Move VerifyCandidate* functions to MappingGenerator. (3ecd8904) · Commits · github_fork / Chromap

src/chromap.cc

+8 −575

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src/chromap.h

+23 −44

Original line number	Diff line number	Diff line
		@@ -31,7 +31,7 @@ class ChromapDriver {
		void ParseArgsAndRun(int argc, char *argv[]);
		};

		template <typename MappingRecord = MappingWithoutBarcode>
		template <typename MappingRecord>
		class Chromap {
		public:
		// For index construction
		@@ -139,28 +139,39 @@ class Chromap {
		}
		}

		// For paired-end read mapping
		void ConstructIndex();

		void MapSingleEndReads();

		void MapPairedEndReads();

		private:
		uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch *read_batch,
		SequenceBatch *barcode_batch);

		uint32_t LoadPairedEndReadsWithBarcodes(SequenceBatch &read_batch1,
		SequenceBatch &read_batch2,
		SequenceBatch &barcode_batch);

		void TrimAdapterForPairedEndRead(uint32_t pair_index,
		SequenceBatch &read_batch1,
		SequenceBatch &read_batch2);

		bool PairedEndReadWithBarcodeIsDuplicate(uint32_t pair_index,
		const SequenceBatch &barcode_batch,
		const SequenceBatch &read_batch1,
		const SequenceBatch &read_batch2);

		// For single-end read mapping
		void MapSingleEndReads();
		void LoadBarcodeWhitelist();

		uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch *read_batch,
		SequenceBatch *barcode_batch);
		void ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes);

		// Supportive functions
		void ConstructIndex();
		void UpdateBarcodeAbundance(uint32_t num_loaded_barcodes,
		const SequenceBatch &barcode_batch);

		bool CorrectBarcodeAt(uint32_t barcode_index, SequenceBatch &barcode_batch,
		uint64_t &num_barcode_in_whitelist,
		uint64_t &num_corrected_barcode);

		size_t FindBestMappingIndexFromDuplicates(
		const std::vector<MappingRecord> &duplicates);
		@@ -170,27 +181,6 @@ class Chromap {
		const SequenceBatch &reference,
		const MappingProcessor<MappingRecord> &mapping_processor);

		void VerifyCandidatesOnOneDirectionUsingSIMD(
		Direction candidate_direction, const SequenceBatch &read_batch,
		uint32_t read_index, const SequenceBatch &reference,
		const std::vector<Candidate> &candidates,
		std::vector<std::pair<int, uint64_t> > &mappings, int &min_num_errors,
		int &num_best_mappings, int &second_min_num_errors,
		int &num_second_best_mappings);

		void VerifyCandidatesOnOneDirection(
		Direction candidate_direction, const SequenceBatch &read_batch,
		uint32_t read_index, const SequenceBatch &reference,
		const std::vector<Candidate> &candidates,
		std::vector<std::pair<int, uint64_t> > &mappings,
		std::vector<int> &split_sites, int &min_num_errors,
		int &num_best_mappings, int &second_min_num_errors,
		int &num_second_best_mappings);

		void VerifyCandidates(const SequenceBatch &read_batch, uint32_t read_index,
		const SequenceBatch &reference,
		MappingMetadata &mapping_metadata);

		uint32_t MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord> > >
		@@ -205,17 +195,6 @@ class Chromap {
		const std::vector<std::vector<MappingRecord> > &uni_mappings,
		const std::vector<std::vector<MappingRecord> > &multi_mappings);

		void LoadBarcodeWhitelist();

		void ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes);

		void UpdateBarcodeAbundance(uint32_t num_loaded_barcodes,
		const SequenceBatch &barcode_batch);

		bool CorrectBarcodeAt(uint32_t barcode_index, SequenceBatch &barcode_batch,
		uint64_t &num_barcode_in_whitelist,
		uint64_t &num_corrected_barcode);

		void OutputTempMappings(
		uint32_t num_reference_sequences,
		const MappingProcessor<MappingRecord> &mapping_processor);
		@@ -224,11 +203,12 @@ class Chromap {
		uint8_t mapq_threshold, uint32_t num_reference_sequences,
		const SequenceBatch &reference,
		const std::vector<std::vector<MappingRecord> > &mappings);

		void OutputMappings(uint32_t num_reference_sequences,
		const SequenceBatch &reference,
		const std::vector<std::vector<MappingRecord> > &mappings);

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

		@@ -236,7 +216,6 @@ class Chromap {

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

		private:
		// Parameters
		int kmer_size_;
		int window_size_;
		@@ -286,8 +265,8 @@ class Chromap {
		std::vector<std::string> read_file2_paths_;
		std::vector<std::string> barcode_file_paths_;
		std::string barcode_whitelist_file_path_;
		int barcode_format_[3]; // 0-start, 1-end (includsive), 2-strand(-1:minus,
		// 1:plus)
		// 0-start, 1-end (includsive), 2-strand(-1:minus, 1:plus)
		int barcode_format_[3];
		int read1_format_[3];
		int read2_format_[3];
		std::string mapping_output_file_path_;

src/mapping_generator.h

+588 −0

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