/* Generated by Cython 0.19.1 on Mon Apr 14 13:01:27 2014 */ #define PY_SSIZE_T_CLEAN #ifndef CYTHON_USE_PYLONG_INTERNALS #ifdef PYLONG_BITS_IN_DIGIT #define CYTHON_USE_PYLONG_INTERNALS 0 #else #include "pyconfig.h" #ifdef PYLONG_BITS_IN_DIGIT #define CYTHON_USE_PYLONG_INTERNALS 1 #else #define CYTHON_USE_PYLONG_INTERNALS 0 #endif #endif #endif #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 < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #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 #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_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #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, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #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 #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX < 0x02060000 #define Py_TPFLAGS_HAVE_VERSION_TAG 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #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_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 #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_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #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 #endif #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #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_CheckExact(obj) || PyUnicode_CheckExact(obj) || \ PyString_Check(obj) || PyUnicode_Check(obj)) #define __Pyx_PyBaseString_CheckExact(obj) (Py_TYPE(obj) == &PyBaseString_Type) #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #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 #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #endif #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ #elif defined(_MSC_VER) #define CYTHON_INLINE __inline #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else #define CYTHON_INLINE #endif #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) #define CYTHON_RESTRICT __restrict__ #elif defined(_MSC_VER) #define CYTHON_RESTRICT __restrict #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_RESTRICT restrict #else #define CYTHON_RESTRICT #endif #endif #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif #if PY_MAJOR_VERSION >= 3 #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 #ifndef __PYX_EXTERN_C #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" #else #define __PYX_EXTERN_C extern #endif #endif #if defined(WIN32) || defined(MS_WINDOWS) #define _USE_MATH_DEFINES #endif #include #define __PYX_HAVE__MACS2__IO__cPeakIO #define __PYX_HAVE_API__MACS2__IO__cPeakIO #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #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 typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 #define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 #define __PYX_DEFAULT_STRING_ENCODING "" #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyBytes_FromString PyBytes_FromString #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(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_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s) #define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s) #define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s) #define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { const Py_UNICODE *u_end = u; while (*u_end++) ; return u_end - u - 1; } #else #define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen #endif #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_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) #define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #if CYTHON_COMPILING_IN_CPYTHON #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 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII static int __Pyx_sys_getdefaultencoding_not_ascii; static int __Pyx_init_sys_getdefaultencoding_params() { PyObject* sys = NULL; PyObject* default_encoding = NULL; PyObject* ascii_chars_u = NULL; PyObject* ascii_chars_b = NULL; sys = PyImport_ImportModule("sys"); if (sys == NULL) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); if (default_encoding == NULL) goto bad; if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) { __Pyx_sys_getdefaultencoding_not_ascii = 0; } else { const char* default_encoding_c = PyBytes_AS_STRING(default_encoding); 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 == NULL) goto bad; ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); if (ascii_chars_b == NULL || strncmp(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 '%s' is not a superset of ascii.", default_encoding_c); goto bad; } } Py_XDECREF(sys); Py_XDECREF(default_encoding); Py_XDECREF(ascii_chars_u); Py_XDECREF(ascii_chars_b); return 0; bad: Py_XDECREF(sys); 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() { PyObject* sys = NULL; PyObject* default_encoding = NULL; char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (sys == NULL) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); if (default_encoding == NULL) goto bad; default_encoding_c = PyBytes_AS_STRING(default_encoding); __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); Py_DECREF(sys); Py_DECREF(default_encoding); return 0; bad: Py_XDECREF(sys); Py_XDECREF(default_encoding); return -1; } #endif #endif #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_d; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; 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[] = { "cPeakIO.pyx", }; /*--- Type declarations ---*/ struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakContent; struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO; struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO; struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region; struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent; struct __pyx_opt_args_5MACS2_2IO_7cPeakIO_6PeakIO_add; /* "MACS2/IO/cPeakIO.pyx":133 * self.peaks = {} * * cpdef add (self, str chromosome, int start, int end, int summit = 0, # <<<<<<<<<<<<<< * float peak_score=0, float pileup=0, * float pscore=0, float fold_change=0, float qscore=0, */ struct __pyx_opt_args_5MACS2_2IO_7cPeakIO_6PeakIO_add { int __pyx_n; int summit; float peak_score; float pileup; float pscore; float fold_change; float qscore; PyObject *name; }; /* "MACS2/IO/cPeakIO.pyx":48 * # ------------------------------------ * * cdef class PeakContent: # <<<<<<<<<<<<<< * cdef: * int start */ struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakContent { PyObject_HEAD int start; int end; int length; int summit; float score; float pileup; float pscore; float fc; float qscore; PyObject *name; }; /* "MACS2/IO/cPeakIO.pyx":789 * * * cdef class BroadPeakIO: # <<<<<<<<<<<<<< * """IO for broad peak information. * */ struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO { PyObject_HEAD PyObject *peaks; }; /* "MACS2/IO/cPeakIO.pyx":123 * return "start:%d;end:%d;score:%f" % ( self.start, self.end, self.score ) * * cdef class PeakIO: # <<<<<<<<<<<<<< * """IO for peak information. * */ struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO { PyObject_HEAD struct __pyx_vtabstruct_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_vtab; PyObject *peaks; }; /* "MACS2/IO/cPeakIO.pyx":647 * return (peaknumber, subpeak) * * cdef class Region: # <<<<<<<<<<<<<< * """For plain region of chrom, start and end * """ */ struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region { PyObject_HEAD }; /* "MACS2/IO/cPeakIO.pyx":716 * * * cdef class BroadPeakContent: # <<<<<<<<<<<<<< * cdef: * long start */ struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent { PyObject_HEAD long start; long end; long length; float score; PyObject *thickStart; PyObject *thickEnd; long blockNum; PyObject *blockSizes; PyObject *blockStarts; float pileup; float pscore; float fc; float qscore; PyObject *name; }; /* "MACS2/IO/cPeakIO.pyx":123 * return "start:%d;end:%d;score:%f" % ( self.start, self.end, self.score ) * * cdef class PeakIO: # <<<<<<<<<<<<<< * """IO for peak information. * */ struct __pyx_vtabstruct_5MACS2_2IO_7cPeakIO_PeakIO { PyObject *(*add)(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *, PyObject *, int, int, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_7cPeakIO_6PeakIO_add *__pyx_optional_args); PyObject *(*add_PeakContent)(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *, PyObject *, PyObject *, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_vtabptr_5MACS2_2IO_7cPeakIO_PeakIO; 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/*proto*/ /* Module declarations from 'MACS2.IO.cPeakIO' */ static PyTypeObject *__pyx_ptype_5MACS2_2IO_7cPeakIO_PeakContent = 0; static PyTypeObject *__pyx_ptype_5MACS2_2IO_7cPeakIO_BroadPeakIO = 0; static PyTypeObject *__pyx_ptype_5MACS2_2IO_7cPeakIO_PeakIO = 0; static PyTypeObject *__pyx_ptype_5MACS2_2IO_7cPeakIO_Region = 0; static PyTypeObject *__pyx_ptype_5MACS2_2IO_7cPeakIO_BroadPeakContent = 0; static PyObject *__pyx_f_5MACS2_2IO_7cPeakIO_subpeak_letters(int); /*proto*/ static PyObject *__pyx_f_5MACS2_2IO_7cPeakIO_parse_peakname(PyObject *, int __pyx_skip_dispatch); /*proto*/ #define __Pyx_MODULE_NAME "MACS2.IO.cPeakIO" int __pyx_module_is_main_MACS2__IO__cPeakIO = 0; /* Implementation of 'MACS2.IO.cPeakIO' */ static PyObject *__pyx_builtin_print; static PyObject *__pyx_builtin_chr; static PyObject *__pyx_builtin_sorted; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_round; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_UserWarning; static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_range; static int __pyx_pf_5MACS2_2IO_7cPeakIO_11PeakContent___init__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakContent *__pyx_v_self, int __pyx_v_start, int __pyx_v_end, int __pyx_v_summit, float __pyx_v_peak_score, float __pyx_v_pileup, float __pyx_v_pscore, float __pyx_v_fold_change, float __pyx_v_qscore, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11PeakContent_2__getitem__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakContent *__pyx_v_self, PyObject *__pyx_v_a); /* proto */ static int __pyx_pf_5MACS2_2IO_7cPeakIO_11PeakContent_4__setitem__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakContent *__pyx_v_self, PyObject *__pyx_v_a, PyObject *__pyx_v_v); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11PeakContent_6__str__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakContent *__pyx_v_self); /* proto */ static int __pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO___init__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_2add(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_chromosome, int __pyx_v_start, int __pyx_v_end, int __pyx_v_summit, float __pyx_v_peak_score, float __pyx_v_pileup, float __pyx_v_pscore, float __pyx_v_fold_change, float __pyx_v_qscore, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_4add_PeakContent(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_chromosome, PyObject *__pyx_v_peakcontent); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_6get_data_from_chrom(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_chrom); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_8get_chr_names(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_lambda_funcdef_lambda1(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_10sort(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_12filter_pscore(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, double __pyx_v_pscore_cut); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_14filter_qscore(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, double __pyx_v_qscore_cut); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_16filter_fc(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_fc_low, PyObject *__pyx_v_fc_up); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_18total(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_20write_to_xls(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_22_to_xls(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_print_func); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_24_to_bed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_description, PyObject *__pyx_v_score_column, PyObject *__pyx_v_print_func, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_26_to_summits_bed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_description, PyObject *__pyx_v_score_column, PyObject *__pyx_v_print_func, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_28tobed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_30to_summits_bed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_32write_to_bed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_description, PyObject *__pyx_v_score_column, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_34write_to_summit_bed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_description, PyObject *__pyx_v_score_column, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_36write_to_narrowPeak(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_score_column, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_38write_to_xls(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_ofhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_40overlap_with_other_peaks(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_peaks2, double __pyx_v_cover); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6PeakIO_42read_from_xls(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_ofhd); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_parse_peakname(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_peakname); /* proto */ static int __pyx_pf_5MACS2_2IO_7cPeakIO_6Region___init__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6Region_2add_loc(struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region *__pyx_v_self, PyObject *__pyx_v_chrom, int __pyx_v_start, int __pyx_v_end); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6Region_4sort(struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6Region_6merge_overlap(struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_6Region_8write_to_bed(struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region *__pyx_v_self, PyObject *__pyx_v_fhd); /* proto */ static int __pyx_pf_5MACS2_2IO_7cPeakIO_16BroadPeakContent___init__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *__pyx_v_self, long __pyx_v_start, long __pyx_v_end, float __pyx_v_score, PyObject *__pyx_v_thickStart, PyObject *__pyx_v_thickEnd, long __pyx_v_blockNum, PyObject *__pyx_v_blockSizes, PyObject *__pyx_v_blockStarts, float __pyx_v_pileup, float __pyx_v_pscore, float __pyx_v_fold_change, float __pyx_v_qscore, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_16BroadPeakContent_2__getitem__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *__pyx_v_self, PyObject *__pyx_v_a); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_16BroadPeakContent_4__str__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *__pyx_v_self); /* proto */ static int __pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO___init__(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO_2add(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self, char *__pyx_v_chromosome, long __pyx_v_start, long __pyx_v_end, long __pyx_v_score, PyObject *__pyx_v_thickStart, PyObject *__pyx_v_thickEnd, long __pyx_v_blockNum, PyObject *__pyx_v_blockSizes, PyObject *__pyx_v_blockStarts, float __pyx_v_pileup, float __pyx_v_pscore, float __pyx_v_fold_change, float __pyx_v_qscore, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO_4total(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO_6write_to_gappedPeak(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_description, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO_8write_to_Bed12(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, PyObject *__pyx_v_description, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO_10write_to_broadPeak(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name, CYTHON_UNUSED PyObject *__pyx_v_description, PyObject *__pyx_v_trackline); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_7cPeakIO_11BroadPeakIO_12write_to_xls(struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakIO *__pyx_v_self, PyObject *__pyx_v_ofhd, PyObject *__pyx_v_name_prefix, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_PeakContent(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_BroadPeakIO(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_PeakIO(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_Region(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_BroadPeakContent(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static char __pyx_k_1[] = "start:%d;end:%d;score:%f"; static char __pyx_k_2[] = "PeakIO.sort.."; static char __pyx_k_3[] = "MACS2.IO.cPeakIO"; static char __pyx_k_4[] = "%s_peak_"; static char __pyx_k_6[] = "\t"; static char __pyx_k_7[] = "-log10(pvalue)"; static char __pyx_k_8[] = "-log10(qvalue)"; static char __pyx_k_11[] = "\n"; static char __pyx_k_13[] = "%s%d%s"; static char __pyx_k_14[] = "%s\t%d\t%d\t%d"; static char __pyx_k_15[] = "\t%d"; static char __pyx_k_16[] = "\t%.2f"; static char __pyx_k_17[] = "\t%.5f"; static char __pyx_k_18[] = "\t%s"; static char __pyx_k_20[] = "%s%d"; static char __pyx_k_22[] = "%s"; static char __pyx_k_25[] = "\""; static char __pyx_k_26[] = "\\\""; static char __pyx_k_29[] = "track name=\"%s (peaks)\" description=\"%s\" visibility=1\n"; static char __pyx_k_30[] = "track name=MACS description=Unknown"; static char __pyx_k_33[] = "%s\t%d\t%d\t%s%d%s\t%.5f\n"; static char __pyx_k_34[] = "%s\t%d\t%d\t%s%d\t%.5f\n"; static char __pyx_k_39[] = "track name=\"%s (summits)\" description=\"%s\" visibility=1\n"; static char __pyx_k_45[] = "track type=narrowPeak name=\"%s\" description=\"%s\" nextItemButton=on\n"; static char __pyx_k_47[] = "%s\t%d\t%d\t%s\t%d\t.\t%.5f\t%.5f\t%.5f\t%d\n"; static char __pyx_k_53[] = ""; static char __pyx_k_54[] = "#"; static char __pyx_k_57[] = "column %s not recognized"; static char __pyx_k_58[] = "Malformed peak at line %d:\n%s"; static char __pyx_k_60[] = "(\\D.*)"; static char __pyx_k_61[] = "%s\t%d\t%d\n"; static char __pyx_k_62[] = "."; static char __pyx_k_64[] = "track name=\"%s\" description=\"%s\" type=gappedPeak nextItemButton=on\n"; static char __pyx_k_65[] = "%s\t%d\t%d\t%s%d\t%d\t.\t%s\t%s\t0\t%d\t%s\t%s\t%.5f\t%.5f\t%.5f\n"; static char __pyx_k_67[] = "track name=\"%s\" description=\"%s\" type=bed nextItemButton=on\n"; static char __pyx_k_68[] = "%s\t%d\t%d\t%s%d\t%d\t.\n"; static char __pyx_k_69[] = "%s\t%d\t%d\t%s%d\t%d\t.\t%s\t%s\t0\t%d\t%s\t%s\n"; static char __pyx_k_71[] = "track type=broadPeak name=\"%s\" description=\"%s\" nextItemButton=on\n"; static char __pyx_k_73[] = "%s\t%d\t%d\t%s\t%d\t.\t%.5f\t%.5f\t%.5f\n"; static char __pyx_k_78[] = "Module for PeakIO IO classes.\n\nCopyright (c) 2010,2011 Tao Liu \n\nThis code is free software; you can redistribute it and/or modify it\nunder the terms of the BSD License (see the file COPYING included\nwith the distribution).\n\n@status: experimental\n@version: $Revision$\n@author: Tao Liu\n@contact: taoliu@jimmy.harvard.edu\n"; static char __pyx_k_79[] = "MACS2.Constants"; static char __pyx_k_80[] = "*"; static char __pyx_k_81[] = "PeakIO $Revision$"; static char __pyx_k_82[] = "Tao Liu "; static char __pyx_k_83[] = "PeakIO class"; static char __pyx_k___[] = "_"; static char __pyx_k__NA[] = "NA"; static char __pyx_k__fc[] = "fc"; static char __pyx_k__re[] = "re"; static char __pyx_k__add[] = "add"; static char __pyx_k__chr[] = "chr"; static char __pyx_k__end[] = "end"; static char __pyx_k__fhd[] = "fhd"; static char __pyx_k__key[] = "key"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__MACS[] = "MACS"; static char __pyx_k__join[] = "join"; static char __pyx_k__keys[] = "keys"; static char __pyx_k__name[] = "name"; static char __pyx_k__next[] = "next"; static char __pyx_k__ofhd[] = "ofhd"; static char __pyx_k__peak[] = "peak"; static char __pyx_k__sort[] = "sort"; static char __pyx_k__chrom[] = "chrom"; static char __pyx_k__count[] = "count"; static char __pyx_k__cover[] = "cover"; static char __pyx_k__fc_up[] = "fc_up"; static char __pyx_k__peak_[] = "peak_"; static char __pyx_k__peaks[] = "peaks"; static char __pyx_k__print[] = "print"; static char __pyx_k__range[] = "range"; static char __pyx_k__round[] = "round"; static char __pyx_k__score[] = "score"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; static char __pyx_k__write[] = "write"; static char __pyx_k__append[] = "append"; static char __pyx_k__fc_low[] = "fc_low"; static char __pyx_k__length[] = "length"; static char __pyx_k__peaks2[] = "peaks2"; static char __pyx_k__pileup[] = "pileup"; static char __pyx_k__pscore[] = "pscore"; static char __pyx_k__qscore[] = "qscore"; static char __pyx_k__rstrip[] = "rstrip"; static char __pyx_k__sorted[] = "sorted"; static char __pyx_k__summit[] = "summit"; static char __pyx_k____doc__[] = "__doc__"; static char __pyx_k___to_bed[] = "_to_bed"; static char __pyx_k___to_xls[] = "_to_xls"; static char __pyx_k__groupby[] = "groupby"; static char __pyx_k__has_key[] = "has_key"; static char __pyx_k__regions[] = "regions"; static char __pyx_k__replace[] = "replace"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__blockNum[] = "blockNum"; static char __pyx_k__operator[] = "operator"; static char __pyx_k__readline[] = "readline"; static char __pyx_k__thickEnd[] = "thickEnd"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__itertools[] = "itertools"; static char __pyx_k__readlines[] = "readlines"; static char __pyx_k__trackline[] = "trackline"; static char __pyx_k__IndexError[] = "IndexError"; static char __pyx_k____author__[] = "__author__"; static char __pyx_k____import__[] = "__import__"; static char __pyx_k__abs_summit[] = "abs_summit"; static char __pyx_k__blockSizes[] = "blockSizes"; static char __pyx_k__chromosome[] = "chromosome"; static char __pyx_k__itemgetter[] = "itemgetter"; static char __pyx_k__peak_score[] = "peak_score"; static char __pyx_k__print_func[] = "print_func"; static char __pyx_k__thickStart[] = "thickStart"; static char __pyx_k__UserWarning[] = "UserWarning"; static char __pyx_k____version__[] = "__version__"; static char __pyx_k__blockStarts[] = "blockStarts"; static char __pyx_k__description[] = "description"; static char __pyx_k__fold_change[] = "fold_change"; static char __pyx_k__name_prefix[] = "name_prefix"; static char __pyx_k__peakcontent[] = "peakcontent"; static char __pyx_k__score_column[] = "score_column"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k____flag_sorted[] = "__flag_sorted"; static char __pyx_k____pyx_vtable__[] = "__pyx_vtable__"; static char __pyx_k___to_summits_bed[] = "_to_summits_bed"; static char __pyx_k__add_PeakContent[] = "add_PeakContent"; static char __pyx_k__fold_enrichment[] = "fold_enrichment"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static PyObject *__pyx_kp_s_1; static PyObject *__pyx_kp_s_11; static PyObject *__pyx_kp_s_13; static PyObject *__pyx_kp_s_14; static PyObject *__pyx_kp_s_15; static PyObject *__pyx_kp_s_16; static PyObject *__pyx_kp_s_17; static PyObject *__pyx_kp_s_18; static PyObject *__pyx_n_s_2; static PyObject *__pyx_kp_s_20; static PyObject *__pyx_kp_s_22; static PyObject *__pyx_kp_s_25; static PyObject *__pyx_kp_s_26; static PyObject *__pyx_kp_s_29; static PyObject *__pyx_n_s_3; static PyObject *__pyx_kp_s_30; static PyObject *__pyx_kp_s_33; static PyObject *__pyx_kp_s_34; static PyObject *__pyx_kp_s_39; static PyObject *__pyx_kp_s_4; static PyObject *__pyx_kp_s_45; static PyObject *__pyx_kp_s_47; static PyObject *__pyx_kp_s_53; static PyObject *__pyx_kp_s_54; 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Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("IO for broad peak information.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5MACS2_2IO_7cPeakIO_BroadPeakIO, /*tp_traverse*/ __pyx_tp_clear_5MACS2_2IO_7cPeakIO_BroadPeakIO, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_2IO_7cPeakIO_BroadPeakIO, /*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_5MACS2_2IO_7cPeakIO_11BroadPeakIO_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_2IO_7cPeakIO_BroadPeakIO, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5MACS2_2IO_7cPeakIO_PeakIO __pyx_vtable_5MACS2_2IO_7cPeakIO_PeakIO; static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_PeakIO(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *p; PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *)o); p->__pyx_vtab = __pyx_vtabptr_5MACS2_2IO_7cPeakIO_PeakIO; p->peaks = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5MACS2_2IO_7cPeakIO_PeakIO(PyObject *o) { struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *p = (struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->peaks); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5MACS2_2IO_7cPeakIO_PeakIO(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *p = (struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *)o; if (p->peaks) { e = (*v)(p->peaks, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5MACS2_2IO_7cPeakIO_PeakIO(PyObject *o) { struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *p = (struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO *)o; PyObject* tmp; tmp = ((PyObject*)p->peaks); p->peaks = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5MACS2_2IO_7cPeakIO_PeakIO[] = { {__Pyx_NAMESTR("add"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_3add, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_2add)}, {__Pyx_NAMESTR("add_PeakContent"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_5add_PeakContent, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("get_data_from_chrom"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_7get_data_from_chrom, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("get_chr_names"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_9get_chr_names, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("sort"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_11sort, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("filter_pscore"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_13filter_pscore, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("filter_qscore"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_15filter_qscore, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("filter_fc"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_17filter_fc, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_16filter_fc)}, {__Pyx_NAMESTR("total"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_19total, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("write_to_xls"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_21write_to_xls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("_to_xls"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_23_to_xls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("_to_bed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_25_to_bed, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_24_to_bed)}, {__Pyx_NAMESTR("_to_summits_bed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_27_to_summits_bed, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_26_to_summits_bed)}, {__Pyx_NAMESTR("tobed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_29tobed, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_28tobed)}, {__Pyx_NAMESTR("to_summits_bed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_31to_summits_bed, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_30to_summits_bed)}, {__Pyx_NAMESTR("write_to_bed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_33write_to_bed, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_32write_to_bed)}, {__Pyx_NAMESTR("write_to_summit_bed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_35write_to_summit_bed, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_34write_to_summit_bed)}, {__Pyx_NAMESTR("write_to_narrowPeak"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_37write_to_narrowPeak, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_36write_to_narrowPeak)}, {__Pyx_NAMESTR("write_to_xls"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_39write_to_xls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_38write_to_xls)}, {__Pyx_NAMESTR("overlap_with_other_peaks"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_41overlap_with_other_peaks, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_40overlap_with_other_peaks)}, {__Pyx_NAMESTR("read_from_xls"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6PeakIO_43read_from_xls, METH_O, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_6PeakIO_42read_from_xls)}, {0, 0, 0, 0} }; static PyTypeObject __pyx_type_5MACS2_2IO_7cPeakIO_PeakIO = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("MACS2.IO.cPeakIO.PeakIO"), /*tp_name*/ sizeof(struct __pyx_obj_5MACS2_2IO_7cPeakIO_PeakIO), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5MACS2_2IO_7cPeakIO_PeakIO, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #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*/ __Pyx_DOCSTR("IO for peak information.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5MACS2_2IO_7cPeakIO_PeakIO, /*tp_traverse*/ __pyx_tp_clear_5MACS2_2IO_7cPeakIO_PeakIO, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_2IO_7cPeakIO_PeakIO, /*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_5MACS2_2IO_7cPeakIO_6PeakIO_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_2IO_7cPeakIO_PeakIO, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_Region(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; return o; } static void __pyx_tp_dealloc_5MACS2_2IO_7cPeakIO_Region(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5MACS2_2IO_7cPeakIO_Region[] = { {__Pyx_NAMESTR("add_loc"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6Region_3add_loc, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("sort"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6Region_5sort, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("merge_overlap"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6Region_7merge_overlap, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("write_to_bed"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_6Region_9write_to_bed, METH_O, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyTypeObject __pyx_type_5MACS2_2IO_7cPeakIO_Region = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("MACS2.IO.cPeakIO.Region"), /*tp_name*/ sizeof(struct __pyx_obj_5MACS2_2IO_7cPeakIO_Region), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5MACS2_2IO_7cPeakIO_Region, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #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*/ __Pyx_DOCSTR("For plain region of chrom, start and end\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_2IO_7cPeakIO_Region, /*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_5MACS2_2IO_7cPeakIO_6Region_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_2IO_7cPeakIO_Region, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5MACS2_2IO_7cPeakIO_BroadPeakContent(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *p; PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *)o); p->thickStart = ((PyObject*)Py_None); Py_INCREF(Py_None); p->thickEnd = ((PyObject*)Py_None); Py_INCREF(Py_None); p->blockSizes = ((PyObject*)Py_None); Py_INCREF(Py_None); p->blockStarts = ((PyObject*)Py_None); Py_INCREF(Py_None); p->name = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5MACS2_2IO_7cPeakIO_BroadPeakContent(PyObject *o) { struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *p = (struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->thickStart); Py_CLEAR(p->thickEnd); Py_CLEAR(p->blockSizes); Py_CLEAR(p->blockStarts); Py_CLEAR(p->name); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5MACS2_2IO_7cPeakIO_BroadPeakContent(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *p = (struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *)o; if (p->thickStart) { e = (*v)(p->thickStart, a); if (e) return e; } if (p->thickEnd) { e = (*v)(p->thickEnd, a); if (e) return e; } if (p->blockSizes) { e = (*v)(p->blockSizes, a); if (e) return e; } if (p->blockStarts) { e = (*v)(p->blockStarts, a); if (e) return e; } if (p->name) { e = (*v)(p->name, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5MACS2_2IO_7cPeakIO_BroadPeakContent(PyObject *o) { struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *p = (struct __pyx_obj_5MACS2_2IO_7cPeakIO_BroadPeakContent *)o; PyObject* tmp; tmp = ((PyObject*)p->thickStart); p->thickStart = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->thickEnd); p->thickEnd = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->blockSizes); p->blockSizes = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->blockStarts); p->blockStarts = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->name); p->name = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5MACS2_2IO_7cPeakIO_BroadPeakContent(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 PyMethodDef __pyx_methods_5MACS2_2IO_7cPeakIO_BroadPeakContent[] = { {0, 0, 0, 0} }; static PySequenceMethods __pyx_tp_as_sequence_BroadPeakContent = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5MACS2_2IO_7cPeakIO_BroadPeakContent, /*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_BroadPeakContent = { 0, /*mp_length*/ __pyx_pw_5MACS2_2IO_7cPeakIO_16BroadPeakContent_3__getitem__, 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__pyx_tp_traverse_5MACS2_2IO_7cPeakIO_BroadPeakContent, /*tp_traverse*/ __pyx_tp_clear_5MACS2_2IO_7cPeakIO_BroadPeakContent, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_2IO_7cPeakIO_BroadPeakContent, /*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_5MACS2_2IO_7cPeakIO_16BroadPeakContent_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_2IO_7cPeakIO_BroadPeakContent, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyMethodDef __pyx_methods[] = { {__Pyx_NAMESTR("parse_peakname"), (PyCFunction)__pyx_pw_5MACS2_2IO_7cPeakIO_1parse_peakname, METH_O, __Pyx_DOCSTR(__pyx_doc_5MACS2_2IO_7cPeakIO_parse_peakname)}, {0, 0, 0, 0} }; static char* 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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; Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_kwdict = NULL; op->defaults_getter = NULL; op->func_annotations = NULL; PyObject_GC_Track(op); 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_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]); PyMem_Free(m->defaults); m->defaults = NULL; } return 0; } static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) { PyObject_GC_UnTrack(m); if (m->func_weakreflist != NULL) PyObject_ClearWeakRefs((PyObject *) m); __Pyx_CyFunction_clear(m); PyObject_GC_Del(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_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) { __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 PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); } if (obj == Py_None) obj = NULL; return PyMethod_New(func, obj, type); } static PyObject* __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromFormat("", op->func_qualname, (void *)op); #else return PyString_FromFormat("", PyString_AsString(op->func_qualname), (void *)op); #endif } #if CYTHON_COMPILING_IN_PYPY static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyCFunctionObject* f = (PyCFunctionObject*)func; PyCFunction meth = PyCFunction_GET_FUNCTION(func); PyObject *self = PyCFunction_GET_SELF(func); Py_ssize_t size; switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { case METH_VARARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) return (*meth)(self, arg); break; case METH_VARARGS | METH_KEYWORDS: return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); case METH_NOARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 0) return (*meth)(self, NULL); PyErr_Format(PyExc_TypeError, "%.200s() takes no arguments (%zd 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 (size == 1) return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); PyErr_Format(PyExc_TypeError, "%.200s() takes exactly one argument (%zd 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; } #else static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { return PyCFunction_Call(func, arg, kw); } #endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ __Pyx_CyFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_CyFunction_methods, /*tp_methods*/ __pyx_CyFunction_members, /*tp_members*/ __pyx_CyFunction_getsets, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ __Pyx_CyFunction_descr_get, /*tp_descr_get*/ 0, /*tp_descr_set*/ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static int __Pyx_CyFunction_init(void) { #if !CYTHON_COMPILING_IN_PYPY __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; #endif if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) return PyErr_NoMemory(); memset(m->defaults, 0, size); m->defaults_pyobjects = pyobjects; 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); } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); 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_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON 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; /* Make sure tstate is in a consistent state when we XDECREF these objects (DECREF may run arbitrary code). */ 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; } static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { PyObject *result; #if CYTHON_COMPILING_IN_CPYTHON result = PyDict_GetItem(__pyx_d, name); if (result) { Py_INCREF(result); } else { #else result = PyObject_GetItem(__pyx_d, name); if (!result) { PyErr_Clear(); #endif result = __Pyx_GetBuiltinName(name); } return result; } 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); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || 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 } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static CYTHON_INLINE 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, int wraparound, int boundscheck) { #if CYTHON_COMPILING_IN_CPYTHON if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { PyObject *r = PyList_GET_ITEM(o, 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, int wraparound, int boundscheck) { #if CYTHON_COMPILING_IN_CPYTHON if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { PyObject *r = PyTuple_GET_ITEM(o, 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, int wraparound, int boundscheck) { #if CYTHON_COMPILING_IN_CPYTHON if (is_list || PyList_CheckExact(o)) { Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if ((!boundscheck) || (likely((n >= 0) & (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((n >= 0) & (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)) PyErr_Clear(); else return NULL; } } 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)); } static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; #if CYTHON_COMPILING_IN_PYPY float_value = PyNumber_Float(obj); #else PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number; if (likely(nb) && likely(nb->nb_float)) { float_value = nb->nb_float(obj); if (likely(float_value) && unlikely(!PyFloat_Check(float_value))) { PyErr_Format(PyExc_TypeError, "__float__ returned non-float (type %.200s)", Py_TYPE(float_value)->tp_name); Py_DECREF(float_value); goto bad; } } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) { #if PY_MAJOR_VERSION >= 3 float_value = PyFloat_FromString(obj); #else float_value = PyFloat_FromString(obj, 0); #endif } else { PyObject* args = PyTuple_New(1); if (unlikely(!args)) goto bad; PyTuple_SET_ITEM(args, 0, obj); float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0); PyTuple_SET_ITEM(args, 0, 0); Py_DECREF(args); } #endif if (likely(float_value)) { double value = PyFloat_AS_DOUBLE(float_value); Py_DECREF(float_value); return value; } bad: return (double)-1; } static CYTHON_INLINE int __Pyx_PyStr_Tailmatch(PyObject* self, PyObject* arg, Py_ssize_t start, Py_ssize_t end, int direction) { if (PY_MAJOR_VERSION < 3) return __Pyx_PyBytes_Tailmatch(self, arg, start, end, direction); else return __Pyx_PyUnicode_Tailmatch(self, arg, start, end, direction); } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); 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); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #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; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else 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; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ 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 *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 = PyEval_CallObject(type, args); 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 PY_VERSION_HEX >= 0x03030000 if (cause) { #else if (cause && cause != Py_None) { #endif 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) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) 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; } 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; } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); 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; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } 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_VERSION_HEX < 0x03030000 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_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(unsigned long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (unsigned long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(unsigned long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(unsigned long) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(unsigned long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(long) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(signed long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (signed long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(signed long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(signed long) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(signed long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) { while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } return *s1 == *s2; } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } 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) / 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, 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); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __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, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } 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 /* Python 3+ has unicode identifiers */ 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; ++t; } return 0; } static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) { return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str)); } static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { Py_ssize_t ignore; return __Pyx_PyObject_AsStringAndSize(o, &ignore); } static CYTHON_INLINE 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)) { #if PY_VERSION_HEX < 0x03030000 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 /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/ *length = PyBytes_GET_SIZE(defenc); return defenc_c; #else /* PY_VERSION_HEX < 0x03030000 */ if (PyUnicode_READY(o) == -1) return NULL; #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII if (PyUnicode_IS_ASCII(o)) { *length = PyUnicode_GET_DATA_SIZE(o); return PyUnicode_AsUTF8(o); } else { PyUnicode_AsASCIIString(o); return NULL; } #else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */ return PyUnicode_AsUTF8AndSize(o, length); #endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */ #endif /* PY_VERSION_HEX < 0x03030000 */ } else #endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */ { char* result; int r = PyBytes_AsStringAndSize(o, &result, length); if (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 PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_MAJOR_VERSION < 3 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_MAJOR_VERSION < 3 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } 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 = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { if ((val != (unsigned PY_LONG_LONG)-1) || !PyErr_Occurred()) PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */