Move Tn5 shift function to MappingProcessor. (1dc57ab4) · Commits · github_fork / Chromap

src/chromap.cc

+4 −43

Original line number	Diff line number	Diff line
		@@ -1289,7 +1289,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		// OutputMappingStatistics(num_reference_sequences,
		// mappings_on_diff_ref_seqs_, mappings_on_diff_ref_seqs_);
		if (Tn5_shift_) {
		ApplyTn5ShiftOnPairedEndMapping(num_reference_sequences,
		mapping_processor.ApplyTn5ShiftOnMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		}

		@@ -1404,24 +1404,6 @@ void Chromap<MappingRecord>::OutputMappings(
		mappings);
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::ApplyTn5ShiftOnPairedEndMapping(
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord>> &mappings) {
		uint64_t num_shifted_mappings = 0;
		for (auto &mappings_on_one_ref_seq : mappings) {
		for (auto &mapping : mappings_on_one_ref_seq) {
		// mapping.fragment_start_position += 4;
		// mapping.positive_alignment_length -= 4;
		// mapping.fragment_length -= 9;
		// mapping.negative_alignment_length -= 5;
		mapping.Tn5Shift();
		++num_shifted_mappings;
		}
		}
		std::cerr << "# shifted mappings: " << num_shifted_mappings << ".\n";
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::MapSingleEndReads() {
		double real_start_time = GetRealTime();
		@@ -1730,8 +1712,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		mapping_processor);
		} else {
		if (Tn5_shift_) {
		ApplyTn5ShiftOnSingleEndMapping(num_reference_sequences,
		&mappings_on_diff_ref_seqs_);
		mapping_processor.ApplyTn5ShiftOnMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		}

		if (remove_pcr_duplicates_) {
		@@ -1768,27 +1750,6 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		std::cerr << "Total time: " << GetRealTime() - real_start_time << "s.\n";
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::ApplyTn5ShiftOnSingleEndMapping(
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord>> *mappings) {
		uint64_t num_shifted_mappings = 0;
		for (auto &mappings_on_one_ref_seq : *mappings) {
		for (auto &mapping : mappings_on_one_ref_seq) {
		mapping.Tn5Shift();
		// uint8_t strand = mapping.direction & 1;
		// if (strand == 1) {
		// mapping.fragment_start_position += 4;
		// mapping.fragment_length -= 4;
		//} else {
		// mapping.fragment_length -= 5;
		//}
		++num_shifted_mappings;
		}
		}
		std::cerr << "# shifted mappings: " << num_shifted_mappings << ".\n";
		}

		template <typename MappingRecord>
		uint32_t Chromap<MappingRecord>::LoadSingleEndReadsWithBarcodes(
		SequenceBatch read_batch, SequenceBatch barcode_batch) {

src/chromap.h

+0 −8

Original line number	Diff line number	Diff line
		@@ -153,20 +153,12 @@ class Chromap {
		const SequenceBatch &read_batch1,
		const SequenceBatch &read_batch2);

		void ApplyTn5ShiftOnPairedEndMapping(
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord> > &mappings);

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

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

		void ApplyTn5ShiftOnSingleEndMapping(
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord> > *mappings);

		// Supportive functions
		void ConstructIndex();

src/mapping_processor.h

+18 −0

Original line number	Diff line number	Diff line
		@@ -56,6 +56,10 @@ class MappingProcessor {
		int multi_mapping_allocation_distance,
		std::vector<std::vector<MappingRecord>> &mappings) const;

		void ApplyTn5ShiftOnMappings(
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord> > &mappings);

		private:
		void BuildAugmentedTree(
		uint32_t ref_id,
		@@ -368,6 +372,20 @@ void MappingProcessor<MappingRecord>::AllocateMultiMappings(
		<< num_multi_mappings_without_overlapping_unique_mappings << ".\n";
		}

		template <typename MappingRecord>
		void MappingProcessor<MappingRecord>::ApplyTn5ShiftOnMappings(
		uint32_t num_reference_sequences,
		std::vector<std::vector<MappingRecord>> &mappings) {
		uint64_t num_shifted_mappings = 0;
		for (auto &mappings_on_one_ref_seq : mappings) {
		for (auto &mapping : mappings_on_one_ref_seq) {
		mapping.Tn5Shift();
		++num_shifted_mappings;
		}
		}
		std::cerr << "# shifted mappings: " << num_shifted_mappings << ".\n";
		}

		} // namespace chromap

		#endif // MAPPING_PROCESSOR_H_

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