/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/bbi/ |
H A D | cirtree_file.c | 2375 PyObject *__pyx_v_rval = 0; in __pyx_pw_2bx_3bbi_12cirtree_file_11CIRTreeFile_5r_find_overlapping() local 2468 __pyx_v_rval = values[5]; in __pyx_pw_2bx_3bbi_12cirtree_file_11CIRTreeFile_5r_find_overlapping() 2894 PyObject *__pyx_v_rval = 0; in __pyx_pw_2bx_3bbi_12cirtree_file_11CIRTreeFile_7r_find_overlapping_leaf() local 2987 __pyx_v_rval = values[4]; in __pyx_pw_2bx_3bbi_12cirtree_file_11CIRTreeFile_7r_find_overlapping_leaf() 3321 PyObject *__pyx_v_rval = 0; in __pyx_pw_2bx_3bbi_12cirtree_file_11CIRTreeFile_9r_find_overlapping_parent() local 3414 __pyx_v_rval = values[4]; in __pyx_pw_2bx_3bbi_12cirtree_file_11CIRTreeFile_9r_find_overlapping_parent() 3905 PyObject *__pyx_v_rval = NULL; in __pyx_pf_2bx_3bbi_12cirtree_file_11CIRTreeFile_10find_overlapping_blocks() local 4003 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_3bbi_12cirtree_file_11CIRTreeFile_10find_overlapping_blocks() 4026 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_3bbi_12cirtree_file_11CIRTreeFile_10find_overlapping_blocks() 4027 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_3bbi_12cirtree_file_11CIRTreeFile_10find_overlapping_blocks() [all …]
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H A D | bbi_file.c | 8414 PyObject *__pyx_v_rval = NULL; in __pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query() local 8628 __pyx_v_rval = ((PyObject*)__pyx_t_1); in __pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query() 8869 __Pyx_INCREF(__pyx_v_rval); in __pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query() 8870 __pyx_r = __pyx_v_rval; in __pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query() 8895 __Pyx_XDECREF(__pyx_v_rval); in __pyx_f_2bx_3bbi_8bbi_file_7BBIFile_query() 10358 PyObject *__pyx_v_rval = NULL; in __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region() local 10417 __pyx_v_rval = __pyx_t_1; in __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region() 11183 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region() 11184 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region() 11209 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region() [all …]
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H A D | bigbed_file.c | 4841 PyObject *__pyx_v_rval = NULL; in __pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get() local 5129 __pyx_v_rval = ((PyObject*)__pyx_t_6); in __pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get() 5329 …__pyx_t_15 = __Pyx_PyList_Append(__pyx_v_rval, __pyx_t_5); if (unlikely(__pyx_t_15 == ((int)-1))) … in __pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get() 5350 __Pyx_INCREF(__pyx_v_rval); in __pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get() 5351 __pyx_r = __pyx_v_rval; in __pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get() 5378 __Pyx_XDECREF(__pyx_v_rval); in __pyx_f_2bx_3bbi_11bigbed_file_10BigBedFile_get()
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/motif/ |
H A D | _pwm.c | 1252 PyArrayObject *__pyx_v_rval = 0; in __pyx_pw_2bx_5motif_4_pwm_1score_string() local 1315 __pyx_v_rval = ((PyArrayObject *)values[3]); in __pyx_pw_2bx_5motif_4_pwm_1score_string() 1327 …if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_rval), __pyx_ptype_2bx_5motif_4_pwm_ndarray, … in __pyx_pw_2bx_5motif_4_pwm_1score_string() 1328 …_pwm_score_string(__pyx_self, __pyx_v_matrix, __pyx_v_char_to_index, __pyx_v_string, __pyx_v_rval); in __pyx_pw_2bx_5motif_4_pwm_1score_string() 1339 …rix, PyArrayObject *__pyx_v_char_to_index, PyObject *__pyx_v_string, PyArrayObject *__pyx_v_rval) { in __pyx_pf_2bx_5motif_4_pwm_score_string() argument 1533 …(((npy_float32 *)(__pyx_v_rval->data + (__pyx_v_i * (__pyx_v_rval->strides[0]))))[0]) = __pyx_v_sc… in __pyx_pf_2bx_5motif_4_pwm_score_string() 1578 PyArrayObject *__pyx_v_rval = 0; in __pyx_pw_2bx_5motif_4_pwm_3score_string_with_gaps() local 1641 __pyx_v_rval = ((PyArrayObject *)values[3]); in __pyx_pw_2bx_5motif_4_pwm_3score_string_with_gaps() 1653 …if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_rval), __pyx_ptype_2bx_5motif_4_pwm_ndarray, … in __pyx_pw_2bx_5motif_4_pwm_3score_string_with_gaps() 1654 …_string_with_gaps(__pyx_self, __pyx_v_matrix, __pyx_v_char_to_index, __pyx_v_string, __pyx_v_rval); in __pyx_pw_2bx_5motif_4_pwm_3score_string_with_gaps() [all …]
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/ |
H A D | _seqmapping.c | 1866 __pyx_v_rval = __pyx_t_2; in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate() 1906 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate() 1907 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate() 2069 __pyx_v_rval = __pyx_t_3; in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_8translate_list() 2246 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_8translate_list() 2247 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_8translate_list() 2531 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_10reverse_map() 3245 __pyx_v_rval = __pyx_t_4; in __pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate() 3347 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate() 4753 __pyx_v_rval = __pyx_t_1; in __pyx_pf_2bx_11_seqmapping_15IntToIntMapping_22get_table() [all …]
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/misc/ |
H A D | _seekbzip2.c | 1826 PyObject *__pyx_v_rval = 0; in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() local 1915 __pyx_v_rval = __pyx_t_2; in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() 1925 __pyx_v_p_rval = PyBytes_AsString(__pyx_v_rval); in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() 2053 …__pyx_t_4 = __Pyx_PyList_Append(__pyx_v_chunks, __pyx_v_rval); if (unlikely(__pyx_t_4 == ((int)-1)… in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() 2101 __Pyx_DECREF_SET(__pyx_v_rval, __pyx_t_2); in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() 2111 __pyx_v_p_rval = PyBytes_AsString(__pyx_v_rval); in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() 2345 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_6readline() 2387 PyObject *__pyx_v_rval = 0; in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_8read() local 2450 __pyx_v_rval = __pyx_t_2; in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_8read() 2460 __pyx_v_p_rval = PyBytes_AsString(__pyx_v_rval); in __pyx_pf_2bx_4misc_10_seekbzip2_9SeekBzip2_8read() [all …]
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H A D | bgzf.c | 1635 PyObject *__pyx_v_rval = 0; in __pyx_pf_2bx_4misc_4bgzf_8BGZFFile_4read() local 1653 __pyx_v_rval = __pyx_t_1; in __pyx_pf_2bx_4misc_4bgzf_8BGZFFile_4read() 1663 (void)(bgzf_read(__pyx_v_self->bgzf, PyBytes_AsString(__pyx_v_rval), __pyx_v_length)); in __pyx_pf_2bx_4misc_4bgzf_8BGZFFile_4read() 1673 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_4misc_4bgzf_8BGZFFile_4read() 1674 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_4misc_4bgzf_8BGZFFile_4read() 1691 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_2bx_4misc_4bgzf_8BGZFFile_4read()
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/intseq/ |
H A D | ngramcount.c | 1377 PyObject *__pyx_v_rval = NULL; in __pyx_pf_2bx_6intseq_10ngramcount_count_ngrams() local 1611 __pyx_v_rval = __pyx_t_7; in __pyx_pf_2bx_6intseq_10ngramcount_count_ngrams() 1643 …__pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_rval, __pyx_n_s_array_struct); if (unlikely(!__pyx_t… in __pyx_pf_2bx_6intseq_10ngramcount_count_ngrams() 1834 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_6intseq_10ngramcount_count_ngrams() 1835 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_6intseq_10ngramcount_count_ngrams() 1857 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_2bx_6intseq_10ngramcount_count_ngrams() 1872 …0ngramcount__count_ngrams(int *__pyx_v_ints, int __pyx_v_n_ints, int *__pyx_v_rval, int __pyx_v_n,… in __pyx_f_2bx_6intseq_10ngramcount__count_ngrams() argument 2030 (__pyx_v_rval[__pyx_v_index]) = ((__pyx_v_rval[__pyx_v_index]) + 1); in __pyx_f_2bx_6intseq_10ngramcount__count_ngrams()
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/seq/ |
H A D | _nib.c | 1303 PyObject *__pyx_v_rval = NULL; in __pyx_pf_2bx_3seq_4_nib_translate_raw_data() local 1356 __pyx_v_rval = __pyx_t_2; in __pyx_pf_2bx_3seq_4_nib_translate_raw_data() 1366 __pyx_v_p_rval = PyBytes_AsString(__pyx_v_rval); in __pyx_pf_2bx_3seq_4_nib_translate_raw_data() 1525 …__pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_rval, __pyx_n_s_decode); if (unlikely(!__pyx_t_4)) _… in __pyx_pf_2bx_3seq_4_nib_translate_raw_data() 1562 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_3seq_4_nib_translate_raw_data() 1563 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_3seq_4_nib_translate_raw_data() 1583 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_2bx_3seq_4_nib_translate_raw_data()
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/arrays/ |
H A D | array_tree.c | 2603 PyObject *__pyx_v_rval = NULL; in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() local 2641 __pyx_v_rval = ((PyObject*)__pyx_t_1); in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() 2802 …__pyx_t_12 = (__Pyx_PyDict_ContainsTF(__pyx_v_chrom, __pyx_v_rval, Py_NE)); if (unlikely(__pyx_t_1… in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() 2875 …if (unlikely(PyDict_SetItem(__pyx_v_rval, __pyx_v_chrom, __pyx_t_7) < 0)) __PYX_ERR(0, 73, __pyx_L… in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() 2894 …__pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_rval, __pyx_v_chrom); if (unlikely(!__pyx_t_7)) __PYX_ERR… in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() 2985 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() 2986 __pyx_r = __pyx_v_rval; in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader() 3010 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader()
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/dports/biology/py-pysam/pysam-0.18.0/pysam/ |
H A D | libchtslib.c | 11185 int __pyx_v_rval; in __pyx_pf_5pysam_10libchtslib_7HTSFile_18add_hts_options() local 11281 __pyx_v_rval = hts_opt_add((&__pyx_v_opts), __pyx_t_6); in __pyx_pf_5pysam_10libchtslib_7HTSFile_18add_hts_options() 11290 __pyx_t_1 = ((__pyx_v_rval != 0) != 0); in __pyx_pf_5pysam_10libchtslib_7HTSFile_18add_hts_options() 11388 __pyx_v_rval = hts_opt_apply(__pyx_v_self->htsfile, __pyx_v_opts); in __pyx_pf_5pysam_10libchtslib_7HTSFile_18add_hts_options() 11397 __pyx_t_1 = ((__pyx_v_rval != 0) != 0); in __pyx_pf_5pysam_10libchtslib_7HTSFile_18add_hts_options()
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/dports/net/py-pynmsg/pynmsg-0.5.0/ |
H A D | _nmsg.c | 7931 PyObject *__pyx_v_rval = NULL; in __pyx_pf_5_nmsg_7message_16to_json() local 8054 __pyx_v_rval = __pyx_t_3; in __pyx_pf_5_nmsg_7message_16to_json() 8076 __Pyx_INCREF(__pyx_v_rval); in __pyx_pf_5_nmsg_7message_16to_json() 8077 __Pyx_GIVEREF(__pyx_v_rval); in __pyx_pf_5_nmsg_7message_16to_json() 8078 PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_rval); in __pyx_pf_5_nmsg_7message_16to_json() 8104 __Pyx_XDECREF(__pyx_v_rval); in __pyx_pf_5_nmsg_7message_16to_json()
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