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#include <LibBlasrConfig.h>
#ifdef USE_PBBAM
#include <alignment/query/SequentialZmwGroupQuery.h>
#include <pbbam/CompositeBamReader.h>
#include <boost/optional.hpp>
#include <cassert>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace PacBio::BAM::internal;
struct SequentialZmwGroupQuery::SequentialZmwGroupQueryPrivate
{
public:
SequentialZmwGroupQueryPrivate(const DataSet& dataset)
: reader_(new SequentialCompositeBamReader(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<SequentialCompositeBamReader> reader_;
boost::optional<BamRecord> nextRecord_;
};
SequentialZmwGroupQuery::SequentialZmwGroupQuery(const DataSet& dataset)
: internal::IGroupQuery(), d_(new SequentialZmwGroupQueryPrivate(dataset))
{
}
SequentialZmwGroupQuery::~SequentialZmwGroupQuery(void) {}
bool SequentialZmwGroupQuery::GetNext(std::vector<BamRecord>& records)
{
return d_->GetNext(records);
}
#endif
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