/* Generated by Cython 0.17.4 on Wed Oct 2 14:10:45 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 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 > 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_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 #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__HTSeq___HTSeq #define __PYX_HAVE_API__HTSeq___HTSeq #include "stdio.h" #include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif /* inline attribute */ #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 /* unused attribute */ #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 long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ /* Type Conversion Predeclarations */ #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) #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)) #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_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; #if !defined(CYTHON_CCOMPLEX) #if defined(__cplusplus) #define CYTHON_CCOMPLEX 1 #elif defined(_Complex_I) #define CYTHON_CCOMPLEX 1 #else #define CYTHON_CCOMPLEX 0 #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus #include #else #include #endif #endif #if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) #undef _Complex_I #define _Complex_I 1.0fj #endif static const char *__pyx_f[] = { "_HTSeq.pyx", "_HTSeq.pxd", "numpy.pxd", "type.pxd", }; #define IS_UNSIGNED(type) (((type) -1) > 0) struct __Pyx_StructField_; #define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) typedef struct { const char* name; /* for error messages only */ struct __Pyx_StructField_* fields; size_t size; /* sizeof(type) */ size_t arraysize[8]; /* length of array in each dimension */ int ndim; char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */ char is_unsigned; int flags; } __Pyx_TypeInfo; typedef struct __Pyx_StructField_ { __Pyx_TypeInfo* type; const char* name; size_t offset; } __Pyx_StructField; typedef struct { __Pyx_StructField* field; size_t parent_offset; } __Pyx_BufFmt_StackElem; typedef struct { __Pyx_StructField root; __Pyx_BufFmt_StackElem* head; size_t fmt_offset; size_t new_count, enc_count; size_t struct_alignment; int is_complex; char enc_type; char new_packmode; char enc_packmode; char is_valid_array; } __Pyx_BufFmt_Context; /* "numpy.pxd":723 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t */ typedef npy_int8 __pyx_t_5numpy_int8_t; /* "numpy.pxd":724 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t */ typedef npy_int16 __pyx_t_5numpy_int16_t; /* "numpy.pxd":725 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< * ctypedef npy_int64 int64_t * #ctypedef npy_int96 int96_t */ typedef npy_int32 __pyx_t_5numpy_int32_t; /* "numpy.pxd":726 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< * #ctypedef npy_int96 int96_t * #ctypedef npy_int128 int128_t */ typedef npy_int64 __pyx_t_5numpy_int64_t; /* "numpy.pxd":730 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; /* "numpy.pxd":731 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; /* "numpy.pxd":732 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< * ctypedef npy_uint64 uint64_t * #ctypedef npy_uint96 uint96_t */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; /* "numpy.pxd":733 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< * #ctypedef npy_uint96 uint96_t * #ctypedef npy_uint128 uint128_t */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; /* "numpy.pxd":737 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t * #ctypedef npy_float80 float80_t */ typedef npy_float32 __pyx_t_5numpy_float32_t; /* "numpy.pxd":738 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< * #ctypedef npy_float80 float80_t * #ctypedef npy_float128 float128_t */ typedef npy_float64 __pyx_t_5numpy_float64_t; /* "numpy.pxd":747 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t */ typedef npy_long __pyx_t_5numpy_int_t; /* "numpy.pxd":748 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< * ctypedef npy_longlong longlong_t * */ typedef npy_longlong __pyx_t_5numpy_long_t; /* "numpy.pxd":749 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< * * ctypedef npy_ulong uint_t */ typedef npy_longlong __pyx_t_5numpy_longlong_t; /* "numpy.pxd":751 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t */ typedef npy_ulong __pyx_t_5numpy_uint_t; /* "numpy.pxd":752 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulonglong_t * */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; /* "numpy.pxd":753 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< * * ctypedef npy_intp intp_t */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; /* "numpy.pxd":755 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< * ctypedef npy_uintp uintp_t * */ typedef npy_intp __pyx_t_5numpy_intp_t; /* "numpy.pxd":756 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< * * ctypedef npy_double float_t */ typedef npy_uintp __pyx_t_5numpy_uintp_t; /* "numpy.pxd":758 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t */ typedef npy_double __pyx_t_5numpy_float_t; /* "numpy.pxd":759 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< * ctypedef npy_longdouble longdouble_t * */ typedef npy_double __pyx_t_5numpy_double_t; /* "numpy.pxd":760 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< * * ctypedef npy_cfloat cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< float > __pyx_t_float_complex; #else typedef float _Complex __pyx_t_float_complex; #endif #else typedef struct { float real, imag; } __pyx_t_float_complex; #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< double > __pyx_t_double_complex; #else typedef double _Complex __pyx_t_double_complex; #endif #else typedef struct { double real, imag; } __pyx_t_double_complex; #endif /*--- Type declarations ---*/ struct __pyx_obj_5HTSeq_6_HTSeq_Alignment; struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal; struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment; struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray; struct __pyx_obj_5HTSeq_6_HTSeq___pyx_scope_struct____iadd__; struct __pyx_obj_5HTSeq_6_HTSeq_Sequence; struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities; struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment; struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector; /* "numpy.pxd":762 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; /* "numpy.pxd":763 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< * ctypedef npy_clongdouble clongdouble_t * */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; /* "numpy.pxd":764 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< * * ctypedef npy_cdouble complex_t */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; /* "numpy.pxd":766 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< * * cdef inline object PyArray_MultiIterNew1(a): */ typedef npy_cdouble __pyx_t_5numpy_complex_t; struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_left_end; struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_right_end; struct __pyx_opt_args_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_left_end_with_quals; struct __pyx_opt_args_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_right_end_with_quals; struct __pyx_opt_args_5HTSeq_6_HTSeq_parse_cigar; struct __pyx_opt_args_5HTSeq_6_HTSeq_build_cigar_list; struct __pyx_opt_args_5HTSeq_6_HTSeq_quotesafe_split; /* "HTSeq/_HTSeq.pxd":25 * cpdef Sequence get_reverse_complement( self ) * cpdef object add_bases_to_count_array( Sequence self, numpy.ndarray count_array_ ) * cpdef Sequence trim_left_end( Sequence self, Sequence pattern, float mismatch_prop = ? ) # <<<<<<<<<<<<<< * cpdef Sequence trim_right_end( Sequence self, Sequence pattern, float mismatch_prop = ? ) * */ struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_left_end { int __pyx_n; float mismatch_prop; }; /* "HTSeq/_HTSeq.pxd":26 * cpdef object add_bases_to_count_array( Sequence self, numpy.ndarray count_array_ ) * cpdef Sequence trim_left_end( Sequence self, Sequence pattern, float mismatch_prop = ? ) * cpdef Sequence trim_right_end( Sequence self, Sequence pattern, float mismatch_prop = ? ) # <<<<<<<<<<<<<< * * */ struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_right_end { int __pyx_n; float mismatch_prop; }; /* "HTSeq/_HTSeq.pxd":36 * cdef _fill_qual_arr( SequenceWithQualities self ) * cpdef object add_qual_to_count_array( SequenceWithQualities self, numpy.ndarray count_array_ ) * cpdef SequenceWithQualities trim_left_end_with_quals( SequenceWithQualities self, # <<<<<<<<<<<<<< * Sequence pattern, int max_mm_qual = ? ) * cpdef SequenceWithQualities trim_right_end_with_quals( SequenceWithQualities self, */ struct __pyx_opt_args_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_left_end_with_quals { int __pyx_n; int max_mm_qual; }; /* "HTSeq/_HTSeq.pxd":38 * cpdef SequenceWithQualities trim_left_end_with_quals( SequenceWithQualities self, * Sequence pattern, int max_mm_qual = ? ) * cpdef SequenceWithQualities trim_right_end_with_quals( SequenceWithQualities self, # <<<<<<<<<<<<<< * Sequence pattern, int max_mm_qual = ? ) * */ struct __pyx_opt_args_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_right_end_with_quals { int __pyx_n; int max_mm_qual; }; /* "HTSeq/_HTSeq.pyx":1110 * _re_cigar_codes = re.compile( '([A-Z])' ) * * cpdef list parse_cigar( str cigar_string, int ref_left = 0, str chrom = "", str strand = "." ): # <<<<<<<<<<<<<< * cdef list split_cigar, cl * cdef int size */ struct __pyx_opt_args_5HTSeq_6_HTSeq_parse_cigar { int __pyx_n; int ref_left; PyObject *chrom; PyObject *strand; }; /* "HTSeq/_HTSeq.pyx":1127 * return build_cigar_list( cl, ref_left, chrom, strand ) * * cpdef list build_cigar_list( list cigar_pairs, int ref_left = 0, str chrom = "", str strand = "." ): # <<<<<<<<<<<<<< * cdef list split_cigar, res * cdef int rpos, qpos, size */ struct __pyx_opt_args_5HTSeq_6_HTSeq_build_cigar_list { int __pyx_n; int ref_left; PyObject *chrom; PyObject *strand; }; /* "HTSeq/_HTSeq.pyx":1425 * ########################### * * cpdef list quotesafe_split( bytes s, bytes split=b';', bytes quote=b'"' ): # <<<<<<<<<<<<<< * cdef list l = [] * cdef int i = 0 */ struct __pyx_opt_args_5HTSeq_6_HTSeq_quotesafe_split { int __pyx_n; PyObject *split; PyObject *quote; }; /* "HTSeq/_HTSeq.pxd":42 * * * cdef class Alignment( object ): # <<<<<<<<<<<<<< * cdef public SequenceWithQualities _read * cdef public GenomicInterval iv */ struct __pyx_obj_5HTSeq_6_HTSeq_Alignment { PyObject_HEAD struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *_read; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *iv; }; /* "HTSeq/_HTSeq.pxd":46 * cdef public GenomicInterval iv * * cdef class AlignmentWithSequenceReversal( Alignment ): # <<<<<<<<<<<<<< * cdef public SequenceWithQualities read_as_aligned * cdef public SequenceWithQualities _read_as_sequenced */ struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal { struct __pyx_obj_5HTSeq_6_HTSeq_Alignment __pyx_base; struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *read_as_aligned; struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *_read_as_sequenced; }; /* "HTSeq/_HTSeq.pyx":1034 * * * cdef class BowtieAlignment( AlignmentWithSequenceReversal ): # <<<<<<<<<<<<<< * * """When reading in a Bowtie file, objects of the class BowtieAlignment */ struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment { struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal __pyx_base; PyObject *reserved; PyObject *substitutions; }; /* "HTSeq/_HTSeq.pyx":1067 * 'P': 'padded' } * * cdef class CigarOperation( object ): # <<<<<<<<<<<<<< * * cdef public str type */ struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation { PyObject_HEAD PyObject *type; int size; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *ref_iv; int query_from; int query_to; }; /* "HTSeq/_HTSeq.pxd":3 * cimport numpy * * cdef class GenomicInterval: # <<<<<<<<<<<<<< * * cdef public str chrom */ struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval { PyObject_HEAD struct __pyx_vtabstruct_5HTSeq_6_HTSeq_GenomicInterval *__pyx_vtab; PyObject *chrom; long start; long end; PyObject *_strand; }; /* "HTSeq/_HTSeq.pxd":15 * cpdef extend_to_include( GenomicInterval self, GenomicInterval iv ) * * cdef class GenomicPosition( GenomicInterval ): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval __pyx_base; }; /* "HTSeq/_HTSeq.pyx":478 * return cv * * cdef class GenomicArray( object ): # <<<<<<<<<<<<<< * * cdef public dict chrom_vectors */ struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray { PyObject_HEAD PyObject *chrom_vectors; int stranded; PyObject *typecode; int auto_add_chroms; PyObject *storage; PyObject *memmap_dir; }; /* "HTSeq/_HTSeq.pyx":437 * raise TypeError, "Illegal index type" * * def __iadd__( self, value ): # <<<<<<<<<<<<<< * if not self.is_vector_of_sets: * self.array[ self.iv.start - self.offset : self.iv.end - self.offset ].__iadd__( value ) */ struct __pyx_obj_5HTSeq_6_HTSeq___pyx_scope_struct____iadd__ { PyObject_HEAD PyObject *__pyx_v_value; }; /* "HTSeq/_HTSeq.pxd":19 * * * cdef class Sequence( object ): # <<<<<<<<<<<<<< * cdef public bytes seq * cdef public str name */ struct __pyx_obj_5HTSeq_6_HTSeq_Sequence { PyObject_HEAD struct __pyx_vtabstruct_5HTSeq_6_HTSeq_Sequence *__pyx_vtab; PyObject *seq; PyObject *name; PyObject *descr; }; /* "HTSeq/_HTSeq.pxd":29 * * * cdef class SequenceWithQualities( Sequence ): # <<<<<<<<<<<<<< * cdef readonly bytes _qualstr * cdef readonly bytes _qualstr_phred */ struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence __pyx_base; PyObject *_qualstr; PyObject *_qualstr_phred; PyObject *_qualscale; PyObject *_qualarr; }; /* "HTSeq/_HTSeq.pxd":50 * cdef public SequenceWithQualities _read_as_sequenced * * cdef class SAM_Alignment( AlignmentWithSequenceReversal ): # <<<<<<<<<<<<<< * cdef public list cigar * cdef public int aQual */ struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment { struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal __pyx_base; PyObject *cigar; int aQual; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *mate_start; PyObject *pe_which; int inferred_insert_size; int proper_pair; int not_primary_alignment; int failed_platform_qc; int pcr_or_optical_duplicate; PyObject *original_sam_line; int _flag; PyObject *optional_fields; }; /* "HTSeq/_HTSeq.pyx":314 * * * cdef class ChromVector( object ): # <<<<<<<<<<<<<< * * cdef public object array */ struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector { PyObject_HEAD PyObject *array; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *iv; int offset; int is_vector_of_sets; PyObject *_storage; }; /* "HTSeq/_HTSeq.pyx":26 * cdef str strand_nostrand = intern( "." ) * * cdef class GenomicInterval: # <<<<<<<<<<<<<< * * """A GenomicInterval specifies an interval (i.e., a range of */ struct __pyx_vtabstruct_5HTSeq_6_HTSeq_GenomicInterval { PyObject *(*is_contained_in)(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, int __pyx_skip_dispatch); PyObject *(*contains)(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, int __pyx_skip_dispatch); PyObject *(*overlaps)(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, int __pyx_skip_dispatch); PyObject *(*extend_to_include)(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_5HTSeq_6_HTSeq_GenomicInterval *__pyx_vtabptr_5HTSeq_6_HTSeq_GenomicInterval; /* "HTSeq/_HTSeq.pyx":634 * base_to_column = { 'A': 0, 'C': 1, 'G': 2, 'T': 3, 'N': 4 } * * cdef class Sequence( object ): # <<<<<<<<<<<<<< * """A Sequence, typically of DNA, with a name. * """ */ struct __pyx_vtabstruct_5HTSeq_6_HTSeq_Sequence { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*get_reverse_complement)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch); PyObject *(*add_bases_to_count_array)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, PyArrayObject *, int __pyx_skip_dispatch); struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*trim_left_end)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_left_end *__pyx_optional_args); struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*trim_right_end)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_right_end *__pyx_optional_args); }; static struct __pyx_vtabstruct_5HTSeq_6_HTSeq_Sequence *__pyx_vtabptr_5HTSeq_6_HTSeq_Sequence; /* "HTSeq/_HTSeq.pyx":754 * * * cdef class SequenceWithQualities( Sequence ): # <<<<<<<<<<<<<< * """A Sequence with base-call quality scores. * It now has property 'qual', an integer NumPy array of Sanger/Phred */ struct __pyx_vtabstruct_5HTSeq_6_HTSeq_SequenceWithQualities { struct __pyx_vtabstruct_5HTSeq_6_HTSeq_Sequence __pyx_base; PyObject *(*_fill_qual_arr)(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *); 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static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_is_dict); static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos, PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict); static int __Pyx_PyUnicode_Tailmatch(PyObject* s, PyObject* substr, Py_ssize_t start, Py_ssize_t end, int direction) { if (unlikely(PyTuple_Check(substr))) { Py_ssize_t i, count = PyTuple_GET_SIZE(substr); for (i = 0; i < count; i++) { int result; #if CYTHON_COMPILING_IN_CPYTHON result = PyUnicode_Tailmatch(s, PyTuple_GET_ITEM(substr, i), start, end, direction); #else PyObject* sub = PySequence_GetItem(substr, i); if (unlikely(!sub)) return -1; result = PyUnicode_Tailmatch(s, sub, start, end, direction); Py_DECREF(sub); #endif if (result) { return result; } } return 0; } return PyUnicode_Tailmatch(s, substr, start, end, direction); } static int __Pyx_PyBytes_SingleTailmatch(PyObject* self, PyObject* arg, Py_ssize_t start, Py_ssize_t end, int direction) { const char* self_ptr = PyBytes_AS_STRING(self); Py_ssize_t self_len = PyBytes_GET_SIZE(self); const char* sub_ptr; Py_ssize_t sub_len; int retval; #if PY_VERSION_HEX >= 0x02060000 Py_buffer view; view.obj = NULL; #endif if ( PyBytes_Check(arg) ) { sub_ptr = PyBytes_AS_STRING(arg); sub_len = PyBytes_GET_SIZE(arg); } #if PY_MAJOR_VERSION < 3 else if ( PyUnicode_Check(arg) ) { return PyUnicode_Tailmatch(self, arg, start, end, direction); } #endif else { #if PY_VERSION_HEX < 0x02060000 if (unlikely(PyObject_AsCharBuffer(arg, &sub_ptr, &sub_len))) return -1; #else if (unlikely(PyObject_GetBuffer(self, &view, PyBUF_SIMPLE) == -1)) return -1; sub_ptr = (const char*) view.buf; sub_len = view.len; #endif } if (end > self_len) end = self_len; else if (end < 0) end += self_len; if (end < 0) end = 0; if (start < 0) start += self_len; if (start < 0) start = 0; if (direction > 0) { if (end-sub_len > start) start = end - sub_len; } if (start + sub_len <= end) retval = !memcmp(self_ptr+start, sub_ptr, sub_len); else retval = 0; #if PY_VERSION_HEX >= 0x02060000 if (view.obj) PyBuffer_Release(&view); #endif return retval; } static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr, Py_ssize_t start, Py_ssize_t end, int direction) { if (unlikely(PyTuple_Check(substr))) { Py_ssize_t i, count = PyTuple_GET_SIZE(substr); for (i = 0; i < count; i++) { int result; #if CYTHON_COMPILING_IN_CPYTHON result = __Pyx_PyBytes_SingleTailmatch(self, PyTuple_GET_ITEM(substr, i), start, end, direction); #else PyObject* sub = PySequence_GetItem(substr, i); if (unlikely(!sub)) return -1; result = __Pyx_PyBytes_SingleTailmatch(self, sub, start, end, direction); Py_DECREF(sub); #endif if (result) { return result; } } return 0; } return __Pyx_PyBytes_SingleTailmatch(self, substr, start, end, direction); } static CYTHON_INLINE int __Pyx_PyStr_Tailmatch(PyObject* self, PyObject* arg, Py_ssize_t start, Py_ssize_t end, int direction); static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); static void __Pyx_RaiseBufferIndexError(int axis); /*proto*/ #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) #define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0) static void __Pyx_RaiseBufferFallbackError(void); /*proto*/ static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyObject_AsDouble(obj) \ (likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \ likely(PyInt_CheckExact(obj)) ? \ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj)) #else #define __Pyx_PyObject_AsDouble(obj) \ ((likely(PyFloat_CheckExact(obj))) ? \ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) #endif static CYTHON_INLINE char __Pyx_PyBytes_GetItemInt(PyObject* bytes, Py_ssize_t index, int check_bounds) { if (check_bounds) { Py_ssize_t size = PyBytes_GET_SIZE(bytes); if (unlikely(index >= size) | ((index < 0) & unlikely(index < -size))) { PyErr_Format(PyExc_IndexError, "string index out of range"); return -1; } } if (index < 0) index += PyBytes_GET_SIZE(bytes); return PyBytes_AS_STRING(bytes)[index]; } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ typedef struct { Py_ssize_t shape, strides, suboffsets; } __Pyx_Buf_DimInfo; typedef struct { size_t refcount; Py_buffer pybuffer; } __Pyx_Buffer; typedef struct { __Pyx_Buffer *rcbuffer; char *data; __Pyx_Buf_DimInfo diminfo[8]; } __Pyx_LocalBuf_ND; #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); static void __Pyx_ReleaseBuffer(Py_buffer *view); #else #define __Pyx_GetBuffer PyObject_GetBuffer #define __Pyx_ReleaseBuffer PyBuffer_Release #endif static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/ #define __Pyx_CyFunction_USED 1 #include #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 #define __Pyx_CYFUNCTION_CCLASS 0x04 #define __Pyx_CyFunction_GetClosure(f) \ (((__pyx_CyFunctionObject *) (f))->func_closure) #define __Pyx_CyFunction_GetClassObj(f) \ (((__pyx_CyFunctionObject *) (f))->func_classobj) #define __Pyx_CyFunction_Defaults(type, f) \ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) #define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) typedef struct { PyCFunctionObject func; int flags; PyObject *func_dict; PyObject *func_weakreflist; PyObject *func_name; PyObject *func_doc; PyObject *func_code; PyObject *func_closure; PyObject *func_classobj; /* No-args super() class cell */ void *defaults; int defaults_pyobjects; PyObject *defaults_tuple; /* Const defaults tuple */ PyObject *(*defaults_getter)(PyObject *); } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; #define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code) static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, int flags, PyObject *self, PyObject *module, PyObject* code); static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, size_t size, int pyobjects); static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, PyObject *tuple); static int __Pyx_CyFunction_init(void); static CYTHON_INLINE Py_intptr_t __Pyx_PyInt_from_py_Py_intptr_t(PyObject *); static CYTHON_INLINE long __Pyx_pow_long(long, long); /* proto */ static CYTHON_INLINE npy_long __Pyx_PyInt_from_py_npy_long(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_Py_intptr_t(Py_intptr_t); #include "descrobject.h" static PyObject* __Pyx_Method_ClassMethod(PyObject *method); /*proto*/ #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) #define __Pyx_CIMAG(z) ((z).imag()) #else #define __Pyx_CREAL(z) (__real__(z)) #define __Pyx_CIMAG(z) (__imag__(z)) #endif #else #define __Pyx_CREAL(z) ((z).real) #define __Pyx_CIMAG(z) ((z).imag) #endif #if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX #define __Pyx_SET_CREAL(z,x) ((z).real(x)) #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) #else #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) #endif static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); #if CYTHON_CCOMPLEX #define __Pyx_c_eqf(a, b) ((a)==(b)) #define __Pyx_c_sumf(a, b) ((a)+(b)) #define __Pyx_c_difff(a, b) ((a)-(b)) #define __Pyx_c_prodf(a, b) ((a)*(b)) #define __Pyx_c_quotf(a, b) ((a)/(b)) #define __Pyx_c_negf(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zerof(z) ((z)==(float)0) #define __Pyx_c_conjf(z) (::std::conj(z)) #if 1 #define __Pyx_c_absf(z) (::std::abs(z)) #define __Pyx_c_powf(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zerof(z) ((z)==0) #define __Pyx_c_conjf(z) (conjf(z)) #if 1 #define __Pyx_c_absf(z) (cabsf(z)) #define __Pyx_c_powf(a, b) (cpowf(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); #endif #endif static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); #if CYTHON_CCOMPLEX #define __Pyx_c_eq(a, b) ((a)==(b)) #define __Pyx_c_sum(a, b) ((a)+(b)) #define __Pyx_c_diff(a, b) ((a)-(b)) #define __Pyx_c_prod(a, b) ((a)*(b)) #define __Pyx_c_quot(a, b) ((a)/(b)) #define __Pyx_c_neg(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zero(z) ((z)==(double)0) #define __Pyx_c_conj(z) (::std::conj(z)) #if 1 #define __Pyx_c_abs(z) (::std::abs(z)) #define __Pyx_c_pow(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zero(z) ((z)==0) #define __Pyx_c_conj(z) (conj(z)) #if 1 #define __Pyx_c_abs(z) (cabs(z)) #define __Pyx_c_pow(a, b) (cpow(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); #endif #endif static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static int __Pyx_check_binary_version(void); static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; /* Module declarations from 'libc.stdlib' */ /* Module declarations from 'numpy' */ /* Module declarations from 'numpy' */ static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ /* Module declarations from 'HTSeq._HTSeq' */ static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_GenomicInterval = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_GenomicPosition = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_Sequence = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_SequenceWithQualities = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_Alignment = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_SAM_Alignment = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_ChromVector = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_GenomicArray = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_BowtieAlignment = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq_CigarOperation = 0; static PyTypeObject *__pyx_ptype_5HTSeq_6_HTSeq___pyx_scope_struct____iadd__ = 0; static PyObject *__pyx_v_5HTSeq_6_HTSeq_strand_plus = 0; static PyObject *__pyx_v_5HTSeq_6_HTSeq_strand_minus = 0; static PyObject *__pyx_v_5HTSeq_6_HTSeq_strand_nostrand = 0; static PyObject *__pyx_v_5HTSeq_6_HTSeq__translation_table_for_complementation = 0; static PyObject *__pyx_f_5HTSeq_6_HTSeq_reverse_complement(PyObject *, int __pyx_skip_dispatch); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq_parse_cigar(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_parse_cigar *__pyx_optional_args); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq_build_cigar_list(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_build_cigar_list *__pyx_optional_args); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq__parse_SAM_optional_field_value(PyObject *); /*proto*/ static PyObject *__pyx_f_5HTSeq_6_HTSeq_quotesafe_split(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_quotesafe_split *__pyx_optional_args); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 }; #define __Pyx_MODULE_NAME "HTSeq._HTSeq" int __pyx_module_is_main_HTSeq___HTSeq = 0; /* Implementation of 'HTSeq._HTSeq' */ static PyObject *__pyx_builtin_property; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_xrange; static PyObject *__pyx_builtin_chr; static PyObject *__pyx_builtin_ord; static PyObject *__pyx_builtin_ImportError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval___init__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, PyObject *__pyx_v_chrom, long __pyx_v_start, long __pyx_v_end, PyObject *__pyx_v_strand); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_6strand___set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_6strand_2__get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_2__reduce__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_4__copy__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_6__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_8__str__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_6length___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_6length_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, long __pyx_v_newLength); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_7start_d___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_7start_d_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, long __pyx_v_newStartd); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_5end_d___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_12start_as_pos___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_10end_as_pos___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_14start_d_as_pos___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_12end_d_as_pos___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_10__richcmp__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_other, int __pyx_v_op); /* proto */ static Py_hash_t __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_12__hash__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_14is_contained_in(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_16contains(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_18overlaps(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_20xrange(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, long __pyx_v_step); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_22xrange_d(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, long __pyx_v_step); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_24extend_to_include(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_26copy(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_5chrom___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_5chrom_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_5chrom_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_5start___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_5start_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_3end___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicInterval_3end_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_GenomicInterval_from_directional(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, long __pyx_v_start_d, long __pyx_v_length, PyObject *__pyx_v_strand); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition___init__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self, PyObject *__pyx_v_chrom, long __pyx_v_pos, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_3pos___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_3pos_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self, long __pyx_v_newValue); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_3end___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_6length___get__(CYTHON_UNUSED struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_2__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_4__str__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_6__reduce__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15GenomicPosition_8copy(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_create(PyObject *__pyx_v_cls, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv, PyObject *__pyx_v_typecode, PyObject *__pyx_v_storage, PyObject *__pyx_v_memmap_dir); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_2_create_view(PyObject *__pyx_v_cls, struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_vec, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_4__getitem__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_6__setitem__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_8__iadd___addval(PyObject *__pyx_self, PyObject *__pyx_v_x); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_8__iadd__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_10__iter__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_12values(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_14steps(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_16apply(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_fun); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_18__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_20__reduce__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_5array___get__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_5array_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_5array_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_2iv___get__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_2iv_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_2iv_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_6offset___get__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_6offset_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_17is_vector_of_sets___get__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_17is_vector_of_sets_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_11ChromVector_8_storage___get__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_8_storage_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_11ChromVector_8_storage_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_2_ChromVector_unpickle(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_array, PyObject *__pyx_v_iv, PyObject *__pyx_v_offset, PyObject *__pyx_v_is_vector_of_sets, PyObject *__pyx_v__storage); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_12GenomicArray___init__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_chroms, int __pyx_v_stranded, PyObject *__pyx_v_typecode, PyObject *__pyx_v_storage, PyObject *__pyx_v_memmap_dir); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_2__getitem__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_4__setitem__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_6add_chrom(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_length, PyObject *__pyx_v_start_index); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_8__reduce__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_10write_bedgraph_file(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_file_or_filename, PyObject *__pyx_v_strand, PyObject *__pyx_v_track_options); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_12steps(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_13chrom_vectors___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_13chrom_vectors_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_13chrom_vectors_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_8stranded___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_8typecode___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_15auto_add_chroms___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_15auto_add_chroms_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_7storage___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12GenomicArray_10memmap_dir___get__(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_4_GenomicArray_unpickle(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_stranded, PyObject *__pyx_v_typecode, PyObject *__pyx_v_chrom_vectors); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_6_make_translation_table_for_complementation(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8reverse_complement(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_seq); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence___init__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyObject *__pyx_v_seq, PyObject *__pyx_v_name); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_2get_reverse_complement(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_4__str__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_6__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static Py_ssize_t __pyx_pf_5HTSeq_6_HTSeq_8Sequence_8__len__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_10__getitem__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_12write_to_fasta_file(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyObject *__pyx_v_fasta_file); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_14add_bases_to_count_array(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyArrayObject *__pyx_v_count_array_); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_16trim_left_end(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_pattern, float __pyx_v_mismatch_prop); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_18trim_right_end(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_pattern, float __pyx_v_mismatch_prop); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_3seq___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence_3seq_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence_3seq_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_4name___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence_4name_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence_4name_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_8Sequence_5descr___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence_5descr_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_8Sequence_5descr_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities___init__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, PyObject *__pyx_v_seq, PyObject *__pyx_v_name, PyObject *__pyx_v_qualstr, PyObject *__pyx_v_qualscale); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_4qual___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_4qual_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, PyObject *__pyx_v_newvalue); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_2__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_4__getitem__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_6qualstr(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_8write_to_fastq_file(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, PyObject *__pyx_v_fastq_file); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_10get_fastq_str(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, int __pyx_v_convert_to_phred); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_12get_reverse_complement(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_14add_qual_to_count_array(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, PyArrayObject *__pyx_v_count_array_); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_16trim_left_end_with_quals(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_pattern, int __pyx_v_max_mm_qual); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_18trim_right_end_with_quals(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *__pyx_v_pattern, int __pyx_v_max_mm_qual); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_8_qualstr___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_14_qualstr_phred___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_10_qualscale___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_21SequenceWithQualities_8_qualarr___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment___init__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v_read, PyObject *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_2read(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_4__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_6paired_end(CYTHON_UNUSED struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_8aligned(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_5_read___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_5_read_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_5_read_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv___get__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_9Alignment_2iv_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal___init__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *__pyx_v_read_as_aligned, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *__pyx_v_iv); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_4read___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced___get__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment___init__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_bowtie_line); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved___get__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions___get__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation___init__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_type_, int __pyx_v_size, int __pyx_v_rfrom, int __pyx_v_rto, int __pyx_v_qfrom, int __pyx_v_qto, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand, int __pyx_v_check); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_2__repr__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4check(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4type___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4type_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4type_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4size___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_4size_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_6ref_iv___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_6ref_iv_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_6ref_iv_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_10query_from___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_10query_from_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8query_to___get__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_14CigarOperation_8query_to_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_10parse_cigar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_cigar_string, int __pyx_v_ref_left, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_12build_cigar_list(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_cigar_pairs, int __pyx_v_ref_left, PyObject *__pyx_v_chrom, PyObject *__pyx_v_strand); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_to_pysam_AlignedRead(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_sf); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_2from_pysam_AlignedRead(CYTHON_UNUSED PyObject *__pyx_v_cls, PyObject *__pyx_v_read, PyObject *__pyx_v_samfile); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_4from_SAM_line(CYTHON_UNUSED PyObject *__pyx_v_cls, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_4flag___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_4flag_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_6paired_end(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_8mate_aligned(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_10get_sam_line(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_12optional_field(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_14raw_optional_fields(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_5cigar___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_5cigar_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_5cigar_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_5aQual___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_5aQual_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_10mate_start___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_10mate_start_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_10mate_start_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_8pe_which___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_8pe_which_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_8pe_which_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_20inferred_insert_size___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_20inferred_insert_size_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_11proper_pair___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_11proper_pair_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_21not_primary_alignment___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_21not_primary_alignment_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_18failed_platform_qc___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_18failed_platform_qc_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_24pcr_or_optical_duplicate___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_24pcr_or_optical_duplicate_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_17original_sam_line___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields___get__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_2__set__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_4__del__(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5HTSeq_6_HTSeq_14quotesafe_split(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_s, PyObject *__pyx_v_split, PyObject *__pyx_v_quote); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static char __pyx_k_2[] = "start is larger than end"; static char __pyx_k_3[] = "Strand must be'+', '-', or '.'."; static char __pyx_k_4[] = "<%s object '%s', [%d,%s), strand '%s'>"; static char __pyx_k_5[] = "%s:[%d,%s)/%s"; static char __pyx_k_6[] = "GenomicInterval_xrange"; static char __pyx_k_7[] = "GenomicInterval_xranged"; static char __pyx_k_8[] = "Cannot extend an interval to include None."; static char __pyx_k_9[] = "Cannot extend an interval to include an interval on another chromosome."; static char __pyx_k_10[] = "Cannot extend an interval to include an interval on another strand."; static char __pyx_k_11[] = "."; static char __pyx_k_12[] = "<%s object '%s':%d, strand '%s'>"; static char __pyx_k_13[] = "%s:%d/%s"; static char __pyx_k_14[] = ""; static char __pyx_k_15[] = ".nmm"; static char __pyx_k_16[] = "w+"; static char __pyx_k_17[] = "Illegal storage mode."; static char __pyx_k_18[] = "Cannot subset to zero-length interval."; static char __pyx_k_19[] = "start too small"; static char __pyx_k_20[] = "stop too large"; static char __pyx_k_21[] = "Illegal index type"; static char __pyx_k_22[] = "Required assignment signature not yet implemented."; static char __pyx_k_23[] = "Start of interval is after its end."; static char __pyx_k_24[] = "Cannot assign to zero-length interval."; static char __pyx_k_25[] = "Chromosome name mismatch."; static char __pyx_k_26[] = "Strand mismatch."; static char __pyx_k_29[] = "/home/anders/work/code/htseq/src/HTSeq/_HTSeq.pyx"; static char __pyx_k_30[] = "HTSeq._HTSeq"; static char __pyx_k_31[] = "<%s object, %s, %s>"; static char __pyx_k_32[] = "_ChromVector_unpickle"; static char __pyx_k_33[] = "Automatic adding of chromosomes can "; static char __pyx_k_34[] = " only be used with storage type 'StepVector'."; static char __pyx_k_35[] = "Indefinite-length chromosomes can "; static char __pyx_k_36[] = "'chroms' must be a list or a dict or 'auto'."; static char __pyx_k_37[] = "Non-stranded index used for stranded GenomicArray."; static char __pyx_k_38[] = "Illegal index type."; static char __pyx_k_40[] = "+"; static char __pyx_k_41[] = "-"; static char __pyx_k_42[] = "_GenomicArray_unpickle"; static char __pyx_k_43[] = "Strand specified in unstranded GenomicArray."; static char __pyx_k_44[] = "Strand must be specified for stranded GenomicArray."; static char __pyx_k_45[] = "track type=bedGraph\n"; static char __pyx_k_47[] = "track type=bedGraph %s\n"; static char __pyx_k_48[] = "%s\t%d\t%d\t%f\n"; static char __pyx_k_50[] = "get_reverse_complement"; static char __pyx_k_51[] = "<%s object '%s' (length %d)>"; static char __pyx_k_52[] = "[part]"; static char __pyx_k_53[] = ">%s %s\n"; static char __pyx_k_54[] = ">%s\n"; static char __pyx_k_55[] = "\n"; static char __pyx_k_56[] = "add_bases_to_count_array"; static char __pyx_k_57[] = "'count_array' too small for sequence."; static char __pyx_k_58[] = "'count_array' has too few columns."; static char __pyx_k_59[] = "Illegal base letter encountered."; static char __pyx_k_60[] = "'seq' and 'qualstr' do not have the same length."; static char __pyx_k_61[] = "Quality string missing."; static char __pyx_k_62[] = "Quality string has not the same length as sequence."; static char __pyx_k_63[] = "solexa-old"; static char __pyx_k_64[] = "Illegal quality scale '%s'."; static char __pyx_k_65[] = "qual can only be assigned a numpy array of type numpy.int"; static char __pyx_k_66[] = "assignment to qual with illegal shape"; static char __pyx_k_67[] = "<%s object '%s'>"; static char __pyx_k_68[] = "Quality string missing"; static char __pyx_k_69[] = " "; static char __pyx_k_70[] = "@%s %s\n"; static char __pyx_k_71[] = "@%s\n"; static char __pyx_k_72[] = "+\n"; static char __pyx_k_76[] = "add_qual_to_count_array"; static char __pyx_k_77[] = "Too large quality value encountered."; static char __pyx_k_78[] = "trim_left_end_with_quals"; static char __pyx_k_79[] = "trim_right_end_with_quals"; static char __pyx_k_80[] = "Paired-end read"; static char __pyx_k_81[] = "<%s object: %s '%s' aligned to %s>"; static char __pyx_k_82[] = "<%s object: %s '%s', not aligned>"; static char __pyx_k_83[] = "\t"; static char __pyx_k_85[] = "Inconsistent CIGAR operation."; static char __pyx_k_86[] = "< %s: %d base(s) %s on ref iv %s, query iv [%d,%d) >"; static char __pyx_k_87[] = "cigar_operation_names"; static char __pyx_k_88[] = "Illegal CIGAR string '%s'"; static char __pyx_k_89[] = "Unknown CIGAR code '%s' encountered."; static char __pyx_k_90[] = ":"; static char __pyx_k_91[] = "Malformatted SAM optional field '%'"; static char __pyx_k_92[] = "SAM optional field with illegal type letter '%s'"; static char __pyx_k_93[] = "Please Install PySam to use this functionality (http://code.google.com/p/pysam/)"; static char __pyx_k_95[] = "cigar_operation_code_dict"; static char __pyx_k_96[] = "*"; static char __pyx_k_97[] = "cigar_operation_codes"; static char __pyx_k_99[] = "SAM line does not contain at least 11 tab-delimited fields."; static char __pyx_k__A[] = "A"; static char __pyx_k__B[] = "B"; static char __pyx_k__C[] = "C"; static char __pyx_k__D[] = "D"; static char __pyx_k__G[] = "G"; static char __pyx_k__H[] = "H"; static char __pyx_k__I[] = "I"; static char __pyx_k__L[] = "L"; static char __pyx_k__M[] = "M"; static char __pyx_k__N[] = "N"; static char __pyx_k__O[] = "O"; static char __pyx_k__P[] = "P"; static char __pyx_k__Q[] = "Q"; static char __pyx_k__S[] = "S"; static char __pyx_k__T[] = "T"; static char __pyx_k__X[] = "X"; static char __pyx_k__Z[] = "Z"; static char __pyx_k__a[] = "a"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__d[] = "d"; static char __pyx_k__f[] = "f"; static char __pyx_k__g[] = "g"; static char __pyx_k__h[] = "h"; static char __pyx_k__i[] = "i"; static char __pyx_k__j[] = "j"; static char __pyx_k__l[] = "l"; static char __pyx_k__q[] = "q"; static char __pyx_k__s[] = "s"; static char __pyx_k__t[] = "t"; static char __pyx_k__w[] = "w"; static char __pyx_k__x[] = "x"; static char __pyx_k__y[] = "y"; static char __pyx_k_100[] = "="; static char __pyx_k_102[] = "Sequence in SAM file contains '=', which is not supported."; static char __pyx_k_104[] = "Sequence in SAM file contains '.', which is not supported."; static char __pyx_k_105[] = "Malformed SAM line: RNAME != '*' although flag bit &0x0004 set"; static char __pyx_k_107[] = "Malformed SAM line: RNAME == '*' although flag bit &0x0004 cleared"; static char __pyx_k_108[] = "Malformed SAM line: MRNM != '*' although flag bit &0x0008 set"; static char __pyx_k_110[] = "Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared"; static char __pyx_k_111[] = "Malformed SAM line: MRNM == '=' although read is not aligned."; static char __pyx_k_115[] = "SAM optional field tag %s not found"; static char __pyx_k_116[] = "SAM optional field tag %s not unique"; static char __pyx_k_117[] = ";"; static char __pyx_k_118[] = "\""; static char __pyx_k_119[] = "'split' must be length 1"; static char __pyx_k_120[] = "'quote' must be length 1"; static char __pyx_k_121[] = "unmatched quote"; static char __pyx_k_122[] = "ndarray is not C contiguous"; static char __pyx_k_124[] = "ndarray is not Fortran contiguous"; static char __pyx_k_126[] = "Non-native byte order not supported"; static char __pyx_k_128[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_129[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_132[] = "Format string allocated too short."; static char __pyx_k_134[] = "The length is calculated as end - start. If you set the length, \n 'start_d' will be preserved, i.e., 'end' is changed, unless the strand\n is '-', in which case 'start' is changed."; static char __pyx_k_135[] = "See the class docstring for the meaning of the 'directional start'.\n Note that if you set 'start_d', both the start and the end are changed, \n such the interval gets the requested new directional start and its\n length stays unchanged."; static char __pyx_k_136[] = "As GenomicPosition is a subclass of GenomicInterval, 'pos' is actually\n just an alias for 'start_d'.\n "; static char __pyx_k_139[] = "GenomicInterval_from_directional"; static char __pyx_k_146[] = "_make_translation_table_for_complementation"; static char __pyx_k_147[] = "soft-clipped"; static char __pyx_k_148[] = "hard-clipped"; static char __pyx_k_149[] = "([A-Z])"; static char __pyx_k_151[] = "from_pysam_AlignedRead"; static char __pyx_k__Zd[] = "Zd"; static char __pyx_k__Zf[] = "Zf"; static char __pyx_k__Zg[] = "Zg"; static char __pyx_k__cv[] = "cv"; static char __pyx_k__ga[] = "ga"; static char __pyx_k__iv[] = "iv"; static char __pyx_k__os[] = "os"; static char __pyx_k__re[] = "re"; static char __pyx_k__se[] = "se"; static char __pyx_k__Inf[] = "Inf"; static char __pyx_k__add[] = "add"; static char __pyx_k__chr[] = "chr"; static char __pyx_k__csv[] = "csv"; static char __pyx_k__end[] = "end"; static char __pyx_k__int[] = "int"; static char __pyx_k__ord[] = "ord"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__qto[] = "qto"; static char __pyx_k__rto[] = "rto"; static char __pyx_k__seq[] = "seq"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__tid[] = "tid"; static char __pyx_k__vec[] = "vec"; static char __pyx_k__Read[] = "Read"; static char __pyx_k__aend[] = "aend"; static char __pyx_k__auto[] = "auto"; static char __pyx_k__copy[] = "copy"; static char __pyx_k__flag[] = "flag"; static char __pyx_k__gzip[] = "gzip"; static char __pyx_k__join[] = "join"; static char __pyx_k__mapq[] = "mapq"; static char __pyx_k__math[] = "math"; static char __pyx_k__mode[] = "mode"; static char __pyx_k__mpos[] = "mpos"; static char __pyx_k__mrnm[] = "mrnm"; static char __pyx_k__name[] = "name"; static char __pyx_k__none[] = "none"; static char __pyx_k__open[] = "open"; static char __pyx_k__path[] = "path"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__read[] = "read"; static char __pyx_k__size[] = "size"; static char __pyx_k__step[] = "step"; static char __pyx_k__stop[] = "stop"; static char __pyx_k__tags[] = "tags"; static char __pyx_k__type[] = "type"; static char __pyx_k__warn[] = "warn"; static char __pyx_k__apply[] = "apply"; static char __pyx_k__array[] = "array"; static char __pyx_k__check[] = "check"; static char __pyx_k__chrom[] = "chrom"; static char __pyx_k__cigar[] = "cigar"; static char __pyx_k__close[] = "close"; static char __pyx_k__count[] = "count"; static char __pyx_k__descr[] = "descr"; static char __pyx_k__dtype[] = "dtype"; static char __pyx_k__empty[] = "empty"; static char __pyx_k__end_d[] = "end_d"; static char __pyx_k__first[] = "first"; static char __pyx_k__index[] = "index"; static char __pyx_k__isize[] = "isize"; static char __pyx_k__log10[] = "log10"; static char __pyx_k__numpy[] = "numpy"; static char __pyx_k__phred[] = "phred"; static char __pyx_k__pysam[] = "pysam"; static char __pyx_k__qfrom[] = "qfrom"; static char __pyx_k__qname[] = "qname"; static char __pyx_k__quote[] = "quote"; static char __pyx_k__range[] = "range"; static char __pyx_k__rfrom[] = "rfrom"; static char __pyx_k__shape[] = "shape"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__steps[] = "steps"; static char __pyx_k__type_[] = "type_"; static char __pyx_k__upper[] = "upper"; static char __pyx_k__write[] = "write"; static char __pyx_k__zeros[] = "zeros"; static char __pyx_k__addval[] = "addval"; static char __pyx_k__chroms[] = "chroms"; static char __pyx_k__create[] = "create"; static char __pyx_k__gettid[] = "gettid"; static char __pyx_k__length[] = "length"; static char __pyx_k__maxint[] = "maxint"; static char __pyx_k__memmap[] = "memmap"; static char __pyx_k__offset[] = "offset"; static char __pyx_k__padded[] = "padded"; static char __pyx_k__ref_iv[] = "ref_iv"; static char __pyx_k__rstrip[] = "rstrip"; static char __pyx_k__second[] = "second"; static char __pyx_k__solexa[] = "solexa"; static char __pyx_k__stderr[] = "stderr"; static char __pyx_k__strand[] = "strand"; static char __pyx_k__values[] = "values"; static char __pyx_k__xrange[] = "xrange"; static char __pyx_k__aligned[] = "aligned"; static char __pyx_k__compile[] = "compile"; static char __pyx_k__deleted[] = "deleted"; static char __pyx_k__matched[] = "matched"; static char __pyx_k__missing[] = "missing"; static char __pyx_k__ndarray[] = "ndarray"; static char __pyx_k__noquals[] = "noquals"; static char __pyx_k__pattern[] = "pattern"; static char __pyx_k__qualstr[] = "qualstr"; static char __pyx_k__samfile[] = "samfile"; static char __pyx_k__skipped[] = "skipped"; static char __pyx_k__start_d[] = "start_d"; static char __pyx_k__storage[] = "storage"; static char __pyx_k__unknown[] = "unknown"; static char __pyx_k__unnamed[] = "unnamed"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k__StringIO[] = "StringIO"; static char __pyx_k____iadd__[] = "__iadd__"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____name__[] = "__name__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k___qualarr[] = "_qualarr"; static char __pyx_k___qualstr[] = "_qualstr"; static char __pyx_k___storage[] = "_storage"; static char __pyx_k__contains[] = "contains"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__getrname[] = "getrname"; static char __pyx_k__getvalue[] = "getvalue"; static char __pyx_k__inserted[] = "inserted"; static char __pyx_k__is_read1[] = "is_read1"; static char __pyx_k__is_read2[] = "is_read2"; static char __pyx_k__overlaps[] = "overlaps"; static char __pyx_k__property[] = "property"; static char __pyx_k__ref_left[] = "ref_left"; static char __pyx_k__stranded[] = "stranded"; static char __pyx_k__typecode[] = "typecode"; static char __pyx_k__warnings[] = "warnings"; static char __pyx_k__TypeError[] = "TypeError"; static char __pyx_k____class__[] = "__class__"; static char __pyx_k__add_chrom[] = "add_chrom"; static char __pyx_k__cStringIO[] = "cStringIO"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__is_paired[] = "is_paired"; static char __pyx_k__is_qcfail[] = "is_qcfail"; static char __pyx_k__itertools[] = "itertools"; static char __pyx_k__qualscale[] = "qualscale"; static char __pyx_k__translate[] = "translate"; static char __pyx_k__IndexError[] = "IndexError"; static char __pyx_k__StepVector[] = "StepVector"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k____reduce__[] = "__reduce__"; static char __pyx_k___qualscale[] = "_qualscale"; static char __pyx_k__is_reverse[] = "is_reverse"; static char __pyx_k__memmap_dir[] = "memmap_dir"; static char __pyx_k__paired_end[] = "paired_end"; static char __pyx_k__AlignedRead[] = "AlignedRead"; static char __pyx_k__ImportError[] = "ImportError"; static char __pyx_k__bowtie_line[] = "bowtie_line"; static char __pyx_k__cigar_pairs[] = "cigar_pairs"; static char __pyx_k__collections[] = "collections"; static char __pyx_k__is_unmapped[] = "is_unmapped"; static char __pyx_k__max_mm_qual[] = "max_mm_qual"; static char __pyx_k__revcomp_of_[] = "revcomp_of_"; static char __pyx_k__start_index[] = "start_index"; static char __pyx_k__RuntimeError[] = "RuntimeError"; static char __pyx_k___create_view[] = "_create_view"; static char __pyx_k__cigar_string[] = "cigar_string"; static char __pyx_k__is_duplicate[] = "is_duplicate"; static char __pyx_k__is_secondary[] = "is_secondary"; static char __pyx_k__mate_aligned[] = "mate_aligned"; static char __pyx_k__chrom_vectors[] = "chrom_vectors"; static char __pyx_k__from_SAM_line[] = "from_SAM_line"; static char __pyx_k__mismatch_prop[] = "mismatch_prop"; static char __pyx_k__track_options[] = "track_options"; static char __pyx_k__trim_left_end[] = "trim_left_end"; static char __pyx_k__base_to_column[] = "base_to_column"; static char __pyx_k__is_proper_pair[] = "is_proper_pair"; static char __pyx_k__not_paired_end[] = "not_paired_end"; static char __pyx_k__trim_right_end[] = "trim_right_end"; static char __pyx_k___HTSeq_internal[] = "_HTSeq_internal"; static char __pyx_k___re_cigar_codes[] = "_re_cigar_codes"; static char __pyx_k__is_contained_in[] = "is_contained_in"; static char __pyx_k__mate_is_reverse[] = "mate_is_reverse"; static char __pyx_k__read_as_aligned[] = "read_as_aligned"; static char __pyx_k__convert_to_phred[] = "convert_to_phred"; static char __pyx_k__file_or_filename[] = "file_or_filename"; static char __pyx_k__mate_is_unmapped[] = "mate_is_unmapped"; static char __pyx_k__ChromVector_steps[] = "ChromVector_steps"; static char __pyx_k__extend_to_include[] = "extend_to_include"; static char __pyx_k__is_vector_of_sets[] = "is_vector_of_sets"; static char __pyx_k__GenomicArray_steps[] = "GenomicArray_steps"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__raw_optional_fields[] = "raw_optional_fields"; static char __pyx_k__write_to_fastq_file[] = "write_to_fastq_file"; static PyObject *__pyx_kp_s_10; static PyObject *__pyx_kp_s_100; static PyObject *__pyx_kp_s_102; static PyObject *__pyx_kp_s_104; static PyObject *__pyx_kp_s_105; static PyObject *__pyx_kp_s_107; static PyObject *__pyx_kp_s_108; static PyObject *__pyx_kp_s_11; static PyObject *__pyx_kp_s_110; static PyObject *__pyx_kp_s_111; static PyObject *__pyx_kp_s_115; static PyObject *__pyx_kp_s_116; static PyObject *__pyx_kp_b_117; static PyObject *__pyx_kp_b_118; static PyObject *__pyx_kp_s_119; static PyObject *__pyx_kp_s_12; static PyObject *__pyx_kp_s_120; static PyObject *__pyx_kp_s_121; static PyObject *__pyx_kp_u_122; static PyObject *__pyx_kp_u_124; static PyObject *__pyx_kp_u_126; static PyObject *__pyx_kp_u_128; static PyObject *__pyx_kp_u_129; static PyObject *__pyx_kp_s_13; static PyObject *__pyx_kp_u_132; static PyObject *__pyx_n_s_139; static PyObject *__pyx_kp_b_14; static PyObject *__pyx_kp_s_14; static PyObject *__pyx_n_s_146; static PyObject *__pyx_kp_s_147; static PyObject *__pyx_kp_s_148; static PyObject *__pyx_kp_s_149; static PyObject *__pyx_kp_s_15; static PyObject *__pyx_n_s_151; static PyObject *__pyx_kp_s_16; static PyObject *__pyx_kp_s_17; static PyObject *__pyx_kp_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_2; static PyObject *__pyx_kp_s_20; static PyObject *__pyx_kp_s_21; static PyObject *__pyx_kp_s_22; static PyObject *__pyx_kp_s_23; static PyObject *__pyx_kp_s_24; static PyObject *__pyx_kp_s_25; static PyObject *__pyx_kp_s_26; static PyObject *__pyx_kp_s_29; static PyObject *__pyx_kp_s_3; static PyObject *__pyx_n_s_30; static PyObject *__pyx_kp_s_31; static PyObject *__pyx_n_s_32; static PyObject *__pyx_kp_s_33; static PyObject *__pyx_kp_s_34; static PyObject *__pyx_kp_s_35; static PyObject *__pyx_kp_s_36; 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static PyObject *__pyx_kp_s_69; static PyObject *__pyx_n_s_7; static PyObject *__pyx_kp_s_70; static PyObject *__pyx_kp_s_71; static PyObject *__pyx_kp_s_72; static PyObject *__pyx_n_s_76; static PyObject *__pyx_kp_s_77; static PyObject *__pyx_n_s_78; static PyObject *__pyx_n_s_79; static PyObject *__pyx_kp_s_8; static PyObject *__pyx_kp_s_80; static PyObject *__pyx_kp_s_81; static PyObject *__pyx_kp_s_82; static PyObject *__pyx_kp_s_83; static PyObject *__pyx_kp_s_85; static PyObject *__pyx_kp_s_86; static PyObject *__pyx_n_s_87; static PyObject *__pyx_kp_s_88; static PyObject *__pyx_kp_s_89; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_kp_s_90; static PyObject *__pyx_kp_s_91; static PyObject *__pyx_kp_s_92; static PyObject *__pyx_kp_s_93; static PyObject *__pyx_n_s_95; static PyObject *__pyx_kp_s_96; static PyObject *__pyx_n_s_97; static PyObject *__pyx_kp_s_99; static PyObject *__pyx_n_s__A; static PyObject *__pyx_n_s__AlignedRead; static PyObject *__pyx_n_s__C; static PyObject *__pyx_n_s__ChromVector_steps; 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} static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_chrom(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_5chrom_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_chrom(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_5chrom_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_5chrom_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_start(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_5start_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_5start_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_end(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_3end_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_end(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_3end_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_GenomicInterval[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_3__reduce__, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("__copy__"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_5__copy__, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("is_contained_in"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_15is_contained_in, METH_O, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval_14is_contained_in)}, {__Pyx_NAMESTR("contains"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_17contains, METH_O, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval_16contains)}, {__Pyx_NAMESTR("overlaps"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_19overlaps, METH_O, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval_18overlaps)}, {__Pyx_NAMESTR("xrange"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_21xrange, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval_20xrange)}, {__Pyx_NAMESTR("xrange_d"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_23xrange_d, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval_22xrange_d)}, {__Pyx_NAMESTR("extend_to_include"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_25extend_to_include, METH_O, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval_24extend_to_include)}, {__Pyx_NAMESTR("copy"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_27copy, METH_NOARGS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_GenomicInterval[] = { {(char *)"strand", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_strand, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_strand, 0, 0}, {(char *)"length", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_length, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_length, __Pyx_DOCSTR(__pyx_k_134), 0}, {(char *)"start_d", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_start_d, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_start_d, __Pyx_DOCSTR(__pyx_k_135), 0}, {(char *)"end_d", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_end_d, 0, 0, 0}, {(char *)"start_as_pos", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_start_as_pos, 0, 0, 0}, {(char *)"end_as_pos", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_end_as_pos, 0, 0, 0}, {(char *)"start_d_as_pos", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_start_d_as_pos, 0, 0, 0}, {(char *)"end_d_as_pos", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_end_d_as_pos, 0, 0, 0}, {(char *)"chrom", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_chrom, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_chrom, 0, 0}, {(char *)"start", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_start, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_start, 0, 0}, {(char *)"end", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicInterval_end, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicInterval_end, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_GenomicInterval = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_GenomicInterval = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_GenomicInterval = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_GenomicInterval = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_GenomicInterval = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.GenomicInterval"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicInterval, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_7__repr__, /*tp_repr*/ &__pyx_tp_as_number_GenomicInterval, /*tp_as_number*/ &__pyx_tp_as_sequence_GenomicInterval, /*tp_as_sequence*/ &__pyx_tp_as_mapping_GenomicInterval, /*tp_as_mapping*/ __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_13__hash__, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_9__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_GenomicInterval, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("A GenomicInterval specifies an interval (i.e., a range of \n consecutive positions) on a reference genome.\n \n A GenomicInterval object has the following slots, some of which \n are calculated from the other:\n \n chrom: The name of a sequence (i.e., chromosome, contig, or \n the like). \n start: The start of the interval. Even on the reverse strand,\n this is always the smaller of the two values 'start' and 'end'.\n Note that all positions should be given as 0-based value!\n end: The end of the interval. Following Python convention for \n ranges, this in one more than the coordinate of the last base\n that is considered part of the sequence.\n strand: The strand, as a single character, '+' or '-'. '.' indicates\n that the strand is irrelavant. (Alternatively, pass a Strand object.)\n length: The length of the interval, i.e., end - start\n start_d: The \"directional start\" position. This is the position of the\n first base of the interval, taking the strand into account. Hence, \n this is the same as 'start' except when strand == '-', in which \n case it is end-1.\n end_d: The \"directional end\": Usually, the same as 'end', but for \n strand=='-1', it is start-1.\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_GenomicInterval, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_GenomicInterval, /*tp_clear*/ __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_11__richcmp__, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_GenomicInterval, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_GenomicInterval, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_15GenomicInterval_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_GenomicInterval, /*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_5HTSeq_6_HTSeq_GenomicPosition __pyx_vtable_5HTSeq_6_HTSeq_GenomicPosition; static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_GenomicPosition(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *p; PyObject *o = __pyx_tp_new_5HTSeq_6_HTSeq_GenomicInterval(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5HTSeq_6_HTSeq_GenomicInterval*)__pyx_vtabptr_5HTSeq_6_HTSeq_GenomicPosition; return o; } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15GenomicPosition_pos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_3pos_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_15GenomicPosition_pos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_3pos_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15GenomicPosition_end(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_3end_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15GenomicPosition_length(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_6length_1__get__(o); } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_GenomicPosition[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_7__reduce__, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("copy"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_9copy, METH_NOARGS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_GenomicPosition[] = { {(char *)"pos", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicPosition_pos, __pyx_setprop_5HTSeq_6_HTSeq_15GenomicPosition_pos, __Pyx_DOCSTR(__pyx_k_136), 0}, {(char *)"end", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicPosition_end, 0, 0, 0}, {(char *)"length", __pyx_getprop_5HTSeq_6_HTSeq_15GenomicPosition_length, 0, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_GenomicPosition = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_GenomicPosition = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_GenomicPosition = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_GenomicPosition = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_GenomicPosition = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.GenomicPosition"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicInterval, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_3__repr__, /*tp_repr*/ &__pyx_tp_as_number_GenomicPosition, /*tp_as_number*/ &__pyx_tp_as_sequence_GenomicPosition, /*tp_as_sequence*/ &__pyx_tp_as_mapping_GenomicPosition, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_5__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_GenomicPosition, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("A GenomicPosition specifies the position of a nucleotide or\n base pair on a reference genome.\n \n It has the following slots:\n chrom: The name of a sequence (i.e., chromosome, contig, or \n the like). \n pos: The position on the sequence specified by seqname.\n The position should always be given as 0-based value!\n strand: The strand, as a single character, '+' or '-'. '.' indicates\n that the strand is irrelavant.\n\n The GenomicPosition class is derived from GenomicInterval. Hence,\n a GenomicPosition is always a GenomicInterval of length 1. Do not tinker\n with the exposed GenomeInterval slots.\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_GenomicInterval, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_GenomicInterval, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_GenomicPosition, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_GenomicPosition, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_15GenomicPosition_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_GenomicPosition, /*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_5HTSeq_6_HTSeq_Sequence __pyx_vtable_5HTSeq_6_HTSeq_Sequence; static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_Sequence(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *)o); p->__pyx_vtab = __pyx_vtabptr_5HTSeq_6_HTSeq_Sequence; p->seq = ((PyObject*)Py_None); Py_INCREF(Py_None); p->name = ((PyObject*)Py_None); Py_INCREF(Py_None); p->descr = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_Sequence(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->seq); Py_CLEAR(p->name); Py_CLEAR(p->descr); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_Sequence(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *)o; if (p->seq) { e = (*v)(p->seq, a); if (e) return e; } if (p->name) { e = (*v)(p->name, a); if (e) return e; } if (p->descr) { e = (*v)(p->descr, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_Sequence(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *)o; PyObject* tmp; tmp = ((PyObject*)p->seq); p->seq = ((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); tmp = ((PyObject*)p->descr); p->descr = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5HTSeq_6_HTSeq_Sequence(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 PyObject *__pyx_getprop_5HTSeq_6_HTSeq_8Sequence_seq(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_3seq_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_8Sequence_seq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_3seq_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_3seq_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_8Sequence_name(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_4name_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_8Sequence_name(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_4name_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_4name_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_8Sequence_descr(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_5descr_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_8Sequence_descr(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_5descr_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_8Sequence_5descr_5__del__(o); } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_Sequence[] = { {__Pyx_NAMESTR("get_reverse_complement"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_8Sequence_3get_reverse_complement, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("write_to_fasta_file"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_8Sequence_13write_to_fasta_file, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("add_bases_to_count_array"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_8Sequence_15add_bases_to_count_array, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("trim_left_end"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_8Sequence_17trim_left_end, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("trim_right_end"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_8Sequence_19trim_right_end, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_Sequence[] = { {(char *)"seq", __pyx_getprop_5HTSeq_6_HTSeq_8Sequence_seq, __pyx_setprop_5HTSeq_6_HTSeq_8Sequence_seq, 0, 0}, {(char *)"name", __pyx_getprop_5HTSeq_6_HTSeq_8Sequence_name, __pyx_setprop_5HTSeq_6_HTSeq_8Sequence_name, 0, 0}, {(char *)"descr", __pyx_getprop_5HTSeq_6_HTSeq_8Sequence_descr, __pyx_setprop_5HTSeq_6_HTSeq_8Sequence_descr, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Sequence = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_Sequence = { __pyx_pw_5HTSeq_6_HTSeq_8Sequence_9__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5HTSeq_6_HTSeq_Sequence, /*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_Sequence = { __pyx_pw_5HTSeq_6_HTSeq_8Sequence_9__len__, /*mp_length*/ __pyx_pw_5HTSeq_6_HTSeq_8Sequence_11__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Sequence = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_Sequence = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.Sequence"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_Sequence, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_8Sequence_7__repr__, /*tp_repr*/ &__pyx_tp_as_number_Sequence, /*tp_as_number*/ &__pyx_tp_as_sequence_Sequence, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Sequence, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5HTSeq_6_HTSeq_8Sequence_5__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Sequence, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("A Sequence, typically of DNA, with a name.\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_Sequence, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_Sequence, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_Sequence, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_Sequence, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_8Sequence_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_Sequence, /*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_5HTSeq_6_HTSeq_SequenceWithQualities __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities; static PyObject *__pyx_tp_new_5HTSeq_6_HTSeq_SequenceWithQualities(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *p; PyObject *o = __pyx_tp_new_5HTSeq_6_HTSeq_Sequence(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5HTSeq_6_HTSeq_Sequence*)__pyx_vtabptr_5HTSeq_6_HTSeq_SequenceWithQualities; p->_qualstr = ((PyObject*)Py_None); Py_INCREF(Py_None); p->_qualstr_phred = ((PyObject*)Py_None); Py_INCREF(Py_None); p->_qualscale = ((PyObject*)Py_None); Py_INCREF(Py_None); p->_qualarr = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_SequenceWithQualities(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->_qualstr); Py_CLEAR(p->_qualstr_phred); Py_CLEAR(p->_qualscale); Py_CLEAR(p->_qualarr); PyObject_GC_Track(o); __pyx_tp_dealloc_5HTSeq_6_HTSeq_Sequence(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_SequenceWithQualities(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)o; e = __pyx_tp_traverse_5HTSeq_6_HTSeq_Sequence(o, v, a); if (e) return e; if (p->_qualstr) { e = (*v)(p->_qualstr, a); if (e) return e; } if (p->_qualstr_phred) { e = (*v)(p->_qualstr_phred, a); if (e) return e; } if (p->_qualscale) { e = (*v)(p->_qualscale, a); if (e) return e; } if (p->_qualarr) { e = (*v)(p->_qualarr, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_SequenceWithQualities(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)o; PyObject* tmp; __pyx_tp_clear_5HTSeq_6_HTSeq_Sequence(o); tmp = ((PyObject*)p->_qualstr); p->_qualstr = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->_qualstr_phred); p->_qualstr_phred = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->_qualscale); p->_qualscale = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->_qualarr); p->_qualarr = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5HTSeq_6_HTSeq_SequenceWithQualities(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 PyObject *__pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities_qual(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_4qual_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_21SequenceWithQualities_qual(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_4qual_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualstr(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_8_qualstr_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualstr_phred(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_14_qualstr_phred_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualscale(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_10_qualscale_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualarr(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_8_qualarr_1__get__(o); } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_SequenceWithQualities[] = { {__Pyx_NAMESTR("qualstr"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_7qualstr, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("write_to_fastq_file"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_9write_to_fastq_file, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("get_fastq_str"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_11get_fastq_str, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("get_reverse_complement"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_13get_reverse_complement, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("add_qual_to_count_array"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_15add_qual_to_count_array, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("trim_left_end_with_quals"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_17trim_left_end_with_quals, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("trim_right_end_with_quals"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_19trim_right_end_with_quals, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_SequenceWithQualities[] = { {(char *)"qual", __pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities_qual, __pyx_setprop_5HTSeq_6_HTSeq_21SequenceWithQualities_qual, 0, 0}, {(char *)"_qualstr", __pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualstr, 0, 0, 0}, {(char *)"_qualstr_phred", __pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualstr_phred, 0, 0, 0}, {(char *)"_qualscale", __pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualscale, 0, 0, 0}, {(char *)"_qualarr", __pyx_getprop_5HTSeq_6_HTSeq_21SequenceWithQualities__qualarr, 0, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_SequenceWithQualities = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_SequenceWithQualities = { #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_8Sequence_9__len__, /*sq_length*/ #else 0, /*sq_length*/ #endif 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5HTSeq_6_HTSeq_SequenceWithQualities, /*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_SequenceWithQualities = { #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_8Sequence_9__len__, /*mp_length*/ #else 0, /*mp_length*/ #endif __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_5__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_SequenceWithQualities = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.SequenceWithQualities"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_SequenceWithQualities, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_3__repr__, /*tp_repr*/ &__pyx_tp_as_number_SequenceWithQualities, /*tp_as_number*/ &__pyx_tp_as_sequence_SequenceWithQualities, /*tp_as_sequence*/ &__pyx_tp_as_mapping_SequenceWithQualities, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_8Sequence_5__str__, /*tp_str*/ #else 0, /*tp_str*/ #endif 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_SequenceWithQualities, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("A Sequence with base-call quality scores.\n It now has property 'qual', an integer NumPy array of Sanger/Phred \n quality scores of the base calls.\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_SequenceWithQualities, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_SequenceWithQualities, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_SequenceWithQualities, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_SequenceWithQualities, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_21SequenceWithQualities_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_SequenceWithQualities, /*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_5HTSeq_6_HTSeq_Alignment(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o); p->_read = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)Py_None); Py_INCREF(Py_None); p->iv = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->_read); Py_CLEAR(p->iv); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_Alignment(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; if (p->_read) { e = (*v)(((PyObject*)p->_read), a); if (e) return e; } if (p->iv) { e = (*v)(((PyObject*)p->iv), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_Alignment *)o; PyObject* tmp; tmp = ((PyObject*)p->_read); p->_read = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->iv); p->iv = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_9Alignment__read(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5_read_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_9Alignment__read(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5_read_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5_read_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_9Alignment_iv(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_9Alignment_2iv_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_9Alignment_iv(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_9Alignment_2iv_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_9Alignment_2iv_5__del__(o); } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_Alignment[] = { {__Pyx_NAMESTR("read"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_3read, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("paired_end"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_7paired_end, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("aligned"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_9Alignment_9aligned, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5HTSeq_6_HTSeq_9Alignment_8aligned)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_Alignment[] = { {(char *)"_read", __pyx_getprop_5HTSeq_6_HTSeq_9Alignment__read, __pyx_setprop_5HTSeq_6_HTSeq_9Alignment__read, 0, 0}, {(char *)"iv", __pyx_getprop_5HTSeq_6_HTSeq_9Alignment_iv, __pyx_setprop_5HTSeq_6_HTSeq_9Alignment_iv, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Alignment = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_Alignment = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_Alignment = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Alignment = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_Alignment = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.Alignment"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_Alignment), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_Alignment, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__repr__, /*tp_repr*/ &__pyx_tp_as_number_Alignment, /*tp_as_number*/ &__pyx_tp_as_sequence_Alignment, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Alignment, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Alignment, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("Alignment base type:\n\n An alignment object can be defined in different ways but will always\n provide these attributes:\n read: a SequenceWithQualities object with the read\n aligned: whether the read is aligned\n iv: a GenomicInterval object with the alignment position \n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_Alignment, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_Alignment, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_Alignment, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_Alignment, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_9Alignment_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_Alignment, /*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_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *p; PyObject *o = __pyx_tp_new_5HTSeq_6_HTSeq_Alignment(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *)o); p->read_as_aligned = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)Py_None); Py_INCREF(Py_None); p->_read_as_sequenced = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *p = (struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->read_as_aligned); Py_CLEAR(p->_read_as_sequenced); PyObject_GC_Track(o); __pyx_tp_dealloc_5HTSeq_6_HTSeq_Alignment(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *p = (struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *)o; e = __pyx_tp_traverse_5HTSeq_6_HTSeq_Alignment(o, v, a); if (e) return e; if (p->read_as_aligned) { e = (*v)(((PyObject*)p->read_as_aligned), a); if (e) return e; } if (p->_read_as_sequenced) { e = (*v)(((PyObject*)p->_read_as_sequenced), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *p = (struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal *)o; PyObject* tmp; __pyx_tp_clear_5HTSeq_6_HTSeq_Alignment(o); tmp = ((PyObject*)p->read_as_aligned); p->read_as_aligned = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->_read_as_sequenced); p->_read_as_sequenced = ((struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_read(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_4read_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_read_as_aligned(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_read_as_aligned(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_15read_as_aligned_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal__read_as_sequenced(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal__read_as_sequenced(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_18_read_as_sequenced_5__del__(o); } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal[] = { {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal[] = { {(char *)"read", __pyx_getprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_read, 0, 0, 0}, {(char *)"read_as_aligned", __pyx_getprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_read_as_aligned, __pyx_setprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_read_as_aligned, 0, 0}, {(char *)"_read_as_sequenced", __pyx_getprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal__read_as_sequenced, __pyx_setprop_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal__read_as_sequenced, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_AlignmentWithSequenceReversal = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_AlignmentWithSequenceReversal = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_AlignmentWithSequenceReversal = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_AlignmentWithSequenceReversal = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.AlignmentWithSequenceReversal"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__repr__, /*tp_repr*/ #else 0, /*tp_repr*/ #endif &__pyx_tp_as_number_AlignmentWithSequenceReversal, /*tp_as_number*/ &__pyx_tp_as_sequence_AlignmentWithSequenceReversal, /*tp_as_sequence*/ &__pyx_tp_as_mapping_AlignmentWithSequenceReversal, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_AlignmentWithSequenceReversal, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("Many aligners report the read's sequence in reverse-complemented form\n when it was mapped to the reverse strand. For such alignments, a \n daughter class of this one should be used.\n \n Then, the read is stored as aligned in the 'read_as_aligned' field,\n and get reverse-complemented back to the sequenced form when the 'read'\n attribute is sequenced.\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal, /*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_5HTSeq_6_HTSeq_SAM_Alignment(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *p; PyObject *o = __pyx_tp_new_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *)o); p->cigar = ((PyObject*)Py_None); Py_INCREF(Py_None); p->mate_start = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *)Py_None); Py_INCREF(Py_None); p->pe_which = ((PyObject*)Py_None); Py_INCREF(Py_None); p->original_sam_line = ((PyObject*)Py_None); Py_INCREF(Py_None); p->optional_fields = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->cigar); Py_CLEAR(p->mate_start); Py_CLEAR(p->pe_which); Py_CLEAR(p->original_sam_line); Py_CLEAR(p->optional_fields); PyObject_GC_Track(o); __pyx_tp_dealloc_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *)o; e = __pyx_tp_traverse_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(o, v, a); if (e) return e; if (p->cigar) { e = (*v)(p->cigar, a); if (e) return e; } if (p->mate_start) { e = (*v)(((PyObject*)p->mate_start), a); if (e) return e; } if (p->pe_which) { e = (*v)(p->pe_which, a); if (e) return e; } if (p->original_sam_line) { e = (*v)(p->original_sam_line, a); if (e) return e; } if (p->optional_fields) { e = (*v)(p->optional_fields, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_SAM_Alignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment *)o; PyObject* tmp; __pyx_tp_clear_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(o); tmp = ((PyObject*)p->cigar); p->cigar = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->mate_start); p->mate_start = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicPosition *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->pe_which); p->pe_which = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->original_sam_line); p->original_sam_line = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->optional_fields); p->optional_fields = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_flag(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_4flag_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_flag(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_4flag_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_cigar(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_5cigar_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_cigar(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_5cigar_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_5cigar_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_aQual(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_5aQual_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_aQual(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_5aQual_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_mate_start(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_10mate_start_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_mate_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_10mate_start_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_10mate_start_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_pe_which(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_8pe_which_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_pe_which(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_8pe_which_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_8pe_which_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_inferred_insert_size(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_20inferred_insert_size_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_inferred_insert_size(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_20inferred_insert_size_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_proper_pair(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_11proper_pair_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_proper_pair(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_11proper_pair_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_not_primary_alignment(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_21not_primary_alignment_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_not_primary_alignment(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_21not_primary_alignment_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_failed_platform_qc(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_18failed_platform_qc_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_failed_platform_qc(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_18failed_platform_qc_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_pcr_or_optical_duplicate(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_24pcr_or_optical_duplicate_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_pcr_or_optical_duplicate(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_24pcr_or_optical_duplicate_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_original_sam_line(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_17original_sam_line_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_optional_fields(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_optional_fields(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_15optional_fields_5__del__(o); } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_SAM_Alignment[] = { {__Pyx_NAMESTR("to_pysam_AlignedRead"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_1to_pysam_AlignedRead, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("from_pysam_AlignedRead"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_3from_pysam_AlignedRead, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("from_SAM_line"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_5from_SAM_line, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("paired_end"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_7paired_end, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("mate_aligned"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_9mate_aligned, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("get_sam_line"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_11get_sam_line, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("optional_field"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_13optional_field, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("raw_optional_fields"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_13SAM_Alignment_15raw_optional_fields, METH_NOARGS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_SAM_Alignment[] = { {(char *)"flag", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_flag, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_flag, 0, 0}, {(char *)"cigar", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_cigar, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_cigar, 0, 0}, {(char *)"aQual", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_aQual, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_aQual, 0, 0}, {(char *)"mate_start", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_mate_start, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_mate_start, 0, 0}, {(char *)"pe_which", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_pe_which, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_pe_which, 0, 0}, {(char *)"inferred_insert_size", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_inferred_insert_size, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_inferred_insert_size, 0, 0}, {(char *)"proper_pair", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_proper_pair, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_proper_pair, 0, 0}, {(char *)"not_primary_alignment", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_not_primary_alignment, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_not_primary_alignment, 0, 0}, {(char *)"failed_platform_qc", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_failed_platform_qc, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_failed_platform_qc, 0, 0}, {(char *)"pcr_or_optical_duplicate", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_pcr_or_optical_duplicate, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_pcr_or_optical_duplicate, 0, 0}, {(char *)"original_sam_line", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_original_sam_line, 0, 0, 0}, {(char *)"optional_fields", __pyx_getprop_5HTSeq_6_HTSeq_13SAM_Alignment_optional_fields, __pyx_setprop_5HTSeq_6_HTSeq_13SAM_Alignment_optional_fields, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_SAM_Alignment = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_SAM_Alignment = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_SAM_Alignment = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_SAM_Alignment = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_SAM_Alignment = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.SAM_Alignment"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_SAM_Alignment), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_SAM_Alignment, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__repr__, /*tp_repr*/ #else 0, /*tp_repr*/ #endif &__pyx_tp_as_number_SAM_Alignment, /*tp_as_number*/ &__pyx_tp_as_sequence_SAM_Alignment, /*tp_as_sequence*/ &__pyx_tp_as_mapping_SAM_Alignment, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_SAM_Alignment, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("When reading in a SAM file, objects of the class SAM_Alignment\n are returned. In addition to the 'read', 'iv' and 'aligned' fields (see \n Alignment class), the following fields are provided:\n - aQual: the alignment quality score\n - cigar: a list of CigarOperatio objects, describing the alignment\n - tags: the extra information tags [not yet implemented]\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_SAM_Alignment, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_SAM_Alignment, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_SAM_Alignment, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_SAM_Alignment, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_29AlignmentWithSequenceReversal_1__init__, /*tp_init*/ #else 0, /*tp_init*/ #endif 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_SAM_Alignment, /*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_5HTSeq_6_HTSeq_ChromVector(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *)o); p->array = Py_None; Py_INCREF(Py_None); p->iv = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)Py_None); Py_INCREF(Py_None); p->_storage = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_ChromVector(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *p = (struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->array); Py_CLEAR(p->iv); Py_CLEAR(p->_storage); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_ChromVector(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *p = (struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *)o; if (p->array) { e = (*v)(p->array, a); if (e) return e; } if (p->iv) { e = (*v)(((PyObject*)p->iv), a); if (e) return e; } if (p->_storage) { e = (*v)(p->_storage, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_ChromVector(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *p = (struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector *)o; PyObject* tmp; tmp = ((PyObject*)p->array); p->array = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->iv); p->iv = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->_storage); p->_storage = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5HTSeq_6_HTSeq_ChromVector(PyObject *o, Py_ssize_t i) { PyObject *r; PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); Py_DECREF(x); return r; } static int __pyx_mp_ass_subscript_5HTSeq_6_HTSeq_ChromVector(PyObject *o, PyObject *i, PyObject *v) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_7__setitem__(o, i, v); } else { PyErr_Format(PyExc_NotImplementedError, "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_array(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_5array_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_array(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_5array_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_5array_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_iv(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_2iv_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_iv(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_2iv_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_2iv_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_offset(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_6offset_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_offset(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_6offset_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_is_vector_of_sets(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_17is_vector_of_sets_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_is_vector_of_sets(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_17is_vector_of_sets_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_11ChromVector__storage(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_8_storage_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector__storage(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_8_storage_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_8_storage_5__del__(o); } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_ChromVector[] = { {__Pyx_NAMESTR("create"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_1create, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("_create_view"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_3_create_view, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("values"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_13values, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("steps"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_15steps, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("apply"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_17apply, METH_O, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_11ChromVector_21__reduce__, METH_NOARGS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_ChromVector[] = { {(char *)"array", __pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_array, __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_array, 0, 0}, {(char *)"iv", __pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_iv, __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_iv, 0, 0}, {(char *)"offset", __pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_offset, __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_offset, 0, 0}, {(char *)"is_vector_of_sets", __pyx_getprop_5HTSeq_6_HTSeq_11ChromVector_is_vector_of_sets, __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector_is_vector_of_sets, 0, 0}, {(char *)"_storage", __pyx_getprop_5HTSeq_6_HTSeq_11ChromVector__storage, __pyx_setprop_5HTSeq_6_HTSeq_11ChromVector__storage, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_ChromVector = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_9__iadd__, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_ChromVector = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5HTSeq_6_HTSeq_ChromVector, /*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_ChromVector = { 0, /*mp_length*/ __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_5__getitem__, /*mp_subscript*/ __pyx_mp_ass_subscript_5HTSeq_6_HTSeq_ChromVector, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_ChromVector = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_ChromVector = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.ChromVector"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_ChromVector), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_ChromVector, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_19__repr__, /*tp_repr*/ &__pyx_tp_as_number_ChromVector, /*tp_as_number*/ &__pyx_tp_as_sequence_ChromVector, /*tp_as_sequence*/ &__pyx_tp_as_mapping_ChromVector, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_ChromVector, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_ChromVector, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_ChromVector, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5HTSeq_6_HTSeq_11ChromVector_11__iter__, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_ChromVector, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_ChromVector, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_ChromVector, /*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_5HTSeq_6_HTSeq_GenomicArray(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *)o); p->chrom_vectors = ((PyObject*)Py_None); Py_INCREF(Py_None); p->typecode = ((PyObject*)Py_None); Py_INCREF(Py_None); p->storage = ((PyObject*)Py_None); Py_INCREF(Py_None); p->memmap_dir = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicArray(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *p = (struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->chrom_vectors); Py_CLEAR(p->typecode); Py_CLEAR(p->storage); Py_CLEAR(p->memmap_dir); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_GenomicArray(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *p = (struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *)o; if (p->chrom_vectors) { e = (*v)(p->chrom_vectors, a); if (e) return e; } if (p->typecode) { e = (*v)(p->typecode, a); if (e) return e; } if (p->storage) { e = (*v)(p->storage, a); if (e) return e; } if (p->memmap_dir) { e = (*v)(p->memmap_dir, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_GenomicArray(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *p = (struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray *)o; PyObject* tmp; tmp = ((PyObject*)p->chrom_vectors); p->chrom_vectors = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->typecode); p->typecode = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->storage); p->storage = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->memmap_dir); p->memmap_dir = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5HTSeq_6_HTSeq_GenomicArray(PyObject *o, Py_ssize_t i) { PyObject *r; PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); Py_DECREF(x); return r; } static int __pyx_mp_ass_subscript_5HTSeq_6_HTSeq_GenomicArray(PyObject *o, PyObject *i, PyObject *v) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_5__setitem__(o, i, v); } else { PyErr_Format(PyExc_NotImplementedError, "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_chrom_vectors(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_13chrom_vectors_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_12GenomicArray_chrom_vectors(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_13chrom_vectors_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_13chrom_vectors_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_stranded(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_8stranded_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_typecode(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_8typecode_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_auto_add_chroms(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_15auto_add_chroms_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_12GenomicArray_auto_add_chroms(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_15auto_add_chroms_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_storage(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7storage_1__get__(o); } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_memmap_dir(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_10memmap_dir_1__get__(o); } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_GenomicArray[] = { {__Pyx_NAMESTR("add_chrom"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_7add_chrom, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_9__reduce__, METH_NOARGS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("write_bedgraph_file"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_11write_bedgraph_file, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("steps"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_13steps, METH_NOARGS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_GenomicArray[] = { {(char *)"chrom_vectors", __pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_chrom_vectors, __pyx_setprop_5HTSeq_6_HTSeq_12GenomicArray_chrom_vectors, 0, 0}, {(char *)"stranded", __pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_stranded, 0, 0, 0}, {(char *)"typecode", __pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_typecode, 0, 0, 0}, {(char *)"auto_add_chroms", __pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_auto_add_chroms, __pyx_setprop_5HTSeq_6_HTSeq_12GenomicArray_auto_add_chroms, 0, 0}, {(char *)"storage", __pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_storage, 0, 0, 0}, {(char *)"memmap_dir", __pyx_getprop_5HTSeq_6_HTSeq_12GenomicArray_memmap_dir, 0, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_GenomicArray = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_GenomicArray = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5HTSeq_6_HTSeq_GenomicArray, /*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_GenomicArray = { 0, /*mp_length*/ __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_3__getitem__, /*mp_subscript*/ __pyx_mp_ass_subscript_5HTSeq_6_HTSeq_GenomicArray, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_GenomicArray = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_GenomicArray = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.GenomicArray"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicArray), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_GenomicArray, /*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*/ &__pyx_tp_as_number_GenomicArray, /*tp_as_number*/ &__pyx_tp_as_sequence_GenomicArray, /*tp_as_sequence*/ &__pyx_tp_as_mapping_GenomicArray, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_GenomicArray, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_GenomicArray, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_GenomicArray, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_GenomicArray, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_GenomicArray, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_12GenomicArray_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_GenomicArray, /*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_5HTSeq_6_HTSeq_BowtieAlignment(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *p; PyObject *o = __pyx_tp_new_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *)o); p->reserved = ((PyObject*)Py_None); Py_INCREF(Py_None); p->substitutions = ((PyObject*)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_BowtieAlignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->reserved); Py_CLEAR(p->substitutions); PyObject_GC_Track(o); __pyx_tp_dealloc_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_BowtieAlignment(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *)o; e = __pyx_tp_traverse_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(o, v, a); if (e) return e; if (p->reserved) { e = (*v)(p->reserved, a); if (e) return e; } if (p->substitutions) { e = (*v)(p->substitutions, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_BowtieAlignment(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *p = (struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment *)o; PyObject* tmp; __pyx_tp_clear_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal(o); tmp = ((PyObject*)p->reserved); p->reserved = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->substitutions); p->substitutions = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15BowtieAlignment_reserved(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_15BowtieAlignment_reserved(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_8reserved_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_15BowtieAlignment_substitutions(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_15BowtieAlignment_substitutions(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_13substitutions_5__del__(o); } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_BowtieAlignment[] = { {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_BowtieAlignment[] = { {(char *)"reserved", __pyx_getprop_5HTSeq_6_HTSeq_15BowtieAlignment_reserved, __pyx_setprop_5HTSeq_6_HTSeq_15BowtieAlignment_reserved, 0, 0}, {(char *)"substitutions", __pyx_getprop_5HTSeq_6_HTSeq_15BowtieAlignment_substitutions, __pyx_setprop_5HTSeq_6_HTSeq_15BowtieAlignment_substitutions, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_BowtieAlignment = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_BowtieAlignment = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_BowtieAlignment = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_BowtieAlignment = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_BowtieAlignment = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.BowtieAlignment"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_BowtieAlignment), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_BowtieAlignment, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5HTSeq_6_HTSeq_9Alignment_5__repr__, /*tp_repr*/ #else 0, /*tp_repr*/ #endif &__pyx_tp_as_number_BowtieAlignment, /*tp_as_number*/ &__pyx_tp_as_sequence_BowtieAlignment, /*tp_as_sequence*/ &__pyx_tp_as_mapping_BowtieAlignment, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_BowtieAlignment, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("When reading in a Bowtie file, objects of the class BowtieAlignment\n are returned. In addition to the 'read' and 'iv' fields (see Alignment\n class), the fields 'reserved' and 'substitutions' are provided. These \n contain the content of the respective columns of the Bowtie output \n \n [A parser for the substitutions field will be added soon.]\n "), /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_BowtieAlignment, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_BowtieAlignment, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_BowtieAlignment, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_BowtieAlignment, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5HTSeq_6_HTSeq_15BowtieAlignment_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5HTSeq_6_HTSeq_BowtieAlignment, /*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_5HTSeq_6_HTSeq_CigarOperation(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o); p->type = ((PyObject*)Py_None); Py_INCREF(Py_None); p->ref_iv = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5HTSeq_6_HTSeq_CigarOperation(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->type); Py_CLEAR(p->ref_iv); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5HTSeq_6_HTSeq_CigarOperation(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; if (p->type) { e = (*v)(p->type, a); if (e) return e; } if (p->ref_iv) { e = (*v)(((PyObject*)p->ref_iv), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5HTSeq_6_HTSeq_CigarOperation(PyObject *o) { struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *p = (struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation *)o; PyObject* tmp; tmp = ((PyObject*)p->type); p->type = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->ref_iv); p->ref_iv = ((struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_type(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_4type_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_type(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_4type_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_4type_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_size(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_4size_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_size(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_4size_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_ref_iv(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_6ref_iv_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_ref_iv(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_6ref_iv_3__set__(o, v); } else { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_6ref_iv_5__del__(o); } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_query_from(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_10query_from_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_query_from(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_10query_from_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_query_to(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_8query_to_1__get__(o); } static int __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_query_to(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_8query_to_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyMethodDef __pyx_methods_5HTSeq_6_HTSeq_CigarOperation[] = { {__Pyx_NAMESTR("check"), (PyCFunction)__pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_5check, METH_NOARGS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5HTSeq_6_HTSeq_CigarOperation[] = { {(char *)"type", __pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_type, __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_type, 0, 0}, {(char *)"size", __pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_size, __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_size, 0, 0}, {(char *)"ref_iv", __pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_ref_iv, __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_ref_iv, 0, 0}, {(char *)"query_from", __pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_query_from, __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_query_from, 0, 0}, {(char *)"query_to", __pyx_getprop_5HTSeq_6_HTSeq_14CigarOperation_query_to, __pyx_setprop_5HTSeq_6_HTSeq_14CigarOperation_query_to, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_CigarOperation = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_CigarOperation = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*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_CigarOperation = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_CigarOperation = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5HTSeq_6_HTSeq_CigarOperation = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("HTSeq._HTSeq.CigarOperation"), /*tp_name*/ sizeof(struct __pyx_obj_5HTSeq_6_HTSeq_CigarOperation), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5HTSeq_6_HTSeq_CigarOperation, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_5HTSeq_6_HTSeq_14CigarOperation_3__repr__, /*tp_repr*/ &__pyx_tp_as_number_CigarOperation, /*tp_as_number*/ &__pyx_tp_as_sequence_CigarOperation, /*tp_as_sequence*/ &__pyx_tp_as_mapping_CigarOperation, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_CigarOperation, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ __pyx_tp_traverse_5HTSeq_6_HTSeq_CigarOperation, /*tp_traverse*/ __pyx_tp_clear_5HTSeq_6_HTSeq_CigarOperation, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5HTSeq_6_HTSeq_CigarOperation, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5HTSeq_6_HTSeq_CigarOperation, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, 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__pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_15GenomicInterval_contains; __pyx_vtable_5HTSeq_6_HTSeq_GenomicInterval.overlaps = (PyObject *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_15GenomicInterval_overlaps; __pyx_vtable_5HTSeq_6_HTSeq_GenomicInterval.extend_to_include = (PyObject *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, struct __pyx_obj_5HTSeq_6_HTSeq_GenomicInterval *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_15GenomicInterval_extend_to_include; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_GenomicInterval) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5HTSeq_6_HTSeq_GenomicInterval, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5HTSeq_6_HTSeq_15GenomicInterval___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5HTSeq_6_HTSeq_15GenomicInterval___init__.doc = __pyx_doc_5HTSeq_6_HTSeq_15GenomicInterval___init__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5HTSeq_6_HTSeq_15GenomicInterval___init__; } } #endif if (__Pyx_SetVtable(__pyx_type_5HTSeq_6_HTSeq_GenomicInterval.tp_dict, __pyx_vtabptr_5HTSeq_6_HTSeq_GenomicInterval) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "GenomicInterval", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_GenomicInterval) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5HTSeq_6_HTSeq_GenomicInterval = &__pyx_type_5HTSeq_6_HTSeq_GenomicInterval; __pyx_vtabptr_5HTSeq_6_HTSeq_GenomicPosition = &__pyx_vtable_5HTSeq_6_HTSeq_GenomicPosition; __pyx_vtable_5HTSeq_6_HTSeq_GenomicPosition.__pyx_base = *__pyx_vtabptr_5HTSeq_6_HTSeq_GenomicInterval; __pyx_type_5HTSeq_6_HTSeq_GenomicPosition.tp_base = __pyx_ptype_5HTSeq_6_HTSeq_GenomicInterval; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_GenomicPosition) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5HTSeq_6_HTSeq_GenomicPosition.tp_dict, __pyx_vtabptr_5HTSeq_6_HTSeq_GenomicPosition) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "GenomicPosition", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_GenomicPosition) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5HTSeq_6_HTSeq_GenomicPosition = &__pyx_type_5HTSeq_6_HTSeq_GenomicPosition; __pyx_vtabptr_5HTSeq_6_HTSeq_Sequence = &__pyx_vtable_5HTSeq_6_HTSeq_Sequence; __pyx_vtable_5HTSeq_6_HTSeq_Sequence.get_reverse_complement = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_8Sequence_get_reverse_complement; __pyx_vtable_5HTSeq_6_HTSeq_Sequence.add_bases_to_count_array = (PyObject *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_8Sequence_add_bases_to_count_array; __pyx_vtable_5HTSeq_6_HTSeq_Sequence.trim_left_end = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_left_end *__pyx_optional_args))__pyx_f_5HTSeq_6_HTSeq_8Sequence_trim_left_end; __pyx_vtable_5HTSeq_6_HTSeq_Sequence.trim_right_end = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_8Sequence_trim_right_end *__pyx_optional_args))__pyx_f_5HTSeq_6_HTSeq_8Sequence_trim_right_end; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_Sequence) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5HTSeq_6_HTSeq_Sequence.tp_dict, __pyx_vtabptr_5HTSeq_6_HTSeq_Sequence) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "Sequence", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_Sequence) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5HTSeq_6_HTSeq_Sequence = &__pyx_type_5HTSeq_6_HTSeq_Sequence; __pyx_vtabptr_5HTSeq_6_HTSeq_SequenceWithQualities = &__pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities.__pyx_base = *__pyx_vtabptr_5HTSeq_6_HTSeq_Sequence; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities.__pyx_base.get_reverse_complement = (struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities_get_reverse_complement__pyx_wrap_1; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities._fill_qual_arr = (PyObject *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *))__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities__fill_qual_arr; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities.add_qual_to_count_array = (PyObject *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities_add_qual_to_count_array; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities.trim_left_end_with_quals = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_left_end_with_quals *__pyx_optional_args))__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_left_end_with_quals; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities.trim_right_end_with_quals = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *, struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch, struct __pyx_opt_args_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_right_end_with_quals *__pyx_optional_args))__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities_trim_right_end_with_quals; __pyx_vtable_5HTSeq_6_HTSeq_SequenceWithQualities.get_reverse_complement = (struct __pyx_obj_5HTSeq_6_HTSeq_SequenceWithQualities *(*)(struct __pyx_obj_5HTSeq_6_HTSeq_Sequence *, int __pyx_skip_dispatch))__pyx_f_5HTSeq_6_HTSeq_21SequenceWithQualities_get_reverse_complement; __pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities.tp_base = __pyx_ptype_5HTSeq_6_HTSeq_Sequence; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5HTSeq_6_HTSeq_21SequenceWithQualities___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5HTSeq_6_HTSeq_21SequenceWithQualities___init__.doc = __pyx_doc_5HTSeq_6_HTSeq_21SequenceWithQualities___init__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5HTSeq_6_HTSeq_21SequenceWithQualities___init__; } } #endif if (__Pyx_SetVtable(__pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities.tp_dict, __pyx_vtabptr_5HTSeq_6_HTSeq_SequenceWithQualities) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "SequenceWithQualities", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5HTSeq_6_HTSeq_SequenceWithQualities = &__pyx_type_5HTSeq_6_HTSeq_SequenceWithQualities; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_Alignment) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "Alignment", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_Alignment) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5HTSeq_6_HTSeq_Alignment = &__pyx_type_5HTSeq_6_HTSeq_Alignment; __pyx_type_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal.tp_base = __pyx_ptype_5HTSeq_6_HTSeq_Alignment; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "AlignmentWithSequenceReversal", (PyObject *)&__pyx_type_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal = &__pyx_type_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal; __pyx_type_5HTSeq_6_HTSeq_SAM_Alignment.tp_base = __pyx_ptype_5HTSeq_6_HTSeq_AlignmentWithSequenceReversal; if (PyType_Ready(&__pyx_type_5HTSeq_6_HTSeq_SAM_Alignment) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "SAM_Alignment", (PyObject 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"" : "s", num_found); } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static PyObject* __Pyx_Intern(PyObject* s) { if (!(likely(PyString_CheckExact(s)))) { PyErr_Format(PyExc_TypeError, "Expected str, got %s", Py_TYPE(s)->tp_name); return 0; } Py_INCREF(s); #if PY_MAJOR_VERSION >= 3 PyUnicode_InternInPlace(&s); #else PyString_InternInPlace(&s); #endif return s; } 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 (cause && cause != Py_None) { PyObject *fixed_cause; 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 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 int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else if (s1 == s2) { return (equals == Py_EQ); } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyBytes_GET_SIZE(s1) == 1) { if (equals == Py_EQ) return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]); else return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]); } else { int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1)); return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } #endif } static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else if (s1 == s2) { return (equals == Py_EQ); } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { #if CYTHON_PEP393_ENABLED if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) return -1; if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { return (equals == Py_NE); } else if (PyUnicode_GET_LENGTH(s1) == 1) { Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); #else if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyUnicode_GET_SIZE(s1) == 1) { Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); #endif } else { int result = PyUnicode_Compare(s1, s2); if ((result == -1) && unlikely(PyErr_Occurred())) return -1; return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } #endif } static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { if (t == Py_None) { __Pyx_RaiseNoneNotIterableError(); } else if (PyTuple_GET_SIZE(t) < index) { __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); } else { __Pyx_RaiseTooManyValuesError(index); } } static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int is_tuple, int has_known_size, int decref_tuple) { Py_ssize_t index; PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; if (!is_tuple && unlikely(!PyTuple_Check(tuple))) { iternextfunc iternext; iter = PyObject_GetIter(tuple); if (unlikely(!iter)) goto bad; if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } iternext = Py_TYPE(iter)->tp_iternext; value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; Py_DECREF(iter); } else { if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) { __Pyx_UnpackTupleError(tuple, 2); goto bad; } #if CYTHON_COMPILING_IN_PYPY value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad; value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad; #else value1 = PyTuple_GET_ITEM(tuple, 0); value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value1); Py_INCREF(value2); #endif if (decref_tuple) { Py_DECREF(tuple); } } *pvalue1 = value1; *pvalue2 = value2; return 0; unpacking_failed: if (!has_known_size && __Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); bad: Py_XDECREF(iter); Py_XDECREF(value1); Py_XDECREF(value2); if (decref_tuple) { Py_XDECREF(tuple); } return -1; } static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_source_is_dict) { is_dict = is_dict || likely(PyDict_CheckExact(iterable)); *p_source_is_dict = is_dict; #if !CYTHON_COMPILING_IN_PYPY if (is_dict) { *p_orig_length = PyDict_Size(iterable); Py_INCREF(iterable); return iterable; } #endif *p_orig_length = 0; if (method_name) { PyObject* iter; iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL); if (!iterable) return NULL; #if !CYTHON_COMPILING_IN_PYPY if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) return iterable; #endif iter = PyObject_GetIter(iterable); Py_DECREF(iterable); return iter; } return PyObject_GetIter(iterable); } static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos, PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { PyObject* next_item; #if !CYTHON_COMPILING_IN_PYPY if (source_is_dict) { PyObject *key, *value; if (unlikely(orig_length != PyDict_Size(iter_obj))) { PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); return -1; } if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { return 0; } if (pitem) { PyObject* tuple = PyTuple_New(2); if (unlikely(!tuple)) { return -1; } Py_INCREF(key); Py_INCREF(value); PyTuple_SET_ITEM(tuple, 0, key); PyTuple_SET_ITEM(tuple, 1, value); *pitem = tuple; } else { if (pkey) { Py_INCREF(key); *pkey = key; } if (pvalue) { Py_INCREF(value); *pvalue = value; } } return 1; } else if (PyTuple_CheckExact(iter_obj)) { Py_ssize_t pos = *ppos; if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; *ppos = pos + 1; next_item = PyTuple_GET_ITEM(iter_obj, pos); Py_INCREF(next_item); } else if (PyList_CheckExact(iter_obj)) { Py_ssize_t pos = *ppos; if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; *ppos = pos + 1; next_item = PyList_GET_ITEM(iter_obj, pos); Py_INCREF(next_item); } else #endif { next_item = PyIter_Next(iter_obj); if (unlikely(!next_item)) { return __Pyx_IterFinish(); } } if (pitem) { *pitem = next_item; } else if (pkey && pvalue) { if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1)) return -1; } else if (pkey) { *pkey = next_item; } else { *pvalue = next_item; } return 1; } 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 int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, __Pyx_TypeInfo* type) { stack[0].field = &ctx->root; stack[0].parent_offset = 0; ctx->root.type = type; ctx->root.name = "buffer dtype"; ctx->root.offset = 0; ctx->head = stack; ctx->head->field = &ctx->root; ctx->fmt_offset = 0; ctx->head->parent_offset = 0; ctx->new_packmode = '@'; ctx->enc_packmode = '@'; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->is_complex = 0; ctx->is_valid_array = 0; ctx->struct_alignment = 0; while (type->typegroup == 'S') { ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = 0; type = type->fields->type; } } static int __Pyx_BufFmt_ParseNumber(const char** ts) { int count; const char* t = *ts; if (*t < '0' || *t > '9') { return -1; } else { count = *t++ - '0'; while (*t >= '0' && *t < '9') { count *= 10; count += *t++ - '0'; } } *ts = t; return count; } static int __Pyx_BufFmt_ExpectNumber(const char **ts) { int number = __Pyx_BufFmt_ParseNumber(ts); if (number == -1) /* First char was not a digit */ PyErr_Format(PyExc_ValueError,\ "Does not understand character buffer dtype format string ('%c')", **ts); return number; } static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%c'", ch); } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; case 'h': return "'short'"; case 'H': return "'unsigned short'"; case 'i': return "'int'"; case 'I': return "'unsigned int'"; case 'l': return "'long'"; case 'L': return "'unsigned long'"; case 'q': return "'long long'"; case 'Q': return "'unsigned long long'"; case 'f': return (is_complex ? "'complex float'" : "'float'"); case 'd': return (is_complex ? "'complex double'" : "'double'"); case 'g': return (is_complex ? "'complex long double'" : "'long double'"); case 'T': return "a struct"; case 'O': return "Python object"; case 'P': return "a pointer"; case 's': case 'p': return "a string"; case 0: return "end"; default: return "unparseable format string"; } } static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return 2; case 'i': case 'I': case 'l': case 'L': return 4; case 'q': case 'Q': return 8; case 'f': return (is_complex ? 8 : 4); case 'd': return (is_complex ? 16 : 8); case 'g': { PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); return 0; } case 'O': case 'P': return sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(float) * (is_complex ? 2 : 1); case 'd': return sizeof(double) * (is_complex ? 2 : 1); case 'g': return sizeof(long double) * (is_complex ? 2 : 1); case 'O': case 'P': return sizeof(void*); default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } typedef struct { char c; short x; } __Pyx_st_short; typedef struct { char c; int x; } __Pyx_st_int; typedef struct { char c; long x; } __Pyx_st_long; typedef struct { char c; float x; } __Pyx_st_float; typedef struct { char c; double x; } __Pyx_st_double; typedef struct { char c; long double x; } __Pyx_st_longdouble; typedef struct { char c; void *x; } __Pyx_st_void_p; #ifdef HAVE_LONG_LONG typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_st_float) - sizeof(float); case 'd': return sizeof(__Pyx_st_double) - sizeof(double); case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } /* These are for computing the padding at the end of the struct to align on the first member of the struct. This will probably the same as above, but we don't have any guarantees. */ typedef struct { short x; char c; } __Pyx_pad_short; typedef struct { int x; char c; } __Pyx_pad_int; typedef struct { long x; char c; } __Pyx_pad_long; typedef struct { float x; char c; } __Pyx_pad_float; typedef struct { double x; char c; } __Pyx_pad_double; typedef struct { long double x; char c; } __Pyx_pad_longdouble; typedef struct { void *x; char c; } __Pyx_pad_void_p; #ifdef HAVE_LONG_LONG typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { switch (ch) { case 'c': return 'H'; case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); case 'O': return 'O'; case 'P': return 'P'; default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { if (ctx->head == NULL || ctx->head->field == &ctx->root) { const char* expected; const char* quote; if (ctx->head == NULL) { expected = "end"; quote = ""; } else { expected = ctx->head->field->type->name; quote = "'"; } PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected %s%s%s but got %s", quote, expected, quote, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); } else { __Pyx_StructField* field = ctx->head->field; __Pyx_StructField* parent = (ctx->head - 1)->field; PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), parent->type->name, field->name); } } static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { char group; size_t size, offset, arraysize = 1; if (ctx->enc_type == 0) return 0; if (ctx->head->field->type->arraysize[0]) { int i, ndim = 0; if (ctx->enc_type == 's' || ctx->enc_type == 'p') { ctx->is_valid_array = ctx->head->field->type->ndim == 1; ndim = 1; if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %zu", ctx->head->field->type->arraysize[0], ctx->enc_count); return -1; } } if (!ctx->is_valid_array) { PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", ctx->head->field->type->ndim, ndim); return -1; } for (i = 0; i < ctx->head->field->type->ndim; i++) { arraysize *= ctx->head->field->type->arraysize[i]; } ctx->is_valid_array = 0; ctx->enc_count = 1; } group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); do { __Pyx_StructField* field = ctx->head->field; __Pyx_TypeInfo* type = field->type; if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); } else { size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); } if (ctx->enc_packmode == '@') { size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); size_t align_mod_offset; if (align_at == 0) return -1; align_mod_offset = ctx->fmt_offset % align_at; if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; if (ctx->struct_alignment == 0) ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, ctx->is_complex); } if (type->size != size || type->typegroup != group) { if (type->typegroup == 'C' && type->fields != NULL) { size_t parent_offset = ctx->head->parent_offset + field->offset; ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = parent_offset; continue; } if ((type->typegroup == 'H' || group == 'H') && type->size == size) { } else { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } } offset = ctx->head->parent_offset + field->offset; if (ctx->fmt_offset != offset) { PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); return -1; } ctx->fmt_offset += size; if (arraysize) ctx->fmt_offset += (arraysize - 1) * size; --ctx->enc_count; /* Consume from buffer string */ while (1) { if (field == &ctx->root) { ctx->head = NULL; if (ctx->enc_count != 0) { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } break; /* breaks both loops as ctx->enc_count == 0 */ } ctx->head->field = ++field; if (field->type == NULL) { --ctx->head; field = ctx->head->field; continue; } else if (field->type->typegroup == 'S') { size_t parent_offset = ctx->head->parent_offset + field->offset; if (field->type->fields->type == NULL) continue; /* empty struct */ field = field->type->fields; ++ctx->head; ctx->head->field = field; ctx->head->parent_offset = parent_offset; break; } else { break; } } } while (ctx->enc_count); ctx->enc_type = 0; ctx->is_complex = 0; return 0; } static CYTHON_INLINE PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; int i = 0, number; int ndim = ctx->head->field->type->ndim; ; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, "Cannot handle repeated arrays in format string"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; while (*ts && *ts != ')') { if (isspace(*ts)) continue; number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) return PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %d", ctx->head->field->type->arraysize[i], number); if (*ts != ',' && *ts != ')') return PyErr_Format(PyExc_ValueError, "Expected a comma in format string, got '%c'", *ts); if (*ts == ',') ts++; i++; } if (i != ndim) return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", ctx->head->field->type->ndim, i); if (!*ts) { PyErr_SetString(PyExc_ValueError, "Unexpected end of format string, expected ')'"); return NULL; } ctx->is_valid_array = 1; ctx->new_count = 1; *tsp = ++ts; return Py_None; } static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { int got_Z = 0; while (1) { switch(*ts) { case 0: if (ctx->enc_type != 0 && ctx->head == NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; if (ctx->head != NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } return ts; case ' ': case 10: case 13: ++ts; break; case '<': if (!__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '>': case '!': if (__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '=': case '@': case '^': ctx->new_packmode = *ts++; break; case 'T': /* substruct */ { const char* ts_after_sub; size_t i, struct_count = ctx->new_count; size_t struct_alignment = ctx->struct_alignment; ctx->new_count = 1; ++ts; if (*ts != '{') { PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ ctx->enc_count = 0; ctx->struct_alignment = 0; ++ts; ts_after_sub = ts; for (i = 0; i != struct_count; ++i) { ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); if (!ts_after_sub) return NULL; } ts = ts_after_sub; if (struct_alignment) ctx->struct_alignment = struct_alignment; } break; case '}': /* end of substruct; either repeat or move on */ { size_t alignment = ctx->struct_alignment; ++ts; if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ if (alignment && ctx->fmt_offset % alignment) { ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); } } return ts; case 'x': if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->fmt_offset += ctx->new_count; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->enc_packmode = ctx->new_packmode; ++ts; break; case 'Z': got_Z = 1; ++ts; if (*ts != 'f' && *ts != 'd' && *ts != 'g') { __Pyx_BufFmt_RaiseUnexpectedChar('Z'); return NULL; } /* fall through */ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 's': case 'p': if (ctx->enc_type == *ts && got_Z == ctx->is_complex && ctx->enc_packmode == ctx->new_packmode) { ctx->enc_count += ctx->new_count; } else { if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_count = ctx->new_count; ctx->enc_packmode = ctx->new_packmode; ctx->enc_type = *ts; ctx->is_complex = got_Z; } ++ts; ctx->new_count = 1; got_Z = 0; break; case ':': ++ts; while(*ts != ':') ++ts; ++ts; break; case '(': if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; break; default: { int number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; ctx->new_count = (size_t)number; } } } } static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { buf->buf = NULL; buf->obj = NULL; buf->strides = __Pyx_zeros; buf->shape = __Pyx_zeros; buf->suboffsets = __Pyx_minusones; } static CYTHON_INLINE int __Pyx_GetBufferAndValidate( Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) { if (obj == Py_None || obj == NULL) { __Pyx_ZeroBuffer(buf); return 0; } buf->buf = NULL; if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; if (buf->ndim != nd) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", nd, buf->ndim); goto fail; } if (!cast) { __Pyx_BufFmt_Context ctx; __Pyx_BufFmt_Init(&ctx, stack, dtype); if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; } if ((unsigned)buf->itemsize != dtype->size) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", buf->itemsize, (buf->itemsize > 1) ? "s" : "", dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); goto fail; } if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; return 0; fail:; __Pyx_ZeroBuffer(buf); return -1; } static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { if (info->buf == NULL) return; if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; __Pyx_ReleaseBuffer(info); } static void __Pyx_RaiseBufferIndexError(int axis) { PyErr_Format(PyExc_IndexError, "Out of bounds on buffer access (axis %d)", axis); } static void __Pyx_RaiseBufferFallbackError(void) { PyErr_Format(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } static CYTHON_INLINE Py_ssize_t __Pyx_mod_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t r = a % b; r += ((r != 0) & ((r ^ b) < 0)) * b; return r; } static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t q = a / b; Py_ssize_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } 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 double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; #if CYTHON_COMPILING_IN_PYPY float_value = PyNumber_Float(obj); #else if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) { return PyFloat_AsDouble(obj); } 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 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 } #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { CYTHON_UNUSED PyObject *getbuffer_cobj; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, "__pyx_getbuffer"))) { getbufferproc func; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)"); #else func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj); #endif Py_DECREF(getbuffer_cobj); if (!func) goto fail; return func(obj, view, flags); } else { PyErr_Clear(); } #endif PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name); #if PY_VERSION_HEX < 0x02060000 fail: #endif return -1; } static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyObject *obj = view->obj; CYTHON_UNUSED PyObject *releasebuffer_cobj; if (!obj) return; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) { PyBuffer_Release(view); return; } #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, "__pyx_releasebuffer"))) { releasebufferproc func; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)"); #else func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj); #endif Py_DECREF(releasebuffer_cobj); if (!func) goto fail; func(obj, view); return; } else { PyErr_Clear(); } #endif goto nofail; #if PY_VERSION_HEX < 0x02060000 fail: #endif PyErr_WriteUnraisable(obj); nofail: Py_DECREF(obj); view->obj = NULL; } #endif /* PY_MAJOR_VERSION < 3 */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; 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, '.')) { /* try package relative import first */ 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); if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { 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 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: Py_XDECREF(empty_list); Py_XDECREF(py_import); Py_XDECREF(empty_dict); return module; } static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (op->func_doc == NULL && op->func.m_ml->ml_doc) { #if PY_MAJOR_VERSION >= 3 op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); #else op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); #endif } if (op->func_doc == 0) { Py_INCREF(Py_None); return Py_None; } Py_INCREF(op->func_doc); return op->func_doc; } static int __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp = op->func_doc; if (value == NULL) op->func_doc = Py_None; /* Mark as deleted */ else op->func_doc = value; Py_INCREF(op->func_doc); Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) { if (op->func_name == NULL) { #if PY_MAJOR_VERSION >= 3 op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); #else op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); #endif } Py_INCREF(op->func_name); return op->func_name; } static int __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (value == NULL || !PyUnicode_Check(value)) { #else if (value == NULL || !PyString_Check(value)) { #endif PyErr_SetString(PyExc_TypeError, "__name__ must be set to a string object"); return -1; } tmp = op->func_name; Py_INCREF(value); op->func_name = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) { PyObject *self; self = m->func_closure; if (self == NULL) self = Py_None; Py_INCREF(self); return self; } static PyObject * __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) { if (op->func_dict == NULL) { op->func_dict = PyDict_New(); if (op->func_dict == NULL) return NULL; } Py_INCREF(op->func_dict); return op->func_dict; } static int __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; if (value == NULL) { PyErr_SetString(PyExc_TypeError, "function's dictionary may not be deleted"); return -1; } if (!PyDict_Check(value)) { PyErr_SetString(PyExc_TypeError, "setting function's dictionary to a non-dict"); return -1; } tmp = op->func_dict; Py_INCREF(value); op->func_dict = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) { PyObject* dict = PyModule_GetDict(__pyx_m); Py_XINCREF(dict); return dict; } static PyObject * __Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) { Py_INCREF(Py_None); return Py_None; } static PyObject * __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) { PyObject* result = (op->func_code) ? op->func_code : Py_None; Py_INCREF(result); return result; } static PyObject * __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { if (op->defaults_tuple) { Py_INCREF(op->defaults_tuple); return op->defaults_tuple; } if (op->defaults_getter) { PyObject *res = op->defaults_getter((PyObject *) op); if (res) { Py_INCREF(res); op->defaults_tuple = res; } return res; } Py_INCREF(Py_None); return Py_None; } static PyGetSetDef __pyx_CyFunction_getsets[] = { {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {0, 0, 0, 0, 0} }; #ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ #define PY_WRITE_RESTRICTED WRITE_RESTRICTED #endif static PyMemberDef __pyx_CyFunction_members[] = { {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, {0, 0, 0, 0, 0} }; static PyObject * __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromString(m->func.m_ml->ml_name); #else return PyString_FromString(m->func.m_ml->ml_name); #endif } static PyMethodDef __pyx_CyFunction_methods[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, {0, 0, 0, 0} }; static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject *closure, PyObject *module, PyObject* code) { __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); if (op == NULL) return NULL; op->flags = flags; op->func_weakreflist = NULL; op->func.m_ml = ml; op->func.m_self = (PyObject *) op; Py_XINCREF(closure); op->func_closure = closure; Py_XINCREF(module); op->func.m_module = module; op->func_dict = NULL; op->func_name = NULL; 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_getter = 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_doc); Py_CLEAR(m->func_code); Py_CLEAR(m->func_classobj); Py_CLEAR(m->defaults_tuple); 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_doc); Py_VISIT(m->func_code); Py_VISIT(m->func_classobj); Py_VISIT(m->defaults_tuple); 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) { PyObject *func_name = __Pyx_CyFunction_get_name(op); #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromFormat("", func_name, (void *)op); #else return PyString_FromFormat("", PyString_AsString(func_name), (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, sizeof(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 Py_intptr_t __Pyx_PyInt_from_py_Py_intptr_t(PyObject* x) { const Py_intptr_t neg_one = (Py_intptr_t)-1, const_zero = (Py_intptr_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(Py_intptr_t) == sizeof(char)) { if (is_unsigned) return (Py_intptr_t)__Pyx_PyInt_AsUnsignedChar(x); else return (Py_intptr_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(Py_intptr_t) == sizeof(short)) { if (is_unsigned) return (Py_intptr_t)__Pyx_PyInt_AsUnsignedShort(x); else return (Py_intptr_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(Py_intptr_t) == sizeof(int)) { if (is_unsigned) return (Py_intptr_t)__Pyx_PyInt_AsUnsignedInt(x); else return (Py_intptr_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(Py_intptr_t) == sizeof(long)) { if (is_unsigned) return (Py_intptr_t)__Pyx_PyInt_AsUnsignedLong(x); else return (Py_intptr_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(Py_intptr_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (Py_intptr_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (Py_intptr_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else Py_intptr_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (Py_intptr_t)-1; } } static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { long t = b; switch (e) { case 3: t *= b; case 2: t *= b; case 1: return t; case 0: return 1; } if (unlikely(e<0)) return 0; t = 1; while (likely(e)) { t *= (b * (e&1)) | ((~e)&1); /* 1 or b */ b *= b; e >>= 1; } return t; } static CYTHON_INLINE npy_long __Pyx_PyInt_from_py_npy_long(PyObject* x) { const npy_long neg_one = (npy_long)-1, const_zero = (npy_long)0; const int is_unsigned = const_zero < neg_one; if (sizeof(npy_long) == sizeof(char)) { if (is_unsigned) return (npy_long)__Pyx_PyInt_AsUnsignedChar(x); else return (npy_long)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(npy_long) == sizeof(short)) { if (is_unsigned) return (npy_long)__Pyx_PyInt_AsUnsignedShort(x); else return (npy_long)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(npy_long) == sizeof(int)) { if (is_unsigned) return (npy_long)__Pyx_PyInt_AsUnsignedInt(x); else return (npy_long)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(npy_long) == sizeof(long)) { if (is_unsigned) return (npy_long)__Pyx_PyInt_AsUnsignedLong(x); else return (npy_long)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(npy_long) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (npy_long)__Pyx_PyInt_AsUnsignedLongLong(x); else return (npy_long)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else npy_long val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (npy_long)-1; } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_Py_intptr_t(Py_intptr_t val) { const Py_intptr_t neg_one = (Py_intptr_t)-1, const_zero = (Py_intptr_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(Py_intptr_t) == sizeof(char)) || (sizeof(Py_intptr_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(Py_intptr_t) == sizeof(int)) || (sizeof(Py_intptr_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(Py_intptr_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(Py_intptr_t), little, !is_unsigned); } } static PyObject* __Pyx_Method_ClassMethod(PyObject *method) { #if CYTHON_COMPILING_IN_PYPY if (PyObject_TypeCheck(method, &PyWrapperDescr_Type)) { /* cdef classes */ return PyClassMethod_New(method); } #else static PyTypeObject *methoddescr_type = NULL; if (methoddescr_type == NULL) { PyObject *meth = __Pyx_GetAttrString((PyObject*)&PyList_Type, "append"); if (!meth) return NULL; methoddescr_type = Py_TYPE(meth); Py_DECREF(meth); } if (PyObject_TypeCheck(method, methoddescr_type)) { /* cdef classes */ PyMethodDescrObject *descr = (PyMethodDescrObject *)method; #if PY_VERSION_HEX < 0x03020000 PyTypeObject *d_type = descr->d_type; #else PyTypeObject *d_type = descr->d_common.d_type; #endif return PyDescr_NewClassMethod(d_type, descr->d_method); } #endif else if (PyMethod_Check(method)) { /* python classes */ return PyClassMethod_New(PyMethod_GET_FUNCTION(method)); } else if (PyCFunction_Check(method)) { return PyClassMethod_New(method); } #ifdef __Pyx_CyFunction_USED else if (PyObject_TypeCheck(method, __pyx_CyFunctionType)) { return PyClassMethod_New(method); } #endif PyErr_Format(PyExc_TypeError, "Class-level classmethod() can only be called on " "a method_descriptor or instance method."); return NULL; } #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); } #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return x + y*(__pyx_t_float_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { __pyx_t_float_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrtf(z.real*z.real + z.imag*z.imag); #else return hypotf(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { float denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(a, a); case 3: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, a); case 4: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_absf(a); theta = atan2f(a.imag, a.real); } lnr = logf(r); z_r = expf(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cosf(z_theta); z.imag = z_r * sinf(z_theta); return z; } #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); } #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return x + y*(__pyx_t_double_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { __pyx_t_double_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrt(z.real*z.real + z.imag*z.imag); #else return hypot(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { double denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(a, a); case 3: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, a); case 4: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_abs(a); theta = atan2(a.imag, a.real); } lnr = log(r); z_r = exp(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cos(z_theta); z.imag = z_r * sin(z_theta); return z; } #endif #endif 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); } 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_VERSION_HEX < 0x03000000 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 (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 { 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; } } 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_VERSION_HEX < 0x03000000 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 (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 { 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; } } 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_VERSION_HEX < 0x03000000 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 (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 { 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; } } 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_VERSION_HEX < 0x03000000 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 (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 { 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; } } 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_VERSION_HEX < 0x03000000 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 (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 { 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; } } 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_VERSION_HEX < 0x03000000 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 (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 { 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 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_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_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif 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; } /* Type Conversion Functions */ 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_VERSION_HEX < 0x03000000 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_VERSION_HEX < 0x03000000 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_VERSION_HEX < 0x03000000 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)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */