/dports/biology/bcftools/bcftools-1.14/plugins/ |
H A D | tag2tag.c | 129 …init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Desc… in init() 131 …init_header(out_hdr,drop_source_tag?"GL":NULL,BCF_HL_FMT,"##FORMAT=<ID=PL,Number=G,Type=Integer,De… in init() 133 …init_header(out_hdr,drop_source_tag?"PL":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Desc… in init() 137 …init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GT,Number=1,Type=String,Des… in init() 143 bcf_hdr_remove(out_hdr,BCF_HL_FMT,"QR"); in init() 144 bcf_hdr_remove(out_hdr,BCF_HL_FMT,"QA"); in init() 150 …d=bcf_hdr_id2int(in_hdr,BCF_DT_ID,src_tag))<0 || !bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,tag_id) ) in init() 152 if ( bcf_hdr_id2type(in_hdr,BCF_HL_FMT,tag_id) != src_type ) in init() 157 …d=bcf_hdr_id2int(in_hdr,BCF_DT_ID,src_tag))<0 || !bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,tag_id) ) in init() 159 if ( bcf_hdr_id2type(in_hdr,BCF_HL_FMT,tag_id) != src_type ) in init()
|
H A D | dosage.c | 254 if ( bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,id) ) in init() 256 pl_type = bcf_hdr_id2type(in_hdr,BCF_HL_FMT,id); in init() 269 if ( bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,id) ) in init() 271 gl_type = bcf_hdr_id2type(in_hdr,BCF_HL_FMT,id); in init()
|
H A D | parental-origin.c | 121 …=bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL"))<0 || !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) in init_data() 123 …=bcf_hdr_id2int(args->hdr, BCF_DT_ID, "AD"))<0 || !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) in init_data() 125 …=bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT"))<0 || !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) in init_data()
|
H A D | split.c | 409 if ( is_fmt && bcf_hdr_idinfo_exists(args->hdr_in,BCF_HL_FMT,id) ) in init_data() 429 if ( hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FMT ) continue; in init_data() 438 if ( hrec->type==BCF_HL_FMT && args->nfmt_tags ) in init_data()
|
/dports/biology/bio-mocha/bcftools-1.14/plugins/ |
H A D | tag2tag.c | 129 …init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Desc… in init() 131 …init_header(out_hdr,drop_source_tag?"GL":NULL,BCF_HL_FMT,"##FORMAT=<ID=PL,Number=G,Type=Integer,De… in init() 133 …init_header(out_hdr,drop_source_tag?"PL":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Desc… in init() 137 …init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GT,Number=1,Type=String,Des… in init() 143 bcf_hdr_remove(out_hdr,BCF_HL_FMT,"QR"); in init() 144 bcf_hdr_remove(out_hdr,BCF_HL_FMT,"QA"); in init() 150 …d=bcf_hdr_id2int(in_hdr,BCF_DT_ID,src_tag))<0 || !bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,tag_id) ) in init() 152 if ( bcf_hdr_id2type(in_hdr,BCF_HL_FMT,tag_id) != src_type ) in init() 157 …d=bcf_hdr_id2int(in_hdr,BCF_DT_ID,src_tag))<0 || !bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,tag_id) ) in init() 159 if ( bcf_hdr_id2type(in_hdr,BCF_HL_FMT,tag_id) != src_type ) in init()
|
H A D | score.c | 564 if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, gt_id)) use_tag = SCORE_GT; in run() 565 if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, ds_id)) use_tag = SCORE_DS; in run() 566 if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, hds_id)) use_tag = SCORE_HDS; in run() 567 …if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, ap1_id) && bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, ap2_i… in run() 569 if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, gp_id)) use_tag = SCORE_GP; in run() 574 if (!bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, gt_id)) in run() 578 if (!bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, ds_id)) in run() 582 if (!bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, hds_id)) in run() 586 …if (!bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, ap1_id) || !bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, ap2… in run() 590 if (!bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, gp_id)) in run() [all …]
|
H A D | mochatools.c | 362 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->gt_id)) args->gt_id = -1; in init() 365 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->ad_id)) args->ad_id = -1; in init() 366 if (args->ad_id >= 0 && bcf_hdr_id2type(args->in_hdr, BCF_HL_FMT, args->ad_id) != BCF_HT_INT) in init() 368 if (args->ad_id >= 0 && bcf_hdr_id2length(args->in_hdr, BCF_HL_FMT, args->ad_id) != BCF_VL_R) in init() 372 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->baf_id)) args->baf_id = -1; in init() 373 if (args->baf_id >= 0 && bcf_hdr_id2type(args->in_hdr, BCF_HL_FMT, args->baf_id) != BCF_HT_REAL) in init() 377 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->lrr_id)) args->lrr_id = -1; in init() 382 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->gt_id)) in init() 384 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->baf_id)) in init() 452 if (!bcf_hdr_idinfo_exists(args->in_hdr, BCF_HL_FMT, args->as_id)) in init() [all …]
|
H A D | dosage.c | 254 if ( bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,id) ) in init() 256 pl_type = bcf_hdr_id2type(in_hdr,BCF_HL_FMT,id); in init() 269 if ( bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,id) ) in init() 271 gl_type = bcf_hdr_id2type(in_hdr,BCF_HL_FMT,id); in init()
|
H A D | parental-origin.c | 121 …=bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL"))<0 || !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) in init_data() 123 …=bcf_hdr_id2int(args->hdr, BCF_DT_ID, "AD"))<0 || !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) in init_data() 125 …=bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT"))<0 || !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) in init_data()
|
/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | vcfannotate.c | 266 if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in remove_hdr_lines() 316 else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; } in init_remove_annots() 317 else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; } in init_remove_annots() 371 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 388 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 438 if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue; in init_remove_annots() 2352 if ( hrec->type!=BCF_HL_FMT) continue; in init_columns() 2383 col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); in init_columns() 2411 if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() 2432 switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() [all …]
|
H A D | mcall.c | 117 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 120 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 270 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) error("No such FORMAT tag \"%s\"\n", c… in init_sample_groups() 275 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 279 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 1235 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1238 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1386 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles() 1390 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles()
|
H A D | reheader.c | 515 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 523 …ec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->typ… in strip_header() 547 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 642 if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; in reheader_bcf()
|
/dports/biology/bcftools/bcftools-1.14/ |
H A D | vcfannotate.c | 266 if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in remove_hdr_lines() 316 else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; } in init_remove_annots() 317 else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; } in init_remove_annots() 371 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 388 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 438 if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue; in init_remove_annots() 2352 if ( hrec->type!=BCF_HL_FMT) continue; in init_columns() 2383 col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); in init_columns() 2411 if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() 2432 switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() [all …]
|
H A D | mcall.c | 117 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 120 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 270 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) error("No such FORMAT tag \"%s\"\n", c… in init_sample_groups() 275 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 279 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 1235 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1238 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1386 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles() 1390 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles()
|
H A D | reheader.c | 515 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 523 …ec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->typ… in strip_header() 547 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 642 if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; in reheader_bcf()
|
/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | vcfannotate.c | 266 if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in remove_hdr_lines() 316 else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; } in init_remove_annots() 317 else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; } in init_remove_annots() 371 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 388 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 438 if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue; in init_remove_annots() 2352 if ( hrec->type!=BCF_HL_FMT) continue; in init_columns() 2383 col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); in init_columns() 2411 if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() 2432 switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() [all …]
|
H A D | vcfannotate.c.pysam.c | 268 if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in remove_hdr_lines() 318 else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; } in init_remove_annots() 319 else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; } in init_remove_annots() 373 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 390 else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag; in init_remove_annots() 440 if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue; in init_remove_annots() 2354 if ( hrec->type!=BCF_HL_FMT) continue; in init_columns() 2385 col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id); in init_columns() 2413 if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() 2434 switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) ) in init_columns() [all …]
|
H A D | mcall.c | 117 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 120 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 270 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) error("No such FORMAT tag \"%s\"\n", c… in init_sample_groups() 275 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 279 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 1235 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1238 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1386 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles() 1390 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles()
|
H A D | mcall.c.pysam.c | 119 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 122 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call-… in mcall_init_trios() 272 …if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) error("No such FORMAT tag \"%s\"\n", c… in init_sample_groups() 277 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 281 …if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag =… in init_sample_groups() 1237 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1240 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_trim_and_update_numberR() 1388 int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles() 1392 int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id); in mcall_constrain_alleles()
|
H A D | reheader.c | 515 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 523 …ec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->typ… in strip_header() 547 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 642 if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; in reheader_bcf()
|
H A D | reheader.c.pysam.c | 517 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 525 …ec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->typ… in strip_header() 549 …ec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->typ… in strip_header() 644 if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; in reheader_bcf()
|
/dports/biology/vt/vt-0.57721/lib/htslib/ |
H A D | vcf.c | 450 else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT; in bcf_hdr_register_hrec() 498 if (hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT) { in bcf_hdr_register_hrec() 622 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 631 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 735 if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in bcf_hdr_remove() 1916 if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) { in vcf_parse_format() 1941 fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT]; in vcf_parse_format() 2783 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_combine() 2863 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_merge() 3408 if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,fmt_id) ) in bcf_update_format() [all …]
|
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
H A D | vcf.c | 450 else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT; in bcf_hdr_register_hrec() 498 if (hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT) { in bcf_hdr_register_hrec() 622 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 631 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 735 if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in bcf_hdr_remove() 1916 if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) { in vcf_parse_format() 1941 fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT]; in vcf_parse_format() 2783 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_combine() 2863 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_merge() 3408 if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,fmt_id) ) in bcf_update_format() [all …]
|
/dports/biology/stacks/stacks-2.4/htslib/ |
H A D | vcf.c | 450 else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT; in bcf_hdr_register_hrec() 498 if (hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT) { in bcf_hdr_register_hrec() 622 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 631 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 735 if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in bcf_hdr_remove() 1916 if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) { in vcf_parse_format() 1941 fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT]; in vcf_parse_format() 2783 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_combine() 2863 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_merge() 3394 if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,fmt_id) ) in bcf_update_format() [all …]
|
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
H A D | vcf.c | 455 else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT; in bcf_hdr_register_hrec() 615 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 624 … if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G ) in bcf_hdr_check_sanity() 709 if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in bcf_hdr_remove() 730 if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG ) in bcf_hdr_remove() 1919 if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) { in vcf_parse_format() 1944 fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT]; in vcf_parse_format() 2779 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_combine() 2857 else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT ) in bcf_hdr_merge() 3384 if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,fmt_id) ) in bcf_update_format() [all …]
|