Searched refs:aln_res (Results 1 – 4 of 4) sorted by relevance
991 AlignRes aln_res; in process() local1041 << '\t' << aln_res.subj_pos + 1 << ':' << aln_res.cigar in process()1070 << '\t' << aln_res.subj_pos + 1 << ':' << aln_res.cigar in process()1317 aln_res.cigar = c; in align_reads_to_contig()1329 aln_res = g_aln->result(); in align_reads_to_contig()1332 if (aln_res.pct_id < min_aln_cov) in align_reads_to_contig()1448 AlignRes aln_res; in find_locus_overlap() local1504 aln_res.pct_id = 1; in find_locus_overlap()1559 overlap += aln_res.subj_pos; in find_locus_overlap()1787 AlignRes aln_res; in assemble_locus_contig() local[all …]
798 AlignRes aln_res; in search_for_gaps() local937 aln_res = aln->result(); in search_for_gaps()944 if (aln_res.cigar.find('D') != string::npos) in search_for_gaps()951 if (aln_res.gap_cnt <= (max_gaps + 1) && in search_for_gaps()952 aln_res.pct_id >= min_match_len && in search_for_gaps()955 query_hits[query_allele][cat_allele] = aln_res; in search_for_gaps()1011 AlignRes aln_res; in verify_gapped_match() local
265 AlignRes& aln_res,271 …bool align_reads_to_contig(SuffixTree *st, GappedAln *g_aln, DNASeq4 &query, AlignRes &aln_res) co…
797 AlignRes aln_res; in search_for_gaps() local919 aln_res = aln->result(); in search_for_gaps()925 if (aln_res.gap_cnt <= (max_gaps + 1)) { in search_for_gaps()929 if (aln_res.pct_id >= min_match_len) { in search_for_gaps()932 … tag_1->add_match(tag_2->id, cat_hit.first, allele->first, d, invert_cigar(aln_res.cigar)); in search_for_gaps()