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
}
