/usr/include/pbseq/alignment/query/SequentialZmwGroupQuery.h is in libblasr-dev 0~20161219-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | #include "../../pbdata/libconfig.h"
#ifdef USE_PBBAM
#ifndef SEQUENTIAL_ZMWGROUPQUERY_H
#define SEQUENTIAL_ZMWGROUPQUERY_H
#include <pbbam/internal/QueryBase.h>
#include <memory>
namespace PacBio {
namespace BAM {
/// This class operates on a name-sorted BAM file, with each iteration of the query
/// returning each contiguous block of records that share a name.
///
/// \note Iterate over zmws, return vector of subreads of a zmw each time.
///
class PBBAM_EXPORT SequentialZmwGroupQuery : public internal::IGroupQuery
{
public:
SequentialZmwGroupQuery(const DataSet& dataset);
~SequentialZmwGroupQuery(void);
public:
bool GetNext(std::vector<BamRecord>& records);
private:
struct SequentialZmwGroupQueryPrivate;
std::unique_ptr<SequentialZmwGroupQueryPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#endif // SEQUENTIAL_ZMWGROUPQUERY_H
#endif
|