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Searched refs:FLT_EXCLUDE (Results 1 – 25 of 76) sorted by relevance

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/dports/biology/bcftools/bcftools-1.14/plugins/
H A Dfill-from-fasta.c91 #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()
H A Dremove-overlaps.c42 #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()
H A Dguess-ploidy.c41 #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()
H A DsetGT.c38 #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()
H A Dparental-origin.c47 #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()
H A Dprune.c50 #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()
H A Dscatter.c36 #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()
/dports/biology/bio-mocha/bcftools-1.14/plugins/
H A Dfill-from-fasta.c91 #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()
H A Dremove-overlaps.c42 #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()
H A Dguess-ploidy.c41 #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()
H A DsetGT.c38 #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()
H A Dparental-origin.c47 #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()
H A Dscatter.c36 #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()
H A Dprune.c50 #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()
/dports/biology/bio-mocha/bcftools-1.14/
H A Dvcfview.c44 #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 …]
H A Dvcffilter.c45 #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()
H A Dvcfquery.c44 #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()
/dports/biology/bcftools/bcftools-1.14/
H A Dvcfview.c44 #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 …]
H A Dvcffilter.c45 #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()
H A Dvcfquery.c44 #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()
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dvcfview.c44 #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 …]
H A Dvcfview.c.pysam.c46 #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 …]
H A Dvcffilter.c45 #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()
H A Dvcffilter.c.pysam.c47 #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()
H A Dvcfquery.c44 #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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