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Searched refs:cigar_len (Results 1 – 25 of 29) sorted by relevance

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/dports/biology/hisat2/hisat2-2.2.1/evaluation/tests/one_snp_test/
H A Dsimulate_one_snp_reads.py150 cigar_len, cigar_op = cigars[i]
152 partial_ref_seq = chr_seq[ref_pos:ref_pos+cigar_len]
164 ref_pos += cigar_len
165 read_pos += cigar_len
170 ann_read_rel += (["-"] * cigar_len)
171 ann_read_seq += (["-"] * cigar_len)
172 ref_pos += cigar_len
175 ann_ref_rel += (["-"] * cigar_len)
176 ann_ref_seq += (["-"] * cigar_len)
179 read_pos += cigar_len
[all …]
/dports/biology/iolib/io_lib-io_lib-1-14-10/progs/
H A Dscram_pileup.c136 if (p->cigar_len == 0) { in get_next_base()
151 p->pos += p->cigar_len; in get_next_base()
152 p->cigar_len = 0; in get_next_base()
163 p->cigar_len--; in get_next_base()
172 p->cigar_len = 0; in get_next_base()
184 if (p->cigar_len == 0) { in get_next_base()
208 p->cigar_len--; in get_next_base()
213 p->cigar_len = 0; in get_next_base()
298 if (p->cigar_len == 0) { in get_next_base()
315 *is_insert = p->cigar_len; in get_next_base()
[all …]
H A Dscram_pileup.h55 int cigar_len; // Remaining length of this cigar op member
/dports/biology/bioparser/bioparser-3.0.15/include/bioparser/
H A Dsam_parser.hpp40 std::uint32_t cigar_len = 0; in Parse() local
83 cigar_len = end_ptr - begin_ptr; in Parse()
122 cigar_len = this->RightStrip(cigar, cigar_len); in Parse()
131 if (q_name_len == 0 || t_name_len == 0 || cigar_len == 0 || in Parse()
143 cigar, cigar_len, in Parse()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/
H A Dcg_tools.h69 uint32_t cigar_len; member
127 rc_t discover_rna_splicing_candidates( uint32_t cigar_len, const char * cigar, uint32_t min_len, rn…
134 rc_t change_rna_splicing_cigar( uint32_t cigar_len, char * cigar, rna_splice_candidates * candidate…
135 rc_t cg_canonical_print_cigar( const char * cigar, size_t cigar_len);
H A Dmd_flag.c123 struct cigar_t * make_cigar_t( const char * cigar_str, const size_t cigar_len ) in make_cigar_t() argument
129 if ( cigar_str != NULL && cigar_str[ 0 ] != 0 && cigar_len > 0 ) in make_cigar_t()
130 size = cigar_len; in make_cigar_t()
252 const size_t cigar_len, in kout_md_tag_from_cigar_string() argument
259 struct cigar_t * cigar = make_cigar_t( cigar_str, cigar_len ); in kout_md_tag_from_cigar_string()
H A Dcg_tools.c505 output->cigar_len = j; in adjust_cigar()
520 output->cigar_len = input->p_cigar.len; in make_cg_cigar()
521 output->cigar[ output->cigar_len ] = 0; in make_cg_cigar()
524 output->p_cigar.len = output->cigar_len; in make_cg_cigar()
768 output->cigar_len = input->p_cigar.len; in merge_cg_cigar()
769 output->cigar[ output->cigar_len ] = 0; in merge_cg_cigar()
805 output->cigar_len = input->p_cigar.len; in make_cg_merge()
806 output->cigar[ output->cigar_len ] = 0; in make_cg_merge()
1625 candidates->cigops_len = ( cigar_len / 2 ) + 1; in discover_rna_splicing_candidates()
1695 if ( cigar_len > 0 ) in cg_canonical_print_cigar()
[all …]
H A Dmd_flag.h38 const size_t cigar_len,
H A Dsam-aligned.c878 size_t cigar_len, in modify_and_print_cigar() argument
885 if ( cigar_len > 0 ) in modify_and_print_cigar()
889 ExplodeCIGAR( al_cig, 1024, cigar, cigar_len ); in modify_and_print_cigar()
951 cgc_output->p_cigar.len = cgc_output->cigar_len; in cg_cigar_treatments()
969 cgc_output->p_cigar.len = cgc_output->cigar_len; in cg_cigar_treatments()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/test/
H A Dsamtools.cpp136 int cigar_len = bam->core.n_cigar; in bam_collect_func() local
138 if ( cigar_len && (cigar[0]&15) == 4 /* S */ ) { in bam_collect_func()
140 --cigar_len; in bam_collect_func()
143 if ( cigar_len && (cigar[cigar_len-1]&15) == 4 /* S */ ) { in bam_collect_func()
144 --cigar_len; in bam_collect_func()
146 aln.CIGAR.assign(cigar, cigar+cigar_len); in bam_collect_func()
/dports/biology/hisat2/hisat2-2.2.1/
H A Dhisat2_simulate_reads.py536 cur_trans_pos += cigar_len
577 cigar_len, cigar_op = cigars[i]
591 ref_pos += cigar_len
592 read_pos += cigar_len
597 ann_read_rel += (["-"] * cigar_len)
598 ann_read_seq += (["-"] * cigar_len)
599 ref_pos += cigar_len
602 ann_ref_rel += (["-"] * cigar_len)
603 ann_ref_seq += (["-"] * cigar_len)
606 read_pos += cigar_len
[all …]
/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/
H A Dbam.h91 uint32_t cigar_len:16, flag:16; member
241 #define bam_cigar_len(b) (((b)->flag & BAM_CIGAR32 ? ((b)->bin<<16) : 0) + (b)->cigar_len)
255 …(((b)->flag |= BAM_CIGAR32), (b)->bin = ((v)>>16), (b)->cigar_len = (v)&0xffff) : ((b)->cigar_len …
H A Dbam.c1231 int cigar_len; in sam_next_seq() local
1353 cigar_len = 0; in sam_next_seq()
1391 cigar_len++; in sam_next_seq()
1395 bam_set_cigar_len(bs, cigar_len); in sam_next_seq()
1714 bs->cigar_len = i32 & 0xffff; in bam_get_seq()
1722 int i, cigar_len = bam_cigar_len(bs); in bam_get_seq() local
1724 for (i = 0; i < cigar_len; i++) { in bam_get_seq()
1782 bs->cigar_len = i32 & 0xffff; in bam_get_seq()
1818 int i, cigar_len = bam_cigar_len(bs); in bam_get_seq() local
1820 for (i = 0; i < cigar_len; i++) { in bam_get_seq()
[all …]
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/align/
H A Dwriter-reference.h112 uint32_t cigar_len,
139 uint32_t cigar_len,
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/align/
H A Dwriter-reference.h112 uint32_t cigar_len,
139 uint32_t cigar_len,
/dports/biology/bioparser/bioparser-3.0.15/test/
H A Dsam_parser_test.cpp22 const char* cigar, std::uint32_t cigar_len, in SamOverlap()
32 cigar, cigar_len), in SamOverlap()
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/align/
H A Dwriter-reference.c2369 rc_t cigar2offset_2(unsigned const cigar_len, in cigar2offset_2() argument
2383 for (i = 0; i < cigar_len; ++i) { in cigar2offset_2()
2482 unsigned const cigar_len, in cigar_bin() argument
2489 for (i = 0; i < cigar_len; ++i) { in cigar_bin()
2509 ALIGN_C_DBGF(("'[%u]\n", cigar_len)); in cigar_bin()
2515 unsigned const cigar_len, in cigar_string() argument
2523 for (i = j = 0; j < cigar_len; ++j) { in cigar_string()
2602 unsigned const cigar_len, in cigar2offset() argument
2819 uint32_t cigar_len, in ReferenceMgr_Compress() argument
2858 const void* cigar, uint32_t cigar_len, in ReferenceSeq_Compress() argument
[all …]
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/align/
H A Dwriter-reference.c2369 rc_t cigar2offset_2(unsigned const cigar_len, in cigar2offset_2() argument
2383 for (i = 0; i < cigar_len; ++i) { in cigar2offset_2()
2482 unsigned const cigar_len, in cigar_bin() argument
2489 for (i = 0; i < cigar_len; ++i) { in cigar_bin()
2509 ALIGN_C_DBGF(("'[%u]\n", cigar_len)); in cigar_bin()
2515 unsigned const cigar_len, in cigar_string() argument
2523 for (i = j = 0; j < cigar_len; ++j) { in cigar_string()
2602 unsigned const cigar_len, in cigar2offset() argument
2819 uint32_t cigar_len, in ReferenceMgr_Compress() argument
2858 const void* cigar, uint32_t cigar_len, in ReferenceSeq_Compress() argument
[all …]
/dports/biology/subread/subread-2.0.2-source/src/longread-one/
H A DLRMfile-io.c533 int cigar_len = strlen(cigar); in LRMwrite_chunk_add_buffered_output() local
536 read_binlen = cigar_len+rname_len+2.5*iteration_context->read_length+500; in LRMwrite_chunk_add_buffered_output()
/dports/biology/subread/subread-2.0.2-source/src/
H A Dgene-algorithms.c662 int cigar_len = strlen(cigar); in compress_cigar() local
663 cigar_len = min(cigar_len, EXON_MAX_CIGAR_LEN); in compress_cigar()
664 cigar[cigar_len]=0; in compress_cigar()
678 for(i=0; i < cigar_len; i++) in compress_cigar()
H A Dcore.h640 int bincigar2cigar(char * cigar, int cigar_len, char * bincigar, int bincigar_max_len, int read_len…
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/axf/
H A Dcigar.c527 INSDC_coord_len *cigar_len = NULL; in cigar_impl_2() local
541 rslt->data->elem_bits = sizeof(cigar_len[0]) * 8; in cigar_impl_2()
548 cigar_len = rslt->data->base; in cigar_impl_2()
550 memset(cigar_len, 0, sizeof(cigar_len[0]) * nreads); in cigar_impl_2()
561 INSDC_coord_len *const count = (self->version & 0x04) ? cigar_len + n : &cnt; in cigar_impl_2()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/axf/
H A Dcigar.c527 INSDC_coord_len *cigar_len = NULL; in cigar_impl_2() local
541 rslt->data->elem_bits = sizeof(cigar_len[0]) * 8; in cigar_impl_2()
548 cigar_len = rslt->data->base; in cigar_impl_2()
550 memset(cigar_len, 0, sizeof(cigar_len[0]) * nreads); in cigar_impl_2()
561 INSDC_coord_len *const count = (self->version & 0x04) ? cigar_len + n : &cnt; in cigar_impl_2()
/dports/biology/hisat2/hisat2-2.2.1/evaluation/real/
H A Dcalculate_read_cost.py294 cigar_len = int(cigar[:-1])
297 pos += cigar_len
299 right = pos + cigar_len
/dports/biology/hisat2/hisat2-2.2.1/evaluation/simulation/
H A Dcalculate_read_cost.py562 cigar_len = int(cigar[:-1])
563 cigar_list.append([cigar_op, cigar_len])
603 cigar_len = int(cigar[:-1])
609 if cigar_len <= min_exon_len:

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