diff --git a/CRISPResso2/CRISPRessoCOREResources.c b/CRISPResso2/CRISPRessoCOREResources.c index f7231760..b98cef4a 100644 --- a/CRISPResso2/CRISPRessoCOREResources.c +++ b/CRISPResso2/CRISPRessoCOREResources.c @@ -1,31 +1,5 @@ /* Generated by Cython 0.29.22 */ -/* BEGIN: Cython Metadata -{ - "distutils": { - "depends": [ - "/Users/cole/miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h", - "/Users/cole/miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/core/include/numpy/arrayscalars.h", - "/Users/cole/miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h", - "/Users/cole/miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h", - "/Users/cole/miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/core/include/numpy/ufuncobject.h" - ], - "extra_compile_args": [ - "-w", - "-Ofast" - ], - "include_dirs": [ - "/Users/cole/miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/core/include" - ], - "name": "CRISPResso2.CRISPRessoCOREResources", - "sources": [ - "CRISPResso2/CRISPRessoCOREResources.pyx" - ] - }, - "module_name": "CRISPResso2.CRISPRessoCOREResources" -} -END: Cython Metadata */ - #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H @@ -35,7 +9,7 @@ END: Cython Metadata */ #else #define CYTHON_ABI "0_29_22" #define CYTHON_HEX_VERSION 0x001D16F0 -#define CYTHON_FUTURE_DIVISION 1 +#define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -872,12 +846,12 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { - "CRISPResso2/CRISPRessoCOREResources.pyx", + "CRISPRessoCOREResources.pyx", "__init__.pxd", "type.pxd", }; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":690 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":690 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -886,7 +860,7 @@ static const char *__pyx_f[] = { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":691 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":691 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -895,7 +869,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":692 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":692 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -904,7 +878,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":693 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":693 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -913,7 +887,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":697 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":697 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -922,7 +896,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":698 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":698 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -931,7 +905,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":699 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":699 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -940,7 +914,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":700 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":700 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -949,7 +923,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":704 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":704 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -958,7 +932,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":705 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":705 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -967,7 +941,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":714 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":714 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -976,7 +950,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":715 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":715 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -985,7 +959,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":716 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":716 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -994,7 +968,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":718 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":718 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1003,7 +977,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":719 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":719 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1012,7 +986,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":720 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":720 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1021,7 +995,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":722 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":722 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1030,7 +1004,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":723 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":723 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1039,7 +1013,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":725 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":725 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1048,7 +1022,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":726 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":726 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1057,7 +1031,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":727 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":727 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1092,7 +1066,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":729 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":729 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1101,7 +1075,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":730 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":730 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1110,7 +1084,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":731 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":731 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1119,7 +1093,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":733 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":733 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1202,18 +1176,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject /* GetBuiltinName.proto */ static PyObject *__Pyx_GetBuiltinName(PyObject *name); -/* RaiseArgTupleInvalid.proto */ -static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, - Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); - -/* RaiseDoubleKeywords.proto */ -static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); - -/* ParseKeywords.proto */ -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ - const char* function_name); - /* IncludeStringH.proto */ #include @@ -1223,6 +1185,13 @@ static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int eq /* UnicodeEquals.proto */ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); +/* StrEquals.proto */ +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif + /* ListAppend.proto */ #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { @@ -1311,6 +1280,44 @@ static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* #define __Pyx_CallUnboundCMethod1(cfunc, self, arg) __Pyx__CallUnboundCMethod1(cfunc, self, arg) #endif +/* PyCFunctionFastCall.proto */ +#if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); +#else +#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) +#endif + +/* PyFunctionFastCall.proto */ +#if CYTHON_FAST_PYCALL +#define __Pyx_PyFunction_FastCall(func, args, nargs)\ + __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); +#else +#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) +#endif +#define __Pyx_BUILD_ASSERT_EXPR(cond)\ + (sizeof(char [1 - 2*!(cond)]) - 1) +#ifndef Py_MEMBER_SIZE +#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) +#endif + static size_t __pyx_pyframe_localsplus_offset = 0; + #include "frameobject.h" + #define __Pxy_PyFrame_Initialize_Offsets()\ + ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ + (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) + #define __Pyx_PyFrame_GetLocalsplus(frame)\ + (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) +#endif + +/* PyObjectCallMethO.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +/* PyObjectCallOneArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + /* PyDictVersioning.proto */ #if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS #define __PYX_DICT_VERSION_INIT ((PY_UINT64_T) -1) @@ -1358,46 +1365,20 @@ static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_ve static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); #endif -/* PyCFunctionFastCall.proto */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); -#else -#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) -#endif - -/* PyFunctionFastCall.proto */ -#if CYTHON_FAST_PYCALL -#define __Pyx_PyFunction_FastCall(func, args, nargs)\ - __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); -#else -#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) -#endif -#define __Pyx_BUILD_ASSERT_EXPR(cond)\ - (sizeof(char [1 - 2*!(cond)]) - 1) -#ifndef Py_MEMBER_SIZE -#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) -#endif - static size_t __pyx_pyframe_localsplus_offset = 0; - #include "frameobject.h" - #define __Pxy_PyFrame_Initialize_Offsets()\ - ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ - (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) - #define __Pyx_PyFrame_GetLocalsplus(frame)\ - (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) -#endif - /* PyObjectCall2Args.proto */ static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif +/* RaiseArgTupleInvalid.proto */ +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); -/* PyObjectCallOneArg.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); +/* RaiseDoubleKeywords.proto */ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +/* ParseKeywords.proto */ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ + const char* function_name); /* PyObjectCallNoArg.proto */ #if CYTHON_COMPILING_IN_CPYTHON @@ -1638,12 +1619,12 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); /* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - /* CIntFromPy.proto */ static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *); +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + /* CIntFromPy.proto */ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); @@ -1708,6 +1689,7 @@ static PyTypeObject *__pyx_ptype_5numpy_character = 0; static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; /* Module declarations from 'CRISPResso2.CRISPRessoCOREResources' */ +static PyObject *__pyx_f_11CRISPResso2_23CRISPRessoCOREResources_find_indels_substitutions(PyObject *, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/ #define __Pyx_MODULE_NAME "CRISPResso2.CRISPRessoCOREResources" extern int __pyx_module_is_main_CRISPResso2__CRISPRessoCOREResources; int __pyx_module_is_main_CRISPResso2__CRISPRessoCOREResources = 0; @@ -1715,6 +1697,7 @@ int __pyx_module_is_main_CRISPResso2__CRISPRessoCOREResources = 0; /* Implementation of 'CRISPResso2.CRISPRessoCOREResources' */ static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_ImportError; static const char __pyx_k_[] = "-"; static const char __pyx_k_A[] = "A"; @@ -1752,7 +1735,6 @@ static const char __pyx_k_ref_en[] = "ref_en"; static const char __pyx_k_ref_st[] = "ref_st"; static const char __pyx_k_compile[] = "compile"; static const char __pyx_k_retDict[] = "retDict"; -static const char __pyx_k_seq_len[] = "seq_len"; static const char __pyx_k_sub_seq[] = "sub_seq"; static const char __pyx_k_finditer[] = "finditer"; static const char __pyx_k_enumerate[] = "enumerate"; @@ -1762,16 +1744,13 @@ static const char __pyx_k_ImportError[] = "ImportError"; static const char __pyx_k_inc_del_pos[] = "inc_del_pos"; static const char __pyx_k_insertion_n[] = "insertion_n"; static const char __pyx_k_read_seq_al[] = "read_seq_al"; -static const char __pyx_k_end_deletion[] = "end_deletion"; static const char __pyx_k_include_indx[] = "_include_indx"; static const char __pyx_k_intersection[] = "intersection"; static const char __pyx_k_ref_positions[] = "ref_positions"; static const char __pyx_k_deletion_sizes[] = "deletion_sizes"; static const char __pyx_k_re_find_indels[] = "re_find_indels"; -static const char __pyx_k_start_deletion[] = "start_deletion"; static const char __pyx_k_substitution_n[] = "substitution_n"; static const char __pyx_k_insertion_sizes[] = "insertion_sizes"; -static const char __pyx_k_start_insertion[] = "start_insertion"; static const char __pyx_k_include_indx_set[] = "include_indx_set"; static const char __pyx_k_calculate_homology[] = "calculate_homology"; static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; @@ -1784,36 +1763,30 @@ static const char __pyx_k_all_deletion_positions[] = "all_deletion_positions"; static const char __pyx_k_substitution_positions[] = "substitution_positions"; static const char __pyx_k_all_insertion_positions[] = "all_insertion_positions"; static const char __pyx_k_all_substitution_values[] = "all_substitution_values"; -static const char __pyx_k_find_indels_substitutions[] = "find_indels_substitutions"; static const char __pyx_k_all_substitution_positions[] = "all_substitution_positions"; static const char __pyx_k_all_insertion_left_positions[] = "all_insertion_left_positions"; +static const char __pyx_k_Users_cole_code_edylitics_CRISP[] = "/Users/cole/code/edylitics/CRISPResso/CRISPResso2/CRISPRessoCOREResources.pyx"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour[] = "CRISPResso2/CRISPRessoCOREResources.pyx"; +static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour[] = "CRISPResso2.CRISPRessoCOREResources"; static const char __pyx_k_find_indels_substitutions_legacy[] = "find_indels_substitutions_legacy"; static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour_2[] = "CRISPResso2.CRISPRessoCOREResources"; -static PyObject *__pyx_kp_u_; -static PyObject *__pyx_n_u_A; -static PyObject *__pyx_n_u_C; -static PyObject *__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour; -static PyObject *__pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2; -static PyObject *__pyx_n_u_G; +static PyObject *__pyx_kp_s_; +static PyObject *__pyx_n_s_A; +static PyObject *__pyx_n_s_C; +static PyObject *__pyx_n_s_CRISPResso2_CRISPRessoCOREResour; +static PyObject *__pyx_n_s_G; static PyObject *__pyx_n_s_ImportError; -static PyObject *__pyx_n_u_N; -static PyObject *__pyx_n_u_T; -static PyObject *__pyx_kp_u__4; +static PyObject *__pyx_n_s_N; +static PyObject *__pyx_n_s_T; +static PyObject *__pyx_kp_s_Users_cole_code_edylitics_CRISP; +static PyObject *__pyx_kp_s__4; static PyObject *__pyx_n_s_a; static PyObject *__pyx_n_s_al; static PyObject *__pyx_n_s_all_deletion_positions; -static PyObject *__pyx_n_u_all_deletion_positions; static PyObject *__pyx_n_s_all_insertion_left_positions; -static PyObject *__pyx_n_u_all_insertion_left_positions; static PyObject *__pyx_n_s_all_insertion_positions; -static PyObject *__pyx_n_u_all_insertion_positions; static PyObject *__pyx_n_s_all_substitution_positions; -static PyObject *__pyx_n_u_all_substitution_positions; static PyObject *__pyx_n_s_all_substitution_values; -static PyObject *__pyx_n_u_all_substitution_values; static PyObject *__pyx_n_s_array; static PyObject *__pyx_n_s_b; static PyObject *__pyx_n_s_bl; @@ -1822,17 +1795,11 @@ static PyObject *__pyx_n_s_calculate_homology; static PyObject *__pyx_n_s_cline_in_traceback; static PyObject *__pyx_n_s_compile; static PyObject *__pyx_n_s_deletion_coordinates; -static PyObject *__pyx_n_u_deletion_coordinates; static PyObject *__pyx_n_s_deletion_n; -static PyObject *__pyx_n_u_deletion_n; static PyObject *__pyx_n_s_deletion_positions; -static PyObject *__pyx_n_u_deletion_positions; static PyObject *__pyx_n_s_deletion_sizes; -static PyObject *__pyx_n_u_deletion_sizes; static PyObject *__pyx_n_s_en; -static PyObject *__pyx_n_s_end_deletion; static PyObject *__pyx_n_s_enumerate; -static PyObject *__pyx_n_s_find_indels_substitutions; static PyObject *__pyx_n_s_find_indels_substitutions_legacy; static PyObject *__pyx_n_s_finditer; static PyObject *__pyx_n_s_i; @@ -1843,13 +1810,9 @@ static PyObject *__pyx_n_s_inc_del_pos; static PyObject *__pyx_n_s_include_indx; static PyObject *__pyx_n_s_include_indx_set; static PyObject *__pyx_n_s_insertion_coordinates; -static PyObject *__pyx_n_u_insertion_coordinates; static PyObject *__pyx_n_s_insertion_n; -static PyObject *__pyx_n_u_insertion_n; static PyObject *__pyx_n_s_insertion_positions; -static PyObject *__pyx_n_u_insertion_positions; static PyObject *__pyx_n_s_insertion_sizes; -static PyObject *__pyx_n_u_insertion_sizes; static PyObject *__pyx_n_s_intersection; static PyObject *__pyx_n_s_l; static PyObject *__pyx_n_s_main; @@ -1857,8 +1820,8 @@ static PyObject *__pyx_n_s_name; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_nucSet; static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_u_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_u_numpy_core_umath_failed_to_impor; +static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; +static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; static PyObject *__pyx_n_s_p; static PyObject *__pyx_n_s_range; static PyObject *__pyx_n_s_re; @@ -1866,23 +1829,16 @@ static PyObject *__pyx_n_s_re_find_indels; static PyObject *__pyx_n_s_read_seq_al; static PyObject 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"../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":933 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":933 * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) # <<<<<<<<<<<<<< @@ -5507,7 +5458,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ (void)(PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_base)); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":931 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":931 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -5519,7 +5470,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":935 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":935 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -5534,7 +5485,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":936 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":936 * * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) # <<<<<<<<<<<<<< @@ -5543,7 +5494,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ __pyx_v_base = PyArray_BASE(__pyx_v_arr); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":937 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":937 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -5553,7 +5504,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":938 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":938 * base = PyArray_BASE(arr) * if base is NULL: * return None # <<<<<<<<<<<<<< @@ -5564,7 +5515,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":937 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":937 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -5573,7 +5524,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":939 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":939 * if base is NULL: * return None * return base # <<<<<<<<<<<<<< @@ -5585,7 +5536,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = ((PyObject *)__pyx_v_base); goto __pyx_L0; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":935 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":935 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -5600,7 +5551,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":943 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":943 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -5624,7 +5575,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":944 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":944 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5640,7 +5591,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":945 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":945 * cdef inline int import_array() except -1: * try: * __pyx_import_array() # <<<<<<<<<<<<<< @@ -5649,7 +5600,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 945, __pyx_L3_error) - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":944 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":944 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5663,7 +5614,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":946 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":946 * try: * __pyx_import_array() * except Exception: # <<<<<<<<<<<<<< @@ -5678,7 +5629,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":947 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":947 * __pyx_import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -5694,7 +5645,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":944 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":944 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5709,7 +5660,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":943 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":943 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -5732,7 +5683,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":949 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":949 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -5756,7 +5707,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { int __pyx_clineno = 0; 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"../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":950 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -5795,7 +5746,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":952 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":952 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -5810,7 +5761,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":953 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":953 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -5826,7 +5777,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":950 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":950 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -5841,7 +5792,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":949 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":949 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -5864,7 +5815,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":955 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":955 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -5888,7 +5839,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":956 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":956 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -5904,7 +5855,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":957 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":957 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -5913,7 +5864,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 957, __pyx_L3_error) - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":956 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":956 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -5927,7 +5878,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":958 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":958 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -5942,7 +5893,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":959 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":959 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -5958,7 +5909,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":956 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":956 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -5973,7 +5924,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":955 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":955 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -5996,7 +5947,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":969 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":969 * * * cdef inline bint is_timedelta64_object(object obj): # <<<<<<<<<<<<<< @@ -6009,7 +5960,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("is_timedelta64_object", 0); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":981 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":981 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< @@ -6019,7 +5970,7 @@ static CYTHON_INLINE int 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"../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":996 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":996 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< @@ -6056,7 +6007,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyDatetimeArrType_Type)); goto __pyx_L0; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":984 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":984 * * * cdef inline bint is_datetime64_object(object obj): # <<<<<<<<<<<<<< @@ -6070,7 +6021,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":999 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":999 * * * cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<< @@ -6081,7 +6032,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *__pyx_v_obj) { npy_datetime __pyx_r; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1006 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1006 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -6091,7 +6042,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":999 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":999 * * * cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<< @@ -6104,7 +6055,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1009 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1009 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<< @@ -6115,7 +6066,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject *__pyx_v_obj) { npy_timedelta __pyx_r; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1013 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1013 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -6125,7 +6076,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1009 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1009 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<< @@ -6138,7 +6089,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1016 +/* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1016 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<< @@ -6149,7 +6100,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObject *__pyx_v_obj) { NPY_DATETIMEUNIT __pyx_r; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1020 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1020 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< @@ -6157,7 +6108,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec __pyx_r = ((NPY_DATETIMEUNIT)((PyDatetimeScalarObject *)__pyx_v_obj)->obmeta.base); goto __pyx_L0; - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":1016 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":1016 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<< @@ -6171,6 +6122,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec } static PyMethodDef __pyx_methods[] = { + {"find_indels_substitutions", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, METH_VARARGS|METH_KEYWORDS, 0}, {0, 0, 0, 0} }; @@ -6216,28 +6168,23 @@ static struct PyModuleDef __pyx_moduledef = { #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { - {&__pyx_kp_u_, __pyx_k_, sizeof(__pyx_k_), 0, 1, 0, 0}, - {&__pyx_n_u_A, __pyx_k_A, sizeof(__pyx_k_A), 0, 1, 0, 1}, - {&__pyx_n_u_C, __pyx_k_C, sizeof(__pyx_k_C), 0, 1, 0, 1}, - {&__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour, __pyx_k_CRISPResso2_CRISPRessoCOREResour, sizeof(__pyx_k_CRISPResso2_CRISPRessoCOREResour), 0, 0, 1, 0}, - {&__pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_k_CRISPResso2_CRISPRessoCOREResour_2, sizeof(__pyx_k_CRISPResso2_CRISPRessoCOREResour_2), 0, 0, 1, 1}, - {&__pyx_n_u_G, __pyx_k_G, sizeof(__pyx_k_G), 0, 1, 0, 1}, + {&__pyx_kp_s_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 1, 0}, + {&__pyx_n_s_A, __pyx_k_A, sizeof(__pyx_k_A), 0, 0, 1, 1}, + {&__pyx_n_s_C, __pyx_k_C, sizeof(__pyx_k_C), 0, 0, 1, 1}, + {&__pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_k_CRISPResso2_CRISPRessoCOREResour, sizeof(__pyx_k_CRISPResso2_CRISPRessoCOREResour), 0, 0, 1, 1}, + {&__pyx_n_s_G, __pyx_k_G, sizeof(__pyx_k_G), 0, 0, 1, 1}, {&__pyx_n_s_ImportError, __pyx_k_ImportError, sizeof(__pyx_k_ImportError), 0, 0, 1, 1}, - {&__pyx_n_u_N, __pyx_k_N, sizeof(__pyx_k_N), 0, 1, 0, 1}, - {&__pyx_n_u_T, __pyx_k_T, sizeof(__pyx_k_T), 0, 1, 0, 1}, - {&__pyx_kp_u__4, __pyx_k__4, sizeof(__pyx_k__4), 0, 1, 0, 0}, + {&__pyx_n_s_N, __pyx_k_N, sizeof(__pyx_k_N), 0, 0, 1, 1}, + {&__pyx_n_s_T, __pyx_k_T, sizeof(__pyx_k_T), 0, 0, 1, 1}, + {&__pyx_kp_s_Users_cole_code_edylitics_CRISP, __pyx_k_Users_cole_code_edylitics_CRISP, sizeof(__pyx_k_Users_cole_code_edylitics_CRISP), 0, 0, 1, 0}, + {&__pyx_kp_s__4, __pyx_k__4, sizeof(__pyx_k__4), 0, 0, 1, 0}, {&__pyx_n_s_a, __pyx_k_a, sizeof(__pyx_k_a), 0, 0, 1, 1}, {&__pyx_n_s_al, __pyx_k_al, sizeof(__pyx_k_al), 0, 0, 1, 1}, {&__pyx_n_s_all_deletion_positions, __pyx_k_all_deletion_positions, sizeof(__pyx_k_all_deletion_positions), 0, 0, 1, 1}, - {&__pyx_n_u_all_deletion_positions, __pyx_k_all_deletion_positions, sizeof(__pyx_k_all_deletion_positions), 0, 1, 0, 1}, {&__pyx_n_s_all_insertion_left_positions, __pyx_k_all_insertion_left_positions, sizeof(__pyx_k_all_insertion_left_positions), 0, 0, 1, 1}, - {&__pyx_n_u_all_insertion_left_positions, __pyx_k_all_insertion_left_positions, sizeof(__pyx_k_all_insertion_left_positions), 0, 1, 0, 1}, {&__pyx_n_s_all_insertion_positions, __pyx_k_all_insertion_positions, sizeof(__pyx_k_all_insertion_positions), 0, 0, 1, 1}, - {&__pyx_n_u_all_insertion_positions, __pyx_k_all_insertion_positions, sizeof(__pyx_k_all_insertion_positions), 0, 1, 0, 1}, {&__pyx_n_s_all_substitution_positions, __pyx_k_all_substitution_positions, sizeof(__pyx_k_all_substitution_positions), 0, 0, 1, 1}, - {&__pyx_n_u_all_substitution_positions, __pyx_k_all_substitution_positions, sizeof(__pyx_k_all_substitution_positions), 0, 1, 0, 1}, {&__pyx_n_s_all_substitution_values, __pyx_k_all_substitution_values, sizeof(__pyx_k_all_substitution_values), 0, 0, 1, 1}, - {&__pyx_n_u_all_substitution_values, __pyx_k_all_substitution_values, sizeof(__pyx_k_all_substitution_values), 0, 1, 0, 1}, {&__pyx_n_s_array, __pyx_k_array, sizeof(__pyx_k_array), 0, 0, 1, 1}, {&__pyx_n_s_b, __pyx_k_b, sizeof(__pyx_k_b), 0, 0, 1, 1}, {&__pyx_n_s_bl, __pyx_k_bl, sizeof(__pyx_k_bl), 0, 0, 1, 1}, @@ -6246,17 +6193,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, {&__pyx_n_s_compile, __pyx_k_compile, sizeof(__pyx_k_compile), 0, 0, 1, 1}, {&__pyx_n_s_deletion_coordinates, __pyx_k_deletion_coordinates, sizeof(__pyx_k_deletion_coordinates), 0, 0, 1, 1}, - {&__pyx_n_u_deletion_coordinates, __pyx_k_deletion_coordinates, sizeof(__pyx_k_deletion_coordinates), 0, 1, 0, 1}, {&__pyx_n_s_deletion_n, __pyx_k_deletion_n, sizeof(__pyx_k_deletion_n), 0, 0, 1, 1}, - {&__pyx_n_u_deletion_n, __pyx_k_deletion_n, sizeof(__pyx_k_deletion_n), 0, 1, 0, 1}, {&__pyx_n_s_deletion_positions, __pyx_k_deletion_positions, sizeof(__pyx_k_deletion_positions), 0, 0, 1, 1}, - {&__pyx_n_u_deletion_positions, __pyx_k_deletion_positions, sizeof(__pyx_k_deletion_positions), 0, 1, 0, 1}, {&__pyx_n_s_deletion_sizes, __pyx_k_deletion_sizes, sizeof(__pyx_k_deletion_sizes), 0, 0, 1, 1}, - {&__pyx_n_u_deletion_sizes, __pyx_k_deletion_sizes, sizeof(__pyx_k_deletion_sizes), 0, 1, 0, 1}, {&__pyx_n_s_en, __pyx_k_en, sizeof(__pyx_k_en), 0, 0, 1, 1}, - {&__pyx_n_s_end_deletion, __pyx_k_end_deletion, sizeof(__pyx_k_end_deletion), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, - {&__pyx_n_s_find_indels_substitutions, __pyx_k_find_indels_substitutions, sizeof(__pyx_k_find_indels_substitutions), 0, 0, 1, 1}, {&__pyx_n_s_find_indels_substitutions_legacy, __pyx_k_find_indels_substitutions_legacy, sizeof(__pyx_k_find_indels_substitutions_legacy), 0, 0, 1, 1}, {&__pyx_n_s_finditer, __pyx_k_finditer, sizeof(__pyx_k_finditer), 0, 0, 1, 1}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, @@ -6267,13 +6208,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_include_indx, __pyx_k_include_indx, sizeof(__pyx_k_include_indx), 0, 0, 1, 1}, {&__pyx_n_s_include_indx_set, __pyx_k_include_indx_set, sizeof(__pyx_k_include_indx_set), 0, 0, 1, 1}, {&__pyx_n_s_insertion_coordinates, __pyx_k_insertion_coordinates, sizeof(__pyx_k_insertion_coordinates), 0, 0, 1, 1}, - {&__pyx_n_u_insertion_coordinates, __pyx_k_insertion_coordinates, sizeof(__pyx_k_insertion_coordinates), 0, 1, 0, 1}, {&__pyx_n_s_insertion_n, __pyx_k_insertion_n, sizeof(__pyx_k_insertion_n), 0, 0, 1, 1}, - {&__pyx_n_u_insertion_n, __pyx_k_insertion_n, sizeof(__pyx_k_insertion_n), 0, 1, 0, 1}, {&__pyx_n_s_insertion_positions, __pyx_k_insertion_positions, sizeof(__pyx_k_insertion_positions), 0, 0, 1, 1}, - {&__pyx_n_u_insertion_positions, __pyx_k_insertion_positions, sizeof(__pyx_k_insertion_positions), 0, 1, 0, 1}, {&__pyx_n_s_insertion_sizes, __pyx_k_insertion_sizes, sizeof(__pyx_k_insertion_sizes), 0, 0, 1, 1}, - {&__pyx_n_u_insertion_sizes, __pyx_k_insertion_sizes, sizeof(__pyx_k_insertion_sizes), 0, 1, 0, 1}, {&__pyx_n_s_intersection, __pyx_k_intersection, sizeof(__pyx_k_intersection), 0, 0, 1, 1}, {&__pyx_n_s_l, __pyx_k_l, sizeof(__pyx_k_l), 0, 0, 1, 1}, {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, @@ -6281,8 +6218,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1}, {&__pyx_n_s_nucSet, __pyx_k_nucSet, sizeof(__pyx_k_nucSet), 0, 0, 1, 1}, {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, - {&__pyx_kp_u_numpy_core_multiarray_failed_to, __pyx_k_numpy_core_multiarray_failed_to, sizeof(__pyx_k_numpy_core_multiarray_failed_to), 0, 1, 0, 0}, - {&__pyx_kp_u_numpy_core_umath_failed_to_impor, __pyx_k_numpy_core_umath_failed_to_impor, sizeof(__pyx_k_numpy_core_umath_failed_to_impor), 0, 1, 0, 0}, + {&__pyx_kp_s_numpy_core_multiarray_failed_to, __pyx_k_numpy_core_multiarray_failed_to, sizeof(__pyx_k_numpy_core_multiarray_failed_to), 0, 0, 1, 0}, + {&__pyx_kp_s_numpy_core_umath_failed_to_impor, __pyx_k_numpy_core_umath_failed_to_impor, sizeof(__pyx_k_numpy_core_umath_failed_to_impor), 0, 0, 1, 0}, {&__pyx_n_s_p, __pyx_k_p, sizeof(__pyx_k_p), 0, 0, 1, 1}, {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, {&__pyx_n_s_re, __pyx_k_re, sizeof(__pyx_k_re), 0, 0, 1, 1}, @@ -6290,23 +6227,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_read_seq_al, __pyx_k_read_seq_al, sizeof(__pyx_k_read_seq_al), 0, 0, 1, 1}, {&__pyx_n_s_ref_en, __pyx_k_ref_en, sizeof(__pyx_k_ref_en), 0, 0, 1, 1}, {&__pyx_n_s_ref_positions, __pyx_k_ref_positions, sizeof(__pyx_k_ref_positions), 0, 0, 1, 1}, - {&__pyx_n_u_ref_positions, __pyx_k_ref_positions, sizeof(__pyx_k_ref_positions), 0, 1, 0, 1}, {&__pyx_n_s_ref_seq_al, __pyx_k_ref_seq_al, sizeof(__pyx_k_ref_seq_al), 0, 0, 1, 1}, {&__pyx_n_s_ref_st, __pyx_k_ref_st, sizeof(__pyx_k_ref_st), 0, 0, 1, 1}, {&__pyx_n_s_retDict, __pyx_k_retDict, sizeof(__pyx_k_retDict), 0, 0, 1, 1}, {&__pyx_n_s_score, __pyx_k_score, sizeof(__pyx_k_score), 0, 0, 1, 1}, - {&__pyx_n_s_seq_len, __pyx_k_seq_len, sizeof(__pyx_k_seq_len), 0, 0, 1, 1}, {&__pyx_n_s_span, __pyx_k_span, sizeof(__pyx_k_span), 0, 0, 1, 1}, {&__pyx_n_s_st, __pyx_k_st, sizeof(__pyx_k_st), 0, 0, 1, 1}, - {&__pyx_n_s_start_deletion, __pyx_k_start_deletion, sizeof(__pyx_k_start_deletion), 0, 0, 1, 1}, - {&__pyx_n_s_start_insertion, __pyx_k_start_insertion, sizeof(__pyx_k_start_insertion), 0, 0, 1, 1}, {&__pyx_n_s_sub_seq, __pyx_k_sub_seq, sizeof(__pyx_k_sub_seq), 0, 0, 1, 1}, {&__pyx_n_s_substitution_n, __pyx_k_substitution_n, sizeof(__pyx_k_substitution_n), 0, 0, 1, 1}, - {&__pyx_n_u_substitution_n, __pyx_k_substitution_n, sizeof(__pyx_k_substitution_n), 0, 1, 0, 1}, {&__pyx_n_s_substitution_positions, __pyx_k_substitution_positions, sizeof(__pyx_k_substitution_positions), 0, 0, 1, 1}, - {&__pyx_n_u_substitution_positions, __pyx_k_substitution_positions, sizeof(__pyx_k_substitution_positions), 0, 1, 0, 1}, {&__pyx_n_s_substitution_values, __pyx_k_substitution_values, sizeof(__pyx_k_substitution_values), 0, 0, 1, 1}, - {&__pyx_n_u_substitution_values, __pyx_k_substitution_values, sizeof(__pyx_k_substitution_values), 0, 1, 0, 1}, {&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1}, {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} @@ -6314,6 +6244,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 57, __pyx_L1_error) __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 92, __pyx_L1_error) + __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) __PYX_ERR(0, 100, __pyx_L1_error) __pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(1, 947, __pyx_L1_error) return 0; __pyx_L1_error:; @@ -6324,25 +6255,25 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":947 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":947 * __pyx_import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< * * cdef inline int import_umath() except -1: */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_numpy_core_multiarray_failed_to); if (unlikely(!__pyx_tuple__2)) __PYX_ERR(1, 947, __pyx_L1_error) + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_numpy_core_multiarray_failed_to); if (unlikely(!__pyx_tuple__2)) __PYX_ERR(1, 947, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../miniconda3/envs/crispresso/lib/python3.8/site-packages/numpy/__init__.pxd":953 + /* "../../../../miniconda3/envs/CRISPResso/lib/python3.8/site-packages/numpy/__init__.pxd":953 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< * * cdef inline int import_ufunc() except -1: */ - 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/* "CRISPResso2/CRISPRessoCOREResources.pyx":22 - * @cython.nonecheck(False) - * @cython.wraparound(False) - * def find_indels_substitutions(read_seq_al, ref_seq_al, _include_indx): # <<<<<<<<<<<<<< - * - * #ref_positions holds the indices for which positions map back to the original reference - */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 22, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_find_indels_substitutions, __pyx_t_1) < 0) __PYX_ERR(0, 22, __pyx_L1_error) - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":130 * @cython.nonecheck(False) * @cython.wraparound(False) @@ -6788,7 +6695,7 @@ if (!__Pyx_RefNanny) { * * cdef char* sub_seq='' */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 130, __pyx_L1_error) + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 130, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_find_indels_substitutions_legacy, __pyx_t_1) < 0) __PYX_ERR(0, 130, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -6800,7 +6707,7 @@ if (!__Pyx_RefNanny) { * cdef char *al = a * cdef char *bl = b */ - 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(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 { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; + 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; } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); +#endif } -/* RaiseDoubleKeywords */ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, - PyObject* kw_name) -{ - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION >= 3 - "%s() got multiple values for keyword argument '%U'", func_name, kw_name); - #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AsString(kw_name)); - #endif -} - -/* ParseKeywords */ -static int __Pyx_ParseOptionalKeywords( - PyObject *kwds, - PyObject **argnames[], - PyObject *kwds2, - PyObject *values[], - Py_ssize_t num_pos_args, - const char* function_name) -{ - PyObject *key = 0, *value = 0; - Py_ssize_t pos = 0; - PyObject*** name; - PyObject*** first_kw_arg = argnames + num_pos_args; - while (PyDict_Next(kwds, &pos, &key, &value)) { - name = first_kw_arg; - while (*name && (**name != key)) name++; - if (*name) { - values[name-argnames] = value; - continue; - } - name = first_kw_arg; - #if PY_MAJOR_VERSION < 3 - if (likely(PyString_Check(key))) { - while (*name) { - if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) - && _PyString_Eq(**name, key)) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - if ((**argname == key) || ( - (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) - && _PyString_Eq(**argname, key))) { - goto arg_passed_twice; - } - argname++; - } - } - } else - #endif - if (likely(PyUnicode_Check(key))) { - while (*name) { - int cmp = (**name == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**name, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) { - values[name-argnames] = value; - break; - } - name++; - } - if (*name) continue; - else { - PyObject*** argname = argnames; - while (argname != first_kw_arg) { - int cmp = (**argname == key) ? 0 : - #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 - (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : - #endif - PyUnicode_Compare(**argname, key); - if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; - if (cmp == 0) goto arg_passed_twice; - argname++; - } - } - } else - goto invalid_keyword_type; - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; - } - } - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -/* BytesEquals */ -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - const char *ps1, *ps2; - Py_ssize_t length = PyBytes_GET_SIZE(s1); - if (length != PyBytes_GET_SIZE(s2)) - return (equals == Py_NE); - ps1 = PyBytes_AS_STRING(s1); - ps2 = PyBytes_AS_STRING(s2); - if (ps1[0] != ps2[0]) { - return (equals == Py_NE); - } else if (length == 1) { - return (equals == Py_EQ); - } else { - int result; -#if CYTHON_USE_UNICODE_INTERNALS - Py_hash_t hash1, hash2; - hash1 = ((PyBytesObject*)s1)->ob_shash; - hash2 = ((PyBytesObject*)s2)->ob_shash; - if (hash1 != hash2 && hash1 != -1 && hash2 != -1) { - return (equals == Py_NE); - } -#endif - result = memcmp(ps1, ps2, (size_t)length); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -#endif -} - -/* UnicodeEquals */ -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { -#if CYTHON_COMPILING_IN_PYPY - return PyObject_RichCompareBool(s1, s2, equals); -#else -#if PY_MAJOR_VERSION < 3 - PyObject* owned_ref = NULL; -#endif - int s1_is_unicode, s2_is_unicode; - if (s1 == s2) { - goto return_eq; - } - s1_is_unicode = PyUnicode_CheckExact(s1); - s2_is_unicode = PyUnicode_CheckExact(s2); -#if PY_MAJOR_VERSION < 3 - if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { - owned_ref = PyUnicode_FromObject(s2); - if (unlikely(!owned_ref)) - return -1; - s2 = owned_ref; - s2_is_unicode = 1; - } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { - owned_ref = PyUnicode_FromObject(s1); - if (unlikely(!owned_ref)) - return -1; - s1 = owned_ref; - s1_is_unicode = 1; - } else if (((!s2_is_unicode) & (!s1_is_unicode))) { - return __Pyx_PyBytes_Equals(s1, s2, equals); - } -#endif - if (s1_is_unicode & s2_is_unicode) { - Py_ssize_t length; - int kind; - void *data1, *data2; - if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) - return -1; - length = __Pyx_PyUnicode_GET_LENGTH(s1); - if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { - goto return_ne; - } -#if CYTHON_USE_UNICODE_INTERNALS - { - Py_hash_t hash1, hash2; - #if CYTHON_PEP393_ENABLED - hash1 = ((PyASCIIObject*)s1)->hash; - hash2 = ((PyASCIIObject*)s2)->hash; +/* UnicodeEquals */ +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } +#if CYTHON_USE_UNICODE_INTERNALS + { + Py_hash_t hash1, hash2; + #if CYTHON_PEP393_ENABLED + hash1 = ((PyASCIIObject*)s1)->hash; + hash2 = ((PyASCIIObject*)s2)->hash; #else hash1 = ((PyUnicodeObject*)s1)->hash; hash2 = ((PyUnicodeObject*)s2)->hash; @@ -7418,67 +7183,6 @@ static PyObject* __Pyx__CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObje return result; } -/* PyDictVersioning */ -#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS -static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; -} -static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { - PyObject **dictptr = NULL; - Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; - if (offset) { -#if CYTHON_COMPILING_IN_CPYTHON - dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); -#else - dictptr = _PyObject_GetDictPtr(obj); -#endif - } - return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; -} -static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { - PyObject *dict = Py_TYPE(obj)->tp_dict; - if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) - return 0; - return obj_dict_version == __Pyx_get_object_dict_version(obj); -} -#endif - -/* GetModuleGlobalName */ -#if CYTHON_USE_DICT_VERSIONS -static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) -#else -static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) -#endif -{ - PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS -#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 - result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } else if (unlikely(PyErr_Occurred())) { - return NULL; - } -#else - result = PyDict_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } -#endif -#else - result = PyObject_GetItem(__pyx_d, name); - __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) - if (likely(result)) { - return __Pyx_NewRef(result); - } - PyErr_Clear(); -#endif - return __Pyx_GetBuiltinName(name); -} - /* PyCFunctionFastCall */ #if CYTHON_FAST_PYCCALL static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { @@ -7621,35 +7325,6 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, #endif #endif -/* PyObjectCall2Args */ -static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { - PyObject *args, *result = NULL; - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyFunction_FastCall(function, args, 2); - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {arg1, arg2}; - return __Pyx_PyCFunction_FastCall(function, args, 2); - } - #endif - args = PyTuple_New(2); - if (unlikely(!args)) goto done; - Py_INCREF(arg1); - PyTuple_SET_ITEM(args, 0, arg1); - Py_INCREF(arg2); - PyTuple_SET_ITEM(args, 1, arg2); - Py_INCREF(function); - result = __Pyx_PyObject_Call(function, args, NULL); - Py_DECREF(args); - Py_DECREF(function); -done: - return result; -} - /* PyObjectCallMethO */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { @@ -7682,33 +7357,265 @@ static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { Py_DECREF(args); return result; } -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, &arg, 1); + } +#endif + if (likely(PyCFunction_Check(func))) { + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); +#if CYTHON_FAST_PYCCALL + } else if (__Pyx_PyFastCFunction_Check(func)) { + return __Pyx_PyCFunction_FastCall(func, &arg, 1); +#endif + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +#endif + +/* PyDictVersioning */ +#if CYTHON_USE_DICT_VERSIONS && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PY_UINT64_T __Pyx_get_tp_dict_version(PyObject *obj) { + PyObject *dict = Py_TYPE(obj)->tp_dict; + return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; +} +static CYTHON_INLINE PY_UINT64_T __Pyx_get_object_dict_version(PyObject *obj) { + PyObject **dictptr = NULL; + Py_ssize_t offset = Py_TYPE(obj)->tp_dictoffset; + if (offset) { +#if CYTHON_COMPILING_IN_CPYTHON + dictptr = (likely(offset > 0)) ? (PyObject **) ((char *)obj + offset) : _PyObject_GetDictPtr(obj); +#else + dictptr = _PyObject_GetDictPtr(obj); +#endif + } + return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; +} +static CYTHON_INLINE int __Pyx_object_dict_version_matches(PyObject* obj, PY_UINT64_T tp_dict_version, PY_UINT64_T obj_dict_version) { + PyObject *dict = Py_TYPE(obj)->tp_dict; + if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) + return 0; + return obj_dict_version == __Pyx_get_object_dict_version(obj); +} +#endif + +/* GetModuleGlobalName */ +#if CYTHON_USE_DICT_VERSIONS +static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_version, PyObject **dict_cached_value) +#else +static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) +#endif +{ + PyObject *result; +#if !CYTHON_AVOID_BORROWED_REFS +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 + result = _PyDict_GetItem_KnownHash(__pyx_d, name, ((PyASCIIObject *) name)->hash); + __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) + if (likely(result)) { + return __Pyx_NewRef(result); + } else if (unlikely(PyErr_Occurred())) { + return NULL; + } +#else + result = PyDict_GetItem(__pyx_d, name); + __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) + if (likely(result)) { + return __Pyx_NewRef(result); + } +#endif +#else + result = PyObject_GetItem(__pyx_d, name); + __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) + if (likely(result)) { + return __Pyx_NewRef(result); + } + PyErr_Clear(); +#endif + return __Pyx_GetBuiltinName(name); +} + +/* PyObjectCall2Args */ +static CYTHON_UNUSED PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { + PyObject *args, *result = NULL; + #if CYTHON_FAST_PYCALL + if (PyFunction_Check(function)) { + PyObject *args[2] = {arg1, arg2}; + return __Pyx_PyFunction_FastCall(function, args, 2); + } + #endif + #if CYTHON_FAST_PYCCALL + if (__Pyx_PyFastCFunction_Check(function)) { + PyObject *args[2] = {arg1, arg2}; + return __Pyx_PyCFunction_FastCall(function, args, 2); + } + #endif + args = PyTuple_New(2); + if (unlikely(!args)) goto done; + Py_INCREF(arg1); + PyTuple_SET_ITEM(args, 0, arg1); + Py_INCREF(arg2); + PyTuple_SET_ITEM(args, 1, arg2); + Py_INCREF(function); + result = __Pyx_PyObject_Call(function, args, NULL); + Py_DECREF(args); + Py_DECREF(function); +done: + return result; +} + +/* RaiseArgTupleInvalid */ +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; } -#endif - if (likely(PyCFunction_Check(func))) { - if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { - return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (__Pyx_PyFastCFunction_Check(func)) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif - } + if (exact) { + more_or_less = "exactly"; } - return __Pyx__PyObject_CallOneArg(func, arg); + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); } -#else -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; + +/* RaiseDoubleKeywords */ +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +/* ParseKeywords */ +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (__Pyx_PyUnicode_GET_LENGTH(**name) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (__Pyx_PyUnicode_GET_LENGTH(**argname) != __Pyx_PyUnicode_GET_LENGTH(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; } -#endif /* PyObjectCallNoArg */ #if CYTHON_COMPILING_IN_CPYTHON @@ -9027,44 +8934,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { } } -/* CIntToPy */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic push -#pragma GCC diagnostic ignored "-Wconversion" -#endif - const long neg_one = (long) -1, const_zero = (long) 0; -#ifdef __Pyx_HAS_GCC_DIAGNOSTIC -#pragma GCC diagnostic pop -#endif - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - /* CIntFromPy */ static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC @@ -9261,6 +9130,44 @@ static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) { return (size_t) -1; } +/* CIntToPy */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wconversion" +#endif + const long neg_one = (long) -1, const_zero = (long) 0; +#ifdef __Pyx_HAS_GCC_DIAGNOSTIC +#pragma GCC diagnostic pop +#endif + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); +#endif + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); +#ifdef HAVE_LONG_LONG + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); +#endif + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + /* CIntFromPy */ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { #ifdef __Pyx_HAS_GCC_DIAGNOSTIC diff --git a/CRISPResso2/CRISPRessoCOREResources.pyx b/CRISPResso2/CRISPRessoCOREResources.pyx index 555ed511..ba826089 100644 --- a/CRISPResso2/CRISPRessoCOREResources.pyx +++ b/CRISPResso2/CRISPRessoCOREResources.pyx @@ -19,7 +19,7 @@ re_find_indels = re.compile("(-*-)") @cython.boundscheck(False) @cython.nonecheck(False) @cython.wraparound(False) -def find_indels_substitutions(read_seq_al, ref_seq_al, _include_indx): +cpdef find_indels_substitutions(read_seq_al, ref_seq_al, _include_indx): #ref_positions holds the indices for which positions map back to the original reference # for example, @@ -49,7 +49,7 @@ def find_indels_substitutions(read_seq_al, ref_seq_al, _include_indx): insertion_sizes = [] cdef int start_insertion = -1 # the -1 value indicates that there currently isn't an insertion - cdef int seq_len = len(ref_seq_al) + cdef size_t seq_len = len(ref_seq_al) include_indx_set = set(_include_indx) nucSet = set(['A', 'T', 'C', 'G', 'N']) cdef int idx = 0 @@ -96,9 +96,9 @@ def find_indels_substitutions(read_seq_al, ref_seq_al, _include_indx): deletion_sizes.append(end_deletion - start_deletion) start_deletion = -1 - substitution_n = len(substitution_positions) - deletion_n = np.sum(deletion_sizes) - insertion_n = np.sum(insertion_sizes) + cdef size_t substitution_n = len(substitution_positions) + cdef size_t deletion_n = sum(deletion_sizes) + cdef size_t insertion_n = sum(insertion_sizes) return { 'all_insertion_positions': all_insertion_positions,