Generated by Cython 0.25.2
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
+0026: import numpy as np
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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
+0042: cdef double NAN = np.nan
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+0052: cdef char COMMA = b','
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+0053: cdef char SLASH = b'/'
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struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *ref_parser;
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *alt_parser;
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *qual_parser;
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *filter_parser;
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *info_parser;
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *format_parser;
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *calldata_parser;
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int region_end;
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/* … */
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if (__pyx_t_8) {
/* … */
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__pyx_t_7 = (__pyx_t_8 != 0);
if (__pyx_t_7) {
/* … */
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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, 628, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 628, __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__13 = PyTuple_Pack(1, __pyx_kp_s_variants_is_snp); if (unlikely(!__pyx_tuple__13)) __PYX_ERR(0, 628, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__13); __Pyx_GIVEREF(__pyx_tuple__13);
0629:
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goto __pyx_L8_bool_binop_done;
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if (!__pyx_t_8) {
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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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+0731: calldata_parser = VCFCallDataParser(format_keys=format_keys,
__pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 731, __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, 731, __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, 731, __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, 731, __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, 731, __pyx_L1_error)
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__pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->chunk_length); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 734, __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, 731, __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, 735, __pyx_L1_error)
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__pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_5allel_3opt_11io_vcf_read_VCFSkipAllCallDataParser), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 739, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_v_calldata_parser = ((struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFFieldParserBase *)__pyx_t_5); __pyx_t_5 = 0; } __pyx_L10:;
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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 == -1)) __PYX_ERR(0, 740, __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 == -1)) __PYX_ERR(0, 741, __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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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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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse", 0);
/* … */
/* function exit code */
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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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0746: """Parse to end of current chunk or EOF."""
0747:
0748: # with nogil:
0749:
+0750: while True:
while (1) {
0751:
+0752: if context.state == VCFState.EOF:
switch (__pyx_v_context->state) {
case __pyx_e_5allel_3opt_11io_vcf_read_EOF:
/* … */
break;
+0753: break
goto __pyx_L4_break;
0754:
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case __pyx_e_5allel_3opt_11io_vcf_read_EOL:
/* … */
break;
0756:
0757: # 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;
}
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__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 == -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_CR) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L5;
}
+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 == -1)) __PYX_ERR(0, 761, __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) {
/* … */
}
+0763: 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 == -1)) __PYX_ERR(0, 763, __pyx_L1_error)
0764: else:
0765: # shouldn't ever happen
0766: # with gil:
+0767: warn('unexpected EOL character', context)
/*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 == -1)) __PYX_ERR(0, 767, __pyx_L1_error)
+0768: break
goto __pyx_L4_break;
}
__pyx_L5:;
0769:
0770: # advance state
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_CHROM;
0772:
0773: # 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) {
/* … */
}
0775: # we're done
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goto __pyx_L4_break;
0777:
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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 == -1)) __PYX_ERR(0, 779, __pyx_L1_error)
0780:
+0781: elif context.state == VCFState.ID:
case __pyx_e_5allel_3opt_11io_vcf_read_ID:
/* … */
break;
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__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 == -1)) __PYX_ERR(0, 782, __pyx_L1_error)
0783:
+0784: elif context.state == VCFState.REF:
case __pyx_e_5allel_3opt_11io_vcf_read_REF:
/* … */
break;
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__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 == -1)) __PYX_ERR(0, 785, __pyx_L1_error)
0786:
+0787: elif context.state == VCFState.ALT:
case __pyx_e_5allel_3opt_11io_vcf_read_ALT:
/* … */
break;
+0788: self.alt_parser.parse(stream, context)
__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 == -1)) __PYX_ERR(0, 788, __pyx_L1_error)
0789:
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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 == -1)) __PYX_ERR(0, 791, __pyx_L1_error)
0792:
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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 == -1)) __PYX_ERR(0, 794, __pyx_L1_error)
0795:
+0796: 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 == -1)) __PYX_ERR(0, 797, __pyx_L1_error)
0798:
+0799: elif context.state == VCFState.FORMAT:
case __pyx_e_5allel_3opt_11io_vcf_read_FORMAT:
/* … */
break;
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__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 == -1)) __PYX_ERR(0, 800, __pyx_L1_error)
0801:
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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 == -1)) __PYX_ERR(0, 803, __pyx_L1_error)
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goto __pyx_L4_break;
break;
}
}
__pyx_L4_break:;
0810:
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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_RefNannyDeclarations
__Pyx_RefNannySetupContext("malloc_chunk", 0);
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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 == -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, 920, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 920, __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, 920, __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, 920, __pyx_L1_error)
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0922:
0923:
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
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/* … */
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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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goto __pyx_L4_break;
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append(__pyx_v_dest, __pyx_v_stream->c);
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0949: # advance input stream
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0951:
0952:
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__Pyx_RefNannySetupContext("vcf_parse_missing", 0);
/* … */
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/* … */
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/* … */
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goto __pyx_L4_break;
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if (__pyx_t_1) {
/* … */
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0974:
0975:
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__Pyx_RefNannyDeclarations
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/* … */
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/* … */
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goto __pyx_L4_break;
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0987:
0988:
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/* … */
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0990:
0991: cdef:
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+1018: 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) {
int __pyx_v_i;
int __pyx_v_n;
int __pyx_v_cmp;
int __pyx_v_memory_offset;
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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse", 0);
/* … */
/* function exit code */
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1023:
1024: # reset context
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->chrom));
+1026: context.pos = 0
__pyx_v_context->pos = 0;
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__pyx_v_context->ref_len = 0;
1028:
1029: # check for EOF early - important to handle file with no final line terminator
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__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1031: context.state = VCFState.EOF
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goto __pyx_L0;
1033:
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__pyx_t_1 = ((__pyx_v_context->chrom.size == 0) != 0);
if (__pyx_t_1) {
/* … */
}
1037: # with gil:
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__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_empty_CHROM, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1038, __pyx_L1_error)
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_terminate((&__pyx_v_context->chrom));
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__pyx_t_1 = ((__pyx_v_context->state == __pyx_e_5allel_3opt_11io_vcf_read_CHROM) != 0);
if (__pyx_t_1) {
/* … */
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__pyx_t_1 = ((__pyx_v_context->temp.size == 0) != 0);
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/* … */
goto __pyx_L6;
}
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1049: else:
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__pyx_L6:;
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__pyx_t_1 = ((__pyx_v_context->state == __pyx_e_5allel_3opt_11io_vcf_read_POS) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_v_context->state = (__pyx_v_context->state + 1);
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__pyx_t_1 = ((__pyx_v_self->region_chrom != NULL) != 0);
if (__pyx_t_1) {
/* … */
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if (__pyx_t_1) {
/* … */
}
+1062: return vcf_skip_variant(stream, context)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_skip_variant(__pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1062, __pyx_L1_error)
__pyx_r = __pyx_t_2;
goto __pyx_L0;
1063:
+1064: if cmp > 0:
__pyx_t_1 = ((__pyx_v_cmp > 0) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_r = 0;
goto __pyx_L0;
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__pyx_t_3 = ((__pyx_v_self->region_begin > 0) != 0);
if (__pyx_t_3) {
} else {
__pyx_t_1 = __pyx_t_3;
goto __pyx_L12_bool_binop_done;
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__pyx_t_1 = __pyx_t_3;
__pyx_L12_bool_binop_done:;
if (__pyx_t_1) {
/* … */
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+1070: return vcf_skip_variant(stream, context)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_skip_variant(__pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1070, __pyx_L1_error)
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goto __pyx_L0;
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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);
}
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if (__pyx_t_3) {
/* … */
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
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goto __pyx_L0;
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__pyx_v_context->sample_index = 0;
+1079: context.sample_field_index = 0
__pyx_v_context->sample_field_index = 0;
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__pyx_v_context->sample_output_index = -1;
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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);
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__pyx_t_3 = (__pyx_v_self->store_chrom != 0);
if (__pyx_t_3) {
/* … */
}
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+1087: if self.dtype.kind == 'S':
__pyx_t_3 = ((__pyx_v_self->__pyx_base.dtype->kind == 'S') != 0);
if (__pyx_t_3) {
/* … */
goto __pyx_L16;
}
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__pyx_t_5 = __pyx_t_4;
}
__pyx_v_n = __pyx_t_5;
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__pyx_t_2 = __pyx_v_n;
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_2; __pyx_t_6+=1) {
__pyx_v_i = __pyx_t_6;
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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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1099: else:
1100: # with gil:
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__pyx_t_3 = (__pyx_v_self->store_pos != 0);
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/* … */
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1286:
1287:
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__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 1307, __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, 1307, __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, 1307, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1307, __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, 1307, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_v_dtype) < 0) __PYX_ERR(0, 1307, __pyx_L1_error) if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_number, __pyx_v_number) < 0) __PYX_ERR(0, 1307, __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, 1307, __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;
+1308: chunk_length=chunk_length)
if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_chunk_length, __pyx_v_chunk_length) < 0) __PYX_ERR(0, 1307, __pyx_L1_error)
+1309: 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, 1309, __pyx_L1_error) __pyx_v_self->store_alt = __pyx_t_1;
+1310: self.store_numalt = store_numalt
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_numalt); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1310, __pyx_L1_error) __pyx_v_self->store_numalt = __pyx_t_1;
+1311: self.store_svlen = store_svlen
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_svlen); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1311, __pyx_L1_error) __pyx_v_self->store_svlen = __pyx_t_1;
+1312: self.store_is_snp = store_is_snp
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_store_is_snp); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1312, __pyx_L1_error) __pyx_v_self->store_is_snp = __pyx_t_1;
1313:
+1314: 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) {
int __pyx_v_alt_index;
int __pyx_v_memory_offset;
int __pyx_v_memory_index;
int __pyx_v_chars_stored;
int __pyx_v_alt_len;
int __pyx_v_is_snp;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse", 0);
/* … */
/* function exit code */
__pyx_r = 0;
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:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
1315: cdef:
1316: # index of alt values
+1317: int alt_index = 0
__pyx_v_alt_index = 0;
1318: # index into memory view
1319: int memory_offset, memory_index
1320: # number of characters read into current value
+1321: int chars_stored = 0
__pyx_v_chars_stored = 0;
1322: # size of alt allel
+1323: int alt_len = 0
__pyx_v_alt_len = 0;
1324: # is the variant a SNP?
+1325: bint is_snp = context.ref_len == 1
__pyx_v_is_snp = (__pyx_v_context->ref_len == 1);
1326:
1327: # bail out early for missing value
+1328: if stream.c == PERIOD:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PERIOD) != 0);
if (__pyx_t_1) {
/* … */
}
1329: # treat period as missing value, regardless of what comes next
+1330: return 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 == -1)) __PYX_ERR(0, 1330, __pyx_L1_error)
__pyx_r = __pyx_t_2;
goto __pyx_L0;
1331:
1332: # bail out early for empty value
+1333: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1334: 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 == -1)) __PYX_ERR(0, 1334, __pyx_L1_error)
+1335: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1336: return 0
__pyx_r = 0;
goto __pyx_L0;
1337:
1338: # initialise memory offset and index
+1339: 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);
+1340: memory_index = memory_offset
__pyx_v_memory_index = __pyx_v_memory_offset;
1341:
+1342: while True:
while (1) {
1343:
+1344: if stream.c == 0:
__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1345: 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;
+1346: 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) {
/* … */
}
+1347: 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);
1348: alt_len - context.ref_len
+1349: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+1350: break
goto __pyx_L6_break;
1351:
+1352: 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) {
/* … */
}
+1353: 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;
+1354: 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_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) {
/* … */
}
+1355: 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);
1356: alt_len - context.ref_len
+1357: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+1358: break
goto __pyx_L6_break;
1359:
+1360: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1361: 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;
+1362: 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) {
/* … */
}
+1363: 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);
1364: alt_len - context.ref_len
+1365: 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 == -1)) __PYX_ERR(0, 1365, __pyx_L1_error)
+1366: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1367: break
goto __pyx_L6_break;
1368:
+1369: 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_L20;
}
+1370: 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_L26_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_len == 1) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L26_bool_binop_done:;
__pyx_v_is_snp = __pyx_t_1;
+1371: 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_L29_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_alt_index < __pyx_v_self->__pyx_base.number) != 0);
__pyx_t_1 = __pyx_t_3;
__pyx_L29_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1372: self.svlen_memory[context.chunk_variant_index, alt_index] = \
__pyx_t_10 = __pyx_v_context->chunk_variant_index;
__pyx_t_11 = __pyx_v_alt_index;
*((__pyx_t_5numpy_int32_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_self->svlen_memory.data + __pyx_t_10 * __pyx_v_self->svlen_memory.strides[0]) ) + __pyx_t_11 * __pyx_v_self->svlen_memory.strides[1]) )) = (__pyx_v_alt_len - __pyx_v_context->ref_len);
1373: alt_len - context.ref_len
1374: # advance value index
+1375: alt_index += 1
__pyx_v_alt_index = (__pyx_v_alt_index + 1);
1376: # reset alt_len
+1377: alt_len = 0
__pyx_v_alt_len = 0;
1378: # set memory index to beginning of next item
+1379: memory_index = memory_offset + (alt_index * self.itemsize)
__pyx_v_memory_index = (__pyx_v_memory_offset + (__pyx_v_alt_index * __pyx_v_self->__pyx_base.itemsize));
1380: # reset chars stored
+1381: chars_stored = 0
__pyx_v_chars_stored = 0;
1382:
1383: else:
+1384: 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_L32_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_L32_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1385: alt_len += 1
__pyx_v_alt_len = (__pyx_v_alt_len + 1);
+1386: if self.store_alt and chars_stored < self.itemsize 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_L35_bool_binop_done;
}
__pyx_t_3 = ((__pyx_v_chars_stored < __pyx_v_self->__pyx_base.itemsize) != 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);
__pyx_t_1 = __pyx_t_3;
__pyx_L35_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
}
__pyx_L20:;
1387: # store value
+1388: self.memory[memory_index] = stream.c
__pyx_t_12 = __pyx_v_stream->c;
__pyx_t_13 = __pyx_v_memory_index;
*((__pyx_t_5numpy_uint8_t *) ( /* dim=0 */ (__pyx_v_self->memory.data + __pyx_t_13 * __pyx_v_self->memory.strides[0]) )) = __pyx_t_12;
1389: # advance number of characters stored
+1390: chars_stored += 1
__pyx_v_chars_stored = (__pyx_v_chars_stored + 1);
1391: # advance memory index
+1392: memory_index += 1
__pyx_v_memory_index = (__pyx_v_memory_index + 1);
1393:
1394: # advance input stream
+1395: 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 == -1)) __PYX_ERR(0, 1395, __pyx_L1_error) } __pyx_L6_break:;
1396:
+1397: if self.store_numalt:
__pyx_t_1 = (__pyx_v_self->store_numalt != 0);
if (__pyx_t_1) {
/* … */
}
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+1483: return 0
__pyx_r = 0;
goto __pyx_L0;
1484:
1485: # setup temp
+1486: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
1487:
+1488: while True:
while (1) {
1489:
+1490: if stream.c == 0:
__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1491: 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;
+1492: 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) {
/* … */
}
+1493: 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);
1494: alt_len - context.ref_len
+1495: 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) {
/* … */
}
1496: # with gil:
+1497: 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, 1497, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6);
__pyx_t_6 = 0;
+1498: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1498, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1498, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1498, __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, 1498, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+1499: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+1500: break
goto __pyx_L6_break;
1501:
+1502: 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) {
/* … */
}
+1503: 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;
+1504: 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) {
/* … */
}
+1505: 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);
1506: alt_len - context.ref_len
+1507: 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) {
/* … */
}
1508: # with gil:
+1509: 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, 1509, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_8);
__pyx_t_8 = 0;
+1510: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1510, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1510, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1510, __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, 1510, __pyx_L1_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+1511: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+1512: break
goto __pyx_L6_break;
1513:
+1514: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1515: 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;
+1516: 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) {
/* … */
}
+1517: 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);
1518: alt_len - context.ref_len
+1519: 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) {
/* … */
}
1520: # with gil:
+1521: 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, 1521, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_6);
__pyx_t_6 = 0;
+1522: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1522, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1522, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1522, __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, 1522, __pyx_L1_error) __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+1523: 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 == -1)) __PYX_ERR(0, 1523, __pyx_L1_error)
+1524: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1525: break
goto __pyx_L6_break;
1526:
+1527: 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;
}
+1528: 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;
+1529: 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_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) {
/* … */
}
+1530: 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);
1531: alt_len - context.ref_len
+1532: 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_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) {
/* … */
}
1533: # with gil:
+1534: 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, 1534, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF_SET(__pyx_v_v, __pyx_t_8);
__pyx_t_8 = 0;
+1535: self.values[context.chunk_variant_index, alt_index] = v
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_context->chunk_variant_index); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 1535, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_alt_index); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 1535, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 1535, __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, 1535, __pyx_L1_error) __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
1536: # advance value index
+1537: alt_index += 1
__pyx_v_alt_index = (__pyx_v_alt_index + 1);
1538: # reset
+1539: CharVector_clear(&context.temp)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->temp));
+1540: alt_len = 0
__pyx_v_alt_len = 0;
1541:
1542: else:
+1543: 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) {
/* … */
}
+1544: alt_len += 1
__pyx_v_alt_len = (__pyx_v_alt_len + 1);
+1545: 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:;
+1546: CharVector_append(&context.temp, stream.c)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->temp), __pyx_v_stream->c);
1547:
1548: # advance input stream
+1549: 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 == -1)) __PYX_ERR(0, 1549, __pyx_L1_error) } __pyx_L6_break:;
1550:
+1551: if self.store_numalt:
__pyx_t_1 = (__pyx_v_self->store_numalt != 0);
if (__pyx_t_1) {
/* … */
}
+1552: 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);
+1553: if self.store_is_snp:
__pyx_t_1 = (__pyx_v_self->store_is_snp != 0);
if (__pyx_t_1) {
/* … */
}
+1554: self.is_snp_memory[context.chunk_variant_index] = is_snp
__pyx_t_16 = __pyx_v_context->chunk_variant_index;
*((__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;
1555:
+1556: 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) {
PyObject *__pyx_v_shape = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("malloc_chunk", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
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/* … */
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1700: cdef:
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_key));
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_val));
1839:
1840: # check for missing value
+1841: if stream.c == PERIOD:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_PERIOD) != 0);
if (__pyx_t_1) {
/* … */
}
1842: # treat leading period as missing, regardless of what comes next
+1843: return 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 == -1)) __PYX_ERR(0, 1843, __pyx_L1_error)
__pyx_r = __pyx_t_2;
goto __pyx_L0;
1844:
1845: # check for empty value
+1846: if stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
1847: # not strictly kosher, treat as missing/empty
+1848: 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 == -1)) __PYX_ERR(0, 1848, __pyx_L1_error)
+1849: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1850: return 0
__pyx_r = 0;
goto __pyx_L0;
1851:
+1852: while True:
while (1) {
1853:
+1854: if stream.c == 0:
__pyx_t_1 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_1) {
/* … */
}
+1855: if context.info_key.size > 0:
__pyx_t_1 = ((__pyx_v_context->info_key.size > 0) != 0);
if (__pyx_t_1) {
/* … */
}
1856: # handle flag
+1857: self.parse_info(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParser *)__pyx_v_self->__pyx_base.__pyx_vtab)->parse_info(__pyx_v_self, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1857, __pyx_L1_error)
+1858: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
+1859: break
goto __pyx_L6_break;
1860:
+1861: 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_L9_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_L9_bool_binop_done:;
if (__pyx_t_1) {
/* … */
}
+1862: if context.info_key.size > 0:
__pyx_t_1 = ((__pyx_v_context->info_key.size > 0) != 0);
if (__pyx_t_1) {
/* … */
}
1863: # handle flag
+1864: self.parse_info(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParser *)__pyx_v_self->__pyx_base.__pyx_vtab)->parse_info(__pyx_v_self, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1864, __pyx_L1_error)
+1865: context.state = VCFState.EOL
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
+1866: break
goto __pyx_L6_break;
1867:
+1868: elif stream.c == TAB:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_TAB) != 0);
if (__pyx_t_1) {
/* … */
}
+1869: if context.info_key.size > 0:
__pyx_t_1 = ((__pyx_v_context->info_key.size > 0) != 0);
if (__pyx_t_1) {
/* … */
}
1870: # handle flag
+1871: self.parse_info(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParser *)__pyx_v_self->__pyx_base.__pyx_vtab)->parse_info(__pyx_v_self, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1871, __pyx_L1_error)
1872: # advance input stream beyond tab
+1873: 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 == -1)) __PYX_ERR(0, 1873, __pyx_L1_error)
+1874: context.state += 1
__pyx_v_context->state = (__pyx_v_context->state + 1);
+1875: break
goto __pyx_L6_break;
1876:
+1877: elif stream.c == SEMICOLON:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_SEMICOLON) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L7;
}
+1878: if context.info_key.size > 0:
__pyx_t_1 = ((__pyx_v_context->info_key.size > 0) != 0);
if (__pyx_t_1) {
/* … */
}
1879: # handle flag
+1880: self.parse_info(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParser *)__pyx_v_self->__pyx_base.__pyx_vtab)->parse_info(__pyx_v_self, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1880, __pyx_L1_error)
+1881: 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 == -1)) __PYX_ERR(0, 1881, __pyx_L1_error)
1882:
+1883: elif stream.c == EQUALS:
__pyx_t_1 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_EQUALS) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L7;
}
1884: # advance input stream beyond '='
+1885: 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 == -1)) __PYX_ERR(0, 1885, __pyx_L1_error)
+1886: if context.info_key.size > 0:
__pyx_t_1 = ((__pyx_v_context->info_key.size > 0) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L14;
}
+1887: self.parse_info(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParser *)__pyx_v_self->__pyx_base.__pyx_vtab)->parse_info(__pyx_v_self, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1887, __pyx_L1_error)
1888: else:
1889: # with gil:
+1890: warn('missing INFO key', context)
/*else*/ {
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_missing_INFO_key, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1890, __pyx_L1_error)
+1891: self.skip_parser.parse(stream, context)
__pyx_t_2 = ((struct __pyx_vtabstruct_5allel_3opt_11io_vcf_read_VCFInfoParserBase *)__pyx_v_self->skip_parser->__pyx_vtab)->parse(__pyx_v_self->skip_parser, __pyx_v_stream, __pyx_v_context); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 1891, __pyx_L1_error)
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__pyx_L14:;
1892:
1893: else:
1894:
+1895: CharVector_append(&context.info_key, stream.c)
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_key), __pyx_v_stream->c);
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__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 == -1)) __PYX_ERR(0, 1896, __pyx_L1_error)
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__pyx_L7:;
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__pyx_L6_break:;
1897:
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__Pyx_RefNannyDeclarations
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goto __pyx_L0;
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__Pyx_AddTraceback("allel.opt.io_vcf_read.VCFInfoParser.parse_info", __pyx_clineno, __pyx_lineno, __pyx_filename);
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1899: InputStreamBase stream,
1900: VCFContext context) except -1: # nogil
1901:
1902: cdef:
1903: int parser_index
1904: PyObject* parser
1905:
1906: # terminate key
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_terminate((&__pyx_v_context->info_key));
1908:
1909: # search for index of current INFO key
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1911:
1912: # clear out key for good measure
+1913: CharVector_clear(&context.info_key)
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_clear((&__pyx_v_context->info_key));
1914:
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__pyx_t_1 = ((__pyx_v_parser_index >= 0) != 0);
if (__pyx_t_1) {
/* … */
goto __pyx_L3;
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1919: else:
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1921:
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static int __pyx_f_5allel_3opt_11io_vcf_read_13VCFInfoParser_malloc_chunk(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoParser *__pyx_v_self) {
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1923: cdef VCFInfoParserBase parser
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__PYX_ERR(0, 1924, __pyx_L1_error)
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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1926:
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1928: cdef VCFInfoParserBase parser
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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1931:
1932:
+1933: cdef class VCFInfoParserBase:
struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoParserBase {
PyObject_HEAD
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int (*make_chunk)(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFInfoParserBase *, PyObject *, struct __pyx_opt_args_5allel_3opt_11io_vcf_read_17VCFInfoParserBase_make_chunk *__pyx_optional_args);
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1934:
1935: cdef:
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static int __pyx_fuse_5__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_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) {
int __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_info_parse_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
static int __pyx_fuse_6__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_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) {
int __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_6vcf_info_parse_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
static int __pyx_fuse_7__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_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) {
int __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_info_parse_integer", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_parse_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
2319: VCFContext context,
2320: integer[:, :] memory) except -1: # nogil
2321: cdef:
+2322: int 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; /* … */ __pyx_v_value_index = 0;
2323:
2324: # reset temporary buffer
+2325: 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));
2326:
+2327: while True:
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
2328:
+2329: 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) {
/* … */
}
+2330: 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;
}
+2331: 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;
}
+2332: 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;
}
+2333: 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:;
+2334: 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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __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 == -1)) __PYX_ERR(0, 2334, __pyx_L1_error)
+2335: 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;
2336:
+2337: 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;
}
+2338: 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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __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 == -1)) __PYX_ERR(0, 2338, __pyx_L1_error)
+2339: 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));
+2340: 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);
2341:
2342: else:
+2343: CharVector_append(&context.info_val, stream.c)
/*else*/ {
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__pyx_L5:;
/* … */
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
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__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);
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__pyx_L5:;
/* … */
/*else*/ {
__pyx_f_5allel_3opt_11io_vcf_read_CharVector_append((&__pyx_v_context->info_val), __pyx_v_stream->c);
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__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:;
2344:
+2345: 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 == -1)) __PYX_ERR(0, 2345, __pyx_L1_error)
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__pyx_L4_break:;
/* … */
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__pyx_L4_break:;
/* … */
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__pyx_L4_break:;
/* … */
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__pyx_L4_break:;
/* … */
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__pyx_L4_break:;
/* … */
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__pyx_L4_break:;
/* … */
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__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 == -1)) __PYX_ERR(0, 2345, __pyx_L1_error)
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__pyx_L4_break:;
2346:
2347:
+2348: 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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_v_parsed;
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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_info_store_integer", 0);
/* … */
/* function exit code */
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__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_integer", __pyx_clineno, __pyx_lineno, __pyx_filename);
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __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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__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_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_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_2vcf_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_3__pyx_f_5allel_3opt_11io_vcf_read_vcf_info_store_integer(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_3vcf_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();
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_4vcf_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();
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __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();
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __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;
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__Pyx_RefNannyFinishContext();
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2349: int value_index,
2350: integer[:, :] memory) except -1: # nogil
2351: cdef:
2352: int parsed
2353: long value
2354:
+2355: 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) {
/* … */
}
2356: # more values than we have room for, ignore
+2357: 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;
2358:
2359: # parse string as integer
+2360: 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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __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 == -1)) __PYX_ERR(0, 2360, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
2361:
+2362: 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) {
/* … */
}
2363: # store value
+2364: 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;
2365:
2366:
+2367: 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) {
int __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_info_parse_floating", 0);
/* … */
/* function exit code */
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goto __pyx_L0;
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_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_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) {
int __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);
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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2368: VCFContext context,
2369: floating[:, :] memory) except -1: # nogil
2370: cdef:
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__pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0;
2372:
2373: # reset temporary buffer
+2374: 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));
2375:
+2376: while True:
while (1) {
/* … */
while (1) {
2377:
+2378: 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) {
/* … */
}
+2379: 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;
}
+2380: 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;
}
+2381: 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;
}
+2382: 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:;
+2383: 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 == -1)) __PYX_ERR(0, 2383, __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 == -1)) __PYX_ERR(0, 2383, __pyx_L1_error)
+2384: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
2385:
+2386: 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;
}
+2387: 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 == -1)) __PYX_ERR(0, 2387, __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 == -1)) __PYX_ERR(0, 2387, __pyx_L1_error)
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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));
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__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
2390:
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/*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);
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__pyx_L5:;
2393:
+2394: 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 == -1)) __PYX_ERR(0, 2394, __pyx_L1_error)
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__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 == -1)) __PYX_ERR(0, 2394, __pyx_L1_error)
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__pyx_L4_break:;
2395:
2396:
+2397: 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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_info_store_floating", 0);
/* … */
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__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
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int __pyx_v_parsed;
double __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_info_store_floating", 0);
/* … */
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goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_info_store_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
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2398: int value_index,
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+2404: if value_index >= memory.shape[1]:
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
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/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[1])) != 0);
if (__pyx_t_1) {
/* … */
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__pyx_r = 0;
goto __pyx_L0;
/* … */
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goto __pyx_L0;
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__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 == -1)) __PYX_ERR(0, 2409, __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 == -1)) __PYX_ERR(0, 2409, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
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/* … */
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/* … */
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if (__pyx_t_1) {
/* … */
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*((__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_5numpy_float64_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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2419:
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/* … */
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2421:
2422: cdef:
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2424: int n_formats
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/* Python wrapper */
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static int __pyx_pw_5allel_3opt_11io_vcf_read_15VCFFormatParser_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 2427, __pyx_L3_error)
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__Pyx_RefNannySetupContext("__cinit__", 0);
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__Pyx_XDECREF(__pyx_t_2);
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__pyx_t_2 = __pyx_v_self->format_keys; __Pyx_INCREF(__pyx_t_2); if (unlikely(__pyx_t_2 == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); __PYX_ERR(0, 2432, __pyx_L1_error) } __pyx_t_4 = PyTuple_GET_SIZE(__pyx_t_2); if (unlikely(__pyx_t_4 == -1)) __PYX_ERR(0, 2432, __pyx_L1_error) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_v_self->n_formats = __pyx_t_4;
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2434: # setup FORMAT keys as C strings for nogil searching
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__pyx_v_i = __pyx_t_6;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
__PYX_ERR(0, 2437, __pyx_L1_error)
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__pyx_t_7 = __Pyx_PyObject_AsString(PyTuple_GET_ITEM(__pyx_v_self->format_keys, __pyx_v_i)); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) __PYX_ERR(0, 2437, __pyx_L1_error)
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2438:
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/* … */
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/* … */
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/* Python wrapper */
static void __pyx_pw_5allel_3opt_11io_vcf_read_17VCFCallDataParser_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
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/* … */
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free(__pyx_v_self->parsers_cptr);
2656:
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__pyx_v_context->sample_index = 0;
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__pyx_v_context->sample_output_index = -1;
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__pyx_v_context->sample_field_index = 0;
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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);
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/* … */
goto __pyx_L3;
}
+2669: context.sample_output_index += 1
__pyx_v_context->sample_output_index = (__pyx_v_context->sample_output_index + 1);
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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;
+2673: 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 == -1)) __PYX_ERR(0, 2673, __pyx_L1_error)
}
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__pyx_L3:;
2674:
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while (1) {
2676:
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__pyx_t_2 = ((__pyx_v_context->sample_index >= __pyx_v_self->n_samples) != 0);
if (__pyx_t_2) {
/* … */
}
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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 == -1)) __PYX_ERR(0, 2679, __pyx_L1_error)
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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;
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__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 == -1)) __PYX_ERR(0, 2681, __pyx_L1_error)
}
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+2683: if stream.c == 0:
__pyx_t_2 = ((__pyx_v_stream->c == 0) != 0);
if (__pyx_t_2) {
/* … */
}
+2684: context.state = VCFState.EOF
__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOF;
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goto __pyx_L11_break;
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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_2 = __pyx_t_3;
goto __pyx_L19_bool_binop_done;
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__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) {
/* … */
}
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__pyx_v_context->state = __pyx_e_5allel_3opt_11io_vcf_read_EOL;
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goto __pyx_L11_break;
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+2691: 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;
}
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__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 == -1)) __PYX_ERR(0, 2692, __pyx_L1_error)
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__pyx_v_context->sample_index = (__pyx_v_context->sample_index + 1);
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__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;
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__pyx_v_context->sample_output_index = (__pyx_v_context->sample_output_index + 1);
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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;
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__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_LF) != 0);
if (__pyx_t_3) {
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__pyx_t_2 = __pyx_t_3;
goto __pyx_L24_bool_binop_done;
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__pyx_t_3 = ((__pyx_v_stream->c != __pyx_v_5allel_3opt_11io_vcf_read_CR) != 0);
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__pyx_t_2 = __pyx_t_3;
goto __pyx_L24_bool_binop_done;
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__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 == -1)) __PYX_ERR(0, 2700, __pyx_L1_error)
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__pyx_L21:;
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__pyx_t_2 = ((__pyx_v_stream->c == __pyx_v_5allel_3opt_11io_vcf_read_COLON) != 0);
if (__pyx_t_2) {
/* … */
goto __pyx_L18;
}
+2703: context.sample_field_index += 1
__pyx_v_context->sample_field_index = (__pyx_v_context->sample_field_index + 1);
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__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 == -1)) __PYX_ERR(0, 2704, __pyx_L1_error)
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+2706: 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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if (__pyx_t_2) {
/* … */
goto __pyx_L28;
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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;
}
+2967: 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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __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 == -1)) __PYX_ERR(0, 2967, __pyx_L1_error)
+2968: 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);
+2969: 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));
2970:
+2971: 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) {
/* … */
}
+2972: 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;
}
+2973: 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;
}
+2974: 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;
}
+2975: 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:;
+2976: 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 == -1)) __PYX_ERR(0, 2976, __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 == -1)) __PYX_ERR(0, 2976, __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 == -1)) __PYX_ERR(0, 2976, __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 == -1)) __PYX_ERR(0, 2976, __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 == -1)) __PYX_ERR(0, 2976, __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 == -1)) __PYX_ERR(0, 2976, __pyx_L1_error)
/* … */
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goto __pyx_L4_break;
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/* … */
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/* … */
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/* … */
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2978:
2979: else:
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2983:
2984:
+2985: 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, int __pyx_v_value_index) {
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2986: integer[:, :, :] memory,
2987: int value_index) except -1: # nogil
2988: cdef:
2989: int parsed
2990: long allele
2991:
+2992: 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) {
/* … */
}
2993: # more values than we've made room for, ignore
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__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;
2995:
2996: # attempt to parse allele
+2997: parsed = vcf_strtol(&context.temp, context, &allele)
__pyx_t_2 = __pyx_f_5allel_3opt_11io_vcf_read_vcf_strtol((&__pyx_v_context->temp), __pyx_v_context, (&__pyx_v_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __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_allele)); if (unlikely(__pyx_t_2 == -1)) __PYX_ERR(0, 2997, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
2998:
2999: # store value
+3000: 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) {
/* … */
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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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/* … */
__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) {
/* … */
}
+3001: memory[context.chunk_variant_index, context.sample_output_index, value_index] = allele
__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_allele;
/* … */
__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_allele;
/* … */
__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_allele;
/* … */
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__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_allele;
/* … */
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*((__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_allele;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
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*((__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_allele;
/* … */
__pyx_t_3 = __pyx_v_context->chunk_variant_index;
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*((__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_allele;
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3162:
3163:
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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_genotype_ac_parse", 0);
/* … */
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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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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_genotype_ac_parse", 0);
/* … */
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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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int __pyx_r;
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/* … */
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int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_genotype_ac_parse", 0);
/* … */
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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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3165: VCFContext context,
3166: integer[:, :, :] memory) except -1: # nogil
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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));
3169:
+3170: while True:
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
3171:
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__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;
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/* … */
__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;
}
+3173: 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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __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 == -1)) __PYX_ERR(0, 3173, __pyx_L1_error)
+3174: 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));
3175:
+3176: 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) {
/* … */
}
+3177: 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;
}
+3178: 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;
}
+3179: 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;
}
+3180: 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:;
+3181: 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 == -1)) __PYX_ERR(0, 3181, __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 == -1)) __PYX_ERR(0, 3181, __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 == -1)) __PYX_ERR(0, 3181, __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 == -1)) __PYX_ERR(0, 3181, __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 == -1)) __PYX_ERR(0, 3181, __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 == -1)) __PYX_ERR(0, 3181, __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 == -1)) __PYX_ERR(0, 3181, __pyx_L1_error)
/* … */
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+3182: 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;
3183:
3184: else:
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/*else*/ {
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__pyx_L5:;
3186:
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/* … */
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/* … */
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__pyx_L4_break:;
/* … */
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3188:
3189:
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3191: integer[:, :, :] memory) except -1: # nogil
3192: cdef:
3193: int parsed
3194: long allele
3195:
3196: # attempt to parse allele
+3197: parsed = vcf_strtol(&context.temp, context, &allele)
__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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __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 == -1)) __PYX_ERR(0, 3197, __pyx_L1_error) __pyx_v_parsed = __pyx_t_1;
3198:
3199: # 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;
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__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);
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__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
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__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) {
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__pyx_t_2 = __pyx_t_3;
goto __pyx_L4_bool_binop_done;
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/* … */
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/* … */
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goto __pyx_L4_bool_binop_done;
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/* … */
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*((__pyx_t_5numpy_int8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_4 * __pyx_v_memory.strides[0]) ) + __pyx_t_5 * __pyx_v_memory.strides[1]) ) + __pyx_t_6 * __pyx_v_memory.strides[2]) )) += 1;
/* … */
__pyx_t_4 = __pyx_v_context->chunk_variant_index;
__pyx_t_5 = __pyx_v_context->sample_output_index;
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*((__pyx_t_5numpy_int16_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_4 * __pyx_v_memory.strides[0]) ) + __pyx_t_5 * __pyx_v_memory.strides[1]) ) + __pyx_t_6 * __pyx_v_memory.strides[2]) )) += 1;
/* … */
__pyx_t_4 = __pyx_v_context->chunk_variant_index;
__pyx_t_5 = __pyx_v_context->sample_output_index;
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*((__pyx_t_5numpy_int32_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_4 * __pyx_v_memory.strides[0]) ) + __pyx_t_5 * __pyx_v_memory.strides[1]) ) + __pyx_t_6 * __pyx_v_memory.strides[2]) )) += 1;
/* … */
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/* … */
__pyx_t_4 = __pyx_v_context->chunk_variant_index;
__pyx_t_5 = __pyx_v_context->sample_output_index;
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*((__pyx_t_5numpy_uint8_t *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_memory.data + __pyx_t_4 * __pyx_v_memory.strides[0]) ) + __pyx_t_5 * __pyx_v_memory.strides[1]) ) + __pyx_t_6 * __pyx_v_memory.strides[2]) )) += 1;
/* … */
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3202:
3203:
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struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFCallDataParserBase __pyx_base;
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3392:
3393:
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int __pyx_v_value_index;
int __pyx_r;
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__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_calldata_parse_integer", 0);
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3395: VCFContext context,
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3397:
3398: 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;
3400:
3401: # reset temporary buffer
+3402: 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));
3403:
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while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
/* … */
while (1) {
3405:
+3406: 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;
}
+3407: 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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __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 == -1)) __PYX_ERR(0, 3407, __pyx_L1_error)
+3408: 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));
+3409: 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);
3410:
+3411: 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) {
/* … */
}
+3412: 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;
}
+3413: 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;
}
+3414: 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;
}
+3415: 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:;
+3416: 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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __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 == -1)) __PYX_ERR(0, 3416, __pyx_L1_error)
+3417: 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;
3418:
3419: else:
+3420: 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);
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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);
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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:;
3421:
+3422: 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 == -1)) __PYX_ERR(0, 3422, __pyx_L1_error)
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__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 == -1)) __PYX_ERR(0, 3422, __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 == -1)) __PYX_ERR(0, 3422, __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 == -1)) __PYX_ERR(0, 3422, __pyx_L1_error)
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__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 == -1)) __PYX_ERR(0, 3422, __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 == -1)) __PYX_ERR(0, 3422, __pyx_L1_error)
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__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 == -1)) __PYX_ERR(0, 3422, __pyx_L1_error)
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__pyx_L4_break:;
/* … */
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}
__pyx_L4_break:;
3423:
3424:
+3425: 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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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long __pyx_v_value;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_calldata_store_integer", 0);
/* … */
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long __pyx_v_value;
int __pyx_r;
__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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__pyx_L0:;
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_2vcf_calldata_store_integer", 0);
/* … */
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__pyx_L0:;
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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__Pyx_RefNannyDeclarations
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/* … */
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
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/* … */
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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_v_parsed;
long __pyx_v_value;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_5vcf_calldata_store_integer", 0);
/* … */
/* function exit code */
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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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__pyx_L0:;
__Pyx_RefNannyFinishContext();
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int __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_6vcf_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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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, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_v_parsed;
long __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_7vcf_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_L0:;
__Pyx_RefNannyFinishContext();
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3426: int value_index,
3427: integer[:, :, :] memory) except -1: # nogil
3428: cdef:
3429: int parsed
3430: long value
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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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/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
}
/* … */
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if (__pyx_t_1) {
/* … */
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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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/* … */
__pyx_t_1 = ((__pyx_v_value_index >= (__pyx_v_memory.shape[2])) != 0);
if (__pyx_t_1) {
/* … */
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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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/* … */
__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) {
/* … */
}
3433: # more values than we have room for, ignore
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__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;
3435:
+3436: 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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __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 == -1)) __PYX_ERR(0, 3436, __pyx_L1_error) __pyx_v_parsed = __pyx_t_2;
3437:
3438: # store value
+3439: 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) {
/* … */
}
+3440: 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;
3441:
3442:
+3443: 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) {
int __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_calldata_parse_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__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) {
int __pyx_v_value_index;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_1vcf_calldata_parse_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("allel.opt.io_vcf_read.vcf_calldata_parse_floating", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
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3444: VCFContext context,
3445: floating[:, :, :] memory) except -1: # nogil
3446:
3447: cdef:
+3448: int value_index = 0
__pyx_v_value_index = 0; /* … */ __pyx_v_value_index = 0;
3449:
3450: # reset temporary buffer
+3451: 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));
3452:
+3453: while True:
while (1) {
/* … */
while (1) {
3454:
+3455: 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;
}
+3456: 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 == -1)) __PYX_ERR(0, 3456, __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 == -1)) __PYX_ERR(0, 3456, __pyx_L1_error)
+3457: 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));
+3458: value_index += 1
__pyx_v_value_index = (__pyx_v_value_index + 1);
/* … */
__pyx_v_value_index = (__pyx_v_value_index + 1);
3459:
+3460: 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) {
/* … */
}
+3461: 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;
}
+3462: 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;
}
+3463: 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;
}
+3464: 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:;
+3465: 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 == -1)) __PYX_ERR(0, 3465, __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 == -1)) __PYX_ERR(0, 3465, __pyx_L1_error)
+3466: break
goto __pyx_L4_break;
/* … */
goto __pyx_L4_break;
3467:
3468: else:
+3469: 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:;
3470:
+3471: 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 == -1)) __PYX_ERR(0, 3471, __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 == -1)) __PYX_ERR(0, 3471, __pyx_L1_error)
}
__pyx_L4_break:;
3472:
3473:
+3474: cdef int vcf_calldata_store_floating(VCFContext context,
static int __pyx_fuse_0__pyx_f_5allel_3opt_11io_vcf_read_vcf_calldata_store_floating(struct __pyx_obj_5allel_3opt_11io_vcf_read_VCFContext *__pyx_v_context, int __pyx_v_value_index, __Pyx_memviewslice __pyx_v_memory) {
int __pyx_v_parsed;
double __pyx_v_value;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__pyx_fuse_0vcf_calldata_store_floating", 0);
/* … */
/* function exit code */
__pyx_r = 0;
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/* … */
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3675:
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__pyx_t_2 = ((__pyx_v_value->size == 1) != 0);
if (__pyx_t_2) {
} else {
__pyx_t_1 = __pyx_t_2;
goto __pyx_L5_bool_binop_done;
}
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__pyx_t_1 = __pyx_t_2;
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if (__pyx_t_1) {
/* … */
}
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goto __pyx_L0;
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__pyx_f_5allel_3opt_11io_vcf_read_CharVector_terminate(__pyx_v_value);
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(__pyx_v_d[0]) = strtod(__pyx_v_value->data, (&__pyx_v_str_end));
3685:
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3688:
3689: # check success
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if (__pyx_t_1) {
/* … */
}
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goto __pyx_L0;
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__pyx_t_1 = ((__pyx_v_parsed > 0) != 0);
if (__pyx_t_1) {
/* … */
}
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__pyx_r = __pyx_v_parsed;
goto __pyx_L0;
3697:
3698: else:
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/*else*/ {
__pyx_t_3 = __pyx_f_5allel_3opt_11io_vcf_read_warn(__pyx_kp_s_error_parsing_floating_point_val, __pyx_v_context); if (unlikely(__pyx_t_3 == -1)) __PYX_ERR(0, 3700, __pyx_L1_error)
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__pyx_r = 0;
goto __pyx_L0;
}
3702:
3703:
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3706:
3707:
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3709: 'CHROM',
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3711: 'ID',
3712: 'REF',
3713: 'ALT',
3714: 'QUAL',
3715: 'FILTER',
3716: 'INFO',
3717: 'FORMAT',
3718: 'CALLDATA',
3719: 'EOL',
3720: 'EOF'
3721: ]
3722:
3723:
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int __pyx_v_format_index;
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PyObject *__pyx_v_format = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("warn", 0);
__Pyx_INCREF(__pyx_v_message);
/* … */
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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_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_AddTraceback("allel.opt.io_vcf_read.warn", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__pyx_L0:;
__Pyx_XDECREF(__pyx_v_chrom);
__Pyx_XDECREF(__pyx_v_sample);
__Pyx_XDECREF(__pyx_v_format);
__Pyx_XDECREF(__pyx_v_message);
__Pyx_RefNannyFinishContext();
return __pyx_r;
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3725: cdef int format_index
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if (__pyx_t_3) {
/* … */
}
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__Pyx_GOTREF(__pyx_t_2);
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__pyx_t_4 = ((__pyx_v_context->state == __pyx_e_5allel_3opt_11io_vcf_read_CALLDATA) != 0);
if (__pyx_t_4) {
/* … */
}
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__pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_context->headers, __pyx_n_s_samples); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 3737, __pyx_L1_error)
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/* … */
goto __pyx_L7;
}
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__PYX_ERR(0, 3742, __pyx_L1_error)
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__Pyx_INCREF(__pyx_t_1);
__pyx_v_format = __pyx_t_1;
__pyx_t_1 = 0;
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3748:
3749:
3750: # import sys
3751: #
3752: #
3753: # cdef int debug(message, vars=None) except -1:
3754: # message = '[DEBUG] ' + str(message)
3755: # if vars:
3756: # message = message % vars
3757: # print(message, file=sys.stderr)
3758: # sys.stderr.flush()
3759:
3760:
3761: ##########################################################################################
3762: # EXPERIMENTAL support for multi-threaded parsing
3763: # N.B., this is not used for the moment, because use of object dtype for strings
3764: # requires GIL acquisition, and this may hurt performance in a single-threaded
3765: # context. I'm not completely certain that is the case, but I am out of time to
3766: # explore further.
3767:
3768:
3769: # import itertools
3770: # import time
3771: #
3772: #
3773: # cdef class VCFParallelParser:
3774: #
3775: # cdef:
3776: # FileInputStream stream
3777: # CharVectorInputStream buffer
3778: # VCFContext context
3779: # VCFParser parser
3780: # int chunk_length
3781: # int block_length
3782: # object pool
3783: # object result
3784: #
3785: # def __cinit__(self, stream, parser, chunk_length, block_length, pool, headers, fields):
3786: # self.buffer = CharVectorInputStream(2**14)
3787: # self.context = VCFContext(headers, fields)
3788: # self.stream = stream
3789: # self.parser = parser
3790: # self.chunk_length = chunk_length
3791: # self.block_length = block_length
3792: # self.pool = pool
3793: # self.result = None
3794: #
3795: # def read(self, n_lines):
3796: # self.buffer.clear()
3797: # n_lines_read = self.stream.read_lines_into(&(self.buffer.vector), n_lines)
3798: # self.buffer.advance()
3799: # return n_lines_read
3800: #
3801: # def parse_async(self, block_index, chunk_index):
3802: # self.result = self.pool.apply_async(self.parse, args=(block_index, chunk_index))
3803: #
3804: # def join(self):
3805: # if self.result is not None:
3806: # self.result.get()
3807: #
3808: # def parse(self, block_index, chunk_index):
3809: # before = time.time()
3810: # # set initial state
3811: # self.context.state = VCFState.CHROM
3812: # self.context.chunk_variant_index = block_index * self.block_length - 1
3813: # self.context.variant_index = (chunk_index * self.chunk_length +
3814: # self.context.chunk_variant_index)
3815: # # parse the block of data stored in the buffer
3816: # self.parser.parse(self.buffer, self.context)
3817: # after = time.time()
3818: #
3819: #
3820: # cdef class VCFParallelChunkIterator:
3821: #
3822: # cdef:
3823: # FileInputStream stream
3824: # VCFParser parser
3825: # object pool
3826: # int chunk_length
3827: # int block_length
3828: # int n_threads
3829: # int n_workers
3830: # int chunk_index
3831: # list workers
3832: #
3833: # def __cinit__(self,
3834: # FileInputStream stream,
3835: # int chunk_length, int block_length, int n_threads,
3836: # headers, fields, types, numbers, fills, region, loc_samples):
3837: #
3838: # fields = sorted(fields)
3839: # self.stream = stream
3840: # self.chunk_length = chunk_length
3841: # self.n_threads = n_threads
3842: # self.pool = ThreadPool(n_threads)
3843: # # allow one more worker than number of threads in pool to allow for sync
3844: # # reading of data in the main thread
3845: # self.n_workers = n_threads + 1
3846: # # only makes sense to have block length at most fraction chunk length if we want
3847: # # some parallelism
3848: # self.block_length = min(block_length, chunk_length//self.n_workers)
3849: # if self.block_length < 1:
3850: # self.block_length = 1
3851: # loc_samples = check_samples(loc_samples, headers)
3852: # self.parser = VCFParser(
3853: # fields=fields, types=types, numbers=numbers, chunk_length=chunk_length, loc_samples=loc_samples, fills=fills,
3854: # region=region
3855: # )
3856: # self.chunk_index = -1
3857: # self.workers = [VCFParallelParser(stream=stream, parser=self.parser, chunk_length=self.chunk_length,
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3859: # fields=fields)
3860: # for _ in range(self.n_workers)]
3861: #
3862: # def __iter__(self):
3863: # return self
3864: #
3865: # def __next__(self):
3866: # cdef:
3867: # int block_index = 0
3868: # int i = 0
3869: # int n_lines
3870: # int n_lines_read = 0
3871: # VCFParallelParser worker
3872: #
3873: # # increment the current chunk index
3874: # self.chunk_index += 1
3875: #
3876: # # allocate arrays for next chunk
3877: # self.parser.malloc_chunk()
3878: #
3879: # # cycle around the workers
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3893: #
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3908: #
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3912: #
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3915: #
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3918: # self.pool.close()
3919: # self.pool.join()
3920: # self.pool.terminate()
3921: # raise StopIteration
3922: #
3923: # else:
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3927:
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3931:
3932:
3933: # ANN field indices
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__pyx_e_5allel_3opt_11io_vcf_read_ANNOTATION_IMPACT = 2,
__pyx_e_5allel_3opt_11io_vcf_read_GENE_NAME = 3,
__pyx_e_5allel_3opt_11io_vcf_read_GENE_ID = 4,
__pyx_e_5allel_3opt_11io_vcf_read_FEATURE_TYPE = 5,
__pyx_e_5allel_3opt_11io_vcf_read_FEATURE_ID = 6,
__pyx_e_5allel_3opt_11io_vcf_read_TRANSCRIPT_BIOTYPE = 7,
__pyx_e_5allel_3opt_11io_vcf_read_RANK = 8,
__pyx_e_5allel_3opt_11io_vcf_read_HGVS_C = 9,
__pyx_e_5allel_3opt_11io_vcf_read_HGVS_P = 10,
__pyx_e_5allel_3opt_11io_vcf_read_CDNA = 11,
__pyx_e_5allel_3opt_11io_vcf_read_CDS = 12,
__pyx_e_5allel_3opt_11io_vcf_read_AA = 13,
__pyx_e_5allel_3opt_11io_vcf_read_DISTANCE = 14
};
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3936: ANNOTATION = 1,
3937: ANNOTATION_IMPACT = 2,
3938: GENE_NAME = 3,
3939: GENE_ID = 4,
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3941: FEATURE_ID = 6,
3942: TRANSCRIPT_BIOTYPE = 7,
3943: RANK = 8,
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3945: HGVS_P = 10,
3946: CDNA = 11,
3947: CDS = 12,
3948: AA = 13,
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3950:
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__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4170, __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_ascii); __Pyx_GIVEREF(__pyx_n_s_ascii); PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_n_s_ascii); __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyString_Type)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 4170, __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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__pyx_L16_bool_binop_done:;
if (__pyx_t_3) {
/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
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__pyx_t_3 = __pyx_t_11;
goto __pyx_L19_bool_binop_done;
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__pyx_L19_bool_binop_done:;
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
__PYX_ERR(0, 4184, __pyx_L1_error)
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PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
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PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_5);
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__pyx_t_12 = (__pyx_t_11 != 0);
if (__pyx_t_12) {
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__pyx_t_3 = __pyx_t_12;
goto __pyx_L22_bool_binop_done;
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__pyx_L22_bool_binop_done:;
if (__pyx_t_3) {
/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
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if (unlikely(PyObject_SetItem(__pyx_v_annotation_impact, __pyx_t_2, __pyx_t_1) < 0)) __PYX_ERR(0, 4186, __pyx_L1_error)
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__pyx_t_12 = (__pyx_v_gene_name != Py_None);
__pyx_t_11 = (__pyx_t_12 != 0);
if (__pyx_t_11) {
} else {
__pyx_t_3 = __pyx_t_11;
goto __pyx_L25_bool_binop_done;
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__pyx_t_11 = ((__pyx_v_n_vals > __pyx_e_5allel_3opt_11io_vcf_read_GENE_NAME) != 0);
__pyx_t_3 = __pyx_t_11;
__pyx_L25_bool_binop_done:;
if (__pyx_t_3) {
/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
__PYX_ERR(0, 4188, __pyx_L1_error)
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if (unlikely(PyObject_SetItem(__pyx_v_gene_name, __pyx_t_6, __pyx_t_2) < 0)) __PYX_ERR(0, 4188, __pyx_L1_error)
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goto __pyx_L28_bool_binop_done;
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__pyx_t_12 = ((__pyx_v_n_vals > __pyx_e_5allel_3opt_11io_vcf_read_GENE_ID) != 0);
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__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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if (unlikely(PyObject_SetItem(__pyx_v_gene_id, __pyx_t_1, __pyx_t_6) < 0)) __PYX_ERR(0, 4190, __pyx_L1_error)
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goto __pyx_L31_bool_binop_done;
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__pyx_t_11 = ((__pyx_v_n_vals > __pyx_e_5allel_3opt_11io_vcf_read_FEATURE_TYPE) != 0);
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/* … */
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
__PYX_ERR(0, 4192, __pyx_L1_error)
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goto __pyx_L34_bool_binop_done;
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/* … */
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goto __pyx_L37_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_L47_bool_binop_done;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
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/* … */
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