Fix an issue of keeping wrong mapq read during deduplication (8a275c17) · Commits · github_fork / Chromap

src/mapping_processor.h

+6 −4

Original line number	Diff line number	Diff line
		@@ -118,23 +118,25 @@ void MappingProcessor<MappingRecord>::RemovePCRDuplicate(
		for (uint32_t ri = 0; ri < num_reference_sequences; ++ri) {
		deduped_mappings.push_back(std::vector<MappingRecord>());
		if (mappings[ri].size() != 0) {
		// Ideally I should output the last of the dups of first mappings.
		deduped_mappings[ri].emplace_back(mappings[ri].front());
		// Haowen: Ideally I should output the last of the dups of first mappings.
		// Li: The mappings' mapq are sorted in increasing order, so we should put the last
		// map
		auto last_it = mappings[ri].begin();
		uint32_t last_dup_count = 1;

		for (auto it = ++(mappings[ri].begin()); it != mappings[ri].end(); ++it) {
		if (!((it) == (last_it))) {
		deduped_mappings[ri].emplace_back((*last_it));
		deduped_mappings[ri].back().num_dups_ = std::min(
		(uint32_t)std::numeric_limits<uint8_t>::max(), last_dup_count);
		last_dup_count = 1;
		deduped_mappings[ri].emplace_back((*it));
		last_it = it;
		} else {
		++last_dup_count;
		}
		last_it = it;
		}

		deduped_mappings[ri].emplace_back((*last_it));
		deduped_mappings[ri].back().num_dups_ = std::min(
		(uint32_t)std::numeric_limits<uint8_t>::max(), last_dup_count);
		num_mappings += deduped_mappings[ri].size();

+4 −1

Original line number	Diff line number	Diff line
		@@ -251,7 +251,6 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(
		const bool current_mapping_is_duplicated =
		last_rid == min_rid && (current_mapping_is_duplicated_at_cell_level \|\|
		current_mapping_is_duplicated_at_bulk_level);

		if (mapping_parameters_.remove_pcr_duplicates &&
		current_mapping_is_duplicated) {
		++num_last_mapping_dups;
		@@ -266,6 +265,9 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(
		temp_dups_for_bulk_level_dedup.back().num_dups_ = 1;
		}
		}
		if (current_min_mapping.mapq_ > last_mapping.mapq_) {
		last_mapping = current_min_mapping ;
		}
		} else {
		if (!is_first_iteration) {
		if (deduplicate_at_bulk_level_for_single_cell_data) {
		@@ -283,6 +285,7 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(
		if (mapping_parameters_.Tn5_shift) {
		last_mapping.Tn5Shift();
		}

		AppendMapping(last_rid, reference, last_mapping);
		++num_mappings_passing_filters;
		if (!mapping_parameters_.summary_metadata_file_path.empty())