diff --git a/CRISPResso2/CRISPResso2Align.c b/CRISPResso2/CRISPResso2Align.c index 32bb20a2..fcce51c4 100644 --- a/CRISPResso2/CRISPResso2Align.c +++ b/CRISPResso2/CRISPResso2Align.c @@ -4,18 +4,18 @@ { "distutils": { "depends": [ - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayscalars.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ufuncobject.h" + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayscalars.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-w", "-Ofast" ], "include_dirs": [ - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include" + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include" ], "name": "CRISPResso2.CRISPResso2Align", "sources": [ @@ -1677,7 +1677,7 @@ typedef struct { /* #### Code section: numeric_typedefs ### */ -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -1686,7 +1686,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":770 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":770 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -1695,7 +1695,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -1704,7 +1704,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":772 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":772 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1713,7 +1713,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1722,7 +1722,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":777 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":777 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1731,7 +1731,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":778 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":778 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1740,7 +1740,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1749,7 +1749,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":783 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":783 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1758,7 +1758,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":784 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":784 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1767,7 +1767,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":791 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":791 * ctypedef double complex complex128_t * * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1776,7 +1776,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 * * ctypedef npy_longlong longlong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1785,7 +1785,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1794,7 +1794,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1803,7 +1803,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1812,7 +1812,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":798 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":798 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1821,7 +1821,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":799 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":799 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1883,7 +1883,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1095 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1095 * * # Iterator API added in v1.6 * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil # <<<<<<<<<<<<<< @@ -1892,7 +1892,7 @@ struct __pyx_memoryviewslice_obj; */ typedef int (*__pyx_t_5numpy_NpyIter_IterNextFunc)(NpyIter *); -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 * # Iterator API added in v1.6 * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil # <<<<<<<<<<<<<< @@ -18596,7 +18596,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 * * @property * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18607,7 +18607,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":287 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":287 * @property * cdef inline npy_intp itemsize(self) noexcept nogil: * return PyDataType_ELSIZE(self) # <<<<<<<<<<<<<< @@ -18617,7 +18617,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D __pyx_r = PyDataType_ELSIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 * * @property * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18630,7 +18630,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 * * @property * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18641,7 +18641,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":291 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":291 * @property * cdef inline npy_intp alignment(self) noexcept nogil: * return PyDataType_ALIGNMENT(self) # <<<<<<<<<<<<<< @@ -18651,7 +18651,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 * * @property * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18664,7 +18664,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 * # for this using PyDataType_HASFIELDS. * @property * cdef inline object fields(self): # <<<<<<<<<<<<<< @@ -18678,7 +18678,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("fields", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":297 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":297 * @property * cdef inline object fields(self): * return PyDataType_FIELDS(self) # <<<<<<<<<<<<<< @@ -18691,7 +18691,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc __pyx_r = ((PyObject *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 * # for this using PyDataType_HASFIELDS. * @property * cdef inline object fields(self): # <<<<<<<<<<<<<< @@ -18706,7 +18706,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 * * @property * cdef inline tuple names(self): # <<<<<<<<<<<<<< @@ -18720,7 +18720,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("names", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":301 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":301 * @property * cdef inline tuple names(self): * return PyDataType_NAMES(self) # <<<<<<<<<<<<<< @@ -18733,7 +18733,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr __pyx_r = ((PyObject*)__pyx_t_1); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 * * @property * cdef inline tuple names(self): # <<<<<<<<<<<<<< @@ -18748,7 +18748,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 * # this field via the inline helper method PyDataType_SHAPE. * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18759,7 +18759,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self) { PyArray_ArrayDescr *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":308 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":308 * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: * return PyDataType_SUBARRAY(self) # <<<<<<<<<<<<<< @@ -18769,7 +18769,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra __pyx_r = PyDataType_SUBARRAY(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 * # this field via the inline helper method PyDataType_SHAPE. * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18782,7 +18782,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 * * @property * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18793,7 +18793,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self) { npy_uint64 __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":313 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":313 * cdef inline npy_uint64 flags(self) noexcept nogil: * """The data types flags.""" * return PyDataType_FLAGS(self) # <<<<<<<<<<<<<< @@ -18803,7 +18803,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr __pyx_r = PyDataType_FLAGS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 * * @property * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18816,7 +18816,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 * * @property * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18827,7 +18827,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":325 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":325 * cdef inline int numiter(self) noexcept nogil: * """The number of arrays that need to be broadcast to the same shape.""" * return PyArray_MultiIter_NUMITER(self) # <<<<<<<<<<<<<< @@ -18837,7 +18837,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 * * @property * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18850,7 +18850,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18861,7 +18861,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":330 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":330 * cdef inline npy_intp size(self) noexcept nogil: * """The total broadcasted size.""" * return PyArray_MultiIter_SIZE(self) # <<<<<<<<<<<<<< @@ -18871,7 +18871,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18884,7 +18884,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 * * @property * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18895,7 +18895,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":335 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":335 * cdef inline npy_intp index(self) noexcept nogil: * """The current (1-d) index into the broadcasted result.""" * return PyArray_MultiIter_INDEX(self) # <<<<<<<<<<<<<< @@ -18905,7 +18905,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 * * @property * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18918,7 +18918,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 * * @property * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18929,7 +18929,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":340 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":340 * cdef inline int nd(self) noexcept nogil: * """The number of dimensions in the broadcasted result.""" * return PyArray_MultiIter_NDIM(self) # <<<<<<<<<<<<<< @@ -18939,7 +18939,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 * * @property * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18952,7 +18952,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 * * @property * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18963,7 +18963,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":345 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":345 * cdef inline npy_intp* dimensions(self) noexcept nogil: * """The shape of the broadcasted result.""" * return PyArray_MultiIter_DIMS(self) # <<<<<<<<<<<<<< @@ -18973,7 +18973,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 * * @property * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18986,7 +18986,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 * * @property * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -18997,7 +18997,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self) { void **__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":351 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":351 * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. * On return, the iterators are adjusted for broadcasting.""" * return PyArray_MultiIter_ITERS(self) # <<<<<<<<<<<<<< @@ -19007,7 +19007,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 * * @property * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19020,7 +19020,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 * * @property * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19031,7 +19031,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self) { PyObject *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":369 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":369 * """Returns a borrowed reference to the object owning the data/memory. * """ * return PyArray_BASE(self) # <<<<<<<<<<<<<< @@ -19041,7 +19041,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject __pyx_r = PyArray_BASE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 * * @property * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19054,7 +19054,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< @@ -19068,7 +19068,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray PyArray_Descr *__pyx_t_1; __Pyx_RefNannySetupContext("descr", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":375 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":375 * """Returns an owned reference to the dtype of the array. * """ * return PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -19081,7 +19081,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray __pyx_r = ((PyArray_Descr *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< @@ -19096,7 +19096,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 * * @property * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19107,7 +19107,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":381 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":381 * """Returns the number of dimensions in the array. * """ * return PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -19117,7 +19117,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx __pyx_r = PyArray_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 * * @property * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19130,7 +19130,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 * * @property * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19141,7 +19141,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":389 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":389 * Can return NULL for 0-dimensional arrays. * """ * return PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -19151,7 +19151,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec __pyx_r = PyArray_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 * * @property * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19164,7 +19164,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 * * @property * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19175,7 +19175,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":396 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":396 * The number of elements matches the number of dimensions of the array (ndim). * """ * return PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -19185,7 +19185,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO __pyx_r = PyArray_STRIDES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 * * @property * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19198,7 +19198,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19209,7 +19209,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":402 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":402 * """Returns the total size (in number of elements) of the array. * """ * return PyArray_SIZE(self) # <<<<<<<<<<<<<< @@ -19219,7 +19219,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * __pyx_r = PyArray_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19232,7 +19232,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 * * @property * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19243,7 +19243,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__pyx_v_self) { char *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":411 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":411 * of `PyArray_DATA()` instead, which returns a 'void*'. * """ * return PyArray_BYTES(self) # <<<<<<<<<<<<<< @@ -19253,7 +19253,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p __pyx_r = PyArray_BYTES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 * * @property * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< @@ -19266,7 +19266,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 * ctypedef long double complex clongdouble_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -19283,7 +19283,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":807 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":807 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -19297,7 +19297,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 * ctypedef long double complex clongdouble_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -19316,7 +19316,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -19333,7 +19333,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":810 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":810 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< @@ -19347,7 +19347,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -19366,7 +19366,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -19383,7 +19383,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":813 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":813 * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< @@ -19397,7 +19397,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -19416,7 +19416,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -19433,7 +19433,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":816 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":816 * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< @@ -19447,7 +19447,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -19466,7 +19466,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -19483,7 +19483,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":819 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":819 * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< @@ -19497,7 +19497,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -19516,7 +19516,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -19531,7 +19531,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ PyObject *__pyx_t_2; __Pyx_RefNannySetupContext("PyDataType_SHAPE", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -19541,7 +19541,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_t_1 = PyDataType_HASSUBARRAY(__pyx_v_d); if (__pyx_t_1) { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":823 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":823 * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): * return d.subarray.shape # <<<<<<<<<<<<<< @@ -19554,7 +19554,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_r = ((PyObject*)__pyx_t_2); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -19563,7 +19563,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":825 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":825 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -19577,7 +19577,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -19592,7 +19592,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base) except *: # <<<<<<<<<<<<<< @@ -19606,7 +19606,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1010 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1010 * * cdef inline void set_array_base(ndarray arr, object base) except *: * Py_INCREF(base) # important to do this before stealing the reference below! # <<<<<<<<<<<<<< @@ -19615,7 +19615,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_INCREF(__pyx_v_base); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1011 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1011 * cdef inline void set_array_base(ndarray arr, object base) except *: * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) # <<<<<<<<<<<<<< @@ -19624,7 +19624,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_t_1 = PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_base); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(2, 1011, __pyx_L1_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base) except *: # <<<<<<<<<<<<<< @@ -19639,7 +19639,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_L0:; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -19654,7 +19654,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 * * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) # <<<<<<<<<<<<<< @@ -19663,7 +19663,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ __pyx_v_base = PyArray_BASE(__pyx_v_arr); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -19673,7 +19673,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = (__pyx_v_base == NULL); if (__pyx_t_1) { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1016 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1016 * base = PyArray_BASE(arr) * if base is NULL: * return None # <<<<<<<<<<<<<< @@ -19684,7 +19684,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -19693,7 +19693,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1017 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1017 * if base is NULL: * return None * return base # <<<<<<<<<<<<<< @@ -19705,7 +19705,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = ((PyObject *)__pyx_v_base); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -19720,7 +19720,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -19744,7 +19744,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_array", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -19760,7 +19760,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1023 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1023 * cdef inline int import_array() except -1: * try: * __pyx_import_array() # <<<<<<<<<<<<<< @@ -19769,7 +19769,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1023, __pyx_L3_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -19783,7 +19783,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1024 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1024 * try: * __pyx_import_array() * except Exception: # <<<<<<<<<<<<<< @@ -19798,7 +19798,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 * __pyx_import_array() * except Exception: * raise ImportError("numpy._core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -19813,7 +19813,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { } goto __pyx_L5_except_error; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -19829,7 +19829,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -19852,7 +19852,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 * raise ImportError("numpy._core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -19876,7 +19876,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_umath", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -19892,7 +19892,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -19901,7 +19901,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1029, __pyx_L3_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -19915,7 +19915,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1030 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1030 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -19930,7 +19930,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< @@ -19945,7 +19945,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { } goto __pyx_L5_except_error; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -19961,7 +19961,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 * raise ImportError("numpy._core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -19984,7 +19984,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -20008,7 +20008,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_ufunc", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -20024,7 +20024,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1035 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1035 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -20033,7 +20033,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1035, __pyx_L3_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -20047,7 +20047,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -20062,7 +20062,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1037 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1037 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< @@ -20077,7 +20077,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { } goto __pyx_L5_except_error; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -20093,7 +20093,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -20116,7 +20116,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 * * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -20127,7 +20127,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1052 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1052 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< @@ -20137,7 +20137,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyTimedeltaArrType_Type)); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 * * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -20150,7 +20150,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 * * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -20161,7 +20161,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1067 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1067 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< @@ -20171,7 +20171,7 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 * * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -20184,7 +20184,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 * * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -20195,7 +20195,7 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1077 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1077 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -20205,7 +20205,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 * * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -20218,7 +20218,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -20229,7 +20229,7 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1084 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1084 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -20239,7 +20239,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -20252,7 +20252,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -20263,7 +20263,7 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1091 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1091 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< @@ -20273,7 +20273,7 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -26909,7 +26909,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 * __pyx_import_array() * except Exception: * raise ImportError("numpy._core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -26920,7 +26920,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py index 6c21ee52..88ea14bb 100644 --- a/CRISPResso2/CRISPRessoCORE.py +++ b/CRISPResso2/CRISPRessoCORE.py @@ -486,10 +486,12 @@ def variant_file_generator_process(seq_list, get_new_variant_object, args, refs, Nothing """ - def numpy_encoder(obj): - """ Custom encoding for numpy arrays and other non-serializable types """ + def custom_encoder(obj): + """ Custom encoding for non-serializable types """ if isinstance(obj, np.ndarray): - return obj.tolist() # Convert numpy arrays to lists + return obj.tolist() + if isinstance(obj, CRISPRessoCOREResources.ResultsSlotsDict): + return {key: obj[key] for key in obj.__slots__} raise TypeError(f"Object of type {obj.__class__.__name__} is not JSON serializable") variant_file_path = os.path.join(variants_dir, f"variants_{process_id}.tsv") @@ -500,7 +502,7 @@ def numpy_encoder(obj): for index, fastq_seq in enumerate(seq_list): new_variant = get_new_variant_object(args, fastq_seq, refs, ref_names, aln_matrix, pe_scaffold_dna_info) # Convert the complex object to a JSON string - json_string = json.dumps(new_variant, default=numpy_encoder) + json_string = json.dumps(new_variant, default=custom_encoder) variant_lines += f"{fastq_seq}\t{json_string}\n" if index % 10000 == 0 and index != 0: info(f"Process {process_id + 1} has processed {index} unique reads", {'percent_complete': 10}) diff --git a/CRISPResso2/CRISPRessoCOREResources.c b/CRISPResso2/CRISPRessoCOREResources.c index b227f38b..1a35f659 100644 --- a/CRISPResso2/CRISPRessoCOREResources.c +++ b/CRISPResso2/CRISPRessoCOREResources.c @@ -4,18 +4,18 @@ { "distutils": { "depends": [ - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayscalars.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h", - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ufuncobject.h" + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayobject.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/arrayscalars.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h", + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-w", "-Ofast" ], "include_dirs": [ - "/private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/_core/include" + "/private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/_core/include" ], "name": "CRISPResso2.CRISPRessoCOREResources", "sources": [ @@ -1249,7 +1249,7 @@ static CYTHON_INLINE float __PYX_NAN() { #include /* Using NumPy API declarations from "numpy/__init__.cython-30.pxd" */ - + #include "numpy/arrayobject.h" #include "numpy/ndarrayobject.h" #include "numpy/ndarraytypes.h" @@ -1538,17 +1538,17 @@ static const char *__pyx_f[] = { /* #### Code section: numeric_typedefs ### */ -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":769 * # 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; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":770 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":770 + * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< * ctypedef npy_int32 int32_t @@ -1556,7 +1556,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":771 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -1565,7 +1565,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":772 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":772 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1574,17 +1574,17 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":776 * #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; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":777 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":777 + * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< * ctypedef npy_uint32 uint32_t @@ -1592,7 +1592,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":778 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":778 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1601,7 +1601,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":779 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1610,17 +1610,17 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":783 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":783 * #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; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":784 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":784 + * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< * #ctypedef npy_float80 float80_t @@ -1628,65 +1628,65 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":791 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":791 * ctypedef double complex complex128_t - * + * * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulonglong_t - * + * */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":792 + * * ctypedef npy_longlong longlong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< - * + * * ctypedef npy_intp intp_t */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 * ctypedef npy_ulonglong ulonglong_t - * + * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< * ctypedef npy_uintp uintp_t - * + * */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 + * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< - * + * * ctypedef npy_double float_t */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 * 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; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":798 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":798 + * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< * ctypedef npy_longdouble longdouble_t - * + * */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":799 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":799 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< - * + * * ctypedef float complex cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; @@ -1731,20 +1731,20 @@ static CYTHON_INLINE __pyx_t_long_double_complex __pyx_t_long_double_complex_fro /*--- Type declarations ---*/ -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1095 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1095 + * * # Iterator API added in v1.6 * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil # <<<<<<<<<<<<<< * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil - * + * */ typedef int (*__pyx_t_5numpy_NpyIter_IterNextFunc)(NpyIter *); -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 * # Iterator API added in v1.6 * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil # <<<<<<<<<<<<<< - * + * * cdef extern from "numpy/arrayobject.h": */ typedef void (*__pyx_t_5numpy_NpyIter_GetMultiIndexFunc)(NpyIter *, npy_intp *); @@ -1992,10 +1992,6 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int #define __Pyx_ArgsSlice_FASTCALL(args, start, stop) PyTuple_GetSlice(args, start, stop) #endif -/* RaiseArgTupleInvalid.proto */ -static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, - Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); - /* RaiseDoubleKeywords.proto */ static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); @@ -2005,6 +2001,105 @@ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject *const *kwvalues PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); +/* RaiseArgTupleInvalid.proto */ +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +/* IterFinish.proto */ +static CYTHON_INLINE int __Pyx_IterFinish(void); + +/* PyFunctionFastCall.proto */ +#if CYTHON_FAST_PYCALL +#if !CYTHON_VECTORCALL +#define __Pyx_PyFunction_FastCall(func, args, nargs)\ + __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); +#endif +#define __Pyx_BUILD_ASSERT_EXPR(cond)\ + (sizeof(char [1 - 2*!(cond)]) - 1) +#ifndef Py_MEMBER_SIZE +#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) +#endif +#if !CYTHON_VECTORCALL +#if PY_VERSION_HEX >= 0x03080000 + #include "frameobject.h" +#if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API + #ifndef Py_BUILD_CORE + #define Py_BUILD_CORE 1 + #endif + #include "internal/pycore_frame.h" +#endif + #define __Pxy_PyFrame_Initialize_Offsets() + #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus) +#else + static size_t __pyx_pyframe_localsplus_offset = 0; + #include "frameobject.h" + #define __Pxy_PyFrame_Initialize_Offsets()\ + ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ + (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) + #define __Pyx_PyFrame_GetLocalsplus(frame)\ + (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) +#endif +#endif +#endif + +/* PyObjectCallMethO.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +/* PyObjectFastCall.proto */ +#define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL) +static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs); + +/* PyObjectCallNoArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); + +/* PyObjectCallOneArg.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +/* PyObjectGetMethod.proto */ +static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method); + +/* PyObjectCallMethod0.proto */ +static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name); + +/* RaiseNeedMoreValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +/* RaiseTooManyValuesToUnpack.proto */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +/* UnpackItemEndCheck.proto */ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); + +/* RaiseNoneIterError.proto */ +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +/* UnpackTupleError.proto */ +static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); + +/* UnpackTuple2.proto */ +#define __Pyx_unpack_tuple2(tuple, value1, value2, is_tuple, has_known_size, decref_tuple)\ + (likely(is_tuple || PyTuple_Check(tuple)) ?\ + (likely(has_known_size || PyTuple_GET_SIZE(tuple) == 2) ?\ + __Pyx_unpack_tuple2_exact(tuple, value1, value2, decref_tuple) :\ + (__Pyx_UnpackTupleError(tuple, 2), -1)) :\ + __Pyx_unpack_tuple2_generic(tuple, value1, value2, has_known_size, decref_tuple)) +static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( + PyObject* tuple, PyObject** value1, PyObject** value2, int decref_tuple); +static int __Pyx_unpack_tuple2_generic( + PyObject* tuple, PyObject** value1, PyObject** value2, int has_known_size, int decref_tuple); + +/* dict_iter.proto */ +static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name, + Py_ssize_t* p_orig_length, int* p_is_dict); +static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos, + PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict); + +/* GetAttr.proto */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + /* ListAppend.proto */ #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { @@ -2090,53 +2185,6 @@ static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* #define __Pyx_CallUnboundCMethod1(cfunc, self, arg) __Pyx__CallUnboundCMethod1(cfunc, self, arg) #endif -/* PyFunctionFastCall.proto */ -#if CYTHON_FAST_PYCALL -#if !CYTHON_VECTORCALL -#define __Pyx_PyFunction_FastCall(func, args, nargs)\ - __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs); -#endif -#define __Pyx_BUILD_ASSERT_EXPR(cond)\ - (sizeof(char [1 - 2*!(cond)]) - 1) -#ifndef Py_MEMBER_SIZE -#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member) -#endif -#if !CYTHON_VECTORCALL -#if PY_VERSION_HEX >= 0x03080000 - #include "frameobject.h" -#if PY_VERSION_HEX >= 0x030b00a6 && !CYTHON_COMPILING_IN_LIMITED_API - #ifndef Py_BUILD_CORE - #define Py_BUILD_CORE 1 - #endif - #include "internal/pycore_frame.h" -#endif - #define __Pxy_PyFrame_Initialize_Offsets() - #define __Pyx_PyFrame_GetLocalsplus(frame) ((frame)->f_localsplus) -#else - static size_t __pyx_pyframe_localsplus_offset = 0; - #include "frameobject.h" - #define __Pxy_PyFrame_Initialize_Offsets()\ - ((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\ - (void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus))) - #define __Pyx_PyFrame_GetLocalsplus(frame)\ - (assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset)) -#endif -#endif -#endif - -/* PyObjectCallMethO.proto */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); -#endif - -/* PyObjectFastCall.proto */ -#define __Pyx_PyObject_FastCall(func, args, nargs) __Pyx_PyObject_FastCallDict(func, args, (size_t)(nargs), NULL) -static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs); - -/* 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) @@ -2184,18 +2232,6 @@ static PyObject *__Pyx__GetModuleGlobalName(PyObject *name, PY_UINT64_T *dict_ve static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); #endif -/* RaiseTooManyValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); - -/* RaiseNeedMoreValuesToUnpack.proto */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); - -/* IterFinish.proto */ -static CYTHON_INLINE int __Pyx_IterFinish(void); - -/* UnpackItemEndCheck.proto */ -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); - /* TypeImport.proto */ #ifndef __PYX_HAVE_RT_ImportType_proto_3_0_11 #define __PYX_HAVE_RT_ImportType_proto_3_0_11 @@ -2224,6 +2260,17 @@ static PyObject *__Pyx_ImportDottedModule(PyObject *name, PyObject *parts_tuple) static PyObject *__Pyx_ImportDottedModule_WalkParts(PyObject *module, PyObject *name, PyObject *parts_tuple); #endif +/* SetNameInClass.proto */ +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030500A1 && PY_VERSION_HEX < 0x030d0000 +#define __Pyx_SetNameInClass(ns, name, value)\ + (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value)) +#elif CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_SetNameInClass(ns, name, value)\ + (likely(PyDict_CheckExact(ns)) ? PyDict_SetItem(ns, name, value) : PyObject_SetItem(ns, name, value)) +#else +#define __Pyx_SetNameInClass(ns, name, value) PyObject_SetItem(ns, name, value) +#endif + /* IncludeStructmemberH.proto */ #include @@ -2372,6 +2419,28 @@ static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, PyObject *module, PyObject *globals, PyObject* code); +/* CalculateMetaclass.proto */ +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); + +/* PyObjectCall2Args.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2); + +/* PyObjectLookupSpecial.proto */ +#if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS +#define __Pyx_PyObject_LookupSpecialNoError(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 0) +#define __Pyx_PyObject_LookupSpecial(obj, attr_name) __Pyx__PyObject_LookupSpecial(obj, attr_name, 1) +static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error); +#else +#define __Pyx_PyObject_LookupSpecialNoError(o,n) __Pyx_PyObject_GetAttrStrNoError(o,n) +#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) +#endif + +/* Py3ClassCreate.proto */ +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, + PyObject *mkw, PyObject *modname, PyObject *doc); +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, + PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); + /* CLineInTraceback.proto */ #ifdef CYTHON_CLINE_IN_TRACEBACK #define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0) @@ -2668,31 +2737,54 @@ static const char __pyx_k_en[] = "en"; static const char __pyx_k_np[] = "np"; static const char __pyx_k_re[] = "re"; static const char __pyx_k_st[] = "st"; -static const char __pyx_k__13[] = "?"; +static const char __pyx_k__20[] = "?"; +static const char __pyx_k_doc[] = "__doc__"; static const char __pyx_k_idx[] = "idx"; +static const char __pyx_k_key[] = "key"; static const char __pyx_k_sum[] = "sum"; +static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_init[] = "__init__"; static const char __pyx_k_main[] = "__main__"; static const char __pyx_k_name[] = "__name__"; +static const char __pyx_k_self[] = "self"; static const char __pyx_k_span[] = "span"; static const char __pyx_k_spec[] = "__spec__"; static const char __pyx_k_test[] = "__test__"; static const char __pyx_k_array[] = "array"; static const char __pyx_k_idx_c[] = "idx_c"; +static const char __pyx_k_items[] = "items"; static const char __pyx_k_numpy[] = "numpy"; static const char __pyx_k_range[] = "range"; static const char __pyx_k_score[] = "score"; +static const char __pyx_k_slots[] = "__slots__"; +static const char __pyx_k_super[] = "super"; +static const char __pyx_k_value[] = "value"; static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_kwargs[] = "kwargs"; +static const char __pyx_k_module[] = "__module__"; static const char __pyx_k_nucSet[] = "nucSet"; static const char __pyx_k_ref_en[] = "ref_en"; static const char __pyx_k_ref_st[] = "ref_st"; +static const char __pyx_k_aln_ref[] = "aln_ref"; +static const char __pyx_k_aln_seq[] = "aln_seq"; static const char __pyx_k_compile[] = "compile"; +static const char __pyx_k_getitem[] = "__getitem__"; +static const char __pyx_k_prepare[] = "__prepare__"; static const char __pyx_k_retDict[] = "retDict"; static const char __pyx_k_seq_len[] = "seq_len"; +static const char __pyx_k_setitem[] = "__setitem__"; static const char __pyx_k_sub_seq[] = "sub_seq"; static const char __pyx_k_finditer[] = "finditer"; +static const char __pyx_k_qualname[] = "__qualname__"; +static const char __pyx_k_ref_name[] = "ref_name"; +static const char __pyx_k_set_name[] = "__set_name__"; static const char __pyx_k_enumerate[] = "enumerate"; +static const char __pyx_k_metaclass[] = "__metaclass__"; +static const char __pyx_k_aln_scores[] = "aln_scores"; +static const char __pyx_k_aln_strand[] = "aln_strand"; static const char __pyx_k_deletion_n[] = "deletion_n"; static const char __pyx_k_ref_seq_al[] = "ref_seq_al"; +static const char __pyx_k_total_mods[] = "total_mods"; 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"; @@ -2702,37 +2794,52 @@ static const char __pyx_k_include_indx[] = "_include_indx"; static const char __pyx_k_initializing[] = "_initializing"; static const char __pyx_k_intersection[] = "intersection"; static const char __pyx_k_is_coroutine[] = "_is_coroutine"; +static const char __pyx_k_init_subclass[] = "__init_subclass__"; static const char __pyx_k_ref_positions[] = "ref_positions"; +static const char __pyx_k_classification[] = "classification"; static const char __pyx_k_deletion_sizes[] = "deletion_sizes"; +static const char __pyx_k_irregular_ends[] = "irregular_ends"; +static const char __pyx_k_mods_in_window[] = "mods_in_window"; 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_ResultsSlotsDict[] = "ResultsSlotsDict"; static const char __pyx_k_include_indx_set[] = "include_indx_set"; static const char __pyx_k_asyncio_coroutines[] = "asyncio.coroutines"; static const char __pyx_k_calculate_homology[] = "calculate_homology"; static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback"; static const char __pyx_k_deletion_positions[] = "deletion_positions"; static const char __pyx_k_insertion_positions[] = "insertion_positions"; +static const char __pyx_k_mods_outside_window[] = "mods_outside_window"; static const char __pyx_k_substitution_values[] = "substitution_values"; static const char __pyx_k_deletion_coordinates[] = "deletion_coordinates"; static const char __pyx_k_insertion_coordinates[] = "insertion_coordinates"; static const char __pyx_k_all_deletion_positions[] = "all_deletion_positions"; static const char __pyx_k_current_insertion_size[] = "current_insertion_size"; static const char __pyx_k_substitution_positions[] = "substitution_positions"; +static const char __pyx_k_ResultsSlotsDict___init[] = "ResultsSlotsDict.__init__"; 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_all_deletion_coordinates[] = "all_deletion_coordinates"; +static const char __pyx_k_deletions_outside_window[] = "deletions_outside_window"; static const char __pyx_k_find_indels_substitutions[] = "find_indels_substitutions"; +static const char __pyx_k_insertions_outside_window[] = "insertions_outside_window"; +static const char __pyx_k_ResultsSlotsDict___getitem[] = "ResultsSlotsDict.__getitem__"; +static const char __pyx_k_ResultsSlotsDict___setitem[] = "ResultsSlotsDict.__setitem__"; 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_CRISPResso2_CRISPRessoCOREResour[] = "CRISPResso2/CRISPRessoCOREResources.pyx"; +static const char __pyx_k_substitutions_outside_window[] = "substitutions_outside_window"; +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_multiarray_failed_to[] = "numpy._core.multiarray failed to import"; static const char __pyx_k_numpy__core_umath_failed_to_impo[] = "numpy._core.umath failed to import"; -static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour_2[] = "CRISPResso2.CRISPRessoCOREResources"; +static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour_2[] = "CRISPResso2/CRISPRessoCOREResources.pyx"; /* #### Code section: decls ### */ +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_kwargs); /* proto */ +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_2__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_4__setitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_substitutions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_read_seq_al, PyObject *__pyx_v_ref_seq_al, PyObject *__pyx_v__include_indx); /* proto */ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_substitutions_legacy(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_read_seq_al, PyObject *__pyx_v_ref_seq_al, PyObject *__pyx_v__include_indx); /* proto */ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_homology(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b); /* proto */ @@ -2804,13 +2911,17 @@ typedef struct { #endif PyObject *__pyx_n_u_A; PyObject *__pyx_n_u_C; - PyObject *__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour; - PyObject *__pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2; + PyObject *__pyx_n_s_CRISPResso2_CRISPRessoCOREResour; + PyObject *__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2; PyObject *__pyx_n_u_G; PyObject *__pyx_n_s_ImportError; PyObject *__pyx_n_u_N; + PyObject *__pyx_n_s_ResultsSlotsDict; + PyObject *__pyx_n_s_ResultsSlotsDict___getitem; + PyObject *__pyx_n_s_ResultsSlotsDict___init; + PyObject *__pyx_n_s_ResultsSlotsDict___setitem; PyObject *__pyx_n_u_T; - PyObject *__pyx_n_s__13; + PyObject *__pyx_n_s__20; PyObject *__pyx_kp_u__3; PyObject *__pyx_n_s__4; PyObject *__pyx_kp_u__5; @@ -2828,12 +2939,17 @@ typedef struct { PyObject *__pyx_n_u_all_substitution_positions; PyObject *__pyx_n_s_all_substitution_values; PyObject *__pyx_n_u_all_substitution_values; + PyObject *__pyx_n_u_aln_ref; + PyObject *__pyx_n_u_aln_scores; + PyObject *__pyx_n_u_aln_seq; + PyObject *__pyx_n_u_aln_strand; PyObject *__pyx_n_s_array; PyObject *__pyx_n_s_asyncio_coroutines; PyObject *__pyx_n_s_b; PyObject *__pyx_n_s_bl; PyObject *__pyx_n_s_c; PyObject *__pyx_n_s_calculate_homology; + PyObject *__pyx_n_u_classification; PyObject *__pyx_n_s_cline_in_traceback; PyObject *__pyx_n_s_compile; PyObject *__pyx_n_s_current_insertion_size; @@ -2845,12 +2961,16 @@ typedef struct { PyObject *__pyx_n_u_deletion_positions; PyObject *__pyx_n_s_deletion_sizes; PyObject *__pyx_n_u_deletion_sizes; + PyObject *__pyx_n_u_deletions_outside_window; + PyObject *__pyx_n_s_dict; + PyObject *__pyx_n_s_doc; PyObject *__pyx_n_s_en; PyObject *__pyx_n_s_end_deletion; PyObject *__pyx_n_s_enumerate; PyObject *__pyx_n_s_find_indels_substitutions; PyObject *__pyx_n_s_find_indels_substitutions_legacy; PyObject *__pyx_n_s_finditer; + PyObject *__pyx_n_s_getitem; PyObject *__pyx_n_s_i; PyObject *__pyx_n_s_idx; PyObject *__pyx_n_s_idx_c; @@ -2858,6 +2978,8 @@ typedef struct { PyObject *__pyx_n_s_inc_del_pos; PyObject *__pyx_n_s_include_indx; PyObject *__pyx_n_s_include_indx_set; + PyObject *__pyx_n_s_init; + PyObject *__pyx_n_s_init_subclass; PyObject *__pyx_n_s_initializing; PyObject *__pyx_n_s_insertion_coordinates; PyObject *__pyx_n_u_insertion_coordinates; @@ -2867,10 +2989,19 @@ typedef struct { PyObject *__pyx_n_u_insertion_positions; PyObject *__pyx_n_s_insertion_sizes; PyObject *__pyx_n_u_insertion_sizes; + PyObject *__pyx_n_u_insertions_outside_window; PyObject *__pyx_n_s_intersection; + PyObject *__pyx_n_u_irregular_ends; PyObject *__pyx_n_s_is_coroutine; + PyObject *__pyx_n_s_items; + PyObject *__pyx_n_s_key; + PyObject *__pyx_n_s_kwargs; PyObject *__pyx_n_s_l; PyObject *__pyx_n_s_main; + PyObject *__pyx_n_s_metaclass; + PyObject *__pyx_n_u_mods_in_window; + PyObject *__pyx_n_u_mods_outside_window; + PyObject *__pyx_n_s_module; PyObject *__pyx_n_s_name; PyObject *__pyx_n_s_np; PyObject *__pyx_n_s_nucSet; @@ -2878,18 +3009,25 @@ typedef struct { PyObject *__pyx_kp_u_numpy__core_multiarray_failed_to; PyObject *__pyx_kp_u_numpy__core_umath_failed_to_impo; PyObject *__pyx_n_s_p; + PyObject *__pyx_n_s_prepare; + PyObject *__pyx_n_s_qualname; PyObject *__pyx_n_s_range; PyObject *__pyx_n_s_re; PyObject *__pyx_n_s_re_find_indels; PyObject *__pyx_n_s_read_seq_al; PyObject *__pyx_n_s_ref_en; + PyObject *__pyx_n_u_ref_name; PyObject *__pyx_n_s_ref_positions; PyObject *__pyx_n_u_ref_positions; PyObject *__pyx_n_s_ref_seq_al; PyObject *__pyx_n_s_ref_st; PyObject *__pyx_n_s_retDict; PyObject *__pyx_n_s_score; + PyObject *__pyx_n_s_self; PyObject *__pyx_n_s_seq_len; + PyObject *__pyx_n_s_set_name; + PyObject *__pyx_n_s_setitem; + PyObject *__pyx_n_s_slots; PyObject *__pyx_n_s_span; PyObject *__pyx_n_s_spec; PyObject *__pyx_n_s_st; @@ -2902,19 +3040,30 @@ typedef struct { PyObject *__pyx_n_u_substitution_positions; PyObject *__pyx_n_s_substitution_values; PyObject *__pyx_n_u_substitution_values; + PyObject *__pyx_n_u_substitutions_outside_window; PyObject *__pyx_n_s_sum; + PyObject *__pyx_n_s_super; PyObject *__pyx_n_s_test; + PyObject *__pyx_n_u_total_mods; + PyObject *__pyx_n_s_value; PyObject *__pyx_int_0; PyObject *__pyx_int_neg_1; PyObject *__pyx_tuple_; PyObject *__pyx_tuple__2; PyObject *__pyx_tuple__6; PyObject *__pyx_tuple__7; - PyObject *__pyx_tuple__9; - PyObject *__pyx_tuple__11; - PyObject *__pyx_codeobj__8; - PyObject *__pyx_codeobj__10; - PyObject *__pyx_codeobj__12; + PyObject *__pyx_tuple__8; + PyObject *__pyx_tuple__10; + PyObject *__pyx_tuple__12; + PyObject *__pyx_tuple__14; + PyObject *__pyx_tuple__16; + PyObject *__pyx_tuple__18; + PyObject *__pyx_codeobj__9; + PyObject *__pyx_codeobj__11; + PyObject *__pyx_codeobj__13; + PyObject *__pyx_codeobj__15; + PyObject *__pyx_codeobj__17; + PyObject *__pyx_codeobj__19; } __pyx_mstate; #if CYTHON_USE_MODULE_STATE @@ -2975,13 +3124,17 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_ptype_5numpy_ufunc); Py_CLEAR(clear_module_state->__pyx_n_u_A); Py_CLEAR(clear_module_state->__pyx_n_u_C); - Py_CLEAR(clear_module_state->__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour); - Py_CLEAR(clear_module_state->__pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2); + Py_CLEAR(clear_module_state->__pyx_n_s_CRISPResso2_CRISPRessoCOREResour); + Py_CLEAR(clear_module_state->__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2); Py_CLEAR(clear_module_state->__pyx_n_u_G); Py_CLEAR(clear_module_state->__pyx_n_s_ImportError); Py_CLEAR(clear_module_state->__pyx_n_u_N); + Py_CLEAR(clear_module_state->__pyx_n_s_ResultsSlotsDict); + Py_CLEAR(clear_module_state->__pyx_n_s_ResultsSlotsDict___getitem); + Py_CLEAR(clear_module_state->__pyx_n_s_ResultsSlotsDict___init); + Py_CLEAR(clear_module_state->__pyx_n_s_ResultsSlotsDict___setitem); Py_CLEAR(clear_module_state->__pyx_n_u_T); - Py_CLEAR(clear_module_state->__pyx_n_s__13); + Py_CLEAR(clear_module_state->__pyx_n_s__20); Py_CLEAR(clear_module_state->__pyx_kp_u__3); Py_CLEAR(clear_module_state->__pyx_n_s__4); Py_CLEAR(clear_module_state->__pyx_kp_u__5); @@ -2999,12 +3152,17 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_u_all_substitution_positions); Py_CLEAR(clear_module_state->__pyx_n_s_all_substitution_values); Py_CLEAR(clear_module_state->__pyx_n_u_all_substitution_values); + Py_CLEAR(clear_module_state->__pyx_n_u_aln_ref); + Py_CLEAR(clear_module_state->__pyx_n_u_aln_scores); + Py_CLEAR(clear_module_state->__pyx_n_u_aln_seq); + Py_CLEAR(clear_module_state->__pyx_n_u_aln_strand); Py_CLEAR(clear_module_state->__pyx_n_s_array); Py_CLEAR(clear_module_state->__pyx_n_s_asyncio_coroutines); Py_CLEAR(clear_module_state->__pyx_n_s_b); Py_CLEAR(clear_module_state->__pyx_n_s_bl); Py_CLEAR(clear_module_state->__pyx_n_s_c); Py_CLEAR(clear_module_state->__pyx_n_s_calculate_homology); + Py_CLEAR(clear_module_state->__pyx_n_u_classification); Py_CLEAR(clear_module_state->__pyx_n_s_cline_in_traceback); Py_CLEAR(clear_module_state->__pyx_n_s_compile); Py_CLEAR(clear_module_state->__pyx_n_s_current_insertion_size); @@ -3016,12 +3174,16 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_u_deletion_positions); Py_CLEAR(clear_module_state->__pyx_n_s_deletion_sizes); Py_CLEAR(clear_module_state->__pyx_n_u_deletion_sizes); + Py_CLEAR(clear_module_state->__pyx_n_u_deletions_outside_window); + Py_CLEAR(clear_module_state->__pyx_n_s_dict); + Py_CLEAR(clear_module_state->__pyx_n_s_doc); Py_CLEAR(clear_module_state->__pyx_n_s_en); Py_CLEAR(clear_module_state->__pyx_n_s_end_deletion); Py_CLEAR(clear_module_state->__pyx_n_s_enumerate); Py_CLEAR(clear_module_state->__pyx_n_s_find_indels_substitutions); Py_CLEAR(clear_module_state->__pyx_n_s_find_indels_substitutions_legacy); Py_CLEAR(clear_module_state->__pyx_n_s_finditer); + Py_CLEAR(clear_module_state->__pyx_n_s_getitem); Py_CLEAR(clear_module_state->__pyx_n_s_i); Py_CLEAR(clear_module_state->__pyx_n_s_idx); Py_CLEAR(clear_module_state->__pyx_n_s_idx_c); @@ -3029,6 +3191,8 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_s_inc_del_pos); Py_CLEAR(clear_module_state->__pyx_n_s_include_indx); Py_CLEAR(clear_module_state->__pyx_n_s_include_indx_set); + Py_CLEAR(clear_module_state->__pyx_n_s_init); + Py_CLEAR(clear_module_state->__pyx_n_s_init_subclass); Py_CLEAR(clear_module_state->__pyx_n_s_initializing); Py_CLEAR(clear_module_state->__pyx_n_s_insertion_coordinates); Py_CLEAR(clear_module_state->__pyx_n_u_insertion_coordinates); @@ -3038,10 +3202,19 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_u_insertion_positions); Py_CLEAR(clear_module_state->__pyx_n_s_insertion_sizes); Py_CLEAR(clear_module_state->__pyx_n_u_insertion_sizes); + Py_CLEAR(clear_module_state->__pyx_n_u_insertions_outside_window); Py_CLEAR(clear_module_state->__pyx_n_s_intersection); + Py_CLEAR(clear_module_state->__pyx_n_u_irregular_ends); Py_CLEAR(clear_module_state->__pyx_n_s_is_coroutine); + Py_CLEAR(clear_module_state->__pyx_n_s_items); + Py_CLEAR(clear_module_state->__pyx_n_s_key); + Py_CLEAR(clear_module_state->__pyx_n_s_kwargs); Py_CLEAR(clear_module_state->__pyx_n_s_l); Py_CLEAR(clear_module_state->__pyx_n_s_main); + Py_CLEAR(clear_module_state->__pyx_n_s_metaclass); + Py_CLEAR(clear_module_state->__pyx_n_u_mods_in_window); + Py_CLEAR(clear_module_state->__pyx_n_u_mods_outside_window); + Py_CLEAR(clear_module_state->__pyx_n_s_module); Py_CLEAR(clear_module_state->__pyx_n_s_name); Py_CLEAR(clear_module_state->__pyx_n_s_np); Py_CLEAR(clear_module_state->__pyx_n_s_nucSet); @@ -3049,18 +3222,25 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_kp_u_numpy__core_multiarray_failed_to); Py_CLEAR(clear_module_state->__pyx_kp_u_numpy__core_umath_failed_to_impo); Py_CLEAR(clear_module_state->__pyx_n_s_p); + Py_CLEAR(clear_module_state->__pyx_n_s_prepare); + Py_CLEAR(clear_module_state->__pyx_n_s_qualname); Py_CLEAR(clear_module_state->__pyx_n_s_range); Py_CLEAR(clear_module_state->__pyx_n_s_re); Py_CLEAR(clear_module_state->__pyx_n_s_re_find_indels); Py_CLEAR(clear_module_state->__pyx_n_s_read_seq_al); Py_CLEAR(clear_module_state->__pyx_n_s_ref_en); + Py_CLEAR(clear_module_state->__pyx_n_u_ref_name); Py_CLEAR(clear_module_state->__pyx_n_s_ref_positions); Py_CLEAR(clear_module_state->__pyx_n_u_ref_positions); Py_CLEAR(clear_module_state->__pyx_n_s_ref_seq_al); Py_CLEAR(clear_module_state->__pyx_n_s_ref_st); Py_CLEAR(clear_module_state->__pyx_n_s_retDict); Py_CLEAR(clear_module_state->__pyx_n_s_score); + Py_CLEAR(clear_module_state->__pyx_n_s_self); Py_CLEAR(clear_module_state->__pyx_n_s_seq_len); + Py_CLEAR(clear_module_state->__pyx_n_s_set_name); + Py_CLEAR(clear_module_state->__pyx_n_s_setitem); + Py_CLEAR(clear_module_state->__pyx_n_s_slots); Py_CLEAR(clear_module_state->__pyx_n_s_span); Py_CLEAR(clear_module_state->__pyx_n_s_spec); Py_CLEAR(clear_module_state->__pyx_n_s_st); @@ -3073,19 +3253,30 @@ static int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_n_u_substitution_positions); Py_CLEAR(clear_module_state->__pyx_n_s_substitution_values); Py_CLEAR(clear_module_state->__pyx_n_u_substitution_values); + Py_CLEAR(clear_module_state->__pyx_n_u_substitutions_outside_window); Py_CLEAR(clear_module_state->__pyx_n_s_sum); + Py_CLEAR(clear_module_state->__pyx_n_s_super); Py_CLEAR(clear_module_state->__pyx_n_s_test); + Py_CLEAR(clear_module_state->__pyx_n_u_total_mods); + Py_CLEAR(clear_module_state->__pyx_n_s_value); Py_CLEAR(clear_module_state->__pyx_int_0); Py_CLEAR(clear_module_state->__pyx_int_neg_1); Py_CLEAR(clear_module_state->__pyx_tuple_); Py_CLEAR(clear_module_state->__pyx_tuple__2); Py_CLEAR(clear_module_state->__pyx_tuple__6); Py_CLEAR(clear_module_state->__pyx_tuple__7); - Py_CLEAR(clear_module_state->__pyx_tuple__9); - Py_CLEAR(clear_module_state->__pyx_tuple__11); - Py_CLEAR(clear_module_state->__pyx_codeobj__8); - Py_CLEAR(clear_module_state->__pyx_codeobj__10); - Py_CLEAR(clear_module_state->__pyx_codeobj__12); + Py_CLEAR(clear_module_state->__pyx_tuple__8); + Py_CLEAR(clear_module_state->__pyx_tuple__10); + Py_CLEAR(clear_module_state->__pyx_tuple__12); + Py_CLEAR(clear_module_state->__pyx_tuple__14); + Py_CLEAR(clear_module_state->__pyx_tuple__16); + Py_CLEAR(clear_module_state->__pyx_tuple__18); + Py_CLEAR(clear_module_state->__pyx_codeobj__9); + Py_CLEAR(clear_module_state->__pyx_codeobj__11); + Py_CLEAR(clear_module_state->__pyx_codeobj__13); + Py_CLEAR(clear_module_state->__pyx_codeobj__15); + Py_CLEAR(clear_module_state->__pyx_codeobj__17); + Py_CLEAR(clear_module_state->__pyx_codeobj__19); return 0; } #endif @@ -3124,13 +3315,17 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_ptype_5numpy_ufunc); Py_VISIT(traverse_module_state->__pyx_n_u_A); Py_VISIT(traverse_module_state->__pyx_n_u_C); - Py_VISIT(traverse_module_state->__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour); - Py_VISIT(traverse_module_state->__pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2); + Py_VISIT(traverse_module_state->__pyx_n_s_CRISPResso2_CRISPRessoCOREResour); + Py_VISIT(traverse_module_state->__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2); Py_VISIT(traverse_module_state->__pyx_n_u_G); Py_VISIT(traverse_module_state->__pyx_n_s_ImportError); Py_VISIT(traverse_module_state->__pyx_n_u_N); + Py_VISIT(traverse_module_state->__pyx_n_s_ResultsSlotsDict); + Py_VISIT(traverse_module_state->__pyx_n_s_ResultsSlotsDict___getitem); + Py_VISIT(traverse_module_state->__pyx_n_s_ResultsSlotsDict___init); + Py_VISIT(traverse_module_state->__pyx_n_s_ResultsSlotsDict___setitem); Py_VISIT(traverse_module_state->__pyx_n_u_T); - Py_VISIT(traverse_module_state->__pyx_n_s__13); + Py_VISIT(traverse_module_state->__pyx_n_s__20); Py_VISIT(traverse_module_state->__pyx_kp_u__3); Py_VISIT(traverse_module_state->__pyx_n_s__4); Py_VISIT(traverse_module_state->__pyx_kp_u__5); @@ -3148,12 +3343,17 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_u_all_substitution_positions); Py_VISIT(traverse_module_state->__pyx_n_s_all_substitution_values); Py_VISIT(traverse_module_state->__pyx_n_u_all_substitution_values); + Py_VISIT(traverse_module_state->__pyx_n_u_aln_ref); + Py_VISIT(traverse_module_state->__pyx_n_u_aln_scores); + Py_VISIT(traverse_module_state->__pyx_n_u_aln_seq); + Py_VISIT(traverse_module_state->__pyx_n_u_aln_strand); Py_VISIT(traverse_module_state->__pyx_n_s_array); Py_VISIT(traverse_module_state->__pyx_n_s_asyncio_coroutines); Py_VISIT(traverse_module_state->__pyx_n_s_b); Py_VISIT(traverse_module_state->__pyx_n_s_bl); Py_VISIT(traverse_module_state->__pyx_n_s_c); Py_VISIT(traverse_module_state->__pyx_n_s_calculate_homology); + Py_VISIT(traverse_module_state->__pyx_n_u_classification); Py_VISIT(traverse_module_state->__pyx_n_s_cline_in_traceback); Py_VISIT(traverse_module_state->__pyx_n_s_compile); Py_VISIT(traverse_module_state->__pyx_n_s_current_insertion_size); @@ -3165,12 +3365,16 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_u_deletion_positions); Py_VISIT(traverse_module_state->__pyx_n_s_deletion_sizes); Py_VISIT(traverse_module_state->__pyx_n_u_deletion_sizes); + Py_VISIT(traverse_module_state->__pyx_n_u_deletions_outside_window); + Py_VISIT(traverse_module_state->__pyx_n_s_dict); + Py_VISIT(traverse_module_state->__pyx_n_s_doc); Py_VISIT(traverse_module_state->__pyx_n_s_en); Py_VISIT(traverse_module_state->__pyx_n_s_end_deletion); Py_VISIT(traverse_module_state->__pyx_n_s_enumerate); Py_VISIT(traverse_module_state->__pyx_n_s_find_indels_substitutions); Py_VISIT(traverse_module_state->__pyx_n_s_find_indels_substitutions_legacy); Py_VISIT(traverse_module_state->__pyx_n_s_finditer); + Py_VISIT(traverse_module_state->__pyx_n_s_getitem); Py_VISIT(traverse_module_state->__pyx_n_s_i); Py_VISIT(traverse_module_state->__pyx_n_s_idx); Py_VISIT(traverse_module_state->__pyx_n_s_idx_c); @@ -3178,6 +3382,8 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_s_inc_del_pos); Py_VISIT(traverse_module_state->__pyx_n_s_include_indx); Py_VISIT(traverse_module_state->__pyx_n_s_include_indx_set); + Py_VISIT(traverse_module_state->__pyx_n_s_init); + Py_VISIT(traverse_module_state->__pyx_n_s_init_subclass); Py_VISIT(traverse_module_state->__pyx_n_s_initializing); Py_VISIT(traverse_module_state->__pyx_n_s_insertion_coordinates); Py_VISIT(traverse_module_state->__pyx_n_u_insertion_coordinates); @@ -3187,10 +3393,19 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_u_insertion_positions); Py_VISIT(traverse_module_state->__pyx_n_s_insertion_sizes); Py_VISIT(traverse_module_state->__pyx_n_u_insertion_sizes); + Py_VISIT(traverse_module_state->__pyx_n_u_insertions_outside_window); Py_VISIT(traverse_module_state->__pyx_n_s_intersection); + Py_VISIT(traverse_module_state->__pyx_n_u_irregular_ends); Py_VISIT(traverse_module_state->__pyx_n_s_is_coroutine); + Py_VISIT(traverse_module_state->__pyx_n_s_items); + Py_VISIT(traverse_module_state->__pyx_n_s_key); + Py_VISIT(traverse_module_state->__pyx_n_s_kwargs); Py_VISIT(traverse_module_state->__pyx_n_s_l); Py_VISIT(traverse_module_state->__pyx_n_s_main); + Py_VISIT(traverse_module_state->__pyx_n_s_metaclass); + Py_VISIT(traverse_module_state->__pyx_n_u_mods_in_window); + Py_VISIT(traverse_module_state->__pyx_n_u_mods_outside_window); + Py_VISIT(traverse_module_state->__pyx_n_s_module); Py_VISIT(traverse_module_state->__pyx_n_s_name); Py_VISIT(traverse_module_state->__pyx_n_s_np); Py_VISIT(traverse_module_state->__pyx_n_s_nucSet); @@ -3198,18 +3413,25 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_kp_u_numpy__core_multiarray_failed_to); Py_VISIT(traverse_module_state->__pyx_kp_u_numpy__core_umath_failed_to_impo); Py_VISIT(traverse_module_state->__pyx_n_s_p); + Py_VISIT(traverse_module_state->__pyx_n_s_prepare); + Py_VISIT(traverse_module_state->__pyx_n_s_qualname); Py_VISIT(traverse_module_state->__pyx_n_s_range); Py_VISIT(traverse_module_state->__pyx_n_s_re); Py_VISIT(traverse_module_state->__pyx_n_s_re_find_indels); Py_VISIT(traverse_module_state->__pyx_n_s_read_seq_al); Py_VISIT(traverse_module_state->__pyx_n_s_ref_en); + Py_VISIT(traverse_module_state->__pyx_n_u_ref_name); Py_VISIT(traverse_module_state->__pyx_n_s_ref_positions); Py_VISIT(traverse_module_state->__pyx_n_u_ref_positions); Py_VISIT(traverse_module_state->__pyx_n_s_ref_seq_al); Py_VISIT(traverse_module_state->__pyx_n_s_ref_st); Py_VISIT(traverse_module_state->__pyx_n_s_retDict); Py_VISIT(traverse_module_state->__pyx_n_s_score); + Py_VISIT(traverse_module_state->__pyx_n_s_self); Py_VISIT(traverse_module_state->__pyx_n_s_seq_len); + Py_VISIT(traverse_module_state->__pyx_n_s_set_name); + Py_VISIT(traverse_module_state->__pyx_n_s_setitem); + Py_VISIT(traverse_module_state->__pyx_n_s_slots); Py_VISIT(traverse_module_state->__pyx_n_s_span); Py_VISIT(traverse_module_state->__pyx_n_s_spec); Py_VISIT(traverse_module_state->__pyx_n_s_st); @@ -3222,19 +3444,30 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { Py_VISIT(traverse_module_state->__pyx_n_u_substitution_positions); Py_VISIT(traverse_module_state->__pyx_n_s_substitution_values); Py_VISIT(traverse_module_state->__pyx_n_u_substitution_values); + Py_VISIT(traverse_module_state->__pyx_n_u_substitutions_outside_window); Py_VISIT(traverse_module_state->__pyx_n_s_sum); + Py_VISIT(traverse_module_state->__pyx_n_s_super); Py_VISIT(traverse_module_state->__pyx_n_s_test); + Py_VISIT(traverse_module_state->__pyx_n_u_total_mods); + Py_VISIT(traverse_module_state->__pyx_n_s_value); Py_VISIT(traverse_module_state->__pyx_int_0); Py_VISIT(traverse_module_state->__pyx_int_neg_1); Py_VISIT(traverse_module_state->__pyx_tuple_); Py_VISIT(traverse_module_state->__pyx_tuple__2); Py_VISIT(traverse_module_state->__pyx_tuple__6); Py_VISIT(traverse_module_state->__pyx_tuple__7); - Py_VISIT(traverse_module_state->__pyx_tuple__9); - Py_VISIT(traverse_module_state->__pyx_tuple__11); - Py_VISIT(traverse_module_state->__pyx_codeobj__8); - Py_VISIT(traverse_module_state->__pyx_codeobj__10); - Py_VISIT(traverse_module_state->__pyx_codeobj__12); + Py_VISIT(traverse_module_state->__pyx_tuple__8); + Py_VISIT(traverse_module_state->__pyx_tuple__10); + Py_VISIT(traverse_module_state->__pyx_tuple__12); + Py_VISIT(traverse_module_state->__pyx_tuple__14); + Py_VISIT(traverse_module_state->__pyx_tuple__16); + Py_VISIT(traverse_module_state->__pyx_tuple__18); + Py_VISIT(traverse_module_state->__pyx_codeobj__9); + Py_VISIT(traverse_module_state->__pyx_codeobj__11); + Py_VISIT(traverse_module_state->__pyx_codeobj__13); + Py_VISIT(traverse_module_state->__pyx_codeobj__15); + Py_VISIT(traverse_module_state->__pyx_codeobj__17); + Py_VISIT(traverse_module_state->__pyx_codeobj__19); return 0; } #endif @@ -3303,13 +3536,17 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #endif #define __pyx_n_u_A __pyx_mstate_global->__pyx_n_u_A #define __pyx_n_u_C __pyx_mstate_global->__pyx_n_u_C -#define __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour __pyx_mstate_global->__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour -#define __pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2 __pyx_mstate_global->__pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2 +#define __pyx_n_s_CRISPResso2_CRISPRessoCOREResour __pyx_mstate_global->__pyx_n_s_CRISPResso2_CRISPRessoCOREResour +#define __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2 __pyx_mstate_global->__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2 #define __pyx_n_u_G __pyx_mstate_global->__pyx_n_u_G #define __pyx_n_s_ImportError __pyx_mstate_global->__pyx_n_s_ImportError #define __pyx_n_u_N __pyx_mstate_global->__pyx_n_u_N +#define __pyx_n_s_ResultsSlotsDict __pyx_mstate_global->__pyx_n_s_ResultsSlotsDict +#define __pyx_n_s_ResultsSlotsDict___getitem __pyx_mstate_global->__pyx_n_s_ResultsSlotsDict___getitem +#define __pyx_n_s_ResultsSlotsDict___init __pyx_mstate_global->__pyx_n_s_ResultsSlotsDict___init +#define __pyx_n_s_ResultsSlotsDict___setitem __pyx_mstate_global->__pyx_n_s_ResultsSlotsDict___setitem #define __pyx_n_u_T __pyx_mstate_global->__pyx_n_u_T -#define __pyx_n_s__13 __pyx_mstate_global->__pyx_n_s__13 +#define __pyx_n_s__20 __pyx_mstate_global->__pyx_n_s__20 #define __pyx_kp_u__3 __pyx_mstate_global->__pyx_kp_u__3 #define __pyx_n_s__4 __pyx_mstate_global->__pyx_n_s__4 #define __pyx_kp_u__5 __pyx_mstate_global->__pyx_kp_u__5 @@ -3327,12 +3564,17 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_u_all_substitution_positions __pyx_mstate_global->__pyx_n_u_all_substitution_positions #define __pyx_n_s_all_substitution_values __pyx_mstate_global->__pyx_n_s_all_substitution_values #define __pyx_n_u_all_substitution_values __pyx_mstate_global->__pyx_n_u_all_substitution_values +#define __pyx_n_u_aln_ref __pyx_mstate_global->__pyx_n_u_aln_ref +#define __pyx_n_u_aln_scores __pyx_mstate_global->__pyx_n_u_aln_scores +#define __pyx_n_u_aln_seq __pyx_mstate_global->__pyx_n_u_aln_seq +#define __pyx_n_u_aln_strand __pyx_mstate_global->__pyx_n_u_aln_strand #define __pyx_n_s_array __pyx_mstate_global->__pyx_n_s_array #define __pyx_n_s_asyncio_coroutines __pyx_mstate_global->__pyx_n_s_asyncio_coroutines #define __pyx_n_s_b __pyx_mstate_global->__pyx_n_s_b #define __pyx_n_s_bl __pyx_mstate_global->__pyx_n_s_bl #define __pyx_n_s_c __pyx_mstate_global->__pyx_n_s_c #define __pyx_n_s_calculate_homology __pyx_mstate_global->__pyx_n_s_calculate_homology +#define __pyx_n_u_classification __pyx_mstate_global->__pyx_n_u_classification #define __pyx_n_s_cline_in_traceback __pyx_mstate_global->__pyx_n_s_cline_in_traceback #define __pyx_n_s_compile __pyx_mstate_global->__pyx_n_s_compile #define __pyx_n_s_current_insertion_size __pyx_mstate_global->__pyx_n_s_current_insertion_size @@ -3344,12 +3586,16 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_u_deletion_positions __pyx_mstate_global->__pyx_n_u_deletion_positions #define __pyx_n_s_deletion_sizes __pyx_mstate_global->__pyx_n_s_deletion_sizes #define __pyx_n_u_deletion_sizes __pyx_mstate_global->__pyx_n_u_deletion_sizes +#define __pyx_n_u_deletions_outside_window __pyx_mstate_global->__pyx_n_u_deletions_outside_window +#define __pyx_n_s_dict __pyx_mstate_global->__pyx_n_s_dict +#define __pyx_n_s_doc __pyx_mstate_global->__pyx_n_s_doc #define __pyx_n_s_en __pyx_mstate_global->__pyx_n_s_en #define __pyx_n_s_end_deletion __pyx_mstate_global->__pyx_n_s_end_deletion #define __pyx_n_s_enumerate __pyx_mstate_global->__pyx_n_s_enumerate #define __pyx_n_s_find_indels_substitutions __pyx_mstate_global->__pyx_n_s_find_indels_substitutions #define __pyx_n_s_find_indels_substitutions_legacy __pyx_mstate_global->__pyx_n_s_find_indels_substitutions_legacy #define __pyx_n_s_finditer __pyx_mstate_global->__pyx_n_s_finditer +#define __pyx_n_s_getitem __pyx_mstate_global->__pyx_n_s_getitem #define __pyx_n_s_i __pyx_mstate_global->__pyx_n_s_i #define __pyx_n_s_idx __pyx_mstate_global->__pyx_n_s_idx #define __pyx_n_s_idx_c __pyx_mstate_global->__pyx_n_s_idx_c @@ -3357,6 +3603,8 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_s_inc_del_pos __pyx_mstate_global->__pyx_n_s_inc_del_pos #define __pyx_n_s_include_indx __pyx_mstate_global->__pyx_n_s_include_indx #define __pyx_n_s_include_indx_set __pyx_mstate_global->__pyx_n_s_include_indx_set +#define __pyx_n_s_init __pyx_mstate_global->__pyx_n_s_init +#define __pyx_n_s_init_subclass __pyx_mstate_global->__pyx_n_s_init_subclass #define __pyx_n_s_initializing __pyx_mstate_global->__pyx_n_s_initializing #define __pyx_n_s_insertion_coordinates __pyx_mstate_global->__pyx_n_s_insertion_coordinates #define __pyx_n_u_insertion_coordinates __pyx_mstate_global->__pyx_n_u_insertion_coordinates @@ -3366,10 +3614,19 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_u_insertion_positions __pyx_mstate_global->__pyx_n_u_insertion_positions #define __pyx_n_s_insertion_sizes __pyx_mstate_global->__pyx_n_s_insertion_sizes #define __pyx_n_u_insertion_sizes __pyx_mstate_global->__pyx_n_u_insertion_sizes +#define __pyx_n_u_insertions_outside_window __pyx_mstate_global->__pyx_n_u_insertions_outside_window #define __pyx_n_s_intersection __pyx_mstate_global->__pyx_n_s_intersection +#define __pyx_n_u_irregular_ends __pyx_mstate_global->__pyx_n_u_irregular_ends #define __pyx_n_s_is_coroutine __pyx_mstate_global->__pyx_n_s_is_coroutine +#define __pyx_n_s_items __pyx_mstate_global->__pyx_n_s_items +#define __pyx_n_s_key __pyx_mstate_global->__pyx_n_s_key +#define __pyx_n_s_kwargs __pyx_mstate_global->__pyx_n_s_kwargs #define __pyx_n_s_l __pyx_mstate_global->__pyx_n_s_l #define __pyx_n_s_main __pyx_mstate_global->__pyx_n_s_main +#define __pyx_n_s_metaclass __pyx_mstate_global->__pyx_n_s_metaclass +#define __pyx_n_u_mods_in_window __pyx_mstate_global->__pyx_n_u_mods_in_window +#define __pyx_n_u_mods_outside_window __pyx_mstate_global->__pyx_n_u_mods_outside_window +#define __pyx_n_s_module __pyx_mstate_global->__pyx_n_s_module #define __pyx_n_s_name __pyx_mstate_global->__pyx_n_s_name #define __pyx_n_s_np __pyx_mstate_global->__pyx_n_s_np #define __pyx_n_s_nucSet __pyx_mstate_global->__pyx_n_s_nucSet @@ -3377,18 +3634,25 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_kp_u_numpy__core_multiarray_failed_to __pyx_mstate_global->__pyx_kp_u_numpy__core_multiarray_failed_to #define __pyx_kp_u_numpy__core_umath_failed_to_impo __pyx_mstate_global->__pyx_kp_u_numpy__core_umath_failed_to_impo #define __pyx_n_s_p __pyx_mstate_global->__pyx_n_s_p +#define __pyx_n_s_prepare __pyx_mstate_global->__pyx_n_s_prepare +#define __pyx_n_s_qualname __pyx_mstate_global->__pyx_n_s_qualname #define __pyx_n_s_range __pyx_mstate_global->__pyx_n_s_range #define __pyx_n_s_re __pyx_mstate_global->__pyx_n_s_re #define __pyx_n_s_re_find_indels __pyx_mstate_global->__pyx_n_s_re_find_indels #define __pyx_n_s_read_seq_al __pyx_mstate_global->__pyx_n_s_read_seq_al #define __pyx_n_s_ref_en __pyx_mstate_global->__pyx_n_s_ref_en +#define __pyx_n_u_ref_name __pyx_mstate_global->__pyx_n_u_ref_name #define __pyx_n_s_ref_positions __pyx_mstate_global->__pyx_n_s_ref_positions #define __pyx_n_u_ref_positions __pyx_mstate_global->__pyx_n_u_ref_positions #define __pyx_n_s_ref_seq_al __pyx_mstate_global->__pyx_n_s_ref_seq_al #define __pyx_n_s_ref_st __pyx_mstate_global->__pyx_n_s_ref_st #define __pyx_n_s_retDict __pyx_mstate_global->__pyx_n_s_retDict #define __pyx_n_s_score __pyx_mstate_global->__pyx_n_s_score +#define __pyx_n_s_self __pyx_mstate_global->__pyx_n_s_self #define __pyx_n_s_seq_len __pyx_mstate_global->__pyx_n_s_seq_len +#define __pyx_n_s_set_name __pyx_mstate_global->__pyx_n_s_set_name +#define __pyx_n_s_setitem __pyx_mstate_global->__pyx_n_s_setitem +#define __pyx_n_s_slots __pyx_mstate_global->__pyx_n_s_slots #define __pyx_n_s_span __pyx_mstate_global->__pyx_n_s_span #define __pyx_n_s_spec __pyx_mstate_global->__pyx_n_s_spec #define __pyx_n_s_st __pyx_mstate_global->__pyx_n_s_st @@ -3401,48 +3665,59 @@ static int __pyx_m_traverse(PyObject *m, visitproc visit, void *arg) { #define __pyx_n_u_substitution_positions __pyx_mstate_global->__pyx_n_u_substitution_positions #define __pyx_n_s_substitution_values __pyx_mstate_global->__pyx_n_s_substitution_values #define __pyx_n_u_substitution_values __pyx_mstate_global->__pyx_n_u_substitution_values +#define __pyx_n_u_substitutions_outside_window __pyx_mstate_global->__pyx_n_u_substitutions_outside_window #define __pyx_n_s_sum __pyx_mstate_global->__pyx_n_s_sum +#define __pyx_n_s_super __pyx_mstate_global->__pyx_n_s_super #define __pyx_n_s_test __pyx_mstate_global->__pyx_n_s_test +#define __pyx_n_u_total_mods __pyx_mstate_global->__pyx_n_u_total_mods +#define __pyx_n_s_value __pyx_mstate_global->__pyx_n_s_value #define __pyx_int_0 __pyx_mstate_global->__pyx_int_0 #define __pyx_int_neg_1 __pyx_mstate_global->__pyx_int_neg_1 #define __pyx_tuple_ __pyx_mstate_global->__pyx_tuple_ #define __pyx_tuple__2 __pyx_mstate_global->__pyx_tuple__2 #define __pyx_tuple__6 __pyx_mstate_global->__pyx_tuple__6 #define __pyx_tuple__7 __pyx_mstate_global->__pyx_tuple__7 -#define __pyx_tuple__9 __pyx_mstate_global->__pyx_tuple__9 -#define __pyx_tuple__11 __pyx_mstate_global->__pyx_tuple__11 -#define __pyx_codeobj__8 __pyx_mstate_global->__pyx_codeobj__8 -#define __pyx_codeobj__10 __pyx_mstate_global->__pyx_codeobj__10 -#define __pyx_codeobj__12 __pyx_mstate_global->__pyx_codeobj__12 +#define __pyx_tuple__8 __pyx_mstate_global->__pyx_tuple__8 +#define __pyx_tuple__10 __pyx_mstate_global->__pyx_tuple__10 +#define __pyx_tuple__12 __pyx_mstate_global->__pyx_tuple__12 +#define __pyx_tuple__14 __pyx_mstate_global->__pyx_tuple__14 +#define __pyx_tuple__16 __pyx_mstate_global->__pyx_tuple__16 +#define __pyx_tuple__18 __pyx_mstate_global->__pyx_tuple__18 +#define __pyx_codeobj__9 __pyx_mstate_global->__pyx_codeobj__9 +#define __pyx_codeobj__11 __pyx_mstate_global->__pyx_codeobj__11 +#define __pyx_codeobj__13 __pyx_mstate_global->__pyx_codeobj__13 +#define __pyx_codeobj__15 __pyx_mstate_global->__pyx_codeobj__15 +#define __pyx_codeobj__17 __pyx_mstate_global->__pyx_codeobj__17 +#define __pyx_codeobj__19 __pyx_mstate_global->__pyx_codeobj__19 /* #### Code section: module_code ### */ -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + * * @property * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< * return PyDataType_ELSIZE(self) - * + * */ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":287 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":287 * @property * cdef inline npy_intp itemsize(self) noexcept nogil: * return PyDataType_ELSIZE(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyDataType_ELSIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + * * @property * cdef inline npy_intp itemsize(self) noexcept nogil: # <<<<<<<<<<<<<< * return PyDataType_ELSIZE(self) - * + * */ /* function exit code */ @@ -3450,33 +3725,33 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + * * @property * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< * return PyDataType_ALIGNMENT(self) - * + * */ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":291 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":291 * @property * cdef inline npy_intp alignment(self) noexcept nogil: * return PyDataType_ALIGNMENT(self) # <<<<<<<<<<<<<< - * + * * # Use fields/names with care as they may be NULL. You must check */ __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + * * @property * cdef inline npy_intp alignment(self) noexcept nogil: # <<<<<<<<<<<<<< * return PyDataType_ALIGNMENT(self) - * + * */ /* function exit code */ @@ -3484,12 +3759,12 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 * # for this using PyDataType_HASFIELDS. * @property * cdef inline object fields(self): # <<<<<<<<<<<<<< * return PyDataType_FIELDS(self) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Descr *__pyx_v_self) { @@ -3498,11 +3773,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("fields", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":297 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":297 * @property * cdef inline object fields(self): * return PyDataType_FIELDS(self) # <<<<<<<<<<<<<< - * + * * @property */ __Pyx_XDECREF(__pyx_r); @@ -3511,12 +3786,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc __pyx_r = ((PyObject *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 * # for this using PyDataType_HASFIELDS. * @property * cdef inline object fields(self): # <<<<<<<<<<<<<< * return PyDataType_FIELDS(self) - * + * */ /* function exit code */ @@ -3526,12 +3801,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + * * @property * cdef inline tuple names(self): # <<<<<<<<<<<<<< * return PyDataType_NAMES(self) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr *__pyx_v_self) { @@ -3540,11 +3815,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("names", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":301 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":301 * @property * cdef inline tuple names(self): * return PyDataType_NAMES(self) # <<<<<<<<<<<<<< - * + * * # Use PyDataType_HASSUBARRAY to test whether this field is */ __Pyx_XDECREF(__pyx_r); @@ -3553,12 +3828,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr __pyx_r = ((PyObject*)__pyx_t_1); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + * * @property * cdef inline tuple names(self): # <<<<<<<<<<<<<< * return PyDataType_NAMES(self) - * + * */ /* function exit code */ @@ -3568,33 +3843,33 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 * # this field via the inline helper method PyDataType_SHAPE. * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< * return PyDataType_SUBARRAY(self) - * + * */ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self) { PyArray_ArrayDescr *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":308 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":308 * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: * return PyDataType_SUBARRAY(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyDataType_SUBARRAY(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 * # this field via the inline helper method PyDataType_SHAPE. * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: # <<<<<<<<<<<<<< * return PyDataType_SUBARRAY(self) - * + * */ /* function exit code */ @@ -3602,8 +3877,8 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + * * @property * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< * """The data types flags.""" @@ -3613,18 +3888,18 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self) { npy_uint64 __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":313 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":313 * cdef inline npy_uint64 flags(self) noexcept nogil: * """The data types flags.""" * return PyDataType_FLAGS(self) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyDataType_FLAGS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + * * @property * cdef inline npy_uint64 flags(self) noexcept nogil: # <<<<<<<<<<<<<< * """The data types flags.""" @@ -3636,8 +3911,8 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + * * @property * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< * """The number of arrays that need to be broadcast to the same shape.""" @@ -3647,18 +3922,18 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":325 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":325 * cdef inline int numiter(self) noexcept nogil: * """The number of arrays that need to be broadcast to the same shape.""" * return PyArray_MultiIter_NUMITER(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + * * @property * cdef inline int numiter(self) noexcept nogil: # <<<<<<<<<<<<<< * """The number of arrays that need to be broadcast to the same shape.""" @@ -3670,8 +3945,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """The total broadcasted size.""" @@ -3681,18 +3956,18 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":330 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":330 * cdef inline npy_intp size(self) noexcept nogil: * """The total broadcasted size.""" * return PyArray_MultiIter_SIZE(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """The total broadcasted size.""" @@ -3704,8 +3979,8 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + * * @property * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< * """The current (1-d) index into the broadcasted result.""" @@ -3715,18 +3990,18 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":335 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":335 * cdef inline npy_intp index(self) noexcept nogil: * """The current (1-d) index into the broadcasted result.""" * return PyArray_MultiIter_INDEX(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + * * @property * cdef inline npy_intp index(self) noexcept nogil: # <<<<<<<<<<<<<< * """The current (1-d) index into the broadcasted result.""" @@ -3738,8 +4013,8 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + * * @property * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< * """The number of dimensions in the broadcasted result.""" @@ -3749,18 +4024,18 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":340 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":340 * cdef inline int nd(self) noexcept nogil: * """The number of dimensions in the broadcasted result.""" * return PyArray_MultiIter_NDIM(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + * * @property * cdef inline int nd(self) noexcept nogil: # <<<<<<<<<<<<<< * """The number of dimensions in the broadcasted result.""" @@ -3772,8 +4047,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + * * @property * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< * """The shape of the broadcasted result.""" @@ -3783,18 +4058,18 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":345 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":345 * cdef inline npy_intp* dimensions(self) noexcept nogil: * """The shape of the broadcasted result.""" * return PyArray_MultiIter_DIMS(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + * * @property * cdef inline npy_intp* dimensions(self) noexcept nogil: # <<<<<<<<<<<<<< * """The shape of the broadcasted result.""" @@ -3806,8 +4081,8 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + * * @property * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. @@ -3817,18 +4092,18 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self) { void **__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":351 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":351 * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. * On return, the iterators are adjusted for broadcasting.""" * return PyArray_MultiIter_ITERS(self) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + * * @property * cdef inline void** iters(self) noexcept nogil: # <<<<<<<<<<<<<< * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. @@ -3840,8 +4115,8 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 + * * @property * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a borrowed reference to the object owning the data/memory. @@ -3851,18 +4126,18 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self) { PyObject *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":369 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":369 * """Returns a borrowed reference to the object owning the data/memory. * """ * return PyArray_BASE(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_BASE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 + * * @property * cdef inline PyObject* base(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a borrowed reference to the object owning the data/memory. @@ -3874,8 +4149,8 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 + * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< * """Returns an owned reference to the dtype of the array. @@ -3888,11 +4163,11 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray PyArray_Descr *__pyx_t_1; __Pyx_RefNannySetupContext("descr", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":375 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":375 * """Returns an owned reference to the dtype of the array. * """ * return PyArray_DESCR(self) # <<<<<<<<<<<<<< - * + * * @property */ __Pyx_XDECREF((PyObject *)__pyx_r); @@ -3901,8 +4176,8 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray __pyx_r = ((PyArray_Descr *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 + * * @property * cdef inline dtype descr(self): # <<<<<<<<<<<<<< * """Returns an owned reference to the dtype of the array. @@ -3916,8 +4191,8 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 + * * @property * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the number of dimensions in the array. @@ -3927,18 +4202,18 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":381 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":381 * """Returns the number of dimensions in the array. * """ * return PyArray_NDIM(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 + * * @property * cdef inline int ndim(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the number of dimensions in the array. @@ -3950,8 +4225,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 + * * @property * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the dimensions/shape of the array. @@ -3961,18 +4236,18 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":389 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":389 * Can return NULL for 0-dimensional arrays. * """ * return PyArray_DIMS(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 + * * @property * cdef inline npy_intp *shape(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the dimensions/shape of the array. @@ -3984,8 +4259,8 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 + * * @property * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the strides of the array. @@ -3995,18 +4270,18 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":396 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":396 * The number of elements matches the number of dimensions of the array (ndim). * """ * return PyArray_STRIDES(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_STRIDES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 + * * @property * cdef inline npy_intp *strides(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns a pointer to the strides of the array. @@ -4018,8 +4293,8 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 + * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the total size (in number of elements) of the array. @@ -4029,18 +4304,18 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":402 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":402 * """Returns the total size (in number of elements) of the array. * """ * return PyArray_SIZE(self) # <<<<<<<<<<<<<< - * + * * @property */ __pyx_r = PyArray_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 + * * @property * cdef inline npy_intp size(self) noexcept nogil: # <<<<<<<<<<<<<< * """Returns the total size (in number of elements) of the array. @@ -4052,8 +4327,8 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 + * * @property * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< * """The pointer to the data buffer as a char*. @@ -4063,18 +4338,18 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__pyx_v_self) { char *__pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":411 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":411 * of `PyArray_DATA()` instead, which returns a 'void*'. * """ * return PyArray_BYTES(self) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyArray_BYTES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":405 + * * @property * cdef inline char* data(self) noexcept nogil: # <<<<<<<<<<<<<< * """The pointer to the data buffer as a char*. @@ -4086,12 +4361,12 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 * ctypedef long double complex clongdouble_t - * + * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(1, a) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) { @@ -4103,11 +4378,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":807 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":807 + * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< - * + * * cdef inline object PyArray_MultiIterNew2(a, b): */ __Pyx_XDECREF(__pyx_r); @@ -4117,12 +4392,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":806 * ctypedef long double complex clongdouble_t - * + * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(1, a) - * + * */ /* function exit code */ @@ -4136,12 +4411,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 * return PyArray_MultiIterNew(1, a) - * + * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(2, a, b) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) { @@ -4153,11 +4428,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":810 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":810 + * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< - * + * * cdef inline object PyArray_MultiIterNew3(a, b, c): */ __Pyx_XDECREF(__pyx_r); @@ -4167,12 +4442,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 * return PyArray_MultiIterNew(1, a) - * + * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(2, a, b) - * + * */ /* function exit code */ @@ -4186,12 +4461,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 * return PyArray_MultiIterNew(2, a, b) - * + * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(3, a, b, c) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) { @@ -4203,11 +4478,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":813 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":813 + * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< - * + * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): */ __Pyx_XDECREF(__pyx_r); @@ -4217,12 +4492,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 * return PyArray_MultiIterNew(2, a, b) - * + * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(3, a, b, c) - * + * */ /* function exit code */ @@ -4236,12 +4511,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 * return PyArray_MultiIterNew(3, a, b, c) - * + * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(4, a, b, c, d) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) { @@ -4253,11 +4528,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":816 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":816 + * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< - * + * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): */ __Pyx_XDECREF(__pyx_r); @@ -4267,12 +4542,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 * return PyArray_MultiIterNew(3, a, b, c) - * + * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(4, a, b, c, d) - * + * */ /* function exit code */ @@ -4286,12 +4561,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 * return PyArray_MultiIterNew(4, a, b, c, d) - * + * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(5, a, b, c, d, e) - * + * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) { @@ -4303,11 +4578,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":819 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":819 + * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< - * + * * cdef inline tuple PyDataType_SHAPE(dtype d): */ __Pyx_XDECREF(__pyx_r); @@ -4317,12 +4592,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":818 * return PyArray_MultiIterNew(4, a, b, c, d) - * + * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(5, a, b, c, d, e) - * + * */ /* function exit code */ @@ -4336,9 +4611,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 * return PyArray_MultiIterNew(5, a, b, c, d, e) - * + * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< * if PyDataType_HASSUBARRAY(d): * return d.subarray.shape @@ -4351,8 +4626,8 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ PyObject *__pyx_t_2; __Pyx_RefNannySetupContext("PyDataType_SHAPE", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 + * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< * return d.subarray.shape @@ -4361,7 +4636,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_t_1 = PyDataType_HASSUBARRAY(__pyx_v_d); if (__pyx_t_1) { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":823 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":823 * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): * return d.subarray.shape # <<<<<<<<<<<<<< @@ -4374,8 +4649,8 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_r = ((PyObject*)__pyx_t_2); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":822 + * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< * return d.subarray.shape @@ -4383,12 +4658,12 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":825 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":825 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< - * - * + * + * */ /*else*/ { __Pyx_XDECREF(__pyx_r); @@ -4397,9 +4672,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":821 * return PyArray_MultiIterNew(5, a, b, c, d, e) - * + * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< * if PyDataType_HASSUBARRAY(d): * return d.subarray.shape @@ -4412,9 +4687,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 * int _import_umath() except -1 - * + * * cdef inline void set_array_base(ndarray arr, object base) except *: # <<<<<<<<<<<<<< * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) @@ -4426,27 +4701,27 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1010 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1010 + * * cdef inline void set_array_base(ndarray arr, object base) except *: * Py_INCREF(base) # important to do this before stealing the reference below! # <<<<<<<<<<<<<< * PyArray_SetBaseObject(arr, base) - * + * */ Py_INCREF(__pyx_v_base); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1011 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1011 * cdef inline void set_array_base(ndarray arr, object base) except *: * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) # <<<<<<<<<<<<<< - * + * * cdef inline object get_array_base(ndarray arr): */ __pyx_t_1 = PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_base); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(1, 1011, __pyx_L1_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1009 * int _import_umath() except -1 - * + * * cdef inline void set_array_base(ndarray arr, object base) except *: # <<<<<<<<<<<<<< * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) @@ -4459,9 +4734,9 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_L0:; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 * PyArray_SetBaseObject(arr, base) - * + * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< * base = PyArray_BASE(arr) * if base is NULL: @@ -4474,8 +4749,8 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1014 + * * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) # <<<<<<<<<<<<<< * if base is NULL: @@ -4483,7 +4758,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ __pyx_v_base = PyArray_BASE(__pyx_v_arr); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -4493,18 +4768,18 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = (__pyx_v_base == NULL); if (__pyx_t_1) { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1016 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1016 * base = PyArray_BASE(arr) * if base is NULL: * return None # <<<<<<<<<<<<<< * return base - * + * */ __Pyx_XDECREF(__pyx_r); __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1015 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -4513,11 +4788,11 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1017 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1017 * if base is NULL: * return None * return base # <<<<<<<<<<<<<< - * + * * # Versions of the import_* functions which are more suitable for */ __Pyx_XDECREF(__pyx_r); @@ -4525,9 +4800,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = ((PyObject *)__pyx_v_base); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1013 * PyArray_SetBaseObject(arr, base) - * + * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< * base = PyArray_BASE(arr) * if base is NULL: @@ -4540,7 +4815,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -4564,7 +4839,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_array", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4580,7 +4855,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1023 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1023 * cdef inline int import_array() except -1: * try: * __pyx_import_array() # <<<<<<<<<<<<<< @@ -4589,7 +4864,7 @@ 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, 1023, __pyx_L3_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4603,12 +4878,12 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1024 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1024 * try: * __pyx_import_array() * except Exception: # <<<<<<<<<<<<<< * raise ImportError("numpy._core.multiarray failed to import") - * + * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { @@ -4618,11 +4893,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 * __pyx_import_array() * except Exception: * raise ImportError("numpy._core.multiarray failed to import") # <<<<<<<<<<<<<< - * + * * cdef inline int import_umath() except -1: */ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 1025, __pyx_L5_except_error) @@ -4633,7 +4908,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { } goto __pyx_L5_except_error; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1022 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -4649,7 +4924,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1021 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -4672,9 +4947,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 * raise ImportError("numpy._core.multiarray failed to import") - * + * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4696,8 +4971,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_umath", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4712,7 +4987,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1029 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -4721,8 +4996,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1029, __pyx_L3_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4735,12 +5010,12 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1030 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1030 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< * raise ImportError("numpy._core.umath failed to import") - * + * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { @@ -4750,11 +5025,11 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< - * + * * cdef inline int import_ufunc() except -1: */ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 1031, __pyx_L5_except_error) @@ -4765,8 +5040,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { } goto __pyx_L5_except_error; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1028 + * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4781,9 +5056,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1027 * raise ImportError("numpy._core.multiarray failed to import") - * + * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4804,9 +5079,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 * raise ImportError("numpy._core.umath failed to import") - * + * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4828,8 +5103,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_ufunc", 1); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4844,7 +5119,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1035 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1035 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -4853,8 +5128,8 @@ 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, 1035, __pyx_L3_error) - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4867,12 +5142,12 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1036 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< * raise ImportError("numpy._core.umath failed to import") - * + * */ __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(&((PyTypeObject*)PyExc_Exception)[0]))); if (__pyx_t_4) { @@ -4882,12 +5157,12 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1037 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1037 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ImportError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(1, 1037, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); @@ -4897,8 +5172,8 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { } goto __pyx_L5_except_error; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1034 + * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< * _import_umath() @@ -4913,9 +5188,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1033 * raise ImportError("numpy._core.umath failed to import") - * + * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< * try: * _import_umath() @@ -4936,9 +5211,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 - * - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 + * + * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.timedelta64)` @@ -4947,19 +5222,19 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1052 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1052 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyTimedeltaArrType_Type)); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 - * - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1040 + * + * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.timedelta64)` @@ -4970,9 +5245,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 - * - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 + * + * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.datetime64)` @@ -4981,19 +5256,19 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1067 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1067 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyDatetimeArrType_Type)); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 - * - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1055 + * + * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< * """ * Cython equivalent of `isinstance(obj, np.datetime64)` @@ -5004,9 +5279,9 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 - * - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 + * + * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy datetime64 object @@ -5015,19 +5290,19 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1077 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1077 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 - * - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1070 + * + * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy datetime64 object @@ -5038,9 +5313,9 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 - * - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 + * + * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy timedelta64 object @@ -5049,19 +5324,19 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1084 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1084 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 - * - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1080 + * + * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the int64 value underlying scalar numpy timedelta64 object @@ -5072,9 +5347,9 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 - * - * +/* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 + * + * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the unit part of the dtype for a numpy datetime64 object. @@ -5083,19 +5358,19 @@ 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; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1091 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1091 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< - * - * + * + * */ __pyx_r = ((NPY_DATETIMEUNIT)((PyDatetimeScalarObject *)__pyx_v_obj)->obmeta.base); goto __pyx_L0; - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 - * - * + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1087 + * + * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< * """ * returns the unit part of the dtype for a numpy datetime64 object. @@ -5106,44 +5381,43 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec return __pyx_r; } -/* "CRISPResso2/CRISPRessoCOREResources.pyx":18 - * re_find_indels = re.compile("(-*-)") - * - * @cython.boundscheck(False) # <<<<<<<<<<<<<< - * @cython.nonecheck(False) - * @cython.wraparound(False) +/* "CRISPResso2/CRISPRessoCOREResources.pyx":53 + * ) + * + * def __init__(self, **kwargs): # <<<<<<<<<<<<<< + * for key, value in kwargs.items(): + * setattr(self, key, value) */ /* Python wrapper */ -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_1__init__(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else PyObject *__pyx_args, PyObject *__pyx_kwds #endif ); /*proto*/ -static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions = {"find_indels_substitutions", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, +static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_1__init__ = {"__init__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_1__init__, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_1__init__(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else PyObject *__pyx_args, PyObject *__pyx_kwds #endif ) { - PyObject *__pyx_v_read_seq_al = 0; - PyObject *__pyx_v_ref_seq_al = 0; - PyObject *__pyx_v__include_indx = 0; + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_kwargs = 0; #if !CYTHON_METH_FASTCALL CYTHON_UNUSED Py_ssize_t __pyx_nargs; #endif CYTHON_UNUSED PyObject *const *__pyx_kwvalues; - PyObject* values[3] = {0,0,0}; + PyObject* values[1] = {0}; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("find_indels_substitutions (wrapper)", 0); + __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); #if !CYTHON_METH_FASTCALL #if CYTHON_ASSUME_SAFE_MACROS __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); @@ -5152,15 +5426,13 @@ PyObject *__pyx_args, PyObject *__pyx_kwds #endif #endif __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL; + __Pyx_GOTREF(__pyx_v_kwargs); { - PyObject **__pyx_pyargnames[] = {&__pyx_n_s_read_seq_al,&__pyx_n_s_ref_seq_al,&__pyx_n_s_include_indx,0}; + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,0}; if (__pyx_kwds) { Py_ssize_t kw_args; switch (__pyx_nargs) { - case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); - CYTHON_FALLTHROUGH; - case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); - CYTHON_FALLTHROUGH; case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); CYTHON_FALLTHROUGH; case 0: break; @@ -5169,51 +5441,27 @@ PyObject *__pyx_args, PyObject *__pyx_kwds kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); switch (__pyx_nargs) { case 0: - if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_read_seq_al)) != 0)) { + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 18, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 53, __pyx_L3_error) else goto __pyx_L5_argtuple_error; - CYTHON_FALLTHROUGH; - case 1: - if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_ref_seq_al)) != 0)) { - (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); - kw_args--; - } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 18, __pyx_L3_error) - else { - __Pyx_RaiseArgtupleInvalid("find_indels_substitutions", 1, 3, 3, 1); __PYX_ERR(0, 18, __pyx_L3_error) - } - CYTHON_FALLTHROUGH; - case 2: - if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_include_indx)) != 0)) { - (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); - kw_args--; - } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 18, __pyx_L3_error) - else { - __Pyx_RaiseArgtupleInvalid("find_indels_substitutions", 1, 3, 3, 2); __PYX_ERR(0, 18, __pyx_L3_error) - } } if (unlikely(kw_args > 0)) { const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "find_indels_substitutions") < 0)) __PYX_ERR(0, 18, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, __pyx_v_kwargs, values + 0, kwd_pos_args, "__init__") < 0)) __PYX_ERR(0, 53, __pyx_L3_error) } - } else if (unlikely(__pyx_nargs != 3)) { + } else if (unlikely(__pyx_nargs != 1)) { goto __pyx_L5_argtuple_error; } else { values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); - values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); - values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); } - __pyx_v_read_seq_al = values[0]; - __pyx_v_ref_seq_al = values[1]; - __pyx_v__include_indx = values[2]; + __pyx_v_self = values[0]; } goto __pyx_L6_skip; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("find_indels_substitutions", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 18, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, __pyx_nargs); __PYX_ERR(0, 53, __pyx_L3_error) __pyx_L6_skip:; goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; @@ -5223,13 +5471,15 @@ PyObject *__pyx_args, PyObject *__pyx_kwds __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); } } - __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.find_indels_substitutions", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0; + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.ResultsSlotsDict.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_substitutions(__pyx_self, __pyx_v_read_seq_al, __pyx_v_ref_seq_al, __pyx_v__include_indx); + __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict___init__(__pyx_self, __pyx_v_self, __pyx_v_kwargs); /* function exit code */ + __Pyx_DECREF(__pyx_v_kwargs); { Py_ssize_t __pyx_temp; for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { @@ -5240,293 +5490,839 @@ PyObject *__pyx_args, PyObject *__pyx_kwds return __pyx_r; } -static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_substitutions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_read_seq_al, PyObject *__pyx_v_ref_seq_al, PyObject *__pyx_v__include_indx) { - PyObject *__pyx_v_ref_positions = NULL; - PyObject *__pyx_v_all_substitution_positions = NULL; - PyObject *__pyx_v_substitution_positions = NULL; - PyObject *__pyx_v_all_substitution_values = NULL; - PyObject *__pyx_v_substitution_values = NULL; - PyObject *__pyx_v_all_deletion_positions = NULL; - PyObject *__pyx_v_all_deletion_coordinates = NULL; - PyObject *__pyx_v_deletion_positions = NULL; - PyObject *__pyx_v_deletion_coordinates = NULL; - PyObject *__pyx_v_deletion_sizes = NULL; - int __pyx_v_start_deletion; - PyObject *__pyx_v_all_insertion_positions = NULL; - PyObject *__pyx_v_all_insertion_left_positions = NULL; - PyObject *__pyx_v_insertion_positions = NULL; - PyObject *__pyx_v_insertion_coordinates = NULL; - PyObject *__pyx_v_insertion_sizes = NULL; - int __pyx_v_start_insertion; - size_t __pyx_v_seq_len; - PyObject *__pyx_v_include_indx_set = NULL; - CYTHON_UNUSED PyObject *__pyx_v_nucSet = NULL; - int __pyx_v_idx; - int __pyx_v_idx_c; - int __pyx_v_current_insertion_size; - PyObject *__pyx_v_c = NULL; - PyObject *__pyx_v_end_deletion = NULL; - size_t __pyx_v_substitution_n; - size_t __pyx_v_deletion_n; - size_t __pyx_v_insertion_n; +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_kwargs) { + PyObject *__pyx_v_key = NULL; + PyObject *__pyx_v_value = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; Py_ssize_t __pyx_t_2; - int __pyx_t_3; - PyObject *(*__pyx_t_4)(PyObject *); + Py_ssize_t __pyx_t_3; + int __pyx_t_4; PyObject *__pyx_t_5 = NULL; - int __pyx_t_6; + PyObject *__pyx_t_6 = NULL; int __pyx_t_7; - PyObject *__pyx_t_8 = NULL; - PyObject *__pyx_t_9 = NULL; - int __pyx_t_10; - int __pyx_t_11; - size_t __pyx_t_12; - unsigned int __pyx_t_13; + int __pyx_t_8; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; - __Pyx_RefNannySetupContext("find_indels_substitutions", 1); + __Pyx_RefNannySetupContext("__init__", 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":32 - * # aln A - T T T G G C C - * # 1 2 3 4-4 5 6 7 8 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__getitem__") < 0)) __PYX_ERR(0, 57, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 2)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + } + __pyx_v_self = values[0]; + __pyx_v_key = values[1]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__getitem__", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 57, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.ResultsSlotsDict.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_2__getitem__(__pyx_self, __pyx_v_self, __pyx_v_key); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_2__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__getitem__", 1); + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":58 + * + * def __getitem__(self, key): + * return getattr(self, key) # <<<<<<<<<<<<<< + * + * def __setitem__(self, key, value): + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_GetAttr(__pyx_v_self, __pyx_v_key); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 58, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":57 + * setattr(self, key, value) + * + * def __getitem__(self, key): # <<<<<<<<<<<<<< + * return getattr(self, key) + * + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.ResultsSlotsDict.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "CRISPResso2/CRISPRessoCOREResources.pyx":60 + * return getattr(self, key) + * + * def __setitem__(self, key, value): # <<<<<<<<<<<<<< + * setattr(self, key, value) + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_5__setitem__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_5__setitem__ = {"__setitem__", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_5__setitem__, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_5__setitem__(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_self = 0; + PyObject *__pyx_v_key = 0; + PyObject *__pyx_v_value = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[3] = {0,0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("__setitem__ (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_self,&__pyx_n_s_key,&__pyx_n_s_value,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_self)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 60, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_key)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 60, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__setitem__", 1, 3, 3, 1); __PYX_ERR(0, 60, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_value)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 60, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("__setitem__", 1, 3, 3, 2); __PYX_ERR(0, 60, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "__setitem__") < 0)) __PYX_ERR(0, 60, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 3)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + } + __pyx_v_self = values[0]; + __pyx_v_key = values[1]; + __pyx_v_value = values[2]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("__setitem__", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 60, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.ResultsSlotsDict.__setitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_4__setitem__(__pyx_self, __pyx_v_self, __pyx_v_key, __pyx_v_value); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_4__setitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("__setitem__", 1); + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":61 + * + * def __setitem__(self, key, value): + * setattr(self, key, value) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = PyObject_SetAttr(__pyx_v_self, __pyx_v_key, __pyx_v_value); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 61, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":60 + * return getattr(self, key) + * + * def __setitem__(self, key, value): # <<<<<<<<<<<<<< + * setattr(self, key, value) + * + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.ResultsSlotsDict.__setitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "CRISPResso2/CRISPRessoCOREResources.pyx":64 + * + * + * @cython.boundscheck(False) # <<<<<<<<<<<<<< + * @cython.nonecheck(False) + * @cython.wraparound(False) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +); /*proto*/ +static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions = {"find_indels_substitutions", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions(PyObject *__pyx_self, +#if CYTHON_METH_FASTCALL +PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds +#else +PyObject *__pyx_args, PyObject *__pyx_kwds +#endif +) { + PyObject *__pyx_v_read_seq_al = 0; + PyObject *__pyx_v_ref_seq_al = 0; + PyObject *__pyx_v__include_indx = 0; + #if !CYTHON_METH_FASTCALL + CYTHON_UNUSED Py_ssize_t __pyx_nargs; + #endif + CYTHON_UNUSED PyObject *const *__pyx_kwvalues; + PyObject* values[3] = {0,0,0}; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("find_indels_substitutions (wrapper)", 0); + #if !CYTHON_METH_FASTCALL + #if CYTHON_ASSUME_SAFE_MACROS + __pyx_nargs = PyTuple_GET_SIZE(__pyx_args); + #else + __pyx_nargs = PyTuple_Size(__pyx_args); if (unlikely(__pyx_nargs < 0)) return NULL; + #endif + #endif + __pyx_kwvalues = __Pyx_KwValues_FASTCALL(__pyx_args, __pyx_nargs); + { + PyObject **__pyx_pyargnames[] = {&__pyx_n_s_read_seq_al,&__pyx_n_s_ref_seq_al,&__pyx_n_s_include_indx,0}; + if (__pyx_kwds) { + Py_ssize_t kw_args; + switch (__pyx_nargs) { + case 3: values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + CYTHON_FALLTHROUGH; + case 2: values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + CYTHON_FALLTHROUGH; + case 1: values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + CYTHON_FALLTHROUGH; + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = __Pyx_NumKwargs_FASTCALL(__pyx_kwds); + switch (__pyx_nargs) { + case 0: + if (likely((values[0] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_read_seq_al)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 64, __pyx_L3_error) + else goto __pyx_L5_argtuple_error; + CYTHON_FALLTHROUGH; + case 1: + if (likely((values[1] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_ref_seq_al)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 64, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("find_indels_substitutions", 1, 3, 3, 1); __PYX_ERR(0, 64, __pyx_L3_error) + } + CYTHON_FALLTHROUGH; + case 2: + if (likely((values[2] = __Pyx_GetKwValue_FASTCALL(__pyx_kwds, __pyx_kwvalues, __pyx_n_s_include_indx)) != 0)) { + (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); + kw_args--; + } + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 64, __pyx_L3_error) + else { + __Pyx_RaiseArgtupleInvalid("find_indels_substitutions", 1, 3, 3, 2); __PYX_ERR(0, 64, __pyx_L3_error) + } + } + if (unlikely(kw_args > 0)) { + const Py_ssize_t kwd_pos_args = __pyx_nargs; + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "find_indels_substitutions") < 0)) __PYX_ERR(0, 64, __pyx_L3_error) + } + } else if (unlikely(__pyx_nargs != 3)) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = __Pyx_Arg_FASTCALL(__pyx_args, 0); + values[1] = __Pyx_Arg_FASTCALL(__pyx_args, 1); + values[2] = __Pyx_Arg_FASTCALL(__pyx_args, 2); + } + __pyx_v_read_seq_al = values[0]; + __pyx_v_ref_seq_al = values[1]; + __pyx_v__include_indx = values[2]; + } + goto __pyx_L6_skip; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("find_indels_substitutions", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 64, __pyx_L3_error) + __pyx_L6_skip:; + goto __pyx_L4_argument_unpacking_done; + __pyx_L3_error:; + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.find_indels_substitutions", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_substitutions(__pyx_self, __pyx_v_read_seq_al, __pyx_v_ref_seq_al, __pyx_v__include_indx); + + /* function exit code */ + { + Py_ssize_t __pyx_temp; + for (__pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) { + __Pyx_Arg_XDECREF_FASTCALL(values[__pyx_temp]); + } + } + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_substitutions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_read_seq_al, PyObject *__pyx_v_ref_seq_al, PyObject *__pyx_v__include_indx) { + PyObject *__pyx_v_ref_positions = NULL; + PyObject *__pyx_v_all_substitution_positions = NULL; + PyObject *__pyx_v_substitution_positions = NULL; + PyObject *__pyx_v_all_substitution_values = NULL; + PyObject *__pyx_v_substitution_values = NULL; + PyObject *__pyx_v_all_deletion_positions = NULL; + PyObject *__pyx_v_all_deletion_coordinates = NULL; + PyObject *__pyx_v_deletion_positions = NULL; + PyObject *__pyx_v_deletion_coordinates = NULL; + PyObject *__pyx_v_deletion_sizes = NULL; + int __pyx_v_start_deletion; + PyObject *__pyx_v_all_insertion_positions = NULL; + PyObject *__pyx_v_all_insertion_left_positions = NULL; + PyObject *__pyx_v_insertion_positions = NULL; + PyObject *__pyx_v_insertion_coordinates = NULL; + PyObject *__pyx_v_insertion_sizes = NULL; + int __pyx_v_start_insertion; + size_t __pyx_v_seq_len; + PyObject *__pyx_v_include_indx_set = NULL; + CYTHON_UNUSED PyObject *__pyx_v_nucSet = NULL; + int __pyx_v_idx; + int __pyx_v_idx_c; + int __pyx_v_current_insertion_size; + PyObject *__pyx_v_c = NULL; + PyObject *__pyx_v_end_deletion = NULL; + size_t __pyx_v_substitution_n; + size_t __pyx_v_deletion_n; + size_t __pyx_v_insertion_n; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + Py_ssize_t __pyx_t_2; + int __pyx_t_3; + PyObject *(*__pyx_t_4)(PyObject *); + PyObject *__pyx_t_5 = NULL; + int __pyx_t_6; + int __pyx_t_7; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + int __pyx_t_10; + int __pyx_t_11; + size_t __pyx_t_12; + PyObject *__pyx_t_13 = NULL; + unsigned int __pyx_t_14; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("find_indels_substitutions", 1); + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":78 + * # aln A - T T T G G C C + * # 1 2 3 4-4 5 6 7 8 = __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 58, __pyx_L1_error) + __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 104, __pyx_L1_error) #else - __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 58, __pyx_L1_error) + __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 104, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif } else { { Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1); #if !CYTHON_ASSUME_SAFE_MACROS - if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 58, __pyx_L1_error) + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 104, __pyx_L1_error) #endif if (__pyx_t_2 >= __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 58, __pyx_L1_error) + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++; if (unlikely((0 < 0))) __PYX_ERR(0, 104, __pyx_L1_error) #else - __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 58, __pyx_L1_error) + __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 104, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif } @@ -5598,7 +6394,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else __PYX_ERR(0, 58, __pyx_L1_error) + else __PYX_ERR(0, 104, __pyx_L1_error) } break; } @@ -5609,128 +6405,128 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_v_idx_c = __pyx_t_3; __pyx_t_3 = (__pyx_t_3 + 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":59 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":105 * cdef int current_insertion_size = 0 * for idx_c, c in enumerate(ref_seq_al): * if c != '-': # <<<<<<<<<<<<<< * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': */ - __pyx_t_6 = (__Pyx_PyUnicode_Equals(__pyx_v_c, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 59, __pyx_L1_error) + __pyx_t_6 = (__Pyx_PyUnicode_Equals(__pyx_v_c, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 105, __pyx_L1_error) if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":60 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":106 * for idx_c, c in enumerate(ref_seq_al): * if c != '-': * ref_positions.append(idx) # <<<<<<<<<<<<<< * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': * all_substitution_positions.append(idx) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 60, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 106, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 60, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 106, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":61 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":107 * if c != '-': * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': # <<<<<<<<<<<<<< * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) */ - __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_ref_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_ref_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = PyObject_RichCompare(__pyx_t_5, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_9 = PyObject_RichCompare(__pyx_t_5, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_10) { } else { __pyx_t_6 = __pyx_t_10; goto __pyx_L7_bool_binop_done; } - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_10) { } else { __pyx_t_6 = __pyx_t_10; goto __pyx_L7_bool_binop_done; } - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_n_u_N, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 61, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_n_u_N, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 107, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_6 = __pyx_t_10; __pyx_L7_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":62 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":108 * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': * all_substitution_positions.append(idx) # <<<<<<<<<<<<<< * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 62, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 108, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 62, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 108, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":63 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":109 * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) # <<<<<<<<<<<<<< * if idx in _include_indx: * substitution_positions.append(idx) */ - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 63, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 109, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 63, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 109, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":64 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":110 * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: # <<<<<<<<<<<<<< * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 64, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 110, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = (__Pyx_PySequence_ContainsTF(__pyx_t_9, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 64, __pyx_L1_error) + __pyx_t_6 = (__Pyx_PySequence_ContainsTF(__pyx_t_9, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 110, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":65 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":111 * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: * substitution_positions.append(idx) # <<<<<<<<<<<<<< * substitution_values.append(read_seq_al[idx_c]) * if start_insertion != -1: # this is the end of an insertion */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 65, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 111, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 65, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 111, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":66 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":112 * if idx in _include_indx: * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) # <<<<<<<<<<<<<< * if start_insertion != -1: # this is the end of an insertion * all_insertion_left_positions.append(start_insertion) */ - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 66, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 112, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 66, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 112, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":64 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":110 * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: # <<<<<<<<<<<<<< @@ -5739,7 +6535,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":61 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":107 * if c != '-': * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': # <<<<<<<<<<<<<< @@ -5748,7 +6544,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":67 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":113 * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) * if start_insertion != -1: # this is the end of an insertion # <<<<<<<<<<<<<< @@ -5758,125 +6554,125 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_6 = (__pyx_v_start_insertion != -1L); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":68 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":114 * substitution_values.append(read_seq_al[idx_c]) * if start_insertion != -1: # this is the end of an insertion * all_insertion_left_positions.append(start_insertion) # <<<<<<<<<<<<<< * all_insertion_positions.append(start_insertion) * all_insertion_positions.append(idx) */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 68, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 114, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_left_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 68, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_left_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 114, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":69 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":115 * if start_insertion != -1: # this is the end of an insertion * all_insertion_left_positions.append(start_insertion) * all_insertion_positions.append(start_insertion) # <<<<<<<<<<<<<< * all_insertion_positions.append(idx) * if start_insertion in include_indx_set and idx in include_indx_set: */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 69, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 115, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 69, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 115, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":70 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":116 * all_insertion_left_positions.append(start_insertion) * all_insertion_positions.append(start_insertion) * all_insertion_positions.append(idx) # <<<<<<<<<<<<<< * if start_insertion in include_indx_set and idx in include_indx_set: * insertion_coordinates.append((start_insertion, idx)) */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 70, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 116, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 70, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 116, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":71 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":117 * all_insertion_positions.append(start_insertion) * all_insertion_positions.append(idx) * if start_insertion in include_indx_set and idx in include_indx_set: # <<<<<<<<<<<<<< * insertion_coordinates.append((start_insertion, idx)) * insertion_positions.append(start_insertion) */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 71, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 117, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = (__Pyx_PySet_ContainsTF(__pyx_t_9, __pyx_v_include_indx_set, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 71, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PySet_ContainsTF(__pyx_t_9, __pyx_v_include_indx_set, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 117, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_10) { } else { __pyx_t_6 = __pyx_t_10; goto __pyx_L13_bool_binop_done; } - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 71, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 117, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = (__Pyx_PySet_ContainsTF(__pyx_t_9, __pyx_v_include_indx_set, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 71, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PySet_ContainsTF(__pyx_t_9, __pyx_v_include_indx_set, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 117, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_6 = __pyx_t_10; __pyx_L13_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":72 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":118 * all_insertion_positions.append(idx) * if start_insertion in include_indx_set and idx in include_indx_set: * insertion_coordinates.append((start_insertion, idx)) # <<<<<<<<<<<<<< * insertion_positions.append(start_insertion) * insertion_positions.append(idx) */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 72, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 118, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 72, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 118, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 72, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 118, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_9); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_9)) __PYX_ERR(0, 72, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_9)) __PYX_ERR(0, 118, __pyx_L1_error); __Pyx_GIVEREF(__pyx_t_8); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_8)) __PYX_ERR(0, 72, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_8)) __PYX_ERR(0, 118, __pyx_L1_error); __pyx_t_9 = 0; __pyx_t_8 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 72, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 118, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":73 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":119 * if start_insertion in include_indx_set and idx in include_indx_set: * insertion_coordinates.append((start_insertion, idx)) * insertion_positions.append(start_insertion) # <<<<<<<<<<<<<< * insertion_positions.append(idx) * insertion_sizes.append(current_insertion_size) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 73, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_insertion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 119, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 73, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 119, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":74 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":120 * insertion_coordinates.append((start_insertion, idx)) * insertion_positions.append(start_insertion) * insertion_positions.append(idx) # <<<<<<<<<<<<<< * insertion_sizes.append(current_insertion_size) * start_insertion = -1 */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 74, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 120, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 74, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 120, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":75 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":121 * insertion_positions.append(start_insertion) * insertion_positions.append(idx) * insertion_sizes.append(current_insertion_size) # <<<<<<<<<<<<<< * start_insertion = -1 * current_insertion_size = 0 */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_current_insertion_size); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 75, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_current_insertion_size); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 121, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_sizes, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 75, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_sizes, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 121, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":71 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":117 * all_insertion_positions.append(start_insertion) * all_insertion_positions.append(idx) * if start_insertion in include_indx_set and idx in include_indx_set: # <<<<<<<<<<<<<< @@ -5885,7 +6681,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":76 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":122 * insertion_positions.append(idx) * insertion_sizes.append(current_insertion_size) * start_insertion = -1 # <<<<<<<<<<<<<< @@ -5894,7 +6690,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ __pyx_v_start_insertion = -1; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":67 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":113 * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) * if start_insertion != -1: # this is the end of an insertion # <<<<<<<<<<<<<< @@ -5903,7 +6699,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":77 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":123 * insertion_sizes.append(current_insertion_size) * start_insertion = -1 * current_insertion_size = 0 # <<<<<<<<<<<<<< @@ -5912,7 +6708,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ __pyx_v_current_insertion_size = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":78 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":124 * start_insertion = -1 * current_insertion_size = 0 * idx += 1 # <<<<<<<<<<<<<< @@ -5921,7 +6717,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ __pyx_v_idx = (__pyx_v_idx + 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":59 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":105 * cdef int current_insertion_size = 0 * for idx_c, c in enumerate(ref_seq_al): * if c != '-': # <<<<<<<<<<<<<< @@ -5931,7 +6727,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su goto __pyx_L5; } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":80 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":126 * idx += 1 * else: # the current ref position is - * if idx == 0: # <<<<<<<<<<<<<< @@ -5942,16 +6738,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_6 = (__pyx_v_idx == 0); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":81 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":127 * else: # the current ref position is - * if idx == 0: * ref_positions.append(-1) # <<<<<<<<<<<<<< * else: * ref_positions.append(-idx) */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_int_neg_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 81, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_int_neg_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 127, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":80 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":126 * idx += 1 * else: # the current ref position is - * if idx == 0: # <<<<<<<<<<<<<< @@ -5961,7 +6757,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su goto __pyx_L15; } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":83 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":129 * ref_positions.append(-1) * else: * ref_positions.append(-idx) # <<<<<<<<<<<<<< @@ -5969,14 +6765,14 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * start_insertion = idx - 1 */ /*else*/ { - __pyx_t_5 = __Pyx_PyInt_From_int((-__pyx_v_idx)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 83, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int((-__pyx_v_idx)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 129, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 83, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 129, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __pyx_L15:; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":84 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":130 * else: * ref_positions.append(-idx) * if idx > 0 and start_insertion == -1: # this is the first index of an insertion # <<<<<<<<<<<<<< @@ -5994,16 +6790,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_L17_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":85 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":131 * ref_positions.append(-idx) * if idx > 0 and start_insertion == -1: # this is the first index of an insertion * start_insertion = idx - 1 # <<<<<<<<<<<<<< * current_insertion_size += 1 - * + * */ __pyx_v_start_insertion = (__pyx_v_idx - 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":84 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":130 * else: * ref_positions.append(-idx) * if idx > 0 and start_insertion == -1: # this is the first index of an insertion # <<<<<<<<<<<<<< @@ -6012,27 +6808,27 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":86 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":132 * if idx > 0 and start_insertion == -1: # this is the first index of an insertion * start_insertion = idx - 1 * current_insertion_size += 1 # <<<<<<<<<<<<<< - * + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion */ __pyx_v_current_insertion_size = (__pyx_v_current_insertion_size + 1); } __pyx_L5:; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":88 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":134 * current_insertion_size += 1 - * + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion # <<<<<<<<<<<<<< * if idx_c - 1 > 0: * start_deletion = ref_positions[idx_c] */ - __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 88, __pyx_L1_error) + __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 134, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_5, __pyx_kp_u__3, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 88, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_5, __pyx_kp_u__3, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 134, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_10) { } else { @@ -6044,8 +6840,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_L20_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":89 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":135 + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion * if idx_c - 1 > 0: # <<<<<<<<<<<<<< * start_deletion = ref_positions[idx_c] @@ -6054,18 +6850,18 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_6 = ((__pyx_v_idx_c - 1) > 0); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":90 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":136 * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion * if idx_c - 1 > 0: * start_deletion = ref_positions[idx_c] # <<<<<<<<<<<<<< * else: * start_deletion = 0 */ - __pyx_t_11 = __Pyx_PyInt_As_int(PyList_GET_ITEM(__pyx_v_ref_positions, __pyx_v_idx_c)); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 90, __pyx_L1_error) + __pyx_t_11 = __Pyx_PyInt_As_int(PyList_GET_ITEM(__pyx_v_ref_positions, __pyx_v_idx_c)); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 136, __pyx_L1_error) __pyx_v_start_deletion = __pyx_t_11; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":89 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":135 + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion * if idx_c - 1 > 0: # <<<<<<<<<<<<<< * start_deletion = ref_positions[idx_c] @@ -6074,7 +6870,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su goto __pyx_L22; } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":92 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":138 * start_deletion = ref_positions[idx_c] * else: * start_deletion = 0 # <<<<<<<<<<<<<< @@ -6086,9 +6882,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su } __pyx_L22:; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":88 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":134 * current_insertion_size += 1 - * + * * if read_seq_al[idx_c] == '-' and start_deletion == -1: # this is the first part of a deletion # <<<<<<<<<<<<<< * if idx_c - 1 > 0: * start_deletion = ref_positions[idx_c] @@ -6096,16 +6892,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su goto __pyx_L19; } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":93 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":139 * else: * start_deletion = 0 * elif read_seq_al[idx_c] != '-' and start_deletion != -1: # this is the end of a deletion # <<<<<<<<<<<<<< * end_deletion = ref_positions[idx_c] * all_deletion_positions.extend(range(start_deletion, end_deletion)) */ - __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 93, __pyx_L1_error) + __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 139, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_5, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 93, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_5, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 139, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_10) { } else { @@ -6117,7 +6913,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_L23_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":94 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":140 * start_deletion = 0 * elif read_seq_al[idx_c] != '-' and start_deletion != -1: # this is the end of a deletion * end_deletion = ref_positions[idx_c] # <<<<<<<<<<<<<< @@ -6129,135 +6925,135 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_XDECREF_SET(__pyx_v_end_deletion, __pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":95 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":141 * elif read_seq_al[idx_c] != '-' and start_deletion != -1: # this is the end of a deletion * end_deletion = ref_positions[idx_c] * all_deletion_positions.extend(range(start_deletion, end_deletion)) # <<<<<<<<<<<<<< * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 95, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 141, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 95, __pyx_L1_error) + __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 141, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_GIVEREF(__pyx_t_5); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 95, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 141, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 95, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 141, __pyx_L1_error); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 95, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 141, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_all_deletion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 95, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_all_deletion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 141, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":96 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":142 * end_deletion = ref_positions[idx_c] * all_deletion_positions.extend(range(start_deletion, end_deletion)) * all_deletion_coordinates.append((start_deletion, end_deletion)) # <<<<<<<<<<<<<< * if include_indx_set.intersection(range(start_deletion, end_deletion)): * deletion_positions.extend(range(start_deletion, end_deletion)) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 96, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 142, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 96, __pyx_L1_error) + __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 142, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_GIVEREF(__pyx_t_5); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 96, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 142, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 96, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 142, __pyx_L1_error); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_deletion_coordinates, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 96, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_deletion_coordinates, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 142, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":97 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":143 * all_deletion_positions.extend(range(start_deletion, end_deletion)) * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): # <<<<<<<<<<<<<< * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) */ - __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 97, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 143, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 97, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 143, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_8); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_8)) __PYX_ERR(0, 97, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_8)) __PYX_ERR(0, 143, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 97, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 143, __pyx_L1_error); __pyx_t_8 = 0; - __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 97, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 143, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PySet_Type_intersection, __pyx_v_include_indx_set, __pyx_t_8); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 97, __pyx_L1_error) + __pyx_t_5 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PySet_Type_intersection, __pyx_v_include_indx_set, __pyx_t_8); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 143, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 97, __pyx_L1_error) + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 143, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":98 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":144 * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): * deletion_positions.extend(range(start_deletion, end_deletion)) # <<<<<<<<<<<<<< * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 98, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 144, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 98, __pyx_L1_error) + __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 144, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_GIVEREF(__pyx_t_5); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 98, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 144, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 98, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 144, __pyx_L1_error); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 98, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 144, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_deletion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 98, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_deletion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 144, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":99 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":145 * if include_indx_set.intersection(range(start_deletion, end_deletion)): * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) # <<<<<<<<<<<<<< * deletion_sizes.append(end_deletion - start_deletion) * start_deletion = -1 */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 99, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 145, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 99, __pyx_L1_error) + __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 145, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_GIVEREF(__pyx_t_5); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 99, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5)) __PYX_ERR(0, 145, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 99, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 145, __pyx_L1_error); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_coordinates, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 99, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_coordinates, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 145, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":100 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":146 * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) # <<<<<<<<<<<<<< * start_deletion = -1 - * + * */ - __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 100, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 146, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = PyNumber_Subtract(__pyx_v_end_deletion, __pyx_t_8); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 100, __pyx_L1_error) + __pyx_t_5 = PyNumber_Subtract(__pyx_v_end_deletion, __pyx_t_8); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 146, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_sizes, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 100, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_sizes, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 146, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":97 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":143 * all_deletion_positions.extend(range(start_deletion, end_deletion)) * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): # <<<<<<<<<<<<<< @@ -6266,16 +7062,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":101 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":147 * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) * start_deletion = -1 # <<<<<<<<<<<<<< - * + * * if start_deletion != -1: */ __pyx_v_start_deletion = -1; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":93 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":139 * else: * start_deletion = 0 * elif read_seq_al[idx_c] != '-' and start_deletion != -1: # this is the end of a deletion # <<<<<<<<<<<<<< @@ -6285,7 +7081,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su } __pyx_L19:; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":58 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":104 * cdef int idx_c * cdef int current_insertion_size = 0 * for idx_c, c in enumerate(ref_seq_al): # <<<<<<<<<<<<<< @@ -6295,9 +7091,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":103 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":149 * start_deletion = -1 - * + * * if start_deletion != -1: # <<<<<<<<<<<<<< * end_deletion = ref_positions[seq_len - 1] * all_deletion_positions.extend(range(start_deletion, end_deletion)) @@ -6305,8 +7101,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __pyx_t_6 = (__pyx_v_start_deletion != -1L); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":104 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":150 + * * if start_deletion != -1: * end_deletion = ref_positions[seq_len - 1] # <<<<<<<<<<<<<< * all_deletion_positions.extend(range(start_deletion, end_deletion)) @@ -6318,135 +7114,135 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_XDECREF_SET(__pyx_v_end_deletion, __pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":105 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":151 * if start_deletion != -1: * end_deletion = ref_positions[seq_len - 1] * all_deletion_positions.extend(range(start_deletion, end_deletion)) # <<<<<<<<<<<<<< * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): */ - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 105, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 151, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 105, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 151, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_1); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 105, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 151, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 105, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 151, __pyx_L1_error); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 105, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 151, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_all_deletion_positions, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 105, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_all_deletion_positions, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 151, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":106 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":152 * end_deletion = ref_positions[seq_len - 1] * all_deletion_positions.extend(range(start_deletion, end_deletion)) * all_deletion_coordinates.append((start_deletion, end_deletion)) # <<<<<<<<<<<<<< * if include_indx_set.intersection(range(start_deletion, end_deletion)): * deletion_positions.extend(range(start_deletion, end_deletion)) */ - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 106, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 152, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 106, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 152, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_1); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 106, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 152, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 106, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 152, __pyx_L1_error); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_deletion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 106, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_deletion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 152, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":107 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":153 * all_deletion_positions.extend(range(start_deletion, end_deletion)) * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): # <<<<<<<<<<<<<< * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 107, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 153, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 107, __pyx_L1_error) + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 153, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_GIVEREF(__pyx_t_5); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5)) __PYX_ERR(0, 107, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5)) __PYX_ERR(0, 153, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 107, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 153, __pyx_L1_error); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 107, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 153, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PySet_Type_intersection, __pyx_v_include_indx_set, __pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 107, __pyx_L1_error) + __pyx_t_1 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PySet_Type_intersection, __pyx_v_include_indx_set, __pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 153, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 107, __pyx_L1_error) + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 153, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":108 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":154 * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): * deletion_positions.extend(range(start_deletion, end_deletion)) # <<<<<<<<<<<<<< * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) */ - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 108, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 154, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 108, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 154, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_1); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 108, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 154, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 108, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 154, __pyx_L1_error); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 108, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 154, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_deletion_positions, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 108, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_deletion_positions, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 154, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":109 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":155 * if include_indx_set.intersection(range(start_deletion, end_deletion)): * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) # <<<<<<<<<<<<<< * deletion_sizes.append(end_deletion - start_deletion) - * + * */ - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 109, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 155, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 109, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 155, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_1); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 109, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1)) __PYX_ERR(0, 155, __pyx_L1_error); __Pyx_INCREF(__pyx_v_end_deletion); __Pyx_GIVEREF(__pyx_v_end_deletion); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 109, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_end_deletion)) __PYX_ERR(0, 155, __pyx_L1_error); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 109, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 155, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":110 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":156 * deletion_positions.extend(range(start_deletion, end_deletion)) * deletion_coordinates.append((start_deletion, end_deletion)) * deletion_sizes.append(end_deletion - start_deletion) # <<<<<<<<<<<<<< - * + * * cdef size_t substitution_n = len(substitution_positions) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 110, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start_deletion); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 156, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = PyNumber_Subtract(__pyx_v_end_deletion, __pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 110, __pyx_L1_error) + __pyx_t_1 = PyNumber_Subtract(__pyx_v_end_deletion, __pyx_t_5); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 156, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_sizes, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 110, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_sizes, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 156, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":107 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":153 * all_deletion_positions.extend(range(start_deletion, end_deletion)) * all_deletion_coordinates.append((start_deletion, end_deletion)) * if include_indx_set.intersection(range(start_deletion, end_deletion)): # <<<<<<<<<<<<<< @@ -6455,295 +7251,309 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":103 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":149 * start_deletion = -1 - * + * * if start_deletion != -1: # <<<<<<<<<<<<<< * end_deletion = ref_positions[seq_len - 1] * all_deletion_positions.extend(range(start_deletion, end_deletion)) */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":112 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":158 * deletion_sizes.append(end_deletion - start_deletion) - * + * * cdef size_t substitution_n = len(substitution_positions) # <<<<<<<<<<<<<< * cdef size_t deletion_n = sum(deletion_sizes) * cdef size_t insertion_n = sum(insertion_sizes) */ - __pyx_t_2 = __Pyx_PyList_GET_SIZE(__pyx_v_substitution_positions); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1))) __PYX_ERR(0, 112, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyList_GET_SIZE(__pyx_v_substitution_positions); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1))) __PYX_ERR(0, 158, __pyx_L1_error) __pyx_v_substitution_n = __pyx_t_2; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":113 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":159 + * * cdef size_t substitution_n = len(substitution_positions) * cdef size_t deletion_n = sum(deletion_sizes) # <<<<<<<<<<<<<< * cdef size_t insertion_n = sum(insertion_sizes) - * + * */ - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_sum, __pyx_v_deletion_sizes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 113, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_sum, __pyx_v_deletion_sizes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 159, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_12 = __Pyx_PyInt_As_size_t(__pyx_t_1); if (unlikely((__pyx_t_12 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 113, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyInt_As_size_t(__pyx_t_1); if (unlikely((__pyx_t_12 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 159, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_deletion_n = __pyx_t_12; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":114 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":160 * 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 { + * + * return ResultsSlotsDict( */ - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_sum, __pyx_v_insertion_sizes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 114, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_builtin_sum, __pyx_v_insertion_sizes); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 160, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_12 = __Pyx_PyInt_As_size_t(__pyx_t_1); if (unlikely((__pyx_t_12 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 114, __pyx_L1_error) + __pyx_t_12 = __Pyx_PyInt_As_size_t(__pyx_t_1); if (unlikely((__pyx_t_12 == (size_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 160, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_insertion_n = __pyx_t_12; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":116 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":162 * cdef size_t insertion_n = sum(insertion_sizes) - * - * return { # <<<<<<<<<<<<<< - * 'all_insertion_positions': all_insertion_positions, - * 'all_insertion_left_positions': all_insertion_left_positions, + * + * return ResultsSlotsDict( # <<<<<<<<<<<<<< + * all_insertion_positions=all_insertion_positions, + * all_insertion_left_positions=all_insertion_left_positions, */ __Pyx_XDECREF(__pyx_r); + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_ResultsSlotsDict); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 162, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":117 - * - * return { - * 'all_insertion_positions': all_insertion_positions, # <<<<<<<<<<<<<< - * 'all_insertion_left_positions': all_insertion_left_positions, - * 'insertion_positions': insertion_positions, + /* "CRISPResso2/CRISPRessoCOREResources.pyx":163 + * + * return ResultsSlotsDict( + * all_insertion_positions=all_insertion_positions, # <<<<<<<<<<<<<< + * all_insertion_left_positions=all_insertion_left_positions, + * insertion_positions=insertion_positions, */ - __pyx_t_1 = __Pyx_PyDict_NewPresized(18); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 117, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_insertion_positions, __pyx_v_all_insertion_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":118 - * return { - * 'all_insertion_positions': all_insertion_positions, - * 'all_insertion_left_positions': all_insertion_left_positions, # <<<<<<<<<<<<<< - * 'insertion_positions': insertion_positions, - * 'insertion_coordinates': insertion_coordinates, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_insertion_left_positions, __pyx_v_all_insertion_left_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":119 - * 'all_insertion_positions': all_insertion_positions, - * 'all_insertion_left_positions': all_insertion_left_positions, - * 'insertion_positions': insertion_positions, # <<<<<<<<<<<<<< - * 'insertion_coordinates': insertion_coordinates, - * 'insertion_sizes': insertion_sizes, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_positions, __pyx_v_insertion_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":120 - * 'all_insertion_left_positions': all_insertion_left_positions, - * 'insertion_positions': insertion_positions, - * 'insertion_coordinates': insertion_coordinates, # <<<<<<<<<<<<<< - * 'insertion_sizes': insertion_sizes, - * 'insertion_n': insertion_n, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_coordinates, __pyx_v_insertion_coordinates) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":121 - * 'insertion_positions': insertion_positions, - * 'insertion_coordinates': insertion_coordinates, - * 'insertion_sizes': insertion_sizes, # <<<<<<<<<<<<<< - * 'insertion_n': insertion_n, - * - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_sizes, __pyx_v_insertion_sizes) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":122 - * 'insertion_coordinates': insertion_coordinates, - * 'insertion_sizes': insertion_sizes, - * 'insertion_n': insertion_n, # <<<<<<<<<<<<<< - * - * 'all_deletion_positions': all_deletion_positions, - */ - __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_insertion_n); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 122, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyDict_NewPresized(18); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 163, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_n, __pyx_t_5) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_all_insertion_positions, __pyx_v_all_insertion_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":124 - * 'insertion_n': insertion_n, - * - * 'all_deletion_positions': all_deletion_positions, # <<<<<<<<<<<<<< - * 'all_deletion_coordinates': all_deletion_coordinates, - * 'deletion_positions': deletion_positions, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_positions, __pyx_v_all_deletion_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":125 - * - * 'all_deletion_positions': all_deletion_positions, - * 'all_deletion_coordinates': all_deletion_coordinates, # <<<<<<<<<<<<<< - * 'deletion_positions': deletion_positions, - * 'deletion_coordinates': deletion_coordinates, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_coordinates, __pyx_v_all_deletion_coordinates) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":126 - * 'all_deletion_positions': all_deletion_positions, - * 'all_deletion_coordinates': all_deletion_coordinates, - * 'deletion_positions': deletion_positions, # <<<<<<<<<<<<<< - * 'deletion_coordinates': deletion_coordinates, - * 'deletion_sizes': deletion_sizes, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_positions, __pyx_v_deletion_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":127 - * 'all_deletion_coordinates': all_deletion_coordinates, - * 'deletion_positions': deletion_positions, - * 'deletion_coordinates': deletion_coordinates, # <<<<<<<<<<<<<< - * 'deletion_sizes': deletion_sizes, - * 'deletion_n': deletion_n, - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_coordinates, __pyx_v_deletion_coordinates) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":128 - * 'deletion_positions': deletion_positions, - * 'deletion_coordinates': deletion_coordinates, - * 'deletion_sizes': deletion_sizes, # <<<<<<<<<<<<<< - * 'deletion_n': deletion_n, - * - */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_sizes, __pyx_v_deletion_sizes) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - - /* "CRISPResso2/CRISPRessoCOREResources.pyx":129 - * 'deletion_coordinates': deletion_coordinates, - * 'deletion_sizes': deletion_sizes, - * 'deletion_n': deletion_n, # <<<<<<<<<<<<<< - * - * 'all_substitution_positions': all_substitution_positions, - */ - __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_deletion_n); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 129, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_5); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_n, __pyx_t_5) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + /* "CRISPResso2/CRISPRessoCOREResources.pyx":164 + * return ResultsSlotsDict( + * all_insertion_positions=all_insertion_positions, + * all_insertion_left_positions=all_insertion_left_positions, # <<<<<<<<<<<<<< + * insertion_positions=insertion_positions, + * insertion_coordinates=insertion_coordinates, + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_all_insertion_left_positions, __pyx_v_all_insertion_left_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":165 + * all_insertion_positions=all_insertion_positions, + * all_insertion_left_positions=all_insertion_left_positions, + * insertion_positions=insertion_positions, # <<<<<<<<<<<<<< + * insertion_coordinates=insertion_coordinates, + * insertion_sizes=insertion_sizes, + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_insertion_positions, __pyx_v_insertion_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":131 - * 'deletion_n': deletion_n, - * - * 'all_substitution_positions': all_substitution_positions, # <<<<<<<<<<<<<< - * 'substitution_positions': substitution_positions, - * 'all_substitution_values': np.array(all_substitution_values), + /* "CRISPResso2/CRISPRessoCOREResources.pyx":166 + * all_insertion_left_positions=all_insertion_left_positions, + * insertion_positions=insertion_positions, + * insertion_coordinates=insertion_coordinates, # <<<<<<<<<<<<<< + * insertion_sizes=insertion_sizes, + * insertion_n=insertion_n, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_substitution_positions, __pyx_v_all_substitution_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_insertion_coordinates, __pyx_v_insertion_coordinates) < 0) __PYX_ERR(0, 163, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":132 - * - * 'all_substitution_positions': all_substitution_positions, - * 'substitution_positions': substitution_positions, # <<<<<<<<<<<<<< - * 'all_substitution_values': np.array(all_substitution_values), - * 'substitution_values': np.array(substitution_values), + /* "CRISPResso2/CRISPRessoCOREResources.pyx":167 + * insertion_positions=insertion_positions, + * insertion_coordinates=insertion_coordinates, + * insertion_sizes=insertion_sizes, # <<<<<<<<<<<<<< + * insertion_n=insertion_n, + * */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_positions, __pyx_v_substitution_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_insertion_sizes, __pyx_v_insertion_sizes) < 0) __PYX_ERR(0, 163, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":133 - * 'all_substitution_positions': all_substitution_positions, - * 'substitution_positions': substitution_positions, - * 'all_substitution_values': np.array(all_substitution_values), # <<<<<<<<<<<<<< - * 'substitution_values': np.array(substitution_values), - * 'substitution_n': substitution_n, + /* "CRISPResso2/CRISPRessoCOREResources.pyx":168 + * insertion_coordinates=insertion_coordinates, + * insertion_sizes=insertion_sizes, + * insertion_n=insertion_n, # <<<<<<<<<<<<<< + * + * all_deletion_positions=all_deletion_positions, */ - __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_np); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 133, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_insertion_n); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 168, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_array); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 133, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_9); + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_insertion_n, __pyx_t_8) < 0) __PYX_ERR(0, 163, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = NULL; - __pyx_t_13 = 0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":170 + * insertion_n=insertion_n, + * + * all_deletion_positions=all_deletion_positions, # <<<<<<<<<<<<<< + * all_deletion_coordinates=all_deletion_coordinates, + * deletion_positions=deletion_positions, + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_all_deletion_positions, __pyx_v_all_deletion_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":171 + * + * all_deletion_positions=all_deletion_positions, + * all_deletion_coordinates=all_deletion_coordinates, # <<<<<<<<<<<<<< + * deletion_positions=deletion_positions, + * deletion_coordinates=deletion_coordinates, + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_all_deletion_coordinates, __pyx_v_all_deletion_coordinates) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":172 + * all_deletion_positions=all_deletion_positions, + * all_deletion_coordinates=all_deletion_coordinates, + * deletion_positions=deletion_positions, # <<<<<<<<<<<<<< + * deletion_coordinates=deletion_coordinates, + * deletion_sizes=deletion_sizes, + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_deletion_positions, __pyx_v_deletion_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":173 + * all_deletion_coordinates=all_deletion_coordinates, + * deletion_positions=deletion_positions, + * deletion_coordinates=deletion_coordinates, # <<<<<<<<<<<<<< + * deletion_sizes=deletion_sizes, + * deletion_n=deletion_n, + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_deletion_coordinates, __pyx_v_deletion_coordinates) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":174 + * deletion_positions=deletion_positions, + * deletion_coordinates=deletion_coordinates, + * deletion_sizes=deletion_sizes, # <<<<<<<<<<<<<< + * deletion_n=deletion_n, + * + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_deletion_sizes, __pyx_v_deletion_sizes) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":175 + * deletion_coordinates=deletion_coordinates, + * deletion_sizes=deletion_sizes, + * deletion_n=deletion_n, # <<<<<<<<<<<<<< + * + * all_substitution_positions=all_substitution_positions, + */ + __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_deletion_n); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 175, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_deletion_n, __pyx_t_8) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":177 + * deletion_n=deletion_n, + * + * all_substitution_positions=all_substitution_positions, # <<<<<<<<<<<<<< + * substitution_positions=substitution_positions, + * all_substitution_values=np.array(all_substitution_values), + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_all_substitution_positions, __pyx_v_all_substitution_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":178 + * + * all_substitution_positions=all_substitution_positions, + * substitution_positions=substitution_positions, # <<<<<<<<<<<<<< + * all_substitution_values=np.array(all_substitution_values), + * substitution_values=np.array(substitution_values), + */ + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_substitution_positions, __pyx_v_substitution_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":179 + * all_substitution_positions=all_substitution_positions, + * substitution_positions=substitution_positions, + * all_substitution_values=np.array(all_substitution_values), # <<<<<<<<<<<<<< + * substitution_values=np.array(substitution_values), + * substitution_n=substitution_n, + */ + __Pyx_GetModuleGlobalName(__pyx_t_9, __pyx_n_s_np); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 179, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_13 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_array); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 179, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_13); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = NULL; + __pyx_t_14 = 0; #if CYTHON_UNPACK_METHODS - if (unlikely(PyMethod_Check(__pyx_t_9))) { - __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_9); - if (likely(__pyx_t_8)) { - PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9); - __Pyx_INCREF(__pyx_t_8); + if (unlikely(PyMethod_Check(__pyx_t_13))) { + __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_13); + if (likely(__pyx_t_9)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_13); + __Pyx_INCREF(__pyx_t_9); __Pyx_INCREF(function); - __Pyx_DECREF_SET(__pyx_t_9, function); - __pyx_t_13 = 1; + __Pyx_DECREF_SET(__pyx_t_13, function); + __pyx_t_14 = 1; } } #endif { - PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_v_all_substitution_values}; - __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); - __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; - if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 133, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_all_substitution_values}; + __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_13, __pyx_callargs+1-__pyx_t_14, 1+__pyx_t_14); + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 179, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; } - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_substitution_values, __pyx_t_5) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_all_substitution_values, __pyx_t_8) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":134 - * 'substitution_positions': substitution_positions, - * 'all_substitution_values': np.array(all_substitution_values), - * 'substitution_values': np.array(substitution_values), # <<<<<<<<<<<<<< - * 'substitution_n': substitution_n, - * 'ref_positions': ref_positions, + /* "CRISPResso2/CRISPRessoCOREResources.pyx":180 + * substitution_positions=substitution_positions, + * all_substitution_values=np.array(all_substitution_values), + * substitution_values=np.array(substitution_values), # <<<<<<<<<<<<<< + * substitution_n=substitution_n, + * */ - __Pyx_GetModuleGlobalName(__pyx_t_9, __pyx_n_s_np); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 134, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_13, __pyx_n_s_np); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_13); + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_13, __pyx_n_s_array); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 180, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 134, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = NULL; - __pyx_t_13 = 0; + __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; + __pyx_t_13 = NULL; + __pyx_t_14 = 0; #if CYTHON_UNPACK_METHODS - if (unlikely(PyMethod_Check(__pyx_t_8))) { - __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_8); - if (likely(__pyx_t_9)) { - PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_8); - __Pyx_INCREF(__pyx_t_9); + if (unlikely(PyMethod_Check(__pyx_t_9))) { + __pyx_t_13 = PyMethod_GET_SELF(__pyx_t_9); + if (likely(__pyx_t_13)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9); + __Pyx_INCREF(__pyx_t_13); __Pyx_INCREF(function); - __Pyx_DECREF_SET(__pyx_t_8, function); - __pyx_t_13 = 1; + __Pyx_DECREF_SET(__pyx_t_9, function); + __pyx_t_14 = 1; } } #endif { - PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_substitution_values}; - __pyx_t_5 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_13, 1+__pyx_t_13); - __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 134, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + PyObject *__pyx_callargs[2] = {__pyx_t_13, __pyx_v_substitution_values}; + __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_14, 1+__pyx_t_14); + __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 180, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_values, __pyx_t_5) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_substitution_values, __pyx_t_8) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":135 - * 'all_substitution_values': np.array(all_substitution_values), - * 'substitution_values': np.array(substitution_values), - * 'substitution_n': substitution_n, # <<<<<<<<<<<<<< - * 'ref_positions': ref_positions, - * } + /* "CRISPResso2/CRISPRessoCOREResources.pyx":181 + * all_substitution_values=np.array(all_substitution_values), + * substitution_values=np.array(substitution_values), + * substitution_n=substitution_n, # <<<<<<<<<<<<<< + * + * ref_positions=ref_positions, */ - __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_substitution_n); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 135, __pyx_L1_error) - __Pyx_GOTREF(__pyx_t_5); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_n, __pyx_t_5) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_substitution_n); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 181, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_substitution_n, __pyx_t_8) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":136 - * 'substitution_values': np.array(substitution_values), - * 'substitution_n': substitution_n, - * 'ref_positions': ref_positions, # <<<<<<<<<<<<<< - * } - * @cython.boundscheck(False) + /* "CRISPResso2/CRISPRessoCOREResources.pyx":183 + * substitution_n=substitution_n, + * + * ref_positions=ref_positions, # <<<<<<<<<<<<<< + * ) + * */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_ref_positions, __pyx_v_ref_positions) < 0) __PYX_ERR(0, 117, __pyx_L1_error) - __pyx_r = __pyx_t_1; - __pyx_t_1 = 0; + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_ref_positions, __pyx_v_ref_positions) < 0) __PYX_ERR(0, 163, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":162 + * cdef size_t insertion_n = sum(insertion_sizes) + * + * return ResultsSlotsDict( # <<<<<<<<<<<<<< + * all_insertion_positions=all_insertion_positions, + * all_insertion_left_positions=all_insertion_left_positions, + */ + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_empty_tuple, __pyx_t_5); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 162, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_r = __pyx_t_8; + __pyx_t_8 = 0; goto __pyx_L0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":18 - * re_find_indels = re.compile("(-*-)") - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":64 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) @@ -6755,6 +7565,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_8); __Pyx_XDECREF(__pyx_t_9); + __Pyx_XDECREF(__pyx_t_13); __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.find_indels_substitutions", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; @@ -6782,16 +7593,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su return __pyx_r; } -/* "CRISPResso2/CRISPRessoCOREResources.pyx":138 - * 'ref_positions': ref_positions, - * } +/* "CRISPResso2/CRISPRessoCOREResources.pyx":187 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) */ /* Python wrapper */ -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -6799,7 +7610,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds #endif ); /*proto*/ static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy = {"find_indels_substitutions_legacy", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -6849,7 +7660,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 138, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 187, __pyx_L3_error) else goto __pyx_L5_argtuple_error; CYTHON_FALLTHROUGH; case 1: @@ -6857,9 +7668,9 @@ PyObject *__pyx_args, PyObject *__pyx_kwds (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 138, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 187, __pyx_L3_error) else { - __Pyx_RaiseArgtupleInvalid("find_indels_substitutions_legacy", 1, 3, 3, 1); __PYX_ERR(0, 138, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("find_indels_substitutions_legacy", 1, 3, 3, 1); __PYX_ERR(0, 187, __pyx_L3_error) } CYTHON_FALLTHROUGH; case 2: @@ -6867,14 +7678,14 @@ PyObject *__pyx_args, PyObject *__pyx_kwds (void)__Pyx_Arg_NewRef_FASTCALL(values[2]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 138, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 187, __pyx_L3_error) else { - __Pyx_RaiseArgtupleInvalid("find_indels_substitutions_legacy", 1, 3, 3, 2); __PYX_ERR(0, 138, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("find_indels_substitutions_legacy", 1, 3, 3, 2); __PYX_ERR(0, 187, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "find_indels_substitutions_legacy") < 0)) __PYX_ERR(0, 138, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "find_indels_substitutions_legacy") < 0)) __PYX_ERR(0, 187, __pyx_L3_error) } } else if (unlikely(__pyx_nargs != 3)) { goto __pyx_L5_argtuple_error; @@ -6889,7 +7700,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds } goto __pyx_L6_skip; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("find_indels_substitutions_legacy", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 138, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("find_indels_substitutions_legacy", 1, 3, 3, __pyx_nargs); __PYX_ERR(0, 187, __pyx_L3_error) __pyx_L6_skip:; goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; @@ -6971,93 +7782,93 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("find_indels_substitutions_legacy", 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":145 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":192 * def find_indels_substitutions_legacy(read_seq_al, ref_seq_al, _include_indx): - * + * * cdef char* sub_seq='' # <<<<<<<<<<<<<< - * + * * cdef int st */ __pyx_v_sub_seq = ((char *)""); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":162 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":209 * # aln A - T T T G G C C * # 1 2 3 4-4 5 6 7 8 = __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 169, __pyx_L1_error) + __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 216, __pyx_L1_error) #else - __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 169, __pyx_L1_error) + __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 216, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif } else { { Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1); #if !CYTHON_ASSUME_SAFE_MACROS - if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 169, __pyx_L1_error) + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 216, __pyx_L1_error) #endif if (__pyx_t_3 >= __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 169, __pyx_L1_error) + __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 216, __pyx_L1_error) #else - __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 169, __pyx_L1_error) + __pyx_t_5 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 216, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif } @@ -7120,7 +7931,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else __PYX_ERR(0, 169, __pyx_L1_error) + else __PYX_ERR(0, 216, __pyx_L1_error) } break; } @@ -7131,128 +7942,128 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_v_idx_c = __pyx_t_2; __pyx_t_2 = (__pyx_t_2 + 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":170 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":217 * idx=0 * for idx_c, c in enumerate(ref_seq_al): * if c in nucSet: # <<<<<<<<<<<<<< * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': */ - __pyx_t_6 = (__Pyx_PySet_ContainsTF(__pyx_v_c, __pyx_v_nucSet, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 170, __pyx_L1_error) + __pyx_t_6 = (__Pyx_PySet_ContainsTF(__pyx_v_c, __pyx_v_nucSet, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 217, __pyx_L1_error) if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":171 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":218 * for idx_c, c in enumerate(ref_seq_al): * if c in nucSet: * ref_positions.append(idx) # <<<<<<<<<<<<<< * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': * all_substitution_positions.append(idx) */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 171, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 218, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 171, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 218, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":172 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":219 * if c in nucSet: * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': # <<<<<<<<<<<<<< * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) */ - __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_ref_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_ref_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = PyObject_RichCompare(__pyx_t_5, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_9 = PyObject_RichCompare(__pyx_t_5, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_10) { } else { __pyx_t_6 = __pyx_t_10; goto __pyx_L7_bool_binop_done; } - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_kp_u__3, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_10) { } else { __pyx_t_6 = __pyx_t_10; goto __pyx_L7_bool_binop_done; } - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_n_u_N, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 172, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PyUnicode_Equals(__pyx_t_9, __pyx_n_u_N, Py_NE)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 219, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_6 = __pyx_t_10; __pyx_L7_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":173 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":220 * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': * all_substitution_positions.append(idx) # <<<<<<<<<<<<<< * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 173, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 220, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 173, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 220, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":174 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":221 * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) # <<<<<<<<<<<<<< * if idx in _include_indx: * substitution_positions.append(idx) */ - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 174, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 221, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 174, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 221, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":175 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":222 * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: # <<<<<<<<<<<<<< * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 175, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 222, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = (__Pyx_PySequence_ContainsTF(__pyx_t_9, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 175, __pyx_L1_error) + __pyx_t_6 = (__Pyx_PySequence_ContainsTF(__pyx_t_9, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_6 < 0))) __PYX_ERR(0, 222, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":176 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":223 * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: * substitution_positions.append(idx) # <<<<<<<<<<<<<< * substitution_values.append(read_seq_al[idx_c]) - * + * */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 176, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_idx); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 223, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 176, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 223, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":177 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":224 * if idx in _include_indx: * substitution_positions.append(idx) * substitution_values.append(read_seq_al[idx_c]) # <<<<<<<<<<<<<< - * + * * idx+=1 */ - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 177, __pyx_L1_error) + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_read_seq_al, __pyx_v_idx_c, int, 1, __Pyx_PyInt_From_int, 0, 0, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 224, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 177, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_substitution_values, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 224, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":175 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":222 * all_substitution_positions.append(idx) * all_substitution_values.append(read_seq_al[idx_c]) * if idx in _include_indx: # <<<<<<<<<<<<<< @@ -7261,7 +8072,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":172 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":219 * if c in nucSet: * ref_positions.append(idx) * if ref_seq_al[idx_c]!=read_seq_al[idx_c] and read_seq_al[idx_c] != '-' and read_seq_al[idx_c] != 'N': # <<<<<<<<<<<<<< @@ -7270,16 +8081,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":179 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":226 * substitution_values.append(read_seq_al[idx_c]) - * + * * idx+=1 # <<<<<<<<<<<<<< - * + * * else: */ __pyx_v_idx = (__pyx_v_idx + 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":170 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":217 * idx=0 * for idx_c, c in enumerate(ref_seq_al): * if c in nucSet: # <<<<<<<<<<<<<< @@ -7289,8 +8100,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s goto __pyx_L5; } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":182 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":229 + * * else: * if idx==0: # <<<<<<<<<<<<<< * ref_positions.append(-1) @@ -7300,17 +8111,17 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_t_6 = (__pyx_v_idx == 0); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":183 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":230 * else: * if idx==0: * ref_positions.append(-1) # <<<<<<<<<<<<<< * else: * ref_positions.append(-idx) */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_int_neg_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 183, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_int_neg_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 230, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":182 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":229 + * * else: * if idx==0: # <<<<<<<<<<<<<< * ref_positions.append(-1) @@ -7319,24 +8130,24 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s goto __pyx_L11; } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":185 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":232 * ref_positions.append(-1) * else: * ref_positions.append(-idx) # <<<<<<<<<<<<<< - * + * * substitution_n = len(substitution_positions) */ /*else*/ { - __pyx_t_9 = __Pyx_PyInt_From_int((-__pyx_v_idx)); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 185, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyInt_From_int((-__pyx_v_idx)); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 232, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 185, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_ref_positions, __pyx_t_9); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 232, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } __pyx_L11:; } __pyx_L5:; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":169 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":216 * nucSet = set(['A', 'T', 'C', 'G', 'N']) * idx=0 * for idx_c, c in enumerate(ref_seq_al): # <<<<<<<<<<<<<< @@ -7346,158 +8157,158 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":187 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":234 * ref_positions.append(-idx) - * + * * substitution_n = len(substitution_positions) # <<<<<<<<<<<<<< - * + * * #the remainder of positions are with reference to the original reference sequence indexes we calculated above */ - __pyx_t_3 = __Pyx_PyList_GET_SIZE(__pyx_v_substitution_positions); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 187, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyList_GET_SIZE(__pyx_v_substitution_positions); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1))) __PYX_ERR(0, 234, __pyx_L1_error) __pyx_v_substitution_n = __pyx_t_3; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":190 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":237 + * * #the remainder of positions are with reference to the original reference sequence indexes we calculated above * all_deletion_positions=[] # <<<<<<<<<<<<<< * deletion_positions=[] * deletion_coordinates=[] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 190, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 237, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_all_deletion_positions = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":191 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":238 * #the remainder of positions are with reference to the original reference sequence indexes we calculated above * all_deletion_positions=[] * deletion_positions=[] # <<<<<<<<<<<<<< * deletion_coordinates=[] * all_deletion_coordinates=[] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 191, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 238, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_deletion_positions = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":192 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":239 * all_deletion_positions=[] * deletion_positions=[] * deletion_coordinates=[] # <<<<<<<<<<<<<< * all_deletion_coordinates=[] * deletion_sizes=[] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 192, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 239, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_deletion_coordinates = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":193 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":240 * deletion_positions=[] * deletion_coordinates=[] * all_deletion_coordinates=[] # <<<<<<<<<<<<<< * deletion_sizes=[] - * + * */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 193, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 240, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_all_deletion_coordinates = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":194 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":241 * deletion_coordinates=[] * all_deletion_coordinates=[] * deletion_sizes=[] # <<<<<<<<<<<<<< - * + * * all_insertion_positions=[] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 194, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 241, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_deletion_sizes = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":196 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":243 * deletion_sizes=[] - * + * * all_insertion_positions=[] # <<<<<<<<<<<<<< * all_insertion_left_positions=[] * insertion_positions=[] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 196, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 243, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_all_insertion_positions = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":197 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":244 + * * all_insertion_positions=[] * all_insertion_left_positions=[] # <<<<<<<<<<<<<< * insertion_positions=[] * insertion_coordinates = [] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 197, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 244, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_all_insertion_left_positions = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":198 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":245 * all_insertion_positions=[] * all_insertion_left_positions=[] * insertion_positions=[] # <<<<<<<<<<<<<< * insertion_coordinates = [] * insertion_sizes=[] */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 198, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 245, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_insertion_positions = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":199 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":246 * all_insertion_left_positions=[] * insertion_positions=[] * insertion_coordinates = [] # <<<<<<<<<<<<<< * insertion_sizes=[] - * + * */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 199, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 246, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_insertion_coordinates = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":200 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":247 * insertion_positions=[] * insertion_coordinates = [] * insertion_sizes=[] # <<<<<<<<<<<<<< - * + * * include_indx_set = set(_include_indx) */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 200, __pyx_L1_error) + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 247, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_insertion_sizes = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":202 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":249 * insertion_sizes=[] - * + * * include_indx_set = set(_include_indx) # <<<<<<<<<<<<<< * for p in re_find_indels.finditer(read_seq_al): * st,en=p.span() */ - __pyx_t_1 = PySet_New(__pyx_v__include_indx); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 202, __pyx_L1_error) + __pyx_t_1 = PySet_New(__pyx_v__include_indx); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 249, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_v_include_indx_set = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":203 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":250 + * * include_indx_set = set(_include_indx) * for p in re_find_indels.finditer(read_seq_al): # <<<<<<<<<<<<<< * st,en=p.span() * ref_st = 0 */ - __Pyx_GetModuleGlobalName(__pyx_t_9, __pyx_n_s_re_find_indels); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 203, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_9, __pyx_n_s_re_find_indels); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 250, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_finditer); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_9, __pyx_n_s_finditer); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 250, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_9 = NULL; @@ -7518,7 +8329,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_v_read_seq_al}; __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_11, 1+__pyx_t_11); __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 203, __pyx_L1_error) + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 250, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } @@ -7527,9 +8338,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_t_3 = 0; __pyx_t_4 = NULL; } else { - __pyx_t_3 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_3 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 250, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_4 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_8); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_8); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 250, __pyx_L1_error) } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; for (;;) { @@ -7538,28 +8349,28 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s { Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_8); #if !CYTHON_ASSUME_SAFE_MACROS - if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 203, __pyx_L1_error) + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 250, __pyx_L1_error) #endif if (__pyx_t_3 >= __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_1 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 250, __pyx_L1_error) #else - __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_8, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_8, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 250, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); #endif } else { { Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_8); #if !CYTHON_ASSUME_SAFE_MACROS - if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 203, __pyx_L1_error) + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 250, __pyx_L1_error) #endif if (__pyx_t_3 >= __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 250, __pyx_L1_error) #else - __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_8, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_1 = __Pyx_PySequence_ITEM(__pyx_t_8, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 250, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); #endif } @@ -7569,7 +8380,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else __PYX_ERR(0, 203, __pyx_L1_error) + else __PYX_ERR(0, 250, __pyx_L1_error) } break; } @@ -7578,14 +8389,14 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_XDECREF_SET(__pyx_v_p, __pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":204 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":251 * include_indx_set = set(_include_indx) * for p in re_find_indels.finditer(read_seq_al): * st,en=p.span() # <<<<<<<<<<<<<< * ref_st = 0 * if st-1 > 0: */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_p, __pyx_n_s_span); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 204, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_p, __pyx_n_s_span); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_5 = NULL; __pyx_t_11 = 0; @@ -7605,7 +8416,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_5, NULL}; __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_11, 0+__pyx_t_11); __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 204, __pyx_L1_error) + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } @@ -7615,28 +8426,28 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s if (unlikely(size != 2)) { if (size > 2) __Pyx_RaiseTooManyValuesError(2); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - __PYX_ERR(0, 204, __pyx_L1_error) + __PYX_ERR(0, 251, __pyx_L1_error) } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS if (likely(PyTuple_CheckExact(sequence))) { - __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0); - __pyx_t_5 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_5 = PyTuple_GET_ITEM(sequence, 1); } else { - __pyx_t_9 = PyList_GET_ITEM(sequence, 0); - __pyx_t_5 = PyList_GET_ITEM(sequence, 1); + __pyx_t_9 = PyList_GET_ITEM(sequence, 0); + __pyx_t_5 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_9); __Pyx_INCREF(__pyx_t_5); #else - __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 204, __pyx_L1_error) + __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 204, __pyx_L1_error) + __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); #endif __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } else { Py_ssize_t index = -1; - __pyx_t_12 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_12 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_12); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_13 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_12); @@ -7644,7 +8455,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_GOTREF(__pyx_t_9); index = 1; __pyx_t_5 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_5)) goto __pyx_L15_unpacking_failed; __Pyx_GOTREF(__pyx_t_5); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) __PYX_ERR(0, 203, __pyx_L1_error) + if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) __PYX_ERR(0, 251, __pyx_L1_error) __pyx_t_13 = NULL; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; goto __pyx_L16_unpacking_done; @@ -7652,17 +8463,17 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; __pyx_t_13 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - __PYX_ERR(0, 204, __pyx_L1_error) + __PYX_ERR(0, 251, __pyx_L1_error) __pyx_L16_unpacking_done:; } - __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 204, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 203, __pyx_L1_error) + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 251, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_st = __pyx_t_2; __pyx_v_en = __pyx_t_14; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":205 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":252 * for p in re_find_indels.finditer(read_seq_al): * st,en=p.span() * ref_st = 0 # <<<<<<<<<<<<<< @@ -7672,7 +8483,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_INCREF(__pyx_int_0); __Pyx_XDECREF_SET(__pyx_v_ref_st, __pyx_int_0); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":206 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":253 * st,en=p.span() * ref_st = 0 * if st-1 > 0: # <<<<<<<<<<<<<< @@ -7682,7 +8493,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_t_6 = ((__pyx_v_st - 1) > 0); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":207 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":254 * ref_st = 0 * if st-1 > 0: * ref_st = ref_positions[st] # <<<<<<<<<<<<<< @@ -7694,7 +8505,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_DECREF_SET(__pyx_v_ref_st, __pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":206 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":253 * st,en=p.span() * ref_st = 0 * if st-1 > 0: # <<<<<<<<<<<<<< @@ -7703,30 +8514,30 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":208 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":255 * if st-1 > 0: * ref_st = ref_positions[st] * ref_en = idx-1 # <<<<<<<<<<<<<< * if en < len(ref_positions): * ref_en = ref_positions[en] */ - __pyx_t_1 = __Pyx_PyInt_From_long((__pyx_v_idx - 1)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 208, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_long((__pyx_v_idx - 1)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 255, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_XDECREF_SET(__pyx_v_ref_en, __pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":209 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":256 * ref_st = ref_positions[st] * ref_en = idx-1 * if en < len(ref_positions): # <<<<<<<<<<<<<< * ref_en = ref_positions[en] * all_deletion_positions.extend(range(ref_st,ref_en)) */ - __pyx_t_15 = __Pyx_PyList_GET_SIZE(__pyx_v_ref_positions); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 208, __pyx_L1_error) + __pyx_t_15 = __Pyx_PyList_GET_SIZE(__pyx_v_ref_positions); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 256, __pyx_L1_error) __pyx_t_6 = (__pyx_v_en < __pyx_t_15); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":210 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":257 * ref_en = idx-1 * if en < len(ref_positions): * ref_en = ref_positions[en] # <<<<<<<<<<<<<< @@ -7738,7 +8549,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_DECREF_SET(__pyx_v_ref_en, __pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":209 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":256 * ref_st = ref_positions[st] * ref_en = idx-1 * if en < len(ref_positions): # <<<<<<<<<<<<<< @@ -7747,132 +8558,132 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":211 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":258 * if en < len(ref_positions): * ref_en = ref_positions[en] * all_deletion_positions.extend(range(ref_st,ref_en)) # <<<<<<<<<<<<<< * all_deletion_coordinates.append((ref_st,ref_en)) * inc_del_pos = include_indx_set.intersection(range(ref_st,ref_en)) */ - __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 211, __pyx_L1_error) + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 258, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_ref_st); __Pyx_GIVEREF(__pyx_v_ref_st); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_ref_st)) __PYX_ERR(0, 211, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_ref_st)) __PYX_ERR(0, 258, __pyx_L1_error); __Pyx_INCREF(__pyx_v_ref_en); __Pyx_GIVEREF(__pyx_v_ref_en); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_ref_en)) __PYX_ERR(0, 211, __pyx_L1_error); - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 211, __pyx_L1_error) + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_ref_en)) __PYX_ERR(0, 258, __pyx_L1_error); + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 258, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_all_deletion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 211, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_all_deletion_positions, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 258, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":212 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":259 * ref_en = ref_positions[en] * all_deletion_positions.extend(range(ref_st,ref_en)) * all_deletion_coordinates.append((ref_st,ref_en)) # <<<<<<<<<<<<<< * inc_del_pos = include_indx_set.intersection(range(ref_st,ref_en)) * if(len(inc_del_pos)>0): */ - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 212, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 259, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_ref_st); __Pyx_GIVEREF(__pyx_v_ref_st); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ref_st)) __PYX_ERR(0, 212, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ref_st)) __PYX_ERR(0, 259, __pyx_L1_error); __Pyx_INCREF(__pyx_v_ref_en); __Pyx_GIVEREF(__pyx_v_ref_en); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_ref_en)) __PYX_ERR(0, 212, __pyx_L1_error); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_deletion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 212, __pyx_L1_error) + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_ref_en)) __PYX_ERR(0, 259, __pyx_L1_error); + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_deletion_coordinates, __pyx_t_5); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 259, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":213 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":260 * all_deletion_positions.extend(range(ref_st,ref_en)) * all_deletion_coordinates.append((ref_st,ref_en)) * inc_del_pos = include_indx_set.intersection(range(ref_st,ref_en)) # <<<<<<<<<<<<<< * if(len(inc_del_pos)>0): * deletion_positions.extend(range(ref_st,ref_en)) */ - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 213, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 260, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_ref_st); __Pyx_GIVEREF(__pyx_v_ref_st); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ref_st)) __PYX_ERR(0, 213, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ref_st)) __PYX_ERR(0, 260, __pyx_L1_error); __Pyx_INCREF(__pyx_v_ref_en); __Pyx_GIVEREF(__pyx_v_ref_en); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_ref_en)) __PYX_ERR(0, 213, __pyx_L1_error); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 213, __pyx_L1_error) + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_ref_en)) __PYX_ERR(0, 260, __pyx_L1_error); + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 260, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PySet_Type_intersection, __pyx_v_include_indx_set, __pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 213, __pyx_L1_error) + __pyx_t_5 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PySet_Type_intersection, __pyx_v_include_indx_set, __pyx_t_1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 260, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF_SET(__pyx_v_inc_del_pos, __pyx_t_5); __pyx_t_5 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":214 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":261 * all_deletion_coordinates.append((ref_st,ref_en)) * inc_del_pos = include_indx_set.intersection(range(ref_st,ref_en)) * if(len(inc_del_pos)>0): # <<<<<<<<<<<<<< * deletion_positions.extend(range(ref_st,ref_en)) * deletion_coordinates.append((ref_st,ref_en)) */ - __pyx_t_15 = PyObject_Length(__pyx_v_inc_del_pos); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 212, __pyx_L1_error) + __pyx_t_15 = PyObject_Length(__pyx_v_inc_del_pos); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 261, __pyx_L1_error) __pyx_t_6 = (__pyx_t_15 > 0); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":215 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":262 * inc_del_pos = include_indx_set.intersection(range(ref_st,ref_en)) * if(len(inc_del_pos)>0): * deletion_positions.extend(range(ref_st,ref_en)) # <<<<<<<<<<<<<< * deletion_coordinates.append((ref_st,ref_en)) * deletion_sizes.append(en-st) */ - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 215, __pyx_L1_error) + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 262, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_ref_st); __Pyx_GIVEREF(__pyx_v_ref_st); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ref_st)) __PYX_ERR(0, 215, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ref_st)) __PYX_ERR(0, 262, __pyx_L1_error); __Pyx_INCREF(__pyx_v_ref_en); __Pyx_GIVEREF(__pyx_v_ref_en); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_ref_en)) __PYX_ERR(0, 215, __pyx_L1_error); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 215, __pyx_L1_error) + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_ref_en)) __PYX_ERR(0, 262, __pyx_L1_error); + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_range, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 262, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_deletion_positions, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 215, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Extend(__pyx_v_deletion_positions, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 262, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":216 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":263 * if(len(inc_del_pos)>0): * deletion_positions.extend(range(ref_st,ref_en)) * deletion_coordinates.append((ref_st,ref_en)) # <<<<<<<<<<<<<< * deletion_sizes.append(en-st) - * + * */ - __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 216, __pyx_L1_error) + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 263, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_ref_st); __Pyx_GIVEREF(__pyx_v_ref_st); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_ref_st)) __PYX_ERR(0, 216, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_ref_st)) __PYX_ERR(0, 263, __pyx_L1_error); __Pyx_INCREF(__pyx_v_ref_en); __Pyx_GIVEREF(__pyx_v_ref_en); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_ref_en)) __PYX_ERR(0, 216, __pyx_L1_error); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_coordinates, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 216, __pyx_L1_error) + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_ref_en)) __PYX_ERR(0, 263, __pyx_L1_error); + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_coordinates, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 263, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":217 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":264 * deletion_positions.extend(range(ref_st,ref_en)) * deletion_coordinates.append((ref_st,ref_en)) * deletion_sizes.append(en-st) # <<<<<<<<<<<<<< - * + * * deletion_n = np.sum(deletion_sizes) */ - __pyx_t_1 = __Pyx_PyInt_From_int((__pyx_v_en - __pyx_v_st)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 217, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyInt_From_int((__pyx_v_en - __pyx_v_st)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 264, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_sizes, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 217, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_deletion_sizes, __pyx_t_1); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 264, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":214 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":261 * all_deletion_coordinates.append((ref_st,ref_en)) * inc_del_pos = include_indx_set.intersection(range(ref_st,ref_en)) * if(len(inc_del_pos)>0): # <<<<<<<<<<<<<< @@ -7881,8 +8692,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":203 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":250 + * * include_indx_set = set(_include_indx) * for p in re_find_indels.finditer(read_seq_al): # <<<<<<<<<<<<<< * st,en=p.span() @@ -7891,16 +8702,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s } __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":219 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":266 * deletion_sizes.append(en-st) - * + * * deletion_n = np.sum(deletion_sizes) # <<<<<<<<<<<<<< - * + * * for p in re_find_indels.finditer(ref_seq_al): */ - __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 219, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 266, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 219, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 266, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = NULL; @@ -7921,23 +8732,23 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_1, __pyx_v_deletion_sizes}; __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_11, 1+__pyx_t_11); __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; - if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 219, __pyx_L1_error) + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 266, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __pyx_v_deletion_n = __pyx_t_8; __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":221 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":268 * deletion_n = np.sum(deletion_sizes) - * + * * for p in re_find_indels.finditer(ref_seq_al): # <<<<<<<<<<<<<< * st,en=p.span() * #sometimes insertions run off the end of the reference */ - __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_re_find_indels); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 221, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_re_find_indels); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 268, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_finditer); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_finditer); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 268, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -7958,7 +8769,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_ref_seq_al}; __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_1, __pyx_callargs+1-__pyx_t_11, 1+__pyx_t_11); __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 221, __pyx_L1_error) + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 268, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } @@ -7967,9 +8778,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_t_3 = 0; __pyx_t_4 = NULL; } else { - __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 268, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_4 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 268, __pyx_L1_error) } __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; for (;;) { @@ -7978,28 +8789,28 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s { Py_ssize_t __pyx_temp = __Pyx_PyList_GET_SIZE(__pyx_t_1); #if !CYTHON_ASSUME_SAFE_MACROS - if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 221, __pyx_L1_error) + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 268, __pyx_L1_error) #endif if (__pyx_t_3 >= __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_8 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 268, __pyx_L1_error) #else - __pyx_t_8 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_8 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 268, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); #endif } else { { Py_ssize_t __pyx_temp = __Pyx_PyTuple_GET_SIZE(__pyx_t_1); #if !CYTHON_ASSUME_SAFE_MACROS - if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 221, __pyx_L1_error) + if (unlikely((__pyx_temp < 0))) __PYX_ERR(0, 268, __pyx_L1_error) #endif if (__pyx_t_3 >= __pyx_temp) break; } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely((0 < 0))) __PYX_ERR(0, 268, __pyx_L1_error) #else - __pyx_t_8 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 221, __pyx_L1_error) + __pyx_t_8 = __Pyx_PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 268, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); #endif } @@ -8009,7 +8820,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else __PYX_ERR(0, 221, __pyx_L1_error) + else __PYX_ERR(0, 268, __pyx_L1_error) } break; } @@ -8018,14 +8829,14 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_XDECREF_SET(__pyx_v_p, __pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":222 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":269 + * * for p in re_find_indels.finditer(ref_seq_al): * st,en=p.span() # <<<<<<<<<<<<<< * #sometimes insertions run off the end of the reference * if st == 0: # if insertion happened before ref */ - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_p, __pyx_n_s_span); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 222, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_p, __pyx_n_s_span); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_t_9 = NULL; __pyx_t_11 = 0; @@ -8045,7 +8856,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_9, NULL}; __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_11, 0+__pyx_t_11); __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 222, __pyx_L1_error) + if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } @@ -8055,28 +8866,28 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s if (unlikely(size != 2)) { if (size > 2) __Pyx_RaiseTooManyValuesError(2); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - __PYX_ERR(0, 222, __pyx_L1_error) + __PYX_ERR(0, 269, __pyx_L1_error) } #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS if (likely(PyTuple_CheckExact(sequence))) { - __pyx_t_5 = PyTuple_GET_ITEM(sequence, 0); - __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_5 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1); } else { - __pyx_t_5 = PyList_GET_ITEM(sequence, 0); - __pyx_t_9 = PyList_GET_ITEM(sequence, 1); + __pyx_t_5 = PyList_GET_ITEM(sequence, 0); + __pyx_t_9 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_5); __Pyx_INCREF(__pyx_t_9); #else - __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 222, __pyx_L1_error) + __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 222, __pyx_L1_error) + __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); #endif __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } else { Py_ssize_t index = -1; - __pyx_t_12 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 220, __pyx_L1_error) + __pyx_t_12 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_12); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_13 = __Pyx_PyObject_GetIterNextFunc(__pyx_t_12); @@ -8084,7 +8895,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_GOTREF(__pyx_t_5); index = 1; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L23_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) __PYX_ERR(0, 220, __pyx_L1_error) + if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) __PYX_ERR(0, 269, __pyx_L1_error) __pyx_t_13 = NULL; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; goto __pyx_L24_unpacking_done; @@ -8092,17 +8903,17 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; __pyx_t_13 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - __PYX_ERR(0, 222, __pyx_L1_error) + __PYX_ERR(0, 269, __pyx_L1_error) __pyx_L24_unpacking_done:; } - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 220, __pyx_L1_error) + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 222, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 269, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_st = __pyx_t_14; __pyx_v_en = __pyx_t_2; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":224 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":271 * st,en=p.span() * #sometimes insertions run off the end of the reference * if st == 0: # if insertion happened before ref # <<<<<<<<<<<<<< @@ -8112,7 +8923,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __pyx_t_6 = (__pyx_v_st == 0); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":225 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":272 * #sometimes insertions run off the end of the reference * if st == 0: # if insertion happened before ref * continue # <<<<<<<<<<<<<< @@ -8121,7 +8932,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ goto __pyx_L21_continue; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":224 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":271 * st,en=p.span() * #sometimes insertions run off the end of the reference * if st == 0: # if insertion happened before ref # <<<<<<<<<<<<<< @@ -8130,18 +8941,18 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":226 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":273 * if st == 0: # if insertion happened before ref * continue * if en == len(ref_seq_al): # if insertion happened after ref # <<<<<<<<<<<<<< * continue * ref_st = ref_positions[st-1] */ - __pyx_t_15 = PyObject_Length(__pyx_v_ref_seq_al); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 224, __pyx_L1_error) + __pyx_t_15 = PyObject_Length(__pyx_v_ref_seq_al); if (unlikely(__pyx_t_15 == ((Py_ssize_t)-1))) __PYX_ERR(0, 273, __pyx_L1_error) __pyx_t_6 = (__pyx_v_en == __pyx_t_15); if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":227 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":274 * continue * if en == len(ref_seq_al): # if insertion happened after ref * continue # <<<<<<<<<<<<<< @@ -8150,7 +8961,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ goto __pyx_L21_continue; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":226 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":273 * if st == 0: # if insertion happened before ref * continue * if en == len(ref_seq_al): # if insertion happened after ref # <<<<<<<<<<<<<< @@ -8159,12 +8970,12 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":228 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":275 * if en == len(ref_seq_al): # if insertion happened after ref * continue * ref_st = ref_positions[st-1] # <<<<<<<<<<<<<< * ref_en = ref_positions[en] - * + * */ __pyx_t_16 = (__pyx_v_st - 1); __pyx_t_8 = PyList_GET_ITEM(__pyx_v_ref_positions, __pyx_t_16); @@ -8172,11 +8983,11 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_XDECREF_SET(__pyx_v_ref_st, __pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":229 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":276 * continue * ref_st = ref_positions[st-1] * ref_en = ref_positions[en] # <<<<<<<<<<<<<< - * + * * all_insertion_left_positions.append(ref_st) */ __pyx_t_8 = PyList_GET_ITEM(__pyx_v_ref_positions, __pyx_v_en); @@ -8184,100 +8995,100 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s __Pyx_XDECREF_SET(__pyx_v_ref_en, __pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":231 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":278 * ref_en = ref_positions[en] - * + * * all_insertion_left_positions.append(ref_st) # <<<<<<<<<<<<<< * all_insertion_positions.append(ref_st) * all_insertion_positions.append(ref_en) */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_left_positions, __pyx_v_ref_st); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 231, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_left_positions, __pyx_v_ref_st); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 278, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":232 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":279 + * * all_insertion_left_positions.append(ref_st) * all_insertion_positions.append(ref_st) # <<<<<<<<<<<<<< * all_insertion_positions.append(ref_en) * if(ref_st in _include_indx or ref_en in _include_indx): */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_v_ref_st); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 232, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_v_ref_st); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 279, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":233 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":280 * all_insertion_left_positions.append(ref_st) * all_insertion_positions.append(ref_st) * all_insertion_positions.append(ref_en) # <<<<<<<<<<<<<< * if(ref_st in _include_indx or ref_en in _include_indx): * insertion_coordinates.append((ref_st,ref_en)) */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_v_ref_en); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 233, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_all_insertion_positions, __pyx_v_ref_en); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 280, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":234 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":281 * all_insertion_positions.append(ref_st) * all_insertion_positions.append(ref_en) * if(ref_st in _include_indx or ref_en in _include_indx): # <<<<<<<<<<<<<< * insertion_coordinates.append((ref_st,ref_en)) * insertion_positions.append(ref_st) */ - __pyx_t_10 = (__Pyx_PySequence_ContainsTF(__pyx_v_ref_st, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 234, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PySequence_ContainsTF(__pyx_v_ref_st, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 281, __pyx_L1_error) if (!__pyx_t_10) { } else { __pyx_t_6 = __pyx_t_10; goto __pyx_L28_bool_binop_done; } - __pyx_t_10 = (__Pyx_PySequence_ContainsTF(__pyx_v_ref_en, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 234, __pyx_L1_error) + __pyx_t_10 = (__Pyx_PySequence_ContainsTF(__pyx_v_ref_en, __pyx_v__include_indx, Py_EQ)); if (unlikely((__pyx_t_10 < 0))) __PYX_ERR(0, 281, __pyx_L1_error) __pyx_t_6 = __pyx_t_10; __pyx_L28_bool_binop_done:; if (__pyx_t_6) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":235 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":282 * all_insertion_positions.append(ref_en) * if(ref_st in _include_indx or ref_en in _include_indx): * insertion_coordinates.append((ref_st,ref_en)) # <<<<<<<<<<<<<< * insertion_positions.append(ref_st) * insertion_positions.append(ref_en) */ - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 235, __pyx_L1_error) + __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 282, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_INCREF(__pyx_v_ref_st); __Pyx_GIVEREF(__pyx_v_ref_st); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_ref_st)) __PYX_ERR(0, 235, __pyx_L1_error); + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_ref_st)) __PYX_ERR(0, 282, __pyx_L1_error); __Pyx_INCREF(__pyx_v_ref_en); __Pyx_GIVEREF(__pyx_v_ref_en); - if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_ref_en)) __PYX_ERR(0, 235, __pyx_L1_error); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_coordinates, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 235, __pyx_L1_error) + if (__Pyx_PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_ref_en)) __PYX_ERR(0, 282, __pyx_L1_error); + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_coordinates, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 282, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":236 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":283 * if(ref_st in _include_indx or ref_en in _include_indx): * insertion_coordinates.append((ref_st,ref_en)) * insertion_positions.append(ref_st) # <<<<<<<<<<<<<< * insertion_positions.append(ref_en) * insertion_sizes.append(en-st) */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_v_ref_st); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 236, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_v_ref_st); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 283, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":237 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":284 * insertion_coordinates.append((ref_st,ref_en)) * insertion_positions.append(ref_st) * insertion_positions.append(ref_en) # <<<<<<<<<<<<<< * insertion_sizes.append(en-st) - * + * */ - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_v_ref_en); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 237, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_positions, __pyx_v_ref_en); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 284, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":238 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":285 * insertion_positions.append(ref_st) * insertion_positions.append(ref_en) * insertion_sizes.append(en-st) # <<<<<<<<<<<<<< - * + * * insertion_n = np.sum(insertion_sizes) */ - __pyx_t_8 = __Pyx_PyInt_From_int((__pyx_v_en - __pyx_v_st)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 238, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyInt_From_int((__pyx_v_en - __pyx_v_st)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 285, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_sizes, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 238, __pyx_L1_error) + __pyx_t_7 = __Pyx_PyList_Append(__pyx_v_insertion_sizes, __pyx_t_8); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 285, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":234 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":281 * all_insertion_positions.append(ref_st) * all_insertion_positions.append(ref_en) * if(ref_st in _include_indx or ref_en in _include_indx): # <<<<<<<<<<<<<< @@ -8286,9 +9097,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s */ } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":221 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":268 * deletion_n = np.sum(deletion_sizes) - * + * * for p in re_find_indels.finditer(ref_seq_al): # <<<<<<<<<<<<<< * st,en=p.span() * #sometimes insertions run off the end of the reference @@ -8297,16 +9108,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":240 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":287 * insertion_sizes.append(en-st) - * + * * insertion_n = np.sum(insertion_sizes) # <<<<<<<<<<<<<< - * + * * retDict = { */ - __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_np); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 240, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_np); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 287, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_sum); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 240, __pyx_L1_error) + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_sum); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 287, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_8 = NULL; @@ -8327,151 +9138,151 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_v_insertion_sizes}; __pyx_t_1 = __Pyx_PyObject_FastCall(__pyx_t_9, __pyx_callargs+1-__pyx_t_11, 1+__pyx_t_11); __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; - if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 240, __pyx_L1_error) + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 287, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } __pyx_v_insertion_n = __pyx_t_1; __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":243 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":290 + * * retDict = { * 'all_insertion_positions':all_insertion_positions, # <<<<<<<<<<<<<< * 'all_insertion_left_positions':all_insertion_left_positions, * 'insertion_positions':insertion_positions, */ - __pyx_t_1 = __Pyx_PyDict_NewPresized(18); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 243, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyDict_NewPresized(18); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 290, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_insertion_positions, __pyx_v_all_insertion_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_insertion_positions, __pyx_v_all_insertion_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":244 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":291 * retDict = { * 'all_insertion_positions':all_insertion_positions, * 'all_insertion_left_positions':all_insertion_left_positions, # <<<<<<<<<<<<<< * 'insertion_positions':insertion_positions, * 'insertion_coordinates':insertion_coordinates, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_insertion_left_positions, __pyx_v_all_insertion_left_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_insertion_left_positions, __pyx_v_all_insertion_left_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":245 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":292 * 'all_insertion_positions':all_insertion_positions, * 'all_insertion_left_positions':all_insertion_left_positions, * 'insertion_positions':insertion_positions, # <<<<<<<<<<<<<< * 'insertion_coordinates':insertion_coordinates, * 'insertion_sizes':insertion_sizes, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_positions, __pyx_v_insertion_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_positions, __pyx_v_insertion_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":246 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":293 * 'all_insertion_left_positions':all_insertion_left_positions, * 'insertion_positions':insertion_positions, * 'insertion_coordinates':insertion_coordinates, # <<<<<<<<<<<<<< * 'insertion_sizes':insertion_sizes, * 'insertion_n':insertion_n, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_coordinates, __pyx_v_insertion_coordinates) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_coordinates, __pyx_v_insertion_coordinates) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":247 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":294 * 'insertion_positions':insertion_positions, * 'insertion_coordinates':insertion_coordinates, * 'insertion_sizes':insertion_sizes, # <<<<<<<<<<<<<< * 'insertion_n':insertion_n, * 'all_deletion_positions':all_deletion_positions, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_sizes, __pyx_v_insertion_sizes) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_sizes, __pyx_v_insertion_sizes) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":248 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":295 * 'insertion_coordinates':insertion_coordinates, * 'insertion_sizes':insertion_sizes, * 'insertion_n':insertion_n, # <<<<<<<<<<<<<< * 'all_deletion_positions':all_deletion_positions, - * + * */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_n, __pyx_v_insertion_n) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_insertion_n, __pyx_v_insertion_n) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":249 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":296 * 'insertion_sizes':insertion_sizes, * 'insertion_n':insertion_n, * 'all_deletion_positions':all_deletion_positions, # <<<<<<<<<<<<<< - * + * * 'deletion_positions':deletion_positions, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_positions, __pyx_v_all_deletion_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_positions, __pyx_v_all_deletion_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":251 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":298 * 'all_deletion_positions':all_deletion_positions, - * + * * 'deletion_positions':deletion_positions, # <<<<<<<<<<<<<< * 'deletion_coordinates':deletion_coordinates, * 'all_deletion_coordinates':all_deletion_coordinates, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_positions, __pyx_v_deletion_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_positions, __pyx_v_deletion_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":252 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":299 + * * 'deletion_positions':deletion_positions, * 'deletion_coordinates':deletion_coordinates, # <<<<<<<<<<<<<< * 'all_deletion_coordinates':all_deletion_coordinates, * 'deletion_sizes':deletion_sizes, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_coordinates, __pyx_v_deletion_coordinates) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_coordinates, __pyx_v_deletion_coordinates) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":253 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":300 * 'deletion_positions':deletion_positions, * 'deletion_coordinates':deletion_coordinates, * 'all_deletion_coordinates':all_deletion_coordinates, # <<<<<<<<<<<<<< * 'deletion_sizes':deletion_sizes, * 'deletion_n':deletion_n, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_coordinates, __pyx_v_all_deletion_coordinates) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_deletion_coordinates, __pyx_v_all_deletion_coordinates) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":254 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":301 * 'deletion_coordinates':deletion_coordinates, * 'all_deletion_coordinates':all_deletion_coordinates, * 'deletion_sizes':deletion_sizes, # <<<<<<<<<<<<<< * 'deletion_n':deletion_n, - * + * */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_sizes, __pyx_v_deletion_sizes) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_sizes, __pyx_v_deletion_sizes) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":255 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":302 * 'all_deletion_coordinates':all_deletion_coordinates, * 'deletion_sizes':deletion_sizes, * 'deletion_n':deletion_n, # <<<<<<<<<<<<<< - * + * * 'all_substitution_positions':all_substitution_positions, */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_n, __pyx_v_deletion_n) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_deletion_n, __pyx_v_deletion_n) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":257 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":304 * 'deletion_n':deletion_n, - * + * * 'all_substitution_positions':all_substitution_positions, # <<<<<<<<<<<<<< * 'substitution_positions':substitution_positions, * 'all_substitution_values':np.array(all_substitution_values), */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_substitution_positions, __pyx_v_all_substitution_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_substitution_positions, __pyx_v_all_substitution_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":258 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":305 + * * 'all_substitution_positions':all_substitution_positions, * 'substitution_positions':substitution_positions, # <<<<<<<<<<<<<< * 'all_substitution_values':np.array(all_substitution_values), * 'substitution_values':np.array(substitution_values), */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_positions, __pyx_v_substitution_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_positions, __pyx_v_substitution_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":259 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":306 * 'all_substitution_positions':all_substitution_positions, * 'substitution_positions':substitution_positions, * 'all_substitution_values':np.array(all_substitution_values), # <<<<<<<<<<<<<< * 'substitution_values':np.array(substitution_values), * 'substitution_n':substitution_n, */ - __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_np); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 259, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_np); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 306, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_array); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 259, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_array); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 306, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_8 = NULL; @@ -8492,23 +9303,23 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_8, __pyx_v_all_substitution_values}; __pyx_t_9 = __Pyx_PyObject_FastCall(__pyx_t_5, __pyx_callargs+1-__pyx_t_11, 1+__pyx_t_11); __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; - if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 259, __pyx_L1_error) + if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 306, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_substitution_values, __pyx_t_9) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_all_substitution_values, __pyx_t_9) < 0) __PYX_ERR(0, 290, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":260 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":307 * 'substitution_positions':substitution_positions, * 'all_substitution_values':np.array(all_substitution_values), * 'substitution_values':np.array(substitution_values), # <<<<<<<<<<<<<< * 'substitution_n':substitution_n, - * + * */ - __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_np); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 260, __pyx_L1_error) + __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_np); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 307, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 260, __pyx_L1_error) + __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 307, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -8529,51 +9340,51 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s PyObject *__pyx_callargs[2] = {__pyx_t_5, __pyx_v_substitution_values}; __pyx_t_9 = __Pyx_PyObject_FastCall(__pyx_t_8, __pyx_callargs+1-__pyx_t_11, 1+__pyx_t_11); __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 260, __pyx_L1_error) + if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 307, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_values, __pyx_t_9) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_values, __pyx_t_9) < 0) __PYX_ERR(0, 290, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":261 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":308 * 'all_substitution_values':np.array(all_substitution_values), * 'substitution_values':np.array(substitution_values), * 'substitution_n':substitution_n, # <<<<<<<<<<<<<< - * + * * 'ref_positions':ref_positions, */ - __pyx_t_9 = PyInt_FromSsize_t(__pyx_v_substitution_n); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 261, __pyx_L1_error) + __pyx_t_9 = PyInt_FromSsize_t(__pyx_v_substitution_n); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 308, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_n, __pyx_t_9) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_substitution_n, __pyx_t_9) < 0) __PYX_ERR(0, 290, __pyx_L1_error) __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":263 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":310 * 'substitution_n':substitution_n, - * + * * 'ref_positions':ref_positions, # <<<<<<<<<<<<<< * } * return retDict */ - if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_ref_positions, __pyx_v_ref_positions) < 0) __PYX_ERR(0, 243, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_1, __pyx_n_u_ref_positions, __pyx_v_ref_positions) < 0) __PYX_ERR(0, 290, __pyx_L1_error) __pyx_v_retDict = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":265 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":312 * 'ref_positions':ref_positions, * } * return retDict # <<<<<<<<<<<<<< - * - * + * + * */ __Pyx_XDECREF(__pyx_r); __Pyx_INCREF(__pyx_v_retDict); __pyx_r = __pyx_v_retDict; goto __pyx_L0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":138 - * 'ref_positions': ref_positions, - * } + /* "CRISPResso2/CRISPRessoCOREResources.pyx":187 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) @@ -8619,16 +9430,16 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2find_indels_s return __pyx_r; } -/* "CRISPResso2/CRISPRessoCOREResources.pyx":268 - * - * +/* "CRISPResso2/CRISPRessoCOREResources.pyx":315 + * + * * def calculate_homology(a, b): # <<<<<<<<<<<<<< * cdef char *al = a * cdef char *bl = b */ /* Python wrapper */ -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -8636,7 +9447,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds #endif ); /*proto*/ static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology = {"calculate_homology", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology(PyObject *__pyx_self, +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology(PyObject *__pyx_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else @@ -8683,7 +9494,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds (void)__Pyx_Arg_NewRef_FASTCALL(values[0]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 268, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 315, __pyx_L3_error) else goto __pyx_L5_argtuple_error; CYTHON_FALLTHROUGH; case 1: @@ -8691,14 +9502,14 @@ PyObject *__pyx_args, PyObject *__pyx_kwds (void)__Pyx_Arg_NewRef_FASTCALL(values[1]); kw_args--; } - else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 268, __pyx_L3_error) + else if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 315, __pyx_L3_error) else { - __Pyx_RaiseArgtupleInvalid("calculate_homology", 1, 2, 2, 1); __PYX_ERR(0, 268, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calculate_homology", 1, 2, 2, 1); __PYX_ERR(0, 315, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "calculate_homology") < 0)) __PYX_ERR(0, 268, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values + 0, kwd_pos_args, "calculate_homology") < 0)) __PYX_ERR(0, 315, __pyx_L3_error) } } else if (unlikely(__pyx_nargs != 2)) { goto __pyx_L5_argtuple_error; @@ -8711,7 +9522,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds } goto __pyx_L6_skip; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("calculate_homology", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 268, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calculate_homology", 1, 2, 2, __pyx_nargs); __PYX_ERR(0, 315, __pyx_L3_error) __pyx_L6_skip:; goto __pyx_L4_argument_unpacking_done; __pyx_L3_error:; @@ -8757,47 +9568,47 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_hom int __pyx_clineno = 0; __Pyx_RefNannySetupContext("calculate_homology", 1); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":269 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":316 + * * def calculate_homology(a, b): * cdef char *al = a # <<<<<<<<<<<<<< * cdef char *bl = b * cdef size_t l = strlen(al) */ - __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_a); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 269, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_a); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 316, __pyx_L1_error) __pyx_v_al = __pyx_t_1; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":270 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":317 * def calculate_homology(a, b): * cdef char *al = a * cdef char *bl = b # <<<<<<<<<<<<<< * cdef size_t l = strlen(al) * cdef float score = 0.0 */ - __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_b); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 270, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_b); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 317, __pyx_L1_error) __pyx_v_bl = __pyx_t_1; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":271 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":318 * cdef char *al = a * cdef char *bl = b * cdef size_t l = strlen(al) # <<<<<<<<<<<<<< * cdef float score = 0.0 - * + * */ __pyx_v_l = strlen(__pyx_v_al); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":272 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":319 * cdef char *bl = b * cdef size_t l = strlen(al) * cdef float score = 0.0 # <<<<<<<<<<<<<< - * + * * for i in range(l): */ __pyx_v_score = 0.0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":274 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":321 * cdef float score = 0.0 - * + * * for i in range(l): # <<<<<<<<<<<<<< * if al[i] == bl[i]: * score+=1 @@ -8807,8 +9618,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_hom for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":275 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":322 + * * for i in range(l): * if al[i] == bl[i]: # <<<<<<<<<<<<<< * score+=1 @@ -8817,7 +9628,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_hom __pyx_t_5 = ((__pyx_v_al[__pyx_v_i]) == (__pyx_v_bl[__pyx_v_i])); if (__pyx_t_5) { - /* "CRISPResso2/CRISPRessoCOREResources.pyx":276 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":323 * for i in range(l): * if al[i] == bl[i]: * score+=1 # <<<<<<<<<<<<<< @@ -8825,8 +9636,8 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_hom */ __pyx_v_score = (__pyx_v_score + 1.0); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":275 - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":322 + * * for i in range(l): * if al[i] == bl[i]: # <<<<<<<<<<<<<< * score+=1 @@ -8835,7 +9646,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_hom } } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":277 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":324 * if al[i] == bl[i]: * score+=1 * return score/l # <<<<<<<<<<<<<< @@ -8843,17 +9654,17 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_hom __Pyx_XDECREF(__pyx_r); if (unlikely(__pyx_v_l == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 277, __pyx_L1_error) + __PYX_ERR(0, 324, __pyx_L1_error) } - __pyx_t_6 = PyFloat_FromDouble((__pyx_v_score / ((float)__pyx_v_l))); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 277, __pyx_L1_error) + __pyx_t_6 = PyFloat_FromDouble((__pyx_v_score / ((float)__pyx_v_l))); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 324, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_r = __pyx_t_6; __pyx_t_6 = 0; goto __pyx_L0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":268 - * - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":315 + * + * * def calculate_homology(a, b): # <<<<<<<<<<<<<< * cdef char *al = a * cdef char *bl = b @@ -8888,13 +9699,17 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { __Pyx_StringTabEntry __pyx_string_tab[] = { {&__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_s_CRISPResso2_CRISPRessoCOREResour, __pyx_k_CRISPResso2_CRISPRessoCOREResour, sizeof(__pyx_k_CRISPResso2_CRISPRessoCOREResour), 0, 0, 1, 1}, + {&__pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_k_CRISPResso2_CRISPRessoCOREResour_2, sizeof(__pyx_k_CRISPResso2_CRISPRessoCOREResour_2), 0, 0, 1, 0}, {&__pyx_n_u_G, __pyx_k_G, sizeof(__pyx_k_G), 0, 1, 0, 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_s_ResultsSlotsDict, __pyx_k_ResultsSlotsDict, sizeof(__pyx_k_ResultsSlotsDict), 0, 0, 1, 1}, + {&__pyx_n_s_ResultsSlotsDict___getitem, __pyx_k_ResultsSlotsDict___getitem, sizeof(__pyx_k_ResultsSlotsDict___getitem), 0, 0, 1, 1}, + {&__pyx_n_s_ResultsSlotsDict___init, __pyx_k_ResultsSlotsDict___init, sizeof(__pyx_k_ResultsSlotsDict___init), 0, 0, 1, 1}, + {&__pyx_n_s_ResultsSlotsDict___setitem, __pyx_k_ResultsSlotsDict___setitem, sizeof(__pyx_k_ResultsSlotsDict___setitem), 0, 0, 1, 1}, {&__pyx_n_u_T, __pyx_k_T, sizeof(__pyx_k_T), 0, 1, 0, 1}, - {&__pyx_n_s__13, __pyx_k__13, sizeof(__pyx_k__13), 0, 0, 1, 1}, + {&__pyx_n_s__20, __pyx_k__20, sizeof(__pyx_k__20), 0, 0, 1, 1}, {&__pyx_kp_u__3, __pyx_k__3, sizeof(__pyx_k__3), 0, 1, 0, 0}, {&__pyx_n_s__4, __pyx_k__4, sizeof(__pyx_k__4), 0, 0, 1, 1}, {&__pyx_kp_u__5, __pyx_k__5, sizeof(__pyx_k__5), 0, 1, 0, 0}, @@ -8912,12 +9727,17 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { {&__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_u_aln_ref, __pyx_k_aln_ref, sizeof(__pyx_k_aln_ref), 0, 1, 0, 1}, + {&__pyx_n_u_aln_scores, __pyx_k_aln_scores, sizeof(__pyx_k_aln_scores), 0, 1, 0, 1}, + {&__pyx_n_u_aln_seq, __pyx_k_aln_seq, sizeof(__pyx_k_aln_seq), 0, 1, 0, 1}, + {&__pyx_n_u_aln_strand, __pyx_k_aln_strand, sizeof(__pyx_k_aln_strand), 0, 1, 0, 1}, {&__pyx_n_s_array, __pyx_k_array, sizeof(__pyx_k_array), 0, 0, 1, 1}, {&__pyx_n_s_asyncio_coroutines, __pyx_k_asyncio_coroutines, sizeof(__pyx_k_asyncio_coroutines), 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}, {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1}, {&__pyx_n_s_calculate_homology, __pyx_k_calculate_homology, sizeof(__pyx_k_calculate_homology), 0, 0, 1, 1}, + {&__pyx_n_u_classification, __pyx_k_classification, sizeof(__pyx_k_classification), 0, 1, 0, 1}, {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, {&__pyx_n_s_compile, __pyx_k_compile, sizeof(__pyx_k_compile), 0, 0, 1, 1}, {&__pyx_n_s_current_insertion_size, __pyx_k_current_insertion_size, sizeof(__pyx_k_current_insertion_size), 0, 0, 1, 1}, @@ -8929,12 +9749,16 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { {&__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_u_deletions_outside_window, __pyx_k_deletions_outside_window, sizeof(__pyx_k_deletions_outside_window), 0, 1, 0, 1}, + {&__pyx_n_s_dict, __pyx_k_dict, sizeof(__pyx_k_dict), 0, 0, 1, 1}, + {&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1}, {&__pyx_n_s_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_getitem, __pyx_k_getitem, sizeof(__pyx_k_getitem), 0, 0, 1, 1}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, {&__pyx_n_s_idx, __pyx_k_idx, sizeof(__pyx_k_idx), 0, 0, 1, 1}, {&__pyx_n_s_idx_c, __pyx_k_idx_c, sizeof(__pyx_k_idx_c), 0, 0, 1, 1}, @@ -8942,6 +9766,8 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { {&__pyx_n_s_inc_del_pos, __pyx_k_inc_del_pos, sizeof(__pyx_k_inc_del_pos), 0, 0, 1, 1}, {&__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_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1}, + {&__pyx_n_s_init_subclass, __pyx_k_init_subclass, sizeof(__pyx_k_init_subclass), 0, 0, 1, 1}, {&__pyx_n_s_initializing, __pyx_k_initializing, sizeof(__pyx_k_initializing), 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}, @@ -8951,10 +9777,19 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { {&__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_u_insertions_outside_window, __pyx_k_insertions_outside_window, sizeof(__pyx_k_insertions_outside_window), 0, 1, 0, 1}, {&__pyx_n_s_intersection, __pyx_k_intersection, sizeof(__pyx_k_intersection), 0, 0, 1, 1}, + {&__pyx_n_u_irregular_ends, __pyx_k_irregular_ends, sizeof(__pyx_k_irregular_ends), 0, 1, 0, 1}, {&__pyx_n_s_is_coroutine, __pyx_k_is_coroutine, sizeof(__pyx_k_is_coroutine), 0, 0, 1, 1}, + {&__pyx_n_s_items, __pyx_k_items, sizeof(__pyx_k_items), 0, 0, 1, 1}, + {&__pyx_n_s_key, __pyx_k_key, sizeof(__pyx_k_key), 0, 0, 1, 1}, + {&__pyx_n_s_kwargs, __pyx_k_kwargs, sizeof(__pyx_k_kwargs), 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}, + {&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1}, + {&__pyx_n_u_mods_in_window, __pyx_k_mods_in_window, sizeof(__pyx_k_mods_in_window), 0, 1, 0, 1}, + {&__pyx_n_u_mods_outside_window, __pyx_k_mods_outside_window, sizeof(__pyx_k_mods_outside_window), 0, 1, 0, 1}, + {&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1}, {&__pyx_n_s_name, __pyx_k_name, sizeof(__pyx_k_name), 0, 0, 1, 1}, {&__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}, @@ -8962,18 +9797,25 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { {&__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_impo, __pyx_k_numpy__core_umath_failed_to_impo, sizeof(__pyx_k_numpy__core_umath_failed_to_impo), 0, 1, 0, 0}, {&__pyx_n_s_p, __pyx_k_p, sizeof(__pyx_k_p), 0, 0, 1, 1}, + {&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1}, + {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 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}, {&__pyx_n_s_re_find_indels, __pyx_k_re_find_indels, sizeof(__pyx_k_re_find_indels), 0, 0, 1, 1}, {&__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_u_ref_name, __pyx_k_ref_name, sizeof(__pyx_k_ref_name), 0, 1, 0, 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_self, __pyx_k_self, sizeof(__pyx_k_self), 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_set_name, __pyx_k_set_name, sizeof(__pyx_k_set_name), 0, 0, 1, 1}, + {&__pyx_n_s_setitem, __pyx_k_setitem, sizeof(__pyx_k_setitem), 0, 0, 1, 1}, + {&__pyx_n_s_slots, __pyx_k_slots, sizeof(__pyx_k_slots), 0, 0, 1, 1}, {&__pyx_n_s_span, __pyx_k_span, sizeof(__pyx_k_span), 0, 0, 1, 1}, {&__pyx_n_s_spec, __pyx_k_spec, sizeof(__pyx_k_spec), 0, 0, 1, 1}, {&__pyx_n_s_st, __pyx_k_st, sizeof(__pyx_k_st), 0, 0, 1, 1}, @@ -8986,17 +9828,21 @@ static int __Pyx_CreateStringTabAndInitStrings(void) { {&__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_u_substitutions_outside_window, __pyx_k_substitutions_outside_window, sizeof(__pyx_k_substitutions_outside_window), 0, 1, 0, 1}, {&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1}, + {&__pyx_n_s_super, __pyx_k_super, sizeof(__pyx_k_super), 0, 0, 1, 1}, {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, + {&__pyx_n_u_total_mods, __pyx_k_total_mods, sizeof(__pyx_k_total_mods), 0, 1, 0, 1}, + {&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; return __Pyx_InitStrings(__pyx_string_tab); } /* #### Code section: cached_builtins ### */ static CYTHON_SMALL_CODE int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 58, __pyx_L1_error) - __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 95, __pyx_L1_error) - __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) __PYX_ERR(0, 113, __pyx_L1_error) + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 104, __pyx_L1_error) + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 141, __pyx_L1_error) + __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) __PYX_ERR(0, 159, __pyx_L1_error) __pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(1, 1025, __pyx_L1_error) return 0; __pyx_L1_error:; @@ -9008,22 +9854,22 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1025 * __pyx_import_array() * except Exception: * raise ImportError("numpy._core.multiarray failed to import") # <<<<<<<<<<<<<< - * + * * cdef inline int import_umath() except -1: */ __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_numpy__core_multiarray_failed_to); if (unlikely(!__pyx_tuple_)) __PYX_ERR(1, 1025, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "../../../../../private/var/folders/cq/cgtzxhc95lsfrydd_8w72_d80000gn/T/pip-build-env-qejot30v/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 + /* "../../../../private/var/folders/2h/hd7rhf_x5sj4cld2mxs9wczm0000gn/T/pip-build-env-_z1ridrf/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1031 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< - * + * * cdef inline int import_ufunc() except -1: */ __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_numpy__core_umath_failed_to_impo); if (unlikely(!__pyx_tuple__2)) __PYX_ERR(1, 1031, __pyx_L1_error) @@ -9031,51 +9877,98 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(__pyx_tuple__2); /* "CRISPResso2/CRISPRessoCOREResources.pyx":16 - * - * + * + * * re_find_indels = re.compile("(-*-)") # <<<<<<<<<<<<<< - * - * @cython.boundscheck(False) + * + * class ResultsSlotsDict(): */ __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u__5); if (unlikely(!__pyx_tuple__6)) __PYX_ERR(0, 16, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":18 - * re_find_indels = re.compile("(-*-)") - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":20 + * class ResultsSlotsDict(): + * __slots__ = ( + * 'all_insertion_positions', # <<<<<<<<<<<<<< + * 'all_insertion_left_positions', + * 'insertion_positions', + */ + __pyx_tuple__7 = PyTuple_Pack(31, __pyx_n_u_all_insertion_positions, __pyx_n_u_all_insertion_left_positions, __pyx_n_u_insertion_positions, __pyx_n_u_insertion_coordinates, __pyx_n_u_insertion_sizes, __pyx_n_u_insertion_n, __pyx_n_u_all_deletion_positions, __pyx_n_u_all_deletion_coordinates, __pyx_n_u_deletion_positions, __pyx_n_u_deletion_coordinates, __pyx_n_u_deletion_sizes, __pyx_n_u_deletion_n, __pyx_n_u_all_substitution_positions, __pyx_n_u_substitution_positions, __pyx_n_u_all_substitution_values, __pyx_n_u_substitution_values, __pyx_n_u_substitution_n, __pyx_n_u_ref_positions, __pyx_n_u_ref_name, __pyx_n_u_aln_scores, __pyx_n_u_classification, __pyx_n_u_aln_seq, __pyx_n_u_aln_ref, __pyx_n_u_aln_strand, __pyx_n_u_irregular_ends, __pyx_n_u_insertions_outside_window, __pyx_n_u_deletions_outside_window, __pyx_n_u_substitutions_outside_window, __pyx_n_u_total_mods, __pyx_n_u_mods_in_window, __pyx_n_u_mods_outside_window); if (unlikely(!__pyx_tuple__7)) __PYX_ERR(0, 20, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__7); + __Pyx_GIVEREF(__pyx_tuple__7); + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":53 + * ) + * + * def __init__(self, **kwargs): # <<<<<<<<<<<<<< + * for key, value in kwargs.items(): + * setattr(self, key, value) + */ + __pyx_tuple__8 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_kwargs, __pyx_n_s_key, __pyx_n_s_value); if (unlikely(!__pyx_tuple__8)) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__8); + __Pyx_GIVEREF(__pyx_tuple__8); + __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(1, 0, 0, 4, 0, CO_OPTIMIZED|CO_NEWLOCALS|CO_VARKEYWORDS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_n_s_init, 53, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) __PYX_ERR(0, 53, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":57 + * setattr(self, key, value) + * + * def __getitem__(self, key): # <<<<<<<<<<<<<< + * return getattr(self, key) + * + */ + __pyx_tuple__10 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_key); if (unlikely(!__pyx_tuple__10)) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__10); + __Pyx_GIVEREF(__pyx_tuple__10); + __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__10, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_n_s_getitem, 57, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) __PYX_ERR(0, 57, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":60 + * return getattr(self, key) + * + * def __setitem__(self, key, value): # <<<<<<<<<<<<<< + * setattr(self, key, value) + * + */ + __pyx_tuple__12 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_key, __pyx_n_s_value); if (unlikely(!__pyx_tuple__12)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__12); + __Pyx_GIVEREF(__pyx_tuple__12); + __pyx_codeobj__13 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 3, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__12, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_n_s_setitem, 60, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__13)) __PYX_ERR(0, 60, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":64 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) */ - __pyx_tuple__7 = PyTuple_Pack(31, __pyx_n_s_read_seq_al, __pyx_n_s_ref_seq_al, __pyx_n_s_include_indx, __pyx_n_s_ref_positions, __pyx_n_s_all_substitution_positions, __pyx_n_s_substitution_positions, __pyx_n_s_all_substitution_values, __pyx_n_s_substitution_values, __pyx_n_s_all_deletion_positions, __pyx_n_s_all_deletion_coordinates, __pyx_n_s_deletion_positions, __pyx_n_s_deletion_coordinates, __pyx_n_s_deletion_sizes, __pyx_n_s_start_deletion, __pyx_n_s_all_insertion_positions, __pyx_n_s_all_insertion_left_positions, __pyx_n_s_insertion_positions, __pyx_n_s_insertion_coordinates, __pyx_n_s_insertion_sizes, __pyx_n_s_start_insertion, __pyx_n_s_seq_len, __pyx_n_s_include_indx_set, __pyx_n_s_nucSet, __pyx_n_s_idx, __pyx_n_s_idx_c, __pyx_n_s_current_insertion_size, __pyx_n_s_c, __pyx_n_s_end_deletion, __pyx_n_s_substitution_n, __pyx_n_s_deletion_n, __pyx_n_s_insertion_n); if (unlikely(!__pyx_tuple__7)) __PYX_ERR(0, 18, __pyx_L1_error) - __Pyx_GOTREF(__pyx_tuple__7); - __Pyx_GIVEREF(__pyx_tuple__7); - __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 31, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour, __pyx_n_s_find_indels_substitutions, 18, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 18, __pyx_L1_error) + __pyx_tuple__14 = PyTuple_Pack(31, __pyx_n_s_read_seq_al, __pyx_n_s_ref_seq_al, __pyx_n_s_include_indx, __pyx_n_s_ref_positions, __pyx_n_s_all_substitution_positions, __pyx_n_s_substitution_positions, __pyx_n_s_all_substitution_values, __pyx_n_s_substitution_values, __pyx_n_s_all_deletion_positions, __pyx_n_s_all_deletion_coordinates, __pyx_n_s_deletion_positions, __pyx_n_s_deletion_coordinates, __pyx_n_s_deletion_sizes, __pyx_n_s_start_deletion, __pyx_n_s_all_insertion_positions, __pyx_n_s_all_insertion_left_positions, __pyx_n_s_insertion_positions, __pyx_n_s_insertion_coordinates, __pyx_n_s_insertion_sizes, __pyx_n_s_start_insertion, __pyx_n_s_seq_len, __pyx_n_s_include_indx_set, __pyx_n_s_nucSet, __pyx_n_s_idx, __pyx_n_s_idx_c, __pyx_n_s_current_insertion_size, __pyx_n_s_c, __pyx_n_s_end_deletion, __pyx_n_s_substitution_n, __pyx_n_s_deletion_n, __pyx_n_s_insertion_n); if (unlikely(!__pyx_tuple__14)) __PYX_ERR(0, 64, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__14); + __Pyx_GIVEREF(__pyx_tuple__14); + __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 31, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_n_s_find_indels_substitutions, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) __PYX_ERR(0, 64, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":138 - * 'ref_positions': ref_positions, - * } + /* "CRISPResso2/CRISPRessoCOREResources.pyx":187 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) */ - __pyx_tuple__9 = PyTuple_Pack(34, __pyx_n_s_read_seq_al, __pyx_n_s_ref_seq_al, __pyx_n_s_include_indx, __pyx_n_s_sub_seq, __pyx_n_s_st, __pyx_n_s_en, __pyx_n_s_idx_c, __pyx_n_s_idx, __pyx_n_s_ref_positions, __pyx_n_s_all_substitution_positions, __pyx_n_s_substitution_positions, __pyx_n_s_all_substitution_values, __pyx_n_s_substitution_values, __pyx_n_s_nucSet, __pyx_n_s_c, __pyx_n_s_substitution_n, __pyx_n_s_all_deletion_positions, __pyx_n_s_deletion_positions, __pyx_n_s_deletion_coordinates, __pyx_n_s_all_deletion_coordinates, __pyx_n_s_deletion_sizes, __pyx_n_s_all_insertion_positions, __pyx_n_s_all_insertion_left_positions, __pyx_n_s_insertion_positions, __pyx_n_s_insertion_coordinates, __pyx_n_s_insertion_sizes, __pyx_n_s_include_indx_set, __pyx_n_s_p, __pyx_n_s_ref_st, __pyx_n_s_ref_en, __pyx_n_s_inc_del_pos, __pyx_n_s_deletion_n, __pyx_n_s_insertion_n, __pyx_n_s_retDict); if (unlikely(!__pyx_tuple__9)) __PYX_ERR(0, 138, __pyx_L1_error) - __Pyx_GOTREF(__pyx_tuple__9); - __Pyx_GIVEREF(__pyx_tuple__9); - __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 34, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour, __pyx_n_s_find_indels_substitutions_legacy, 138, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 138, __pyx_L1_error) + __pyx_tuple__16 = PyTuple_Pack(34, __pyx_n_s_read_seq_al, __pyx_n_s_ref_seq_al, __pyx_n_s_include_indx, __pyx_n_s_sub_seq, __pyx_n_s_st, __pyx_n_s_en, __pyx_n_s_idx_c, __pyx_n_s_idx, __pyx_n_s_ref_positions, __pyx_n_s_all_substitution_positions, __pyx_n_s_substitution_positions, __pyx_n_s_all_substitution_values, __pyx_n_s_substitution_values, __pyx_n_s_nucSet, __pyx_n_s_c, __pyx_n_s_substitution_n, __pyx_n_s_all_deletion_positions, __pyx_n_s_deletion_positions, __pyx_n_s_deletion_coordinates, __pyx_n_s_all_deletion_coordinates, __pyx_n_s_deletion_sizes, __pyx_n_s_all_insertion_positions, __pyx_n_s_all_insertion_left_positions, __pyx_n_s_insertion_positions, __pyx_n_s_insertion_coordinates, __pyx_n_s_insertion_sizes, __pyx_n_s_include_indx_set, __pyx_n_s_p, __pyx_n_s_ref_st, __pyx_n_s_ref_en, __pyx_n_s_inc_del_pos, __pyx_n_s_deletion_n, __pyx_n_s_insertion_n, __pyx_n_s_retDict); if (unlikely(!__pyx_tuple__16)) __PYX_ERR(0, 187, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__16); + __Pyx_GIVEREF(__pyx_tuple__16); + __pyx_codeobj__17 = (PyObject*)__Pyx_PyCode_New(3, 0, 0, 34, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__16, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_n_s_find_indels_substitutions_legacy, 187, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) __PYX_ERR(0, 187, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":268 - * - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":315 + * + * * def calculate_homology(a, b): # <<<<<<<<<<<<<< * cdef char *al = a * cdef char *bl = b */ - __pyx_tuple__11 = PyTuple_Pack(7, __pyx_n_s_a, __pyx_n_s_b, __pyx_n_s_al, __pyx_n_s_bl, __pyx_n_s_l, __pyx_n_s_score, __pyx_n_s_i); if (unlikely(!__pyx_tuple__11)) __PYX_ERR(0, 268, __pyx_L1_error) - __Pyx_GOTREF(__pyx_tuple__11); - __Pyx_GIVEREF(__pyx_tuple__11); - __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour, __pyx_n_s_calculate_homology, 268, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) __PYX_ERR(0, 268, __pyx_L1_error) + __pyx_tuple__18 = PyTuple_Pack(7, __pyx_n_s_a, __pyx_n_s_b, __pyx_n_s_al, __pyx_n_s_bl, __pyx_n_s_l, __pyx_n_s_score, __pyx_n_s_i); if (unlikely(!__pyx_tuple__18)) __PYX_ERR(0, 315, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__18); + __Pyx_GIVEREF(__pyx_tuple__18); + __pyx_codeobj__19 = (PyObject*)__Pyx_PyCode_New(2, 0, 0, 7, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__18, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_n_s_calculate_homology, 315, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__19)) __PYX_ERR(0, 315, __pyx_L1_error) __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -9172,7 +10065,7 @@ static int __Pyx_modinit_type_import_code(void) { /*--- Type import code ---*/ __pyx_t_1 = PyImport_ImportModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 9, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType_3_0_11(__pyx_t_1, __Pyx_BUILTIN_MODULE_NAME, "type", #if defined(PYPY_VERSION_NUM) && PYPY_VERSION_NUM < 0x050B0000 sizeof(PyTypeObject), __PYX_GET_STRUCT_ALIGNMENT_3_0_11(PyTypeObject), #elif CYTHON_COMPILING_IN_LIMITED_API @@ -9518,7 +10411,7 @@ if (!__Pyx_RefNanny) { * import numpy as np * cimport numpy as np * import re # <<<<<<<<<<<<<< - * + * * cdef extern from "stdlib.h": */ __pyx_t_2 = __Pyx_ImportDottedModule(__pyx_n_s_re, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 4, __pyx_L1_error) @@ -9527,11 +10420,11 @@ if (!__Pyx_RefNanny) { __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "CRISPResso2/CRISPRessoCOREResources.pyx":16 - * - * + * + * * re_find_indels = re.compile("(-*-)") # <<<<<<<<<<<<<< - * - * @cython.boundscheck(False) + * + * class ResultsSlotsDict(): */ __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_re); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 16, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); @@ -9546,38 +10439,106 @@ if (!__Pyx_RefNanny) { /* "CRISPResso2/CRISPRessoCOREResources.pyx":18 * re_find_indels = re.compile("(-*-)") - * + * + * class ResultsSlotsDict(): # <<<<<<<<<<<<<< + * __slots__ = ( + * 'all_insertion_positions', + */ + __pyx_t_2 = __Pyx_Py3MetaclassPrepare((PyObject *) NULL, __pyx_empty_tuple, __pyx_n_s_ResultsSlotsDict, __pyx_n_s_ResultsSlotsDict, (PyObject *) NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, (PyObject *) NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 18, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_2); + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":20 + * class ResultsSlotsDict(): + * __slots__ = ( + * 'all_insertion_positions', # <<<<<<<<<<<<<< + * 'all_insertion_left_positions', + * 'insertion_positions', + */ + if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_slots, __pyx_tuple__7) < 0) __PYX_ERR(0, 19, __pyx_L1_error) + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":53 + * ) + * + * def __init__(self, **kwargs): # <<<<<<<<<<<<<< + * for key, value in kwargs.items(): + * setattr(self, key, value) + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_1__init__, 0, __pyx_n_s_ResultsSlotsDict___init, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_d, ((PyObject *)__pyx_codeobj__9)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_init, __pyx_t_3) < 0) __PYX_ERR(0, 53, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":57 + * setattr(self, key, value) + * + * def __getitem__(self, key): # <<<<<<<<<<<<<< + * return getattr(self, key) + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_3__getitem__, 0, __pyx_n_s_ResultsSlotsDict___getitem, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_d, ((PyObject *)__pyx_codeobj__11)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_getitem, __pyx_t_3) < 0) __PYX_ERR(0, 57, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":60 + * return getattr(self, key) + * + * def __setitem__(self, key, value): # <<<<<<<<<<<<<< + * setattr(self, key, value) + * + */ + __pyx_t_3 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_16ResultsSlotsDict_5__setitem__, 0, __pyx_n_s_ResultsSlotsDict___setitem, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_d, ((PyObject *)__pyx_codeobj__13)); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_SetNameInClass(__pyx_t_2, __pyx_n_s_setitem, __pyx_t_3) < 0) __PYX_ERR(0, 60, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":18 + * re_find_indels = re.compile("(-*-)") + * + * class ResultsSlotsDict(): # <<<<<<<<<<<<<< + * __slots__ = ( + * 'all_insertion_positions', + */ + __pyx_t_3 = __Pyx_Py3ClassCreate(((PyObject*)&PyType_Type), __pyx_n_s_ResultsSlotsDict, __pyx_empty_tuple, __pyx_t_2, NULL, 0, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 18, __pyx_L1_error) + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ResultsSlotsDict, __pyx_t_3) < 0) __PYX_ERR(0, 18, __pyx_L1_error) + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "CRISPResso2/CRISPRessoCOREResources.pyx":64 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) */ - __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, 0, __pyx_n_s_find_indels_substitutions, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_d, ((PyObject *)__pyx_codeobj__8)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 18, __pyx_L1_error) + __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_1find_indels_substitutions, 0, __pyx_n_s_find_indels_substitutions, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_d, ((PyObject *)__pyx_codeobj__15)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 64, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_find_indels_substitutions, __pyx_t_2) < 0) __PYX_ERR(0, 18, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_find_indels_substitutions, __pyx_t_2) < 0) __PYX_ERR(0, 64, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":138 - * 'ref_positions': ref_positions, - * } + /* "CRISPResso2/CRISPRessoCOREResources.pyx":187 + * + * * @cython.boundscheck(False) # <<<<<<<<<<<<<< * @cython.nonecheck(False) * @cython.wraparound(False) */ - __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy, 0, __pyx_n_s_find_indels_substitutions_legacy, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_d, ((PyObject *)__pyx_codeobj__10)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 138, __pyx_L1_error) + __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3find_indels_substitutions_legacy, 0, __pyx_n_s_find_indels_substitutions_legacy, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_d, ((PyObject *)__pyx_codeobj__17)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 187, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_find_indels_substitutions_legacy, __pyx_t_2) < 0) __PYX_ERR(0, 138, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_find_indels_substitutions_legacy, __pyx_t_2) < 0) __PYX_ERR(0, 187, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":268 - * - * + /* "CRISPResso2/CRISPRessoCOREResources.pyx":315 + * + * * def calculate_homology(a, b): # <<<<<<<<<<<<<< * cdef char *al = a * cdef char *bl = b */ - __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology, 0, __pyx_n_s_calculate_homology, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour_2, __pyx_d, ((PyObject *)__pyx_codeobj__12)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 268, __pyx_L1_error) + __pyx_t_2 = __Pyx_CyFunction_New(&__pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology, 0, __pyx_n_s_calculate_homology, NULL, __pyx_n_s_CRISPResso2_CRISPRessoCOREResour, __pyx_d, ((PyObject *)__pyx_codeobj__19)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 315, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_calculate_homology, __pyx_t_2) < 0) __PYX_ERR(0, 268, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_calculate_homology, __pyx_t_2) < 0) __PYX_ERR(0, 315, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "CRISPResso2/CRISPRessoCOREResources.pyx":1 @@ -10406,32 +11367,6 @@ CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, Py #endif #endif -/* RaiseArgTupleInvalid */ -static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *more_or_less; - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - PyErr_Format(PyExc_TypeError, - "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", - func_name, more_or_less, num_expected, - (num_expected == 1) ? "" : "s", num_found); -} - /* RaiseDoubleKeywords */ static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, @@ -10576,525 +11511,909 @@ static int __Pyx_ParseOptionalKeywords( goto invalid_keyword; } } - Py_XDECREF(key); - Py_XDECREF(value); - return 0; -arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, key); - goto bad; -invalid_keyword_type: - PyErr_Format(PyExc_TypeError, - "%.200s() keywords must be strings", function_name); - goto bad; -invalid_keyword: + Py_XDECREF(key); + Py_XDECREF(value); + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + #if PY_MAJOR_VERSION < 3 + PyErr_Format(PyExc_TypeError, + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + PyErr_Format(PyExc_TypeError, + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + Py_XDECREF(key); + Py_XDECREF(value); + return -1; +} + +/* RaiseArgTupleInvalid */ +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +/* IterFinish */ +static CYTHON_INLINE int __Pyx_IterFinish(void) { + PyObject* exc_type; + __Pyx_PyThreadState_declare + __Pyx_PyThreadState_assign + exc_type = __Pyx_PyErr_CurrentExceptionType(); + if (unlikely(exc_type)) { + if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) + return -1; + __Pyx_PyErr_Clear(); + return 0; + } + return 0; +} + +/* PyFunctionFastCall */ +#if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL +static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, + PyObject *globals) { + PyFrameObject *f; + PyThreadState *tstate = __Pyx_PyThreadState_Current; + PyObject **fastlocals; + Py_ssize_t i; + PyObject *result; + assert(globals != NULL); + /* XXX Perhaps we should create a specialized + PyFrame_New() that doesn't take locals, but does + take builtins without sanity checking them. + */ + assert(tstate != NULL); + f = PyFrame_New(tstate, co, globals, NULL); + if (f == NULL) { + return NULL; + } + fastlocals = __Pyx_PyFrame_GetLocalsplus(f); + for (i = 0; i < na; i++) { + Py_INCREF(*args); + fastlocals[i] = *args++; + } + result = PyEval_EvalFrameEx(f,0); + ++tstate->recursion_depth; + Py_DECREF(f); + --tstate->recursion_depth; + return result; +} +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { + PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); + PyObject *globals = PyFunction_GET_GLOBALS(func); + PyObject *argdefs = PyFunction_GET_DEFAULTS(func); + PyObject *closure; +#if PY_MAJOR_VERSION >= 3 + PyObject *kwdefs; +#endif + PyObject *kwtuple, **k; + PyObject **d; + Py_ssize_t nd; + Py_ssize_t nk; + PyObject *result; + assert(kwargs == NULL || PyDict_Check(kwargs)); + nk = kwargs ? PyDict_Size(kwargs) : 0; + #if PY_MAJOR_VERSION < 3 + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) { + return NULL; + } + #else + if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) { + return NULL; + } + #endif + if ( +#if PY_MAJOR_VERSION >= 3 + co->co_kwonlyargcount == 0 && +#endif + likely(kwargs == NULL || nk == 0) && + co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { + if (argdefs == NULL && co->co_argcount == nargs) { + result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); + goto done; + } + else if (nargs == 0 && argdefs != NULL + && co->co_argcount == Py_SIZE(argdefs)) { + /* function called with no arguments, but all parameters have + a default value: use default values as arguments .*/ + args = &PyTuple_GET_ITEM(argdefs, 0); + result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); + goto done; + } + } + if (kwargs != NULL) { + Py_ssize_t pos, i; + kwtuple = PyTuple_New(2 * nk); + if (kwtuple == NULL) { + result = NULL; + goto done; + } + k = &PyTuple_GET_ITEM(kwtuple, 0); + pos = i = 0; + while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { + Py_INCREF(k[i]); + Py_INCREF(k[i+1]); + i += 2; + } + nk = i / 2; + } + else { + kwtuple = NULL; + k = NULL; + } + closure = PyFunction_GET_CLOSURE(func); +#if PY_MAJOR_VERSION >= 3 + kwdefs = PyFunction_GET_KW_DEFAULTS(func); +#endif + if (argdefs != NULL) { + d = &PyTuple_GET_ITEM(argdefs, 0); + nd = Py_SIZE(argdefs); + } + else { + d = NULL; + nd = 0; + } +#if PY_MAJOR_VERSION >= 3 + result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, + args, (int)nargs, + k, (int)nk, + d, (int)nd, kwdefs, closure); +#else + result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, + args, (int)nargs, + k, (int)nk, + d, (int)nd, closure); +#endif + Py_XDECREF(kwtuple); +done: + Py_LeaveRecursiveCall(); + return result; +} +#endif + +/* PyObjectCallMethO */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func); + self = __Pyx_CyOrPyCFunction_GET_SELF(func); #if PY_MAJOR_VERSION < 3 - PyErr_Format(PyExc_TypeError, - "%.200s() got an unexpected keyword argument '%.200s'", - function_name, PyString_AsString(key)); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; #else - PyErr_Format(PyExc_TypeError, - "%s() got an unexpected keyword argument '%U'", - function_name, key); + if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) + return NULL; #endif -bad: - Py_XDECREF(key); - Py_XDECREF(value); - return -1; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; } +#endif -/* GetItemInt */ -static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { - PyObject *r; - if (unlikely(!j)) return NULL; - r = PyObject_GetItem(o, j); - Py_DECREF(j); - return r; -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyList_GET_SIZE(o); - } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; +/* PyObjectFastCall */ +#if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API +static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) { + PyObject *argstuple; + PyObject *result = 0; + size_t i; + argstuple = PyTuple_New((Py_ssize_t)nargs); + if (unlikely(!argstuple)) return NULL; + for (i = 0; i < nargs; i++) { + Py_INCREF(args[i]); + if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad; } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); -#endif + result = __Pyx_PyObject_Call(func, argstuple, kwargs); + bad: + Py_DECREF(argstuple); + return result; } -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - Py_ssize_t wrapped_i = i; - if (wraparound & unlikely(i < 0)) { - wrapped_i += PyTuple_GET_SIZE(o); +#endif +static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) { + Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs); +#if CYTHON_COMPILING_IN_CPYTHON + if (nargs == 0 && kwargs == NULL) { + if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS)) + return __Pyx_PyObject_CallMethO(func, NULL); } - if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); - Py_INCREF(r); - return r; + else if (nargs == 1 && kwargs == NULL) { + if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O)) + return __Pyx_PyObject_CallMethO(func, args[0]); } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); -#else - return PySequence_GetItem(o, i); #endif -} -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS - if (is_list || PyList_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; + #if PY_VERSION_HEX < 0x030800B1 + #if CYTHON_FAST_PYCCALL + if (PyCFunction_Check(func)) { + if (kwargs) { + return _PyCFunction_FastCallDict(func, args, nargs, kwargs); + } else { + return _PyCFunction_FastCallKeywords(func, args, nargs, NULL); } } - else if (PyTuple_CheckExact(o)) { - Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } - } else { - PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping; - PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence; - if (mm && mm->mp_subscript) { - PyObject *r, *key = PyInt_FromSsize_t(i); - if (unlikely(!key)) return NULL; - r = mm->mp_subscript(o, key); - Py_DECREF(key); - return r; + #if PY_VERSION_HEX >= 0x030700A1 + if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) { + return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL); + } + #endif + #endif + #if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs); + } + #endif + #endif + if (kwargs == NULL) { + #if CYTHON_VECTORCALL + #if PY_VERSION_HEX < 0x03090000 + vectorcallfunc f = _PyVectorcall_Function(func); + #else + vectorcallfunc f = PyVectorcall_Function(func); + #endif + if (f) { + return f(func, args, (size_t)nargs, NULL); } - if (likely(sm && sm->sq_item)) { - if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) { - Py_ssize_t l = sm->sq_length(o); - if (likely(l >= 0)) { - i += l; - } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) - return NULL; - PyErr_Clear(); - } - } - return sm->sq_item(o, i); + #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL + if (__Pyx_CyFunction_CheckExact(func)) { + __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func); + if (f) return f(func, args, (size_t)nargs, NULL); } + #endif } -#else - if (is_list || !PyMapping_Check(o)) { - return PySequence_GetItem(o, i); + if (nargs == 0) { + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs); } -#endif - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); + #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API + return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs); + #else + return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs); + #endif } -/* pyfrozenset_new */ -static CYTHON_INLINE PyObject* __Pyx_PyFrozenSet_New(PyObject* it) { - if (it) { - PyObject* result; -#if CYTHON_COMPILING_IN_PYPY - PyObject* args; - args = PyTuple_Pack(1, it); - if (unlikely(!args)) - return NULL; - result = PyObject_Call((PyObject*)&PyFrozenSet_Type, args, NULL); - Py_DECREF(args); - return result; +/* PyObjectCallNoArg */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { + PyObject *arg[2] = {NULL, NULL}; + return __Pyx_PyObject_FastCall(func, arg + 1, 0 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +} + +/* PyObjectCallOneArg */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *args[2] = {NULL, arg}; + return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +} + +/* PyObjectGetMethod */ +static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **method) { + PyObject *attr; +#if CYTHON_UNPACK_METHODS && CYTHON_COMPILING_IN_CPYTHON && CYTHON_USE_PYTYPE_LOOKUP + __Pyx_TypeName type_name; + PyTypeObject *tp = Py_TYPE(obj); + PyObject *descr; + descrgetfunc f = NULL; + PyObject **dictptr, *dict; + int meth_found = 0; + assert (*method == NULL); + if (unlikely(tp->tp_getattro != PyObject_GenericGetAttr)) { + attr = __Pyx_PyObject_GetAttrStr(obj, name); + goto try_unpack; + } + if (unlikely(tp->tp_dict == NULL) && unlikely(PyType_Ready(tp) < 0)) { + return 0; + } + descr = _PyType_Lookup(tp, name); + if (likely(descr != NULL)) { + Py_INCREF(descr); +#if defined(Py_TPFLAGS_METHOD_DESCRIPTOR) && Py_TPFLAGS_METHOD_DESCRIPTOR + if (__Pyx_PyType_HasFeature(Py_TYPE(descr), Py_TPFLAGS_METHOD_DESCRIPTOR)) +#elif PY_MAJOR_VERSION >= 3 + #ifdef __Pyx_CyFunction_USED + if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type) || __Pyx_CyFunction_Check(descr))) + #else + if (likely(PyFunction_Check(descr) || __Pyx_IS_TYPE(descr, &PyMethodDescr_Type))) + #endif #else - if (PyFrozenSet_CheckExact(it)) { - Py_INCREF(it); - return it; - } - result = PyFrozenSet_New(it); - if (unlikely(!result)) - return NULL; - if ((PY_VERSION_HEX >= 0x031000A1) || likely(PySet_GET_SIZE(result))) - return result; - Py_DECREF(result); + #ifdef __Pyx_CyFunction_USED + if (likely(PyFunction_Check(descr) || __Pyx_CyFunction_Check(descr))) + #else + if (likely(PyFunction_Check(descr))) + #endif #endif + { + meth_found = 1; + } else { + f = Py_TYPE(descr)->tp_descr_get; + if (f != NULL && PyDescr_IsData(descr)) { + attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); + Py_DECREF(descr); + goto try_unpack; + } + } + } + dictptr = _PyObject_GetDictPtr(obj); + if (dictptr != NULL && (dict = *dictptr) != NULL) { + Py_INCREF(dict); + attr = __Pyx_PyDict_GetItemStr(dict, name); + if (attr != NULL) { + Py_INCREF(attr); + Py_DECREF(dict); + Py_XDECREF(descr); + goto try_unpack; + } + Py_DECREF(dict); + } + if (meth_found) { + *method = descr; + return 1; + } + if (f != NULL) { + attr = f(descr, obj, (PyObject *)Py_TYPE(obj)); + Py_DECREF(descr); + goto try_unpack; + } + if (likely(descr != NULL)) { + *method = descr; + return 0; } -#if CYTHON_USE_TYPE_SLOTS - return PyFrozenSet_Type.tp_new(&PyFrozenSet_Type, __pyx_empty_tuple, NULL); + type_name = __Pyx_PyType_GetName(tp); + PyErr_Format(PyExc_AttributeError, +#if PY_MAJOR_VERSION >= 3 + "'" __Pyx_FMT_TYPENAME "' object has no attribute '%U'", + type_name, name); #else - return PyObject_Call((PyObject*)&PyFrozenSet_Type, __pyx_empty_tuple, NULL); + "'" __Pyx_FMT_TYPENAME "' object has no attribute '%.400s'", + type_name, PyString_AS_STRING(name)); +#endif + __Pyx_DECREF_TypeName(type_name); + return 0; +#else + attr = __Pyx_PyObject_GetAttrStr(obj, name); + goto try_unpack; +#endif +try_unpack: +#if CYTHON_UNPACK_METHODS + if (likely(attr) && PyMethod_Check(attr) && likely(PyMethod_GET_SELF(attr) == obj)) { + PyObject *function = PyMethod_GET_FUNCTION(attr); + Py_INCREF(function); + Py_DECREF(attr); + *method = function; + return 1; + } #endif + *method = attr; + return 0; } -/* PySetContains */ -static int __Pyx_PySet_ContainsUnhashable(PyObject *set, PyObject *key) { - int result = -1; - if (PySet_Check(key) && PyErr_ExceptionMatches(PyExc_TypeError)) { - PyObject *tmpkey; - PyErr_Clear(); - tmpkey = __Pyx_PyFrozenSet_New(key); - if (tmpkey != NULL) { - result = PySet_Contains(set, tmpkey); - Py_DECREF(tmpkey); - } +/* PyObjectCallMethod0 */ +static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { + PyObject *method = NULL, *result = NULL; + int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); + if (likely(is_method)) { + result = __Pyx_PyObject_CallOneArg(method, obj); + Py_DECREF(method); + return result; } + if (unlikely(!method)) goto bad; + result = __Pyx_PyObject_CallNoArg(method); + Py_DECREF(method); +bad: return result; } -static CYTHON_INLINE int __Pyx_PySet_ContainsTF(PyObject* key, PyObject* set, int eq) { - int result = PySet_Contains(set, key); - if (unlikely(result < 0)) { - result = __Pyx_PySet_ContainsUnhashable(set, key); - } - return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); + +/* RaiseNeedMoreValuesToUnpack */ +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); } -/* UnpackUnboundCMethod */ -static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) { - PyObject *result; - PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args)); - if (unlikely(!selfless_args)) return NULL; - result = PyObject_Call(method, selfless_args, kwargs); - Py_DECREF(selfless_args); - return result; +/* RaiseTooManyValuesToUnpack */ +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } -static PyMethodDef __Pyx_UnboundCMethod_Def = { - "CythonUnboundCMethod", - __PYX_REINTERPRET_FUNCION(PyCFunction, __Pyx_SelflessCall), - METH_VARARGS | METH_KEYWORDS, - NULL -}; -static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) { - PyObject *method; - method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name); - if (unlikely(!method)) + +/* UnpackItemEndCheck */ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); + __Pyx_RaiseTooManyValuesError(expected); return -1; - target->method = method; -#if CYTHON_COMPILING_IN_CPYTHON - #if PY_MAJOR_VERSION >= 3 - if (likely(__Pyx_TypeCheck(method, &PyMethodDescr_Type))) - #else - if (likely(!__Pyx_CyOrPyCFunction_Check(method))) - #endif - { - PyMethodDescrObject *descr = (PyMethodDescrObject*) method; - target->func = descr->d_method->ml_meth; - target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_STACKLESS); - } else -#endif + } + return __Pyx_IterFinish(); +} + +/* RaiseNoneIterError */ +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +/* UnpackTupleError */ +static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { + if (t == Py_None) { + __Pyx_RaiseNoneNotIterableError(); + } else if (PyTuple_GET_SIZE(t) < index) { + __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); + } else { + __Pyx_RaiseTooManyValuesError(index); + } +} + +/* UnpackTuple2 */ +static CYTHON_INLINE int __Pyx_unpack_tuple2_exact( + PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int decref_tuple) { + PyObject *value1 = NULL, *value2 = NULL; #if CYTHON_COMPILING_IN_PYPY + value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad; + value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad; #else - if (PyCFunction_Check(method)) -#endif - { - PyObject *self; - int self_found; -#if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY - self = PyObject_GetAttrString(method, "__self__"); - if (!self) { - PyErr_Clear(); - } -#else - self = PyCFunction_GET_SELF(method); -#endif - self_found = (self && self != Py_None); -#if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY - Py_XDECREF(self); + value1 = PyTuple_GET_ITEM(tuple, 0); Py_INCREF(value1); + value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value2); #endif - if (self_found) { - PyObject *unbound_method = PyCFunction_New(&__Pyx_UnboundCMethod_Def, method); - if (unlikely(!unbound_method)) return -1; - Py_DECREF(method); - target->method = unbound_method; - } + if (decref_tuple) { + Py_DECREF(tuple); } + *pvalue1 = value1; + *pvalue2 = value2; + return 0; +#if CYTHON_COMPILING_IN_PYPY +bad: + Py_XDECREF(value1); + Py_XDECREF(value2); + if (decref_tuple) { Py_XDECREF(tuple); } + return -1; +#endif +} +static int __Pyx_unpack_tuple2_generic(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, + int has_known_size, int decref_tuple) { + Py_ssize_t index; + PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; + iternextfunc iternext; + iter = PyObject_GetIter(tuple); + if (unlikely(!iter)) goto bad; + if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } + iternext = __Pyx_PyObject_GetIterNextFunc(iter); + value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } + value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } + if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; + Py_DECREF(iter); + *pvalue1 = value1; + *pvalue2 = value2; return 0; +unpacking_failed: + if (!has_known_size && __Pyx_IterFinish() == 0) + __Pyx_RaiseNeedMoreValuesError(index); +bad: + Py_XDECREF(iter); + Py_XDECREF(value1); + Py_XDECREF(value2); + if (decref_tuple) { Py_XDECREF(tuple); } + return -1; } -/* CallUnboundCMethod1 */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg) { - if (likely(cfunc->func)) { - int flag = cfunc->flag; - if (flag == METH_O) { - return (*(cfunc->func))(self, arg); - } else if ((PY_VERSION_HEX >= 0x030600B1) && flag == METH_FASTCALL) { - #if PY_VERSION_HEX >= 0x030700A0 - return (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)cfunc->func)(self, &arg, 1); - #else - return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); - #endif - } else if ((PY_VERSION_HEX >= 0x030700A0) && flag == (METH_FASTCALL | METH_KEYWORDS)) { - return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); +/* dict_iter */ +#if CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 +#include +#endif +static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, + Py_ssize_t* p_orig_length, int* p_source_is_dict) { + is_dict = is_dict || likely(PyDict_CheckExact(iterable)); + *p_source_is_dict = is_dict; + if (is_dict) { +#if !CYTHON_COMPILING_IN_PYPY + *p_orig_length = PyDict_Size(iterable); + Py_INCREF(iterable); + return iterable; +#elif PY_MAJOR_VERSION >= 3 + static PyObject *py_items = NULL, *py_keys = NULL, *py_values = NULL; + PyObject **pp = NULL; + if (method_name) { + const char *name = PyUnicode_AsUTF8(method_name); + if (strcmp(name, "iteritems") == 0) pp = &py_items; + else if (strcmp(name, "iterkeys") == 0) pp = &py_keys; + else if (strcmp(name, "itervalues") == 0) pp = &py_values; + if (pp) { + if (!*pp) { + *pp = PyUnicode_FromString(name + 4); + if (!*pp) + return NULL; + } + method_name = *pp; + } } +#endif } - return __Pyx__CallUnboundCMethod1(cfunc, self, arg); + *p_orig_length = 0; + if (method_name) { + PyObject* iter; + iterable = __Pyx_PyObject_CallMethod0(iterable, method_name); + if (!iterable) + return NULL; +#if !CYTHON_COMPILING_IN_PYPY + if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) + return iterable; +#endif + iter = PyObject_GetIter(iterable); + Py_DECREF(iterable); + return iter; + } + return PyObject_GetIter(iterable); } +static CYTHON_INLINE int __Pyx_dict_iter_next( + PyObject* iter_obj, CYTHON_NCP_UNUSED Py_ssize_t orig_length, CYTHON_NCP_UNUSED Py_ssize_t* ppos, + PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { + PyObject* next_item; +#if !CYTHON_COMPILING_IN_PYPY + if (source_is_dict) { + PyObject *key, *value; + if (unlikely(orig_length != PyDict_Size(iter_obj))) { + PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); + return -1; + } + if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { + return 0; + } + if (pitem) { + PyObject* tuple = PyTuple_New(2); + if (unlikely(!tuple)) { + return -1; + } + Py_INCREF(key); + Py_INCREF(value); + PyTuple_SET_ITEM(tuple, 0, key); + PyTuple_SET_ITEM(tuple, 1, value); + *pitem = tuple; + } else { + if (pkey) { + Py_INCREF(key); + *pkey = key; + } + if (pvalue) { + Py_INCREF(value); + *pvalue = value; + } + } + return 1; + } else if (PyTuple_CheckExact(iter_obj)) { + Py_ssize_t pos = *ppos; + if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; + *ppos = pos + 1; + next_item = PyTuple_GET_ITEM(iter_obj, pos); + Py_INCREF(next_item); + } else if (PyList_CheckExact(iter_obj)) { + Py_ssize_t pos = *ppos; + if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; + *ppos = pos + 1; + next_item = PyList_GET_ITEM(iter_obj, pos); + Py_INCREF(next_item); + } else #endif -static PyObject* __Pyx__CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg){ - PyObject *args, *result = NULL; - if (unlikely(!cfunc->func && !cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; -#if CYTHON_COMPILING_IN_CPYTHON - if (cfunc->func && (cfunc->flag & METH_VARARGS)) { - args = PyTuple_New(1); - if (unlikely(!args)) goto bad; - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 0, arg); - if (cfunc->flag & METH_KEYWORDS) - result = (*(PyCFunctionWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, NULL); - else - result = (*cfunc->func)(self, args); + { + 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 { - args = PyTuple_New(2); - if (unlikely(!args)) goto bad; - Py_INCREF(self); - PyTuple_SET_ITEM(args, 0, self); - Py_INCREF(arg); - PyTuple_SET_ITEM(args, 1, arg); - result = __Pyx_PyObject_Call(cfunc->method, args, NULL); + *pvalue = next_item; } + return 1; +} + +/* GetAttr */ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_USE_TYPE_SLOTS +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) #else - args = PyTuple_Pack(2, self, arg); - if (unlikely(!args)) goto bad; - result = __Pyx_PyObject_Call(cfunc->method, args, NULL); + if (likely(PyString_Check(n))) #endif -bad: - Py_XDECREF(args); - return result; + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); } -/* PyFunctionFastCall */ -#if CYTHON_FAST_PYCALL && !CYTHON_VECTORCALL -static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, - PyObject *globals) { - PyFrameObject *f; - PyThreadState *tstate = __Pyx_PyThreadState_Current; - PyObject **fastlocals; - Py_ssize_t i; - PyObject *result; - assert(globals != NULL); - /* XXX Perhaps we should create a specialized - PyFrame_New() that doesn't take locals, but does - take builtins without sanity checking them. - */ - assert(tstate != NULL); - f = PyFrame_New(tstate, co, globals, NULL); - if (f == NULL) { - return NULL; +/* GetItemInt */ +static PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (unlikely(!j)) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyList_GET_SIZE(o); } - fastlocals = __Pyx_PyFrame_GetLocalsplus(f); - for (i = 0; i < na; i++) { - Py_INCREF(*args); - fastlocals[i] = *args++; + if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; } - result = PyEval_EvalFrameEx(f,0); - ++tstate->recursion_depth; - Py_DECREF(f); - --tstate->recursion_depth; - return result; -} -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, Py_ssize_t nargs, PyObject *kwargs) { - PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); - PyObject *globals = PyFunction_GET_GLOBALS(func); - PyObject *argdefs = PyFunction_GET_DEFAULTS(func); - PyObject *closure; -#if PY_MAJOR_VERSION >= 3 - PyObject *kwdefs; -#endif - PyObject *kwtuple, **k; - PyObject **d; - Py_ssize_t nd; - Py_ssize_t nk; - PyObject *result; - assert(kwargs == NULL || PyDict_Check(kwargs)); - nk = kwargs ? PyDict_Size(kwargs) : 0; - #if PY_MAJOR_VERSION < 3 - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) { - return NULL; + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + Py_ssize_t wrapped_i = i; + if (wraparound & unlikely(i < 0)) { + wrapped_i += PyTuple_GET_SIZE(o); } - #else - if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) { - return NULL; + if ((!boundscheck) || likely(__Pyx_is_valid_index(wrapped_i, PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, wrapped_i); + Py_INCREF(r); + return r; } - #endif - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); #endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { +#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely(__Pyx_is_valid_index(n, PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; } } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely(__Pyx_is_valid_index(n, PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; + } else { + PyMappingMethods *mm = Py_TYPE(o)->tp_as_mapping; + PySequenceMethods *sm = Py_TYPE(o)->tp_as_sequence; + if (mm && mm->mp_subscript) { + PyObject *r, *key = PyInt_FromSsize_t(i); + if (unlikely(!key)) return NULL; + r = mm->mp_subscript(o, key); + Py_DECREF(key); + return r; + } + if (likely(sm && sm->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(sm->sq_length)) { + Py_ssize_t l = sm->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + return NULL; + PyErr_Clear(); + } + } + return sm->sq_item(o, i); } - nk = i / 2; } - else { - kwtuple = NULL; - k = NULL; +#else + if (is_list || !PyMapping_Check(o)) { + return PySequence_GetItem(o, i); } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); #endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +/* pyfrozenset_new */ +static CYTHON_INLINE PyObject* __Pyx_PyFrozenSet_New(PyObject* it) { + if (it) { + PyObject* result; +#if CYTHON_COMPILING_IN_PYPY + PyObject* args; + args = PyTuple_Pack(1, it); + if (unlikely(!args)) + return NULL; + result = PyObject_Call((PyObject*)&PyFrozenSet_Type, args, NULL); + Py_DECREF(args); + return result; +#else + if (PyFrozenSet_CheckExact(it)) { + Py_INCREF(it); + return it; + } + result = PyFrozenSet_New(it); + if (unlikely(!result)) + return NULL; + if ((PY_VERSION_HEX >= 0x031000A1) || likely(PySet_GET_SIZE(result))) + return result; + Py_DECREF(result); +#endif } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); +#if CYTHON_USE_TYPE_SLOTS + return PyFrozenSet_Type.tp_new(&PyFrozenSet_Type, __pyx_empty_tuple, NULL); #else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, (int)nargs, - k, (int)nk, - d, (int)nd, closure); + return PyObject_Call((PyObject*)&PyFrozenSet_Type, __pyx_empty_tuple, NULL); #endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; } -#endif -/* PyObjectCallMethO */ -#if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { - PyObject *self, *result; - PyCFunction cfunc; - cfunc = __Pyx_CyOrPyCFunction_GET_FUNCTION(func); - self = __Pyx_CyOrPyCFunction_GET_SELF(func); - #if PY_MAJOR_VERSION < 3 - if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) - return NULL; - #else - if (unlikely(Py_EnterRecursiveCall(" while calling a Python object"))) - return NULL; - #endif - result = cfunc(self, arg); - Py_LeaveRecursiveCall(); - if (unlikely(!result) && unlikely(!PyErr_Occurred())) { - PyErr_SetString( - PyExc_SystemError, - "NULL result without error in PyObject_Call"); +/* PySetContains */ +static int __Pyx_PySet_ContainsUnhashable(PyObject *set, PyObject *key) { + int result = -1; + if (PySet_Check(key) && PyErr_ExceptionMatches(PyExc_TypeError)) { + PyObject *tmpkey; + PyErr_Clear(); + tmpkey = __Pyx_PyFrozenSet_New(key); + if (tmpkey != NULL) { + result = PySet_Contains(set, tmpkey); + Py_DECREF(tmpkey); + } } return result; } -#endif - -/* PyObjectFastCall */ -#if PY_VERSION_HEX < 0x03090000 || CYTHON_COMPILING_IN_LIMITED_API -static PyObject* __Pyx_PyObject_FastCall_fallback(PyObject *func, PyObject **args, size_t nargs, PyObject *kwargs) { - PyObject *argstuple; - PyObject *result = 0; - size_t i; - argstuple = PyTuple_New((Py_ssize_t)nargs); - if (unlikely(!argstuple)) return NULL; - for (i = 0; i < nargs; i++) { - Py_INCREF(args[i]); - if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad; +static CYTHON_INLINE int __Pyx_PySet_ContainsTF(PyObject* key, PyObject* set, int eq) { + int result = PySet_Contains(set, key); + if (unlikely(result < 0)) { + result = __Pyx_PySet_ContainsUnhashable(set, key); } - result = __Pyx_PyObject_Call(func, argstuple, kwargs); - bad: - Py_DECREF(argstuple); + return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); +} + +/* UnpackUnboundCMethod */ +static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) { + PyObject *result; + PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args)); + if (unlikely(!selfless_args)) return NULL; + result = PyObject_Call(method, selfless_args, kwargs); + Py_DECREF(selfless_args); return result; } -#endif -static CYTHON_INLINE PyObject* __Pyx_PyObject_FastCallDict(PyObject *func, PyObject **args, size_t _nargs, PyObject *kwargs) { - Py_ssize_t nargs = __Pyx_PyVectorcall_NARGS(_nargs); -#if CYTHON_COMPILING_IN_CPYTHON - if (nargs == 0 && kwargs == NULL) { - if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_NOARGS)) - return __Pyx_PyObject_CallMethO(func, NULL); - } - else if (nargs == 1 && kwargs == NULL) { - if (__Pyx_CyOrPyCFunction_Check(func) && likely( __Pyx_CyOrPyCFunction_GET_FLAGS(func) & METH_O)) - return __Pyx_PyObject_CallMethO(func, args[0]); - } -#endif - #if PY_VERSION_HEX < 0x030800B1 - #if CYTHON_FAST_PYCCALL - if (PyCFunction_Check(func)) { - if (kwargs) { - return _PyCFunction_FastCallDict(func, args, nargs, kwargs); - } else { - return _PyCFunction_FastCallKeywords(func, args, nargs, NULL); - } - } - #if PY_VERSION_HEX >= 0x030700A1 - if (!kwargs && __Pyx_IS_TYPE(func, &PyMethodDescr_Type)) { - return _PyMethodDescr_FastCallKeywords(func, args, nargs, NULL); - } - #endif - #endif - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs); - } - #endif +static PyMethodDef __Pyx_UnboundCMethod_Def = { + "CythonUnboundCMethod", + __PYX_REINTERPRET_FUNCION(PyCFunction, __Pyx_SelflessCall), + METH_VARARGS | METH_KEYWORDS, + NULL +}; +static int __Pyx_TryUnpackUnboundCMethod(__Pyx_CachedCFunction* target) { + PyObject *method; + method = __Pyx_PyObject_GetAttrStr(target->type, *target->method_name); + if (unlikely(!method)) + return -1; + target->method = method; +#if CYTHON_COMPILING_IN_CPYTHON + #if PY_MAJOR_VERSION >= 3 + if (likely(__Pyx_TypeCheck(method, &PyMethodDescr_Type))) + #else + if (likely(!__Pyx_CyOrPyCFunction_Check(method))) #endif - if (kwargs == NULL) { - #if CYTHON_VECTORCALL - #if PY_VERSION_HEX < 0x03090000 - vectorcallfunc f = _PyVectorcall_Function(func); - #else - vectorcallfunc f = PyVectorcall_Function(func); - #endif - if (f) { - return f(func, args, (size_t)nargs, NULL); + { + PyMethodDescrObject *descr = (PyMethodDescrObject*) method; + target->func = descr->d_method->ml_meth; + target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST | METH_STACKLESS); + } else +#endif +#if CYTHON_COMPILING_IN_PYPY +#else + if (PyCFunction_Check(method)) +#endif + { + PyObject *self; + int self_found; +#if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY + self = PyObject_GetAttrString(method, "__self__"); + if (!self) { + PyErr_Clear(); } - #elif defined(__Pyx_CyFunction_USED) && CYTHON_BACKPORT_VECTORCALL - if (__Pyx_CyFunction_CheckExact(func)) { - __pyx_vectorcallfunc f = __Pyx_CyFunction_func_vectorcall(func); - if (f) return f(func, args, (size_t)nargs, NULL); +#else + self = PyCFunction_GET_SELF(method); +#endif + self_found = (self && self != Py_None); +#if CYTHON_COMPILING_IN_LIMITED_API || CYTHON_COMPILING_IN_PYPY + Py_XDECREF(self); +#endif + if (self_found) { + PyObject *unbound_method = PyCFunction_New(&__Pyx_UnboundCMethod_Def, method); + if (unlikely(!unbound_method)) return -1; + Py_DECREF(method); + target->method = unbound_method; } - #endif - } - if (nargs == 0) { - return __Pyx_PyObject_Call(func, __pyx_empty_tuple, kwargs); } - #if PY_VERSION_HEX >= 0x03090000 && !CYTHON_COMPILING_IN_LIMITED_API - return PyObject_VectorcallDict(func, args, (size_t)nargs, kwargs); - #else - return __Pyx_PyObject_FastCall_fallback(func, args, (size_t)nargs, kwargs); - #endif + return 0; } -/* PyObjectCallOneArg */ -static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *args[2] = {NULL, arg}; - return __Pyx_PyObject_FastCall(func, args+1, 1 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +/* CallUnboundCMethod1 */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg) { + if (likely(cfunc->func)) { + int flag = cfunc->flag; + if (flag == METH_O) { + return (*(cfunc->func))(self, arg); + } else if ((PY_VERSION_HEX >= 0x030600B1) && flag == METH_FASTCALL) { + #if PY_VERSION_HEX >= 0x030700A0 + return (*(__Pyx_PyCFunctionFast)(void*)(PyCFunction)cfunc->func)(self, &arg, 1); + #else + return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); + #endif + } else if ((PY_VERSION_HEX >= 0x030700A0) && flag == (METH_FASTCALL | METH_KEYWORDS)) { + return (*(__Pyx_PyCFunctionFastWithKeywords)(void*)(PyCFunction)cfunc->func)(self, &arg, 1, NULL); + } + } + return __Pyx__CallUnboundCMethod1(cfunc, self, arg); +} +#endif +static PyObject* __Pyx__CallUnboundCMethod1(__Pyx_CachedCFunction* cfunc, PyObject* self, PyObject* arg){ + PyObject *args, *result = NULL; + if (unlikely(!cfunc->func && !cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL; +#if CYTHON_COMPILING_IN_CPYTHON + if (cfunc->func && (cfunc->flag & METH_VARARGS)) { + args = PyTuple_New(1); + if (unlikely(!args)) goto bad; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + if (cfunc->flag & METH_KEYWORDS) + result = (*(PyCFunctionWithKeywords)(void*)(PyCFunction)cfunc->func)(self, args, NULL); + else + result = (*cfunc->func)(self, args); + } else { + args = PyTuple_New(2); + if (unlikely(!args)) goto bad; + Py_INCREF(self); + PyTuple_SET_ITEM(args, 0, self); + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 1, arg); + result = __Pyx_PyObject_Call(cfunc->method, args, NULL); + } +#else + args = PyTuple_Pack(2, self, arg); + if (unlikely(!args)) goto bad; + result = __Pyx_PyObject_Call(cfunc->method, args, NULL); +#endif +bad: + Py_XDECREF(args); + return result; } /* PyDictVersioning */ @@ -11166,44 +12485,6 @@ static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name) return __Pyx_GetBuiltinName(name); } -/* RaiseTooManyValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); -} - -/* RaiseNeedMoreValuesToUnpack */ -static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { - PyErr_Format(PyExc_ValueError, - "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", - index, (index == 1) ? "" : "s"); -} - -/* IterFinish */ -static CYTHON_INLINE int __Pyx_IterFinish(void) { - PyObject* exc_type; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign - exc_type = __Pyx_PyErr_CurrentExceptionType(); - if (unlikely(exc_type)) { - if (unlikely(!__Pyx_PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) - return -1; - __Pyx_PyErr_Clear(); - return 0; - } - return 0; -} - -/* UnpackItemEndCheck */ -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { - if (unlikely(retval)) { - Py_DECREF(retval); - __Pyx_RaiseTooManyValuesError(expected); - return -1; - } - return __Pyx_IterFinish(); -} - /* TypeImport */ #ifndef __PYX_HAVE_RT_ImportType_3_0_11 #define __PYX_HAVE_RT_ImportType_3_0_11 @@ -12723,6 +14004,293 @@ static PyObject *__Pyx_CyFunction_New(PyMethodDef *ml, int flags, PyObject* qual return op; } +/* CalculateMetaclass */ +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { + Py_ssize_t i, nbases; +#if CYTHON_ASSUME_SAFE_MACROS + nbases = PyTuple_GET_SIZE(bases); +#else + nbases = PyTuple_Size(bases); + if (nbases < 0) return NULL; +#endif + for (i=0; i < nbases; i++) { + PyTypeObject *tmptype; +#if CYTHON_ASSUME_SAFE_MACROS + PyObject *tmp = PyTuple_GET_ITEM(bases, i); +#else + PyObject *tmp = PyTuple_GetItem(bases, i); + if (!tmp) return NULL; +#endif + tmptype = Py_TYPE(tmp); +#if PY_MAJOR_VERSION < 3 + if (tmptype == &PyClass_Type) + continue; +#endif + if (!metaclass) { + metaclass = tmptype; + continue; + } + if (PyType_IsSubtype(metaclass, tmptype)) + continue; + if (PyType_IsSubtype(tmptype, metaclass)) { + metaclass = tmptype; + continue; + } + PyErr_SetString(PyExc_TypeError, + "metaclass conflict: " + "the metaclass of a derived class " + "must be a (non-strict) subclass " + "of the metaclasses of all its bases"); + return NULL; + } + if (!metaclass) { +#if PY_MAJOR_VERSION < 3 + metaclass = &PyClass_Type; +#else + metaclass = &PyType_Type; +#endif + } + Py_INCREF((PyObject*) metaclass); + return (PyObject*) metaclass; +} + +/* PyObjectCall2Args */ +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call2Args(PyObject* function, PyObject* arg1, PyObject* arg2) { + PyObject *args[3] = {NULL, arg1, arg2}; + return __Pyx_PyObject_FastCall(function, args+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET); +} + +/* PyObjectLookupSpecial */ +#if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx__PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name, int with_error) { + PyObject *res; + PyTypeObject *tp = Py_TYPE(obj); +#if PY_MAJOR_VERSION < 3 + if (unlikely(PyInstance_Check(obj))) + return with_error ? __Pyx_PyObject_GetAttrStr(obj, attr_name) : __Pyx_PyObject_GetAttrStrNoError(obj, attr_name); +#endif + res = _PyType_Lookup(tp, attr_name); + if (likely(res)) { + descrgetfunc f = Py_TYPE(res)->tp_descr_get; + if (!f) { + Py_INCREF(res); + } else { + res = f(res, obj, (PyObject *)tp); + } + } else if (with_error) { + PyErr_SetObject(PyExc_AttributeError, attr_name); + } + return res; +} +#endif + +/* Py3ClassCreate */ +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, + PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { + PyObject *ns; + if (metaclass) { + PyObject *prep = __Pyx_PyObject_GetAttrStrNoError(metaclass, __pyx_n_s_prepare); + if (prep) { + PyObject *pargs[3] = {NULL, name, bases}; + ns = __Pyx_PyObject_FastCallDict(prep, pargs+1, 2 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, mkw); + Py_DECREF(prep); + } else { + if (unlikely(PyErr_Occurred())) + return NULL; + ns = PyDict_New(); + } + } else { + ns = PyDict_New(); + } + if (unlikely(!ns)) + return NULL; + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad; +#if PY_VERSION_HEX >= 0x03030000 + if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad; +#else + CYTHON_MAYBE_UNUSED_VAR(qualname); +#endif + if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad; + return ns; +bad: + Py_DECREF(ns); + return NULL; +} +#if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS +static int __Pyx_SetNamesPEP487(PyObject *type_obj) { + PyTypeObject *type = (PyTypeObject*) type_obj; + PyObject *names_to_set, *key, *value, *set_name, *tmp; + Py_ssize_t i = 0; +#if CYTHON_USE_TYPE_SLOTS + names_to_set = PyDict_Copy(type->tp_dict); +#else + { + PyObject *d = PyObject_GetAttr(type_obj, __pyx_n_s_dict); + names_to_set = NULL; + if (likely(d)) { + PyObject *names_to_set = PyDict_New(); + int ret = likely(names_to_set) ? PyDict_Update(names_to_set, d) : -1; + Py_DECREF(d); + if (unlikely(ret < 0)) + Py_CLEAR(names_to_set); + } + } +#endif + if (unlikely(names_to_set == NULL)) + goto bad; + while (PyDict_Next(names_to_set, &i, &key, &value)) { + set_name = __Pyx_PyObject_LookupSpecialNoError(value, __pyx_n_s_set_name); + if (unlikely(set_name != NULL)) { + tmp = __Pyx_PyObject_Call2Args(set_name, type_obj, key); + Py_DECREF(set_name); + if (unlikely(tmp == NULL)) { + __Pyx_TypeName value_type_name = + __Pyx_PyType_GetName(Py_TYPE(value)); + __Pyx_TypeName type_name = __Pyx_PyType_GetName(type); + PyErr_Format(PyExc_RuntimeError, +#if PY_MAJOR_VERSION >= 3 + "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %R " "in '" __Pyx_FMT_TYPENAME "'", + value_type_name, key, type_name); +#else + "Error calling __set_name__ on '" __Pyx_FMT_TYPENAME "' instance %.100s in '" __Pyx_FMT_TYPENAME "'", + value_type_name, + PyString_Check(key) ? PyString_AS_STRING(key) : "?", + type_name); +#endif + goto bad; + } else { + Py_DECREF(tmp); + } + } + else if (unlikely(PyErr_Occurred())) { + goto bad; + } + } + Py_DECREF(names_to_set); + return 0; +bad: + Py_XDECREF(names_to_set); + return -1; +} +static PyObject *__Pyx_InitSubclassPEP487(PyObject *type_obj, PyObject *mkw) { +#if CYTHON_USE_TYPE_SLOTS && CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + PyTypeObject *type = (PyTypeObject*) type_obj; + PyObject *mro = type->tp_mro; + Py_ssize_t i, nbases; + if (unlikely(!mro)) goto done; + (void) &__Pyx_GetBuiltinName; + Py_INCREF(mro); + nbases = PyTuple_GET_SIZE(mro); + assert(PyTuple_GET_ITEM(mro, 0) == type_obj); + for (i = 1; i < nbases-1; i++) { + PyObject *base, *dict, *meth; + base = PyTuple_GET_ITEM(mro, i); + dict = ((PyTypeObject *)base)->tp_dict; + meth = __Pyx_PyDict_GetItemStrWithError(dict, __pyx_n_s_init_subclass); + if (unlikely(meth)) { + descrgetfunc f = Py_TYPE(meth)->tp_descr_get; + PyObject *res; + Py_INCREF(meth); + if (likely(f)) { + res = f(meth, NULL, type_obj); + Py_DECREF(meth); + if (unlikely(!res)) goto bad; + meth = res; + } + res = __Pyx_PyObject_FastCallDict(meth, NULL, 0, mkw); + Py_DECREF(meth); + if (unlikely(!res)) goto bad; + Py_DECREF(res); + goto done; + } else if (unlikely(PyErr_Occurred())) { + goto bad; + } + } +done: + Py_XDECREF(mro); + return type_obj; +bad: + Py_XDECREF(mro); + Py_DECREF(type_obj); + return NULL; +#else + PyObject *super_type, *super, *func, *res; +#if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type) + super_type = __Pyx_GetBuiltinName(__pyx_n_s_super); +#else + super_type = (PyObject*) &PySuper_Type; + (void) &__Pyx_GetBuiltinName; +#endif + super = likely(super_type) ? __Pyx_PyObject_Call2Args(super_type, type_obj, type_obj) : NULL; +#if CYTHON_COMPILING_IN_PYPY && !defined(PySuper_Type) + Py_XDECREF(super_type); +#endif + if (unlikely(!super)) { + Py_CLEAR(type_obj); + goto done; + } + func = __Pyx_PyObject_GetAttrStrNoError(super, __pyx_n_s_init_subclass); + Py_DECREF(super); + if (likely(!func)) { + if (unlikely(PyErr_Occurred())) + Py_CLEAR(type_obj); + goto done; + } + res = __Pyx_PyObject_FastCallDict(func, NULL, 0, mkw); + Py_DECREF(func); + if (unlikely(!res)) + Py_CLEAR(type_obj); + Py_XDECREF(res); +done: + return type_obj; +#endif +} +#endif +static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, + PyObject *dict, PyObject *mkw, + int calculate_metaclass, int allow_py2_metaclass) { + PyObject *result; + PyObject *owned_metaclass = NULL; + PyObject *margs[4] = {NULL, name, bases, dict}; + if (allow_py2_metaclass) { + owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass); + if (owned_metaclass) { + metaclass = owned_metaclass; + } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) { + PyErr_Clear(); + } else { + return NULL; + } + } + if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) { + metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases); + Py_XDECREF(owned_metaclass); + if (unlikely(!metaclass)) + return NULL; + owned_metaclass = metaclass; + } + result = __Pyx_PyObject_FastCallDict(metaclass, margs+1, 3 | __Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET, +#if PY_VERSION_HEX < 0x030600A4 + (metaclass == (PyObject*)&PyType_Type) ? NULL : mkw +#else + mkw +#endif + ); + Py_XDECREF(owned_metaclass); +#if PY_VERSION_HEX < 0x030600A4 && CYTHON_PEP487_INIT_SUBCLASS + if (likely(result) && likely(PyType_Check(result))) { + if (unlikely(__Pyx_SetNamesPEP487(result) < 0)) { + Py_CLEAR(result); + } else { + result = __Pyx_InitSubclassPEP487(result, mkw); + } + } +#else + (void) &__Pyx_GetBuiltinName; +#endif + return result; +} + /* CLineInTraceback */ #ifndef CYTHON_CLINE_IN_TRACEBACK static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line) { @@ -14210,7 +15778,7 @@ __Pyx_PyType_GetName(PyTypeObject* tp) if (unlikely(name == NULL) || unlikely(!PyUnicode_Check(name))) { PyErr_Clear(); Py_XDECREF(name); - name = __Pyx_NewRef(__pyx_n_s__13); + name = __Pyx_NewRef(__pyx_n_s__20); } return name; } diff --git a/CRISPResso2/CRISPRessoCOREResources.pyx b/CRISPResso2/CRISPRessoCOREResources.pyx index d64480fb..c7c8669f 100644 --- a/CRISPResso2/CRISPRessoCOREResources.pyx +++ b/CRISPResso2/CRISPRessoCOREResources.pyx @@ -15,6 +15,52 @@ cdef extern from "Python.h": re_find_indels = re.compile("(-*-)") +class ResultsSlotsDict(): + __slots__ = ( + 'all_insertion_positions', + 'all_insertion_left_positions', + 'insertion_positions', + 'insertion_coordinates', + 'insertion_sizes', + 'insertion_n', + 'all_deletion_positions', + 'all_deletion_coordinates', + 'deletion_positions', + 'deletion_coordinates', + 'deletion_sizes', + 'deletion_n', + 'all_substitution_positions', + 'substitution_positions', + 'all_substitution_values', + 'substitution_values', + 'substitution_n', + 'ref_positions', + 'ref_name', + 'aln_scores', + 'classification', + 'aln_seq', + 'aln_ref', + 'aln_strand', + 'irregular_ends', + 'insertions_outside_window', + 'deletions_outside_window', + 'substitutions_outside_window', + 'total_mods', + 'mods_in_window', + 'mods_outside_window', + ) + + def __init__(self, **kwargs): + for key, value in kwargs.items(): + setattr(self, key, value) + + def __getitem__(self, key): + return getattr(self, key) + + def __setitem__(self, key, value): + setattr(self, key, value) + + @cython.boundscheck(False) @cython.nonecheck(False) @cython.wraparound(False) @@ -113,33 +159,34 @@ def find_indels_substitutions(read_seq_al, ref_seq_al, _include_indx): cdef size_t deletion_n = sum(deletion_sizes) cdef size_t insertion_n = sum(insertion_sizes) - return { - 'all_insertion_positions': all_insertion_positions, - 'all_insertion_left_positions': all_insertion_left_positions, - 'insertion_positions': insertion_positions, - 'insertion_coordinates': insertion_coordinates, - 'insertion_sizes': insertion_sizes, - 'insertion_n': insertion_n, - - 'all_deletion_positions': all_deletion_positions, - 'all_deletion_coordinates': all_deletion_coordinates, - 'deletion_positions': deletion_positions, - 'deletion_coordinates': deletion_coordinates, - 'deletion_sizes': deletion_sizes, - 'deletion_n': deletion_n, - - 'all_substitution_positions': all_substitution_positions, - 'substitution_positions': substitution_positions, - 'all_substitution_values': np.array(all_substitution_values), - 'substitution_values': np.array(substitution_values), - 'substitution_n': substitution_n, - 'ref_positions': ref_positions, - } + return ResultsSlotsDict( + all_insertion_positions=all_insertion_positions, + all_insertion_left_positions=all_insertion_left_positions, + insertion_positions=insertion_positions, + insertion_coordinates=insertion_coordinates, + insertion_sizes=insertion_sizes, + insertion_n=insertion_n, + + all_deletion_positions=all_deletion_positions, + all_deletion_coordinates=all_deletion_coordinates, + deletion_positions=deletion_positions, + deletion_coordinates=deletion_coordinates, + deletion_sizes=deletion_sizes, + deletion_n=deletion_n, + + all_substitution_positions=all_substitution_positions, + substitution_positions=substitution_positions, + all_substitution_values=np.array(all_substitution_values), + substitution_values=np.array(substitution_values), + substitution_n=substitution_n, + + ref_positions=ref_positions, + ) + + @cython.boundscheck(False) @cython.nonecheck(False) @cython.wraparound(False) - - def find_indels_substitutions_legacy(read_seq_al, ref_seq_al, _include_indx): cdef char* sub_seq=''