Merge branch 'li_dev' into haowen_dev (a99e6272) · Commits · github_fork / Chromap

src/chromap.cc

+18 −10

Original line number	Diff line number	Diff line
		@@ -1463,8 +1463,11 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		split_site1 = split_sites1[i1];
		split_site2 = split_sites2[i2];
		}
		GetRefStartEndPositionForReadFromMapping(first_read_direction, mappings1[i1], effect_read1, read1_length, split_site1, reference, &ref_start_position1, &ref_end_position1, &n_cigar1, &cigar1, &NM1, MD_tag1);
		GetRefStartEndPositionForReadFromMapping(second_read_direction, mappings2[i2], effect_read2, read2_length, split_site2, reference, &ref_start_position2, &ref_end_position2, &n_cigar2, &cigar2, &NM2, MD_tag2);
		GetRefStartEndPositionForReadFromMapping(first_read_direction, mappings1[i1], effect_read1, read1_length, split_site1,
		reference, &ref_start_position1, &ref_end_position1, &n_cigar1, &cigar1, &NM1, MD_tag1) ;
		GetRefStartEndPositionForReadFromMapping(second_read_direction, mappings2[i2], effect_read2, read2_length,
		split_site2, reference, &ref_start_position2, &ref_end_position2,
		&n_cigar2, &cigar2, &NM2, MD_tag2) ;
		/*if (!strcmp(read_batch1.GetSequenceNameAt(pair_index), "XXXX")) {
		printf("%d\n", best_mappings.size());
		printf("%d. %d %d\n", min_sum_errors, i1, i2);
		@@ -1513,13 +1516,17 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		}

		if (rid1 < rid2 \|\| (rid1 == rid2 && position1 < position2)) {
		EmplaceBackMappingRecord(read_id, read1_name, barcode_key, rid1, rid2, position1, position2, direction, direction2, mapq, is_unique, 1, &((*mappings_on_diff_ref_seqs)[rid1]));
		EmplaceBackMappingRecord(read_id, read1_name, barcode_key,
		rid1, rid2, position1, position2, direction, direction2, mapq, is_unique, 1,
		&((*mappings_on_diff_ref_seqs)[rid1])) ;
		} else {
		EmplaceBackMappingRecord(read_id, read1_name, barcode_key, rid2, rid1, position2, position1, direction2, direction, mapq, is_unique, 1, &((*mappings_on_diff_ref_seqs)[rid2]));
		EmplaceBackMappingRecord(read_id, read1_name, barcode_key,
		rid2, rid1, position2, position1, direction2, direction, mapq, is_unique, 1,
		&((*mappings_on_diff_ref_seqs)[rid2])) ;
		}
		} else if (output_mapping_in_PAF_) {
		uint32_t fragment_start_position = ref_start_position1;
		uint16_t fragment_length = ref_end_position2 - ref_start_position1 + 1;
		uint16_t fragment_length = ref_end_position2 - ref_start_position1 + 1;;
		uint16_t positive_alignment_length = ref_end_position1 - ref_start_position1 + 1;
		uint16_t negative_alignment_length = ref_end_position2 - ref_start_position2 + 1;
		if (direction == 0) {
		@@ -1542,7 +1549,7 @@ 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;
		}
		@@ -1550,6 +1557,7 @@ 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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