Move mapping stats functions to MappingProcessor. (2942102a) · Commits · github_fork / Chromap

src/chromap.cc

+4 −26

Original line number	Original line	Diff line number	Diff line
	@@ -1095,8 +1095,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
	num_mappings_in_mem, num_reference_sequences, reference,		num_mappings_in_mem, num_reference_sequences, reference,
	barcode_whitelist_lookup_table_, temp_mapping_file_handles);		barcode_whitelist_lookup_table_, temp_mapping_file_handles);
	} else {		} else {
	// OutputMappingStatistics(num_reference_sequences,
	// mappings_on_diff_ref_seqs, mappings_on_diff_ref_seqs);
	if (mapping_parameters_.Tn5_shift) {		if (mapping_parameters_.Tn5_shift) {
	mapping_processor.ApplyTn5ShiftOnMappings(num_reference_sequences,		mapping_processor.ApplyTn5ShiftOnMappings(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	@@ -1106,7 +1104,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
	mapping_processor.RemovePCRDuplicate(num_reference_sequences,		mapping_processor.RemovePCRDuplicate(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	std::cerr << "After removing PCR duplications, ";		std::cerr << "After removing PCR duplications, ";
	OutputMappingStatistics(num_reference_sequences,		mapping_processor.OutputMappingStatistics(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	} else {		} else {
	mapping_processor.SortOutputMappings(num_reference_sequences,		mapping_processor.SortOutputMappings(num_reference_sequences,
	@@ -1121,7 +1119,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
	mapping_parameters_.multi_mapping_allocation_distance,		mapping_parameters_.multi_mapping_allocation_distance,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	std::cerr << "After allocating multi-mappings, ";		std::cerr << "After allocating multi-mappings, ";
	OutputMappingStatistics(num_reference_sequences,		mapping_processor.OutputMappingStatistics(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	mapping_processor.SortOutputMappings(num_reference_sequences,		mapping_processor.SortOutputMappings(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	@@ -1496,7 +1494,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
	mapping_processor.RemovePCRDuplicate(num_reference_sequences,		mapping_processor.RemovePCRDuplicate(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	std::cerr << "After removing PCR duplications, ";		std::cerr << "After removing PCR duplications, ";
	OutputMappingStatistics(num_reference_sequences,		mapping_processor.OutputMappingStatistics(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	} else {		} else {
	mapping_processor.SortOutputMappings(num_reference_sequences,		mapping_processor.SortOutputMappings(num_reference_sequences,
	@@ -1511,7 +1509,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
	mapping_parameters_.multi_mapping_allocation_distance,		mapping_parameters_.multi_mapping_allocation_distance,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	std::cerr << "After allocating multi-mappings, ";		std::cerr << "After allocating multi-mappings, ";
	OutputMappingStatistics(num_reference_sequences,		mapping_processor.OutputMappingStatistics(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	mapping_processor.SortOutputMappings(num_reference_sequences,		mapping_processor.SortOutputMappings(num_reference_sequences,
	mappings_on_diff_ref_seqs);		mappings_on_diff_ref_seqs);
	@@ -1604,26 +1602,6 @@ void Chromap<MappingRecord>::OutputMappingStatistics() {
	<< num_mappings_ - num_uniquely_mapped_reads_ << ".\n";		<< num_mappings_ - num_uniquely_mapped_reads_ << ".\n";
	}		}

	template <typename MappingRecord>
	void Chromap<MappingRecord>::OutputMappingStatistics(
	uint32_t num_reference_sequences,
	const std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs) {
	uint64_t num_uni_mappings = 0;
	uint64_t num_multi_mappings = 0;
	for (auto &mappings_on_one_ref_seq : mappings_on_diff_ref_seqs) {
	for (auto &mapping : mappings_on_one_ref_seq) {
	if ((mapping.is_unique_) == 1) {
	++num_uni_mappings;
	} else {
	++num_multi_mappings;
	}
	}
	}
	std::cerr << "# uni-mappings: " << num_uni_mappings
	<< ", # multi-mappings: " << num_multi_mappings
	<< ", total: " << num_uni_mappings + num_multi_mappings << ".\n";
	}

	template <typename MappingRecord>		template <typename MappingRecord>
	void Chromap<MappingRecord>::LoadBarcodeWhitelist() {		void Chromap<MappingRecord>::LoadBarcodeWhitelist() {
	double real_start_time = GetRealTime();		double real_start_time = GetRealTime();

src/chromap.h

+1 −4

Original line number	Original line	Diff line number	Diff line
	@@ -105,15 +105,12 @@ class Chromap {

	void OutputMappingStatistics();		void OutputMappingStatistics();

	void OutputMappingStatistics(uint32_t num_reference_sequences,
	const std::vector<std::vector<MappingRecord> >
	&mappings_on_diff_ref_seqs);

	void GenerateCustomizedRidRank(const std::string &rid_order_path,		void GenerateCustomizedRidRank(const std::string &rid_order_path,
	uint32_t num_reference_sequences,		uint32_t num_reference_sequences,
	const SequenceBatch &reference,		const SequenceBatch &reference,
	std::vector<int> &rid_rank);		std::vector<int> &rid_rank);

			// TODO: generate reranked candidates directly.
	void RerankCandidatesRid(std::vector<Candidate> &candidates);		void RerankCandidatesRid(std::vector<Candidate> &candidates);

	void ParseReadFormat(const std::string &read_format);		void ParseReadFormat(const std::string &read_format);

src/mapping_processor.h

+24 −0

Original line number	Original line	Diff line number	Diff line
	@@ -67,6 +67,10 @@ class MappingProcessor {
	&mappings_on_diff_ref_seqs_for_diff_threads_for_saving,		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving,
	std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);		std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);

			void OutputMappingStatistics(
			uint32_t num_reference_sequences,
			const std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);

	private:		private:
	void BuildAugmentedTree(		void BuildAugmentedTree(
	uint32_t ref_id,		uint32_t ref_id,
	@@ -424,6 +428,26 @@ MappingProcessor<MappingRecord>::MoveMappingsInBuffersToMappingContainer(
	return num_moved_mappings;		return num_moved_mappings;
	}		}

			template <typename MappingRecord>
			void MappingProcessor<MappingRecord>::OutputMappingStatistics(
			uint32_t num_reference_sequences,
			const std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs) {
			uint64_t num_uni_mappings = 0;
			uint64_t num_multi_mappings = 0;
			for (auto &mappings_on_one_ref_seq : mappings_on_diff_ref_seqs) {
			for (auto &mapping : mappings_on_one_ref_seq) {
			if ((mapping.is_unique_) == 1) {
			++num_uni_mappings;
			} else {
			++num_multi_mappings;
			}
			}
			}
			std::cerr << "# uni-mappings: " << num_uni_mappings
			<< ", # multi-mappings: " << num_multi_mappings
			<< ", total: " << num_uni_mappings + num_multi_mappings << ".\n";
			}

	} // namespace chromap		} // namespace chromap

	#endif // MAPPING_PROCESSOR_H_		#endif // MAPPING_PROCESSOR_H_

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