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#include <LibBlasrConfig.h>
#ifdef USE_PBBAM
#include <alignment/query/PbiFilterZmwGroupQuery.h>
#include <pbbam/CompositeBamReader.h>
#include <boost/optional.hpp>
#include <cassert>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace PacBio::BAM::internal;
struct PbiFilterZmwGroupQuery::PbiFilterZmwGroupQueryPrivate
{
/// TODO: To ensure that BamRecords of a zmw are always stored
/// sequentially in bam files, such as in movie.subreads.bam.
public:
PbiFilterZmwGroupQueryPrivate(const PbiFilter& filter, const DataSet& dataset)
: reader_(new PbiFilterCompositeBamReader<Compare::None>(filter, dataset))
, nextRecord_(boost::none)
{
}
bool GetNext(std::vector<BamRecord>& records)
{
records.clear();
std::string movieName;
int32_t holeNumber = -1;
if (nextRecord_.is_initialized()) {
BamRecord r = nextRecord_.get();
movieName = r.MovieName();
holeNumber = r.HoleNumber();
records.push_back(std::move(r));
nextRecord_ = boost::none;
}
BamRecord record;
while (reader_->GetNext(record)) {
if (records.empty()) {
movieName = record.MovieName();
holeNumber = record.HoleNumber();
records.push_back(record);
} else {
assert(!records.empty());
if (record.MovieName() == movieName and record.HoleNumber() == holeNumber)
records.push_back(record);
else {
nextRecord_ = record;
return true;
}
}
}
return !records.empty();
}
public:
std::unique_ptr<PbiFilterCompositeBamReader<Compare::None>> reader_;
boost::optional<BamRecord> nextRecord_;
};
PbiFilterZmwGroupQuery::PbiFilterZmwGroupQuery(const DataSet& dataset)
: internal::IGroupQuery()
, d_(new PbiFilterZmwGroupQueryPrivate(PbiFilter::FromDataSet(dataset), dataset))
{
}
PbiFilterZmwGroupQuery::PbiFilterZmwGroupQuery(const PbiFilter& filter, const DataSet& dataset)
: internal::IGroupQuery(), d_(new PbiFilterZmwGroupQueryPrivate(filter, dataset))
{
}
PbiFilterZmwGroupQuery::~PbiFilterZmwGroupQuery(void) {}
bool PbiFilterZmwGroupQuery::GetNext(std::vector<BamRecord>& records)
{
return d_->GetNext(records);
}
#endif
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