Fix an issue of retaining chimeric fragment when the read lengths are different. (60fbe5f7) · Commits · github_fork / Chromap

src/index.cc

+9 −9

Original line number	Diff line number	Diff line
		@@ -432,13 +432,13 @@ int Index::CollectSeedHits(int max_seed_frequency,
		}

		#ifdef LI_DEBUG
		for (uint32_t mi = 0; mi < positive_hits->size(); ++mi)
		printf("+ %llu %d %d\n", positive_hits->at(mi),
		(int)(positive_hits->at(mi) >> 32), (int)(positive_hits->at(mi)));
		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 < negative_hits->size(); ++mi)
		printf("- %llu %d %d\n", negative_hits->at(mi),
		(int)(negative_hits->at(mi) >> 32), (int)(negative_hits->at(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]));
		#endif

		return repetitive_seed_count;
		@@ -622,10 +622,10 @@ int Index::CollectSeedHitsFromRepetitiveReadWithMateInfo(
		std::sort(hits.begin(), hits.end());

		#ifdef LI_DEBUG
		for (uint32_t i = 0; i < hits->size(); ++i)
		printf("%s: %d %d\n", __func__, (int)(hits->at(i) >> 32), (int)hits->at(i));
		for (uint32_t i = 0; i < hits.size(); ++i)
		printf("%s: %d %d\n", __func__, (int)(hits[i] >> 32), (int)hits[i]);
		std::cerr << "Rescue gen on one dir\n ";
		printf("%s: %d\n", __func__, hits->size());
		printf("%s: %d\n", __func__, hits.size());
		#endif

		return max_minimizer_count;

src/mapping_generator.h

+8 −7

Original line number	Diff line number	Diff line
		@@ -380,7 +380,7 @@ void MappingGenerator<MappingRecord>::
		printf("mappings1 %d %d:%d\n", i,
		(int)(mappings1[i].GetReferenceSequenceIndex()),
		(int)mappings1[i].GetReferenceSequencePosition());
		for (int i = 0; i < mappings1.size(); ++i)
		for (int i = 0; i < mappings2.size(); ++i)
		printf("mappings2 %d %d:%d\n", i,
		(int)(mappings2[i].GetReferenceSequenceIndex()),
		(int)mappings2[i].GetReferenceSequencePosition());
		@@ -418,17 +418,17 @@ void MappingGenerator<MappingRecord>::
		if ((first_read_strand == kNegative &&
		mappings1[i1].position > mappings2[i2].position +
		mapping_parameters_.max_insert_size -
		read1_length) \|\|
		read2_length) \|\|
		(first_read_strand == kPositive &&
		mappings1[i1].position >
		mappings2[i2].position + read2_length - min_overlap_length)) {
		mappings2[i2].position + read1_length - min_overlap_length)) {
		++i2;
		} else if ((first_read_strand == kPositive &&
		mappings2[i2].position >
		mappings1[i1].position +
		mapping_parameters_.max_insert_size - read2_length) \|\|
		mapping_parameters_.max_insert_size - read1_length) \|\|
		(first_read_strand == kNegative &&
		mappings2[i2].position > mappings1[i1].position + read1_length -
		mappings2[i2].position > mappings1[i1].position + read2_length -
		min_overlap_length)) {
		++i1;
		} else {
		@@ -447,11 +447,13 @@ void MappingGenerator<MappingRecord>::
		mappings1[i1].position + read1_length - min_overlap_length))) {
		#ifdef LI_DEBUG
		printf(
		"%s passed: %llu %d %llu %d: %d %d %d\n", __func__,
		"%s passed: %llu %d %d %llu %d %d: %d %d %d\n", __func__,
		mappings1[i1].GetReferenceSequenceIndex(),
		int(mappings1[i1].GetReferenceSequencePosition()),
		first_read_strand,
		mappings2[current_i2].GetReferenceSequenceIndex(),
		int(mappings2[current_i2].GetReferenceSequencePosition()),
		second_read_strand,
		mappings1[i1].GetNumErrors() + mappings2[current_i2].GetNumErrors(),
		mappings1[i1].GetNumErrors(), mappings2[current_i2].GetNumErrors());
		#endif
		@@ -594,7 +596,6 @@ void MappingGenerator<MappingRecord>::
		GetRefStartEndPositionForReadFromMapping(
		mappings2[i2], reference,
		paired_end_mapping_in_memory.mapping_in_memory2);

		uint8_t mapq1 = 0;
		uint8_t mapq2 = 0;
		const uint8_t mapq = GetMAPQForPairedEndRead(

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