Searched refs:subj_pos (Results 1 – 8 of 8) sorted by relevance
84 size_t subj_pos; variable93 this->subj_pos = 0; in STAln()99 this->subj_pos = s; in STAln()105 this->subj_pos = s; in STAln()
34 uint subj_pos; variable39 this->subj_pos = 0; in AlignRes()46 this->subj_pos = 0; in AlignRes()53 this->subj_pos = pos; in AlignRes()60 this->subj_pos = 0; in clear()331 … s_start = (alns.front().subj_pos >= (q_len * 2)) ? 1 + alns.front().subj_pos - (q_len * 2) : 1; in align_constrained()332 s_end = 1 + alns.front().subj_pos - 1; in align_constrained()350 for (uint j = alns[n].subj_pos + 1; j <= alns[n].subj_pos + alns[n].aln_len; j++) { in align_constrained()352 s = j - alns[n].subj_pos; in align_constrained()375 s_start = 1 + alns[n].subj_pos + alns[n].aln_len; in align_constrained()[all …]
1001 if (aln_res.subj_pos > 0) { in process()1318 aln_res.subj_pos = alns[0].subj_pos; in align_reads_to_contig()1346 if (a.subj_pos == b.subj_pos) in suffix_tree_hits_to_dag()1349 return a.subj_pos < b.subj_pos; in suffix_tree_hits_to_dag()1367 end_pos = alns[i].subj_pos + alns[i].aln_len - 1; in suffix_tree_hits_to_dag()1374 alns[j].subj_pos > alns[i].subj_pos && in suffix_tree_hits_to_dag()1375 alns[j].subj_pos > (uint) end_pos) { in suffix_tree_hits_to_dag()1378 gap_len = alns[j].subj_pos - end_pos - 1; in suffix_tree_hits_to_dag()1548 total_len += aln_res.subj_pos; in find_locus_overlap()1559 overlap += aln_res.subj_pos; in find_locus_overlap()[all …]
537 return a.subj_pos < b.subj_pos; in compare_staln()
320 int subj_pos = 0; in GetCDSNucleotideSequence() local338 …mRNA.append(subject_seq, subj_pos+chunk.second-(prod_pos_start - next_prod_start), prod_pos_start … in GetCDSNucleotideSequence()342 subj_pos += chunk.first; in GetCDSNucleotideSequence()
3693 ASSERT(subj_pos >= 0); in s_TrimChainStartToSubjPos()3694 if (!chain || subj_pos < 0) { in s_TrimChainStartToSubjPos()3700 while (h && h->hsp->subject.end < subj_pos) { in s_TrimChainStartToSubjPos()3715 if (h->hsp->subject.offset >= subj_pos) { in s_TrimChainStartToSubjPos()3721 num_left = subj_pos - hsp->subject.offset; in s_TrimChainStartToSubjPos()3761 ASSERT(subj_pos >= 0); in s_TrimChainEndToSubjPos()3762 if (!chain || subj_pos <= 0) { in s_TrimChainEndToSubjPos()3768 while (h->next && h->next->hsp->subject.end < subj_pos) { in s_TrimChainEndToSubjPos()3774 if (h->next->hsp->subject.offset < subj_pos) { in s_TrimChainEndToSubjPos()3788 if (h->hsp->subject.end <= subj_pos) { in s_TrimChainEndToSubjPos()[all …]
3987 ASSERT(subj_pos >= 0); in s_TrimChainStartToSubjPos()3988 if (!chain || subj_pos < 0) { in s_TrimChainStartToSubjPos()3997 while (h && h->hsp->subject.end < subj_pos) { in s_TrimChainStartToSubjPos()4012 if (h->hsp->subject.offset >= subj_pos) { in s_TrimChainStartToSubjPos()4018 num_left = subj_pos - hsp->subject.offset; in s_TrimChainStartToSubjPos()4061 ASSERT(subj_pos >= 0); in s_TrimChainEndToSubjPos()4062 if (!chain || subj_pos <= 0 || !query_blk || !query_info) { in s_TrimChainEndToSubjPos()4071 while (h->next && h->next->hsp->subject.end < subj_pos) { in s_TrimChainEndToSubjPos()4077 if (h->next->hsp->subject.offset < subj_pos) { in s_TrimChainEndToSubjPos()4091 if (h->hsp->subject.end <= subj_pos) { in s_TrimChainEndToSubjPos()[all …]