Add low-mem mode for single-end reads. (41ea2d05) · Commits · github_fork / Chromap

src/bed_mapping.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -92,7 +92,7 @@ class MappingWithoutBarcode : public Mapping {
		return std::tie(fragment_start_position_) ==
		std::tie(m.fragment_start_position_);
		}
		bool IsSamePosition(const MappingWithBarcode &m) const {
		bool IsSamePosition(const MappingWithoutBarcode &m) const {
		return std::tie(fragment_start_position_) ==
		std::tie(m.fragment_start_position_);
		}

src/chromap.cc

+53 −31

Original line number	Diff line number	Diff line
		@@ -1483,6 +1483,15 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		barcode_length_, mapping_output_file_path_, mapping_output_format_);
		mapping_writer_.OutputHeader(num_reference_sequences, reference);

		uint32_t num_mappings_in_mem = 0;
		uint64_t max_num_mappings_in_mem =
		1 * ((uint64_t)1 << 30) / sizeof(MappingRecord);
		if (mapping_output_format_ == MAPPINGFORMAT_SAM \|\|
		mapping_output_format_ == MAPPINGFORMAT_PAF \|\|
		mapping_output_format_ == MAPPINGFORMAT_PAIRS) {
		max_num_mappings_in_mem = 1 * ((uint64_t)1 << 29) / sizeof(MappingRecord);
		}

		mm_cache mm_to_candidates_cache(2000003);
		mm_to_candidates_cache.SetKmerLength(kmer_size_);
		struct _mm_history *mm_history = new struct _mm_history[read_batch_size_];
		@@ -1542,7 +1551,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		num_threads_ / num_reference_sequences);
		}
		}
		#pragma omp parallel default(none) shared(barcode_whitelist_file_path_, output_mappings_not_in_whitelist_, window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, max_seed_frequencies_, num_threads_, num_reads_, mm_history, reference, index, read_batch, barcode_batch, read_batch_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_reads_for_loading, num_loaded_reads, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mm_to_candidates_cache, mapping_writer_, candidate_processor, mapping_processor, mapping_generator) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)
		#pragma omp parallel default(none) shared(barcode_whitelist_file_path_, output_mappings_not_in_whitelist_, window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, max_seed_frequencies_, num_threads_, num_reads_, mm_history, reference, index, read_batch, barcode_batch, read_batch_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_reads_for_loading, num_loaded_reads, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mm_to_candidates_cache, mapping_writer_, candidate_processor, mapping_processor, mapping_generator, num_mappings_in_mem, max_num_mappings_in_mem) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)
		{
		thread_num_candidates = 0;
		thread_num_mappings = 0;
		@@ -1675,9 +1684,14 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		#pragma omp task
		{
		MoveMappingsInBuffersToMappingContainer(
		num_mappings_in_mem += MoveMappingsInBuffersToMappingContainer(
		num_reference_sequences,
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		if (low_memory_mode_ &&
		num_mappings_in_mem > max_num_mappings_in_mem) {
		OutputTempMappings(num_reference_sequences, mapping_processor);
		num_mappings_in_mem = 0;
		}
		}
		std::cerr << "Mapped in " << GetRealTime() - real_batch_start_time
		<< "s.\n";
		@@ -1710,6 +1724,11 @@ void Chromap<MappingRecord>::MapSingleEndReads() {

		index.Destroy();

		if (low_memory_mode_) {
		ProcessAndOutputMappingsInLowMemory(num_mappings_in_mem,
		num_reference_sequences, reference,
		mapping_processor);
		} else {
		if (Tn5_shift_) {
		ApplyTn5ShiftOnSingleEndMapping(num_reference_sequences,
		&mappings_on_diff_ref_seqs_);
		@@ -1719,7 +1738,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		mapping_processor.RemovePCRDuplicate(num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		std::cerr << "After removing PCR duplications, ";
		OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_,
		OutputMappingStatistics(num_reference_sequences,
		mappings_on_diff_ref_seqs_,
		mappings_on_diff_ref_seqs_);
		} else {
		mapping_processor.SortOutputMappings(num_reference_sequences,
		@@ -1733,13 +1753,15 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		num_reference_sequences, num_multi_mappings,
		multi_mapping_allocation_distance_, mappings_on_diff_ref_seqs_);
		std::cerr << "After allocating multi-mappings, ";
		OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_,
		OutputMappingStatistics(num_reference_sequences,
		mappings_on_diff_ref_seqs_,
		mappings_on_diff_ref_seqs_);
		mapping_processor.SortOutputMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		}
		OutputMappings(num_reference_sequences, reference,
		mappings_on_diff_ref_seqs_);
		}

		mapping_writer_.FinalizeMappingOutput();
		reference.FinalizeLoading();

Admin message