/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
H A D | bam_plcmd.c | 84 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()
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/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
H A D | bam_plcmd.c | 83 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()
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/variants/src/ |
H A D | AssemblySamtoolsMpileup.h | 57 int max_indel_depth; variable
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H A D | AssemblySamtoolsMpileup.cpp | 275 << QString::number(max_indel_depth) in getMpiliupArgs()
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H A D | SamtoolMpileupWorker.cpp | 880 settings.max_indel_depth = getValue<int>(MAX_INDEL_DEPTH); in getSettings()
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | mpileup.c | 71 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()
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | mpileup.c | 71 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()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | mpileup.c | 71 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()
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H A D | mpileup.c.pysam.c | 73 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()
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_plcmd.c | 202 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()
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H A D | bam_plcmd.c.pysam.c | 204 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()
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam_plcmd.c | 202 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()
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/dports/biology/ugene/ugene-40.1/data/cmdline/ |
H A D | snp.uwl | 137 call_variants.max_indel_depth { 382 call_variants.max_indel_depth {
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/dports/biology/ugene/ugene-40.1/data/workflow_samples/NGS/ |
H A D | ngs_variant_calling.uwl | 228 call_variants.max_indel_depth {
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H A D | ngs_variant_calling_full.uwl | 253 call_variants.max_indel_depth {
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