Compute sequence length using cigar and trim it. (fd4f5d61) · Commits · github_fork / Chromap

src/sam_mapping.h

+24 −3

Original line number	Diff line number	Diff line
		@@ -166,9 +166,17 @@ class SAMMapping : public Mapping {
		NM_(NM),
		n_cigar_(n_cigar),
		cigar_(cigar),
		MD_(MD_tag),
		sequence_(sequence),
		sequence_qual_(sequence_qual) {}
		MD_(MD_tag) {
		uint32_t sequence_length = GetSequenceLength();
		if (sequence_length != sequence.length()) {
		sequence_ = sequence.substr(0, sequence_length);
		sequence_qual_ = sequence_qual.substr(0, sequence_length);
		} else {
		sequence_ = sequence;
		sequence_qual_ = sequence_qual;
		}
		}

		bool operator<(const SAMMapping &m) const {
		int read1_flag = flag_ & BAM_FREAD1;
		int m_read1_flag = m.flag_ & BAM_FREAD1;
		@@ -223,6 +231,19 @@ class SAMMapping : public Mapping {
		}
		return alignment_length;
		}

		uint32_t GetSequenceLength() const {
		uint32_t sequence_length = 0;
		for (int ci = 0; ci < n_cigar_; ++ci) {
		uint32_t op = bam_cigar_op(cigar_[ci]);
		uint32_t op_length = bam_cigar_oplen(cigar_[ci]);
		if ((bam_cigar_type(op) & 0x1) > 0) {
		sequence_length += op_length;
		}
		}
		return sequence_length;
		}

		uint32_t GetStartPosition() const { // inclusive
		return pos_ + 1;
		/*if (IsPositiveStrand()) {