Generated by Cython 0.28.4
Yellow lines hint at Python interaction.
Click on a line that starts with a "+" to see the C code that Cython generated for it.
Raw output: kmer_ext.cpp
+01: # distutils: language=c++
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02:
03: from libcpp.string cimport string
04: from libcpp.vector cimport vector
05:
+06: cdef size_t SIZE_OF_INT64 = 8
__pyx_v_8cortexpy_5graph_6parser_8kmer_ext_SIZE_OF_INT64 = 8;
+07: cdef string NUM_TO_LETTER_LIST = b'ACGT'
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08:
+09: def raw_kmer_to_bytes(unsigned kmer_size, const unsigned char[:] kmer_bytes not None):
/* Python wrapper */
static PyObject *__pyx_pw_8cortexpy_5graph_6parser_8kmer_ext_1raw_kmer_to_bytes(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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unsigned int __pyx_v_kmer_size;
__Pyx_memviewslice __pyx_v_kmer_bytes = { 0, 0, { 0 }, { 0 }, { 0 } };
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std::vector<char> __pyx_v_letters;
std::vector<char> __pyx_v_four_letters;
char __pyx_v_kmer_byte;
size_t __pyx_v_ulong_idx;
size_t __pyx_v_ulong_offset;
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size_t __pyx_v_pair_idx;
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+10: assert kmer_size > 0
#ifndef CYTHON_WITHOUT_ASSERTIONS
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!((__pyx_v_kmer_size > 0) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
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+11: assert kmer_size <= kmer_bytes.shape[0] * 4
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PyErr_SetNone(PyExc_AssertionError);
__PYX_ERR(0, 11, __pyx_L1_error)
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#endif
12: cdef vector[char] letters
13: cdef vector[char] four_letters
+14: four_letters.resize(4,0)
try {
__pyx_v_four_letters.resize(4, 0);
} catch(...) {
__Pyx_CppExn2PyErr();
__PYX_ERR(0, 14, __pyx_L1_error)
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15: cdef char kmer_byte
16: cdef size_t ulong_idx, ulong_offset, byte_offset, pair_offset, pair_idx
+17: for ulong_idx in range(kmer_bytes.shape[0]//SIZE_OF_INT64):
if (unlikely(__pyx_v_8cortexpy_5graph_6parser_8kmer_ext_SIZE_OF_INT64 == 0)) {
PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero");
__PYX_ERR(0, 17, __pyx_L1_error)
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__pyx_t_1 = ((__pyx_v_kmer_bytes.shape[0]) / __pyx_v_8cortexpy_5graph_6parser_8kmer_ext_SIZE_OF_INT64);
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_ulong_idx = __pyx_t_3;
+18: ulong_offset = ulong_idx*SIZE_OF_INT64
__pyx_v_ulong_offset = (__pyx_v_ulong_idx * __pyx_v_8cortexpy_5graph_6parser_8kmer_ext_SIZE_OF_INT64);
+19: for byte_offset in reversed(range(SIZE_OF_INT64)):
for (__pyx_t_4 = __pyx_v_8cortexpy_5graph_6parser_8kmer_ext_SIZE_OF_INT64-1 + 1; __pyx_t_4 >= 0 + 1; ) { __pyx_t_4-=1;
__pyx_v_byte_offset = __pyx_t_4;
+20: kmer_byte = kmer_bytes[ulong_offset + byte_offset]
__pyx_t_5 = (__pyx_v_ulong_offset + __pyx_v_byte_offset);
__pyx_t_6 = -1;
if (unlikely(__pyx_t_5 >= (size_t)__pyx_v_kmer_bytes.shape[0])) __pyx_t_6 = 0;
if (unlikely(__pyx_t_6 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_6);
__PYX_ERR(0, 20, __pyx_L1_error)
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+21: for pair_idx in range(4):
for (__pyx_t_7 = 0; __pyx_t_7 < 4; __pyx_t_7+=1) {
__pyx_v_pair_idx = __pyx_t_7;
+22: four_letters[3-pair_idx] = NUM_TO_LETTER_LIST[kmer_byte & 0x3]
(__pyx_v_four_letters[(3 - __pyx_v_pair_idx)]) = (__pyx_v_8cortexpy_5graph_6parser_8kmer_ext_NUM_TO_LETTER_LIST[(__pyx_v_kmer_byte & 0x3)]);
+23: kmer_byte >>= 2
__pyx_v_kmer_byte = (__pyx_v_kmer_byte >> 2);
}
+24: for kmer_byte in four_letters:
__pyx_t_8 = __pyx_v_four_letters.begin();
for (;;) {
if (!(__pyx_t_8 != __pyx_v_four_letters.end())) break;
__pyx_t_9 = *__pyx_t_8;
++__pyx_t_8;
__pyx_v_kmer_byte = __pyx_t_9;
/* … */
}
}
}
+25: letters.push_back(kmer_byte)
try {
__pyx_v_letters.push_back(__pyx_v_kmer_byte);
} catch(...) {
__Pyx_CppExn2PyErr();
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+26: return bytes(letters[(letters.size() - kmer_size):])
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27:
28: # the above code was reimplemented from this
29: # kmer_as_uint64ts = np.frombuffer(raw_kmer, dtype='<u8')
30: # big_endian_kmer = kmer_as_uint64ts.astype('>u8')
31: # kmer_as_bits = np.unpackbits(np.frombuffer(big_endian_kmer.tobytes(), dtype=np.uint8))
32: # kmer = (kmer_as_bits.reshape(-1, 2) * np.array([2, 1])).sum(1)
33: # return NUM_TO_LETTER[kmer[(len(kmer) - self.kmer_size):]]
34:
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57: # edge_sets = edge_sets.reshape(-1, 8)
58: # edge_sets = [EdgeSet(tuple(edge_set.tolist())) for edge_set in edge_sets]
59: # self._edges = edge_sets
60:
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62: cdef unsigned coverage
63: cdef vector[unsigned] coverages
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70:
71: # originally:
72: # start = self.kmer_container_size_in_uint64ts * UINT64_T
73: # coverage_raw = self._data[start:(start + self.num_colors * UINT32_T)]
74: # fmt_string = ''.join(['I' for _ in range(self.num_colors)])
75: # self._coverage = unpack(fmt_string, coverage_raw)