Fix a bug of adjusting read end for pairs format (075caeb8) · Commits · github_fork / Chromap

src/chromap.cc

+5 −12

Original line number	Diff line number	Diff line
		@@ -1329,19 +1329,10 @@ void Chromap<MappingRecord>::GenerateBestMappingsForPairedEndReadOnOneDirection(
		#endif

		if (split_alignment_) {
		// For split alignment, selecting the pairs whose both single-end are the best.
		if (min_num_errors1 + min_num_errors2 < *min_sum_errors) {
		*num_best_mappings = 0;
		*min_sum_errors = min_num_errors1 + min_num_errors2;
		*second_min_sum_errors = min_num_errors1 + min_num_errors2 + 1;
		best_mappings->clear();
		} else if (min_num_errors1 + min_num_errors2 > *min_sum_errors) {
		return;
		}
		if (mappings1.size() == 0 \|\| mappings2.size() == 0) {
		return;
		}

		// For split alignment, selecting the pairs whose both single-end are the best.
		for (i1 = 0; i1 < mappings1.size(); ++i1) {
		if (mappings1[i1].first != min_num_errors1) {
		continue;
		@@ -1351,6 +1342,8 @@ void Chromap<MappingRecord>::GenerateBestMappingsForPairedEndReadOnOneDirection(
		continue;
		}
		best_mappings->emplace_back(i1, i2);
		*min_sum_errors = min_num_errors1 + min_num_errors2;
		*second_min_sum_errors = min_num_errors1 + min_num_errors2 + 1;
		(*num_best_mappings)++;
		}
		}
		@@ -2079,12 +2072,12 @@ void Chromap<MappingRecord>::GetRefStartEndPositionForReadFromMapping(Direction
		verification_window_start_position + mapping_start_position,
		verification_window_start_position + mapping_end_position - 1, n_cigar, cigar);
		// The returned position is right-closed, so need to plus one to match bed convention
		mapping_end_position = new_ref_end_position + 1 - verification_window_start_position;
		mapping_end_position = new_ref_end_position + 1 - verification_window_start_position - read_start_site;
		read_length = split_site - gap_beginning;
		}
		GenerateMDTag(reference.GetSequenceAt(rid), read + read_start_site, verification_window_start_position + read_start_site + mapping_start_position, n_cigar, cigar, *NM, MD_tag);
		*ref_start_position = verification_window_start_position + read_start_site + mapping_start_position;
		*ref_end_position = verification_window_start_position + mapping_end_position - 1;
		*ref_end_position = verification_window_start_position + read_start_site + mapping_end_position - 1;
		} else {
		//int n_cigar = 0;
		//uint32_t *cigar;

src/output_tools.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -326,7 +326,7 @@ struct PairsMapping {
		uint16_t mapq:8, is_unique:1, num_dups:7;

		bool operator<(const PairsMapping& m) const {
		return std::tie(rid1, rid2, pos1, pos2, mapq) < std::tie(m.rid1, m.rid2, m.pos1, m.pos2, mapq);
		return std::tie(rid1, pos1, rid2, pos2, mapq) < std::tie(m.rid1, m.pos1, m.rid2, m.pos2, mapq);
		}
		bool operator==(const PairsMapping& m) const {
		return std::tie(rid1, pos1, rid2, pos2) == std::tie(m.rid1, m.pos1, m.rid2, m.pos2);

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