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Searched refs:allele_index (Results 1 – 8 of 8) sorted by relevance

/dports/biology/stacks/stacks-2.4/src/
H A Dkmers.cc298 int allele_index = 0; in populate_kmer_hash() local
316 …allele_it = allele_map.insert(allele_it, make_pair(allele_index, make_pair(allele->first, tag->id)… in populate_kmer_hash()
324 map_it->second.push_back(allele_index); in populate_kmer_hash()
327 kmer_map[hash_key].push_back(allele_index); in populate_kmer_hash()
333 allele_index++; in populate_kmer_hash()
358 int allele_index = 0; in populate_kmer_hash() local
376 …allele_it = allele_map.insert(allele_it, make_pair(allele_index, make_pair(allele->first, tag->id)… in populate_kmer_hash()
384 map_it->second.push_back(allele_index); in populate_kmer_hash()
387 kmer_map[hash_key].push_back(allele_index); in populate_kmer_hash()
393 allele_index++; in populate_kmer_hash()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/cg-load/
H A Dfactory-evidence-dnbs.c214 m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, in CGEvidenceDnbs_Read()
252 rc = str2u16(b, p - b, &m->allele_index); in CGEvidenceDnbs_Read()
307 … m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, in CGEvidenceDnbs_Read()
316 … m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, in CGEvidenceDnbs_Read()
370 m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, in CGEvidenceDnbs25_Read()
408 rc = str2u16(b, p - b, &m->allele_index); in CGEvidenceDnbs25_Read()
490 … m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, in CGEvidenceDnbs25_Read()
499 … m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, in CGEvidenceDnbs25_Read()
H A Dwriter-evidence-dnbs.h54 uint16_t allele_index; member
H A Dwriter-evidence-dnbs.c187 uint16_t ai = cself->data.dnbs[i].allele_index; in CGWriterEvdDnbs_Write()
H A Dwriter-evidence-intervals.c237 if(self->data.allele_indexes_to_read_number[dnbs->dnbs[i].allele_index] > 0){ in CGWriterEvdInt_Write()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dsnp_annot_info.cpp219 TAlleleIndex allele_index = annot.x_GetAlleleIndex(qual_val); in ParseSeq_feat() local
220 if ( allele_index == kNo_AlleleIndex ) { in ParseSeq_feat()
223 m_AllelesIndices[alleles_count++] = allele_index; in ParseSeq_feat()
532 TAlleleIndex allele_index = m_AllelesIndices[i]; in x_UpdateSeq_featData() local
543 annot.x_GetAllele(allele_index)); in x_UpdateSeq_featData()
790 TAlleleIndex allele_index = m_AllelesIndices[count]; in GetLabel() local
791 if ( allele_index == kNo_AlleleIndex ) { in GetLabel()
796 const string& allele = annot.x_GetAllele(allele_index); in GetLabel()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dsnp_annot_info.cpp219 TAlleleIndex allele_index = annot.x_GetAlleleIndex(qual_val); in ParseSeq_feat() local
220 if ( allele_index == kNo_AlleleIndex ) { in ParseSeq_feat()
223 m_AllelesIndices[alleles_count++] = allele_index; in ParseSeq_feat()
532 TAlleleIndex allele_index = m_AllelesIndices[i]; in x_UpdateSeq_featData() local
543 annot.x_GetAllele(allele_index)); in x_UpdateSeq_featData()
790 TAlleleIndex allele_index = m_AllelesIndices[count]; in GetLabel() local
791 if ( allele_index == kNo_AlleleIndex ) { in GetLabel()
796 const string& allele = annot.x_GetAllele(allele_index); in GetLabel()
/dports/biology/vt/vt-0.57721/
H A Dhts_utils.cpp948 for (int32_t allele_index=0; allele_index <= max_allele_index; ++allele_index) in bcf_ip2g() local
950 int32_t i = choose(pth+allele_index-1, pth); in bcf_ip2g()
952 if (i>=leftover_genotype_index || allele_index==max_allele_index) in bcf_ip2g()
954 if (i>leftover_genotype_index) --allele_index; in bcf_ip2g()
955 leftover_genotype_index -= choose(pth+allele_index-1, pth); in bcf_ip2g()
957 max_allele_index = allele_index; in bcf_ip2g()
958 genotype[pth] = allele_index; in bcf_ip2g()