, 934, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_same_strand), __pyx_ptype_7cpython_4bool_bool, 1, "same_strand", 0))) __PYX_ERR(0, 934, __pyx_L1_error) + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_16any_hits(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self), __pyx_v_interval, __pyx_v_same_strand, __pyx_v_overlap); + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __pyx_r = NULL; + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_16any_hits(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval, PyBoolObject *__pyx_v_same_strand, float __pyx_v_overlap) { + long __pyx_v_found; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("any_hits", 0); + + /* "pybedtools/cbedtools.pyx":960 + * + * """ + * found = 0 # <<<<<<<<<<<<<< + * self.loadIntoMap() + * + */ + __pyx_v_found = 0; + + /* "pybedtools/cbedtools.pyx":961 + * """ + * found = 0 + * self.loadIntoMap() # <<<<<<<<<<<<<< + * + * if same_strand == False: + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_loadIntoMap); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 961, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 961, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":963 + * self.loadIntoMap() + * + * if same_strand == False: # <<<<<<<<<<<<<< + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), overlap) + * else: + */ + __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_v_same_strand), Py_False, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 963, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 963, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_4) { + + /* "pybedtools/cbedtools.pyx":964 + * + * if same_strand == False: + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), overlap) # <<<<<<<<<<<<<< + * else: + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), same_strand, overlap) + */ + __pyx_v_found = __pyx_v_self->intervalFile_ptr->FindAnyOverlapsPerBin((*__pyx_v_interval->_bed), __pyx_v_overlap); + + /* "pybedtools/cbedtools.pyx":963 + * self.loadIntoMap() + * + * if same_strand == False: # <<<<<<<<<<<<<< + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), overlap) + * else: + */ + goto __pyx_L3; + } + + /* "pybedtools/cbedtools.pyx":966 + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), overlap) + * else: + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), same_strand, overlap) # <<<<<<<<<<<<<< + * + * return found + */ + /*else*/ { + __pyx_v_found = __pyx_v_self->intervalFile_ptr->FindAnyOverlapsPerBin((*__pyx_v_interval->_bed), __pyx_v_same_strand, __pyx_v_overlap); + } + __pyx_L3:; + + /* "pybedtools/cbedtools.pyx":968 + * found = self.intervalFile_ptr.FindAnyOverlapsPerBin(deref(interval._bed), same_strand, overlap) + * + * return found # <<<<<<<<<<<<<< + * + * def count_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_found); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 968, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":934 + * search = all_hits + * + * def any_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): # <<<<<<<<<<<<<< + * """ + * :Signature: `IntervalFile.any_hits(interval, same_strand=False, overlap=0.0)` + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.any_hits", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "pybedtools/cbedtools.pyx":970 + * return found + * + * def count_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): # <<<<<<<<<<<<<< + * """ + * :Signature: `IntervalFile.count_hits(interval, same_strand=False, overlap=0.0)` + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_19count_hits(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_18count_hits[] = "\n :Signature: `IntervalFile.count_hits(interval, same_strand=False, overlap=0.0)`\n\n Return the number of overlaps of the Interval `interval` had with this\n IntervalFile.\n\n `same_strand`, if True, will only consider hits on the same strand as\n `interval`.\n\n `overlap` can be used to specify the fraction of overlap between\n `interval` and each feature in the IntervalFile.\n\n Example usage:\n\n >>> fn = pybedtools.example_filename('a.bed')\n\n >>> # create an Interval to query with\n >>> i = pybedtools.Interval('chr1', 1, 10000, strand='+')\n\n >>> # Create an IntervalFile out of a.bed\n >>> intervalfile = pybedtools.IntervalFile(fn)\n\n >>> # get number of stranded hits\n >>> intervalfile.count_hits(i, same_strand=True)\n 3\n\n "; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_19count_hits(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval = 0; + PyBoolObject *__pyx_v_same_strand = 0; + float __pyx_v_overlap; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("count_hits (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_interval,&__pyx_n_s_same_strand,&__pyx_n_s_overlap,0}; + PyObject* values[3] = {0,0,0}; + values[1] = (PyObject *)((PyBoolObject *)Py_False); + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_interval)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_same_strand); + if (value) { values[1] = value; kw_args--; } + } + CYTHON_FALLTHROUGH; + case 2: + if (kw_args > 0) { + PyObject* value = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_overlap); + if (value) { values[2] = value; kw_args--; } + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "count_hits") < 0)) __PYX_ERR(0, 970, __pyx_L3_error) + } + } else { + switch (PyTuple_GET_SIZE(__pyx_args)) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_interval = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)values[0]); + __pyx_v_same_strand = ((PyBoolObject *)values[1]); + if (values[2]) { + __pyx_v_overlap = __pyx_PyFloat_AsFloat(values[2]); if (unlikely((__pyx_v_overlap == (float)-1) && PyErr_Occurred())) __PYX_ERR(0, 970, __pyx_L3_error) + } else { + __pyx_v_overlap = ((float)0.0); + } + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("count_hits", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 970, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.count_hits", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_interval), __pyx_ptype_10pybedtools_9cbedtools_Interval, 1, "interval", 0))) __PYX_ERR(0, 970, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_same_strand), __pyx_ptype_7cpython_4bool_bool, 1, "same_strand", 0))) __PYX_ERR(0, 970, __pyx_L1_error) + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_18count_hits(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self), __pyx_v_interval, __pyx_v_same_strand, __pyx_v_overlap); + + /* function exit code */ + goto __pyx_L0; + __pyx_L1_error:; + __pyx_r = NULL; + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_18count_hits(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, struct __pyx_obj_10pybedtools_9cbedtools_Interval *__pyx_v_interval, PyBoolObject *__pyx_v_same_strand, float __pyx_v_overlap) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("count_hits", 0); + + /* "pybedtools/cbedtools.pyx":998 + * + * """ + * self.loadIntoMap() # <<<<<<<<<<<<<< + * + * if same_strand == False: + */ + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_loadIntoMap); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 998, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); + if (likely(__pyx_t_3)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); + __Pyx_INCREF(__pyx_t_3); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_2, function); + } + } + __pyx_t_1 = (__pyx_t_3) ? __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3) : __Pyx_PyObject_CallNoArg(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 998, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":1000 + * self.loadIntoMap() + * + * if same_strand == False: # <<<<<<<<<<<<<< + * return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), overlap) + * else: + */ + __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_v_same_strand), Py_False, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1000, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) __PYX_ERR(0, 1000, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_4) { + + /* "pybedtools/cbedtools.pyx":1001 + * + * if same_strand == False: + * return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), overlap) # <<<<<<<<<<<<<< + * else: + * return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), same_strand, overlap) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->intervalFile_ptr->CountOverlapsPerBin((*__pyx_v_interval->_bed), __pyx_v_overlap)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1001, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "pybedtools/cbedtools.pyx":1000 + * self.loadIntoMap() + * + * if same_strand == False: # <<<<<<<<<<<<<< + * return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), overlap) + * else: + */ + } + + /* "pybedtools/cbedtools.pyx":1003 + * return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), overlap) + * else: + * return self.intervalFile_ptr.CountOverlapsPerBin(deref(interval._bed), same_strand, overlap) # <<<<<<<<<<<<<< + */ + /*else*/ { + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->intervalFile_ptr->CountOverlapsPerBin((*__pyx_v_interval->_bed), __pyx_v_same_strand, __pyx_v_overlap)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1003, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + } + + /* "pybedtools/cbedtools.pyx":970 + * return found + * + * def count_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): # <<<<<<<<<<<<<< + * """ + * :Signature: `IntervalFile.count_hits(interval, same_strand=False, overlap=0.0)` + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.count_hits", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_21__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_21__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__reduce_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_20__reduce_cython__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_20__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__reduce_cython__", 0); + + /* "(tree fragment)":2 + * def __reduce_cython__(self): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__28, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(1, 2, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __reduce_cython__(self): # <<<<<<<<<<<<<< + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.__reduce_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_23__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state); /*proto*/ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_23__setstate_cython__(PyObject *__pyx_v_self, PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setstate_cython__ (wrapper)", 0); + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_22__setstate_cython__(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)__pyx_v_self), ((PyObject *)__pyx_v___pyx_state)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_12IntervalFile_22__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__setstate_cython__", 0); + + /* "(tree fragment)":4 + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + */ + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_TypeError, __pyx_tuple__29, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __PYX_ERR(1, 4, __pyx_L1_error) + + /* "(tree fragment)":3 + * def __reduce_cython__(self): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): # <<<<<<<<<<<<<< + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("pybedtools.cbedtools.IntervalFile.__setstate_cython__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":1 + * def __pyx_unpickle_IntervalIterator(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * cdef object __pyx_PickleError + * cdef object __pyx_result + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10pybedtools_9cbedtools_5__pyx_unpickle_IntervalIterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_10pybedtools_9cbedtools_5__pyx_unpickle_IntervalIterator = {"__pyx_unpickle_IntervalIterator", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_5__pyx_unpickle_IntervalIterator, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_10pybedtools_9cbedtools_5__pyx_unpickle_IntervalIterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v___pyx_type = 0; + long __pyx_v___pyx_checksum; + PyObject *__pyx_v___pyx_state = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__pyx_unpickle_IntervalIterator (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_pyx_type,&__pyx_n_s_pyx_checksum,&__pyx_n_s_pyx_state,0}; + PyObject* values[3] = {0,0,0}; + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_pyx_type)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_pyx_checksum)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_IntervalIterator", 1, 3, 3, 1); __PYX_ERR(1, 1, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_pyx_state)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_IntervalIterator", 1, 3, 3, 2); __PYX_ERR(1, 1, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__pyx_unpickle_IntervalIterator") < 0)) __PYX_ERR(1, 1, __pyx_L3_error) + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + } + __pyx_v___pyx_type = values[0]; + __pyx_v___pyx_checksum = __Pyx_PyInt_As_long(values[1]); if (unlikely((__pyx_v___pyx_checksum == (long)-1) && PyErr_Occurred())) __PYX_ERR(1, 1, __pyx_L3_error) + __pyx_v___pyx_state = values[2]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_IntervalIterator", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(1, 1, __pyx_L3_error) + __pyx_L3_error:; + __Pyx_AddTraceback("pybedtools.cbedtools.__pyx_unpickle_IntervalIterator", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10pybedtools_9cbedtools_4__pyx_unpickle_IntervalIterator(__pyx_self, __pyx_v___pyx_type, __pyx_v___pyx_checksum, __pyx_v___pyx_state); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10pybedtools_9cbedtools_4__pyx_unpickle_IntervalIterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v___pyx_type, long __pyx_v___pyx_checksum, PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_v___pyx_PickleError = 0; + PyObject *__pyx_v___pyx_result = 0; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_unpickle_IntervalIterator", 0); + + /* "(tree fragment)":4 + * cdef object __pyx_PickleError + * cdef object __pyx_result + * if __pyx_checksum not in (0x15da9d6, 0xa415738, 0x19b863f): # <<<<<<<<<<<<<< + * from pickle import PickleError as __pyx_PickleError + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) + */ + __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = (__Pyx_PySequence_ContainsTF(__pyx_t_1, __pyx_tuple__30, Py_NE)); if (unlikely(__pyx_t_2 < 0)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = (__pyx_t_2 != 0); + if (__pyx_t_3) { + + /* "(tree fragment)":5 + * cdef object __pyx_result + * if __pyx_checksum not in (0x15da9d6, 0xa415738, 0x19b863f): + * from pickle import PickleError as __pyx_PickleError # <<<<<<<<<<<<<< + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) + * __pyx_result = IntervalIterator.__new__(__pyx_type) + */ + __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(__pyx_n_s_PickleError); + __Pyx_GIVEREF(__pyx_n_s_PickleError); + PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_PickleError); + __pyx_t_4 = __Pyx_Import(__pyx_n_s_pickle, __pyx_t_1, -1); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 5, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_4, __pyx_n_s_PickleError); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 5, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(__pyx_t_1); + __pyx_v___pyx_PickleError = __pyx_t_1; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "(tree fragment)":6 + * if __pyx_checksum not in (0x15da9d6, 0xa415738, 0x19b863f): + * from pickle import PickleError as __pyx_PickleError + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) # <<<<<<<<<<<<<< + * __pyx_result = IntervalIterator.__new__(__pyx_type) + * if __pyx_state is not None: + */ + __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v___pyx_checksum); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 6, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_INCREF(__pyx_v___pyx_PickleError); + __pyx_t_1 = __pyx_v___pyx_PickleError; __pyx_t_6 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_6)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_6); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_4 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_6, __pyx_t_5) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 6, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __PYX_ERR(1, 6, __pyx_L1_error) + + /* "(tree fragment)":4 + * cdef object __pyx_PickleError + * cdef object __pyx_result + * if __pyx_checksum not in (0x15da9d6, 0xa415738, 0x19b863f): # <<<<<<<<<<<<<< + * from pickle import PickleError as __pyx_PickleError + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) + */ + } + + /* "(tree fragment)":7 + * from pickle import PickleError as __pyx_PickleError + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) + * __pyx_result = IntervalIterator.__new__(__pyx_type) # <<<<<<<<<<<<<< + * if __pyx_state is not None: + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) + */ + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_ptype_10pybedtools_9cbedtools_IntervalIterator), __pyx_n_s_new); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 7, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_1))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_1, function); + } + } + __pyx_t_4 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_1, __pyx_t_5, __pyx_v___pyx_type) : __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_v___pyx_type); + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 7, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v___pyx_result = __pyx_t_4; + __pyx_t_4 = 0; + + /* "(tree fragment)":8 + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) + * __pyx_result = IntervalIterator.__new__(__pyx_type) + * if __pyx_state is not None: # <<<<<<<<<<<<<< + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) + * return __pyx_result + */ + __pyx_t_3 = (__pyx_v___pyx_state != Py_None); + __pyx_t_2 = (__pyx_t_3 != 0); + if (__pyx_t_2) { + + /* "(tree fragment)":9 + * __pyx_result = IntervalIterator.__new__(__pyx_type) + * if __pyx_state is not None: + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) # <<<<<<<<<<<<<< + * return __pyx_result + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): + */ + if (!(likely(PyTuple_CheckExact(__pyx_v___pyx_state))||((__pyx_v___pyx_state) == Py_None)||((void)PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_v___pyx_state)->tp_name), 0))) __PYX_ERR(1, 9, __pyx_L1_error) + __pyx_t_4 = __pyx_f_10pybedtools_9cbedtools___pyx_unpickle_IntervalIterator__set_state(((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)__pyx_v___pyx_result), ((PyObject*)__pyx_v___pyx_state)); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 9, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "(tree fragment)":8 + * raise __pyx_PickleError("Incompatible checksums (0x%x vs (0x15da9d6, 0xa415738, 0x19b863f) = (_itemtype, stream))" % __pyx_checksum) + * __pyx_result = IntervalIterator.__new__(__pyx_type) + * if __pyx_state is not None: # <<<<<<<<<<<<<< + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) + * return __pyx_result + */ + } + + /* "(tree fragment)":10 + * if __pyx_state is not None: + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) + * return __pyx_result # <<<<<<<<<<<<<< + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] + */ + __Pyx_XDECREF(__pyx_r); + __Pyx_INCREF(__pyx_v___pyx_result); + __pyx_r = __pyx_v___pyx_result; + goto __pyx_L0; + + /* "(tree fragment)":1 + * def __pyx_unpickle_IntervalIterator(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * cdef object __pyx_PickleError + * cdef object __pyx_result + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_AddTraceback("pybedtools.cbedtools.__pyx_unpickle_IntervalIterator", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v___pyx_PickleError); + __Pyx_XDECREF(__pyx_v___pyx_result); + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "(tree fragment)":11 + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) + * return __pyx_result + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] + * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): + */ + +static PyObject *__pyx_f_10pybedtools_9cbedtools___pyx_unpickle_IntervalIterator__set_state(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *__pyx_v___pyx_result, PyObject *__pyx_v___pyx_state) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_unpickle_IntervalIterator__set_state", 0); + + /* "(tree fragment)":12 + * return __pyx_result + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] # <<<<<<<<<<<<<< + * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): + * __pyx_result.__dict__.update(__pyx_state[2]) + */ + if (unlikely(__pyx_v___pyx_state == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(1, 12, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 12, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_v___pyx_result->_itemtype = __pyx_t_2; + if (unlikely(__pyx_v___pyx_state == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(1, 12, __pyx_L1_error) + } + __pyx_t_1 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 12, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_GIVEREF(__pyx_t_1); + __Pyx_GOTREF(__pyx_v___pyx_result->stream); + __Pyx_DECREF(__pyx_v___pyx_result->stream); + __pyx_v___pyx_result->stream = __pyx_t_1; + __pyx_t_1 = 0; + + /* "(tree fragment)":13 + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] + * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< + * __pyx_result.__dict__.update(__pyx_state[2]) + */ + if (unlikely(__pyx_v___pyx_state == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + __PYX_ERR(1, 13, __pyx_L1_error) + } + __pyx_t_4 = PyTuple_GET_SIZE(__pyx_v___pyx_state); if (unlikely(__pyx_t_4 == ((Py_ssize_t)-1))) __PYX_ERR(1, 13, __pyx_L1_error) + __pyx_t_5 = ((__pyx_t_4 > 2) != 0); + if (__pyx_t_5) { + } else { + __pyx_t_3 = __pyx_t_5; + goto __pyx_L4_bool_binop_done; + } + __pyx_t_5 = __Pyx_HasAttr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(__pyx_t_5 == ((int)-1))) __PYX_ERR(1, 13, __pyx_L1_error) + __pyx_t_6 = (__pyx_t_5 != 0); + __pyx_t_3 = __pyx_t_6; + __pyx_L4_bool_binop_done:; + if (__pyx_t_3) { + + /* "(tree fragment)":14 + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] + * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): + * __pyx_result.__dict__.update(__pyx_state[2]) # <<<<<<<<<<<<<< + */ + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v___pyx_result), __pyx_n_s_dict); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 14, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_update); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 14, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(__pyx_v___pyx_state == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + __PYX_ERR(1, 14, __pyx_L1_error) + } + __pyx_t_7 = __Pyx_GetItemInt_Tuple(__pyx_v___pyx_state, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(!__pyx_t_7)) __PYX_ERR(1, 14, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_9 = NULL; + if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_8))) { + __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_8); + if (likely(__pyx_t_9)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8); + __Pyx_INCREF(__pyx_t_9); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_8, function); + } + } + __pyx_t_1 = (__pyx_t_9) ? __Pyx_PyObject_Call2Args(__pyx_t_8, __pyx_t_9, __pyx_t_7) : __Pyx_PyObject_CallOneArg(__pyx_t_8, __pyx_t_7); + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 14, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "(tree fragment)":13 + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] + * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): # <<<<<<<<<<<<<< + * __pyx_result.__dict__.update(__pyx_state[2]) + */ + } + + /* "(tree fragment)":11 + * __pyx_unpickle_IntervalIterator__set_state(<IntervalIterator> __pyx_result, __pyx_state) + * return __pyx_result + * cdef __pyx_unpickle_IntervalIterator__set_state(IntervalIterator __pyx_result, tuple __pyx_state): # <<<<<<<<<<<<<< + * __pyx_result._itemtype = __pyx_state[0]; __pyx_result.stream = __pyx_state[1] + * if len(__pyx_state) > 2 and hasattr(__pyx_result, '__dict__'): + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_AddTraceback("pybedtools.cbedtools.__pyx_unpickle_IntervalIterator__set_state", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "string.from_py":13 + * + * @cname("__pyx_convert_string_from_py_std__in_string") + * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *: # <<<<<<<<<<<<<< + * cdef Py_ssize_t length = 0 + * cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length) + */ + +static std::string __pyx_convert_string_from_py_std__in_string(PyObject *__pyx_v_o) { + Py_ssize_t __pyx_v_length; + char const *__pyx_v_data; + std::string __pyx_r; + __Pyx_RefNannyDeclarations + char const *__pyx_t_1; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_string_from_py_std__in_string", 0); + + /* "string.from_py":14 + * @cname("__pyx_convert_string_from_py_std__in_string") + * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *: + * cdef Py_ssize_t length = 0 # <<<<<<<<<<<<<< + * cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length) + * return string(data, length) + */ + __pyx_v_length = 0; + + /* "string.from_py":15 + * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *: + * cdef Py_ssize_t length = 0 + * cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length) # <<<<<<<<<<<<<< + * return string(data, length) + * + */ + __pyx_t_1 = __Pyx_PyObject_AsStringAndSize(__pyx_v_o, (&__pyx_v_length)); if (unlikely(__pyx_t_1 == ((char const *)NULL))) __PYX_ERR(1, 15, __pyx_L1_error) + __pyx_v_data = __pyx_t_1; + + /* "string.from_py":16 + * cdef Py_ssize_t length = 0 + * cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length) + * return string(data, length) # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = std::string(__pyx_v_data, __pyx_v_length); + goto __pyx_L0; + + /* "string.from_py":13 + * + * @cname("__pyx_convert_string_from_py_std__in_string") + * cdef string __pyx_convert_string_from_py_std__in_string(object o) except *: # <<<<<<<<<<<<<< + * cdef Py_ssize_t length = 0 + * cdef const char* data = __Pyx_PyObject_AsStringAndSize(o, &length) + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_AddTraceback("string.from_py.__pyx_convert_string_from_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_pretend_to_initialize(&__pyx_r); + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "string.to_py":31 + * + * @cname("__pyx_convert_PyObject_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyObject_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyObject_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + +static CYTHON_INLINE PyObject *__pyx_convert_PyObject_string_to_py_std__in_string(std::string const &__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_PyObject_string_to_py_std__in_string", 0); + + /* "string.to_py":32 + * @cname("__pyx_convert_PyObject_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyObject_string_to_py_std__in_string(const string& s): + * return __Pyx_PyObject_FromStringAndSize(s.data(), s.size()) # <<<<<<<<<<<<<< + * cdef extern from *: + * cdef object __Pyx_PyUnicode_FromStringAndSize(const char*, size_t) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyObject_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 32, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "string.to_py":31 + * + * @cname("__pyx_convert_PyObject_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyObject_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyObject_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("string.to_py.__pyx_convert_PyObject_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "string.to_py":37 + * + * @cname("__pyx_convert_PyUnicode_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyUnicode_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyUnicode_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + +static CYTHON_INLINE PyObject *__pyx_convert_PyUnicode_string_to_py_std__in_string(std::string const &__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_PyUnicode_string_to_py_std__in_string", 0); + + /* "string.to_py":38 + * @cname("__pyx_convert_PyUnicode_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyUnicode_string_to_py_std__in_string(const string& s): + * return __Pyx_PyUnicode_FromStringAndSize(s.data(), s.size()) # <<<<<<<<<<<<<< + * cdef extern from *: + * cdef object __Pyx_PyStr_FromStringAndSize(const char*, size_t) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyUnicode_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 38, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "string.to_py":37 + * + * @cname("__pyx_convert_PyUnicode_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyUnicode_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyUnicode_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("string.to_py.__pyx_convert_PyUnicode_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "string.to_py":43 + * + * @cname("__pyx_convert_PyStr_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyStr_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyStr_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + +static CYTHON_INLINE PyObject *__pyx_convert_PyStr_string_to_py_std__in_string(std::string const &__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_PyStr_string_to_py_std__in_string", 0); + + /* "string.to_py":44 + * @cname("__pyx_convert_PyStr_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyStr_string_to_py_std__in_string(const string& s): + * return __Pyx_PyStr_FromStringAndSize(s.data(), s.size()) # <<<<<<<<<<<<<< + * cdef extern from *: + * cdef object __Pyx_PyBytes_FromStringAndSize(const char*, size_t) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyStr_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 44, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "string.to_py":43 + * + * @cname("__pyx_convert_PyStr_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyStr_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyStr_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("string.to_py.__pyx_convert_PyStr_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "string.to_py":49 + * + * @cname("__pyx_convert_PyBytes_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyBytes_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyBytes_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + +static CYTHON_INLINE PyObject *__pyx_convert_PyBytes_string_to_py_std__in_string(std::string const &__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_PyBytes_string_to_py_std__in_string", 0); + + /* "string.to_py":50 + * @cname("__pyx_convert_PyBytes_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyBytes_string_to_py_std__in_string(const string& s): + * return __Pyx_PyBytes_FromStringAndSize(s.data(), s.size()) # <<<<<<<<<<<<<< + * cdef extern from *: + * cdef object __Pyx_PyByteArray_FromStringAndSize(const char*, size_t) + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyBytes_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 50, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "string.to_py":49 + * + * @cname("__pyx_convert_PyBytes_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyBytes_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyBytes_FromStringAndSize(s.data(), s.size()) + * cdef extern from *: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("string.to_py.__pyx_convert_PyBytes_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "string.to_py":55 + * + * @cname("__pyx_convert_PyByteArray_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyByteArray_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyByteArray_FromStringAndSize(s.data(), s.size()) + * + */ + +static CYTHON_INLINE PyObject *__pyx_convert_PyByteArray_string_to_py_std__in_string(std::string const &__pyx_v_s) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_PyByteArray_string_to_py_std__in_string", 0); + + /* "string.to_py":56 + * @cname("__pyx_convert_PyByteArray_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyByteArray_string_to_py_std__in_string(const string& s): + * return __Pyx_PyByteArray_FromStringAndSize(s.data(), s.size()) # <<<<<<<<<<<<<< + * + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyByteArray_FromStringAndSize(__pyx_v_s.data(), __pyx_v_s.size()); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 56, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "string.to_py":55 + * + * @cname("__pyx_convert_PyByteArray_string_to_py_std__in_string") + * cdef inline object __pyx_convert_PyByteArray_string_to_py_std__in_string(const string& s): # <<<<<<<<<<<<<< + * return __Pyx_PyByteArray_FromStringAndSize(s.data(), s.size()) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("string.to_py.__pyx_convert_PyByteArray_string_to_py_std__in_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "vector.from_py":45 + * + * @cname("__pyx_convert_vector_from_py_std_3a__3a_string") + * cdef vector[X] __pyx_convert_vector_from_py_std_3a__3a_string(object o) except *: # <<<<<<<<<<<<<< + * cdef vector[X] v + * for item in o: + */ + +static std::vector<std::string> __pyx_convert_vector_from_py_std_3a__3a_string(PyObject *__pyx_v_o) { + std::vector<std::string> __pyx_v_v; + PyObject *__pyx_v_item = NULL; + std::vector<std::string> __pyx_r; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + Py_ssize_t __pyx_t_2; + PyObject *(*__pyx_t_3)(PyObject *); + PyObject *__pyx_t_4 = NULL; + std::string __pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__pyx_convert_vector_from_py_std_3a__3a_string", 0); + + /* "vector.from_py":47 + * cdef vector[X] __pyx_convert_vector_from_py_std_3a__3a_string(object o) except *: + * cdef vector[X] v + * for item in o: # <<<<<<<<<<<<<< + * v.push_back(<X>item) + * return v + */ + if (likely(PyList_CheckExact(__pyx_v_o)) || PyTuple_CheckExact(__pyx_v_o)) { + __pyx_t_1 = __pyx_v_o; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; + __pyx_t_3 = NULL; + } else { + __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_o); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 47, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext; if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 47, __pyx_L1_error) + } + for (;;) { + if (likely(!__pyx_t_3)) { + if (likely(PyList_CheckExact(__pyx_t_1))) { + if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 47, __pyx_L1_error) + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 47, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + #endif + } else { + if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) __PYX_ERR(1, 47, __pyx_L1_error) + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 47, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + #endif + } + } else { + __pyx_t_4 = __pyx_t_3(__pyx_t_1); + if (unlikely(!__pyx_t_4)) { + PyObject* exc_type = PyErr_Occurred(); + if (exc_type) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); + else __PYX_ERR(1, 47, __pyx_L1_error) + } + break; + } + __Pyx_GOTREF(__pyx_t_4); + } + __Pyx_XDECREF_SET(__pyx_v_item, __pyx_t_4); + __pyx_t_4 = 0; + + /* "vector.from_py":48 + * cdef vector[X] v + * for item in o: + * v.push_back(<X>item) # <<<<<<<<<<<<<< + * return v + * + */ + __pyx_t_5 = __pyx_convert_string_from_py_std__in_string(__pyx_v_item); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 48, __pyx_L1_error) + __pyx_v_v.push_back(((std::string)__pyx_t_5)); + + /* "vector.from_py":47 + * cdef vector[X] __pyx_convert_vector_from_py_std_3a__3a_string(object o) except *: + * cdef vector[X] v + * for item in o: # <<<<<<<<<<<<<< + * v.push_back(<X>item) + * return v + */ + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "vector.from_py":49 + * for item in o: + * v.push_back(<X>item) + * return v # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_v; + goto __pyx_L0; + + /* "vector.from_py":45 + * + * @cname("__pyx_convert_vector_from_py_std_3a__3a_string") + * cdef vector[X] __pyx_convert_vector_from_py_std_3a__3a_string(object o) except *: # <<<<<<<<<<<<<< + * cdef vector[X] v + * for item in o: + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_AddTraceback("vector.from_py.__pyx_convert_vector_from_py_std_3a__3a_string", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_pretend_to_initialize(&__pyx_r); + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_item); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} +static struct __pyx_vtabstruct_10pybedtools_9cbedtools_Interval __pyx_vtable_10pybedtools_9cbedtools_Interval; + +static PyObject *__pyx_tp_new_10pybedtools_9cbedtools_Interval(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_10pybedtools_9cbedtools_Interval *)o); + p->__pyx_vtab = __pyx_vtabptr_10pybedtools_9cbedtools_Interval; + p->_attrs = Py_None; Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_10pybedtools_9cbedtools_Interval(PyObject *o) { + struct __pyx_obj_10pybedtools_9cbedtools_Interval *p = (struct __pyx_obj_10pybedtools_9cbedtools_Interval *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !__Pyx_PyObject_GC_IsFinalized(o)) { + 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_10pybedtools_9cbedtools_8Interval_15__dealloc__(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->_attrs); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_10pybedtools_9cbedtools_Interval(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_10pybedtools_9cbedtools_Interval *p = (struct __pyx_obj_10pybedtools_9cbedtools_Interval *)o; + if (p->_attrs) { + e = (*v)(p->_attrs, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_10pybedtools_9cbedtools_Interval(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_10pybedtools_9cbedtools_Interval *p = (struct __pyx_obj_10pybedtools_9cbedtools_Interval *)o; + tmp = ((PyObject*)p->_attrs); + p->_attrs = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} +static PyObject *__pyx_sq_item_10pybedtools_9cbedtools_Interval(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_10pybedtools_9cbedtools_Interval(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_21__setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_chrom(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5chrom_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_chrom(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5chrom_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_start(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5start_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5start_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_end(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_3end_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_end(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_3end_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_stop(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_4stop_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_stop(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_4stop_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_strand(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_6strand_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_strand(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_6strand_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_length(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_6length_1__get__(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_fields(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_6fields_1__get__(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_attrs(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5attrs_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_attrs(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5attrs_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_count(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5count_1__get__(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_name(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_4name_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_name(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_4name_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_score(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5score_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_score(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5score_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_file_type(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_9file_type_1__get__(o); +} + +static int __pyx_setprop_10pybedtools_9cbedtools_8Interval_file_type(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { + if (v) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_9file_type_3__set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_o_start(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_7o_start_1__get__(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_o_end(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5o_end_1__get__(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_8Interval_o_amt(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_8Interval_5o_amt_1__get__(o); +} + +static PyMethodDef __pyx_methods_10pybedtools_9cbedtools_Interval[] = { + {"__copy__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_8Interval_3__copy__, METH_NOARGS, 0}, + {"deparse_attrs", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_8Interval_9deparse_attrs, METH_NOARGS, 0}, + {"append", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_8Interval_23append, METH_O, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_8Interval_27__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_8Interval_29__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_10pybedtools_9cbedtools_Interval[] = { + {(char *)"chrom", __pyx_getprop_10pybedtools_9cbedtools_8Interval_chrom, __pyx_setprop_10pybedtools_9cbedtools_8Interval_chrom, (char *)" the chromosome of the feature", 0}, + {(char *)"start", __pyx_getprop_10pybedtools_9cbedtools_8Interval_start, __pyx_setprop_10pybedtools_9cbedtools_8Interval_start, (char *)"The 0-based start of the feature.", 0}, + {(char *)"end", __pyx_getprop_10pybedtools_9cbedtools_8Interval_end, __pyx_setprop_10pybedtools_9cbedtools_8Interval_end, (char *)"The end of the feature", 0}, + {(char *)"stop", __pyx_getprop_10pybedtools_9cbedtools_8Interval_stop, __pyx_setprop_10pybedtools_9cbedtools_8Interval_stop, (char *)" the end of the feature", 0}, + {(char *)"strand", __pyx_getprop_10pybedtools_9cbedtools_8Interval_strand, __pyx_setprop_10pybedtools_9cbedtools_8Interval_strand, (char *)" the strand of the feature", 0}, + {(char *)"length", __pyx_getprop_10pybedtools_9cbedtools_8Interval_length, 0, (char *)" the length of the feature", 0}, + {(char *)"fields", __pyx_getprop_10pybedtools_9cbedtools_8Interval_fields, 0, (char *)0, 0}, + {(char *)"attrs", __pyx_getprop_10pybedtools_9cbedtools_8Interval_attrs, __pyx_setprop_10pybedtools_9cbedtools_8Interval_attrs, (char *)0, 0}, + {(char *)"count", __pyx_getprop_10pybedtools_9cbedtools_8Interval_count, 0, (char *)0, 0}, + {(char *)"name", __pyx_getprop_10pybedtools_9cbedtools_8Interval_name, __pyx_setprop_10pybedtools_9cbedtools_8Interval_name, (char *)"\n >>> import pybedtools\n >>> vcf = pybedtools.example_bedtool('v.vcf')\n >>> [v.name for v in vcf]\n ['rs6054257', 'chr1:16', 'rs6040355', 'chr1:222', 'microsat1']\n\n ", 0}, + {(char *)"score", __pyx_getprop_10pybedtools_9cbedtools_8Interval_score, __pyx_setprop_10pybedtools_9cbedtools_8Interval_score, (char *)0, 0}, + {(char *)"file_type", __pyx_getprop_10pybedtools_9cbedtools_8Interval_file_type, __pyx_setprop_10pybedtools_9cbedtools_8Interval_file_type, (char *)"bed/vcf/gff", 0}, + {(char *)"o_start", __pyx_getprop_10pybedtools_9cbedtools_8Interval_o_start, 0, (char *)0, 0}, + {(char *)"o_end", __pyx_getprop_10pybedtools_9cbedtools_8Interval_o_end, 0, (char *)0, 0}, + {(char *)"o_amt", __pyx_getprop_10pybedtools_9cbedtools_8Interval_o_amt, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_Interval = { + 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_10pybedtools_9cbedtools_8Interval_25__nonzero__, /*nb_nonzero*/ + 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_Interval = { + __pyx_pw_10pybedtools_9cbedtools_8Interval_17__len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_10pybedtools_9cbedtools_Interval, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_Interval = { + __pyx_pw_10pybedtools_9cbedtools_8Interval_17__len__, /*mp_length*/ + __pyx_pw_10pybedtools_9cbedtools_8Interval_19__getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_10pybedtools_9cbedtools_Interval, /*mp_ass_subscript*/ +}; + +static PyTypeObject __pyx_type_10pybedtools_9cbedtools_Interval = { + PyVarObject_HEAD_INIT(0, 0) + "pybedtools.cbedtools.Interval", /*tp_name*/ + sizeof(struct __pyx_obj_10pybedtools_9cbedtools_Interval), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10pybedtools_9cbedtools_Interval, /*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 + __pyx_pw_10pybedtools_9cbedtools_8Interval_13__repr__, /*tp_repr*/ + &__pyx_tp_as_number_Interval, /*tp_as_number*/ + &__pyx_tp_as_sequence_Interval, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_Interval, /*tp_as_mapping*/ + __pyx_pw_10pybedtools_9cbedtools_8Interval_5__hash__, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_pw_10pybedtools_9cbedtools_8Interval_11__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|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + "\n Class to represent a genomic interval.\n\n Constructor::\n\n Interval(chrom, start, end, name=\".\", score=\".\", strand=\".\", otherfields=None)\n\n Class to represent a genomic interval of any format. Requires at least 3\n args: chrom (string), start (int), end (int).\n\n `start` is *always* the 0-based start coordinate. If this Interval is to\n represent a GFF object (which uses a 1-based coordinate system), then\n subtract 1 from the 4th item in the line to get the start position in\n 0-based coords for this Interval. The 1-based GFF coord will still be\n available, albeit as a string, in fields[3].\n\n `otherfields` is a list of fields that don't fit into the other kwargs, and\n will be stored in the `fields` attribute of the Interval.\n\n All the items in `otherfields` must be strings for proper conversion to\n C++.\n\n By convention, for BED files, `otherfields` is everything past the first 6\n items in the line. This allows an Interval to represent composite features\n (e.g., a GFF line concatenated to the end of a BED line)\n\n But for other formats (VCF, GFF, SAM), the entire line should be passed in\n as a list for `otherfields` so that we can always check the\n Interval.file_type and extract the fields we want, knowing that they'll be\n in the right order as passed in with `otherfields`.\n\n Example usage:\n\n >>> from pybedtools import Interval\n >>> i = Interval(\"chr1\", 22, 44, strand='-')\n >>> i\n Interval(chr1:22-44)\n\n\n ", /*tp_doc*/ + __pyx_tp_traverse_10pybedtools_9cbedtools_Interval, /*tp_traverse*/ + __pyx_tp_clear_10pybedtools_9cbedtools_Interval, /*tp_clear*/ + __pyx_pw_10pybedtools_9cbedtools_8Interval_7__richcmp__, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_10pybedtools_9cbedtools_Interval, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_10pybedtools_9cbedtools_Interval, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10pybedtools_9cbedtools_8Interval_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10pybedtools_9cbedtools_Interval, /*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 + 0, /*tp_finalize*/ + #endif + #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) + 0, /*tp_vectorcall*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif + #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, /*tp_pypy_flags*/ + #endif +}; + +static PyObject *__pyx_tp_new_10pybedtools_9cbedtools_IntervalIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)o); + p->stream = Py_None; Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalIterator(PyObject *o) { + struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *p = (struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !__Pyx_PyObject_GC_IsFinalized(o)) { + 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_10pybedtools_9cbedtools_16IntervalIterator_3__dealloc__(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->stream); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_10pybedtools_9cbedtools_IntervalIterator(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *p = (struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)o; + if (p->stream) { + e = (*v)(p->stream, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_10pybedtools_9cbedtools_IntervalIterator(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *p = (struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator *)o; + tmp = ((PyObject*)p->stream); + p->stream = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyObject *__pyx_specialmethod___pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {return __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_7__next__(self);} + +static PyMethodDef __pyx_methods_10pybedtools_9cbedtools_IntervalIterator[] = { + {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_7__next__, METH_NOARGS|METH_COEXIST, 0}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_9__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_11__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_10pybedtools_9cbedtools_IntervalIterator = { + PyVarObject_HEAD_INIT(0, 0) + "pybedtools.cbedtools.IntervalIterator", /*tp_name*/ + sizeof(struct __pyx_obj_10pybedtools_9cbedtools_IntervalIterator), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalIterator, /*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*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_10pybedtools_9cbedtools_IntervalIterator, /*tp_traverse*/ + __pyx_tp_clear_10pybedtools_9cbedtools_IntervalIterator, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_5__iter__, /*tp_iter*/ + __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_7__next__, /*tp_iternext*/ + __pyx_methods_10pybedtools_9cbedtools_IntervalIterator, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10pybedtools_9cbedtools_16IntervalIterator_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10pybedtools_9cbedtools_IntervalIterator, /*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 + 0, /*tp_finalize*/ + #endif + #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) + 0, /*tp_vectorcall*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif + #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, /*tp_pypy_flags*/ + #endif +}; + +static PyObject *__pyx_tp_new_10pybedtools_9cbedtools_IntervalFile(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *p; + PyObject *o; + if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) { + o = (*t->tp_alloc)(t, 0); + } else { + o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0); + } + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)o); + new((void*)&(p->_fn)) std::string(); + return o; +} + +static void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalFile(PyObject *o) { + struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *p = (struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile *)o; + #if CYTHON_USE_TP_FINALIZE + if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !__Pyx_PyObject_GC_IsFinalized(o))) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); + __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_3__dealloc__(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); + PyErr_Restore(etype, eval, etb); + } + __Pyx_call_destructor(p->_fn); + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_12IntervalFile_fn(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_2fn_1__get__(o); +} + +static PyObject *__pyx_getprop_10pybedtools_9cbedtools_12IntervalFile_file_type(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_9file_type_1__get__(o); +} + +static PyObject *__pyx_specialmethod___pyx_pw_10pybedtools_9cbedtools_12IntervalFile_7__next__(PyObject *self, CYTHON_UNUSED PyObject *arg) {return __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_7__next__(self);} + +static PyMethodDef __pyx_methods_10pybedtools_9cbedtools_IntervalFile[] = { + {"__next__", (PyCFunction)__pyx_specialmethod___pyx_pw_10pybedtools_9cbedtools_12IntervalFile_7__next__, METH_NOARGS|METH_COEXIST, 0}, + {"loadIntoMap", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_9loadIntoMap, METH_NOARGS, __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_8loadIntoMap}, + {"rewind", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_11rewind, METH_NOARGS, __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_10rewind}, + {"seek", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_13seek, METH_O, __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_12seek}, + {"all_hits", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_15all_hits, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_14all_hits}, + {"any_hits", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_17any_hits, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_16any_hits}, + {"count_hits", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_19count_hits, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10pybedtools_9cbedtools_12IntervalFile_18count_hits}, + {"__reduce_cython__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_21__reduce_cython__, METH_NOARGS, 0}, + {"__setstate_cython__", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_12IntervalFile_23__setstate_cython__, METH_O, 0}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_10pybedtools_9cbedtools_IntervalFile[] = { + {(char *)"fn", __pyx_getprop_10pybedtools_9cbedtools_12IntervalFile_fn, 0, (char *)0, 0}, + {(char *)"file_type", __pyx_getprop_10pybedtools_9cbedtools_12IntervalFile_file_type, 0, (char *)0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_10pybedtools_9cbedtools_IntervalFile = { + PyVarObject_HEAD_INIT(0, 0) + "pybedtools.cbedtools.IntervalFile", /*tp_name*/ + sizeof(struct __pyx_obj_10pybedtools_9cbedtools_IntervalFile), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalFile, /*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, /*tp_flags*/ + 0, /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_5__iter__, /*tp_iter*/ + __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_7__next__, /*tp_iternext*/ + __pyx_methods_10pybedtools_9cbedtools_IntervalFile, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_10pybedtools_9cbedtools_IntervalFile, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_10pybedtools_9cbedtools_12IntervalFile_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_10pybedtools_9cbedtools_IntervalFile, /*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 + 0, /*tp_finalize*/ + #endif + #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800) + 0, /*tp_vectorcall*/ + #endif + #if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, /*tp_print*/ + #endif + #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, /*tp_pypy_flags*/ + #endif +}; + +static PyMethodDef __pyx_methods[] = { + {"create_interval_from_list", (PyCFunction)__pyx_pw_10pybedtools_9cbedtools_1create_interval_from_list, METH_O, __pyx_doc_10pybedtools_9cbedtools_create_interval_from_list}, + {0, 0, 0, 0} +}; + +#if PY_MAJOR_VERSION >= 3 +#if CYTHON_PEP489_MULTI_PHASE_INIT +static PyObject* __pyx_pymod_create(PyObject *spec, PyModuleDef *def); /*proto*/ +static int __pyx_pymod_exec_cbedtools(PyObject* module); /*proto*/ +static PyModuleDef_Slot __pyx_moduledef_slots[] = { + {Py_mod_create, (void*)__pyx_pymod_create}, + {Py_mod_exec, (void*)__pyx_pymod_exec_cbedtools}, + {0, NULL} +}; +#endif + +static struct PyModuleDef __pyx_moduledef = { + PyModuleDef_HEAD_INIT, + "cbedtools", + 0, /* m_doc */ + #if CYTHON_PEP489_MULTI_PHASE_INIT + 0, /* m_size */ + #else + -1, /* m_size */ + #endif + __pyx_methods /* m_methods */, + #if CYTHON_PEP489_MULTI_PHASE_INIT + __pyx_moduledef_slots, /* m_slots */ + #else + NULL, /* m_reload */ + #endif + NULL, /* m_traverse */ + NULL, /* m_clear */ + NULL /* m_free */ +}; +#endif +#ifndef CYTHON_SMALL_CODE +#if defined(__clang__) + #define CYTHON_SMALL_CODE +#elif defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)) + #define CYTHON_SMALL_CODE __attribute__((cold)) +#else + #define CYTHON_SMALL_CODE +#endif +#endif + +static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_kp_s_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 1, 0}, + {&__pyx_n_s_AttributeError, __pyx_k_AttributeError, sizeof(__pyx_k_AttributeError), 0, 0, 1, 1}, + {&__pyx_n_s_Attributes, __pyx_k_Attributes, sizeof(__pyx_k_Attributes), 0, 0, 1, 1}, + {&__pyx_n_s_Attributes___init, __pyx_k_Attributes___init, sizeof(__pyx_k_Attributes___init), 0, 0, 1, 1}, + {&__pyx_n_s_Attributes___str, __pyx_k_Attributes___str, sizeof(__pyx_k_Attributes___str), 0, 0, 1, 1}, + {&__pyx_n_s_BedToolsFileError, __pyx_k_BedToolsFileError, sizeof(__pyx_k_BedToolsFileError), 0, 0, 1, 1}, + {&__pyx_kp_s_Class_to_map_between_a_dict_of, __pyx_k_Class_to_map_between_a_dict_of, sizeof(__pyx_k_Class_to_map_between_a_dict_of), 0, 0, 1, 0}, + {&__pyx_kp_u_Create_an_Interval_object_from, __pyx_k_Create_an_Interval_object_from, sizeof(__pyx_k_Create_an_Interval_object_from), 0, 1, 0, 0}, + {&__pyx_kp_s_Currently_unsupported_comparison, __pyx_k_Currently_unsupported_comparison, sizeof(__pyx_k_Currently_unsupported_comparison), 0, 0, 1, 0}, + {&__pyx_kp_s_Error_opening_file, __pyx_k_Error_opening_file, sizeof(__pyx_k_Error_opening_file), 0, 0, 1, 0}, + {&__pyx_kp_s_Features_are_nested_comparison_u, __pyx_k_Features_are_nested_comparison_u, sizeof(__pyx_k_Features_are_nested_comparison_u), 0, 0, 1, 0}, + {&__pyx_n_s_ID, __pyx_k_ID, sizeof(__pyx_k_ID), 0, 0, 1, 1}, + {&__pyx_kp_s_Incompatible_checksums_0x_x_vs_0, __pyx_k_Incompatible_checksums_0x_x_vs_0, sizeof(__pyx_k_Incompatible_checksums_0x_x_vs_0), 0, 0, 1, 0}, + {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, + {&__pyx_n_s_Interval, __pyx_k_Interval, sizeof(__pyx_k_Interval), 0, 0, 1, 1}, + {&__pyx_n_s_IntervalFile, __pyx_k_IntervalFile, sizeof(__pyx_k_IntervalFile), 0, 0, 1, 1}, + {&__pyx_kp_u_IntervalFile_all_hits_line_888, __pyx_k_IntervalFile_all_hits_line_888, sizeof(__pyx_k_IntervalFile_all_hits_line_888), 0, 1, 0, 0}, + {&__pyx_kp_u_IntervalFile_any_hits_line_934, __pyx_k_IntervalFile_any_hits_line_934, sizeof(__pyx_k_IntervalFile_any_hits_line_934), 0, 1, 0, 0}, + {&__pyx_kp_u_IntervalFile_count_hits_line_970, __pyx_k_IntervalFile_count_hits_line_970, sizeof(__pyx_k_IntervalFile_count_hits_line_970), 0, 1, 0, 0}, + {&__pyx_kp_s_IntervalFile_objects_do_not_yet, __pyx_k_IntervalFile_objects_do_not_yet, sizeof(__pyx_k_IntervalFile_objects_do_not_yet), 0, 0, 1, 0}, + {&__pyx_n_s_IntervalIterator, __pyx_k_IntervalIterator, sizeof(__pyx_k_IntervalIterator), 0, 0, 1, 1}, + {&__pyx_kp_s_Interval_attrs_was_not_None_but, __pyx_k_Interval_attrs_was_not_None_but, sizeof(__pyx_k_Interval_attrs_was_not_None_but), 0, 0, 1, 0}, + {&__pyx_kp_s_Interval_s_i_i, __pyx_k_Interval_s_i_i, sizeof(__pyx_k_Interval_s_i_i), 0, 0, 1, 0}, + {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1}, + {&__pyx_n_s_MalformedBedLineError, __pyx_k_MalformedBedLineError, sizeof(__pyx_k_MalformedBedLineError), 0, 0, 1, 1}, + {&__pyx_n_s_Name, __pyx_k_Name, sizeof(__pyx_k_Name), 0, 0, 1, 1}, + {&__pyx_n_s_NotImplementedError, __pyx_k_NotImplementedError, sizeof(__pyx_k_NotImplementedError), 0, 0, 1, 1}, + {&__pyx_n_s_PROFILES_TRUE, __pyx_k_PROFILES_TRUE, sizeof(__pyx_k_PROFILES_TRUE), 0, 0, 1, 1}, + {&__pyx_n_s_Parent, __pyx_k_Parent, sizeof(__pyx_k_Parent), 0, 0, 1, 1}, + {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1}, + {&__pyx_kp_u_Signature_IntervalFile_all_hits, __pyx_k_Signature_IntervalFile_all_hits, sizeof(__pyx_k_Signature_IntervalFile_all_hits), 0, 1, 0, 0}, + {&__pyx_kp_u_Signature_IntervalFile_any_hits, __pyx_k_Signature_IntervalFile_any_hits, sizeof(__pyx_k_Signature_IntervalFile_any_hits), 0, 1, 0, 0}, + {&__pyx_kp_u_Signature_IntervalFile_count_hi, __pyx_k_Signature_IntervalFile_count_hi, sizeof(__pyx_k_Signature_IntervalFile_count_hi), 0, 1, 0, 0}, + {&__pyx_kp_s_Start_is_greater_than_stop, __pyx_k_Start_is_greater_than_stop, sizeof(__pyx_k_Start_is_greater_than_stop), 0, 0, 1, 0}, + {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1}, + {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, + {&__pyx_kp_s_UTF_8, __pyx_k_UTF_8, sizeof(__pyx_k_UTF_8), 0, 0, 1, 0}, + {&__pyx_kp_s_Unable_to_detect_format_from_s, __pyx_k_Unable_to_detect_format_from_s, sizeof(__pyx_k_Unable_to_detect_format_from_s), 0, 0, 1, 0}, + {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, + {&__pyx_kp_s__15, __pyx_k__15, sizeof(__pyx_k__15), 0, 0, 1, 0}, + {&__pyx_kp_s__19, __pyx_k__19, sizeof(__pyx_k__19), 0, 0, 1, 0}, + {&__pyx_kp_s__2, __pyx_k__2, sizeof(__pyx_k__2), 0, 0, 1, 0}, + {&__pyx_kp_s__20, __pyx_k__20, sizeof(__pyx_k__20), 0, 0, 1, 0}, + {&__pyx_kp_s__21, __pyx_k__21, sizeof(__pyx_k__21), 0, 0, 1, 0}, + {&__pyx_kp_s__22, __pyx_k__22, sizeof(__pyx_k__22), 0, 0, 1, 0}, + {&__pyx_kp_s__23, __pyx_k__23, sizeof(__pyx_k__23), 0, 0, 1, 0}, + {&__pyx_kp_s__25, __pyx_k__25, sizeof(__pyx_k__25), 0, 0, 1, 0}, + {&__pyx_kp_s__3, __pyx_k__3, sizeof(__pyx_k__3), 0, 0, 1, 0}, + {&__pyx_kp_s__4, __pyx_k__4, sizeof(__pyx_k__4), 0, 0, 1, 0}, + {&__pyx_kp_s__5, __pyx_k__5, sizeof(__pyx_k__5), 0, 0, 1, 0}, + {&__pyx_kp_s__7, __pyx_k__7, sizeof(__pyx_k__7), 0, 0, 1, 0}, + {&__pyx_kp_s__8, __pyx_k__8, sizeof(__pyx_k__8), 0, 0, 1, 0}, + {&__pyx_n_s_all_hits, __pyx_k_all_hits, sizeof(__pyx_k_all_hits), 0, 0, 1, 1}, + {&__pyx_n_s_append, __pyx_k_append, sizeof(__pyx_k_append), 0, 0, 1, 1}, + {&__pyx_n_s_attr_str, __pyx_k_attr_str, sizeof(__pyx_k_attr_str), 0, 0, 1, 1}, + {&__pyx_n_s_attr_str_2, __pyx_k_attr_str_2, sizeof(__pyx_k_attr_str_2), 0, 0, 1, 1}, + {&__pyx_n_s_attrs, __pyx_k_attrs, sizeof(__pyx_k_attrs), 0, 0, 1, 1}, + {&__pyx_n_b_bed, __pyx_k_bed, sizeof(__pyx_k_bed), 0, 0, 0, 1}, + {&__pyx_n_s_bed, __pyx_k_bed, sizeof(__pyx_k_bed), 0, 0, 1, 1}, + {&__pyx_n_s_browser, __pyx_k_browser, sizeof(__pyx_k_browser), 0, 0, 1, 1}, + {&__pyx_n_s_chrom, __pyx_k_chrom, sizeof(__pyx_k_chrom), 0, 0, 1, 1}, + {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, + {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1}, + {&__pyx_n_s_closed, __pyx_k_closed, sizeof(__pyx_k_closed), 0, 0, 1, 1}, + {&__pyx_n_s_cmp, __pyx_k_cmp, sizeof(__pyx_k_cmp), 0, 0, 1, 1}, + {&__pyx_n_s_collections, __pyx_k_collections, sizeof(__pyx_k_collections), 0, 0, 1, 1}, + {&__pyx_n_s_count, __pyx_k_count, sizeof(__pyx_k_count), 0, 0, 1, 1}, + {&__pyx_kp_u_create_interval_from_list_line_5, __pyx_k_create_interval_from_list_line_5, sizeof(__pyx_k_create_interval_from_list_line_5), 0, 1, 0, 0}, + {&__pyx_n_s_defaultdict, __pyx_k_defaultdict, sizeof(__pyx_k_defaultdict), 0, 0, 1, 1}, + {&__pyx_n_s_deparse_attrs, __pyx_k_deparse_attrs, sizeof(__pyx_k_deparse_attrs), 0, 0, 1, 1}, + {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1}, + {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1}, + {&__pyx_n_s_e1, __pyx_k_e1, sizeof(__pyx_k_e1), 0, 0, 1, 1}, + {&__pyx_n_s_e2, __pyx_k_e2, sizeof(__pyx_k_e2), 0, 0, 1, 1}, + {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, + {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, + {&__pyx_n_s_enter, __pyx_k_enter, sizeof(__pyx_k_enter), 0, 0, 1, 1}, + {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1}, + {&__pyx_n_s_field, __pyx_k_field, sizeof(__pyx_k_field), 0, 0, 1, 1}, + {&__pyx_kp_s_field_index_out_of_range, __pyx_k_field_index_out_of_range, sizeof(__pyx_k_field_index_out_of_range), 0, 0, 1, 0}, + {&__pyx_n_s_field_sep, __pyx_k_field_sep, sizeof(__pyx_k_field_sep), 0, 0, 1, 1}, + {&__pyx_n_s_fields, __pyx_k_fields, sizeof(__pyx_k_fields), 0, 0, 1, 1}, + {&__pyx_n_s_file_type, __pyx_k_file_type, sizeof(__pyx_k_file_type), 0, 0, 1, 1}, + {&__pyx_n_s_fn, __pyx_k_fn, sizeof(__pyx_k_fn), 0, 0, 1, 1}, + {&__pyx_n_s_gene_id, __pyx_k_gene_id, sizeof(__pyx_k_gene_id), 0, 0, 1, 1}, + {&__pyx_n_s_gene_name, __pyx_k_gene_name, sizeof(__pyx_k_gene_name), 0, 0, 1, 1}, + {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1}, + {&__pyx_n_b_gff, __pyx_k_gff, sizeof(__pyx_k_gff), 0, 0, 0, 1}, + {&__pyx_n_s_gff, __pyx_k_gff, sizeof(__pyx_k_gff), 0, 0, 1, 1}, + {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, + {&__pyx_n_s_indices, __pyx_k_indices, sizeof(__pyx_k_indices), 0, 0, 1, 1}, + {&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1}, + {&__pyx_n_s_int64, __pyx_k_int64, sizeof(__pyx_k_int64), 0, 0, 1, 1}, + {&__pyx_n_s_integer_types, __pyx_k_integer_types, sizeof(__pyx_k_integer_types), 0, 0, 1, 1}, + {&__pyx_n_s_interval, __pyx_k_interval, sizeof(__pyx_k_interval), 0, 0, 1, 1}, + {&__pyx_n_s_intervalFile, __pyx_k_intervalFile, sizeof(__pyx_k_intervalFile), 0, 0, 1, 1}, + {&__pyx_n_s_isdigit, __pyx_k_isdigit, sizeof(__pyx_k_isdigit), 0, 0, 1, 1}, + {&__pyx_n_s_items, __pyx_k_items, sizeof(__pyx_k_items), 0, 0, 1, 1}, + {&__pyx_n_s_iteritems, __pyx_k_iteritems, sizeof(__pyx_k_iteritems), 0, 0, 1, 1}, + {&__pyx_n_s_join, __pyx_k_join, sizeof(__pyx_k_join), 0, 0, 1, 1}, + {&__pyx_n_s_k, __pyx_k_k, sizeof(__pyx_k_k), 0, 0, 1, 1}, + {&__pyx_n_s_kdict, __pyx_k_kdict, sizeof(__pyx_k_kdict), 0, 0, 1, 1}, + {&__pyx_n_s_ktype, __pyx_k_ktype, sizeof(__pyx_k_ktype), 0, 0, 1, 1}, + {&__pyx_n_s_kv, __pyx_k_kv, sizeof(__pyx_k_kv), 0, 0, 1, 1}, + {&__pyx_n_s_kvs, __pyx_k_kvs, sizeof(__pyx_k_kvs), 0, 0, 1, 1}, + {&__pyx_n_s_loadIntoMap, __pyx_k_loadIntoMap, sizeof(__pyx_k_loadIntoMap), 0, 0, 1, 1}, + {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, + {&__pyx_kp_s_malformed_line_s, __pyx_k_malformed_line_s, sizeof(__pyx_k_malformed_line_s), 0, 0, 1, 0}, + {&__pyx_n_s_map, __pyx_k_map, sizeof(__pyx_k_map), 0, 0, 1, 1}, + {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1}, + {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1}, + {&__pyx_n_s_n_eq, __pyx_k_n_eq, sizeof(__pyx_k_n_eq), 0, 0, 1, 1}, + {&__pyx_n_s_n_quotes, __pyx_k_n_quotes, sizeof(__pyx_k_n_quotes), 0, 0, 1, 1}, + {&__pyx_n_s_n_semi, __pyx_k_n_semi, sizeof(__pyx_k_n_semi), 0, 0, 1, 1}, + {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1}, + {&__pyx_n_s_name_2, __pyx_k_name_2, sizeof(__pyx_k_name_2), 0, 0, 1, 1}, + {&__pyx_n_s_new, __pyx_k_new, sizeof(__pyx_k_new), 0, 0, 1, 1}, + {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1}, + {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, + {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1}, + {&__pyx_n_s_otherfields, __pyx_k_otherfields, sizeof(__pyx_k_otherfields), 0, 0, 1, 1}, + {&__pyx_n_s_overlap, __pyx_k_overlap, sizeof(__pyx_k_overlap), 0, 0, 1, 1}, + {&__pyx_n_s_pairs, __pyx_k_pairs, sizeof(__pyx_k_pairs), 0, 0, 1, 1}, + {&__pyx_n_s_pickle, __pyx_k_pickle, sizeof(__pyx_k_pickle), 0, 0, 1, 1}, + {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1}, + {&__pyx_n_s_pybedtools_cbedtools, __pyx_k_pybedtools_cbedtools, sizeof(__pyx_k_pybedtools_cbedtools), 0, 0, 1, 1}, + {&__pyx_kp_s_pybedtools_cbedtools_pyx, __pyx_k_pybedtools_cbedtools_pyx, sizeof(__pyx_k_pybedtools_cbedtools_pyx), 0, 0, 1, 0}, + {&__pyx_n_s_pyx_PickleError, __pyx_k_pyx_PickleError, sizeof(__pyx_k_pyx_PickleError), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_checksum, __pyx_k_pyx_checksum, sizeof(__pyx_k_pyx_checksum), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_result, __pyx_k_pyx_result, sizeof(__pyx_k_pyx_result), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_state, __pyx_k_pyx_state, sizeof(__pyx_k_pyx_state), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_type, __pyx_k_pyx_type, sizeof(__pyx_k_pyx_type), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_unpickle_IntervalIterator, __pyx_k_pyx_unpickle_IntervalIterator, sizeof(__pyx_k_pyx_unpickle_IntervalIterator), 0, 0, 1, 1}, + {&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1}, + {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1}, + {&__pyx_n_s_quoted, __pyx_k_quoted, sizeof(__pyx_k_quoted), 0, 0, 1, 1}, + {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, + {&__pyx_n_s_readline, __pyx_k_readline, sizeof(__pyx_k_readline), 0, 0, 1, 1}, + {&__pyx_n_s_reduce, __pyx_k_reduce, sizeof(__pyx_k_reduce), 0, 0, 1, 1}, + {&__pyx_n_s_reduce_cython, __pyx_k_reduce_cython, sizeof(__pyx_k_reduce_cython), 0, 0, 1, 1}, + {&__pyx_n_s_reduce_ex, __pyx_k_reduce_ex, sizeof(__pyx_k_reduce_ex), 0, 0, 1, 1}, + {&__pyx_n_s_replace, __pyx_k_replace, sizeof(__pyx_k_replace), 0, 0, 1, 1}, + {&__pyx_n_s_richcmp___locals_cmp, __pyx_k_richcmp___locals_cmp, sizeof(__pyx_k_richcmp___locals_cmp), 0, 0, 1, 1}, + {&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1}, + {&__pyx_n_s_s1, __pyx_k_s1, sizeof(__pyx_k_s1), 0, 0, 1, 1}, + {&__pyx_n_s_s2, __pyx_k_s2, sizeof(__pyx_k_s2), 0, 0, 1, 1}, + {&__pyx_kp_s_s_i, __pyx_k_s_i, sizeof(__pyx_k_s_i), 0, 0, 1, 0}, + {&__pyx_n_s_sam, __pyx_k_sam, sizeof(__pyx_k_sam), 0, 0, 1, 1}, + {&__pyx_n_s_same_strand, __pyx_k_same_strand, sizeof(__pyx_k_same_strand), 0, 0, 1, 1}, + {&__pyx_n_s_score, __pyx_k_score, sizeof(__pyx_k_score), 0, 0, 1, 1}, + {&__pyx_n_s_search, __pyx_k_search, sizeof(__pyx_k_search), 0, 0, 1, 1}, + {&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1}, + {&__pyx_kp_s_self__bed_cannot_be_converted_to, __pyx_k_self__bed_cannot_be_converted_to, sizeof(__pyx_k_self__bed_cannot_be_converted_to), 0, 0, 1, 0}, + {&__pyx_kp_s_self_intervalFile_ptr_cannot_be, __pyx_k_self_intervalFile_ptr_cannot_be, sizeof(__pyx_k_self_intervalFile_ptr_cannot_be), 0, 0, 1, 0}, + {&__pyx_n_s_sep, __pyx_k_sep, sizeof(__pyx_k_sep), 0, 0, 1, 1}, + {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1}, + {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, + {&__pyx_n_s_sort_keys, __pyx_k_sort_keys, sizeof(__pyx_k_sort_keys), 0, 0, 1, 1}, + {&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1}, + {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1}, + {&__pyx_n_s_startswith, __pyx_k_startswith, sizeof(__pyx_k_startswith), 0, 0, 1, 1}, + {&__pyx_n_s_stop, __pyx_k_stop, sizeof(__pyx_k_stop), 0, 0, 1, 1}, + {&__pyx_n_s_str, __pyx_k_str, sizeof(__pyx_k_str), 0, 0, 1, 1}, + {&__pyx_n_s_strand, __pyx_k_strand, sizeof(__pyx_k_strand), 0, 0, 1, 1}, + {&__pyx_n_s_stream, __pyx_k_stream, sizeof(__pyx_k_stream), 0, 0, 1, 1}, + {&__pyx_kp_s_stringsource, __pyx_k_stringsource, sizeof(__pyx_k_stringsource), 0, 0, 1, 0}, + {&__pyx_n_s_strip, __pyx_k_strip, sizeof(__pyx_k_strip), 0, 0, 1, 1}, + {&__pyx_n_s_subprocess, __pyx_k_subprocess, sizeof(__pyx_k_subprocess), 0, 0, 1, 1}, + {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1}, + {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, + {&__pyx_n_s_track, __pyx_k_track, sizeof(__pyx_k_track), 0, 0, 1, 1}, + {&__pyx_n_s_transcript_id, __pyx_k_transcript_id, sizeof(__pyx_k_transcript_id), 0, 0, 1, 1}, + {&__pyx_n_s_update, __pyx_k_update, sizeof(__pyx_k_update), 0, 0, 1, 1}, + {&__pyx_n_s_v, __pyx_k_v, sizeof(__pyx_k_v), 0, 0, 1, 1}, + {&__pyx_n_s_val, __pyx_k_val, sizeof(__pyx_k_val), 0, 0, 1, 1}, + {&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1}, + {&__pyx_n_b_vcf, __pyx_k_vcf, sizeof(__pyx_k_vcf), 0, 0, 0, 1}, + {&__pyx_n_s_vcf, __pyx_k_vcf, sizeof(__pyx_k_vcf), 0, 0, 1, 1}, + {&__pyx_n_s_x, __pyx_k_x, sizeof(__pyx_k_x), 0, 0, 1, 1}, + {&__pyx_n_s_y, __pyx_k_y, sizeof(__pyx_k_y), 0, 0, 1, 1}, + {0, 0, 0, 0, 0, 0, 0} +}; +static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) { + __pyx_builtin_map = __Pyx_GetBuiltinName(__pyx_n_s_map); if (!__pyx_builtin_map) __PYX_ERR(0, 176, __pyx_L1_error) + __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) __PYX_ERR(0, 189, __pyx_L1_error) + __pyx_builtin_NotImplementedError = __Pyx_GetBuiltinName(__pyx_n_s_NotImplementedError); if (!__pyx_builtin_NotImplementedError) __PYX_ERR(0, 301, __pyx_L1_error) + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 312, __pyx_L1_error) + __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) __PYX_ERR(0, 521, __pyx_L1_error) + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 527, __pyx_L1_error) + __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error) + __pyx_builtin_AttributeError = __Pyx_GetBuiltinName(__pyx_n_s_AttributeError); if (!__pyx_builtin_AttributeError) __PYX_ERR(0, 745, __pyx_L1_error) + __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) __PYX_ERR(0, 755, __pyx_L1_error) + __pyx_builtin_open = __Pyx_GetBuiltinName(__pyx_n_s_open); if (!__pyx_builtin_open) __PYX_ERR(0, 850, __pyx_L1_error) + return 0; + __pyx_L1_error:; + return -1; +} + +static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); + + /* "pybedtools/cbedtools.pyx":180 + * if value.count('"') == 2: + * self._quoted[field] = True + * self[field] = value.replace('"', '') # <<<<<<<<<<<<<< + * + * def __str__(self): + */ + __pyx_tuple__6 = PyTuple_Pack(2, __pyx_kp_s__4, __pyx_kp_s_); if (unlikely(!__pyx_tuple__6)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__6); + __Pyx_GIVEREF(__pyx_tuple__6); + + /* "pybedtools/cbedtools.pyx":284 + * return False + * + * def cmp(x, y): # <<<<<<<<<<<<<< + * if x < y: + * return -1 + */ + __pyx_tuple__9 = PyTuple_Pack(2, __pyx_n_s_x, __pyx_n_s_y); if (unlikely(!__pyx_tuple__9)) __PYX_ERR(0, 284, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__9); + __Pyx_GIVEREF(__pyx_tuple__9); + __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pybedtools_cbedtools_pyx, __pyx_n_s_cmp, 284, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 284, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":301 + * try: + * if PROFILES_TRUE[profile] == tuple(): + * raise NotImplementedError('Features are nested -- comparison undefined') # <<<<<<<<<<<<<< + * + * if op != 3: + */ + __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_s_Features_are_nested_comparison_u); if (unlikely(!__pyx_tuple__11)) __PYX_ERR(0, 301, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__11); + __Pyx_GIVEREF(__pyx_tuple__11); + + /* "pybedtools/cbedtools.pyx":312 + * return True + * except KeyError: + * raise ValueError('Currently unsupported comparison -- please ' # <<<<<<<<<<<<<< + * 'submit a bug report') + * + */ + __pyx_tuple__12 = PyTuple_Pack(1, __pyx_kp_s_Currently_unsupported_comparison); if (unlikely(!__pyx_tuple__12)) __PYX_ERR(0, 312, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__12); + __Pyx_GIVEREF(__pyx_tuple__12); + + /* "pybedtools/cbedtools.pyx":369 + * + * if self.file_type != "gff": + * raise ValueError('Interval.attrs was not None, but this was a non-GFF Interval') # <<<<<<<<<<<<<< + * + * s = self._attrs.__str__() + */ + __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_s_Interval_attrs_was_not_None_but); if (unlikely(!__pyx_tuple__13)) __PYX_ERR(0, 369, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__13); + __Pyx_GIVEREF(__pyx_tuple__13); + + /* "pybedtools/cbedtools.pyx":420 + * return attrs[self.name_key] + * """ + * for key in ("ID", "Name", "gene_name", "transcript_id", \ # <<<<<<<<<<<<<< + * "gene_id", "Parent"): + * if key in self.attrs: + */ + __pyx_tuple__14 = PyTuple_Pack(6, __pyx_n_s_ID, __pyx_n_s_Name, __pyx_n_s_gene_name, __pyx_n_s_transcript_id, __pyx_n_s_gene_id, __pyx_n_s_Parent); if (unlikely(!__pyx_tuple__14)) __PYX_ERR(0, 420, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__14); + __Pyx_GIVEREF(__pyx_tuple__14); + + /* "pybedtools/cbedtools.pyx":521 + * nfields = self._bed.fields.size() + * if key >= nfields: + * raise IndexError('field index out of range') # <<<<<<<<<<<<<< + * elif key < 0: + * key = nfields + key + */ + __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_s_field_index_out_of_range); if (unlikely(!__pyx_tuple__16)) __PYX_ERR(0, 521, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__16); + __Pyx_GIVEREF(__pyx_tuple__16); + + /* "(tree fragment)":2 + * def __reduce_cython__(self): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + */ + __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_self__bed_cannot_be_converted_to); if (unlikely(!__pyx_tuple__17)) __PYX_ERR(1, 2, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__17); + __Pyx_GIVEREF(__pyx_tuple__17); + + /* "(tree fragment)":4 + * raise TypeError("self._bed cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self._bed cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + */ + __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_self__bed_cannot_be_converted_to); if (unlikely(!__pyx_tuple__18)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__18); + __Pyx_GIVEREF(__pyx_tuple__18); + + /* "pybedtools/cbedtools.pyx":772 + * + * if self._itemtype == 1: + * if line.startswith(('@', '#', 'track', 'browser')) or len(line.strip()) == 0: # <<<<<<<<<<<<<< + * continue + * break + */ + __pyx_tuple__24 = PyTuple_Pack(4, __pyx_kp_s__22, __pyx_kp_s__23, __pyx_n_s_track, __pyx_n_s_browser); if (unlikely(!__pyx_tuple__24)) __PYX_ERR(0, 772, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__24); + __Pyx_GIVEREF(__pyx_tuple__24); + + /* "pybedtools/cbedtools.pyx":850 + * except MalformedBedLineError: + * # If it's a SAM, raise a meaningful exception. If not, fail. + * with open(self.fn) as fn: # <<<<<<<<<<<<<< + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': + */ + __pyx_tuple__26 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__26)) __PYX_ERR(0, 850, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__26); + __Pyx_GIVEREF(__pyx_tuple__26); + + /* "pybedtools/cbedtools.pyx":853 + * interval = create_interval_from_list(fn.readline().strip().split()) + * if interval.file_type == 'sam': + * raise ValueError('IntervalFile objects do not yet natively support SAM. ' # <<<<<<<<<<<<<< + * 'Please convert to BED/GFF/VCF first if you want to ' + * 'use the low-level API of IntervalFile') + */ + __pyx_tuple__27 = PyTuple_Pack(1, __pyx_kp_s_IntervalFile_objects_do_not_yet); if (unlikely(!__pyx_tuple__27)) __PYX_ERR(0, 853, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__27); + __Pyx_GIVEREF(__pyx_tuple__27); + + /* "(tree fragment)":2 + * def __reduce_cython__(self): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + */ + __pyx_tuple__28 = PyTuple_Pack(1, __pyx_kp_s_self_intervalFile_ptr_cannot_be); if (unlikely(!__pyx_tuple__28)) __PYX_ERR(1, 2, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__28); + __Pyx_GIVEREF(__pyx_tuple__28); + + /* "(tree fragment)":4 + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") + * def __setstate_cython__(self, __pyx_state): + * raise TypeError("self.intervalFile_ptr cannot be converted to a Python object for pickling") # <<<<<<<<<<<<<< + */ + __pyx_tuple__29 = PyTuple_Pack(1, __pyx_kp_s_self_intervalFile_ptr_cannot_be); if (unlikely(!__pyx_tuple__29)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__29); + __Pyx_GIVEREF(__pyx_tuple__29); + __pyx_tuple__30 = PyTuple_Pack(3, __pyx_int_22915542, __pyx_int_172054328, __pyx_int_26969663); if (unlikely(!__pyx_tuple__30)) __PYX_ERR(1, 4, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__30); + __Pyx_GIVEREF(__pyx_tuple__30); + + /* "pybedtools/cbedtools.pyx":67 + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * PROFILES_TRUE = { + * (0, 0, -1, 1): (2, 1, 5), # a == b, a >= b, a <= b # <<<<<<<<<<<<<< + * # a --------- + * # b --------- + */ + __pyx_tuple__31 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_0, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__31)) __PYX_ERR(0, 67, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__31); + __Pyx_GIVEREF(__pyx_tuple__31); + __pyx_tuple__32 = PyTuple_Pack(3, __pyx_int_2, __pyx_int_1, __pyx_int_5); if (unlikely(!__pyx_tuple__32)) __PYX_ERR(0, 67, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__32); + __Pyx_GIVEREF(__pyx_tuple__32); + + /* "pybedtools/cbedtools.pyx":71 + * # b --------- + * + * (-1, -1, -1, -1): (0, 1), # a < b, a <= b # <<<<<<<<<<<<<< + * # a ---- + * # b ----- + */ + __pyx_tuple__33 = PyTuple_Pack(4, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__33)) __PYX_ERR(0, 71, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__33); + __Pyx_GIVEREF(__pyx_tuple__33); + __pyx_tuple__34 = PyTuple_Pack(2, __pyx_int_0, __pyx_int_1); if (unlikely(!__pyx_tuple__34)) __PYX_ERR(0, 71, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__34); + __Pyx_GIVEREF(__pyx_tuple__34); + + /* "pybedtools/cbedtools.pyx":75 + * # b ----- + * + * (-1, -1, -1, 0): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ---- + * # b ----- (book-ended) + */ + __pyx_tuple__35 = PyTuple_Pack(4, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_0); if (unlikely(!__pyx_tuple__35)) __PYX_ERR(0, 75, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__35); + __Pyx_GIVEREF(__pyx_tuple__35); + __pyx_tuple__36 = PyTuple_Pack(1, __pyx_int_1); if (unlikely(!__pyx_tuple__36)) __PYX_ERR(0, 75, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__36); + __Pyx_GIVEREF(__pyx_tuple__36); + + /* "pybedtools/cbedtools.pyx":79 + * # b ----- (book-ended) + * + * (1, 1, 0, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ----- + * # b ---- (book-ended) + */ + __pyx_tuple__37 = PyTuple_Pack(4, __pyx_int_1, __pyx_int_1, __pyx_int_0, __pyx_int_1); if (unlikely(!__pyx_tuple__37)) __PYX_ERR(0, 79, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__37); + __Pyx_GIVEREF(__pyx_tuple__37); + __pyx_tuple__38 = PyTuple_Pack(1, __pyx_int_5); if (unlikely(!__pyx_tuple__38)) __PYX_ERR(0, 79, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__38); + __Pyx_GIVEREF(__pyx_tuple__38); + + /* "pybedtools/cbedtools.pyx":83 + * # b ---- (book-ended) + * + * (1, 1, 1, 1): (4, 5), # a > b, a >= b # <<<<<<<<<<<<<< + * # a ------ + * # b ---- + */ + __pyx_tuple__39 = PyTuple_Pack(4, __pyx_int_1, __pyx_int_1, __pyx_int_1, __pyx_int_1); if (unlikely(!__pyx_tuple__39)) __PYX_ERR(0, 83, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__39); + __Pyx_GIVEREF(__pyx_tuple__39); + __pyx_tuple__40 = PyTuple_Pack(2, __pyx_int_4, __pyx_int_5); if (unlikely(!__pyx_tuple__40)) __PYX_ERR(0, 83, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__40); + __Pyx_GIVEREF(__pyx_tuple__40); + + /* "pybedtools/cbedtools.pyx":87 + * # b ---- + * + * (0, 1, -1, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ------------ + * # b --------- + */ + __pyx_tuple__41 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_1, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__41)) __PYX_ERR(0, 87, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__41); + __Pyx_GIVEREF(__pyx_tuple__41); + + /* "pybedtools/cbedtools.pyx":91 + * # b --------- + * + * (1, 0, -1, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ----------- + * # b ------------- + */ + __pyx_tuple__42 = PyTuple_Pack(4, __pyx_int_1, __pyx_int_0, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__42)) __PYX_ERR(0, 91, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__42); + __Pyx_GIVEREF(__pyx_tuple__42); + + /* "pybedtools/cbedtools.pyx":95 + * # b ------------- + * + * (-1, 0, -1, 1): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ------------- + * # b ----------- + */ + __pyx_tuple__43 = PyTuple_Pack(4, __pyx_int_neg_1, __pyx_int_0, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__43)) __PYX_ERR(0, 95, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__43); + __Pyx_GIVEREF(__pyx_tuple__43); + + /* "pybedtools/cbedtools.pyx":99 + * # b ----------- + * + * (0, -1, -1, 1): (1,), # a <= b # <<<<<<<<<<<<<< + * # a --------- + * # b ------------ + */ + __pyx_tuple__44 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__44)) __PYX_ERR(0, 99, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__44); + __Pyx_GIVEREF(__pyx_tuple__44); + + /* "pybedtools/cbedtools.pyx":103 + * # b ------------ + * + * (-1, -1, -1, 1): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ----------- + * # b ----------- + */ + __pyx_tuple__45 = PyTuple_Pack(4, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__45)) __PYX_ERR(0, 103, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__45); + __Pyx_GIVEREF(__pyx_tuple__45); + + /* "pybedtools/cbedtools.pyx":107 + * # b ----------- + * + * (1, 1, -1, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ----------- + * # b ----------- + */ + __pyx_tuple__46 = PyTuple_Pack(4, __pyx_int_1, __pyx_int_1, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__46)) __PYX_ERR(0, 107, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__46); + __Pyx_GIVEREF(__pyx_tuple__46); + + /* "pybedtools/cbedtools.pyx":111 + * # b ----------- + * + * (1, -1, -1, 1): tuple(), # undef # <<<<<<<<<<<<<< + * # a ---- + * # b ----------- + */ + __pyx_tuple__47 = PyTuple_Pack(4, __pyx_int_1, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__47)) __PYX_ERR(0, 111, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__47); + __Pyx_GIVEREF(__pyx_tuple__47); + + /* "pybedtools/cbedtools.pyx":115 + * # b ----------- + * + * (-1, 1, -1, 1): tuple(), # undef # <<<<<<<<<<<<<< + * # a ----------- + * # b ---- + */ + __pyx_tuple__48 = PyTuple_Pack(4, __pyx_int_neg_1, __pyx_int_1, __pyx_int_neg_1, __pyx_int_1); if (unlikely(!__pyx_tuple__48)) __PYX_ERR(0, 115, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__48); + __Pyx_GIVEREF(__pyx_tuple__48); + + /* "pybedtools/cbedtools.pyx":119 + * # b ---- + * + * (-1, 0, -1, 0): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ----------- + * # b - + */ + __pyx_tuple__49 = PyTuple_Pack(4, __pyx_int_neg_1, __pyx_int_0, __pyx_int_neg_1, __pyx_int_0); if (unlikely(!__pyx_tuple__49)) __PYX_ERR(0, 119, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__49); + __Pyx_GIVEREF(__pyx_tuple__49); + + /* "pybedtools/cbedtools.pyx":123 + * # b - + * + * (1, 0, 0, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a - + * # b ----------- + */ + __pyx_tuple__50 = PyTuple_Pack(4, __pyx_int_1, __pyx_int_0, __pyx_int_0, __pyx_int_1); if (unlikely(!__pyx_tuple__50)) __PYX_ERR(0, 123, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__50); + __Pyx_GIVEREF(__pyx_tuple__50); + + /* "pybedtools/cbedtools.pyx":127 + * # b ----------- + * + * (0, 0, 0, 0): (1, 2, 5), # a == b, a <= b, a >= b # <<<<<<<<<<<<<< + * # a - + * # b - (starts and stops are identical for all features) + */ + __pyx_tuple__51 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_0, __pyx_int_0, __pyx_int_0); if (unlikely(!__pyx_tuple__51)) __PYX_ERR(0, 127, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__51); + __Pyx_GIVEREF(__pyx_tuple__51); + __pyx_tuple__52 = PyTuple_Pack(3, __pyx_int_1, __pyx_int_2, __pyx_int_5); if (unlikely(!__pyx_tuple__52)) __PYX_ERR(0, 127, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__52); + __Pyx_GIVEREF(__pyx_tuple__52); + + /* "pybedtools/cbedtools.pyx":146 + * """ + * + * def __init__(self, attr_str=""): # <<<<<<<<<<<<<< + * attr_str = str(attr_str) + * self._attr_str = attr_str + */ + __pyx_tuple__53 = PyTuple_Pack(9, __pyx_n_s_self, __pyx_n_s_attr_str, __pyx_n_s_n_semi, __pyx_n_s_n_eq, __pyx_n_s_n_quotes, __pyx_n_s_kvs, __pyx_n_s_field, __pyx_n_s_value, __pyx_n_s_kv); if (unlikely(!__pyx_tuple__53)) __PYX_ERR(0, 146, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__53); + __Pyx_GIVEREF(__pyx_tuple__53); + __pyx_codeobj__54 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__53, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pybedtools_cbedtools_pyx, __pyx_n_s_init, 146, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__54)) __PYX_ERR(0, 146, __pyx_L1_error) + __pyx_tuple__55 = PyTuple_Pack(1, ((PyObject*)__pyx_kp_s_)); if (unlikely(!__pyx_tuple__55)) __PYX_ERR(0, 146, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__55); + __Pyx_GIVEREF(__pyx_tuple__55); + + /* "pybedtools/cbedtools.pyx":182 + * self[field] = value.replace('"', '') + * + * def __str__(self): # <<<<<<<<<<<<<< + * # stringify all items first + * items = [] + */ + __pyx_tuple__56 = PyTuple_Pack(7, __pyx_n_s_self, __pyx_n_s_items, __pyx_n_s_field, __pyx_n_s_val, __pyx_n_s_pairs, __pyx_n_s_k, __pyx_n_s_v); if (unlikely(!__pyx_tuple__56)) __PYX_ERR(0, 182, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__56); + __Pyx_GIVEREF(__pyx_tuple__56); + __pyx_codeobj__57 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__56, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pybedtools_cbedtools_pyx, __pyx_n_s_str, 182, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__57)) __PYX_ERR(0, 182, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":725 + * + * + * def overlap(int s1, int s2, int e1, int e2): # <<<<<<<<<<<<<< + * return min(e1, e2) - max(s1, s2) + * + */ + __pyx_tuple__58 = PyTuple_Pack(4, __pyx_n_s_s1, __pyx_n_s_s2, __pyx_n_s_e1, __pyx_n_s_e2); if (unlikely(!__pyx_tuple__58)) __PYX_ERR(0, 725, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__58); + __Pyx_GIVEREF(__pyx_tuple__58); + __pyx_codeobj__59 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__58, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pybedtools_cbedtools_pyx, __pyx_n_s_overlap, 725, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__59)) __PYX_ERR(0, 725, __pyx_L1_error) + + /* "(tree fragment)":1 + * def __pyx_unpickle_IntervalIterator(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * cdef object __pyx_PickleError + * cdef object __pyx_result + */ + __pyx_tuple__60 = PyTuple_Pack(5, __pyx_n_s_pyx_type, __pyx_n_s_pyx_checksum, __pyx_n_s_pyx_state, __pyx_n_s_pyx_PickleError, __pyx_n_s_pyx_result); if (unlikely(!__pyx_tuple__60)) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__60); + __Pyx_GIVEREF(__pyx_tuple__60); + __pyx_codeobj__61 = (PyObject*)__Pyx_PyCode_New(3, 0, 5, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__60, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_stringsource, __pyx_n_s_pyx_unpickle_IntervalIterator, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__61)) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_RefNannyFinishContext(); + return -1; +} + +static CYTHON_SMALL_CODE int __Pyx_InitGlobals(void) { + __pyx_umethod_PyDict_Type_items.type = (PyObject*)&PyDict_Type; + __pyx_umethod_PyDict_Type_iteritems.type = (PyObject*)&PyDict_Type; + if (__Pyx_InitStrings(__pyx_string_tab) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_6 = PyInt_FromLong(6); if (unlikely(!__pyx_int_6)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_22915542 = PyInt_FromLong(22915542L); if (unlikely(!__pyx_int_22915542)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_26969663 = PyInt_FromLong(26969663L); if (unlikely(!__pyx_int_26969663)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_172054328 = PyInt_FromLong(172054328L); if (unlikely(!__pyx_int_172054328)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) __PYX_ERR(0, 1, __pyx_L1_error) + return 0; + __pyx_L1_error:; + return -1; +} + +static CYTHON_SMALL_CODE int __Pyx_modinit_global_init_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_variable_export_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_function_export_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_type_init_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_type_import_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_variable_import_code(void); /*proto*/ +static CYTHON_SMALL_CODE int __Pyx_modinit_function_import_code(void); /*proto*/ + +static int __Pyx_modinit_global_init_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_global_init_code", 0); + /*--- Global init code ---*/ + __pyx_v_10pybedtools_9cbedtools_LOOKUPS = ((PyObject*)Py_None); Py_INCREF(Py_None); + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_variable_export_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_variable_export_code", 0); + /*--- Variable export code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_function_export_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_function_export_code", 0); + /*--- Function export code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_type_init_code(void) { + __Pyx_RefNannyDeclarations + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__Pyx_modinit_type_init_code", 0); + /*--- Type init code ---*/ + __pyx_vtabptr_10pybedtools_9cbedtools_Interval = &__pyx_vtable_10pybedtools_9cbedtools_Interval; + __pyx_vtable_10pybedtools_9cbedtools_Interval.append = (PyObject *(*)(struct __pyx_obj_10pybedtools_9cbedtools_Interval *, PyObject *, int __pyx_skip_dispatch))__pyx_f_10pybedtools_9cbedtools_8Interval_append; + __pyx_vtable_10pybedtools_9cbedtools_Interval.deparse_attrs = (PyObject *(*)(struct __pyx_obj_10pybedtools_9cbedtools_Interval *, int __pyx_skip_dispatch))__pyx_f_10pybedtools_9cbedtools_8Interval_deparse_attrs; + if (PyType_Ready(&__pyx_type_10pybedtools_9cbedtools_Interval) < 0) __PYX_ERR(0, 201, __pyx_L1_error) + #if PY_VERSION_HEX < 0x030800B1 + __pyx_type_10pybedtools_9cbedtools_Interval.tp_print = 0; + #endif + if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_10pybedtools_9cbedtools_Interval.tp_dictoffset && __pyx_type_10pybedtools_9cbedtools_Interval.tp_getattro == PyObject_GenericGetAttr)) { + __pyx_type_10pybedtools_9cbedtools_Interval.tp_getattro = __Pyx_PyObject_GenericGetAttr; + } + #if CYTHON_UPDATE_DESCRIPTOR_DOC + { + PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_10pybedtools_9cbedtools_Interval, "__str__"); if (unlikely(!wrapper)) __PYX_ERR(0, 201, __pyx_L1_error) + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_10pybedtools_9cbedtools_8Interval_10__str__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_10pybedtools_9cbedtools_8Interval_10__str__.doc = __pyx_doc_10pybedtools_9cbedtools_8Interval_10__str__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10pybedtools_9cbedtools_8Interval_10__str__; + } + } + #endif + if (__Pyx_SetVtable(__pyx_type_10pybedtools_9cbedtools_Interval.tp_dict, __pyx_vtabptr_10pybedtools_9cbedtools_Interval) < 0) __PYX_ERR(0, 201, __pyx_L1_error) + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_Interval, (PyObject *)&__pyx_type_10pybedtools_9cbedtools_Interval) < 0) __PYX_ERR(0, 201, __pyx_L1_error) + if (__Pyx_setup_reduce((PyObject*)&__pyx_type_10pybedtools_9cbedtools_Interval) < 0) __PYX_ERR(0, 201, __pyx_L1_error) + __pyx_ptype_10pybedtools_9cbedtools_Interval = &__pyx_type_10pybedtools_9cbedtools_Interval; + if (PyType_Ready(&__pyx_type_10pybedtools_9cbedtools_IntervalIterator) < 0) __PYX_ERR(0, 729, __pyx_L1_error) + #if PY_VERSION_HEX < 0x030800B1 + __pyx_type_10pybedtools_9cbedtools_IntervalIterator.tp_print = 0; + #endif + if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_10pybedtools_9cbedtools_IntervalIterator.tp_dictoffset && __pyx_type_10pybedtools_9cbedtools_IntervalIterator.tp_getattro == PyObject_GenericGetAttr)) { + __pyx_type_10pybedtools_9cbedtools_IntervalIterator.tp_getattro = __Pyx_PyObject_GenericGetAttr; + } + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_IntervalIterator, (PyObject *)&__pyx_type_10pybedtools_9cbedtools_IntervalIterator) < 0) __PYX_ERR(0, 729, __pyx_L1_error) + if (__Pyx_setup_reduce((PyObject*)&__pyx_type_10pybedtools_9cbedtools_IntervalIterator) < 0) __PYX_ERR(0, 729, __pyx_L1_error) + __pyx_ptype_10pybedtools_9cbedtools_IntervalIterator = &__pyx_type_10pybedtools_9cbedtools_IntervalIterator; + if (PyType_Ready(&__pyx_type_10pybedtools_9cbedtools_IntervalFile) < 0) __PYX_ERR(0, 794, __pyx_L1_error) + #if PY_VERSION_HEX < 0x030800B1 + __pyx_type_10pybedtools_9cbedtools_IntervalFile.tp_print = 0; + #endif + if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_10pybedtools_9cbedtools_IntervalFile.tp_dictoffset && __pyx_type_10pybedtools_9cbedtools_IntervalFile.tp_getattro == PyObject_GenericGetAttr)) { + __pyx_type_10pybedtools_9cbedtools_IntervalFile.tp_getattro = __Pyx_PyObject_GenericGetAttr; + } + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_IntervalFile, (PyObject *)&__pyx_type_10pybedtools_9cbedtools_IntervalFile) < 0) __PYX_ERR(0, 794, __pyx_L1_error) + if (__Pyx_setup_reduce((PyObject*)&__pyx_type_10pybedtools_9cbedtools_IntervalFile) < 0) __PYX_ERR(0, 794, __pyx_L1_error) + __pyx_ptype_10pybedtools_9cbedtools_IntervalFile = &__pyx_type_10pybedtools_9cbedtools_IntervalFile; + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_RefNannyFinishContext(); + return -1; +} + +static int __Pyx_modinit_type_import_code(void) { + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__Pyx_modinit_type_import_code", 0); + /*--- Type import code ---*/ + __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 9, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_0_29_37(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", + #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000 + sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_0_29_37(PyTypeObject), + #else + sizeof(PyHeapTypeObject), __PYX_GET_STRUCT_ALIGNMENT_0_29_37(PyHeapTypeObject), + #endif + __Pyx_ImportType_CheckSize_Warn_0_29_37); if (!__pyx_ptype_7cpython_4type_type) __PYX_ERR(2, 9, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(3, 8, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType_0_29_37(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), __PYX_GET_STRUCT_ALIGNMENT_0_29_37(PyBoolObject),__Pyx_ImportType_CheckSize_Warn_0_29_37); if (!__pyx_ptype_7cpython_4bool_bool) __PYX_ERR(3, 8, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(4, 15, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType_0_29_37(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), __PYX_GET_STRUCT_ALIGNMENT_0_29_37(PyComplexObject),__Pyx_ImportType_CheckSize_Warn_0_29_37); if (!__pyx_ptype_7cpython_7complex_complex) __PYX_ERR(4, 15, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_RefNannyFinishContext(); + return 0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_RefNannyFinishContext(); + return -1; +} + +static int __Pyx_modinit_variable_import_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_variable_import_code", 0); + /*--- Variable import code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + +static int __Pyx_modinit_function_import_code(void) { + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__Pyx_modinit_function_import_code", 0); + /*--- Function import code ---*/ + __Pyx_RefNannyFinishContext(); + return 0; +} + + +#ifndef CYTHON_NO_PYINIT_EXPORT +#define __Pyx_PyMODINIT_FUNC PyMODINIT_FUNC +#elif PY_MAJOR_VERSION < 3 +#ifdef __cplusplus +#define __Pyx_PyMODINIT_FUNC extern "C" void +#else +#define __Pyx_PyMODINIT_FUNC void +#endif +#else +#ifdef __cplusplus +#define __Pyx_PyMODINIT_FUNC extern "C" PyObject * +#else +#define __Pyx_PyMODINIT_FUNC PyObject * +#endif +#endif + + +#if PY_MAJOR_VERSION < 3 +__Pyx_PyMODINIT_FUNC initcbedtools(void) CYTHON_SMALL_CODE; /*proto*/ +__Pyx_PyMODINIT_FUNC initcbedtools(void) +#else +__Pyx_PyMODINIT_FUNC PyInit_cbedtools(void) CYTHON_SMALL_CODE; /*proto*/ +__Pyx_PyMODINIT_FUNC PyInit_cbedtools(void) +#if CYTHON_PEP489_MULTI_PHASE_INIT +{ + return PyModuleDef_Init(&__pyx_moduledef); +} +static CYTHON_SMALL_CODE int __Pyx_check_single_interpreter(void) { + #if PY_VERSION_HEX >= 0x030700A1 + static PY_INT64_T main_interpreter_id = -1; + PY_INT64_T current_id = PyInterpreterState_GetID(PyThreadState_Get()->interp); + if (main_interpreter_id == -1) { + main_interpreter_id = current_id; + return (unlikely(current_id == -1)) ? -1 : 0; + } else if (unlikely(main_interpreter_id != current_id)) + #else + static PyInterpreterState *main_interpreter = NULL; + PyInterpreterState *current_interpreter = PyThreadState_Get()->interp; + if (!main_interpreter) { + main_interpreter = current_interpreter; + } else if (unlikely(main_interpreter != current_interpreter)) + #endif + { + PyErr_SetString( + PyExc_ImportError, + "Interpreter change detected - this module can only be loaded into one interpreter per process."); + return -1; + } + return 0; +} +static CYTHON_SMALL_CODE int __Pyx_copy_spec_to_module(PyObject *spec, PyObject *moddict, const char* from_name, const char* to_name, int allow_none) { + PyObject *value = PyObject_GetAttrString(spec, from_name); + int result = 0; + if (likely(value)) { + if (allow_none || value != Py_None) { + result = PyDict_SetItemString(moddict, to_name, value); + } + Py_DECREF(value); + } else if (PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_Clear(); + } else { + result = -1; + } + return result; +} +static CYTHON_SMALL_CODE PyObject* __pyx_pymod_create(PyObject *spec, CYTHON_UNUSED PyModuleDef *def) { + PyObject *module = NULL, *moddict, *modname; + if (__Pyx_check_single_interpreter()) + return NULL; + if (__pyx_m) + return __Pyx_NewRef(__pyx_m); + modname = PyObject_GetAttrString(spec, "name"); + if (unlikely(!modname)) goto bad; + module = PyModule_NewObject(modname); + Py_DECREF(modname); + if (unlikely(!module)) goto bad; + moddict = PyModule_GetDict(module); + if (unlikely(!moddict)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "loader", "__loader__", 1) < 0)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "origin", "__file__", 1) < 0)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "parent", "__package__", 1) < 0)) goto bad; + if (unlikely(__Pyx_copy_spec_to_module(spec, moddict, "submodule_search_locations", "__path__", 0) < 0)) goto bad; + return module; +bad: + Py_XDECREF(module); + return NULL; +} + + +static CYTHON_SMALL_CODE int __pyx_pymod_exec_cbedtools(PyObject *__pyx_pyinit_module) +#endif +#endif +{ + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + Py_ssize_t __pyx_t_3; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *(*__pyx_t_7)(PyObject *); + Py_ssize_t __pyx_t_8; + PyObject *__pyx_t_9 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannyDeclarations + #if CYTHON_PEP489_MULTI_PHASE_INIT + if (__pyx_m) { + if (__pyx_m == __pyx_pyinit_module) return 0; + PyErr_SetString(PyExc_RuntimeError, "Module 'cbedtools' has already been imported. Re-initialisation is not supported."); + return -1; + } + #elif PY_MAJOR_VERSION >= 3 + if (__pyx_m) return __Pyx_NewRef(__pyx_m); + #endif + #if CYTHON_REFNANNY +__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); +if (!__Pyx_RefNanny) { + PyErr_Clear(); + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); + if (!__Pyx_RefNanny) + Py_FatalError("failed to import 'refnanny' module"); +} +#endif + __Pyx_RefNannySetupContext("__Pyx_PyMODINIT_FUNC PyInit_cbedtools(void)", 0); + if (__Pyx_check_binary_version() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #ifdef __Pxy_PyFrame_Initialize_Offsets + __Pxy_PyFrame_Initialize_Offsets(); + #endif + __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) __PYX_ERR(0, 1, __pyx_L1_error) + __pyx_empty_unicode = PyUnicode_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_unicode)) __PYX_ERR(0, 1, __pyx_L1_error) + #ifdef __Pyx_CyFunction_USED + if (__pyx_CyFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_FusedFunction_USED + if (__pyx_FusedFunction_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_Coroutine_USED + if (__pyx_Coroutine_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_Generator_USED + if (__pyx_Generator_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_AsyncGen_USED + if (__pyx_AsyncGen_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + #ifdef __Pyx_StopAsyncIteration_USED + if (__pyx_StopAsyncIteration_init() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + /*--- Library function declarations ---*/ + /*--- Threads initialization code ---*/ + #if defined(WITH_THREAD) && PY_VERSION_HEX < 0x030700F0 && defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + PyEval_InitThreads(); + #endif + /*--- Module creation code ---*/ + #if CYTHON_PEP489_MULTI_PHASE_INIT + __pyx_m = __pyx_pyinit_module; + Py_INCREF(__pyx_m); + #else + #if PY_MAJOR_VERSION < 3 + __pyx_m = Py_InitModule4("cbedtools", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); + #else + __pyx_m = PyModule_Create(&__pyx_moduledef); + #endif + if (unlikely(!__pyx_m)) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) __PYX_ERR(0, 1, __pyx_L1_error) + Py_INCREF(__pyx_d); + __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) __PYX_ERR(0, 1, __pyx_L1_error) + Py_INCREF(__pyx_b); + __pyx_cython_runtime = PyImport_AddModule((char *) "cython_runtime"); if (unlikely(!__pyx_cython_runtime)) __PYX_ERR(0, 1, __pyx_L1_error) + Py_INCREF(__pyx_cython_runtime); + if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + /*--- Initialize various global constants etc. ---*/ + if (__Pyx_InitGlobals() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + if (__pyx_module_is_main_pybedtools__cbedtools) { + if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name_2, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + } + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error) + if (!PyDict_GetItemString(modules, "pybedtools.cbedtools")) { + if (unlikely(PyDict_SetItemString(modules, "pybedtools.cbedtools", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error) + } + } + #endif + /*--- Builtin init code ---*/ + if (__Pyx_InitCachedBuiltins() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + /*--- Constants init code ---*/ + if (__Pyx_InitCachedConstants() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + /*--- Global type/function init code ---*/ + (void)__Pyx_modinit_global_init_code(); + (void)__Pyx_modinit_variable_export_code(); + (void)__Pyx_modinit_function_export_code(); + if (unlikely(__Pyx_modinit_type_init_code() < 0)) __PYX_ERR(0, 1, __pyx_L1_error) + if (unlikely(__Pyx_modinit_type_import_code() < 0)) __PYX_ERR(0, 1, __pyx_L1_error) + (void)__Pyx_modinit_variable_import_code(); + (void)__Pyx_modinit_function_import_code(); + /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error) + #endif + + /* "pybedtools/cbedtools.pyx":17 + * + * from libcpp.string cimport string + * import numpy as np # <<<<<<<<<<<<<< + * + * # Python byte strings automatically coerce to/from C++ strings. + */ + __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 17, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) __PYX_ERR(0, 17, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":38 + * return s.decode('UTF-8', 'strict') + * + * integer_types = (int, long, np.int64) # <<<<<<<<<<<<<< + * + * + */ + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 38, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_int64); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 38, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 38, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(((PyObject *)(&PyInt_Type))); + __Pyx_GIVEREF(((PyObject *)(&PyInt_Type))); + PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)(&PyInt_Type))); + __Pyx_INCREF(((PyObject *)(&PyLong_Type))); + __Pyx_GIVEREF(((PyObject *)(&PyLong_Type))); + PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)(&PyLong_Type))); + __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_t_2); + __pyx_t_2 = 0; + if (PyDict_SetItem(__pyx_d, __pyx_n_s_integer_types, __pyx_t_1) < 0) __PYX_ERR(0, 38, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":50 + * """ + * from cython.operator cimport dereference as deref + * import sys # <<<<<<<<<<<<<< + * import subprocess + * from collections import defaultdict + */ + __pyx_t_1 = __Pyx_Import(__pyx_n_s_sys, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 50, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_sys, __pyx_t_1) < 0) __PYX_ERR(0, 50, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":51 + * from cython.operator cimport dereference as deref + * import sys + * import subprocess # <<<<<<<<<<<<<< + * from collections import defaultdict + * + */ + __pyx_t_1 = __Pyx_Import(__pyx_n_s_subprocess, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 51, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_subprocess, __pyx_t_1) < 0) __PYX_ERR(0, 51, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":52 + * import sys + * import subprocess + * from collections import defaultdict # <<<<<<<<<<<<<< + * + * cdef dict LOOKUPS = { + */ + __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 52, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(__pyx_n_s_defaultdict); + __Pyx_GIVEREF(__pyx_n_s_defaultdict); + PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_defaultdict); + __pyx_t_2 = __Pyx_Import(__pyx_n_s_collections, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 52, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_defaultdict); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 52, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_defaultdict, __pyx_t_1) < 0) __PYX_ERR(0, 52, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":55 + * + * cdef dict LOOKUPS = { + * "gff": {"chrom": 0, "start": 3, "end": 4, "stop": 4, "strand": 6}, # <<<<<<<<<<<<<< + * "vcf": {"chrom": 0, "start": 1}, + * "bed": {"chrom": 0, "start": 1, "end": 2, "stop": 2, "score": 4, "strand": 5} + */ + __pyx_t_2 = __Pyx_PyDict_NewPresized(3); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 55, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = __Pyx_PyDict_NewPresized(5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 55, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_chrom, __pyx_int_0) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_start, __pyx_int_3) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_end, __pyx_int_4) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_stop, __pyx_int_4) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_strand, __pyx_int_6) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_gff, __pyx_t_1) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":56 + * cdef dict LOOKUPS = { + * "gff": {"chrom": 0, "start": 3, "end": 4, "stop": 4, "strand": 6}, + * "vcf": {"chrom": 0, "start": 1}, # <<<<<<<<<<<<<< + * "bed": {"chrom": 0, "start": 1, "end": 2, "stop": 2, "score": 4, "strand": 5} + * } + */ + __pyx_t_1 = __Pyx_PyDict_NewPresized(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 56, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_chrom, __pyx_int_0) < 0) __PYX_ERR(0, 56, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_start, __pyx_int_1) < 0) __PYX_ERR(0, 56, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_vcf, __pyx_t_1) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":57 + * "gff": {"chrom": 0, "start": 3, "end": 4, "stop": 4, "strand": 6}, + * "vcf": {"chrom": 0, "start": 1}, + * "bed": {"chrom": 0, "start": 1, "end": 2, "stop": 2, "score": 4, "strand": 5} # <<<<<<<<<<<<<< + * } + * for ktype, kdict in list(LOOKUPS.items()): + */ + __pyx_t_1 = __Pyx_PyDict_NewPresized(6); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_chrom, __pyx_int_0) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_start, __pyx_int_1) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_end, __pyx_int_2) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_stop, __pyx_int_2) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_score, __pyx_int_4) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_strand, __pyx_int_5) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_bed, __pyx_t_1) < 0) __PYX_ERR(0, 55, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XGOTREF(__pyx_v_10pybedtools_9cbedtools_LOOKUPS); + __Pyx_DECREF_SET(__pyx_v_10pybedtools_9cbedtools_LOOKUPS, ((PyObject*)__pyx_t_2)); + __Pyx_GIVEREF(__pyx_t_2); + __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":59 + * "bed": {"chrom": 0, "start": 1, "end": 2, "stop": 2, "score": 4, "strand": 5} + * } + * for ktype, kdict in list(LOOKUPS.items()): # <<<<<<<<<<<<<< + * for k, v in list(kdict.items()): + * kdict[v] = k + */ + if (unlikely(__pyx_v_10pybedtools_9cbedtools_LOOKUPS == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%.30s'", "items"); + __PYX_ERR(0, 59, __pyx_L1_error) + } + __pyx_t_2 = __Pyx_PyDict_Items(__pyx_v_10pybedtools_9cbedtools_LOOKUPS); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PySequence_List(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + for (;;) { + if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) __PYX_ERR(0, 59, __pyx_L1_error) + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + #endif + if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) { + PyObject* sequence = __pyx_t_1; + Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + __PYX_ERR(0, 59, __pyx_L1_error) + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + if (likely(PyTuple_CheckExact(sequence))) { + __pyx_t_4 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_5 = PyTuple_GET_ITEM(sequence, 1); + } else { + __pyx_t_4 = PyList_GET_ITEM(sequence, 0); + __pyx_t_5 = PyList_GET_ITEM(sequence, 1); + } + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + #else + __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + #endif + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + } else { + Py_ssize_t index = -1; + __pyx_t_6 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext; + index = 0; __pyx_t_4 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_4)) goto __pyx_L4_unpacking_failed; + __Pyx_GOTREF(__pyx_t_4); + index = 1; __pyx_t_5 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_5)) goto __pyx_L4_unpacking_failed; + __Pyx_GOTREF(__pyx_t_5); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) __PYX_ERR(0, 59, __pyx_L1_error) + __pyx_t_7 = NULL; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + goto __pyx_L5_unpacking_done; + __pyx_L4_unpacking_failed:; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_7 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); + __PYX_ERR(0, 59, __pyx_L1_error) + __pyx_L5_unpacking_done:; + } + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ktype, __pyx_t_4) < 0) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + if (PyDict_SetItem(__pyx_d, __pyx_n_s_kdict, __pyx_t_5) < 0) __PYX_ERR(0, 59, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":60 + * } + * for ktype, kdict in list(LOOKUPS.items()): + * for k, v in list(kdict.items()): # <<<<<<<<<<<<<< + * kdict[v] = k + * + */ + __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_kdict); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_items); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_5 = NULL; + if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_5)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + __pyx_t_1 = (__pyx_t_5) ? __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5) : __Pyx_PyObject_CallNoArg(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = PySequence_List(__pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = __pyx_t_4; __Pyx_INCREF(__pyx_t_1); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + for (;;) { + if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_1)) break; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_4); __pyx_t_8++; if (unlikely(0 < 0)) __PYX_ERR(0, 60, __pyx_L1_error) + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + #endif + if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) { + PyObject* sequence = __pyx_t_4; + Py_ssize_t size = __Pyx_PySequence_SIZE(sequence); + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + __PYX_ERR(0, 60, __pyx_L1_error) + } + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + if (likely(PyTuple_CheckExact(sequence))) { + __pyx_t_5 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_6 = PyTuple_GET_ITEM(sequence, 1); + } else { + __pyx_t_5 = PyList_GET_ITEM(sequence, 0); + __pyx_t_6 = PyList_GET_ITEM(sequence, 1); + } + __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); + #else + __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + #endif + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + } else { + Py_ssize_t index = -1; + __pyx_t_9 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_7 = Py_TYPE(__pyx_t_9)->tp_iternext; + index = 0; __pyx_t_5 = __pyx_t_7(__pyx_t_9); if (unlikely(!__pyx_t_5)) goto __pyx_L8_unpacking_failed; + __Pyx_GOTREF(__pyx_t_5); + index = 1; __pyx_t_6 = __pyx_t_7(__pyx_t_9); if (unlikely(!__pyx_t_6)) goto __pyx_L8_unpacking_failed; + __Pyx_GOTREF(__pyx_t_6); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_9), 2) < 0) __PYX_ERR(0, 60, __pyx_L1_error) + __pyx_t_7 = NULL; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + goto __pyx_L9_unpacking_done; + __pyx_L8_unpacking_failed:; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_7 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); + __PYX_ERR(0, 60, __pyx_L1_error) + __pyx_L9_unpacking_done:; + } + if (PyDict_SetItem(__pyx_d, __pyx_n_s_k, __pyx_t_5) < 0) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (PyDict_SetItem(__pyx_d, __pyx_n_s_v, __pyx_t_6) < 0) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + + /* "pybedtools/cbedtools.pyx":61 + * for ktype, kdict in list(LOOKUPS.items()): + * for k, v in list(kdict.items()): + * kdict[v] = k # <<<<<<<<<<<<<< + * + * # Keys are tuples of start/start, stop/stop, start/stop, stop/start. + */ + __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_k); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 61, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_kdict); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 61, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_6); + __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_v); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (unlikely(PyObject_SetItem(__pyx_t_6, __pyx_t_5, __pyx_t_4) < 0)) __PYX_ERR(0, 61, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + + /* "pybedtools/cbedtools.pyx":60 + * } + * for ktype, kdict in list(LOOKUPS.items()): + * for k, v in list(kdict.items()): # <<<<<<<<<<<<<< + * kdict[v] = k + * + */ + } + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":59 + * "bed": {"chrom": 0, "start": 1, "end": 2, "stop": 2, "score": 4, "strand": 5} + * } + * for ktype, kdict in list(LOOKUPS.items()): # <<<<<<<<<<<<<< + * for k, v in list(kdict.items()): + * kdict[v] = k + */ + } + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":67 + * # < 0 | <= 1 | == 2 | != 3 | > 4 | >= 5 + * PROFILES_TRUE = { + * (0, 0, -1, 1): (2, 1, 5), # a == b, a >= b, a <= b # <<<<<<<<<<<<<< + * # a --------- + * # b --------- + */ + __pyx_t_2 = __Pyx_PyDict_NewPresized(16); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 67, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__31, __pyx_tuple__32) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":71 + * # b --------- + * + * (-1, -1, -1, -1): (0, 1), # a < b, a <= b # <<<<<<<<<<<<<< + * # a ---- + * # b ----- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__33, __pyx_tuple__34) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":75 + * # b ----- + * + * (-1, -1, -1, 0): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ---- + * # b ----- (book-ended) + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__35, __pyx_tuple__36) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":79 + * # b ----- (book-ended) + * + * (1, 1, 0, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ----- + * # b ---- (book-ended) + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__37, __pyx_tuple__38) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":83 + * # b ---- (book-ended) + * + * (1, 1, 1, 1): (4, 5), # a > b, a >= b # <<<<<<<<<<<<<< + * # a ------ + * # b ---- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__39, __pyx_tuple__40) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":87 + * # b ---- + * + * (0, 1, -1, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ------------ + * # b --------- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__41, __pyx_tuple__38) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":91 + * # b --------- + * + * (1, 0, -1, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ----------- + * # b ------------- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__42, __pyx_tuple__38) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":95 + * # b ------------- + * + * (-1, 0, -1, 1): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ------------- + * # b ----------- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__43, __pyx_tuple__36) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":99 + * # b ----------- + * + * (0, -1, -1, 1): (1,), # a <= b # <<<<<<<<<<<<<< + * # a --------- + * # b ------------ + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__44, __pyx_tuple__36) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":103 + * # b ------------ + * + * (-1, -1, -1, 1): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ----------- + * # b ----------- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__45, __pyx_tuple__36) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":107 + * # b ----------- + * + * (1, 1, -1, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a ----------- + * # b ----------- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__46, __pyx_tuple__38) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":111 + * # b ----------- + * + * (1, -1, -1, 1): tuple(), # undef # <<<<<<<<<<<<<< + * # a ---- + * # b ----------- + */ + __pyx_t_1 = __Pyx_PyObject_CallNoArg(((PyObject *)(&PyTuple_Type))); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 111, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__47, __pyx_t_1) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":115 + * # b ----------- + * + * (-1, 1, -1, 1): tuple(), # undef # <<<<<<<<<<<<<< + * # a ----------- + * # b ---- + */ + __pyx_t_1 = __Pyx_PyObject_CallNoArg(((PyObject *)(&PyTuple_Type))); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 115, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__48, __pyx_t_1) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + + /* "pybedtools/cbedtools.pyx":119 + * # b ---- + * + * (-1, 0, -1, 0): (1,), # a <= b # <<<<<<<<<<<<<< + * # a ----------- + * # b - + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__49, __pyx_tuple__36) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":123 + * # b - + * + * (1, 0, 0, 1): (5,), # a >= b # <<<<<<<<<<<<<< + * # a - + * # b ----------- + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__50, __pyx_tuple__38) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + + /* "pybedtools/cbedtools.pyx":127 + * # b ----------- + * + * (0, 0, 0, 0): (1, 2, 5), # a == b, a <= b, a >= b # <<<<<<<<<<<<<< + * # a - + * # b - (starts and stops are identical for all features) + */ + if (PyDict_SetItem(__pyx_t_2, __pyx_tuple__51, __pyx_tuple__52) < 0) __PYX_ERR(0, 67, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_PROFILES_TRUE, __pyx_t_2) < 0) __PYX_ERR(0, 66, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":133 + * + * + * class MalformedBedLineError(Exception): # <<<<<<<<<<<<<< + * pass + * + */ + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 133, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); + __Pyx_GIVEREF(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); + __pyx_t_1 = __Pyx_CalculateMetaclass(NULL, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 133, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_4 = __Pyx_Py3MetaclassPrepare(__pyx_t_1, __pyx_t_2, __pyx_n_s_MalformedBedLineError, __pyx_n_s_MalformedBedLineError, (PyObject *) NULL, __pyx_n_s_pybedtools_cbedtools, (PyObject *) NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 133, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_Py3ClassCreate(__pyx_t_1, __pyx_n_s_MalformedBedLineError, __pyx_t_2, __pyx_t_4, NULL, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 133, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_MalformedBedLineError, __pyx_t_5) < 0) __PYX_ERR(0, 133, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":137 + * + * + * class BedToolsFileError(Exception): # <<<<<<<<<<<<<< + * pass + * + */ + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); + __Pyx_GIVEREF(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); + __pyx_t_1 = __Pyx_CalculateMetaclass(NULL, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_4 = __Pyx_Py3MetaclassPrepare(__pyx_t_1, __pyx_t_2, __pyx_n_s_BedToolsFileError, __pyx_n_s_BedToolsFileError, (PyObject *) NULL, __pyx_n_s_pybedtools_cbedtools, (PyObject *) NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_Py3ClassCreate(__pyx_t_1, __pyx_n_s_BedToolsFileError, __pyx_t_2, __pyx_t_4, NULL, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_BedToolsFileError, __pyx_t_5) < 0) __PYX_ERR(0, 137, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":141 + * + * + * class Attributes(dict): # <<<<<<<<<<<<<< + * """ + * Class to map between a dict of attrs and fields[8] of a GFF Interval obj. + */ + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 141, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(((PyObject *)(&PyDict_Type))); + __Pyx_GIVEREF(((PyObject *)(&PyDict_Type))); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)(&PyDict_Type))); + __pyx_t_1 = __Pyx_CalculateMetaclass(NULL, __pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 141, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_4 = __Pyx_Py3MetaclassPrepare(__pyx_t_1, __pyx_t_2, __pyx_n_s_Attributes, __pyx_n_s_Attributes, (PyObject *) NULL, __pyx_n_s_pybedtools_cbedtools, __pyx_kp_s_Class_to_map_between_a_dict_of); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 141, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_4); + + /* "pybedtools/cbedtools.pyx":146 + * """ + * + * def __init__(self, attr_str=""): # <<<<<<<<<<<<<< + * attr_str = str(attr_str) + * self._attr_str = attr_str + */ + __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_10pybedtools_9cbedtools_10Attributes_1__init__, 0, __pyx_n_s_Attributes___init, NULL, __pyx_n_s_pybedtools_cbedtools, __pyx_d, ((PyObject *)__pyx_codeobj__54)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 146, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_5, __pyx_tuple__55); + if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_init, __pyx_t_5) < 0) __PYX_ERR(0, 146, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":182 + * self[field] = value.replace('"', '') + * + * def __str__(self): # <<<<<<<<<<<<<< + * # stringify all items first + * items = [] + */ + __pyx_t_5 = __Pyx_CyFunction_New(&__pyx_mdef_10pybedtools_9cbedtools_10Attributes_3__str__, 0, __pyx_n_s_Attributes___str, NULL, __pyx_n_s_pybedtools_cbedtools, __pyx_d, ((PyObject *)__pyx_codeobj__57)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 182, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (__Pyx_SetNameInClass(__pyx_t_4, __pyx_n_s_str, __pyx_t_5) < 0) __PYX_ERR(0, 182, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "pybedtools/cbedtools.pyx":141 + * + * + * class Attributes(dict): # <<<<<<<<<<<<<< + * """ + * Class to map between a dict of attrs and fields[8] of a GFF Interval obj. + */ + __pyx_t_5 = __Pyx_Py3ClassCreate(__pyx_t_1, __pyx_n_s_Attributes, __pyx_t_2, __pyx_t_4, NULL, 0, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 141, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_5); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attributes, __pyx_t_5) < 0) __PYX_ERR(0, 141, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":725 + * + * + * def overlap(int s1, int s2, int e1, int e2): # <<<<<<<<<<<<<< + * return min(e1, e2) - max(s1, s2) + * + */ + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10pybedtools_9cbedtools_3overlap, NULL, __pyx_n_s_pybedtools_cbedtools); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 725, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_overlap, __pyx_t_2) < 0) __PYX_ERR(0, 725, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":932 + * + * # search() is an alias for all_hits + * search = all_hits # <<<<<<<<<<<<<< + * + * def any_hits(self, Interval interval, bool same_strand=False, float overlap=0.0): + */ + __Pyx_GetNameInClass(__pyx_t_2, (PyObject *)__pyx_ptype_10pybedtools_9cbedtools_IntervalFile, __pyx_n_s_all_hits); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 932, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem((PyObject *)__pyx_ptype_10pybedtools_9cbedtools_IntervalFile->tp_dict, __pyx_n_s_search, __pyx_t_2) < 0) __PYX_ERR(0, 932, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + PyType_Modified(__pyx_ptype_10pybedtools_9cbedtools_IntervalFile); + + /* "(tree fragment)":1 + * def __pyx_unpickle_IntervalIterator(__pyx_type, long __pyx_checksum, __pyx_state): # <<<<<<<<<<<<<< + * cdef object __pyx_PickleError + * cdef object __pyx_result + */ + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_10pybedtools_9cbedtools_5__pyx_unpickle_IntervalIterator, NULL, __pyx_n_s_pybedtools_cbedtools); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_pyx_unpickle_IntervalIterator, __pyx_t_2) < 0) __PYX_ERR(1, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "pybedtools/cbedtools.pyx":1 + * # distutils: language = c++ # <<<<<<<<<<<<<< + * # cython: language_level=2 + * + */ + __pyx_t_2 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_create_interval_from_list_line_5, __pyx_kp_u_Create_an_Interval_object_from) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_IntervalFile_all_hits_line_888, __pyx_kp_u_Signature_IntervalFile_all_hits) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_IntervalFile_any_hits_line_934, __pyx_kp_u_Signature_IntervalFile_any_hits) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_IntervalFile_count_hits_line_970, __pyx_kp_u_Signature_IntervalFile_count_hi) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "vector.from_py":45 + * + * @cname("__pyx_convert_vector_from_py_std_3a__3a_string") + * cdef vector[X] __pyx_convert_vector_from_py_std_3a__3a_string(object o) except *: # <<<<<<<<<<<<<< + * cdef vector[X] v + * for item in o: + */ + + /*--- Wrapped vars code ---*/ + + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_6); + __Pyx_XDECREF(__pyx_t_9); + if (__pyx_m) { + if (__pyx_d) { + __Pyx_AddTraceback("init pybedtools.cbedtools", __pyx_clineno, __pyx_lineno, __pyx_filename); + } + Py_CLEAR(__pyx_m); + } else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_ImportError, "init pybedtools.cbedtools"); + } + __pyx_L0:; + __Pyx_RefNannyFinishContext(); + #if CYTHON_PEP489_MULTI_PHASE_INIT + return (__pyx_m != NULL) ? 0 : -1; + #elif PY_MAJOR_VERSION >= 3 + return __pyx_m; + #else + return; + #endif +} + +/* --- Runtime support code --- */ +/* Refnanny */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + void *r = NULL; + m = PyImport_ImportModule(modname); + if (!m) goto end; + p = PyObject_GetAttrString(m, "RefNannyAPI"); + if (!p) goto end; + r = PyLong_AsVoidPtr(p); +end: + Py_XDECREF(p); + Py_XDECREF(m); + return (__Pyx_RefNannyAPIStruct *)r; +} +#endif + +/* 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 + +/* GetBuiltinName */ +static PyObject *__Pyx_GetBuiltinName(PyObject *name) { + PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); + if (unlikely(!result)) { + 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; +} + +/* 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; + } +#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); +} + +/* PyCFunctionFastCall */ +#if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { + PyCFunctionObject *func = (PyCFunctionObject*)func_obj; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); + int flags = PyCFunction_GET_FLAGS(func); + assert(PyCFunction_Check(func)); + assert(METH_FASTCALL == (flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_KEYWORDS | METH_STACKLESS))); + assert(nargs >= 0); + assert(nargs == 0 || args != NULL); + /* _PyCFunction_FastCallDict() must not be called with an exception set, + because it may clear it (directly or indirectly) and so the + caller loses its exception */ + assert(!PyErr_Occurred()); + if ((PY_VERSION_HEX < 0x030700A0) || unlikely(flags & METH_KEYWORDS)) { + return (*((__Pyx_PyCFunctionFastWithKeywords)(void*)meth)) (self, args, nargs, NULL); + } else { + return (*((__Pyx_PyCFunctionFast)(void*)meth)) (self, args, nargs); + } +} +#endif + +/* PyFunctionFastCall */ +#if CYTHON_FAST_PYCALL +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; +} +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { + PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); + PyObject *globals = PyFunction_GET_GLOBALS(func); + PyObject *argdefs = PyFunction_GET_DEFAULTS(func); + PyObject *closure; +#if PY_MAJOR_VERSION >= 3 + PyObject *kwdefs; +#endif + PyObject *kwtuple, **k; + PyObject **d; + Py_ssize_t nd; + Py_ssize_t nk; + PyObject *result; + assert(kwargs == NULL || PyDict_Check(kwargs)); + nk = kwargs ? PyDict_Size(kwargs) : 0; + if (Py_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 +#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 + +/* PyObjectCallOneArg */ +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, &arg, 1); + } +#endif + if (likely(PyCFunction_Check(func))) { + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); +#if CYTHON_FAST_PYCCALL + } else if (__Pyx_PyFastCFunction_Check(func)) { + return __Pyx_PyCFunction_FastCall(func, &arg, 1); +#endif + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +/* PyObjectCall2Args */ +static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { + PyObject *args, *result = NULL; + #if CYTHON_FAST_PYCALL + if (PyFunction_Check(function)) { + PyObject *args[2] = {arg1, arg2}; + return __Pyx_PyFunction_FastCall(function, args, 2); + } + #endif + #if CYTHON_FAST_PYCCALL + if (__Pyx_PyFastCFunction_Check(function)) { + PyObject *args[2] = {arg1, arg2}; + return __Pyx_PyCFunction_FastCall(function, args, 2); + } + #endif + args = PyTuple_New(2); + if (unlikely(!args)) goto done; + Py_INCREF(arg1); + PyTuple_SET_ITEM(args, 0, arg1); + Py_INCREF(arg2); + PyTuple_SET_ITEM(args, 1, arg2); + Py_INCREF(function); + result = __Pyx_PyObject_Call(function, args, NULL); + Py_DECREF(args); + Py_DECREF(function); +done: + return result; +} + +/* decode_c_bytes */ +static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( + const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + if (unlikely((start < 0) | (stop < 0))) { + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + if (stop > length) + stop = length; + if (unlikely(stop <= start)) + return __Pyx_NewRef(__pyx_empty_unicode); + length = stop - start; + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +/* 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 **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; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + 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; + 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 = (**name == key) ? 0 : + #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; + 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; + } + } + 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: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +/* RaiseArgTupleInvalid */ +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +/* PyObjectSetAttrStr */ +#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_setattro)) + return tp->tp_setattro(obj, attr_name, value); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_setattr)) + return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); +#endif + return PyObject_SetAttr(obj, attr_name, value); +} +#endif + +/* PyIntBinop */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { + (void)inplace; + (void)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 - b); + if (likely((x^a) >= 0 || (x^~b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_subtract(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; +#ifdef HAVE_LONG_LONG + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; +#endif + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + break; +#ifdef HAVE_LONG_LONG + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + goto long_long; +#endif + } + CYTHON_FALLTHROUGH; + default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2); + } + } + x = a - b; + return PyLong_FromLong(x); +#ifdef HAVE_LONG_LONG + long_long: + llx = lla - llb; + return PyLong_FromLongLong(llx); +#endif + + + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("subtract", return NULL) + result = ((double)a) - (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2); +} +#endif + +/* BytesEquals */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + 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 + 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 +} + +/* PyObjectCallNoArg */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, NULL, 0); + } +#endif +#if defined(__Pyx_CyFunction_USED) && defined(NDEBUG) + if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) +#else + if (likely(PyCFunction_Check(func))) +#endif + { + if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { + return __Pyx_PyObject_CallMethO(func, NULL); + } + } + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); +} +#endif + +/* RaiseTooManyValuesToUnpack */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +/* RaiseNeedMoreValuesToUnpack */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +/* IterFinish */ +static CYTHON_INLINE int __Pyx_IterFinish(void) { +#if CYTHON_FAST_THREAD_STATE + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject* exc_type = tstate->curexc_type; + if (unlikely(exc_type)) { + if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) { + PyObject *exc_value, *exc_tb; + exc_value = tstate->curexc_value; + exc_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; + Py_DECREF(exc_type); + Py_XDECREF(exc_value); + Py_XDECREF(exc_tb); + return 0; + } else { + return -1; + } + } + return 0; +#else + if (unlikely(PyErr_Occurred())) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { + PyErr_Clear(); + return 0; + } else { + return -1; + } + } + return 0; +#endif +} + +/* UnpackItemEndCheck */ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); + __Pyx_RaiseTooManyValuesError(expected); + return -1; + } + return __Pyx_IterFinish(); +} + +/* PyIntCompare */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED long inplace) { + if (op1 == op2) { + Py_RETURN_TRUE; + } + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long a = PyInt_AS_LONG(op1); + if (a == b) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS + if (likely(PyLong_CheckExact(op1))) { + int unequal; + unsigned long uintval; + Py_ssize_t size = Py_SIZE(op1); + const digit* digits = ((PyLongObject*)op1)->ob_digit; + if (intval == 0) { + if (size == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } else if (intval < 0) { + if (size >= 0) + Py_RETURN_FALSE; + intval = -intval; + size = -size; + } else { + if (size <= 0) + Py_RETURN_FALSE; + } + uintval = (unsigned long) intval; +#if PyLong_SHIFT * 4 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 4)) { + unequal = (size != 5) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[4] != ((uintval >> (4 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif +#if PyLong_SHIFT * 3 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 3)) { + unequal = (size != 4) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[3] != ((uintval >> (3 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif +#if PyLong_SHIFT * 2 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 2)) { + unequal = (size != 3) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)) | (digits[2] != ((uintval >> (2 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif +#if PyLong_SHIFT * 1 < SIZEOF_LONG*8 + if (uintval >> (PyLong_SHIFT * 1)) { + unequal = (size != 2) || (digits[0] != (uintval & (unsigned long) PyLong_MASK)) + | (digits[1] != ((uintval >> (1 * PyLong_SHIFT)) & (unsigned long) PyLong_MASK)); + } else +#endif + unequal = (size != 1) || (((unsigned long) digits[0]) != (uintval & (unsigned long) PyLong_MASK)); + if (unequal == 0) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + if ((double)a == (double)b) Py_RETURN_TRUE; else Py_RETURN_FALSE; + } + return ( + PyObject_RichCompare(op1, op2, Py_EQ)); +} + +/* UnpackUnboundCMethod */ +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))) + #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); + } +#endif + return 0; +} + +/* CallUnboundCMethod0 */ +static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) { + PyObject *args, *result = NULL; + if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; +#if CYTHON_ASSUME_SAFE_MACROS + args = PyTuple_New(1); + if (unlikely(!args)) goto bad; + Py_INCREF(self); + PyTuple_SET_ITEM(args, 0, self); +#else + args = PyTuple_Pack(1, self); + if (unlikely(!args)) goto bad; +#endif + result = __Pyx_PyObject_Call(cfunc->method, args, NULL); + Py_DECREF(args); +bad: + return result; +} + +/* py_dict_iteritems */ +static CYTHON_INLINE PyObject* __Pyx_PyDict_IterItems(PyObject* d) { + if (PY_MAJOR_VERSION >= 3) + return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_items, d); + else + return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_iteritems, d); +} + +/* GetItemInt */ +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!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 { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return NULL; + PyErr_Clear(); + } + } + return m->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)); +} + +/* ObjectGetItem */ +#if CYTHON_USE_TYPE_SLOTS +static PyObject *__Pyx_PyObject_GetIndex(PyObject *obj, PyObject* index) { + PyObject *runerr = NULL; + Py_ssize_t key_value; + PySequenceMethods *m = Py_TYPE(obj)->tp_as_sequence; + if (unlikely(!(m && m->sq_item))) { + PyErr_Format(PyExc_TypeError, "'%.200s' object is not subscriptable", Py_TYPE(obj)->tp_name); + return NULL; + } + 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)) { + PyErr_Clear(); + PyErr_Format(PyExc_IndexError, "cannot fit '%.200s' into an index-sized integer", Py_TYPE(index)->tp_name); + } + return NULL; +} +static PyObject *__Pyx_PyObject_GetItem(PyObject *obj, PyObject* key) { + PyMappingMethods *m = Py_TYPE(obj)->tp_as_mapping; + if (likely(m && m->mp_subscript)) { + return m->mp_subscript(obj, key); + } + return __Pyx_PyObject_GetIndex(obj, key); +} +#endif + +/* GetTopmostException */ +#if CYTHON_USE_EXC_INFO_STACK +static _PyErr_StackItem * +__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) +{ + _PyErr_StackItem *exc_info = tstate->exc_info; + while ((exc_info->exc_type == NULL || exc_info->exc_type == 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 + _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); + *type = exc_info->exc_type; + *value = exc_info->exc_value; + *tb = exc_info->exc_traceback; + #else + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + #endif + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +} +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + 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 + +/* PyErrExceptionMatches */ +#if CYTHON_FAST_THREAD_STATE +static int __Pyx_PyErr_ExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i<n; i++) { + if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1; + } +#endif + for (i=0; i<n; i++) { + if (__Pyx_PyErr_GivenExceptionMatches(exc_type, PyTuple_GET_ITEM(tuple, i))) return 1; + } + return 0; +} +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) { + PyObject *exc_type = tstate->curexc_type; + if (exc_type == err) return 1; + if (unlikely(!exc_type)) return 0; + if (unlikely(PyTuple_Check(err))) + return __Pyx_PyErr_ExceptionMatchesTuple(exc_type, err); + return __Pyx_PyErr_GivenExceptionMatches(exc_type, err); +} +#endif + +/* PyErrFetchRestore */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + *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 + +/* StringJoin */ +#if !CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) { + return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL); +} +#endif + +/* 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 + +/* FetchCommonType */ +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { + PyObject* fake_module; + PyTypeObject* cached_type = NULL; + fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); + if (!fake_module) return NULL; + Py_INCREF(fake_module); + cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name); + if (cached_type) { + if (!PyType_Check((PyObject*)cached_type)) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s is not a type object", + type->tp_name); + goto bad; + } + if (cached_type->tp_basicsize != type->tp_basicsize) { + PyErr_Format(PyExc_TypeError, + "Shared Cython type %.200s has the wrong size, try recompiling", + type->tp_name); + goto bad; + } + } else { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad; + PyErr_Clear(); + if (PyType_Ready(type) < 0) goto bad; + if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0) + goto bad; + Py_INCREF(type); + cached_type = type; + } +done: + Py_DECREF(fake_module); + return cached_type; +bad: + Py_XDECREF(cached_type); + cached_type = NULL; + goto done; +} + +/* CythonFunctionShared */ +#include <structmember.h> +static PyObject * +__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) +{ + if (unlikely(op->func_doc == NULL)) { + if (op->func.m_ml->ml_doc) { +#if PY_MAJOR_VERSION >= 3 + op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); +#else + op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); +#endif + if (unlikely(op->func_doc == NULL)) + return NULL; + } else { + Py_INCREF(Py_None); + return Py_None; + } + } + Py_INCREF(op->func_doc); + return op->func_doc; +} +static int +__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value, CYTHON_UNUSED void *context) +{ + PyObject *tmp = op->func_doc; + if (value == NULL) { + value = Py_None; + } + Py_INCREF(value); + op->func_doc = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) +{ + if (unlikely(op->func_name == NULL)) { +#if PY_MAJOR_VERSION >= 3 + op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); +#else + op->func_name = PyString_InternFromString(op->func.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, CYTHON_UNUSED void *context) +{ + PyObject *tmp; +#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; + } + tmp = op->func_name; + Py_INCREF(value); + op->func_name = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) +{ + Py_INCREF(op->func_qualname); + return op->func_qualname; +} +static int +__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value, CYTHON_UNUSED void *context) +{ + PyObject *tmp; +#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; + } + tmp = op->func_qualname; + Py_INCREF(value); + op->func_qualname = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) +{ + PyObject *self; + self = m->func_closure; + if (self == NULL) + self = Py_None; + Py_INCREF(self); + return self; +} +static PyObject * +__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *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, CYTHON_UNUSED void *context) +{ + PyObject *tmp; + 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; + } + tmp = op->func_dict; + Py_INCREF(value); + op->func_dict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) +{ + Py_INCREF(op->func_globals); + return op->func_globals; +} +static PyObject * +__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) +{ + Py_INCREF(Py_None); + return Py_None; +} +static PyObject * +__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) +{ + PyObject* result = (op->func_code) ? op->func_code : Py_None; + 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 = PySequence_ITEM(res, 0); + if (unlikely(!op->defaults_tuple)) result = -1; + else { + op->defaults_kwdict = 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, CYTHON_UNUSED void *context) { + PyObject* tmp; + if (!value) { + value = Py_None; + } else if (value != Py_None && !PyTuple_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__defaults__ must be set to a tuple object"); + return -1; + } + Py_INCREF(value); + tmp = op->defaults_tuple; + op->defaults_tuple = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) { + PyObject* result = op->defaults_tuple; + if (unlikely(!result)) { + if (op->defaults_getter) { + if (__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, CYTHON_UNUSED void *context) { + PyObject* tmp; + if (!value) { + value = Py_None; + } else if (value != Py_None && !PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__kwdefaults__ must be set to a dict object"); + return -1; + } + Py_INCREF(value); + tmp = op->defaults_kwdict; + op->defaults_kwdict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) { + PyObject* result = op->defaults_kwdict; + if (unlikely(!result)) { + if (op->defaults_getter) { + if (__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, CYTHON_UNUSED void *context) { + PyObject* tmp; + if (!value || value == Py_None) { + value = NULL; + } else if (!PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "__annotations__ must be set to a dict object"); + return -1; + } + Py_XINCREF(value); + tmp = op->func_annotations; + op->func_annotations = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *context) { + PyObject* result = op->func_annotations; + if (unlikely(!result)) { + result = PyDict_New(); + if (unlikely(!result)) return NULL; + op->func_annotations = result; + } + Py_INCREF(result); + return result; +} +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 *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 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}, + {0, 0, 0, 0, 0} +}; +static PyMemberDef __pyx_CyFunction_members[] = { + {(char *) "__module__", T_OBJECT, offsetof(PyCFunctionObject, m_module), PY_WRITE_RESTRICTED, 0}, + {0, 0, 0, 0, 0} +}; +static PyObject * +__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) +{ +#if PY_MAJOR_VERSION >= 3 + Py_INCREF(m->func_qualname); + return m->func_qualname; +#else + return PyString_FromString(m->func.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 +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func_weakreflist) +#else +#define __Pyx_CyFunction_weakreflist(cyfunc) ((cyfunc)->func.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 (unlikely(op == NULL)) + return NULL; + op->flags = flags; + __Pyx_CyFunction_weakreflist(op) = NULL; + op->func.m_ml = ml; + op->func.m_self = (PyObject *) op; + Py_XINCREF(closure); + op->func_closure = closure; + Py_XINCREF(module); + op->func.m_module = module; + op->func_dict = NULL; + op->func_name = NULL; + Py_INCREF(qualname); + op->func_qualname = qualname; + op->func_doc = NULL; + op->func_classobj = NULL; + 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; + return (PyObject *) op; +} +static int +__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) +{ + Py_CLEAR(m->func_closure); + Py_CLEAR(m->func.m_module); + 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); + Py_CLEAR(m->func_classobj); + Py_CLEAR(m->defaults_tuple); + Py_CLEAR(m->defaults_kwdict); + Py_CLEAR(m->func_annotations); + 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); + PyObject_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); + Py_VISIT(m->func.m_module); + 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); + Py_VISIT(m->func_classobj); + Py_VISIT(m->defaults_tuple); + Py_VISIT(m->defaults_kwdict); + 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_descr_get(PyObject *func, PyObject *obj, PyObject *type) +{ +#if PY_MAJOR_VERSION < 3 + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { + Py_INCREF(func); + return func; + } + if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { + if (type == NULL) + type = (PyObject *)(Py_TYPE(obj)); + return __Pyx_PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); + } + if (obj == Py_None) + obj = NULL; +#endif + return __Pyx_PyMethod_New(func, obj, type); +} +static PyObject* +__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromFormat("<cyfunction %U at %p>", + op->func_qualname, (void *)op); +#else + return PyString_FromFormat("<cyfunction %s at %p>", + PyString_AsString(op->func_qualname), (void *)op); +#endif +} +static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) { + PyCFunctionObject* f = (PyCFunctionObject*)func; + PyCFunction meth = f->m_ml->ml_meth; + Py_ssize_t size; + switch (f->m_ml->ml_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)) { + size = PyTuple_GET_SIZE(arg); + if (likely(size == 0)) + return (*meth)(self, NULL); + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + case METH_O: + if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + size = PyTuple_GET_SIZE(arg); + if (likely(size == 1)) { + PyObject *result, *arg0; + #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + arg0 = PyTuple_GET_ITEM(arg, 0); + #else + arg0 = 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; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags in " + "__Pyx_CyFunction_Call. METH_OLDARGS is no " + "longer supported!"); + return NULL; + } + PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", + f->m_ml->ml_name); + return NULL; +} +static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + return __Pyx_CyFunction_CallMethod(func, ((PyCFunctionObject*)func)->m_self, arg, kw); +} +static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) { + PyObject *result; + __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func; + if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) { + Py_ssize_t argc; + PyObject *new_args; + PyObject *self; + argc = PyTuple_GET_SIZE(args); + 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; +} +static PyTypeObject __pyx_CyFunctionType_type = { + PyVarObject_HEAD_INIT(0, 0) + "cython_function_or_method", + sizeof(__pyx_CyFunctionObject), + 0, + (destructor) __Pyx_CyFunction_dealloc, + 0, + 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, + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, + 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_CyFunction_descr_get, + 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 PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000 + 0, +#endif +#if PY_VERSION_HEX >= 0x030C0000 + 0, +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000 && PY_VERSION_HEX < 0x030a0000 + 0, +#endif +}; +static int __pyx_CyFunction_init(void) { + __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); + 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; +} + +/* RaiseException */ +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + __Pyx_PyThreadState_declare + 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 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 + +/* 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, *local_value, *local_tb; +#if CYTHON_FAST_THREAD_STATE + PyObject *tmp_type, *tmp_value, *tmp_tb; + 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; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if 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; + 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; + } + #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; +} + +/* 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); +} + +/* SliceTupleAndList */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE void __Pyx_crop_slice(Py_ssize_t* _start, Py_ssize_t* _stop, Py_ssize_t* _length) { + Py_ssize_t start = *_start, stop = *_stop, length = *_length; + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + else if (stop > length) + stop = length; + *_length = stop - start; + *_start = start; + *_stop = stop; +} +static CYTHON_INLINE void __Pyx_copy_object_array(PyObject** 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_PyList_GetSlice( + PyObject* src, Py_ssize_t start, Py_ssize_t stop) { + PyObject* dest; + Py_ssize_t length = PyList_GET_SIZE(src); + __Pyx_crop_slice(&start, &stop, &length); + if (unlikely(length <= 0)) + return PyList_New(0); + dest = PyList_New(length); + if (unlikely(!dest)) + return NULL; + __Pyx_copy_object_array( + ((PyListObject*)src)->ob_item + start, + ((PyListObject*)dest)->ob_item, + length); + return dest; +} +static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice( + PyObject* src, Py_ssize_t start, Py_ssize_t stop) { + PyObject* dest; + Py_ssize_t length = PyTuple_GET_SIZE(src); + __Pyx_crop_slice(&start, &stop, &length); + if (unlikely(length <= 0)) + return PyTuple_New(0); + dest = PyTuple_New(length); + if (unlikely(!dest)) + return NULL; + __Pyx_copy_object_array( + ((PyTupleObject*)src)->ob_item + start, + ((PyTupleObject*)dest)->ob_item, + length); + return dest; +} +#endif + +/* PyIntBinop */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AndObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { + (void)inplace; + (void)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 + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + 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 + +/* PyIntBinop */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, int inplace, int zerodivision_check) { + (void)inplace; + (void)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 + 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 + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + 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; + double a = PyFloat_AS_DOUBLE(op1); + 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 + +/* SetItemInt */ +static int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { + int r; + if (!j) return -1; + r = PyObject_SetItem(o, j, v); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, 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) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o)); + if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o)))) { + PyObject* old = PyList_GET_ITEM(o, n); + Py_INCREF(v); + PyList_SET_ITEM(o, n, v); + Py_DECREF(old); + return 1; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_ass_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return -1; + PyErr_Clear(); + } + } + return m->sq_ass_item(o, i, v); + } + } +#else +#if CYTHON_COMPILING_IN_PYPY + if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) +#else + if (is_list || PySequence_Check(o)) +#endif + { + return PySequence_SetItem(o, i, v); + } +#endif + return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); +} + +/* ArgTypeTest */ +static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact) +{ + 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; + } + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); + return 0; +} + +/* WriteUnraisableException */ +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback, CYTHON_UNUSED 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 + __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 +} + +/* 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 (unlikely(!r)) { + PyErr_Clear(); + return 0; + } else { + Py_DECREF(r); + return 1; + } +} + +/* IterNext */ +static PyObject *__Pyx_PyIter_Next2Default(PyObject* defval) { + PyObject* exc_type; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + exc_type = __Pyx_PyErr_Occurred(); + if (unlikely(exc_type)) { + if (!defval || unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) + return NULL; + __Pyx_PyErr_Clear(); + Py_INCREF(defval); + return defval; + } + if (defval) { + Py_INCREF(defval); + return defval; + } + __Pyx_PyErr_SetNone(PyExc_StopIteration); + return NULL; +} +static void __Pyx_PyIter_Next_ErrorNoIterator(PyObject *iterator) { + PyErr_Format(PyExc_TypeError, + "%.200s object is not an iterator", Py_TYPE(iterator)->tp_name); +} +static CYTHON_INLINE PyObject *__Pyx_PyIter_Next2(PyObject* iterator, PyObject* defval) { + PyObject* next; + iternextfunc iternext = Py_TYPE(iterator)->tp_iternext; + if (likely(iternext)) { +#if CYTHON_USE_TYPE_SLOTS || CYTHON_COMPILING_IN_PYPY + next = iternext(iterator); + if (likely(next)) + return next; + #if PY_VERSION_HEX >= 0x02070000 && CYTHON_COMPILING_IN_CPYTHON + if (unlikely(iternext == &_PyObject_NextNotImplemented)) + return NULL; + #endif +#else + next = PyIter_Next(iterator); + if (likely(next)) + return next; +#endif + } else if (CYTHON_USE_TYPE_SLOTS || unlikely(!PyIter_Check(iterator))) { + __Pyx_PyIter_Next_ErrorNoIterator(iterator); + return NULL; + } +#if !CYTHON_USE_TYPE_SLOTS + else { + next = PyIter_Next(iterator); + if (likely(next)) + return next; + } +#endif + return __Pyx_PyIter_Next2Default(defval); +} + +/* None */ +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +/* 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 = __Pyx_GetAttr(o, n); + return (likely(r)) ? r : __Pyx_GetAttr3Default(d); +} + +/* FastTypeChecks */ +#if CYTHON_COMPILING_IN_CPYTHON +static int __Pyx_InBases(PyTypeObject *a, PyTypeObject *b) { + while (a) { + a = a->tp_base; + 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); +} +#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) { + int res = exc_type1 ? __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type1) : 0; + if (!res) { + res = __Pyx_IsSubtype((PyTypeObject*)err, (PyTypeObject*)exc_type2); + } + return res; +} +#endif +static int __Pyx_PyErr_GivenExceptionMatchesTuple(PyObject *exc_type, PyObject *tuple) { + Py_ssize_t i, n; + assert(PyExceptionClass_Check(exc_type)); + n = PyTuple_GET_SIZE(tuple); +#if PY_MAJOR_VERSION >= 3 + for (i=0; i<n; i++) { + if (exc_type == PyTuple_GET_ITEM(tuple, i)) return 1; + } +#endif + for (i=0; i<n; i++) { + PyObject *t = PyTuple_GET_ITEM(tuple, i); + #if PY_MAJOR_VERSION < 3 + if (likely(exc_type == t)) return 1; + #endif + if (likely(PyExceptionClass_Check(t))) { + if (__Pyx_inner_PyErr_GivenExceptionMatches2(exc_type, NULL, t)) return 1; + } else { + } + } + return 0; +} +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject* exc_type) { + if (likely(err == exc_type)) return 1; + if (likely(PyExceptionClass_Check(err))) { + if (likely(PyExceptionClass_Check(exc_type))) { + return __Pyx_inner_PyErr_GivenExceptionMatches2(err, NULL, exc_type); + } else if (likely(PyTuple_Check(exc_type))) { + return __Pyx_PyErr_GivenExceptionMatchesTuple(err, exc_type); + } else { + } + } + return PyErr_GivenExceptionMatches(err, exc_type); +} +static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *exc_type1, PyObject *exc_type2) { + assert(PyExceptionClass_Check(exc_type1)); + assert(PyExceptionClass_Check(exc_type2)); + if (likely(err == exc_type1 || err == exc_type2)) return 1; + if (likely(PyExceptionClass_Check(err))) { + return __Pyx_inner_PyErr_GivenExceptionMatches2(err, exc_type1, exc_type2); + } + return (PyErr_GivenExceptionMatches(err, exc_type1) || PyErr_GivenExceptionMatches(err, exc_type2)); +} +#endif + +/* SwapException */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if CYTHON_USE_EXC_INFO_STACK + _PyErr_StackItem *exc_info = tstate->exc_info; + tmp_type = exc_info->exc_type; + tmp_value = exc_info->exc_value; + tmp_tb = exc_info->exc_traceback; + exc_info->exc_type = *type; + exc_info->exc_value = *value; + exc_info->exc_traceback = *tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; + #endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#else +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} +#endif + +/* Import */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_MAJOR_VERSION < 3 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) { + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + if (!module) { + if (!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 (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, (PyObject *)NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + 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)) { + 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; +} + +/* PyObject_GenericGetAttrNoDict */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject *__Pyx_RaiseGenericGetAttributeError(PyTypeObject *tp, PyObject *attr_name) { + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'%.50s' object has no attribute '%U'", + tp->tp_name, attr_name); +#else + "'%.50s' object has no attribute '%.400s'", + tp->tp_name, PyString_AS_STRING(attr_name)); +#endif + return NULL; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_GenericGetAttrNoDict(PyObject* obj, PyObject* attr_name) { + PyObject *descr; + PyTypeObject *tp = Py_TYPE(obj); + if (unlikely(!PyString_Check(attr_name))) { + return PyObject_GenericGetAttr(obj, attr_name); + } + assert(!tp->tp_dictoffset); + descr = _PyType_Lookup(tp, attr_name); + if (unlikely(!descr)) { + return __Pyx_RaiseGenericGetAttributeError(tp, attr_name); + } + Py_INCREF(descr); + #if PY_MAJOR_VERSION < 3 + if (likely(PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_HAVE_CLASS))) + #endif + { + descrgetfunc f = Py_TYPE(descr)->tp_descr_get; + if (unlikely(f)) { + PyObject *res = f(descr, obj, (PyObject *)tp); + Py_DECREF(descr); + return res; + } + } + return descr; +} +#endif + +/* PyObject_GenericGetAttr */ +#if CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP && PY_VERSION_HEX < 0x03070000 +static PyObject* __Pyx_PyObject_GenericGetAttr(PyObject* obj, PyObject* attr_name) { + if (unlikely(Py_TYPE(obj)->tp_dictoffset)) { + return PyObject_GenericGetAttr(obj, attr_name); + } + return __Pyx_PyObject_GenericGetAttrNoDict(obj, attr_name); +} +#endif + +/* SetVTable */ +static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +/* 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; +} + +/* SetupReduce */ +static int __Pyx_setup_reduce_is_named(PyObject* meth, PyObject* name) { + int ret; + PyObject *name_attr; + name_attr = __Pyx_PyObject_GetAttrStr(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_GetAttrStr(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()) + PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_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; +} + +/* TypeImport */ +#ifndef __PYX_HAVE_RT_ImportType_0_29_37 +#define __PYX_HAVE_RT_ImportType_0_29_37 +static PyTypeObject *__Pyx_ImportType_0_29_37(PyObject *module, const char *module_name, const char *class_name, + size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_0_29_37 check_size) +{ + PyObject *result = 0; + char warning[200]; + Py_ssize_t basicsize; + Py_ssize_t itemsize; +#ifdef Py_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; + } +#ifndef Py_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); + goto bad; + } + if (check_size == __Pyx_ImportType_CheckSize_Error_0_29_37 && (size_t)basicsize != 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); + goto bad; + } + else if (check_size == __Pyx_ImportType_CheckSize_Warn_0_29_37 && (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 + +/* py_dict_items */ +static CYTHON_INLINE PyObject* __Pyx_PyDict_Items(PyObject* d) { + if (PY_MAJOR_VERSION >= 3) + return __Pyx_CallUnboundCMethod0(&__pyx_umethod_PyDict_Type_items, d); + else + return PyDict_Items(d); +} + +/* CalculateMetaclass */ +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { + Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases); + for (i=0; i < nbases; i++) { + PyTypeObject *tmptype; + PyObject *tmp = PyTuple_GET_ITEM(bases, i); + tmptype = Py_TYPE(tmp); +#if PY_MAJOR_VERSION < 3 + if (tmptype == &PyClass_Type) + continue; +#endif + if (!metaclass) { + metaclass = tmptype; + continue; + } + if (PyType_IsSubtype(metaclass, tmptype)) + continue; + if (PyType_IsSubtype(tmptype, metaclass)) { + metaclass = tmptype; + continue; + } + PyErr_SetString(PyExc_TypeError, + "metaclass conflict: " + "the metaclass of a derived class " + "must be a (non-strict) subclass " + "of the metaclasses of all its bases"); + return NULL; + } + if (!metaclass) { +#if PY_MAJOR_VERSION < 3 + metaclass = &PyClass_Type; +#else + metaclass = &PyType_Type; +#endif + } + Py_INCREF((PyObject*) metaclass); + return (PyObject*) metaclass; +} + +/* Py3ClassCreate */ +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, + PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { + PyObject *ns; + if (metaclass) { + PyObject *prep = __Pyx_PyObject_GetAttrStr(metaclass, __pyx_n_s_prepare); + if (prep) { + PyObject *pargs = PyTuple_Pack(2, name, bases); + if (unlikely(!pargs)) { + Py_DECREF(prep); + return NULL; + } + ns = PyObject_Call(prep, pargs, mkw); + Py_DECREF(prep); + Py_DECREF(pargs); + } else { + if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + PyErr_Clear(); + ns = PyDict_New(); + } + } else { + ns = PyDict_New(); + } + if (unlikely(!ns)) + return NULL; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad; + if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad; + return ns; +bad: + Py_DECREF(ns); + return NULL; +} +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, + PyObject *dict, PyObject *mkw, + int calculate_metaclass, int allow_py2_metaclass) { + PyObject *result, *margs; + PyObject *owned_metaclass = NULL; + if (allow_py2_metaclass) { + owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass); + if (owned_metaclass) { + metaclass = owned_metaclass; + } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) { + PyErr_Clear(); + } else { + return NULL; + } + } + if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) { + metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases); + Py_XDECREF(owned_metaclass); + if (unlikely(!metaclass)) + return NULL; + owned_metaclass = metaclass; + } + margs = PyTuple_Pack(3, name, bases, dict); + if (unlikely(!margs)) { + result = NULL; + } else { + result = PyObject_Call(metaclass, margs, mkw); + Py_DECREF(margs); + } + Py_XDECREF(owned_metaclass); + return result; +} + +/* GetNameInClass */ +static PyObject *__Pyx_GetGlobalNameAfterAttributeLookup(PyObject *name) { + PyObject *result; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + if (unlikely(!__Pyx_PyErr_ExceptionMatches(PyExc_AttributeError))) + return NULL; + __Pyx_PyErr_Clear(); + __Pyx_GetModuleGlobalNameUncached(result, name); + return result; +} +static PyObject *__Pyx__GetNameInClass(PyObject *nmspace, PyObject *name) { + PyObject *result; + result = __Pyx_PyObject_GetAttrStr(nmspace, name); + if (!result) { + result = __Pyx_GetGlobalNameAfterAttributeLookup(name); + } + return result; +} + +/* CLineInTraceback */ +#ifndef CYTHON_CLINE_IN_TRACEBACK +static int __Pyx_CLineForTraceback(CYTHON_UNUSED PyThreadState *tstate, int c_line) { + PyObject *use_cline; + PyObject *ptype, *pvalue, *ptraceback; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject **cython_runtime_dict; +#endif + 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_GetAttrStr(__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 */ +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); +} + +/* AddTraceback */ +#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 +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, + __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); +} + +/* 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; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +/* 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 + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + 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 + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + 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 + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + 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 one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + 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; +} + +/* 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 + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + 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 + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + 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 + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + 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 one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + 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; +} + +/* CIntFromPy */ +static CYTHON_INLINE CHRPOS __Pyx_PyInt_As_CHRPOS(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const CHRPOS neg_one = (CHRPOS) -1, const_zero = (CHRPOS) 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(CHRPOS) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(CHRPOS, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (CHRPOS) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (CHRPOS) 0; + case 1: __PYX_VERIFY_RETURN_INT(CHRPOS, digit, digits[0]) + case 2: + if (8 * sizeof(CHRPOS) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(CHRPOS) >= 2 * PyLong_SHIFT) { + return (CHRPOS) (((((CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(CHRPOS) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(CHRPOS) >= 3 * PyLong_SHIFT) { + return (CHRPOS) (((((((CHRPOS)digits[2]) << PyLong_SHIFT) | (CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(CHRPOS) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, 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(CHRPOS) >= 4 * PyLong_SHIFT) { + return (CHRPOS) (((((((((CHRPOS)digits[3]) << PyLong_SHIFT) | (CHRPOS)digits[2]) << PyLong_SHIFT) | (CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)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 (CHRPOS) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(CHRPOS) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(CHRPOS, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(CHRPOS) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(CHRPOS, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (CHRPOS) 0; + case -1: __PYX_VERIFY_RETURN_INT(CHRPOS, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(CHRPOS, digit, +digits[0]) + case -2: + if (8 * sizeof(CHRPOS) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(CHRPOS) - 1 > 2 * PyLong_SHIFT) { + return (CHRPOS) (((CHRPOS)-1)*(((((CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(CHRPOS) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(CHRPOS) - 1 > 2 * PyLong_SHIFT) { + return (CHRPOS) ((((((CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(CHRPOS) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(CHRPOS) - 1 > 3 * PyLong_SHIFT) { + return (CHRPOS) (((CHRPOS)-1)*(((((((CHRPOS)digits[2]) << PyLong_SHIFT) | (CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(CHRPOS) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(CHRPOS) - 1 > 3 * PyLong_SHIFT) { + return (CHRPOS) ((((((((CHRPOS)digits[2]) << PyLong_SHIFT) | (CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(CHRPOS) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, 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(CHRPOS) - 1 > 4 * PyLong_SHIFT) { + return (CHRPOS) (((CHRPOS)-1)*(((((((((CHRPOS)digits[3]) << PyLong_SHIFT) | (CHRPOS)digits[2]) << PyLong_SHIFT) | (CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(CHRPOS) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(CHRPOS, 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(CHRPOS) - 1 > 4 * PyLong_SHIFT) { + return (CHRPOS) ((((((((((CHRPOS)digits[3]) << PyLong_SHIFT) | (CHRPOS)digits[2]) << PyLong_SHIFT) | (CHRPOS)digits[1]) << PyLong_SHIFT) | (CHRPOS)digits[0]))); + } + } + break; + } +#endif + if (sizeof(CHRPOS) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(CHRPOS, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(CHRPOS) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(CHRPOS, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + CHRPOS 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 one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (CHRPOS) -1; + } + } else { + CHRPOS val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (CHRPOS) -1; + val = __Pyx_PyInt_As_CHRPOS(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to CHRPOS"); + return (CHRPOS) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to CHRPOS"); + return (CHRPOS) -1; +} + +/* CIntFromPy */ +static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const size_t neg_one = (size_t) -1, const_zero = (size_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(size_t) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (size_t) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, digits[0]) + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 2 * PyLong_SHIFT) { + return (size_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) >= 3 * PyLong_SHIFT) { + return (size_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_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(size_t) >= 4 * PyLong_SHIFT) { + return (size_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 +#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 (size_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(size_t) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (size_t) 0; + case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +digits[0]) + case -2: + if (8 * sizeof(size_t) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(size_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + return (size_t) ((((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(size_t) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(size_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + return (size_t) ((((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(size_t) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_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(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_t) (((size_t)-1)*(((((((((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(size_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(size_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(size_t) - 1 > 4 * PyLong_SHIFT) { + return (size_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 + if (sizeof(size_t) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(size_t) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(size_t, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + size_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 one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (size_t) -1; + } + } else { + size_t val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (size_t) -1; + val = __Pyx_PyInt_As_size_t(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to size_t"); + return (size_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to size_t"); + return (size_t) -1; +} + +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_CHRPOS(CHRPOS value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const CHRPOS neg_one = (CHRPOS) -1, const_zero = (CHRPOS) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(CHRPOS) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(CHRPOS) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(CHRPOS) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(CHRPOS) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(CHRPOS) <= 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; + return _PyLong_FromByteArray(bytes, sizeof(CHRPOS), + little, !is_unsigned); + } +} + +/* 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; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +/* CIntFromPy */ +static CYTHON_INLINE unsigned long __Pyx_PyInt_As_unsigned_long(PyObject *x) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const unsigned long neg_one = (unsigned long) -1, const_zero = (unsigned 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(unsigned long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(unsigned long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (unsigned long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (unsigned long) 0; + case 1: __PYX_VERIFY_RETURN_INT(unsigned long, digit, digits[0]) + case 2: + if (8 * sizeof(unsigned long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(unsigned long) >= 2 * PyLong_SHIFT) { + return (unsigned long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + } + } + break; + case 3: + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(unsigned long) >= 3 * PyLong_SHIFT) { + return (unsigned long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + } + } + break; + case 4: + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned 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(unsigned long) >= 4 * PyLong_SHIFT) { + return (unsigned long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned 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 (unsigned long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(unsigned long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(unsigned long, unsigned long, PyLong_AsUnsignedLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(unsigned long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(unsigned long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) +#endif + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (unsigned long) 0; + case -1: __PYX_VERIFY_RETURN_INT(unsigned long, sdigit, (sdigit) (-(sdigit)digits[0])) + case 1: __PYX_VERIFY_RETURN_INT(unsigned long, digit, +digits[0]) + case -2: + if (8 * sizeof(unsigned long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(unsigned long) - 1 > 2 * PyLong_SHIFT) { + return (unsigned long) (((unsigned long)-1)*(((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))); + } + } + break; + case 2: + if (8 * sizeof(unsigned long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(unsigned long) - 1 > 2 * PyLong_SHIFT) { + return (unsigned long) ((((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))); + } + } + break; + case -3: + if (8 * sizeof(unsigned long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(unsigned long) - 1 > 3 * PyLong_SHIFT) { + return (unsigned long) (((unsigned long)-1)*(((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))); + } + } + break; + case 3: + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + } else if (8 * sizeof(unsigned long) - 1 > 3 * PyLong_SHIFT) { + return (unsigned long) ((((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))); + } + } + break; + case -4: + if (8 * sizeof(unsigned long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned 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(unsigned long) - 1 > 4 * PyLong_SHIFT) { + return (unsigned long) (((unsigned long)-1)*(((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))); + } + } + break; + case 4: + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(unsigned 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(unsigned long) - 1 > 4 * PyLong_SHIFT) { + return (unsigned long) ((((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))); + } + } + break; + } +#endif + if (sizeof(unsigned long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(unsigned long, long, PyLong_AsLong(x)) +#ifdef HAVE_LONG_LONG + } else if (sizeof(unsigned long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(unsigned long, PY_LONG_LONG, PyLong_AsLongLong(x)) +#endif + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + unsigned 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 one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (unsigned long) -1; + } + } else { + unsigned long val; + PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); + if (!tmp) return (unsigned long) -1; + val = __Pyx_PyInt_As_unsigned_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to unsigned long"); + return (unsigned long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to unsigned long"); + return (unsigned long) -1; +} + +/* CheckBinaryVersion */ +static int __Pyx_check_binary_version(void) { + char ctversion[5]; + int same=1, i, found_dot; + const char* rt_from_call = Py_GetVersion(); + PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + found_dot = 0; + for (i = 0; i < 4; i++) { + if (!ctversion[i]) { + same = (rt_from_call[i] < '0' || rt_from_call[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), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +/* InitStrings */ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + 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); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + if (PyObject_Hash(*t->p) == -1) + return -1; + ++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) || (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) { +#if PY_MAJOR_VERSION >= 3 + if (PyLong_Check(result)) { + if (PyErr_WarnFormat(PyExc_DeprecationWarning, 1, + "__int__ returned non-int (type %.200s). " + "The ability to return an instance of a strict subclass of int " + "is deprecated, and may be removed in a future version of Python.", + Py_TYPE(result)->tp_name)) { + Py_DECREF(result); + return NULL; + } + return result; + } +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + type_name, type_name, Py_TYPE(result)->tp_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 + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + 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); +} + + +#endif /* Py_PYTHON_H */