| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | vcfcall.c | 1114 bcf1_t *bcf_rec; in main_vcfcall() local
1115 while ( (bcf_rec = next_line(&args)) ) in main_vcfcall()
1128 for (i=1; i<bcf_rec->n_allele; i++) in main_vcfcall()
1131 if ( bcf_rec->d.allele[i][0]=='<' ) in main_vcfcall()
1137 int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0; in main_vcfcall()
1142 bcf_unpack(bcf_rec, BCF_UN_ALL); in main_vcfcall()
1148 qcall(&args.aux, bcf_rec); in main_vcfcall()
1154 tgt_flush(&args,bcf_rec); in main_vcfcall()
1162 ret = mcall(&args.aux, bcf_rec); in main_vcfcall()
1164 ret = ccall(&args.aux, bcf_rec); in main_vcfcall()
[all …]
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| H A D | mpileup.c | 97 bcf1_t *bcf_rec; member
567 bcf_clear1(conf->bcf_rec); in mpileup_reg()
568 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, in mpileup_reg()
570 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
582 bcf_clear1(conf->bcf_rec); in mpileup_reg()
583 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); in mpileup_reg()
584 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
887 conf->bcf_rec = bcf_init1(); in mpileup()
930 bcf_destroy1(conf->bcf_rec); in mpileup()
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | vcfcall.c | 1114 bcf1_t *bcf_rec; in main_vcfcall() local
1115 while ( (bcf_rec = next_line(&args)) ) in main_vcfcall()
1128 for (i=1; i<bcf_rec->n_allele; i++) in main_vcfcall()
1131 if ( bcf_rec->d.allele[i][0]=='<' ) in main_vcfcall()
1137 int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0; in main_vcfcall()
1142 bcf_unpack(bcf_rec, BCF_UN_ALL); in main_vcfcall()
1148 qcall(&args.aux, bcf_rec); in main_vcfcall()
1154 tgt_flush(&args,bcf_rec); in main_vcfcall()
1162 ret = mcall(&args.aux, bcf_rec); in main_vcfcall()
1164 ret = ccall(&args.aux, bcf_rec); in main_vcfcall()
[all …]
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| H A D | mpileup.c | 97 bcf1_t *bcf_rec; member
567 bcf_clear1(conf->bcf_rec); in mpileup_reg()
568 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, in mpileup_reg()
570 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
582 bcf_clear1(conf->bcf_rec); in mpileup_reg()
583 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); in mpileup_reg()
584 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
887 conf->bcf_rec = bcf_init1(); in mpileup()
930 bcf_destroy1(conf->bcf_rec); in mpileup()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | vcfcall.c | 1114 bcf1_t *bcf_rec; in main_vcfcall() local
1115 while ( (bcf_rec = next_line(&args)) ) in main_vcfcall()
1128 for (i=1; i<bcf_rec->n_allele; i++) in main_vcfcall()
1131 if ( bcf_rec->d.allele[i][0]=='<' ) in main_vcfcall()
1137 int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0; in main_vcfcall()
1142 bcf_unpack(bcf_rec, BCF_UN_ALL); in main_vcfcall()
1148 qcall(&args.aux, bcf_rec); in main_vcfcall()
1154 tgt_flush(&args,bcf_rec); in main_vcfcall()
1162 ret = mcall(&args.aux, bcf_rec); in main_vcfcall()
1164 ret = ccall(&args.aux, bcf_rec); in main_vcfcall()
[all …]
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| H A D | vcfcall.c.pysam.c | 1116 bcf1_t *bcf_rec; in main_vcfcall() local
1117 while ( (bcf_rec = next_line(&args)) ) in main_vcfcall()
1130 for (i=1; i<bcf_rec->n_allele; i++) in main_vcfcall()
1133 if ( bcf_rec->d.allele[i][0]=='<' ) in main_vcfcall()
1139 int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0; in main_vcfcall()
1144 bcf_unpack(bcf_rec, BCF_UN_ALL); in main_vcfcall()
1150 qcall(&args.aux, bcf_rec); in main_vcfcall()
1156 tgt_flush(&args,bcf_rec); in main_vcfcall()
1164 ret = mcall(&args.aux, bcf_rec); in main_vcfcall()
1166 ret = ccall(&args.aux, bcf_rec); in main_vcfcall()
[all …]
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| H A D | mpileup.c | 97 bcf1_t *bcf_rec; member
567 bcf_clear1(conf->bcf_rec); in mpileup_reg()
568 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, in mpileup_reg()
570 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
582 bcf_clear1(conf->bcf_rec); in mpileup_reg()
583 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); in mpileup_reg()
584 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
887 conf->bcf_rec = bcf_init1(); in mpileup()
930 bcf_destroy1(conf->bcf_rec); in mpileup()
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| H A D | mpileup.c.pysam.c | 99 bcf1_t *bcf_rec; member
569 bcf_clear1(conf->bcf_rec); in mpileup_reg()
570 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, in mpileup_reg()
572 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
584 bcf_clear1(conf->bcf_rec); in mpileup_reg()
585 bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); in mpileup_reg()
586 flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); in mpileup_reg()
889 conf->bcf_rec = bcf_init1(); in mpileup()
932 bcf_destroy1(conf->bcf_rec); in mpileup()
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_plcmd.c | 757 bcf1_t *bcf_rec = bcf_init1(); in mpileup() local
779 bcf_clear1(bcf_rec); in mpileup()
780 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0); in mpileup()
781 if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) { in mpileup()
793 bcf_clear1(bcf_rec); in mpileup()
794 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref); in mpileup()
795 if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) { in mpileup()
1049 bcf_destroy1(bcf_rec); in mpileup()
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| H A D | bam_plcmd.c.pysam.c | 759 bcf1_t *bcf_rec = bcf_init1(); in mpileup() local
781 bcf_clear1(bcf_rec); in mpileup()
782 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0); in mpileup()
783 if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) { in mpileup()
795 bcf_clear1(bcf_rec); in mpileup()
796 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref); in mpileup()
797 if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) { in mpileup()
1051 bcf_destroy1(bcf_rec); in mpileup()
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_plcmd.c | 757 bcf1_t *bcf_rec = bcf_init1(); in mpileup() local
779 bcf_clear1(bcf_rec); in mpileup()
780 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0); in mpileup()
781 if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) { in mpileup()
793 bcf_clear1(bcf_rec); in mpileup()
794 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref); in mpileup()
795 if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) { in mpileup()
1049 bcf_destroy1(bcf_rec); in mpileup()
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