Implement the count for total and unmapped. (8674acf1) · Commits · github_fork / Chromap

src/chromap.h

+25 −0

Original line number	Diff line number	Diff line
		@@ -425,6 +425,18 @@ void Chromap::MapSingleEndReads() {
		}
		// std::cerr<<"cache memusage: " <<
		// mm_to_candidates_cache.GetMemoryBytes() <<"\n" ;
		if (!mapping_parameters_.summary_metadata_file_path.empty()) {
		if (mapping_parameters_.is_bulk_data)
		mapping_writer.UpdateSummaryMetadata(0, SUMMARY_METADATA_TOTAL,
		num_loaded_reads) ;
		else
		{
		for (uint32_t read_index = 0; read_index < num_loaded_reads; ++read_index)
		mapping_writer.UpdateSummaryMetadata(
		barcode_batch.GenerateSeedFromSequenceAt(read_index, 0, barcode_length_),
		SUMMARY_METADATA_TOTAL, 1);
		}
		}
		num_loaded_reads = num_loaded_reads_for_loading;
		read_batch_for_loading.SwapSequenceBatch(read_batch);
		barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);
		@@ -964,6 +976,19 @@ void Chromap::MapPairedEndReads() {
		}
		}

		if (!mapping_parameters_.summary_metadata_file_path.empty()) {
		if (mapping_parameters_.is_bulk_data)
		mapping_writer.UpdateSummaryMetadata(0, SUMMARY_METADATA_TOTAL,
		num_loaded_pairs) ;
		else
		{
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index)
		mapping_writer.UpdateSummaryMetadata(
		barcode_batch.GenerateSeedFromSequenceAt(pair_index, 0, barcode_length_),
		SUMMARY_METADATA_TOTAL, 1);
		}
		}

		std::cerr << "Mapped " << num_loaded_pairs << " read pairs in "
		<< GetRealTime() - real_batch_start_time << "s.\n";
		real_batch_start_time = GetRealTime();

src/mapping_writer.h

+30 −1

Original line number	Diff line number	Diff line
		@@ -69,6 +69,7 @@ class MappingWriter {
		&temp_mapping_file_handles);

		void OutputSummaryMetadata();
		void UpdateSummaryMetadata(uint64_t barcode, int type, int change);

		protected:
		void AppendMapping(uint32_t rid, const SequenceBatch &reference,
		@@ -288,8 +289,13 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(
		} else {
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_LOWMAPQ,
		last_mapping.num_dups_);
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));
		}
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_MAPPED,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));

		if (last_mapping.is_unique_ == 1) {
		++num_uni_mappings;
		@@ -327,7 +333,20 @@ void MappingWriter<MappingRecord>::ProcessAndOutputMappingsInLowMemory(
		}
		AppendMapping(last_rid, reference, last_mapping);
		++num_mappings_passing_filters;

		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_DUP,
		last_mapping.num_dups_ - 1);
		} else {
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_LOWMAPQ,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));
		}
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(last_mapping.GetBarcode(), SUMMARY_METADATA_MAPPED,
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(),
		num_last_mapping_dups));

		if (last_mapping.is_unique_ == 1) {
		++num_uni_mappings;
		@@ -399,6 +418,9 @@ void MappingWriter<MappingRecord>::OutputMappingsInVector(
		summary_metadata_.UpdateCount(it->GetBarcode(), SUMMARY_METADATA_LOWMAPQ,
		it->num_dups_);
		}
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(it->GetBarcode(), SUMMARY_METADATA_MAPPED,
		it->num_dups_);
		}
		}
		std::cerr << "Number of output mappings (passed filters): "
		@@ -421,6 +443,13 @@ void MappingWriter<MappingRecord>::OutputSummaryMetadata() {
		summary_metadata_.Output(mapping_parameters_.summary_metadata_file_path.c_str());
		}

		template <typename MappingRecord>
		void MappingWriter<MappingRecord>::UpdateSummaryMetadata(uint64_t barcode, int type, int change)
		{
		if (!mapping_parameters_.summary_metadata_file_path.empty())
		summary_metadata_.UpdateCount(barcode, type, change);
		}

		// Specialization for BED format.
		template <>
		void MappingWriter<MappingWithBarcode>::OutputHeader(

src/summary_metadata.h

+6 −2

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ namespace chromap {
		enum SummaryMetadataField {
		SUMMARY_METADATA_TOTAL = 0,
		SUMMARY_METADATA_DUP,
		SUMMARY_METADATA_UNMAPPED,
		SUMMARY_METADATA_MAPPED,
		SUMMARY_METADATA_LOWMAPQ,
		SUMMARY_METADATA_FIELDS
		};
		@@ -50,7 +50,11 @@ class SummaryMetadata {
		fprintf(fp, "%s", Seed2Sequence(kh_key(barcode_metadata_, k), barcode_length_).c_str());
		int i;
		for (i = 0; i < SUMMARY_METADATA_FIELDS; ++i) {
		if (i != SUMMARY_METADATA_MAPPED)
		fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[i]);
		else
		fprintf(fp, ",%d", kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_TOTAL]
		- kh_value(barcode_metadata_, k).counts[SUMMARY_METADATA_MAPPED]);
		}
		fprintf(fp, "\n");
		}

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