Generated by Cython 0.27.3
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: io_vcf_read.c
+0001: # cython: linetrace=False
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0002: # cython: profile=False
0003: # cython: binding=False
0004: # cython: boundscheck=False
0005: # cython: wraparound=False
0006: # cython: initializedcheck=False
0007: # cython: nonecheck=False
0008: """
0009: # options for profiling...
0010: # cython: profile=True
0011: # cython: binding=True
0012: # cython: linetrace=True
0013: # distutils: define_macros=CYTHON_TRACE=1
0014: # distutils: define_macros=CYTHON_TRACE_NOGIL=1
0015: """
0016: from __future__ import absolute_import, print_function, division
0017:
0018:
+0019: import warnings
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0020: # noinspection PyUnresolvedReferences
0021: from cpython.bytes cimport PyBytes_AS_STRING, PyBytes_FromStringAndSize
0022: # noinspection PyUnresolvedReferences
0023: from libc.stdlib cimport strtol, strtof, strtod, malloc, free, realloc
0024: # noinspection PyUnresolvedReferences
0025: from libc.string cimport strcmp, memcpy
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0027: cimport numpy as np
0028: from cpython.ref cimport PyObject
0029: cdef extern from "Python.h":
0030: char* PyByteArray_AS_STRING(object string)
0031: # from multiprocessing.pool import ThreadPool
0032:
0033:
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0035:
0036:
0037: #########################################################################################
0038: # Constants.
0039:
0040:
0041: # for Windows compatibility
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+0051: cdef char PERIOD = b'.'
__pyx_v_5allel_3opt_11io_vcf_read_PERIOD = '.';
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__pyx_v_5allel_3opt_11io_vcf_read_COMMA = ',';
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/* … */
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+0162: cdef inline void IntVector_free(IntVector* self) nogil:
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/* … */
/* function exit code */
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/* … */
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free(__pyx_v_self->data);
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0166:
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/* … */
/* function exit code */
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if (__pyx_t_1) {
/* … */
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/* … */
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/* … */
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CYTHON_FALLTHROUGH;
case 8: values[7] = PyTuple_GET_ITEM(__pyx_args, 7);
CYTHON_FALLTHROUGH;
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__pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_fields, __pyx_n_s_remove); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 626, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 626, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* … */ __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_variants_is_snp); if (unlikely(!__pyx_tuple__17)) __PYX_ERR(0, 626, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__17); __Pyx_GIVEREF(__pyx_tuple__17);
0627:
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if (!__pyx_t_8) {
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goto __pyx_L8_bool_binop_done;
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if (!__pyx_t_8) {
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__pyx_t_7 = __pyx_t_8;
goto __pyx_L8_bool_binop_done;
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goto __pyx_L8_bool_binop_done;
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/* … */
goto __pyx_L7;
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/* … */
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__pyx_t_5 = PyObject_GetItem(__pyx_v_fills, __pyx_v_field); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 726, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); if (unlikely(PyDict_SetItem(__pyx_v_format_fills, __pyx_v_key, __pyx_t_5) < 0)) __PYX_ERR(0, 726, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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__pyx_t_8 = (__pyx_v_format_keys != Py_None) && (PyList_GET_SIZE(__pyx_v_format_keys) != 0);
if (__pyx_t_8) {
/* … */
goto __pyx_L10;
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__pyx_t_2 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 728, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_format_keys, __pyx_v_format_keys) < 0) __PYX_ERR(0, 728, __pyx_L1_error) __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFFormatParser), __pyx_empty_tuple, __pyx_t_2); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 728, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_v_format_parser = ((struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_t_5); __pyx_t_5 = 0;
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__pyx_t_5 = __Pyx_PyDict_NewPresized(6); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 729, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_format_keys, __pyx_v_format_keys) < 0) __PYX_ERR(0, 729, __pyx_L1_error) /* … */ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFCallDataParser), __pyx_empty_tuple, __pyx_t_5); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 729, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_calldata_parser = ((struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_t_2); __pyx_t_2 = 0;
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if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_types, __pyx_v_format_types) < 0) __PYX_ERR(0, 729, __pyx_L1_error)
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if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_numbers, __pyx_v_format_numbers) < 0) __PYX_ERR(0, 729, __pyx_L1_error)
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__pyx_t_2 = PyInt_FromSsize_t(__pyx_v_self->chunk_length); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 732, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_chunk_length, __pyx_t_2) < 0) __PYX_ERR(0, 729, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_self->loc_samples, 1, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_5numpy_uint8_t, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_5numpy_uint8_t, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 733, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_loc_samples, __pyx_t_2) < 0) __PYX_ERR(0, 729, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_fills, __pyx_v_format_fills) < 0) __PYX_ERR(0, 729, __pyx_L1_error)
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/*else*/ {
__pyx_t_2 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 736, __pyx_L1_error)
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__pyx_t_11 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_format_parser->__pyx_vtab)->malloc_chunk(__pyx_v_format_parser); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(0, 738, __pyx_L1_error)
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__pyx_t_11 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_calldata_parser->__pyx_vtab)->malloc_chunk(__pyx_v_calldata_parser); if (unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(0, 739, __pyx_L1_error)
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__Pyx_INCREF(((PyObject *)__pyx_v_format_parser)); __Pyx_GIVEREF(((PyObject *)__pyx_v_format_parser)); __Pyx_GOTREF(__pyx_v_self->format_parser); __Pyx_DECREF(((PyObject *)__pyx_v_self->format_parser)); __pyx_v_self->format_parser = __pyx_v_format_parser;
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__Pyx_INCREF(((PyObject *)__pyx_v_calldata_parser)); __Pyx_GIVEREF(((PyObject *)__pyx_v_calldata_parser)); __Pyx_GOTREF(__pyx_v_self->calldata_parser); __Pyx_DECREF(((PyObject *)__pyx_v_self->calldata_parser)); __pyx_v_self->calldata_parser = __pyx_v_calldata_parser;
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static int __pyx_f_5allel_3opt_11io_vcf_read_9VCFParser_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFParser *__pyx_v_self, struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context) {
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/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
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__Pyx_AddTraceback("allel.opt.io_vcf_read.VCFParser.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
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0744: """Parse to end of current chunk or EOF."""
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while (1) {
0749:
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switch (__pyx_v_context->state) {
case __pyx_e_5allel_3opt_11io_vcf_read_EOF:
/* … */
break;
+0751: break
goto __pyx_L4_break;
0752:
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case __pyx_e_5allel_3opt_11io_vcf_read_EOL:
/* … */
break;
0754:
0755: # handle line terminators
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__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+0757: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 757, __pyx_L1_error)
+0758: elif stream.c == CR:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+0759: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 759, __pyx_L1_error)
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__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (__pyx_t_1) {
/* … */
}
+0761: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 761, __pyx_L1_error)
0762: else:
0763: # shouldn't ever happen
0764: # with gil:
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/*else*/ {
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_unexpected_EOL_character, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 765, __pyx_L1_error)
+0766: break
goto __pyx_L4_break;
}
__pyx_L5:;
0767:
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_CHROM;
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0771: # end of chunk?
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__pyx_t_1 = (((__pyx_v_context->chunk_variant_index + 1) == __pyx_v_self->chunk_length) != 0);
if (__pyx_t_1) {
/* … */
}
0773: # we're done
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goto __pyx_L4_break;
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case __pyx_e_5allel_3opt_11io_vcf_read_CHROM:
/* … */
break;
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__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->chrom_pos_parser->__pyx_vtab)->parse(__pyx_v_self->chrom_pos_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 777, __pyx_L1_error)
0778:
+0779: elif context.state == VCFState.ID:
case __pyx_e_5allel_3opt_11io_vcf_read_ID:
/* … */
break;
+0780: self.id_parser.parse(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->id_parser->__pyx_vtab)->parse(__pyx_v_self->id_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 780, __pyx_L1_error)
0781:
+0782: elif context.state == VCFState.REF:
case __pyx_e_5allel_3opt_11io_vcf_read_REF:
/* … */
break;
+0783: self.ref_parser.parse(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->ref_parser->__pyx_vtab)->parse(__pyx_v_self->ref_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 783, __pyx_L1_error)
0784:
+0785: elif context.state == VCFState.ALT:
case __pyx_e_5allel_3opt_11io_vcf_read_ALT:
/* … */
break;
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__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->alt_parser->__pyx_vtab)->parse(__pyx_v_self->alt_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 786, __pyx_L1_error)
0787:
+0788: elif context.state == VCFState.QUAL:
case __pyx_e_5allel_3opt_11io_vcf_read_QUAL:
/* … */
break;
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__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->qual_parser->__pyx_vtab)->parse(__pyx_v_self->qual_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 789, __pyx_L1_error)
0790:
+0791: elif context.state == VCFState.FILTER:
case __pyx_e_5allel_3opt_11io_vcf_read_FILTER:
/* … */
break;
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__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->filter_parser->__pyx_vtab)->parse(__pyx_v_self->filter_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 792, __pyx_L1_error)
0793:
+0794: elif context.state == VCFState.INFO:
case __pyx_e_5allel_3opt_11io_vcf_read_INFO:
/* … */
break;
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__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->info_parser->__pyx_vtab)->parse(__pyx_v_self->info_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 795, __pyx_L1_error)
0796:
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case __pyx_e_5allel_3opt_11io_vcf_read_FORMAT:
/* … */
break;
+0798: self.format_parser.parse(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->format_parser->__pyx_vtab)->parse(__pyx_v_self->format_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 798, __pyx_L1_error)
0799:
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case __pyx_e_5allel_3opt_11io_vcf_read_CALLDATA:
/* … */
break;
default:
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__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->calldata_parser->__pyx_vtab)->parse(__pyx_v_self->calldata_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 801, __pyx_L1_error)
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+0807: break
goto __pyx_L4_break;
break;
}
}
__pyx_L4_break:;
0808:
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static int __pyx_f_5allel_3opt_11io_vcf_read_9VCFParser_malloc_chunk(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFParser *__pyx_v_self) {
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__pyx_t_1 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->ref_parser->__pyx_vtab)->malloc_chunk(__pyx_v_self->ref_parser); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 812, __pyx_L1_error)
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__pyx_t_1 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_v_self->qual_parser->__pyx_vtab)->malloc_chunk(__pyx_v_self->qual_parser); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 814, __pyx_L1_error)
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__pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_expected_string_S_or_object_O_dt, __pyx_v_dtype); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 915, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 915, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 915, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __PYX_ERR(0, 915, __pyx_L1_error)
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__Pyx_XDECREF(__pyx_r); __Pyx_INCREF(__pyx_v_dtype); __pyx_r = __pyx_v_dtype; goto __pyx_L0;
0917:
0918:
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static int __pyx_f_5allel_3opt_11io_vcf_read_vcf_read_field(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, struct __pyx_t_5allel_3opt_11io_vcf_read_CharVector *__pyx_v_dest) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("vcf_read_field", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_read_field", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
0920: VCFContext context,
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear(__pyx_v_dest);
0925:
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while (1) {
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__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+0930: break
goto __pyx_L4_break;
0931:
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+0934: break
goto __pyx_L4_break;
0935:
+0936: elif stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 937, __pyx_L1_error)
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goto __pyx_L4_break;
0940:
0941: else:
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/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append(__pyx_v_dest, __pyx_v_stream->c);
}
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__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 945, __pyx_L1_error)
}
__pyx_L4_break:;
0946:
0947:
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static int __pyx_f_5allel_3opt_11io_vcf_read_vcf_parse_missing(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("vcf_parse_missing", 0);
/* … */
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goto __pyx_L0;
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_parse_missing", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
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while (1) {
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__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+0955: break
goto __pyx_L4_break;
0956:
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+0958: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
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goto __pyx_L4_break;
0960:
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__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
0962: # advance input stream beyond tab
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__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 963, __pyx_L1_error)
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__pyx_v_context->state = (__pyx_v_context->state + 1);
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goto __pyx_L4_break;
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__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 968, __pyx_L1_error)
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__pyx_L4_break:;
0969:
0970:
+0971: cdef int vcf_skip_variant(InputStreamBase stream, VCFContext context) except -1: # nogil
static int __pyx_f_5allel_3opt_11io_vcf_read_vcf_skip_variant(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("vcf_skip_variant", 0);
/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_skip_variant", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
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goto __pyx_L4_break;
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
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goto __pyx_L4_break;
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__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 981, __pyx_L1_error)
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__pyx_L4_break:;
0982:
0983:
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0986: cdef:
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0993: Py_ssize_t region_end
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/* Python wrapper */
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PyObject *__pyx_v_dtype = 0;
PyObject *__pyx_v_store_chrom = 0;
PyObject *__pyx_v_store_pos = 0;
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PyObject *__pyx_v_region_chrom = 0;
PyObject *__pyx_v_region_begin = 0;
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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
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Py_ssize_t kw_args;
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CYTHON_FALLTHROUGH;
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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__Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 2); __PYX_ERR(0, 997, __pyx_L3_error)
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CYTHON_FALLTHROUGH;
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if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_chunk_length)) != 0)) kw_args--;
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CYTHON_FALLTHROUGH;
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if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_region_end)) != 0)) kw_args--;
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__Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, 6); __PYX_ERR(0, 997, __pyx_L3_error)
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__Pyx_RaiseArgtupleInvalid("__init__", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 997, __pyx_L3_error)
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__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1001, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFChromPosParser)); __Pyx_GIVEREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFChromPosParser)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFChromPosParser)); __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_self)); __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_super, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1001, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_init); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1001, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1001, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_key, __pyx_n_b_CHROM) < 0) __PYX_ERR(0, 1001, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_v_dtype) < 0) __PYX_ERR(0, 1001, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_number, __pyx_int_1) < 0) __PYX_ERR(0, 1001, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_chunk_length, __pyx_v_chunk_length) < 0) __PYX_ERR(0, 1001, __pyx_L1_error) __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_empty_tuple, __pyx_t_3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1001, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+1002: self.store_chrom = store_chrom
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_chrom); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1002, __pyx_L1_error) __pyx_v_self->store_chrom = __pyx_t_1;
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__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_pos); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1003, __pyx_L1_error) __pyx_v_self->store_pos = __pyx_t_1;
+1004: if region_chrom:
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_region_chrom); if (unlikely(__pyx_t_1 < 0)) __PYX_ERR(0, 1004, __pyx_L1_error) if (__pyx_t_1) { /* … */ goto __pyx_L4; }
+1005: self.region_chrom = <char*> region_chrom
__pyx_t_6 = __Pyx_PyObject_AsWritableString(__pyx_v_region_chrom); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) __PYX_ERR(0, 1005, __pyx_L1_error) __pyx_v_self->region_chrom = ((char *)__pyx_t_6);
+1006: self.region_begin = region_begin
__pyx_t_7 = __Pyx_PyIndex_AsSsize_t(__pyx_v_region_begin); if (unlikely((__pyx_t_7 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 1006, __pyx_L1_error) __pyx_v_self->region_begin = __pyx_t_7;
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__pyx_t_7 = __Pyx_PyIndex_AsSsize_t(__pyx_v_region_end); if (unlikely((__pyx_t_7 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 1007, __pyx_L1_error) __pyx_v_self->region_end = __pyx_t_7;
1008: else:
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/*else*/ {
__pyx_v_self->region_chrom = NULL;
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__pyx_v_self->region_begin = 0;
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__pyx_v_self->region_end = 0; } __pyx_L4:;
1012:
+1013: cdef int parse(self, InputStreamBase stream, VCFContext context) except -1: # nogil
static int __pyx_f_5allel_3opt_11io_vcf_read_17VCFChromPosParser_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFChromPosParser *__pyx_v_self, struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context) {
Py_ssize_t __pyx_v_i;
Py_ssize_t __pyx_v_n;
Py_ssize_t __pyx_v_cmp;
Py_ssize_t __pyx_v_memory_offset;
PyObject *__pyx_v_v = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
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__Pyx_XDECREF(__pyx_t_8);
__Pyx_AddTraceback("allel.opt.io_vcf_read.VCFChromPosParser.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
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1014: cdef:
1015: Py_ssize_t i, n, cmp
1016: # index into memory view
1017: Py_ssize_t memory_offset
1018:
1019: # reset context
+1020: CharVector_clear(&context.chrom)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->chrom));
+1021: context.pos = 0
__pyx_v_context->pos = 0;
+1022: context.ref_len = 0
__pyx_v_context->ref_len = 0;
1023:
1024: # check for EOF early - important to handle file with no final line terminator
+1025: if stream.c == 0:
__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1026: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+1027: return 0
__pyx_r = 0;
goto __pyx_L0;
1028:
1029: # read chrom
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__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_read_field(__pyx_v_stream, __pyx_v_context, (&__pyx_v_context->chrom)); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1030, __pyx_L1_error)
+1031: if context.chrom.size == 0:
__pyx_t_1 = ((__pyx_v_context->chrom.size == 0) != 0);
if (__pyx_t_1) {
/* … */
}
1032: # with gil:
+1033: warn('empty CHROM', context)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_empty_CHROM, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1033, __pyx_L1_error)
+1034: CharVector_terminate(&context.chrom)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_terminate((&__pyx_v_context->chrom));
1035:
1036: # read pos
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__pyx_t_1 = ((__pyx_v_context->state == __pyx_e_5allel_3opt_11io_vcf_read_CHROM) != 0);
if (__pyx_t_1) {
/* … */
}
+1038: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
1039: # read pos
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__pyx_t_1 = ((__pyx_v_context->temp.size == 0) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L6;
}
1042: # with gil:
+1043: warn('empty POS', context)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_empty_POS, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1043, __pyx_L1_error)
1044: else:
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/*else*/ {
__pyx_t_3 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_context->pos)); if (unlikely(__pyx_t_3 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 1045, __pyx_L1_error)
}
__pyx_L6:;
1046:
+1047: if context.state == VCFState.POS:
__pyx_t_1 = ((__pyx_v_context->state == __pyx_e_5allel_3opt_11io_vcf_read_POS) != 0);
if (__pyx_t_1) {
/* … */
}
+1048: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
1049:
1050: # handle region
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__pyx_t_1 = ((__pyx_v_self->region_chrom != NULL) != 0);
if (__pyx_t_1) {
/* … */
}
1052:
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__pyx_v_cmp = strcmp(__pyx_v_context->chrom.data, __pyx_v_self->region_chrom);
1055:
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__pyx_t_1 = ((__pyx_v_cmp < 0) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_skip_variant(__pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1057, __pyx_L1_error)
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__pyx_r = 0;
goto __pyx_L0;
1059:
+1060: if cmp > 0:
__pyx_t_1 = ((__pyx_v_cmp > 0) != 0);
if (__pyx_t_1) {
/* … */
}
1061: # we're done
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
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__pyx_r = 0;
goto __pyx_L0;
1064:
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__pyx_t_4 = ((__pyx_v_self->region_begin > 0) != 0);
if (__pyx_t_4) {
} else {
__pyx_t_1 = __pyx_t_4;
goto __pyx_L12_bool_binop_done;
}
__pyx_t_4 = ((__pyx_v_context->pos < __pyx_v_self->region_begin) != 0);
__pyx_t_1 = __pyx_t_4;
__pyx_L12_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
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__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_skip_variant(__pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1066, __pyx_L1_error)
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__pyx_r = 0;
goto __pyx_L0;
1068:
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__pyx_t_1 = (0 < __pyx_v_self->region_end);
if (__pyx_t_1) {
__pyx_t_1 = (__pyx_v_self->region_end < __pyx_v_context->pos);
}
__pyx_t_4 = (__pyx_t_1 != 0);
if (__pyx_t_4) {
/* … */
}
1070: # we're done
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
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__pyx_r = 0;
goto __pyx_L0;
1073:
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__pyx_v_context->sample_index = 0;
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__pyx_v_context->sample_field_index = 0;
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__pyx_v_context->sample_output_index = -1L;
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__pyx_v_context->variant_index = (__pyx_v_context->variant_index + 1);
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__pyx_v_context->chunk_variant_index = (__pyx_v_context->chunk_variant_index + 1);
1080:
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__pyx_t_4 = (__pyx_v_self->store_chrom != 0);
if (__pyx_t_4) {
/* … */
}
1083:
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__pyx_t_4 = ((__pyx_v_self->__pyx_base.dtype->kind == 'S') != 0);
if (__pyx_t_4) {
/* … */
goto __pyx_L16;
}
1085:
1086: # initialise memory index
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__pyx_t_6 = __pyx_t_3;
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__pyx_t_6 = __pyx_t_5;
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__pyx_v_n = __pyx_t_6;
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__pyx_t_6 = __pyx_v_n;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_6; __pyx_t_3+=1) {
__pyx_v_i = __pyx_t_3;
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*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_self->chrom_memory.data + __pyx_t_7 * __pyx_v_self->chrom_memory.strides[0]) )) = (__pyx_v_context->chrom.data[__pyx_v_i]);
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1095:
1096: else:
1097: # with gil:
1098: # N.B., don't include terminating null byte
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1101:
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__pyx_t_4 = (__pyx_v_self->store_pos != 0);
if (__pyx_t_4) {
/* … */
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__pyx_t_10 = __pyx_v_context->chunk_variant_index;
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__Pyx_XDECREF(__pyx_t_3);
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/* … */
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CYTHON_FALLTHROUGH;
case 3:
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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CYTHON_FALLTHROUGH;
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+1304: super(VCFAltStringParser, self).__init__(key=b'ALT', dtype=dtype, number=number,
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1304, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFAltStringParser)); __Pyx_GIVEREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFAltStringParser)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFAltStringParser)); __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_v_self)); __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_super, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1304, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_init); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1304, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1304, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_key, __pyx_n_b_ALT) < 0) __PYX_ERR(0, 1304, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_v_dtype) < 0) __PYX_ERR(0, 1304, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_number, __pyx_v_number) < 0) __PYX_ERR(0, 1304, __pyx_L1_error) /* … */ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_empty_tuple, __pyx_t_3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1304, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_chunk_length, __pyx_v_chunk_length) < 0) __PYX_ERR(0, 1304, __pyx_L1_error)
+1306: self.store_alt = store_alt
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_alt); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1306, __pyx_L1_error) __pyx_v_self->store_alt = __pyx_t_1;
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__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_numalt); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1307, __pyx_L1_error) __pyx_v_self->store_numalt = __pyx_t_1;
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__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_svlen); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1308, __pyx_L1_error) __pyx_v_self->store_svlen = __pyx_t_1;
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__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_is_snp); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1309, __pyx_L1_error) __pyx_v_self->store_is_snp = __pyx_t_1;
1310:
+1311: cdef int parse(self, InputStreamBase stream, VCFContext context) except -1: # nogil
static int __pyx_f_5allel_3opt_11io_vcf_read_18VCFAltStringParser_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFAltStringParser *__pyx_v_self, struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context) {
Py_ssize_t __pyx_v_alt_index;
Py_ssize_t __pyx_v_memory_offset;
Py_ssize_t __pyx_v_memory_index;
Py_ssize_t __pyx_v_chars_stored;
Py_ssize_t __pyx_v_alt_len;
int __pyx_v_is_snp;
int __pyx_r;
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__Pyx_RefNannySetupContext("parse", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.VCFAltStringParser.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
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1312: cdef:
1313: # index of alt values
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__pyx_v_alt_index = 0;
1315: # index into memory view
1316: Py_ssize_t memory_offset, memory_index
1317: # number of characters read into current value
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__pyx_v_chars_stored = 0;
1319: # size of alt allel
+1320: Py_ssize_t alt_len = 0
__pyx_v_alt_len = 0;
1321: # is the variant a SNP?
+1322: bint is_snp = context.ref_len == 1
__pyx_v_is_snp = (__pyx_v_context->ref_len == 1);
1323:
1324: # bail out early for missing value
+1325: if stream.c == PERIOD:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PERIOD) != 0);
if (__pyx_t_1) {
/* … */
}
1326: # treat period as missing value, regardless of what comes next
+1327: vcf_parse_missing(stream, context)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_parse_missing(__pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1327, __pyx_L1_error)
+1328: return 0
__pyx_r = 0;
goto __pyx_L0;
1329:
1330: # bail out early for empty value
+1331: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1332: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1332, __pyx_L1_error)
+1333: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1334: return 0
__pyx_r = 0;
goto __pyx_L0;
1335:
1336: # initialise memory offset and index
+1337: memory_offset = context.chunk_variant_index * self.itemsize * self.number
__pyx_v_memory_offset = ((__pyx_v_context->chunk_variant_index * __pyx_v_self->__pyx_base.itemsize) * __pyx_v_self->__pyx_base.number);
+1338: memory_index = memory_offset
__pyx_v_memory_index = __pyx_v_memory_offset;
1339:
+1340: while True:
while (1) {
1341:
+1342: if stream.c == 0:
__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1343: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L8_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L8_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
+1344: if self.store_svlen and alt_index < self.number:
__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L11_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L11_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1345: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_4 = __pyx_v_context->chunk_variant_index;
__pyx_t_5 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_4 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_5 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1346: alt_len - context.ref_len
+1347: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+1348: break
goto __pyx_L6_break;
1349:
+1350: elif stream.c == LF or stream.c == CR:
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L13_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L13_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1351: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L15_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L15_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
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__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L18_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L18_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1353: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_6 = __pyx_v_context->chunk_variant_index;
__pyx_t_7 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_6 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_7 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1354: alt_len - context.ref_len
+1355: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+1356: break
goto __pyx_L6_break;
1357:
+1358: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1359: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L21_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L21_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
+1360: if self.store_svlen and alt_index < self.number:
__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L24_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L24_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1361: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_8 = __pyx_v_context->chunk_variant_index;
__pyx_t_9 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_8 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_9 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1362: alt_len - context.ref_len
+1363: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1363, __pyx_L1_error)
+1364: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1365: break
goto __pyx_L6_break;
1366:
+1367: elif stream.c == COMMA:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
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/* … */
goto __pyx_L20;
}
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if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L26_bool_binop_done;
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__pyx_L26_bool_binop_done:;
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__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
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__pyx_t_1 = __pyx_t_3;
goto __pyx_L29_bool_binop_done;
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__pyx_L29_bool_binop_done:;
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/* … */
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/* … */
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/* … */
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1394:
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/* … */
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/* … */
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__pyx_v_chunk_length = values[1];
__pyx_v_store_alt = values[2];
__pyx_v_store_numalt = values[3];
__pyx_v_store_svlen = values[4];
__pyx_v_store_is_snp = values[5];
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 1452, __pyx_L3_error)
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/* function exit code */
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static int __pyx_pf_5allel_3opt_11io_vcf_read_18VCFAltObjectParser___init__(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFAltObjectParser *__pyx_v_self, PyObject *__pyx_v_number, PyObject *__pyx_v_chunk_length, PyObject *__pyx_v_store_alt, PyObject *__pyx_v_store_numalt, PyObject *__pyx_v_store_svlen, PyObject *__pyx_v_store_is_snp) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
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+1453: super(VCFAltObjectParser, self).__init__(key=b'ALT', dtype=np.dtype('object'), number=number,
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFAltObjectParser)); __Pyx_GIVEREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFAltObjectParser)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFAltObjectParser)); __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_v_self)); __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_super, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_init); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_PyDict_NewPresized(4); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_key, __pyx_n_b_ALT) < 0) __PYX_ERR(0, 1453, __pyx_L1_error) __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5numpy_dtype), __pyx_tuple__38, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_3) < 0) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_number, __pyx_v_number) < 0) __PYX_ERR(0, 1453, __pyx_L1_error) /* … */ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_empty_tuple, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; /* … */ __pyx_tuple__38 = PyTuple_Pack(1, __pyx_n_s_object); if (unlikely(!__pyx_tuple__38)) __PYX_ERR(0, 1453, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__38); __Pyx_GIVEREF(__pyx_tuple__38);
+1454: chunk_length=chunk_length)
if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_chunk_length, __pyx_v_chunk_length) < 0) __PYX_ERR(0, 1453, __pyx_L1_error)
+1455: self.store_alt = store_alt
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_store_alt); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1455, __pyx_L1_error) __pyx_v_self->store_alt = __pyx_t_4;
+1456: self.store_numalt = store_numalt
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_store_numalt); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1456, __pyx_L1_error) __pyx_v_self->store_numalt = __pyx_t_4;
+1457: self.store_svlen = store_svlen
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_store_svlen); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1457, __pyx_L1_error) __pyx_v_self->store_svlen = __pyx_t_4;
+1458: self.store_is_snp = store_is_snp
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_store_is_snp); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1458, __pyx_L1_error) __pyx_v_self->store_is_snp = __pyx_t_4;
1459:
+1460: cdef int parse(self, InputStreamBase stream, VCFContext context) except -1: # nogil
static int __pyx_f_5allel_3opt_11io_vcf_read_18VCFAltObjectParser_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFAltObjectParser *__pyx_v_self, struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context) {
Py_ssize_t __pyx_v_alt_index;
Py_ssize_t __pyx_v_alt_len;
int __pyx_v_is_snp;
PyObject *__pyx_v_v = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_AddTraceback("allel.opt.io_vcf_read.VCFAltObjectParser.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_v);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
1461: cdef:
1462: # index of alt values
+1463: Py_ssize_t alt_index = 0
__pyx_v_alt_index = 0;
1464: # size of alt allele
+1465: Py_ssize_t alt_len = 0
__pyx_v_alt_len = 0;
1466: # is the variant a SNP?
+1467: bint is_snp = context.ref_len == 1
__pyx_v_is_snp = (__pyx_v_context->ref_len == 1);
1468:
1469: # bail out early for missing value
+1470: if stream.c == PERIOD:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PERIOD) != 0);
if (__pyx_t_1) {
/* … */
}
1471: # treat period as missing value, regardless of what comes next
+1472: vcf_parse_missing(stream, context)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_parse_missing(__pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1472, __pyx_L1_error)
+1473: return 0
__pyx_r = 0;
goto __pyx_L0;
1474:
1475: # bail out early for empty value
+1476: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1477: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1477, __pyx_L1_error)
+1478: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1479: return 0
__pyx_r = 0;
goto __pyx_L0;
1480:
1481: # setup temp
+1482: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
1483:
+1484: while True:
while (1) {
1485:
+1486: if stream.c == 0:
__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1487: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L8_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L8_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
+1488: if self.store_svlen and alt_index < self.number:
__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L11_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L11_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1489: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_4 = __pyx_v_context->chunk_variant_index;
__pyx_t_5 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_4 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_5 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1490: alt_len - context.ref_len
+1491: if self.store_alt and alt_index < self.number and context.temp.size > 0:
__pyx_t_3 = (__pyx_v_self->store_alt != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L14_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L14_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_context->temp.size > 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L14_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
1492: # with gil:
+1493: v = CharVector_to_pystr(&context.temp)
__pyx_t_6 = __pyx_f_5allel_3opt_11io_vcf_read_CharVector_to_pystr((&__pyx_v_context->temp)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1493, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6); __pyx_t_6 = 0;
+1494: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_6 = PyInt_FromSsize_t(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1494, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = PyInt_FromSsize_t(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1494, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1494, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); __pyx_t_6 = 0; __pyx_t_7 = 0; if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_self->__pyx_base.values), __pyx_t_8, __pyx_v_v) < 0)) __PYX_ERR(0, 1494, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+1495: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+1496: break
goto __pyx_L6_break;
1497:
+1498: elif stream.c == LF or stream.c == CR:
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L17_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L17_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1499: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L19_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L19_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
+1500: if self.store_svlen and alt_index < self.number:
__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L22_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L22_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1501: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_9 = __pyx_v_context->chunk_variant_index;
__pyx_t_10 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_9 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_10 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1502: alt_len - context.ref_len
+1503: if self.store_alt and alt_index < self.number and context.temp.size > 0:
__pyx_t_3 = (__pyx_v_self->store_alt != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L25_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L25_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_context->temp.size > 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L25_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
1504: # with gil:
+1505: v = CharVector_to_pystr(&context.temp)
__pyx_t_8 = __pyx_f_5allel_3opt_11io_vcf_read_CharVector_to_pystr((&__pyx_v_context->temp)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1505, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_8); __pyx_t_8 = 0;
+1506: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_8 = PyInt_FromSsize_t(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1506, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = PyInt_FromSsize_t(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1506, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1506, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_7); __pyx_t_8 = 0; __pyx_t_7 = 0; if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_self->__pyx_base.values), __pyx_t_6, __pyx_v_v) < 0)) __PYX_ERR(0, 1506, __pyx_L1_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+1507: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+1508: break
goto __pyx_L6_break;
1509:
+1510: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1511: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L29_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L29_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
+1512: if self.store_svlen and alt_index < self.number:
__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L32_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L32_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1513: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_11 = __pyx_v_context->chunk_variant_index;
__pyx_t_12 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_11 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_12 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1514: alt_len - context.ref_len
+1515: if self.store_alt and alt_index < self.number and context.temp.size > 0:
__pyx_t_3 = (__pyx_v_self->store_alt != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L35_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L35_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_context->temp.size > 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L35_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
1516: # with gil:
+1517: v = CharVector_to_pystr(&context.temp)
__pyx_t_6 = __pyx_f_5allel_3opt_11io_vcf_read_CharVector_to_pystr((&__pyx_v_context->temp)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1517, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6); __pyx_t_6 = 0;
+1518: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_6 = PyInt_FromSsize_t(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1518, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = PyInt_FromSsize_t(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1518, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1518, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); __pyx_t_6 = 0; __pyx_t_7 = 0; if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_self->__pyx_base.values), __pyx_t_8, __pyx_v_v) < 0)) __PYX_ERR(0, 1518, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+1519: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1519, __pyx_L1_error)
+1520: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1521: break
goto __pyx_L6_break;
1522:
+1523: elif stream.c == COMMA:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L28;
}
+1524: is_snp = is_snp and alt_len == 1
__pyx_t_3 = (__pyx_v_is_snp != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L38_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L38_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
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__pyx_t_3 = (__pyx_v_self->store_svlen != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L41_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L41_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1526: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_13 = __pyx_v_context->chunk_variant_index;
__pyx_t_14 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_13 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_14 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1527: alt_len - context.ref_len
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__pyx_t_3 = (__pyx_v_self->store_alt != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L44_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L44_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
1529: # with gil:
+1530: v = CharVector_to_pystr(&context.temp)
__pyx_t_8 = __pyx_f_5allel_3opt_11io_vcf_read_CharVector_to_pystr((&__pyx_v_context->temp)); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1530, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_8); __pyx_t_8 = 0;
+1531: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_8 = PyInt_FromSsize_t(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1531, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = PyInt_FromSsize_t(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1531, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1531, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_7); __pyx_t_8 = 0; __pyx_t_7 = 0; if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_self->__pyx_base.values), __pyx_t_6, __pyx_v_v) < 0)) __PYX_ERR(0, 1531, __pyx_L1_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
1532: # advance value index
+1533: alt_index += 1
__pyx_v_alt_index = (__pyx_v_alt_index + 1);
1534: # reset
+1535: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
+1536: alt_len = 0
__pyx_v_alt_len = 0;
1537:
1538: else:
+1539: if stream.c != PERIOD and stream.c != ASTERISK:
/*else*/ {
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_PERIOD) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L47_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_ASTERISK) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L47_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1540: alt_len += 1
__pyx_v_alt_len = (__pyx_v_alt_len + 1);
+1541: if self.store_alt and alt_index < self.number:
__pyx_t_3 = (__pyx_v_self->store_alt != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L50_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L50_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
}
__pyx_L28:;
+1542: CharVector_append(&context.temp, stream.c)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
1543:
1544: # advance input stream
+1545: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 1545, __pyx_L1_error)
}
__pyx_L6_break:;
1546:
+1547: if self.store_numalt:
__pyx_t_1 = (__pyx_v_self->store_numalt != 0);
if (__pyx_t_1) {
/* … */
}
+1548: self.numalt_memory[context.chunk_variant_index] = alt_index + 1
__pyx_t_15 = __pyx_v_context->chunk_variant_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=0 */ (__pyx_v_self->numalt_memory.data + __pyx_t_15 * __pyx_v_self->numalt_memory.strides[0]) )) = (__pyx_v_alt_index + 1);
+1549: if self.store_is_snp:
__pyx_t_1 = (__pyx_v_self->store_is_snp != 0);
if (__pyx_t_1) {
/* … */
}
+1550: self.is_snp_memory[context.chunk_variant_index] = is_snp
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*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_self->is_snp_memory.data + __pyx_t_16 * __pyx_v_self->is_snp_memory.strides[0]) )) = __pyx_v_is_snp;
1551:
+1552: cdef int malloc_chunk(self) except -1:
static int __pyx_f_5allel_3opt_11io_vcf_read_18VCFAltObjectParser_malloc_chunk(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFAltObjectParser *__pyx_v_self) {
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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("malloc_chunk", 0);
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goto __pyx_L0;
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__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_5);
__PYX_XDEC_MEMVIEW(&__pyx_t_6, 1);
__PYX_XDEC_MEMVIEW(&__pyx_t_7, 1);
__PYX_XDEC_MEMVIEW(&__pyx_t_8, 1);
__Pyx_AddTraceback("allel.opt.io_vcf_read.VCFAltObjectParser.malloc_chunk", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_t_4 = (__pyx_v_self->store_alt != 0);
if (__pyx_t_4) {
/* … */
}
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if (__pyx_t_4) {
/* … */
}
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/* … */
}
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/* … */
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1854:
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/* … */
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/* … */
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1857: # handle flag
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
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1861:
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__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
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/* … */
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/* … */
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/* … */
goto __pyx_L7;
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/* … */
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/* … */
goto __pyx_L7;
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/* … */
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/* … */
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/* … */
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/* … */
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__pyx_t_2 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
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__pyx_t_2 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
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+2295: stream.c != CR and \
__pyx_t_2 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
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__pyx_t_2 = ((__pyx_v_stream->c != 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L5_bool_binop_done:;
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2298:
+2299: cdef int malloc_chunk(self) except -1:
static int __pyx_f_5allel_3opt_11io_vcf_read_17VCFInfoSkipParser_malloc_chunk(CYTHON_UNUSED struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoSkipParser *__pyx_v_self) {
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2301:
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/* … */
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2303: pass
2304:
2305:
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Py_ssize_t __pyx_v_value_index;
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/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__Pyx_RefNannyFinishContext();
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Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_info_parse_integer", 0);
/* … */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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2307: VCFContext context,
2308: integer[:, :] memory) except -1: # nogil
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__pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0;
2311:
2312: # reset temporary buffer
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
2314:
+2315: while True:
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
2316:
+2317: if stream.c == 0 or \
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
+2318: stream.c == LF or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
+2319: stream.c == CR or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
+2320: stream.c == TAB or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
+2321: stream.c == SEMICOLON:
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
+2322: vcf_info_store_integer(context, value_index, memory)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2322, __pyx_L1_error)
+2323: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
2324:
+2325: elif stream.c == COMMA:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+2326: vcf_info_store_integer(context, value_index, memory)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2326, __pyx_L1_error)
+2327: CharVector_clear(&context.info_val)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
+2328: value_index += 1
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
2329:
2330: else:
+2331: CharVector_append(&context.info_val, stream.c)
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
2332:
+2333: stream.advance()
__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2333, __pyx_L1_error) } __pyx_L4_break:;
2334:
2335:
+2336: cdef int vcf_info_store_integer(VCFContext context,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_info_store_integer", 0);
/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_info_store_integer", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_2vcf_info_store_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_3vcf_info_store_integer", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_4vcf_info_store_integer", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_info_store_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_6vcf_info_store_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_info_store_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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2337: Py_ssize_t value_index,
2338: integer[:, :] memory) except -1: # nogil
2339: cdef:
2340: Py_ssize_t parsed
2341: long value
2342:
+2343: if value_index >= memory.shape[1]:
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
2344: # more values than we have room for, ignore
+2345: return 0
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
2346:
2347: # parse string as integer
+2348: parsed = vcf_strtol(&context.info_val, context, &value)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2348, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
2349:
+2350: if parsed > 0:
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
2351: # store value
+2352: memory[context.chunk_variant_index, value_index] = value
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_int8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_int16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint8_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
2353:
2354:
+2355: cdef int vcf_info_parse_floating(InputStreamBase stream,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_parse_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_info_parse_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_parse_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_info_parse_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
2356: VCFContext context,
2357: floating[:, :] memory) except -1: # nogil
2358: cdef:
+2359: Py_ssize_t value_index = 0
__pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0;
2360:
2361: # reset temporary buffer
+2362: CharVector_clear(&context.info_val)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
2363:
+2364: while True:
while (1) {
/* … */
while (1) {
2365:
+2366: if stream.c == 0 or \
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
+2367: stream.c == LF or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
+2368: stream.c == CR or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
+2369: stream.c == TAB or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
+2370: stream.c == SEMICOLON:
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
+2371: vcf_info_store_floating(context, value_index, memory)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2371, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2371, __pyx_L1_error)
+2372: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
2373:
+2374: elif stream.c == COMMA:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+2375: vcf_info_store_floating(context, value_index, memory)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2375, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2375, __pyx_L1_error)
+2376: CharVector_clear(&context.info_val)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
+2377: value_index += 1
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
2378:
2379: else:
+2380: CharVector_append(&context.info_val, stream.c)
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
}
__pyx_L5:;
2381:
+2382: stream.advance()
__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2382, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2382, __pyx_L1_error) } __pyx_L4_break:;
2383:
2384:
+2385: cdef int vcf_info_store_floating(VCFContext context,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
double __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_info_store_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
double __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_info_store_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
2386: Py_ssize_t value_index,
2387: floating[:, :] memory) except -1: # nogil
2388: cdef:
2389: Py_ssize_t parsed
2390: double value
2391:
+2392: if value_index >= memory.shape[1]:
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
}
2393: # more values than we have room for, ignore
+2394: return 0
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
2395:
2396: # parse string as floating
+2397: parsed = vcf_strtod(&context.info_val, context, &value)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtod((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2397, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtod((&__pyx_v_context->info_val), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 2397, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
2398:
+2399: if parsed > 0:
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
2400: # store value
+2401: memory[context.chunk_variant_index, value_index] = value
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_value_index;
*((__pyx_t_5numpy_float32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) )) = __pyx_v_value;
/* … */
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__pyx_t_4 = __pyx_v_value_index;
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/* … */
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2462: else:
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__pyx_L4_break:;
2467:
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2631: # store pointers to parsers
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__Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 2636, __pyx_L3_error)
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__Pyx_XDECREF(__pyx_t_3);
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+2637: super(VCFCallDataParser, self).__init__(chunk_length=chunk_length)
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2637, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFCallDataParser)); __Pyx_GIVEREF(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFCallDataParser)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFCallDataParser)); __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_v_self)); __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_super, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2637, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_init); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2637, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2637, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_chunk_length, __pyx_v_chunk_length) < 0) __PYX_ERR(0, 2637, __pyx_L1_error) __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_empty_tuple, __pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 2637, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
2638:
+2639: def __dealloc__(self):
/* Python wrapper */
static void __pyx_pw_5allel_3opt_11io_vcf_read_17VCFCallDataParser_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
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if (__pyx_t_1) {
/* … */
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free(__pyx_v_self->parsers_cptr);
2642:
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2644: cdef:
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2647: # initialise context
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__pyx_v_context->sample_index = 0;
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__pyx_v_context->sample_output_index = -1L;
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__pyx_v_context->sample_field_index = 0;
2651:
2652: # setup output indexing
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__pyx_t_1 = 0;
__pyx_t_2 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_self->loc_samples.data + __pyx_t_1 * __pyx_v_self->loc_samples.strides[0]) ))) != 0);
if (__pyx_t_2) {
/* … */
goto __pyx_L3;
}
+2654: context.sample_output_index += 1
__pyx_v_context->sample_output_index = (__pyx_v_context->sample_output_index + 1);
2655: else:
2656: # skip to next sample
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/*else*/ {
while (1) {
__pyx_t_3 = ((__pyx_v_stream->c != 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
if (!__pyx_t_2) break;
+2658: stream.advance()
__pyx_t_4 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 2658, __pyx_L1_error)
}
}
__pyx_L3:;
2659:
+2660: while True:
while (1) {
2661:
+2662: if context.sample_index >= self.n_samples:
__pyx_t_2 = ((__pyx_v_context->sample_index >= __pyx_v_self->n_samples) != 0);
if (__pyx_t_2) {
/* … */
}
2663: # with gil:
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__pyx_t_4 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_more_samples_than_given_in_heade, __pyx_v_context); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 2664, __pyx_L1_error)
+2665: while stream.c != 0 and stream.c != LF and stream.c != CR:
while (1) {
__pyx_t_3 = ((__pyx_v_stream->c != 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L15_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L15_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L15_bool_binop_done:;
if (!__pyx_t_2) break;
+2666: stream.advance()
__pyx_t_4 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 2666, __pyx_L1_error)
}
2667:
+2668: if stream.c == 0:
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_2) {
/* … */
}
+2669: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+2670: break
goto __pyx_L11_break;
2671:
+2672: elif stream.c == LF or stream.c == CR:
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L19_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L19_bool_binop_done:;
if (__pyx_t_2) {
/* … */
}
+2673: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+2674: break
goto __pyx_L11_break;
2675:
+2676: elif stream.c == TAB:
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_2) {
/* … */
goto __pyx_L18;
}
+2677: stream.advance()
__pyx_t_4 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 2677, __pyx_L1_error)
+2678: context.sample_index += 1
__pyx_v_context->sample_index = (__pyx_v_context->sample_index + 1);
+2679: context.sample_field_index = 0
__pyx_v_context->sample_field_index = 0;
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__pyx_t_5 = __pyx_v_context->sample_index;
__pyx_t_2 = ((*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_self->loc_samples.data + __pyx_t_5 * __pyx_v_self->loc_samples.strides[0]) ))) != 0);
if (__pyx_t_2) {
/* … */
goto __pyx_L21;
}
+2681: context.sample_output_index += 1
__pyx_v_context->sample_output_index = (__pyx_v_context->sample_output_index + 1);
2682: else:
2683: # skip to next sample
+2684: while stream.c != 0 and stream.c != LF and stream.c != CR and stream.c != TAB:
/*else*/ {
while (1) {
__pyx_t_3 = ((__pyx_v_stream->c != 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L24_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L24_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L24_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L24_bool_binop_done:;
if (!__pyx_t_2) break;
+2685: stream.advance()
__pyx_t_4 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 2685, __pyx_L1_error)
}
}
__pyx_L21:;
2686:
+2687: elif stream.c == COLON:
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (__pyx_t_2) {
/* … */
goto __pyx_L18;
}
+2688: context.sample_field_index += 1
__pyx_v_context->sample_field_index = (__pyx_v_context->sample_field_index + 1);
+2689: stream.advance()
__pyx_t_4 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(0, 2689, __pyx_L1_error)
2690:
+2691: elif context.sample_field_index >= context.variant_format_indices.size:
__pyx_t_2 = ((__pyx_v_context->sample_field_index >= __pyx_v_context->variant_format_indices.size) != 0);
if (__pyx_t_2) {
/* … */
goto __pyx_L18;
}
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2935:
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2938: VCFContext context,
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2942:
2943: # reset temporary buffer
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2945:
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while (1) {
/* … */
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/* … */
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/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
2947:
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if (!__pyx_t_2) {
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goto __pyx_L6_bool_binop_done;
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/* … */
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/* … */
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goto __pyx_L6_bool_binop_done;
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__pyx_t_1 = __pyx_t_2;
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if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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/* … */
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if (!__pyx_t_2) {
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goto __pyx_L6_bool_binop_done;
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/* … */
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/* … */
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goto __pyx_L6_bool_binop_done;
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if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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/* … */
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if (!__pyx_t_2) {
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__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
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if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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/* … */
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if (!__pyx_t_2) {
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goto __pyx_L6_bool_binop_done;
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
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if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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/* … */
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goto __pyx_L6_bool_binop_done;
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if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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/* … */
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goto __pyx_L6_bool_binop_done;
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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+2949: vcf_genotype_store(context, memory, value_index)
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+2950: value_index += 1
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
+2951: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
2952:
+2953: elif stream.c == COLON or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
+2954: stream.c == TAB or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
+2955: stream.c == LF or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
+2956: stream.c == CR or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
+2957: stream.c == 0:
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
+2958: vcf_genotype_store(context, memory, value_index)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(__pyx_v_context, __pyx_v_memory, __pyx_v_value_index); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2958, __pyx_L1_error)
+2959: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
2960:
2961: else:
+2962: CharVector_append(&context.temp, stream.c)
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
2963:
+2964: stream.advance()
__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 2964, __pyx_L1_error) } __pyx_L4_break:;
2965:
2966:
+2967: cdef int vcf_genotype_store(VCFContext context,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory, Py_ssize_t __pyx_v_value_index) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_allele;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_genotype_store", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_genotype_store", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory, Py_ssize_t __pyx_v_value_index) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_allele;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_genotype_store", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_genotype_store", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_store(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory, Py_ssize_t __pyx_v_value_index) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_allele;
int __pyx_r;
__Pyx_RefNannyDeclarations
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2968: integer[:, :, :] memory,
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/* … */
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/* … */
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2984:
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static int __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_3vcf_genotype_ac_parse", 0);
/* … */
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static int __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_4vcf_genotype_ac_parse", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_genotype_ac_parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_genotype_ac_parse", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_genotype_ac_parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_6vcf_genotype_ac_parse", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_genotype_ac_parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_parse(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_genotype_ac_parse", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_genotype_ac_parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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3147: VCFContext context,
3148: integer[:, :, :] memory) except -1: # nogil
3149: # reset temporary buffer
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
3151:
+3152: while True:
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
3153:
+3154: if stream.c == SLASH or stream.c == PIPE:
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SLASH) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L6_bool_binop_done;
}
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PIPE) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+3155: vcf_genotype_ac_store(context, memory)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3155, __pyx_L1_error)
+3156: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
3157:
+3158: elif stream.c == COLON or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
+3159: stream.c == TAB or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
+3160: stream.c == LF or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
+3161: stream.c == CR or \
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L8_bool_binop_done;
}
+3162: stream.c == 0:
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
/* … */
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_2;
__pyx_L8_bool_binop_done:;
+3163: vcf_genotype_ac_store(context, memory)
__pyx_t_3 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error) /* … */ __pyx_t_3 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(__pyx_v_context, __pyx_v_memory); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3163, __pyx_L1_error)
+3164: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
3165:
3166: else:
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/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
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__pyx_L5:;
/* … */
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__pyx_L5:;
/* … */
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__pyx_L5:;
/* … */
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
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__pyx_L5:;
/* … */
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
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__pyx_L5:;
/* … */
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
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__pyx_L5:;
/* … */
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__pyx_L5:;
/* … */
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__pyx_L5:;
3168:
+3169: stream.advance()
__pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_3 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_3 == ((int)-1))) __PYX_ERR(0, 3169, __pyx_L1_error) } __pyx_L4_break:;
3170:
3171:
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static int __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_genotype_ac_store(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
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3173: integer[:, :, :] memory) except -1: # nogil
3174: cdef:
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3178: # attempt to parse allele
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__pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1; /* … */ __pyx_t_1 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_1 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3179, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1;
3180:
3181: # store value
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__pyx_t_3 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_allele < (__pyx_v_memory.shape[2])) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L4_bool_binop_done:;
if (__pyx_t_2) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_allele < (__pyx_v_memory.shape[2])) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L4_bool_binop_done:;
if (__pyx_t_2) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_allele < (__pyx_v_memory.shape[2])) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L4_bool_binop_done:;
if (__pyx_t_2) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_allele < (__pyx_v_memory.shape[2])) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L4_bool_binop_done:;
if (__pyx_t_2) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_allele < (__pyx_v_memory.shape[2])) != 0);
__pyx_t_2 = __pyx_t_3;
__pyx_L4_bool_binop_done:;
if (__pyx_t_2) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_2 = __pyx_t_3;
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3185:
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_2vcf_calldata_parse_integer", 0);
/* … */
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_3vcf_calldata_parse_integer", 0);
/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_4vcf_calldata_parse_integer", 0);
/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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static int __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_parse_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_calldata_parse_integer", 0);
/* … */
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__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_parse_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_6vcf_calldata_parse_integer", 0);
/* … */
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static int __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_parse_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_calldata_parse_integer", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
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3377: VCFContext context,
3378: integer[:, :, :] memory) except -1: # nogil
3379:
3380: cdef:
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__pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0;
3382:
3383: # reset temporary buffer
+3384: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
3385:
+3386: while True:
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
3387:
+3388: if stream.c == COMMA:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+3389: vcf_calldata_store_integer(context, value_index, memory)
__pyx_t_2 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3389, __pyx_L1_error)
+3390: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
+3391: value_index += 1
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
3392:
+3393: elif stream.c == COLON or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
+3394: stream.c == TAB or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
+3395: stream.c == LF or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
+3396: stream.c == CR or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
+3397: stream.c == 0:
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
+3398: vcf_calldata_store_integer(context, value_index, memory)
__pyx_t_2 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3398, __pyx_L1_error)
+3399: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
3400:
3401: else:
+3402: CharVector_append(&context.temp, stream.c)
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
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__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
}
__pyx_L5:;
3403:
+3404: stream.advance()
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:; /* … */ __pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_InputStreamBase *)__pyx_v_stream->__pyx_vtab)->advance(__pyx_v_stream); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3404, __pyx_L1_error) } __pyx_L4_break:;
3405:
3406:
+3407: cdef int vcf_calldata_store_integer(VCFContext context,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_calldata_store_integer", 0);
/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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static int __pyx_fuse_2__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannyDeclarations
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/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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static int __pyx_fuse_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannyDeclarations
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/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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static int __pyx_fuse_4__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannySetupContext("__pyx_fuse_4vcf_calldata_store_integer", 0);
/* … */
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__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_calldata_store_integer", 0);
/* … */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_6vcf_calldata_store_integer", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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static int __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_calldata_store_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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3408: Py_ssize_t value_index,
3409: integer[:, :, :] memory) except -1: # nogil
3410: cdef:
3411: Py_ssize_t parsed
3412: long value
3413:
+3414: if value_index >= memory.shape[2]:
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
3415: # more values than we have room for, ignore
+3416: return 0
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
/* … */
__pyx_r = 0;
goto __pyx_L0;
3417:
+3418: parsed = vcf_strtol(&context.temp, context, &value)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2; /* … */ __pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_value)); if (unlikely(__pyx_t_2 == ((Py_ssize_t)-1L))) __PYX_ERR(0, 3418, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
3419:
3420: # store value
+3421: if parsed > 0:
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
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/* … */
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/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
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/* … */
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/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
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/* … */
__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
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+3422: memory[context.chunk_variant_index, context.sample_output_index, value_index] = value
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_int64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
__pyx_t_4 = __pyx_v_context->sample_output_index;
__pyx_t_5 = __pyx_v_value_index;
*((__pyx_t_5numpy_uint64_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_3 * __pyx_v_memory.strides[0]) ) + __pyx_t_4 * __pyx_v_memory.strides[1]) ) + __pyx_t_5 * __pyx_v_memory.strides[2]) )) = __pyx_v_value;
3423:
3424:
+3425: cdef int vcf_calldata_parse_floating(InputStreamBase stream,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_parse_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_calldata_parse_floating", 0);
/* … */
/* function exit code */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
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static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_parse_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_InputStreamBase *__pyx_v_stream, struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_calldata_parse_floating", 0);
/* … */
/* function exit code */
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__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
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__Pyx_RefNannyFinishContext();
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3426: VCFContext context,
3427: floating[:, :, :] memory) except -1: # nogil
3428:
3429: cdef:
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__pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0;
3431:
3432: # reset temporary buffer
+3433: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp)); /* … */ __pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
3434:
+3435: while True:
while (1) {
/* … */
while (1) {
3436:
+3437: if stream.c == COMMA:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
/* … */
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COMMA) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
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+3438: vcf_calldata_store_floating(context, value_index, memory)
__pyx_t_2 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3438, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3438, __pyx_L1_error)
+3439: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
/* … */
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
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__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
3441:
+3442: elif stream.c == COLON or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
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/* … */
if (__pyx_t_1) {
/* … */
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
if (__pyx_t_1) {
/* … */
}
+3443: stream.c == TAB or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
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__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
+3445: stream.c == CR or \
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
}
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
if (!__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L6_bool_binop_done;
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__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
/* … */
__pyx_t_3 = ((__pyx_v_stream->c == 0) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L6_bool_binop_done:;
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__pyx_t_2 = __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3447, __pyx_L1_error) /* … */ __pyx_t_2 = __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_floating(__pyx_v_context, __pyx_v_value_index, __pyx_v_memory); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(0, 3447, __pyx_L1_error)
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goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
3449:
3450: else:
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/* … */
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3454:
3455:
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Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_calldata_store_floating", 0);
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static int __pyx_fuse_1__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, Py_ssize_t __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
Py_ssize_t __pyx_v_parsed;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_calldata_store_floating", 0);
/* … */
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goto __pyx_L0;
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_store_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
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3457: Py_ssize_t value_index,
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3460: Py_ssize_t parsed
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__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
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/* … */
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/* … */
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/* … */
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goto __pyx_L0;
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3473:
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3476: cdef np.uint8_t[:] memory
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3695: 'EOL',
3696: 'EOF'
3697: ]
3698:
3699:
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Py_ssize_t __pyx_v_format_index;
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/* … */
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3701: cdef Py_ssize_t format_index
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__pyx_t_3 = ((__pyx_v_context->state > __pyx_e_5allel_3opt_11io_vcf_read_POS) != 0);
if (__pyx_t_3) {
/* … */
}
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__pyx_t_4 = ((__pyx_v_context->state == __pyx_e_5allel_3opt_11io_vcf_read_CALLDATA) != 0);
if (__pyx_t_4) {
/* … */
}
+3710: if context.sample_index >= len(context.headers.samples):
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if (__pyx_t_4) {
/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
__PYX_ERR(0, 3718, __pyx_L1_error)
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__Pyx_INCREF(__pyx_t_1);
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__pyx_t_1 = 0;
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3721: sample,
3722: format)
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3724:
3725:
3726: # import sys
3727: #
3728: #
3729: # cdef int debug(message, vars=None) except -1:
3730: # message = '[DEBUG] ' + str(message)
3731: # if vars:
3732: # message = message % vars
3733: # print(message, file=sys.stderr)
3734: # sys.stderr.flush()
3735:
3736:
3737: ##########################################################################################
3738: # EXPERIMENTAL support for multi-threaded parsing
3739: # N.B., this is not used for the moment, because use of object dtype for strings
3740: # requires GIL acquisition, and this may hurt performance in a single-threaded
3741: # context. I'm not completely certain that is the case, but I am out of time to
3742: # explore further.
3743:
3744:
3745: # import itertools
3746: # import time
3747: #
3748: #
3749: # cdef class VCFParallelParser:
3750: #
3751: # cdef:
3752: # FileInputStream stream
3753: # CharVectorInputStream buffer
3754: # VCFContext context
3755: # VCFParser parser
3756: # Py_ssize_t chunk_length
3757: # Py_ssize_t block_length
3758: # object pool
3759: # object result
3760: #
3761: # def __cinit__(self, stream, parser, chunk_length, block_length, pool, headers, fields):
3762: # self.buffer = CharVectorInputStream(2**14)
3763: # self.context = VCFContext(headers, fields)
3764: # self.stream = stream
3765: # self.parser = parser
3766: # self.chunk_length = chunk_length
3767: # self.block_length = block_length
3768: # self.pool = pool
3769: # self.result = None
3770: #
3771: # def read(self, n_lines):
3772: # self.buffer.clear()
3773: # n_lines_read = self.stream.read_lines_into(&(self.buffer.vector), n_lines)
3774: # self.buffer.advance()
3775: # return n_lines_read
3776: #
3777: # def parse_async(self, block_index, chunk_index):
3778: # self.result = self.pool.apply_async(self.parse, args=(block_index, chunk_index))
3779: #
3780: # def join(self):
3781: # if self.result is not None:
3782: # self.result.get()
3783: #
3784: # def parse(self, block_index, chunk_index):
3785: # before = time.time()
3786: # # set initial state
3787: # self.context.state = VCFState.CHROM
3788: # self.context.chunk_variant_index = block_index * self.block_length - 1
3789: # self.context.variant_index = (chunk_index * self.chunk_length +
3790: # self.context.chunk_variant_index)
3791: # # parse the block of data stored in the buffer
3792: # self.parser.parse(self.buffer, self.context)
3793: # after = time.time()
3794: #
3795: #
3796: # cdef class VCFParallelChunkIterator:
3797: #
3798: # cdef:
3799: # FileInputStream stream
3800: # VCFParser parser
3801: # object pool
3802: # Py_ssize_t chunk_length
3803: # Py_ssize_t block_length
3804: # int n_threads
3805: # int n_workers
3806: # Py_ssize_t chunk_index
3807: # list workers
3808: #
3809: # def __cinit__(self,
3810: # FileInputStream stream,
3811: # Py_ssize_t chunk_length, Py_ssize_t block_length, int n_threads,
3812: # headers, fields, types, numbers, fills, region, loc_samples):
3813: #
3814: # fields = sorted(fields)
3815: # self.stream = stream
3816: # self.chunk_length = chunk_length
3817: # self.n_threads = n_threads
3818: # self.pool = ThreadPool(n_threads)
3819: # # allow one more worker than number of threads in pool to allow for sync
3820: # # reading of data in the main thread
3821: # self.n_workers = n_threads + 1
3822: # # only makes sense to have block length at most fraction chunk length if we want
3823: # # some parallelism
3824: # self.block_length = min(block_length, chunk_length//self.n_workers)
3825: # if self.block_length < 1:
3826: # self.block_length = 1
3827: # loc_samples = check_samples(loc_samples, headers)
3828: # self.parser = VCFParser(
3829: # fields=fields, types=types, numbers=numbers, chunk_length=chunk_length, loc_samples=loc_samples, fills=fills,
3830: # region=region
3831: # )
3832: # self.chunk_index = -1
3833: # self.workers = [VCFParallelParser(stream=stream, parser=self.parser, chunk_length=self.chunk_length,
3834: # block_length=self.block_length, pool=self.pool, headers=headers,
3835: # fields=fields)
3836: # for _ in range(self.n_workers)]
3837: #
3838: # def __iter__(self):
3839: # return self
3840: #
3841: # def __next__(self):
3842: # cdef:
3843: # Py_ssize_t block_index = 0
3844: # Py_ssize_t i = 0
3845: # Py_ssize_t n_lines
3846: # Py_ssize_t n_lines_read = 0
3847: # VCFParallelParser worker
3848: #
3849: # # increment the current chunk index
3850: # self.chunk_index += 1
3851: #
3852: # # allocate arrays for next chunk
3853: # self.parser.malloc_chunk()
3854: #
3855: # # cycle around the workers
3856: # for i in itertools.cycle(list(range(self.n_workers))):
3857: # worker = self.workers[i]
3858: #
3859: # # wait for the result to finish - this ensures we don't overwrite a
3860: # # worker's buffer while it's still parsing
3861: # worker.join()
3862: #
3863: # # read lines into the worker's buffer - this part has to be synchronous
3864: # n_lines = min(self.block_length, self.chunk_length - n_lines_read)
3865: # n_lines_read += worker.read(n_lines)
3866: #
3867: # # launch parsing of the block in parallel
3868: # worker.parse_async(block_index, self.chunk_index)
3869: #
3870: # # increment the current block index
3871: # block_index += 1
3872: #
3873: # # is the chunk done?
3874: # if n_lines_read >= self.chunk_length:
3875: # break
3876: #
3877: # # is the input stream exhausted?
3878: # if self.stream.c == 0:
3879: # break
3880: #
3881: # # wait for all parallel tasks to complete
3882: # for worker in self.workers:
3883: # worker.join()
3884: #
3885: # # obtain the final chunk length via the last worker
3886: # worker = self.workers[i]
3887: # chunk_length = worker.context.chunk_variant_index + 1
3888: #
3889: # # obtain the chunk
3890: # chunk = self.parser.make_chunk(chunk_length)
3891: #
3892: # if chunk is None:
3893: # # clean up thread pool
3894: # self.pool.close()
3895: # self.pool.join()
3896: # self.pool.terminate()
3897: # raise StopIteration
3898: #
3899: # else:
3900: # chrom = CharVector_to_pybytes(&worker.context.chrom)
3901: # pos = worker.context.pos
3902: # return chunk, chunk_length, chrom, pos
3903:
3904:
3905: ###################################################################
3906: # ANN transformer
3907:
3908:
3909: # ANN field indices
+3910: cdef enum ANNFidx:
enum __pyx_t_5allel_3opt_11io_vcf_read_ANNFidx {
__pyx_e_5allel_3opt_11io_vcf_read_ALLELE = 0,
__pyx_e_5allel_3opt_11io_vcf_read_ANNOTATION = 1,
__pyx_e_5allel_3opt_11io_vcf_read_ANNOTATION_IMPACT = 2,
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__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4146, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_raw); __Pyx_GIVEREF(__pyx_v_raw); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_raw); __Pyx_INCREF(__pyx_n_s_utf8); __Pyx_GIVEREF(__pyx_n_s_utf8); PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_n_s_utf8); __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyString_Type)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 4146, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF_SET(__pyx_v_raw, __pyx_t_2); __pyx_t_2 = 0;
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
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goto __pyx_L16_bool_binop_done;
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
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goto __pyx_L19_bool_binop_done;
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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goto __pyx_L22_bool_binop_done;
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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goto __pyx_L25_bool_binop_done;
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if (__pyx_t_3) {
/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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goto __pyx_L28_bool_binop_done;
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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goto __pyx_L31_bool_binop_done;
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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goto __pyx_L34_bool_binop_done;
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/* … */
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/* … */
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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