Fix a bug in bulk dedup (0999cc45) · Commits · github_fork / Chromap

src/chromap.cc

+8 −5

Original line number	Diff line number	Diff line
		@@ -691,7 +691,8 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		++dup_count;
		if (remove_pcr_duplicates_at_bulk_level_) {
		if (!temp_dups_for_bulk_level_dedup.empty() && current_min_mapping == temp_dups_for_bulk_level_dedup.back()) {
		temp_dups_for_bulk_level_dedup.back().num_dups += 1;
		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;
		} else {
		temp_dups_for_bulk_level_dedup.push_back(current_min_mapping);
		temp_dups_for_bulk_level_dedup.back().num_dups = 1;
		@@ -703,12 +704,13 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		// 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());
		double min_mapping_barcode_abundance = kh_value(barcode_whitelist_lookup_table_, barcode_whitelist_lookup_table_iterator) / (double)num_sample_barcodes_;
		double last_mapping_barcode_abundance = kh_value(barcode_whitelist_lookup_table_, barcode_whitelist_lookup_table_iterator) / (double)num_sample_barcodes_;
		for (uint32_t bulk_dup_i = 1; bulk_dup_i < temp_dups_for_bulk_level_dedup.size(); ++bulk_dup_i) {
		barcode_whitelist_lookup_table_iterator = kh_get(k32, barcode_whitelist_lookup_table_, temp_dups_for_bulk_level_dedup[bulk_dup_i].GetBarcode());
		double current_mapping_barcode_abundance = kh_value(barcode_whitelist_lookup_table_, barcode_whitelist_lookup_table_iterator) / (double)num_sample_barcodes_;
		if (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups > last_mapping.num_dups \|\| (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups == last_mapping.num_dups && current_mapping_barcode_abundance > min_mapping_barcode_abundance)) {
		if (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups > last_mapping.num_dups \|\| (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups == last_mapping.num_dups && current_mapping_barcode_abundance > last_mapping_barcode_abundance)) {
		last_mapping = temp_dups_for_bulk_level_dedup[bulk_dup_i];
		last_mapping_barcode_abundance = current_mapping_barcode_abundance;
		}
		}
		temp_dups_for_bulk_level_dedup.clear();
		@@ -752,12 +754,13 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(uint32_t num_mappings_in_
		// 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());
		double min_mapping_barcode_abundance = kh_value(barcode_whitelist_lookup_table_, barcode_whitelist_lookup_table_iterator) / (double)num_sample_barcodes_;
		double last_mapping_barcode_abundance = kh_value(barcode_whitelist_lookup_table_, barcode_whitelist_lookup_table_iterator) / (double)num_sample_barcodes_;
		for (uint32_t bulk_dup_i = 1; bulk_dup_i < temp_dups_for_bulk_level_dedup.size(); ++bulk_dup_i) {
		barcode_whitelist_lookup_table_iterator = kh_get(k32, barcode_whitelist_lookup_table_, temp_dups_for_bulk_level_dedup[bulk_dup_i].GetBarcode());
		double current_mapping_barcode_abundance = kh_value(barcode_whitelist_lookup_table_, barcode_whitelist_lookup_table_iterator) / (double)num_sample_barcodes_;
		if (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups > last_mapping.num_dups \|\| (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups == last_mapping.num_dups && current_mapping_barcode_abundance > min_mapping_barcode_abundance)) {
		if (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups > last_mapping.num_dups \|\| (temp_dups_for_bulk_level_dedup[bulk_dup_i].num_dups == last_mapping.num_dups && current_mapping_barcode_abundance > last_mapping_barcode_abundance)) {
		last_mapping = temp_dups_for_bulk_level_dedup[bulk_dup_i];
		last_mapping_barcode_abundance = current_mapping_barcode_abundance;
		}
		}
		temp_dups_for_bulk_level_dedup.clear();

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