diff --git a/CRISPResso2/CRISPResso2Align.c b/CRISPResso2/CRISPResso2Align.c index faba1625..a4855d27 100644 --- a/CRISPResso2/CRISPResso2Align.c +++ b/CRISPResso2/CRISPResso2Align.c @@ -1,18 +1,18 @@ -/* Generated by Cython 0.29.14 */ +/* Generated by Cython 0.29.15 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h" + "/home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h", + "/home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-w", "-Ofast" ], "include_dirs": [ - "/home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/numpy/core/include" + "/home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/numpy/core/include" ], "name": "CRISPResso2.CRISPResso2Align", "sources": [ @@ -30,8 +30,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_29_14" -#define CYTHON_HEX_VERSION 0x001D0EF0 +#define CYTHON_ABI "0_29_15" +#define CYTHON_HEX_VERSION 0x001D0FF0 #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -968,7 +968,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; #define __Pyx_FastGilFuncInit() -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -977,7 +977,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -986,7 +986,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -995,7 +995,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1004,7 +1004,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1013,7 +1013,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1022,7 +1022,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1031,7 +1031,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1040,7 +1040,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1049,7 +1049,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1058,7 +1058,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1067,7 +1067,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1076,7 +1076,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1085,7 +1085,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1094,7 +1094,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1103,7 +1103,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1112,7 +1112,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1121,7 +1121,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1130,7 +1130,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1139,7 +1139,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1148,7 +1148,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1214,7 +1214,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1223,7 +1223,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1232,7 +1232,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1241,7 +1241,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -6862,7 +6862,7 @@ __pyx_t_9 = -1; return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -6911,7 +6911,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -6920,7 +6920,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -6929,7 +6929,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -6938,7 +6938,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -6952,7 +6952,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -6963,7 +6963,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -6972,7 +6972,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -6985,7 +6985,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 272, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -6994,7 +6994,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -7008,7 +7008,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -7019,7 +7019,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -7028,7 +7028,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -7041,7 +7041,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 276, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -7050,7 +7050,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -7059,7 +7059,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -7068,7 +7068,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -7078,7 +7078,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -7087,7 +7087,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -7096,7 +7096,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -7108,7 +7108,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -7117,7 +7117,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":287 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -7127,7 +7127,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -7137,7 +7137,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -7147,7 +7147,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -7158,7 +7158,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -7167,7 +7167,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -7176,7 +7176,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -7185,7 +7185,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":296 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -7194,7 +7194,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":297 * cdef int t * cdef char* f = NULL * cdef dtype descr = PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -7207,7 +7207,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":300 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":300 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -7220,7 +7220,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -7230,7 +7230,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":303 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":303 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -7240,7 +7240,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -7260,7 +7260,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":305 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":305 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -7277,7 +7277,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -7286,7 +7286,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -7299,7 +7299,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 306, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -7308,7 +7308,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":307 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":307 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -7321,7 +7321,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_UBYTE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":308 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":308 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -7332,7 +7332,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_SHORT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":309 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":309 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -7343,7 +7343,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_USHORT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":310 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":310 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -7354,7 +7354,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_INT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":311 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":311 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -7365,7 +7365,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_UINT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":312 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":312 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -7376,7 +7376,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":313 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":313 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -7387,7 +7387,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_ULONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":314 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":314 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -7398,7 +7398,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONGLONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":315 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":315 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -7409,7 +7409,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_ULONGLONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":316 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":316 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -7420,7 +7420,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_FLOAT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":317 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":317 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -7431,7 +7431,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_DOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":318 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":318 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -7442,7 +7442,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONGDOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":319 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":319 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -7453,7 +7453,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CFLOAT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":320 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":320 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -7464,7 +7464,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CDOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":321 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":321 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -7475,7 +7475,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CLONGDOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":322 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":322 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -7486,7 +7486,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_OBJECT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":323 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":323 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -7497,7 +7497,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":325 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":325 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -7518,7 +7518,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":326 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":326 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -7527,7 +7527,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":327 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":327 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -7537,7 +7537,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -7546,7 +7546,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":329 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":329 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -7556,7 +7556,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":330 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":330 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -7565,7 +7565,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":331 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":331 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -7574,7 +7574,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":332 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":332 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -7584,7 +7584,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == ((char *)NULL))) __PYX_ERR(1, 332, __pyx_L1_error) __pyx_v_f = __pyx_t_9; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":335 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":335 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -7594,7 +7594,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -7626,7 +7626,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":337 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":337 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -7650,7 +7650,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":338 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":338 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -7660,7 +7660,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":339 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":339 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) # <<<<<<<<<<<<<< @@ -7669,7 +7669,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->format); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":338 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":338 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -7678,7 +7678,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":340 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":340 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -7688,7 +7688,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":341 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":341 * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * PyObject_Free(info.strides) # <<<<<<<<<<<<<< @@ -7697,7 +7697,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ PyObject_Free(__pyx_v_info->strides); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":340 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":340 * if PyArray_HASFIELDS(self): * PyObject_Free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -7706,7 +7706,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":337 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":337 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -7718,7 +7718,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* 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*__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -7765,7 +7765,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":824 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":824 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -7779,7 +7779,7 @@ static 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PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_r = ((PyObject*)__pyx_v_d->subarray->shape); goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -7998,7 +7998,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -8012,7 +8012,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -8027,7 +8027,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< 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<<<<<<<<<<<<<< @@ -8179,7 +8179,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 856, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":855 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -8188,7 +8188,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -8208,7 +8208,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":859 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":859 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -8225,7 +8225,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -8234,7 +8234,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":860 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -8247,7 +8247,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 860, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -8256,7 +8256,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":870 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":870 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -8272,7 +8272,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":871 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":871 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -8281,7 +8281,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":872 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":872 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -8290,7 +8290,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":873 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":873 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -8301,7 +8301,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":875 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":875 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -8311,7 +8311,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -8321,7 +8321,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":878 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":878 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -8333,7 +8333,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -8343,7 +8343,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -8356,7 +8356,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 880, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -8365,7 +8365,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":883 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":883 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -8383,7 +8383,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":884 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":884 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -8401,7 +8401,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":885 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":885 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -8419,7 +8419,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":886 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":886 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -8437,7 +8437,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":887 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":887 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -8455,7 +8455,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":888 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":888 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -8473,7 +8473,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":889 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":889 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -8491,7 +8491,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":890 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":890 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -8509,7 +8509,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":891 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":891 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -8527,7 +8527,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":892 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":892 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -8545,7 +8545,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":893 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":893 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -8563,7 +8563,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":894 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":894 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -8581,7 +8581,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":895 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":895 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -8599,7 +8599,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":896 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":896 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -8619,7 +8619,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":897 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":897 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -8639,7 +8639,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":898 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":898 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -8659,7 +8659,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":899 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":899 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -8677,7 +8677,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":901 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":901 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -8696,7 +8696,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":902 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":902 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -8705,7 +8705,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -8715,7 +8715,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":906 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":906 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -8728,7 +8728,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":851 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -8738,7 +8738,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":907 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":907 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -8748,7 +8748,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -8773,7 +8773,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -8785,7 +8785,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1023 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1023 * * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! # <<<<<<<<<<<<<< @@ -8794,7 +8794,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_INCREF(__pyx_v_base); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1024 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1024 * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) # <<<<<<<<<<<<<< @@ -8803,7 +8803,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ (void)(PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_base)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -8815,7 +8815,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -8830,7 +8830,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1027 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1027 * * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) # <<<<<<<<<<<<<< @@ -8839,7 +8839,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ __pyx_v_base = PyArray_BASE(__pyx_v_arr); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -8849,7 +8849,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_base == NULL) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1029 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1029 * base = PyArray_BASE(arr) * if base is NULL: * return None # <<<<<<<<<<<<<< @@ -8860,7 +8860,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -8869,7 +8869,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1030 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1030 * if base is NULL: * return None * return base # <<<<<<<<<<<<<< @@ -8881,7 +8881,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = ((PyObject *)__pyx_v_base); goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -8896,7 +8896,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -8917,7 +8917,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -8933,7 +8933,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1036 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1036 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -8942,7 +8942,7 @@ 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, 1036, __pyx_L3_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -8956,7 +8956,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1037 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1037 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -8971,7 +8971,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -8987,7 +8987,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -9002,7 +9002,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -9025,7 +9025,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -9046,7 +9046,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -9062,7 +9062,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1042 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1042 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -9071,7 +9071,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1042, __pyx_L3_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -9085,7 +9085,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1043 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1043 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -9100,7 +9100,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -9116,7 +9116,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -9131,7 +9131,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -9154,7 +9154,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -9175,7 +9175,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -9191,7 +9191,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1048 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1048 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -9200,7 +9200,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1048, __pyx_L3_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -9214,7 +9214,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1049 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1049 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -9228,7 +9228,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1050 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1050 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -9242,7 +9242,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -9257,7 +9257,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -23105,7 +23105,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_slice__7); __Pyx_GIVEREF(__pyx_slice__7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -23116,7 +23116,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -23127,7 +23127,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -23138,7 +23138,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__10); __Pyx_GIVEREF(__pyx_tuple__10); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":856 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -23149,7 +23149,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__11); __Pyx_GIVEREF(__pyx_tuple__11); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -23160,7 +23160,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__12); __Pyx_GIVEREF(__pyx_tuple__12); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -23171,7 +23171,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__13); __Pyx_GIVEREF(__pyx_tuple__13); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -26739,43 +26739,43 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { PyObject *setstate = NULL; PyObject *setstate_cython = NULL; #if CYTHON_USE_PYTYPE_LOOKUP - if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto GOOD; + if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #else - if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto GOOD; + if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD; #endif #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #else - object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto BAD; + object_reduce_ex = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD; #endif - reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto BAD; + reduce_ex = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_ex); if (unlikely(!reduce_ex)) goto __PYX_BAD; if (reduce_ex == object_reduce_ex) { #if CYTHON_USE_PYTYPE_LOOKUP - object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #else - object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto BAD; + object_reduce = __Pyx_PyObject_GetAttrStr((PyObject*)&PyBaseObject_Type, __pyx_n_s_reduce); if (!object_reduce) goto __PYX_BAD; #endif - reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto BAD; + reduce = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce); if (unlikely(!reduce)) goto __PYX_BAD; if (reduce == object_reduce || __Pyx_setup_reduce_is_named(reduce, __pyx_n_s_reduce_cython)) { - reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto BAD; + reduce_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_reduce_cython); if (unlikely(!reduce_cython)) goto __PYX_BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce, reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_reduce_cython); if (unlikely(ret < 0)) goto __PYX_BAD; setstate = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate); if (!setstate) PyErr_Clear(); if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) { - setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto BAD; - ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto BAD; - ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto BAD; + setstate_cython = __Pyx_PyObject_GetAttrStr(type_obj, __pyx_n_s_setstate_cython); if (unlikely(!setstate_cython)) goto __PYX_BAD; + ret = PyDict_SetItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate, setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; + ret = PyDict_DelItem(((PyTypeObject*)type_obj)->tp_dict, __pyx_n_s_setstate_cython); if (unlikely(ret < 0)) goto __PYX_BAD; } PyType_Modified((PyTypeObject*)type_obj); } } - goto GOOD; -BAD: + goto __PYX_GOOD; +__PYX_BAD: if (!PyErr_Occurred()) PyErr_Format(PyExc_RuntimeError, "Unable to initialize pickling for %s", ((PyTypeObject*)type_obj)->tp_name); ret = -1; -GOOD: +__PYX_GOOD: #if !CYTHON_USE_PYTYPE_LOOKUP Py_XDECREF(object_reduce); Py_XDECREF(object_reduce_ex); diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py index 327c67a9..d5d351ef 100644 --- a/CRISPResso2/CRISPRessoCORE.py +++ b/CRISPResso2/CRISPRessoCORE.py @@ -253,7 +253,10 @@ def get_new_variant_object(args, fastq_seq, refs, ref_names, aln_matrix, pe_scaf for idx in range(len(best_match_names)): best_match_name = best_match_names[idx] - payload=CRISPRessoCOREResources.find_indels_substitutions(best_match_s1s[idx],best_match_s2s[idx],refs[best_match_name]['include_idxs']) + if args.use_legacy_insertion_quantification: + payload=CRISPRessoCOREResources.find_indels_substitutions_legacy(best_match_s1s[idx],best_match_s2s[idx],refs[best_match_name]['include_idxs']) + else: + payload=CRISPRessoCOREResources.find_indels_substitutions(best_match_s1s[idx],best_match_s2s[idx],refs[best_match_name]['include_idxs']) payload['ref_name'] = best_match_name payload['aln_scores'] = aln_scores @@ -1983,7 +1986,7 @@ def get_prime_editing_guides(this_amp_seq,this_amp_name,ref0_seq,prime_edited_se #operates on variantCache if args.bam_input: aln_stats = process_bam(args.bam_input,args.bam_chr_loc,crispresso2_info['bam_output'],variantCache,ref_names,refs,args) - if args.fastq_output: + elif args.fastq_output: aln_stats = process_fastq_write_out(processed_output_filename,crispresso2_info['fastq_output'],variantCache,ref_names,refs,args) else: aln_stats = process_fastq(processed_output_filename,variantCache,ref_names,refs,args) @@ -2139,7 +2142,9 @@ def get_prime_editing_guides(this_amp_seq,this_amp_name,ref0_seq,prime_edited_se effective_len_dicts [ref_name] = defaultdict(int) hists_inframe [ref_name] = defaultdict(int) + hists_inframe [ref_name][0] = 0 hists_frameshift [ref_name] = defaultdict(int) + hists_frameshift [ref_name][0] = 0 #end initialize data structures for each ref def get_allele_row(reference_name, variant_count, aln_ref_names_str, aln_ref_scores_str, variant_payload, write_detailed_allele_table): """ @@ -2482,7 +2487,10 @@ def get_allele_row(reference_name, variant_count, aln_ref_names_str, aln_ref_sco #align this variant to ref1 sequence ref_aln_name,s1,s2,score = variantCache[variant]['ref_aln_details'][0] - payload=CRISPRessoCOREResources.find_indels_substitutions(s1,s2,refs[ref1_name]['include_idxs']) + if args.use_legacy_insertion_quantification: + payload=CRISPRessoCOREResources.find_indels_substitutions_legacy(s1,s2,refs[ref1_name]['include_idxs']) + else: + payload=CRISPRessoCOREResources.find_indels_substitutions(s1,s2,refs[ref1_name]['include_idxs']) #indels in this alignment against ref1 should be recorded for each ref it was originally assigned to, as well as for ref1 #for example, if this read aligned to ref3, align this read to ref1, and add the resulting indels to ref1_all_insertion_count_vectors[ref3] as well as ref1_all_insertion_count_vectors[ref1] @@ -2618,15 +2626,6 @@ def calculate_99_max(d): refs[ref_name]['hlengths'] = hlengths refs[ref_name]['center_index'] = center_index - if not dict(hists_inframe[ref_name]): - hists_inframe[ref_name]={0:0} - else: - hists_inframe[ref_name]=dict(hists_inframe[ref_name]) - - if not dict(hists_frameshift[ref_name]): - hists_frameshift[ref_name]={0:0} - else: - hists_frameshift[ref_name]=dict(hists_frameshift[ref_name]) count_tot = counts_total[ref_name] if count_tot > 0: @@ -4440,8 +4439,12 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln global_MODIFIED_NON_FRAMESHIFT = 0 global_NON_MODIFIED_NON_FRAMESHIFT = 0 global_SPLICING_SITES_MODIFIED = 0 + global_hists_frameshift = defaultdict(lambda :0) + global_hists_frameshift[0] = 0 #fill with at least the zero value (in case there are no others) + global_hists_inframe = defaultdict(lambda :0) + global_hists_inframe[0] = 0 global_count_total = 0 global_count_modified = 0 diff --git a/CRISPResso2/CRISPRessoCOREResources.c b/CRISPResso2/CRISPRessoCOREResources.c index 8fb78ce6..52518fc1 100644 --- a/CRISPResso2/CRISPRessoCOREResources.c +++ b/CRISPResso2/CRISPRessoCOREResources.c @@ -1,18 +1,18 @@ -/* Generated by Cython 0.29.14 */ +/* Generated by Cython 0.29.15 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h" + "/home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h", + "/home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-w", "-Ofast" ], "include_dirs": [ - "/home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/numpy/core/include" + "/home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/numpy/core/include" ], "name": "CRISPResso2.CRISPRessoCOREResources", "sources": [ @@ -30,8 +30,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_29_14" -#define CYTHON_HEX_VERSION 0x001D0EF0 +#define CYTHON_ABI "0_29_15" +#define CYTHON_HEX_VERSION 0x001D0FF0 #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -856,7 +856,7 @@ static const char *__pyx_f[] = { "type.pxd", }; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -865,7 +865,7 @@ static const char *__pyx_f[] = { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -874,7 +874,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -883,7 +883,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -892,7 +892,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -901,7 +901,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":784 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -910,7 +910,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -919,7 +919,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -928,7 +928,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -937,7 +937,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -946,7 +946,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":800 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -955,7 +955,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -964,7 +964,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -973,7 +973,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -982,7 +982,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -991,7 +991,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1000,7 +1000,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":808 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1009,7 +1009,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":809 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1018,7 +1018,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":811 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1027,7 +1027,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":812 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1036,7 +1036,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1071,7 +1071,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do /*--- Type declarations ---*/ -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1080,7 +1080,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1089,7 +1089,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1098,7 +1098,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1751,6 +1751,7 @@ static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype cod static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour[] = "CRISPResso2/CRISPRessoCOREResources.pyx"; static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static const char __pyx_k_find_indels_substitutions_legacy[] = "find_indels_substitutions_legacy"; static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; static const char __pyx_k_CRISPResso2_CRISPRessoCOREResour_2[] = "CRISPResso2.CRISPRessoCOREResources"; @@ -1790,6 +1791,7 @@ static PyObject *__pyx_n_s_deletion_sizes; static PyObject *__pyx_n_s_en; static PyObject *__pyx_n_s_enumerate; static PyObject *__pyx_n_s_find_indels_substitutions; +static PyObject *__pyx_n_s_find_indels_substitutions_legacy; static PyObject *__pyx_n_s_finditer; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_idx; @@ -1836,7 +1838,8 @@ static PyObject *__pyx_n_s_sum; static PyObject *__pyx_n_s_test; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; 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_2calculate_homology(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b); /* 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 */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static __Pyx_CachedCFunction __pyx_umethod_PySet_Type_intersection = {0, &__pyx_n_s_intersection, 0, 0, 0}; @@ -1852,8 +1855,10 @@ static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__9; static PyObject *__pyx_tuple__10; static PyObject *__pyx_tuple__12; +static PyObject *__pyx_tuple__14; static PyObject *__pyx_codeobj__11; static PyObject *__pyx_codeobj__13; +static PyObject *__pyx_codeobj__15; /* Late includes */ /* "CRISPResso2/CRISPRessoCOREResources.pyx":12 @@ -2319,7 +2324,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su * else: * ref_positions.append(-idx) # <<<<<<<<<<<<<< * - * # ###SLOW PART### + * substitution_n = len(substitution_positions) */ /*else*/ { __pyx_t_2 = __Pyx_PyInt_From_int((-__pyx_v_idx)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 58, __pyx_L1_error) @@ -2341,149 +2346,1792 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + /* "CRISPResso2/CRISPRessoCOREResources.pyx":60 + * ref_positions.append(-idx) + * + * substitution_n = 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__pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.find_indels_substitutions_legacy", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_ref_positions); @@ -3499,7 +5147,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su return __pyx_r; } -/* "CRISPResso2/CRISPRessoCOREResources.pyx":154 +/* "CRISPResso2/CRISPRessoCOREResources.pyx":278 * size_t strlen(char *s) * * def calculate_homology(a, b): # <<<<<<<<<<<<<< @@ -3508,9 +5156,9 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_find_indels_su */ /* Python wrapper */ -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3calculate_homology(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_3calculate_homology = {"calculate_homology", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3calculate_homology, METH_VARARGS|METH_KEYWORDS, 0}; -static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_3calculate_homology(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology = {"calculate_homology", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology, METH_VARARGS|METH_KEYWORDS, 0}; +static PyObject *__pyx_pw_11CRISPResso2_23CRISPRessoCOREResources_5calculate_homology(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_a = 0; PyObject *__pyx_v_b = 0; PyObject *__pyx_r = 0; @@ -3539,11 +5187,11 @@ static PyObject 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__Pyx_RaiseArgtupleInvalid("calculate_homology", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 154, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("calculate_homology", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 278, __pyx_L3_error) __pyx_L3_error:; __Pyx_AddTraceback("CRISPResso2.CRISPRessoCOREResources.calculate_homology", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_homology(__pyx_self, __pyx_v_a, __pyx_v_b); + __pyx_r = __pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_homology(__pyx_self, __pyx_v_a, __pyx_v_b); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_homology(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b) { +static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_4calculate_homology(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_a, PyObject *__pyx_v_b) { char *__pyx_v_al; char *__pyx_v_bl; size_t __pyx_v_l; @@ -3585,27 +5233,27 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_hom PyObject *__pyx_t_6 = NULL; __Pyx_RefNannySetupContext("calculate_homology", 0); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":155 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":279 * * 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, 155, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_AsWritableString(__pyx_v_a); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) __PYX_ERR(0, 279, __pyx_L1_error) __pyx_v_al = __pyx_t_1; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":156 + /* 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score+=1 # <<<<<<<<<<<<<< @@ -3653,7 +5301,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_hom */ __pyx_v_score = (__pyx_v_score + 1.0); - /* "CRISPResso2/CRISPRessoCOREResources.pyx":161 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":285 * * for i in range(l): * if al[i] == bl[i]: # <<<<<<<<<<<<<< @@ -3663,7 +5311,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_hom } } - /* "CRISPResso2/CRISPRessoCOREResources.pyx":163 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":287 * if al[i] == bl[i]: * score+=1 * return score/l # <<<<<<<<<<<<<< @@ -3671,15 +5319,15 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_hom __Pyx_XDECREF(__pyx_r); if (unlikely(__pyx_v_l == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 163, __pyx_L1_error) + __PYX_ERR(0, 287, __pyx_L1_error) } - __pyx_t_6 = PyFloat_FromDouble((__pyx_v_score / __pyx_v_l)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 163, __pyx_L1_error) + __pyx_t_6 = PyFloat_FromDouble((__pyx_v_score / __pyx_v_l)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 287, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_r = __pyx_t_6; __pyx_t_6 = 0; goto __pyx_L0; - /* "CRISPResso2/CRISPRessoCOREResources.pyx":154 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":278 * size_t strlen(char *s) * * def calculate_homology(a, b): # <<<<<<<<<<<<<< @@ -3698,7 +5346,7 @@ static PyObject *__pyx_pf_11CRISPResso2_23CRISPRessoCOREResources_2calculate_hom return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -3747,7 +5395,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -3756,7 +5404,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -3765,7 +5413,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -3774,7 +5422,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3788,7 +5436,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -3799,7 +5447,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3808,7 +5456,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # 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"../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3864,7 +5512,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -3877,7 +5525,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 276, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -3886,7 +5534,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -3895,7 +5543,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -3904,7 +5552,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3914,7 +5562,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -3923,7 +5571,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -3932,7 +5580,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -3944,7 +5592,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -3953,7 +5601,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":287 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -3963,7 +5611,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -3973,7 +5621,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -3983,7 +5631,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -3994,7 +5642,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -4003,7 +5651,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -4012,7 +5660,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -4021,7 +5669,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":296 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -4030,7 +5678,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":297 * cdef int t * cdef char* f = NULL * cdef dtype descr = PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -4043,7 +5691,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":300 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":300 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -4056,7 +5704,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -4066,7 +5714,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":303 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":303 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -4076,7 +5724,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4096,7 +5744,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":305 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":305 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -4113,7 +5761,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4122,7 +5770,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4135,7 +5783,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 306, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -4144,7 +5792,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":307 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":307 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -4157,7 +5805,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_UBYTE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":308 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":308 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -4168,7 +5816,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_SHORT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":309 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":309 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -4179,7 +5827,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_USHORT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":310 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":310 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -4190,7 +5838,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_INT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":311 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":311 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -4201,7 +5849,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_UINT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":312 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":312 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -4212,7 +5860,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":313 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":313 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -4223,7 +5871,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_ULONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":314 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":314 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -4234,7 +5882,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONGLONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":315 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":315 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -4245,7 +5893,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_ULONGLONG: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":316 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":316 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -4256,7 +5904,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_FLOAT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":317 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":317 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -4267,7 +5915,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_DOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":318 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":318 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -4278,7 +5926,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONGDOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":319 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":319 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -4289,7 +5937,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CFLOAT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":320 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":320 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -4300,7 +5948,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CDOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":321 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":321 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -4311,7 +5959,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CLONGDOUBLE: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":322 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":322 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -4322,7 +5970,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_OBJECT: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":323 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":323 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -4333,7 +5981,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":325 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":325 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -4354,7 +6002,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":326 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":326 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -4363,7 +6011,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":327 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":327 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -4373,7 +6021,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":302 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -4382,7 +6030,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":329 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":329 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -4392,7 +6040,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":330 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":330 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -4401,7 +6049,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":331 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":331 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -4410,7 +6058,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":332 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":332 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -4420,7 +6068,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == ((char *)NULL))) __PYX_ERR(1, 332, __pyx_L1_error) __pyx_v_f = __pyx_t_9; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":335 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":335 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -4430,7 +6078,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* 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@@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -4742,7 +6390,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -4756,7 +6404,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< @@ -4770,7 +6418,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -4789,7 +6437,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -4803,7 +6451,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ int __pyx_t_1; __Pyx_RefNannySetupContext("PyDataType_SHAPE", 0); - /* 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PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ __pyx_r = ((PyObject*)__pyx_v_d->subarray->shape); goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -4834,7 +6482,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -4848,7 +6496,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -4863,7 +6511,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< 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"../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":852 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -4950,7 +6598,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":853 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":853 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -4985,7 +6633,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":855 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -5002,7 +6650,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":856 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # 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"../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5070,7 +6718,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":860 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":860 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -5083,7 +6731,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(1, 860, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":858 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -5092,7 +6740,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":870 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":870 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -5108,7 +6756,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":871 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":871 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -5117,7 +6765,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":872 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":872 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -5126,7 +6774,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":873 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":873 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -5137,7 +6785,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":875 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":875 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -5147,7 +6795,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -5157,7 +6805,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":878 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":878 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -5169,7 +6817,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -5179,7 +6827,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -5192,7 +6840,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(1, 880, __pyx_L1_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":879 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -5201,7 +6849,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":883 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":883 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -5219,7 +6867,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":884 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":884 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -5237,7 +6885,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":885 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":885 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -5255,7 +6903,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":886 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":886 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -5273,7 +6921,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":887 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":887 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -5291,7 +6939,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":888 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":888 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -5309,7 +6957,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":889 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":889 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -5327,7 +6975,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":890 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":890 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -5345,7 +6993,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":891 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":891 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -5363,7 +7011,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":892 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":892 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -5381,7 +7029,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":893 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":893 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -5399,7 +7047,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":894 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":894 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -5417,7 +7065,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":895 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":895 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -5435,7 +7083,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":896 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":896 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -5455,7 +7103,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":897 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":897 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -5475,7 +7123,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":898 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":898 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -5495,7 +7143,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":899 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":899 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -5513,7 +7161,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":901 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":901 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -5532,7 +7180,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":902 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":902 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -5541,7 +7189,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":877 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -5551,7 +7199,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":906 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":906 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -5564,7 +7212,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":851 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":851 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -5574,7 +7222,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":907 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":907 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -5584,7 +7232,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -5609,7 +7257,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -5621,7 +7269,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1023 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1023 * * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! # <<<<<<<<<<<<<< @@ -5630,7 +7278,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_INCREF(__pyx_v_base); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1024 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1024 * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) # <<<<<<<<<<<<<< @@ -5639,7 +7287,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ (void)(PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_base)); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1022 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -5651,7 +7299,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -5666,7 +7314,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1027 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1027 * * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) # <<<<<<<<<<<<<< @@ -5675,7 +7323,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ __pyx_v_base = PyArray_BASE(__pyx_v_arr); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -5685,7 +7333,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_base == NULL) != 0); if (__pyx_t_1) { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1029 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1029 * base = PyArray_BASE(arr) * if base is NULL: * return None # <<<<<<<<<<<<<< @@ -5696,7 +7344,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1028 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -5705,7 +7353,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1030 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1030 * if base is NULL: * return None * return base # <<<<<<<<<<<<<< @@ -5717,7 +7365,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = ((PyObject *)__pyx_v_base); goto __pyx_L0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1026 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -5732,7 +7380,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -5753,7 +7401,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5769,7 +7417,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1036 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1036 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -5778,7 +7426,7 @@ 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, 1036, __pyx_L3_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5792,7 +7440,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1037 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1037 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -5807,7 +7455,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -5823,7 +7471,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -5838,7 +7486,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __pyx_L8_try_end:; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1034 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -5861,7 +7509,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -5882,7 +7530,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_umath", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -5898,7 +7546,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1042 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1042 * cdef inline int import_umath() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -5907,7 +7555,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1042, __pyx_L3_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -5921,7 +7569,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1043 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1043 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -5936,7 +7584,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -5952,7 +7600,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1041 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -5967,7 +7615,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1040 * raise ImportError("numpy.core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -5990,7 +7638,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 +/* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -6011,7 +7659,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_t_8 = NULL; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -6027,7 +7675,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1048 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1048 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< @@ -6036,7 +7684,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { */ __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 1048, __pyx_L3_error) - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -6050,7 +7698,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1049 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1049 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -6064,7 +7712,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_7); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1050 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1050 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6078,7 +7726,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L5_except_error; __pyx_L5_except_error:; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1047 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -6093,7 +7741,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 * raise ImportError("numpy.core.umath failed to import") * 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"../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -6270,7 +7919,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -6281,7 +7930,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":306 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -6292,7 +7941,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":856 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":856 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -6303,7 +7952,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":880 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -6314,7 +7963,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1038 * _import_array() * except Exception: * raise ImportError("numpy.core.multiarray failed to import") # <<<<<<<<<<<<<< @@ -6325,7 +7974,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1044 * _import_umath() * except Exception: * raise ImportError("numpy.core.umath failed to import") # <<<<<<<<<<<<<< @@ -6359,17 +8008,29 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(__pyx_tuple__10); __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(3, 0, 35, 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, __pyx_n_s_find_indels_substitutions, 12, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) __PYX_ERR(0, 12, __pyx_L1_error) - /* "CRISPResso2/CRISPRessoCOREResources.pyx":154 + /* "CRISPResso2/CRISPRessoCOREResources.pyx":143 + * @cython.nonecheck(False) + * @cython.wraparound(False) + * def find_indels_substitutions_legacy(_read_seq_al,_ref_seq_al,_include_indx): # <<<<<<<<<<<<<< + * #this legacy function includes insertions if they border the quantification window + * #(e.g. if the quantification window is 1bp then insertions 1bp away from the predicted + */ + __pyx_tuple__12 = PyTuple_Pack(35, __pyx_n_s_read_seq_al, __pyx_n_s_ref_seq_al, __pyx_n_s_include_indx, __pyx_n_s_ref_seq_al_2, __pyx_n_s_read_seq_al_2, __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_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__12)) __PYX_ERR(0, 143, __pyx_L1_error) + __Pyx_GOTREF(__pyx_tuple__12); + __Pyx_GIVEREF(__pyx_tuple__12); + __pyx_codeobj__13 = (PyObject*)__Pyx_PyCode_New(3, 0, 35, 0, 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__PYX_ERR(0, 1, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_test/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 + /* "../../../../../../../home/kendell/miniconda3/envs/crispresso2_dev/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":1046 * raise ImportError("numpy.core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< diff --git a/CRISPResso2/CRISPRessoCOREResources.pyx b/CRISPResso2/CRISPRessoCOREResources.pyx index 0e610390..ac72dc83 100644 --- a/CRISPResso2/CRISPRessoCOREResources.pyx +++ b/CRISPResso2/CRISPRessoCOREResources.pyx @@ -57,15 +57,140 @@ def find_indels_substitutions(_read_seq_al,_ref_seq_al,_include_indx): else: ref_positions.append(-idx) -# ###SLOW PART### -# readSeqAtRef = [] -# for idx_c,c in enumerate(ref_seq_al): -# readSeqAtRef.append(read_seq_al[idx_c]) -# include_seq = [] -# for idx in _include_indx: -# include_seq.append(readSeqAtRef[idx]) -# included_sequence = ''.join(chr(i) for i in include_seq) -# ###END SLOW PART### + substitution_n = len(substitution_positions) + + + #the remainder of positions are with reference to the original reference sequence indexes we calculated above + all_deletion_positions=[] + deletion_positions=[] + deletion_coordinates=[] + deletion_sizes=[] + + all_insertion_positions=[] + all_insertion_left_positions=[] + insertion_positions=[] + insertion_coordinates = [] + insertion_sizes=[] + + + 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: + 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)) + 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) + + deletion_n = np.sum(deletion_sizes) + + for p in re_find_indels.finditer(ref_seq_al): + st,en=p.span() + #sometimes deletions run off the end of the reference + if en > idx: # if insertion happened after ref + continue + if st < 1: #if start starts before ref + continue + ref_st = ref_positions[st-1] + ref_en = ref_positions[en] + + 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 and 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) + + insertion_n = np.sum(insertion_sizes) + + + retDict = { + '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, + '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 retDict + +@cython.boundscheck(False) +@cython.nonecheck(False) +@cython.wraparound(False) +def find_indels_substitutions_legacy(_read_seq_al,_ref_seq_al,_include_indx): + #this legacy function includes insertions if they border the quantification window + #(e.g. if the quantification window is 1bp then insertions 1bp away from the predicted + #cut site will be quantified). In the current version with a 1bp quantification window, + #only insertions at the predicted cut site would be counted. + + cdef char* ref_seq_al = _ref_seq_al + cdef char* read_seq_al = _read_seq_al + cdef char* sub_seq='' + + cdef int st + cdef int en + + cdef int idx_c + cdef int idx + + #ref_positions holds the indices for which positions map back to the original reference + # for example, + # 1 2 3 4 5 6 7 8 + # ref A A T T G G C C + # + # and for a given alignment + # ref A A T T - G G C C + # aln A - T T T G G C C + # 1 2 3 4-4 5 6 7 8