PbiIndexPrivate::PbiIndexPrivate(const PbiRawData& rawIndex)
: filename_(rawIndex.Filename())
, version_(rawIndex.Version())
, sections_(rawIndex.FileSections())
, numReads_(rawIndex.NumReads())
, basicData_(rawIndex.BasicData())
, mappedData_(rawIndex.MappedData())
, referenceData_(rawIndex.ReferenceData())
, barcodeData_(rawIndex.BarcodeData())
{ }
void PbiReferenceNameFilter::Initialize(const PbiRawData& idx) const
{
const auto pbiFilename = idx.Filename();
const auto bamFilename = pbiFilename.substr(0, pbiFilename.length() - 4);
const auto bamFile = BamFile{ bamFilename };
// single-value
if (rnameWhitelist_ == boost::none) {
const auto tId = bamFile.ReferenceId(rname_);
subFilter_ = PbiReferenceIdFilter{ tId, cmp_ };
}
// multi-value whitelist
else {
subFilter_ = PbiFilter(PbiFilter::UNION);
for (const auto& rname : rnameWhitelist_.get())
subFilter_.Add(PbiReferenceIdFilter{ bamFile.ReferenceId(rname) });
}
initialized_ = true;
}