Break ties in bulk dedup only for single cell data (c9635713) · Commits · github_fork / Chromap

src/chromap.cc

+3 −3

Original line number	Diff line number	Diff line
		@@ -737,7 +737,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		MappingRecord &current_min_mapping = temp_mapping_file_handles_[min_handle_index].mappings[temp_mapping_file_handles_[min_handle_index].current_mapping_index];
		if (remove_pcr_duplicates_ && last_rid == min_rid && (current_min_mapping == last_mapping \|\| (remove_pcr_duplicates_at_bulk_level_ && current_min_mapping.HasSamePosition(last_mapping)))) {
		++dup_count;
		if (remove_pcr_duplicates_at_bulk_level_) {
		if (!is_bulk_data_ && remove_pcr_duplicates_at_bulk_level_) {
		if (!temp_dups_for_bulk_level_dedup.empty() && current_min_mapping == temp_dups_for_bulk_level_dedup.back()) {
		current_min_mapping.num_dups = temp_dups_for_bulk_level_dedup.back().num_dups + 1;
		temp_dups_for_bulk_level_dedup.back() = current_min_mapping;
		@@ -748,7 +748,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		}
		} else {
		if (dup_count > 0) {
		if (remove_pcr_duplicates_at_bulk_level_ && temp_dups_for_bulk_level_dedup.size() > 0) {
		if (!is_bulk_data_ && remove_pcr_duplicates_at_bulk_level_ && temp_dups_for_bulk_level_dedup.size() > 0) {
		// Find the best barcode, break ties first by the number of the barcodes in the dups, then by the barcode abundance
		last_mapping = temp_dups_for_bulk_level_dedup[0];
		khiter_t barcode_whitelist_lookup_table_iterator = kh_get(k32, barcode_whitelist_lookup_table_, last_mapping.GetBarcode());
		@@ -802,7 +802,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		}
		}
		if (last_mapping.mapq >= mapq_threshold_) {
		if (remove_pcr_duplicates_at_bulk_level_ && temp_dups_for_bulk_level_dedup.size() > 0) {
		if (!is_bulk_data_ && remove_pcr_duplicates_at_bulk_level_ && temp_dups_for_bulk_level_dedup.size() > 0) {
		// Find the best barcode, break ties first by the number of the barcodes in the dups, then by the barcode abundance
		last_mapping = temp_dups_for_bulk_level_dedup[0];
		khiter_t barcode_whitelist_lookup_table_iterator = kh_get(k32, barcode_whitelist_lookup_table_, last_mapping.GetBarcode());

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