/usr/include/pbbam/virtual/ZmwReadStitcher.h is in libpbbam-dev 0.7.4+ds-1.
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//
// File Description
/// \file ZmwReadStitcher.h
/// \brief Defines the ZmwReadStitcher class.
//
// Author: Derek Barnett
#ifndef ZMWREADSTITCHER_H
#define ZMWREADSTITCHER_H
#include "pbbam/BamRecord.h"
#include "pbbam/Config.h"
#include "pbbam/virtual/VirtualZmwBamRecord.h"
#include <memory>
#include <vector>
#include <string>
namespace PacBio {
namespace BAM {
class DataSet;
class PbiFilter;
/// \brief The ZmwReadStitcher class provides an interface for re-stitching
/// "virtual" polymerase reads from their constituent parts.
///
/// \note This reader requires that any input %BAM files also have associated PBI
/// files available for query. See BamFile::EnsurePacBioIndexExists .
///
class PBBAM_EXPORT ZmwReadStitcher
{
public:
/// \name Constructors & Related Methods
/// \{
/// entire file, from BAM names
ZmwReadStitcher(const std::string& primaryBamFilePath,
const std::string& scrapsBamFilePath);
/// filtered input from BAM names
ZmwReadStitcher(const std::string& primaryBamFilePath,
const std::string& scrapsBamFilePath,
const PbiFilter& filter);
/// maybe filtered, from DataSet input
ZmwReadStitcher(const DataSet& dataset);
ZmwReadStitcher(void) = delete;
ZmwReadStitcher(const ZmwReadStitcher&) = delete;
ZmwReadStitcher(ZmwReadStitcher&&) = delete;
ZmwReadStitcher& operator=(const ZmwReadStitcher&) = delete;
ZmwReadStitcher& operator=(ZmwReadStitcher&&) = delete;
~ZmwReadStitcher(void);
/// \}
public:
/// \name File Headers
/// \{
/// \returns the BamHeader associated with this reader's "primary" %BAM file
BamHeader PrimaryHeader(void) const;
/// \returns the BamHeader associated with this reader's "scraps" %BAM file
BamHeader ScrapsHeader(void) const;
/// \}
public:
/// \name Stitched Record Reading
///
/// \returns true if more ZMWs are available for reading.
bool HasNext(void);
/// \returns the next stitched polymerase read
VirtualZmwBamRecord Next(void);
/// \returns the next set of reads that belong to one ZMW.
/// This enables stitching records in a distinct thread.
///
std::vector<BamRecord> NextRaw(void);
/// \}
private:
struct ZmwReadStitcherPrivate;
std::unique_ptr<ZmwReadStitcherPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#endif // ZMWREADSTITCHER_H
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