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#ifndef _BLASR_HDF_HDFZMWWriter_HPP_
#define _BLASR_HDF_HDFZMWWriter_HPP_
#include <LibBlasrConfig.h>
#ifdef USE_PBBAM
#include <pbbam/BamRecord.h>
#include <hdf/BufferedHDF2DArray.hpp>
#include <hdf/BufferedHDFArray.hpp>
#include <hdf/HDFWriterBase.hpp>
#include <pbdata/SMRTSequence.hpp>
class HDFBaseCallerWriter;
class HDFPulseCallerWriter;
class HDFZMWWriter : public HDFWriterBase
{
friend class HDFBaseCallerWriter;
friend class HDFPulseCallerWriter;
public:
/// \name Constructors and Destructors
/// \{
HDFZMWWriter(const std::string& filename, HDFGroup& parentGroup);
/// \params[in] filename
/// \params[in] parentGroup
/// \params[in] inPulseCalls, true if this ZMW is within PulseCalls.
/// \params[in] baseMap, base to channel index in H5.
HDFZMWWriter(const std::string& filename, HDFGroup& parentGroup, const bool inPulseCalls,
const std::map<char, size_t>& baseMap);
~HDFZMWWriter(void);
/// \}
/// \name Public Methods
/// \{
/// \returns true if this ZMW is within PulseCalls.
bool InPulseCalls(void) const;
/// \returns Whether or not to write BaseLineSigma
bool HasBaseLineSigma(void) const;
/// \note Write info of a SMRTSequence to ZMW,
/// (1) add number of pulses to NumEvent if InPulseCalls();
/// otherwise, add number of bases
/// (2) add zmw hole number (UInt) of the sequence as a UInt to HoleNumber,
/// (3) add hole status (unsigned char) to HoleStatus,
/// (4) add hole coordinate xy as (int16_t, int16_t) to HoleXY
bool WriteOneZmw(const PacBio::BAM::BamRecord& read);
bool WriteOneZmw(const SMRTSequence& read);
/// \brief Write fake datasets under /PulseCalls/ZMW
bool WriteFakeDataSets(void);
uint32_t NumZMWs(void) const { return arrayLength_; }
/// \note Flushes all data from cache to disc.
void Flush(void);
/// \note Closes this zmw group as well as child hdf groups.
void Close(void);
/// \}
private:
/// \name Private Data
/// ZMW/NumEvent
BufferedHDFArray<uint32_t> numEventArray_;
/// ZMW/HoleNumber
BufferedHDFArray<unsigned int> holeNumberArray_;
/// ZMW/HoleStatus
BufferedHDFArray<unsigned char> holeStatusArray_;
/// ZMW/HoleXY
BufferedHDF2DArray<int16_t> holeXYArray_;
/// ZMW/BaseLineSigma
BufferedHDF2DArray<float> baseLineSigmaArray_;
/// ZMW group
HDFGroup zmwGroup_;
/// Parent group PulseCalls or BaseCalls
HDFGroup& parentGroup_;
/// Map 'ACGT' to channel indices, defined in /ScanData/RunInfo/BaseMap
std::map<char, size_t> baseMap_;
/// true if parent gropu is PulseCalls.
bool inPulseCalls_;
/// dataset (array) size.
uint32_t arrayLength_;
/// \}
private:
/// \name Private Methods
/// \{
/// \note Initialize child hdf groups under ZMW, including
/// NumEvent, HoleNumber, HoleStatus, HoleXY, and BaseLineSigma
/// \reutrns bool, whether or not child hdf groups successfully initialized.
bool InitializeChildHDFGroups(void);
/// \note Write number of bases to ZMW/NumEvent if not InPulseCalls();
/// Otherwise, write number of pulses.
bool _WriteNumEvent(const uint32_t numEvent);
/// \note Write HoleNumber
bool _WriteHoleNumber(const uint32_t holeNumber);
/// \note Write HoleXY
bool _WriteHoleXY(const int16_t holeX, const int16_t holeY);
/// \note Always write 'SEQUENCINGZMW' to HoleStatus
bool _WriteHoleStatus(const unsigned char holeStatus);
/// \note Write BaseLineSigma if it is required to write and exists in read
bool _WriteBaseLineSigma(const PacBio::BAM::BamRecord& read);
/// \note Add attributes to HoleNumber, HoleXY, HoleStatus, HoleXY and BaseLineSigma
void _WriteAttributes(void);
/// \}
};
#endif // end of #ifdef USE_PBBAM
#endif // end of #ifndef _BLASR_HDF_HDFZMWWriter_HPP_
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