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#ifndef _BLASR_HDF_ZMW_READER_HPP_
#define _BLASR_HDF_ZMW_READER_HPP_
#include <cstdint>
#include <H5Cpp.h>
#include <hdf/HDF2DArray.hpp>
#include <hdf/HDFArray.hpp>
#include <hdf/HDFGroup.hpp>
#include <pbdata/reads/ZMWGroupEntry.hpp>
class HDFZMWReader
{
public:
HDFGroup *parentGroupPtr;
HDFGroup zmwGroup;
HDFArray<UInt> holeNumberArray;
HDFArray<unsigned char> holeStatusArray;
HDF2DArray<int16_t> xyArray;
HDFArray<DNALength> numEventArray;
bool readHoleNumber, readHoleStatus;
bool readHoleXY;
bool readNumEvent;
UInt curZMW;
UInt nZMWEntries;
bool closeFileOnExit;
H5::H5File hdfPlsFile;
HDFZMWReader();
int Initialize(HDFGroup *parentGroupP);
int Initialize();
int Advance(UInt nSteps);
bool GetNext(ZMWGroupEntry &groupEntry);
void Close();
// Return true if get hole number at ZMW/HoleNumber[index].
bool GetHoleNumberAt(UInt index, UInt &holeNumber);
~HDFZMWReader();
};
#endif
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