Reverse complementary SEQ and reverse QUAL for SAM. (d68adbef) · Commits · github_fork / Chromap

src/chromap.cc

+3 −3

Original line number	Diff line number	Diff line
		@@ -1824,13 +1824,13 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(
		EmplaceBackMappingRecord(
		read_id, read1_name, barcode_key, 1, ref_start_position1, rid1,
		flag1, first_read_direction == kPositive ? 1 : 0, is_unique, mapq,
		NM1, n_cigar1, cigar1, MD_tag1, read1,
		NM1, n_cigar1, cigar1, MD_tag1, effect_read1,
		read_batch1.GetSequenceQualAt(pair_index),
		&(mappings_on_diff_ref_seqs[rid1]));
		EmplaceBackMappingRecord(
		read_id, read2_name, barcode_key, 1, ref_start_position2, rid2,
		flag2, second_read_direction == kPositive ? 1 : 0, is_unique,
		mapq, NM2, n_cigar2, cigar2, MD_tag2, read2,
		mapq, NM2, n_cigar2, cigar2, MD_tag2, effect_read2,
		read_batch2.GetSequenceQualAt(pair_index),
		&(mappings_on_diff_ref_seqs[rid2]));
		} else if (mapping_output_format_ == MAPPINGFORMAT_PAIRS) {
		@@ -2965,7 +2965,7 @@ void Chromap<MappingRecord>::ProcessBestMappingsForSingleEndRead(
		}
		EmplaceBackMappingRecord(read_id, read_name, barcode_key, 1,
		ref_start_position, rid, flag, 0, is_unique,
		mapq, NM, n_cigar, cigar, MD_tag, read,
		mapq, NM, n_cigar, cigar, MD_tag, effect_read,
		read_batch.GetSequenceQualAt(read_index),
		&(mappings_on_diff_ref_seqs[rid]));
		} else if (mapping_output_format_ == MAPPINGFORMAT_PAF) {

+9 −0

Original line number	Diff line number	Diff line
		@@ -168,6 +168,15 @@ class SAMMapping : public Mapping {
		cigar_(cigar),
		MD_(MD_tag) {
		uint32_t sequence_length = GetSequenceLength();

		if (!IsPositiveStrand()) {
		for (uint32_t i = 0; i < sequence_length; ++i) {
		char current_qual = sequence_qual_[i];
		sequence_qual_[i] = sequence_qual_[sequence_length - 1 - i];
		sequence_qual_[sequence_length - 1 - i] = current_qual;
		}
		}

		if (sequence_length != sequence.length()) {
		sequence_ = sequence.substr(0, sequence_length);
		sequence_qual_ = sequence_qual.substr(0, sequence_length);