Mapping(const bam_hdr_t * hdr_p, bam1_t * rec_p) : _rec_p(rec_p) { _query_name = bam_get_qname(rec_p); _flag = rec_p->core.flag; for (int i = 0; i < rec_p->core.l_qseq; ++i) { _seq += seq_nt16_str[bam_seqi(bam_get_seq(rec_p), i)]; } if (is_mapped()) { _chr_name = hdr_p->target_name[rec_p->core.tid]; _rf_start = rec_p->core.pos; _cigar = Cigar(bam_get_cigar(rec_p), rec_p->core.n_cigar); _rf_len = _cigar.rf_len(); } if (is_paired() and mp_is_mapped()) { _mp_chr_name = hdr_p->target_name[rec_p->core.mtid]; _mp_rf_start = rec_p->core.mpos; } }
Cigar getCigar() const { return Cigar(m_dataPtr.get()); // Cache constructed value }