Merge pull request #12 from haowenz/li_dev2 (45de7b40) · Commits · github_fork / Chromap

src/chromap.cc

+2 −2

Original line number	Diff line number	Diff line
		@@ -1744,8 +1744,8 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D
		}
		//mapq \|= (uint8_t)1;
		if (output_mapping_in_SAM_) {
		uint16_t flag1 = 1;
		uint16_t flag2 = 1;
		uint16_t flag1 = 3;
		uint16_t flag2 = 3;
		if (first_read_direction == kNegative) {
		flag1 \|= BAM_FREVERSE;
		flag2 \|= BAM_FMREVERSE;

src/output_tools.h

+7 −6

Original line number	Diff line number	Diff line
		@@ -372,18 +372,20 @@ struct SAMMapping {
		return alignment_length;
		}
		uint32_t GetStartPosition() const { // inclusive
		if (IsPositive()) {
		return pos + 1 ;
		/*if (IsPositive()) {
		return pos + 1;
		} else {
		return pos + 1 - GetAlignmentLength();
		}
		return pos + 1 - GetAlignmentLength() + 1;
		}*/
		}
		uint32_t GetEndPosition() const { // exclusive
		if (IsPositive()) {
		return pos + GetAlignmentLength();
		/*if (IsPositive()) {
		return pos + GetAlignmentLength();
		} else {
		return pos + 1;
		}
		}*/
		}
		uint16_t GetStructSize() const {
		return 2 * sizeof(uint32_t) + 2 * sizeof(uint16_t) + 2 * sizeof(uint8_t) + (read_name.length() + MD.length()) * sizeof(char) + n_cigar * sizeof(uint32_t);
		@@ -1275,7 +1277,6 @@ inline void SAMOutputTools<SAMMapping>::AppendMapping(uint32_t rid, const Sequen
		//uint32_t mapping_end_position = mapping.fragment_start_position + mapping.fragment_length;
		const char reference_sequence_name = (mapping.flag & BAM_FUNMAP) > 0 ? "" : reference.GetSequenceNameAt(rid);
		const uint32_t mapping_start_position = mapping.GetStartPosition();

		this->AppendMappingOutput(mapping.read_name + "\t" + std::to_string(mapping.flag) + "\t" + std::string(reference_sequence_name) + "\t" + std::to_string(mapping_start_position) + "\t" + std::to_string(mapping.mapq) + "\t" + mapping.GenerateCigarString() + "\t*\t" + std::to_string(0) + "\t" + std::to_string(0) + "\t" + mapping.sequence + "\t" + mapping.sequence_qual + "\t" + mapping.GenerateIntTagString("NM", mapping.NM) + "\tMD:Z:" + mapping.MD);
		if (cell_barcode_length_ > 0) {
		this->AppendMappingOutput("\tCB:Z:" + Seed2Sequence(mapping.cell_barcode, cell_barcode_length_));

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