| /dports/biology/vt/vt-0.57721/ |
| H A D | bcf_ordered_writer.cpp | 148 if (bcf_get_pos1(v)>=bcf_get_pos1(*i)) in write()
158 … int32_t cutoff_pos1 = std::max(bcf_get_pos1(buffer.front())-window,(hts_pos_t)1); in write()
159 if (bcf_get_pos1(v)<cutoff_pos1) in write()
167 bcf_get_pos1(v), in write()
169 bcf_get_pos1(buffer.front()), in write()
171 bcf_get_pos1(buffer.front())-bcf_get_pos1(v)+1); in write()
254 int32_t cutoff_pos1 = std::max(bcf_get_pos1(buffer.front())-window,(hts_pos_t)1); in flush()
258 if (bcf_get_pos1(buffer.back())<=cutoff_pos1) in flush()
|
| H A D | ordered_bcf_overlap_matcher.cpp | 113 overlaps = overlaps || (bcf_get_pos1(v)<=end1); in overlaps_with()
115 if (bcf_get_pos1(v)>end1) break; in overlaps_with()
133 overlaps = (bcf_get_pos1(*i)<=end1); in overlaps_with()
155 overlaps = overlaps || (bcf_get_pos1(v)<=end1); in overlaps_with()
157 if (bcf_get_pos1(v)>end1) break; in overlaps_with()
182 int32_t cbeg1 = bcf_get_pos1(*i); in overlaps_with()
236 int32_t cbeg1 = bcf_get_pos1(v); in overlaps_with()
295 int32_t cbeg1 = bcf_get_pos1(*i); in overlaps_with()
348 int32_t cbeg1 = bcf_get_pos1(v); in overlaps_with()
626 return (rid==bcf_get_rid(v) && beg1==bcf_get_pos1(v) && end1==bcf_get_end1(v)); in is_exact_match()
|
| H A D | bcf_synced_reader.cpp | 304 pq.push(new bcfptr(i, bcf_get_rid(v), bcf_get_pos1(v), hdrs[i], v, sync_by_pos)); in insert_into_pq()
505 int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front()); in fill_buffer()
532 pos1 = bcf_get_pos1(v); in fill_buffer()
535 if (bcf_get_pos1(v)!=pos1) in fill_buffer()
571 pos1 = bcf_get_pos1(v); in fill_buffer()
574 if (bcf_get_pos1(v)!=pos1) in fill_buffer()
584 int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front()); in fill_buffer()
610 pos1 = bcf_get_pos1(v); in fill_buffer()
613 if (bcf_get_rid(v)!=rid || bcf_get_pos1(v)!=pos1) in fill_buffer()
|
| H A D | candidate_region_extractor.cpp | 64 vntr.beg1 = bcf_get_pos1(v); in pick_candidate_region()
74 vntr.exact_beg1 = bcf_get_pos1(v); in pick_candidate_region()
84 vntr.fuzzy_beg1 = bcf_get_pos1(v); in pick_candidate_region()
144 int32_t pos1 = bcf_get_pos1(v); in is_homopolymer()
176 int32_t min_beg1 = bcf_get_pos1(v); in extract_regions_by_exact_alignment()
189 int32_t pos1 = bcf_get_pos1(v); in extract_regions_by_exact_alignment()
284 int32_t min_beg1 = bcf_get_pos1(v); in extract_regions_by_fuzzy_alignment()
292 int32_t pos1 = bcf_get_pos1(v); in extract_regions_by_fuzzy_alignment()
|
| H A D | variant.cpp | 38 pos1 = bcf_get_pos1(v); in Variant()
49 beg1 = bcf_get_pos1(v); in Variant()
50 end1 = bcf_get_pos1(v); in Variant()
54 beg1 = bcf_get_pos1(v); in Variant()
63 beg1 = bcf_get_pos1(v); in Variant()
69 beg1 = bcf_get_pos1(v); in Variant()
80 beg1 = bcf_get_pos1(v); in Variant()
215 pos1 = bcf_get_pos1(v); in classify()
654 kputw(bcf_get_pos1(v), &var); in get_variant_string()
|
| H A D | candidate_motif_picker.cpp | 66 uint32_t pos1 = bcf_get_pos1(v); in generate_candidate_motifs()
106 offset = bcf_get_pos1(v) - variant.vntr.exact_beg1; in generate_candidate_motifs()
119 std::cerr << "\tpos1 " << bcf_get_pos1(v) << "\n"; in generate_candidate_motifs()
|
| H A D | vntrize.cpp | 206 int32_t start1 = bcf_get_pos1(v); in vntrize()
236 bcf_set_pos1(v, bcf_get_pos1(overlap_vars[0])); in vntrize()
|
| H A D | sort.cpp | 37 return (bcf_get_pos1(u)-bcf_get_pos1(v)); in bcf_compare()
|
| H A D | consolidate.cpp | 489 bcf_set_pos1(v, bcf_get_pos1(vs[0])); in consolidate_multiallelic()
584 if (bcf_get_pos1(indel_vs[i])==flanks[0]) in consolidate_multiallelic()
592 uint32_t beg1 = bcf_get_pos1(indel_vs[i]); in consolidate_multiallelic()
726 bcf_set_pos1(v, bcf_get_pos1(vs[0])); in consolidate_multiallelic()
|
| H A D | complex_genotyping_record.cpp | 36 this->pos1 = bcf_get_pos1(v); in ComplexGenotypingRecord()
53 beg1 = bcf_get_pos1(v); in ComplexGenotypingRecord()
82 this->beg1 = bcf_get_pos1(v) - 3; in ComplexGenotypingRecord()
107 beg1 = bcf_get_pos1(v) - 1; in ComplexGenotypingRecord()
|
| H A D | vntr_annotator.cpp | 71 variant.pos1 = bcf_get_pos1(v); in annotate()
|
| H A D | indel_annotator.cpp | 71 variant.pos1 = bcf_get_pos1(v); in annotate()
|
| H A D | decompose_blocksub.cpp | 222 int32_t pos1 = bcf_get_pos1(v); in decompose_blocksub()
285 int32_t pos1 = bcf_get_pos1(v); in decompose_blocksub()
|
| H A D | fuzzy_partition.cpp | 260 kputw(bcf_get_pos1(v), var); in bcf_variant2string_with_motif()
306 int32_t beg1 = bcf_get_pos1(v); in fuzzy_partition()
|
| H A D | liftover.cpp | 236 int32_t start1 = bcf_get_pos1(v); in liftover()
|
| H A D | construct_probes.cpp | 151 …var_manip->generate_probes(bcf_get_chrom(odr->hdr, v), bcf_get_pos1(v), 1, alleles, probes, min_fl… in construct_probes()
|
| H A D | validate.cpp | 138 int32_t pos1 = bcf_get_pos1(v); in validate()
|
| H A D | filter_overlap.cpp | 141 int32_t beg1 = bcf_get_pos1(v); in filter_overlap()
|
| H A D | union_variants.cpp | 181 bcf_set_pos1(nv, bcf_get_pos1(v)); in union_variants()
|
| H A D | annotate_variants.cpp | 207 int32_t start1 = bcf_get_pos1(v); in annotate_variants()
|
| H A D | view.cpp | 199 int32_t start1 = bcf_get_pos1(v); in view()
|
| H A D | set_ref.cpp | 202 int32_t pos1 = bcf_get_pos1(v); in set_ref()
|
| H A D | vntr_genotyping_record.cpp | 37 this->pos1 = bcf_get_pos1(v); in VNTRGenotypingRecord()
52 beg1 = bcf_get_pos1(v); in VNTRGenotypingRecord()
|
| H A D | snp_genotyping_record.cpp | 43 this->pos1 = bcf_get_pos1(v); in SNPGenotypingRecord()
59 beg1 = bcf_get_pos1(v); in SNPGenotypingRecord()
|
| H A D | annotate_regions.cpp | 231 int32_t beg1 = bcf_get_pos1(v); in annotate_regions()
|