Output # dups and fix a bug in barcode correction (4531386f) · Commits · github_fork / Chromap

src/chromap.cc

+31 −25

Original line number	Diff line number	Diff line
		@@ -145,7 +145,7 @@ void Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		base_to_change += 1;
		base_to_change &= mask;
		// generate the corrected key
		uint32_t corrected_barcode_key = barcode_key_to_change & (base_to_change << (2 * i));
		uint32_t corrected_barcode_key = barcode_key_to_change \| (base_to_change << (2 * i));
		barcode_whitelist_lookup_table_iterator = kh_get(k32_set, barcode_whitelist_lookup_table_, corrected_barcode_key);
		if (barcode_whitelist_lookup_table_iterator != kh_end(barcode_whitelist_lookup_table_)) {
		// find one possible corrected barcode
		@@ -866,26 +866,26 @@ void Chromap<MappingRecord>::GenerateBestMappingsForPairedEndReadOnOneDirection(
		}

		template<typename MappingRecord>
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {
		}

		template<>
		void Chromap<PairedEndMappingWithoutBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<PairedEndMappingWithoutBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PairedEndMappingWithoutBarcode{read_id, fragment_start_position, fragment_length, mapq, direction, is_unique, positive_alignment_length, negative_alignment_length});
		void Chromap<PairedEndMappingWithoutBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<PairedEndMappingWithoutBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PairedEndMappingWithoutBarcode{read_id, fragment_start_position, fragment_length, mapq, direction, is_unique, num_dups, positive_alignment_length, negative_alignment_length});
		}

		template<>
		void Chromap<PairedEndMappingWithBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<PairedEndMappingWithBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PairedEndMappingWithBarcode{read_id, barcode, fragment_start_position, fragment_length, mapq, direction, is_unique, positive_alignment_length, negative_alignment_length});
		void Chromap<PairedEndMappingWithBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<PairedEndMappingWithBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PairedEndMappingWithBarcode{read_id, barcode, fragment_start_position, fragment_length, mapq, direction, is_unique, num_dups, positive_alignment_length, negative_alignment_length});
		}

		template<typename MappingRecord>
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, const char read1_name, const char read2_name, uint16_t read1_length, uint16_t read2_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, const char read1_name, const char read2_name, uint16_t read1_length, uint16_t read2_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {
		}

		template<>
		void Chromap<PairedPAFMapping>::EmplaceBackMappingRecord(uint32_t read_id, const char read1_name, const char read2_name, uint16_t read1_length, uint16_t read2_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<PairedPAFMapping> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PairedPAFMapping{read_id, std::string(read1_name), std::string(read2_name), read1_length, read2_length, fragment_start_position, fragment_length, positive_alignment_length, negative_alignment_length, mapq, direction, is_unique});
		void Chromap<PairedPAFMapping>::EmplaceBackMappingRecord(uint32_t read_id, const char read1_name, const char read2_name, uint16_t read1_length, uint16_t read2_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<PairedPAFMapping> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PairedPAFMapping{read_id, std::string(read1_name), std::string(read2_name), read1_length, read2_length, fragment_start_position, fragment_length, positive_alignment_length, negative_alignment_length, mapq, direction, is_unique, num_dups});
		}

		template <typename MappingRecord>
		@@ -935,9 +935,9 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		barcode_key = barcode_batch.GenerateSeedFromSequenceAt(pair_index, 0, barcode_batch.GetSequenceLengthAt(pair_index));
		}
		if (output_mapping_in_PAF_) {
		EmplaceBackMappingRecord(read_id, read_batch1.GetSequenceNameAt(pair_index), read_batch2.GetSequenceNameAt(pair_index), (uint16_t)read_batch1.GetSequenceLengthAt(pair_index), (uint16_t)read_batch2.GetSequenceLengthAt(pair_index), barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		EmplaceBackMappingRecord(read_id, read_batch1.GetSequenceNameAt(pair_index), read_batch2.GetSequenceNameAt(pair_index), (uint16_t)read_batch1.GetSequenceLengthAt(pair_index), (uint16_t)read_batch2.GetSequenceLengthAt(pair_index), barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		} else {
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		}
		} else {
		BandedTraceback(mappings1[i1].first, reference.GetSequenceAt(rid1) + verification_window_start_position1, negative_read1.data(), read1_length, &mapping_start_position1);
		@@ -953,9 +953,9 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		barcode_key = barcode_batch.GenerateSeedFromSequenceAt(pair_index, 0, barcode_batch.GetSequenceLengthAt(pair_index));
		}
		if (output_mapping_in_PAF_) {
		EmplaceBackMappingRecord(read_id, read_batch1.GetSequenceNameAt(pair_index), read_batch2.GetSequenceNameAt(pair_index), (uint16_t)read_batch1.GetSequenceLengthAt(pair_index), (uint16_t)read_batch2.GetSequenceLengthAt(pair_index), barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		EmplaceBackMappingRecord(read_id, read_batch1.GetSequenceNameAt(pair_index), read_batch2.GetSequenceNameAt(pair_index), (uint16_t)read_batch1.GetSequenceLengthAt(pair_index), (uint16_t)read_batch2.GetSequenceLengthAt(pair_index), barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		} else {
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, positive_alignment_length, negative_alignment_length, &((*mappings_on_diff_ref_seqs)[rid1]));
		}
		}
		(*num_best_mappings_reported)++;
		@@ -1198,26 +1198,26 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		}

		template<typename MappingRecord>
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {
		}

		template<>
		void Chromap<MappingWithoutBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<MappingWithoutBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(MappingWithoutBarcode{read_id, fragment_start_position, fragment_length, mapq, direction, is_unique});
		void Chromap<MappingWithoutBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<MappingWithoutBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(MappingWithoutBarcode{read_id, fragment_start_position, fragment_length, mapq, direction, is_unique, num_dups});
		}

		template<>
		void Chromap<MappingWithBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<MappingWithBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(MappingWithBarcode{read_id, barcode, fragment_start_position, fragment_length, mapq, direction, is_unique});
		void Chromap<MappingWithBarcode>::EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<MappingWithBarcode> *mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(MappingWithBarcode{read_id, barcode, fragment_start_position, fragment_length, mapq, direction, is_unique, num_dups});
		}

		template<typename MappingRecord>
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, const char read_name, uint16_t read_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<MappingRecord> mappings_on_diff_ref_seqs) {
		void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, const char read_name, uint16_t read_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<MappingRecord> mappings_on_diff_ref_seqs) {
		}

		template<>
		void Chromap<PAFMapping>::EmplaceBackMappingRecord(uint32_t read_id, const char read_name, uint16_t read_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<PAFMapping> mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PAFMapping{read_id, std::string(read_name), read_length, fragment_start_position, fragment_length, mapq, direction, is_unique});
		void Chromap<PAFMapping>::EmplaceBackMappingRecord(uint32_t read_id, const char read_name, uint16_t read_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<PAFMapping> mappings_on_diff_ref_seqs) {
		mappings_on_diff_ref_seqs->emplace_back(PAFMapping{read_id, std::string(read_name), read_length, fragment_start_position, fragment_length, mapq, direction, is_unique, num_dups});
		}

		template <typename MappingRecord>
		@@ -1250,9 +1250,9 @@ void Chromap<MappingRecord>::ProcessBestMappingsForSingleEndRead(Direction mappi
		uint8_t direction = 1;
		//mapq \|= 1;
		if (output_mapping_in_PAF_) {
		EmplaceBackMappingRecord(read_id, read_name, (uint16_t)read_length, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, &((*mappings_on_diff_ref_seqs)[rid]));
		EmplaceBackMappingRecord(read_id, read_name, (uint16_t)read_length, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, &((*mappings_on_diff_ref_seqs)[rid]));
		} else {
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, &((*mappings_on_diff_ref_seqs)[rid]));
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, &((*mappings_on_diff_ref_seqs)[rid]));
		}
		} else {
		BandedTraceback(min_num_errors, reference.GetSequenceAt(rid) + verification_window_start_position, negative_read.data(), read_length, &mapping_start_position);
		@@ -1261,9 +1261,9 @@ void Chromap<MappingRecord>::ProcessBestMappingsForSingleEndRead(Direction mappi
		mapq = GetMAPQ(0, 0, fragment_length, min_num_errors, num_best_mappings, second_min_num_errors, num_second_best_mappings);
		uint8_t direction = 0;
		if (output_mapping_in_PAF_) {
		EmplaceBackMappingRecord(read_id, read_name, (uint16_t)read_length, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, &((*mappings_on_diff_ref_seqs)[rid]));
		EmplaceBackMappingRecord(read_id, read_name, (uint16_t)read_length, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, &((*mappings_on_diff_ref_seqs)[rid]));
		} else {
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, &((*mappings_on_diff_ref_seqs)[rid]));
		EmplaceBackMappingRecord(read_id, barcode_key, fragment_start_position, fragment_length, mapq, direction, is_unique, 1, &((*mappings_on_diff_ref_seqs)[rid]));
		}
		}
		(*num_best_mappings_reported)++;
		@@ -1408,11 +1408,17 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(uint32_t num_reference_sequences
		deduped_mappings_on_diff_ref_seqs_[ri].emplace_back(mappings_on_diff_ref_seqs_[ri].front());
		//std::vector<MappingRecord>::iterator last_it = mappings_on_diff_ref_seqs_[ri].begin();
		auto last_it = mappings_on_diff_ref_seqs_[ri].begin();
		uint8_t last_dup_count = 1;
		//for (std::vector<MappingRecord>::iterator it = ++(mappings_on_diff_ref_seqs_[ri].begin()); it != mappings_on_diff_ref_seqs_[ri].end(); ++it) {
		for (auto it = ++(mappings_on_diff_ref_seqs_[ri].begin()); it != mappings_on_diff_ref_seqs_[ri].end(); ++it) {
		if (!((it) == (last_it))) {
		//last_it->num_dups = last_dup_count;
		deduped_mappings_on_diff_ref_seqs_[ri].back().num_dups = last_dup_count;
		last_dup_count = 1;
		deduped_mappings_on_diff_ref_seqs_[ri].emplace_back((*it));
		last_it = it;
		} else {
		++last_dup_count;
		}
		}
		std::vector<MappingRecord>().swap(mappings_on_diff_ref_seqs_[ri]);

src/chromap.h

+4 −4

Original line number	Diff line number	Diff line
		@@ -122,16 +122,16 @@ class Chromap {
		void RecalibrateBestMappingsForPairedEndReadOnOneDirection(Direction first_read_direction, uint32_t pair_index, int min_sum_errors, int second_min_sum_errors, int min_num_errors1, int num_best_mappings1, int second_min_num_errors1, int num_second_best_mappings1, const SequenceBatch &read_batch1, const std::vector<std::pair<int, uint64_t> > &mappings1, int min_num_errors2, int num_best_mappings2, int second_min_num_errors2, int num_second_best_mappings2, const SequenceBatch &read_batch2, const SequenceBatch &reference, const std::vector<std::pair<int, uint64_t> > &mappings2, const std::vector<std::pair<uint32_t, uint32_t> > &edit_best_mappings, std::vector<std::pair<uint32_t, uint32_t> > best_mappings, int best_alignment_score, int num_best_mappings, int second_best_alignment_score, int *num_second_best_mappings);
		void ProcessBestMappingsForPairedEndReadOnOneDirection(Direction first_read_direction, uint32_t pair_index, uint8_t mapq, int num_candidates1, int min_num_errors1, int num_best_mappings1, int second_min_num_errors1, int num_second_best_mappings1, const SequenceBatch &read_batch1, const std::vector<std::pair<int, uint64_t> > &mappings1, int num_candidates2, int min_num_errors2, int num_best_mappings2, int second_min_num_errors2, int num_second_best_mappings2, const SequenceBatch &read_batch2, const SequenceBatch &reference, const SequenceBatch &barcode_batch, const std::vector<int> &best_mapping_indices, const std::vector<std::pair<int, uint64_t> > &mappings2, const std::vector<std::pair<uint32_t, uint32_t> > &best_mappings, int min_sum_errors, int num_best_mappings, int second_min_sum_errors, int num_second_best_mappings, int best_mapping_index, int num_best_mappings_reported, std::vector<std::vector<MappingRecord> > *mappings_on_diff_ref_seqs);
		void GenerateBestMappingsForPairedEndRead(uint32_t pair_index, int num_positive_candidates1, int num_negative_candidates1, int min_num_errors1, int num_best_mappings1, int second_min_num_errors1, int num_second_best_mappings1, const SequenceBatch &read_batch1, const std::vector<std::pair<int, uint64_t> > &positive_mappings1, const std::vector<std::pair<int, uint64_t> > &negative_mappings1, int num_positive_candidates2, int num_negative_candidates2, int min_num_errors2, int num_best_mappings2, int second_min_num_errors2, int num_second_best_mappings2, const SequenceBatch &read_batch2, const SequenceBatch &reference, const SequenceBatch &barcode_batch, const std::vector<std::pair<int, uint64_t> > &positive_mappings2, const std::vector<std::pair<int, uint64_t> > &negative_mappings2, std::vector<int> best_mapping_indices, std::mt19937 generator, std::vector<std::pair<uint32_t, uint32_t> > F1R2_best_mappings, std::vector<std::pair<uint32_t, uint32_t> > F2R1_best_mappings, int min_sum_errors, int num_best_mappings, int second_min_sum_errors, int num_second_best_mappings, std::vector<std::vector<MappingRecord> > *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, const char read1_name, const char read2_name, uint16_t read1_length, uint16_t read2_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, const char read1_name, const char read2_name, uint16_t read1_length, uint16_t read2_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, uint16_t positive_alignment_length, uint16_t negative_alignment_length, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void ApplyTn5ShiftOnPairedEndMapping(uint32_t num_reference_sequences, std::vector<std::vector<MappingRecord> > *mappings);

		// For single-end read mapping
		void MapSingleEndReads();
		void GenerateBestMappingsForSingleEndRead(int min_num_errors, int num_best_mappings, int second_min_num_errors, int num_second_best_mappings, const SequenceBatch &read_batch, uint32_t read_index, const SequenceBatch &reference, const SequenceBatch &barcode_batch, const std::vector<std::pair<int, uint64_t> > &positive_mappings, const std::vector<std::pair<int, uint64_t> > &negative_mappings, std::vector<std::vector<MappingRecord> > *mappings_on_diff_ref_seqs);
		void ProcessBestMappingsForSingleEndRead(Direction mapping_direction, uint8_t mapq, int min_num_errors, int num_best_mappings, int second_min_num_errors, int num_second_best_mappings, const SequenceBatch &read_batch, uint32_t read_index, const SequenceBatch &reference, const SequenceBatch &barcode_batch, const std::vector<int> &best_mapping_indices, const std::vector<std::pair<int, uint64_t> > &mappings, int best_mapping_index, int num_best_mappings_reported, std::vector<std::vector<MappingRecord> > *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, const char* read_name, uint16_t read_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void EmplaceBackMappingRecord(uint32_t read_id, const char* read_name, uint16_t read_length, uint32_t barcode, uint32_t fragment_start_position, uint16_t fragment_length, uint8_t mapq, uint8_t direction, uint8_t is_unique, uint8_t num_dups, std::vector<MappingRecord> *mappings_on_diff_ref_seqs);
		void ApplyTn5ShiftOnSingleEndMapping(uint32_t num_reference_sequences, std::vector<std::vector<MappingRecord> > *mappings);
		uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch read_batch, SequenceBatch barcode_batch);

src/output_tools.h

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