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#ifndef _BLASR_HDF_PULSE_WRITER_HPP_
#define _BLASR_HDF_PULSE_WRITER_HPP_
#include "../pbdata/libconfig.h"
#ifdef USE_PBBAM
#include <sstream>
#include <memory>
// pbdata/
#include "../pbdata/Enumerations.h"
#include "../pbdata/SMRTSequence.hpp"
#include "HDFWriterBase.hpp"
#include "HDFScanDataWriter.hpp"
#include "HDFBaseCallsWriter.hpp"
#include "HDFPulseCallsWriter.hpp"
#include "HDFRegionsWriter.hpp"
using namespace H5;
using namespace std;
class HDFPulseWriter : public HDFWriterBase {
public:
/// \name Constructor & Related Methods
/// \{
/// \brief Sets output h5 file name, scan data, base caller version
/// QVs to write, and h5 file access property list.
/// \note Set /PulseData/Regions
/// \param[in] filename output h5 file name.
/// \param[in] basecallerVersion meta data string
/// \param[in] qvsToWrite Quality values to include in output h5 file.
/// \param[in] regionTypes, regionTypes as /Regions/RegionTypes
/// \param[in] fileAccPropList H5 file access property list
HDFPulseWriter(const std::string & filename,
const std::string & basecallerVersion,
const std::map<char, size_t>& baseMap,
const std::vector<PacBio::BAM::BaseFeature> & qvsToWrite,
const std::vector<std::string> & regionTypes,
const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT);
/// \note No /PulseData/Regions
HDFPulseWriter(const std::string & filename,
const std::string & basecallerVersion,
const std::map<char, size_t>& baseMap,
const std::vector<PacBio::BAM::BaseFeature> & qvsToWrite,
const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT);
~HDFPulseWriter(void);
/// \brief Write one zmw sequence to output h5 file.
/// \param[in] seq, the SMRTSequence to write
bool WriteOneZmw(const SMRTSequence & seq);
/// \brief Write one zmw sequence and its region table to output h5 file.
/// \param[in] seq, the SMRTSequence to write
/// \param[in] regions, region annotations of this zmw.
bool WriteOneZmw(const SMRTSequence & seq,
const std::vector<RegionAnnotation> & regions);
/// \brief Write fake datasets to create POC/PulseRecognizer compatible plx file.
bool WriteFakeDataSets();
inline bool HasRegions(void) const;
/// \brief Flushes buffered data.
void Flush(void);
/// \returns all errors from all writers.
std::vector<std::string> Errors(void);
/// Pass-through method for setting the inverse gain to PulseCallsWriter
void SetInverseGain(float igain);
/// \}
private:
H5::FileAccPropList fileaccproplist_; ///< H5 file access property list
HDFGroup pulseDataGroup_; ///< /PulseData group
private:
/// Points to base caller writer.
std::unique_ptr<HDFBaseCallsWriter> basecallsWriter_;
/// Points to pulse calls writer.
std::unique_ptr<HDFPulseCallsWriter> pulsecallsWriter_;
/// Points to region table writer.
std::unique_ptr<HDFRegionsWriter> regionsWriter_;
/// \}
private:
/// \name Private Methods.
/// \{
/// \brief Closes HDFPulseWriter.
void Close(void);
/// \}
};
inline bool HDFPulseWriter::HasRegions(void) const
{ return bool(regionsWriter_); }
#endif // USE_PBBAM
#endif
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