Fix a bug of misplacing two lines (34a6ec8d) · Commits · github_fork / Chromap

src/chromap.cc

+5 −4

Original line number	Diff line number	Diff line
		@@ -1552,7 +1552,7 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		}
		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)++;
		if (*num_best_mappings_reported == std::min(max_num_best_mappings_, num_best_mappings)) {
		break;
		}
		@@ -1560,6 +1560,7 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		(*best_mapping_index)++;
		}
		}
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::GenerateBestMappingsForPairedEndRead(uint32_t pair_index, int num_positive_candidates1, int num_negative_candidates1, uint32_t repetitive_seed_length1, 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<int> &positive_split_sites1, const std::vector<std::pair<int, uint64_t> > &negative_mappings1, const std::vector<int> &negative_split_sites1, int num_positive_candidates2, int num_negative_candidates2, uint32_t repetitive_seed_length2, 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<int> &positive_split_sites2, const std::vector<std::pair<int, uint64_t> > &negative_mappings2, const std::vector<int> &negative_split_sites2, 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, std::vector<std::pair<uint32_t, uint32_t> > F1F2_best_mappings, std::vector<std::pair<uint32_t, uint32_t> > R1R2_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) {

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