Move mapping moving functions to MappingProcessor. (025dd8ec) · Commits · github_fork / Chromap

src/chromap.cc

+10 −36

Original line number	Diff line number	Diff line
		@@ -1031,7 +1031,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		#pragma omp task
		{
		// Handle output
		num_mappings_in_mem += MoveMappingsInBuffersToMappingContainer(
		num_mappings_in_mem +=
		mapping_processor.MoveMappingsInBuffersToMappingContainer(
		num_reference_sequences,
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
		mappings_on_diff_ref_seqs);
		@@ -1424,7 +1425,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		#pragma omp task
		{
		num_mappings_in_mem += MoveMappingsInBuffersToMappingContainer(
		num_mappings_in_mem +=
		mapping_processor.MoveMappingsInBuffersToMappingContainer(
		num_reference_sequences,
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
		mappings_on_diff_ref_seqs);
		@@ -1577,34 +1579,6 @@ void Chromap<MappingRecord>::ConstructIndex() {
		reference.FinalizeLoading();
		}

		template <typename MappingRecord>
		uint32_t Chromap<MappingRecord>::MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord>>>
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
		std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs) {
		// double real_start_time = Chromap<>::GetRealTime();
		uint32_t num_moved_mappings = 0;
		for (int ti = 0; ti < num_threads_; ++ti) {
		for (uint32_t i = 0; i < num_reference_sequences; ++i) {
		num_moved_mappings +=
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i].size();
		mappings_on_diff_ref_seqs[i].insert(
		mappings_on_diff_ref_seqs[i].end(),
		std::make_move_iterator(
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i]
		.begin()),
		std::make_move_iterator(
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i]
		.end()));
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i].clear();
		}
		}
		// std::cerr << "Moved mappings in " << Chromap<>::GetRealTime() -
		// real_start_time << "s.\n";
		return num_moved_mappings;
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::OutputBarcodeStatistics() {
		std::cerr << "Number of barcodes in whitelist: " << num_barcode_in_whitelist_

src/chromap.h

+0 −6

Original line number	Diff line number	Diff line
		@@ -173,12 +173,6 @@ class Chromap {
		uint64_t &num_barcode_in_whitelist,
		uint64_t &num_corrected_barcode);

		uint32_t MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord> > >
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
		std::vector<std::vector<MappingRecord> > &mappings_on_diff_ref_seqs);

		void OutputBarcodeStatistics();

		void OutputMappingStatistics();

src/mapping_processor.h

+38 −1

Original line number	Diff line number	Diff line
		@@ -60,6 +60,12 @@ class MappingProcessor {
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord>> &mappings);

		uint32_t MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord>>>
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
		std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);

		private:
		void BuildAugmentedTree(
		uint32_t ref_id,
		@@ -386,6 +392,37 @@ void MappingProcessor<MappingRecord>::ApplyTn5ShiftOnMappings(
		std::cerr << "# shifted mappings: " << num_shifted_mappings << ".\n";
		}

		template <typename MappingRecord>
		uint32_t
		MappingProcessor<MappingRecord>::MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord>>>
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
		std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs) {
		// double real_start_time = Chromap<>::GetRealTime();
		uint32_t num_moved_mappings = 0;
		for (size_t ti = 0;
		ti < mappings_on_diff_ref_seqs_for_diff_threads_for_saving.size();
		++ti) {
		for (uint32_t i = 0; i < num_reference_sequences; ++i) {
		num_moved_mappings +=
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i].size();
		mappings_on_diff_ref_seqs[i].insert(
		mappings_on_diff_ref_seqs[i].end(),
		std::make_move_iterator(
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i]
		.begin()),
		std::make_move_iterator(
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i]
		.end()));
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i].clear();
		}
		}
		// std::cerr << "Moved mappings in " << Chromap<>::GetRealTime() -
		// real_start_time << "s.\n";
		return num_moved_mappings;
		}

		} // namespace chromap

		#endif // MAPPING_PROCESSOR_H_

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