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Searched refs:BCF_HL_FMT (Results 1 – 25 of 101) sorted by relevance

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/dports/biology/bcftools/bcftools-1.14/plugins/
H A Dtag2tag.c129 …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 Ddosage.c254 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 Dparental-origin.c121 …=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 Dsplit.c409 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 Dtag2tag.c129 …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 Dscore.c564 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 Dmochatools.c362 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 Ddosage.c254 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 Dparental-origin.c121 …=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 Dvcfannotate.c266 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 Dmcall.c117 …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 Dreheader.c515 …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 Dvcfannotate.c266 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 Dmcall.c117 …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 Dreheader.c515 …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 Dvcfannotate.c266 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 Dvcfannotate.c.pysam.c268 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 Dmcall.c117 …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 Dmcall.c.pysam.c119 …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 Dreheader.c515 …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 Dreheader.c.pysam.c517 …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 Dvcf.c450 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 Dvcf.c450 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 Dvcf.c450 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 Dvcf.c455 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 …]

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