std::string GenomicRegion::ChrName(const BamHeader& h) const {
std::string cc;
if (!h.isEmpty()) {
if (chr >= h.NumSequences())
throw std::invalid_argument( "GenomicRegion::ChrName - not enough targets in BamHeader to cover ref id");
else
cc = h.IDtoName(chr); // std::string(h->target_name[chr]);
} else {
cc = chrToString(chr);
}
return cc;
}
void Interval(const BamHeader& header,
const GenomicInterval& interval)
{
htsIterator_.reset(nullptr);
if (header.HasSequence(interval.Name())) {
auto id = header.SequenceId(interval.Name());
if (id >= 0 && static_cast<size_t>(id) < header.NumSequences()) {
htsIterator_.reset(bam_itr_queryi(htsIndex_.get(),
id,
interval.Start(),
interval.Stop()));
}
}
if (!htsIterator_)
throw std::runtime_error("could not create iterator for requested region");
}
