/dports/biology/bcftools/bcftools-1.14/plugins/ |
H A D | fill-from-fasta.c | 91 #define FLT_EXCLUDE 2 macro 113 filter_str = optarg; filter_logic |= FLT_EXCLUDE; break; in init() 127 …if ( filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) { fprintf(stderr,"Only one of -i or -e can be giv… in init()
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H A D | remove-overlaps.c | 42 #define FLT_EXCLUDE 2 macro 184 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 216 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in run()
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H A D | guess-ploidy.c | 41 #define FLT_EXCLUDE 2 macro 137 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in smpl_pass() 153 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in process_region_guess() 434 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 465 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of --include or --exclude c… in run()
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H A D | setGT.c | 38 #define FLT_EXCLUDE 2 macro 212 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in init() 463 if ( args->smpl_pass[i] && args->filter_logic==FLT_EXCLUDE ) continue; in process() 490 if ( pass_site && args->filter_logic==FLT_EXCLUDE ) in process()
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H A D | parental-origin.c | 47 #define FLT_EXCLUDE 2 macro 173 if ( args->filter_logic & FLT_EXCLUDE ) in process_record() 357 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run()
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H A D | prune.c | 50 #define FLT_EXCLUDE 2 macro 323 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 428 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in run()
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H A D | scatter.c | 36 #define FLT_EXCLUDE 2 macro 336 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 389 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given\n"… in run()
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/dports/biology/bio-mocha/bcftools-1.14/plugins/ |
H A D | fill-from-fasta.c | 91 #define FLT_EXCLUDE 2 macro 113 filter_str = optarg; filter_logic |= FLT_EXCLUDE; break; in init() 127 …if ( filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) { fprintf(stderr,"Only one of -i or -e can be giv… in init()
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H A D | remove-overlaps.c | 42 #define FLT_EXCLUDE 2 macro 184 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 216 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in run()
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H A D | guess-ploidy.c | 41 #define FLT_EXCLUDE 2 macro 137 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in smpl_pass() 153 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in process_region_guess() 434 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 465 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of --include or --exclude c… in run()
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H A D | setGT.c | 38 #define FLT_EXCLUDE 2 macro 212 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in init() 463 if ( args->smpl_pass[i] && args->filter_logic==FLT_EXCLUDE ) continue; in process() 490 if ( pass_site && args->filter_logic==FLT_EXCLUDE ) in process()
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H A D | parental-origin.c | 47 #define FLT_EXCLUDE 2 macro 173 if ( args->filter_logic & FLT_EXCLUDE ) in process_record() 357 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run()
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H A D | scatter.c | 36 #define FLT_EXCLUDE 2 macro 336 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 389 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given\n"… in run()
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H A D | prune.c | 50 #define FLT_EXCLUDE 2 macro 323 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in run() 428 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in run()
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | vcfview.c | 44 #define FLT_EXCLUDE 2 macro 446 if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled in subset_vcf() 460 if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased in subset_vcf() 660 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfview() 702 case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 704 case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 706 case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased in main_vcfview() 737 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcfview() 738 if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n"); in main_vcfview() 739 if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n"); in main_vcfview() [all …]
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H A D | vcffilter.c | 45 #define FLT_EXCLUDE 2 macro 358 if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return; in set_genotypes() 379 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in set_genotypes() 533 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcffilter() 562 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcffilter() 608 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in main_vcffilter()
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H A D | vcfquery.c | 44 #define FLT_EXCLUDE 2 macro 144 if ( args->filter_logic & FLT_EXCLUDE ) in query_vcf() 308 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfquery()
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | vcfview.c | 44 #define FLT_EXCLUDE 2 macro 446 if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled in subset_vcf() 460 if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased in subset_vcf() 660 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfview() 702 case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 704 case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 706 case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased in main_vcfview() 737 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcfview() 738 if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n"); in main_vcfview() 739 if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n"); in main_vcfview() [all …]
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H A D | vcffilter.c | 45 #define FLT_EXCLUDE 2 macro 358 if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return; in set_genotypes() 379 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in set_genotypes() 533 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcffilter() 562 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcffilter() 608 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in main_vcffilter()
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H A D | vcfquery.c | 44 #define FLT_EXCLUDE 2 macro 144 if ( args->filter_logic & FLT_EXCLUDE ) in query_vcf() 308 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfquery()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | vcfview.c | 44 #define FLT_EXCLUDE 2 macro 446 if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled in subset_vcf() 460 if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased in subset_vcf() 660 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfview() 702 case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 704 case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 706 case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased in main_vcfview() 737 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcfview() 738 if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n"); in main_vcfview() 739 if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n"); in main_vcfview() [all …]
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H A D | vcfview.c.pysam.c | 46 #define FLT_EXCLUDE 2 macro 448 if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled in subset_vcf() 462 if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased in subset_vcf() 662 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfview() 704 case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 706 case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break; in main_vcfview() 708 case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased in main_vcfview() 739 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcfview() 740 if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n"); in main_vcfview() 741 if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n"); in main_vcfview() [all …]
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H A D | vcffilter.c | 45 #define FLT_EXCLUDE 2 macro 358 if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return; in set_genotypes() 379 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in set_genotypes() 533 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcffilter() 562 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcffilter() 608 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in main_vcffilter()
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H A D | vcffilter.c.pysam.c | 47 #define FLT_EXCLUDE 2 macro 360 if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return; in set_genotypes() 381 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in set_genotypes() 535 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcffilter() 564 …if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n… in main_vcffilter() 610 if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1; in main_vcffilter()
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H A D | vcfquery.c | 44 #define FLT_EXCLUDE 2 macro 144 if ( args->filter_logic & FLT_EXCLUDE ) in query_vcf() 308 args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; in main_vcfquery()
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