| /dports/biology/vcftools/vcftools-0.1.16/src/perl/ |
| H A D | VcfStats.pm | 204 my ($alleles,$seps,$is_phased,$is_empty) = $self->parse_haplotype($rec,$sample);
237 $key = $is_phased ? 'phased' : 'unphased';
323 my ($alleles,$seps,$is_phased,$is_empty) = $self->parse_haplotype($rec,$sample);
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| H A D | vcf-subset | 162 my ($alleles,$seps,$is_phased,$is_empty) = $vcf->parse_haplotype($x,$col);
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| H A D | Vcf.pm | 1582 my ($alleles,$seps,$is_phased,$is_empty) = $vcf->parse_haplotype($x,'NA00001');
1909 …Usage : my $x = $vcf->next_data_hash(); my ($alleles,$seps,$is_phased,$is_empty) = $vcf->parse_h…
1928 my $is_phased = 0;
1947 if ( $2 eq '|' ) { $is_phased=1; }
1951 $$rec{_cached_haplotypes}{$gtype} = [\@alleles,\@seps,$is_phased,$is_empty];
1957 …Usage : my ($alleles,$seps,$is_phased,$is_empty) = $vcf->parse_haplotype($x,'NA00001'); print $v…
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| H A D | vcf-query | 382 my ($alleles,$seps,$is_phased,$is_empty) = $vcf->parse_haplotype($x,$col);
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| H A D | vcf-merge | 477 … my ($alleles,$seps,$is_phased,$is_empty) = $vcf->parse_haplotype($line,$ori_name);
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| /dports/biology/plink/plink-ng-79b2df8c/2.0/ |
| H A D | plink2_import.cc | 1904 if (is_phased && (cur_geno == 1)) { in VcfConvertPhasedBiallelicLine()
2122 if (is_phased) { in VcfConvertPhasedMultiallelicLine()
2328 if (is_phased) { in VcfConvertPhasedMultiallelicLine()
10656 const uint32_t is_phased = probs_start[-2]; in Bgen13DosageOrPhaseScanThread() local
10657 if (unlikely(is_phased > 1)) { in Bgen13DosageOrPhaseScanThread()
10721 if (!is_phased) { in Bgen13DosageOrPhaseScanThread()
10812 if (!is_phased) { in Bgen13DosageOrPhaseScanThread()
11145 const uint32_t is_phased = probs_start[-2]; in Bgen13GenoToPgenThread() local
11146 if (unlikely(is_phased > 1)) { in Bgen13GenoToPgenThread()
11188 if (!is_phased) { in Bgen13GenoToPgenThread()
[all …]
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| H A D | plink2_export.cc | 8845 … const uintptr_t is_phased = (phasepresent_word | dphase_present_word) & lowbit; variable
8846 if ((!hds_force) && (!is_phased)) {
8852 if (is_phased) {
8914 … const uintptr_t is_phased = (phasepresent_word | dphase_present_word) & lowbit; variable
8915 if ((!hds_force) && (!is_phased)) {
8920 if (is_phased) {
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| /dports/biology/vt/vt-0.57721/lib/htslib/ |
| H A D | vcf.c | 2039 int32_t is_phased = 0, *x = (int32_t*)(z->buf + z->size * m); in vcf_parse_format() local
2041 if (*t == '.') ++t, x[l++] = is_phased; in vcf_parse_format()
2042 else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased; in vcf_parse_format()
2046 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
| H A D | vcf.c | 2039 int32_t is_phased = 0, *x = (int32_t*)(z->buf + z->size * m); in vcf_parse_format() local
2041 if (*t == '.') ++t, x[l++] = is_phased; in vcf_parse_format()
2042 else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased; in vcf_parse_format()
2046 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/stacks/stacks-2.4/htslib/ |
| H A D | vcf.c | 2039 int32_t is_phased = 0, *x = (int32_t*)(z->buf + z->size * m); in vcf_parse_format() local
2041 if (*t == '.') ++t, x[l++] = is_phased; in vcf_parse_format()
2042 else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased; in vcf_parse_format()
2046 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
| H A D | vcf.c | 2041 int32_t is_phased = 0, *x = (int32_t*)(z->buf + z->size * m); in vcf_parse_format() local
2043 if (*t == '.') ++t, x[l++] = is_phased; in vcf_parse_format()
2044 else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased; in vcf_parse_format()
2048 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | vcf.c | 2492 int32_t is_phased = 0; in vcf_parse_format() local
2499 ++t, x[l++] = is_phased; in vcf_parse_format()
2505 x[l++] = (val + 1) << 1 | is_phased; in vcf_parse_format()
2507 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
| H A D | vcf.c | 2448 int32_t is_phased = 0; in vcf_parse_format() local
2455 ++t, x[l++] = is_phased; in vcf_parse_format()
2461 x[l++] = (val + 1) << 1 | is_phased; in vcf_parse_format()
2463 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | vcf.c | 2492 int32_t is_phased = 0; in vcf_parse_format() local
2499 ++t, x[l++] = is_phased; in vcf_parse_format()
2505 x[l++] = (val + 1) << 1 | is_phased; in vcf_parse_format()
2507 is_phased = (*t == '|'); in vcf_parse_format()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | vcfannotate.c | 1937 int i = 0, is_phased = 0; in vcf_setter_format_str() local
1955 if ( *end=='|' ) is_phased = 1; in vcf_setter_format_str()
1961 dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]); in vcf_setter_format_str()
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | vcfannotate.c | 1937 int i = 0, is_phased = 0; in vcf_setter_format_str() local
1955 if ( *end=='|' ) is_phased = 1; in vcf_setter_format_str()
1961 dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]); in vcf_setter_format_str()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | vcfannotate.c | 1937 int i = 0, is_phased = 0; in vcf_setter_format_str() local
1955 if ( *end=='|' ) is_phased = 1; in vcf_setter_format_str()
1961 dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]); in vcf_setter_format_str()
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| H A D | vcfannotate.c.pysam.c | 1939 int i = 0, is_phased = 0; in vcf_setter_format_str() local
1957 if ( *end=='|' ) is_phased = 1; in vcf_setter_format_str()
1963 dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]); in vcf_setter_format_str()
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