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#ifndef _BLASR_HDF_BAX_WRITER_HPP_
#define _BLASR_HDF_BAX_WRITER_HPP_
#include <LibBlasrConfig.h>
#ifdef USE_PBBAM
#include <memory>
#include <sstream>
#include <pbdata/Enumerations.h>
#include <hdf/HDFBaseCallsWriter.hpp>
#include <hdf/HDFFile.hpp>
#include <hdf/HDFRegionsWriter.hpp>
#include <hdf/HDFScanDataWriter.hpp>
#include <hdf/HDFWriterBase.hpp>
#include <pbdata/SMRTSequence.hpp>
using namespace H5;
class HDFBaxWriter : 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 Should not create /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] fileAccPropList H5 file access property list
HDFBaxWriter(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);
/// \brief Sets output h5 file name, scan data, base caller version
/// QVs to write, regions types and h5 file access property list.
/// \note /PulseData/Regions dataset should be created.
/// \param[in] regionTypes, regionTypes as /Regions/RegionTypes
HDFBaxWriter(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);
~HDFBaxWriter(void);
/// \returns whether or not write region table.
inline bool HasRegions(void) const;
/// \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 for POC compatible bax file.
bool WriteFakeDataSets();
/// \brief Flushes buffered data.
void Flush(void);
/// \returns all errors from all writers.
std::vector<std::string> Errors(void);
/// \}
private:
H5::FileAccPropList fileaccproplist_; ///< H5 file access property list
HDFGroup pulseDataGroup_; ///< /PulseData group
private:
/// Points to scan data writer.
std::unique_ptr<HDFScanDataWriter> scandataWriter_;
/// Points to base caller writer.
std::unique_ptr<HDFBaseCallsWriter> basecallsWriter_;
/// Points to region table writer.
std::unique_ptr<HDFRegionsWriter> regionsWriter_;
/// \}
private:
/// \name Private Methods.
/// \{
/// \brief Closes HDFBaxWriter.
void Close(void);
/// \}
};
inline bool HDFBaxWriter::HasRegions(void) const { return bool(regionsWriter_); }
#endif // end of #ifdef USE_PBBAM
#endif // end of #ifdef _BLASR_HDF_BAX_WRITER_HPP_
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