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#ifndef _BLASR_HDF_ZMW_READER_HPP_
#define _BLASR_HDF_ZMW_READER_HPP_
#include <cstdint>
#include <H5Cpp.h>
#include "../pbdata/reads/ZMWGroupEntry.hpp"
#include "HDFArray.hpp"
#include "HDF2DArray.hpp"
#include "HDFGroup.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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