Fix a serious issue of generating best paired mapping results, especially when... (6cde47a1) · Commits · github_fork / Chromap

src/chromap.h

+1 −1

+6 −6

Original line number	Diff line number	Diff line
		@@ -334,13 +334,13 @@ int Index::GenerateCandidatePositions(
		}

		#ifdef LI_DEBUG
		for (uint32_t mi = 0; mi < positive_hits.size(); ++mi)
		printf("+ %llu %d %d\n", positive_hits[mi],
		(int)(positive_hits[mi] >> 32), (int)(positive_hits[mi]));
		for (uint32_t mi = 0; mi < mapping_metadata.positive_hits_.size(); ++mi)
		printf("+ %llu %d %d\n", mapping_metadata.positive_hits_[mi],
		(int)(mapping_metadata.positive_hits_[mi] >> 32), (int)(mapping_metadata.positive_hits_[mi]));

		for (uint32_t mi = 0; mi < negative_hits.size(); ++mi)
		printf("- %llu %d %d\n", negative_hits[mi],
		(int)(negative_hits[mi] >> 32), (int)(negative_hits[mi]));
		for (uint32_t mi = 0; mi < mapping_metadata.negative_hits_.size(); ++mi)
		printf("- %llu %d %d\n", mapping_metadata.negative_hits_[mi],
		(int)(mapping_metadata.negative_hits_[mi] >> 32), (int)(mapping_metadata.negative_hits_[mi]));
		#endif

		mapping_metadata.repetitive_seed_length_ =

+2 −2

Original line number	Diff line number	Diff line
		@@ -441,10 +441,10 @@ void MappingGenerator<MappingRecord>::
		((first_read_strand == kPositive &&
		mappings2[current_i2].position <=
		mappings1[i1].position + mapping_parameters_.max_insert_size -
		read2_length) \|\|
		read1_length) \|\|
		(first_read_strand == kNegative &&
		mappings2[current_i2].position <=
		mappings1[i1].position + read1_length - min_overlap_length))) {
		mappings1[i1].position + read2_length - min_overlap_length))) {
		#ifdef LI_DEBUG
		printf(
		"%s passed: %llu %d %d %llu %d %d: %d %d %d\n", __func__,