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Searched refs:max_indel_depth (Results 1 – 15 of 15) sorted by relevance

/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dbam_plcmd.c84 int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth; member
121 int max_indel_depth; member
203 …pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth; in mpileup() local
316 max_indel_depth = conf->max_indel_depth * sm->n; in mpileup()
345 …if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp… in mpileup()
474 mplp.max_depth = 250; mplp.max_indel_depth = 250; in bam_mpileup()
497 mplp.max_indel_depth = settings->max_indel_depth; in bam_mpileup()
582 …stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth); in bam_mpileup()
/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/
H A Dbam_plcmd.c83 int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth; member
182 …pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth; in mpileup() local
290 max_indel_depth = conf->max_indel_depth * sm->n; in mpileup()
316 …if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp… in mpileup()
444 mplp.max_depth = 250; mplp.max_indel_depth = 250; in bam_mpileup()
481 case 'L': mplp.max_indel_depth = atoi(optarg); break; in bam_mpileup()
527 …stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth); in bam_mpileup()
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/variants/src/
H A DAssemblySamtoolsMpileup.h57 int max_indel_depth; variable
H A DAssemblySamtoolsMpileup.cpp275 << QString::number(max_indel_depth) in getMpiliupArgs()
H A DSamtoolMpileupWorker.cpp880 settings.max_indel_depth = getValue<int>(MAX_INDEL_DEPTH); in getSettings()
/dports/biology/bcftools/bcftools-1.14/
H A Dmpileup.c71 max_indel_depth, max_read_len, fmt_flag, ambig_reads; member
574 if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth in mpileup_reg()
886 conf->max_indel_depth = conf->max_indel_depth * nsmpl; in mpileup()
1157 … -L, --max-idepth INT Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth); in print_usage()
1203 mplp.max_depth = 250; mplp.max_indel_depth = 250; in main_mpileup()
1401 case 'L': mplp.max_indel_depth = atoi(optarg); break; in main_mpileup()
/dports/biology/bio-mocha/bcftools-1.14/
H A Dmpileup.c71 max_indel_depth, max_read_len, fmt_flag, ambig_reads; member
574 if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth in mpileup_reg()
886 conf->max_indel_depth = conf->max_indel_depth * nsmpl; in mpileup()
1157 … -L, --max-idepth INT Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth); in print_usage()
1203 mplp.max_depth = 250; mplp.max_indel_depth = 250; in main_mpileup()
1401 case 'L': mplp.max_indel_depth = atoi(optarg); break; in main_mpileup()
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dmpileup.c71 max_indel_depth, max_read_len, fmt_flag, ambig_reads; member
574 if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth in mpileup_reg()
886 conf->max_indel_depth = conf->max_indel_depth * nsmpl; in mpileup()
1157 … -L, --max-idepth INT Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth); in print_usage()
1203 mplp.max_depth = 250; mplp.max_indel_depth = 250; in main_mpileup()
1401 case 'L': mplp.max_indel_depth = atoi(optarg); break; in main_mpileup()
H A Dmpileup.c.pysam.c73 max_indel_depth, max_read_len, fmt_flag, ambig_reads; member
576 if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth in mpileup_reg()
888 conf->max_indel_depth = conf->max_indel_depth * nsmpl; in mpileup()
1159 … -L, --max-idepth INT Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth); in print_usage()
1205 mplp.max_depth = 250; mplp.max_indel_depth = 250; in main_mpileup()
1403 case 'L': mplp.max_indel_depth = atoi(optarg); break; in main_mpileup()
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_plcmd.c202 int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag, all, rev_del; member
481 int i, tid, *n_plp, tid0 = 0, max_depth, max_indel_depth; in mpileup() local
755 max_indel_depth = conf->max_indel_depth * sm->n; in mpileup()
787 …if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp… in mpileup()
1261 mplp.max_indel_depth = MPLP_MAX_INDEL_DEPTH; in bam_mpileup()
1429 case 'L': mplp.max_indel_depth = atoi(optarg); deprecated(c); break; in bam_mpileup()
H A Dbam_plcmd.c.pysam.c204 int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag, all, rev_del; member
483 int i, tid, *n_plp, tid0 = 0, max_depth, max_indel_depth; in mpileup() local
757 max_indel_depth = conf->max_indel_depth * sm->n; in mpileup()
789 …if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp… in mpileup()
1263 mplp.max_indel_depth = MPLP_MAX_INDEL_DEPTH; in bam_mpileup()
1431 case 'L': mplp.max_indel_depth = atoi(optarg); deprecated(c); break; in bam_mpileup()
/dports/biology/samtools/samtools-1.14/
H A Dbam_plcmd.c202 int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag, all, rev_del; member
481 int i, tid, *n_plp, tid0 = 0, max_depth, max_indel_depth; in mpileup() local
755 max_indel_depth = conf->max_indel_depth * sm->n; in mpileup()
787 …if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp… in mpileup()
1261 mplp.max_indel_depth = MPLP_MAX_INDEL_DEPTH; in bam_mpileup()
1429 case 'L': mplp.max_indel_depth = atoi(optarg); deprecated(c); break; in bam_mpileup()
/dports/biology/ugene/ugene-40.1/data/cmdline/
H A Dsnp.uwl137 call_variants.max_indel_depth {
382 call_variants.max_indel_depth {
/dports/biology/ugene/ugene-40.1/data/workflow_samples/NGS/
H A Dngs_variant_calling.uwl228 call_variants.max_indel_depth {
H A Dngs_variant_calling_full.uwl253 call_variants.max_indel_depth {