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Searched refs:m_aln (Results 1 – 4 of 4) sorted by relevance

/dports/biology/bwa/bwa-0.7.17/
H A Dbwtgap.c115 int max_entries = 0, j, _j, n_aln, m_aln; in bwt_match_gap() local
118 m_aln = 4; n_aln = 0; in bwt_match_gap()
119 aln = (bwt_aln1_t*)calloc(m_aln, sizeof(bwt_aln1_t)); in bwt_match_gap()
184 if (n_aln == m_aln) { in bwt_match_gap()
185 m_aln <<= 1; in bwt_match_gap()
186 aln = (bwt_aln1_t*)realloc(aln, m_aln * sizeof(bwt_aln1_t)); in bwt_match_gap()
187 memset(aln + m_aln/2, 0, m_aln/2*sizeof(bwt_aln1_t)); in bwt_match_gap()
H A Dbwase.c510 int i, n_seqs, m_aln; in bwa_sai2sam_se_core() local
527 m_aln = 0; in bwa_sai2sam_se_core()
547 if (n_aln > m_aln) { in bwa_sai2sam_se_core()
548 m_aln = n_aln; in bwa_sai2sam_se_core()
549 aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln); in bwa_sai2sam_se_core()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dfeature_generator.hpp160 const CSeq_align& m_aln; member
H A Dgene_model.cpp376 : m_aln(aln), m_scope(scope), m_genomic_row(-1) in SMapper()
423 if(m_aln.GetSegs().IsSpliced()) { in GetRnaLoc()
424 rna_loc = x_GetLocFromSplicedExons(m_aln); in GetRnaLoc()
426 const CSeq_id& id = m_aln.GetSeq_id(GetRnaRow()); in GetRnaLoc()
523 if(m_aln.GetSeqStart(0) > m_allowed_unaligned) { in x_GetLocFromSplicedExons()
530 if(m_aln.GetSeqStop(0) + 1 + m_allowed_unaligned < polya_pos) { in x_GetLocFromSplicedExons()
541 (new CSeq_loc_Mapper(m_aln, m_aln.GetSeq_id(m_genomic_row), in x_Mapper()