| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/variants/src/ |
| H A D | AssemblySamtoolsMpileup.h | 45 bool use_orphan; variable
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| H A D | AssemblySamtoolsMpileup.cpp | 282 if (use_orphan) { in getMpiliupArgs()
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| H A D | SamtoolMpileupWorker.cpp | 868 settings.use_orphan = getValue<bool>(USE_ORPHAN); in getSettings()
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | bam_plcmd.c | 467 int nfiles = 0, use_orphan = 0; in bam_mpileup() local
485 use_orphan = settings->b_use_orphan; in bam_mpileup()
550 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in bam_mpileup()
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| /dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
| H A D | bam_plcmd.c | 437 int nfiles = 0, use_orphan = 0; in bam_mpileup() local
478 case 'A': use_orphan = 1; break; in bam_mpileup()
495 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in bam_mpileup()
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| /dports/biology/ugene/ugene-40.1/data/cmdline/ |
| H A D | snp.uwl | 233 call_variants.use_orphan {
351 call_variants.use_orphan {
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| /dports/biology/ugene/ugene-40.1/data/workflow_samples/NGS/ |
| H A D | ngs_variant_calling.uwl | 197 call_variants.use_orphan {
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| H A D | ngs_variant_calling_full.uwl | 222 call_variants.use_orphan {
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | mpileup.c | 1196 int nfiles = 0, use_orphan = 0, noref = 0; in main_mpileup() local
1398 case 'A': use_orphan = 1; break; in main_mpileup()
1482 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in main_mpileup()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | mpileup.c | 1196 int nfiles = 0, use_orphan = 0, noref = 0; in main_mpileup() local
1398 case 'A': use_orphan = 1; break; in main_mpileup()
1482 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in main_mpileup()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | mpileup.c | 1196 int nfiles = 0, use_orphan = 0, noref = 0; in main_mpileup() local
1398 case 'A': use_orphan = 1; break; in main_mpileup()
1482 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in main_mpileup()
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| H A D | mpileup.c.pysam.c | 1198 int nfiles = 0, use_orphan = 0, noref = 0; in main_mpileup() local
1400 case 'A': use_orphan = 1; break; in main_mpileup()
1484 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in main_mpileup()
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_plcmd.c | 1255 int nfiles = 0, use_orphan = 0, has_index_file = 0; in bam_mpileup() local
1426 case 'A': use_orphan = 1; break; in bam_mpileup()
1462 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in bam_mpileup()
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| H A D | bam_plcmd.c.pysam.c | 1257 int nfiles = 0, use_orphan = 0, has_index_file = 0; in bam_mpileup() local
1428 case 'A': use_orphan = 1; break; in bam_mpileup()
1464 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in bam_mpileup()
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_plcmd.c | 1255 int nfiles = 0, use_orphan = 0, has_index_file = 0; in bam_mpileup() local
1426 case 'A': use_orphan = 1; break; in bam_mpileup()
1462 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; in bam_mpileup()
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