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#ifndef _BLASR_HDF_SMRT_SEQUENCE_READER_HPP_
#define _BLASR_HDF_SMRT_SEQUENCE_READER_HPP_
#error "Where is data/*? Apparently this header is no longer used."
#include <hdf/HDFBasReader.h>
#include <hdf/HDFZMWReader.h>
#include <pbdata/SMRTSequence.h>
template <typename T_SMRT_Sequence>
class HDFSMRTSequenceReader : public HDFBasReader
{
public:
HDFZMWReader zmwReader;
bool readQuality;
int Initialize(std::string hdfBasFileName, bool _readQuality = true,
const H5::FileAccPropList &fileAccProplist = H5::FileAccPropList::DEFAULT)
{
HDFBasReader::Initialize(hdfBasFileName, fileAccPropList);
zmwReader.Initialize(hdfBasFile);
readQuality = _readQuality;
if (baseCallsGroup.ContainsObject("WidthInFrames")) {
useWidthInFrames = InitializeField(baseCallsGroup, "WidthInFrames");
}
if (baseCallsGroup.ContainsObject("PreBaseFrames")) {
usePreBaseFrames = InitializeField(baseCallsGroup, "PreBaseFrames");
}
if (baseCallsGroup.ContainsObject("PulseIndex")) {
usePulseIndex = InitializeField(baseCallsGroup, "PulseIndex");
}
}
int GetNext(T_SMRT_Sequence &seq)
{
int retVal;
//
// Copy the curBasePos from the bas reader since it gets advanced
// in the GetNext function.
//
DNALength curBasePosCopy = curBasePos;
retVal = HDFBasReader::GetNext(seq);
//
// Bail now if the file is already done
if (retVal == 0) {
return retVal;
}
zmwReader.GetNext(seq.zmwData);
return retVal;
}
int Advance(int nSteps)
{
int retVal;
retVal = HDFBasReader::Advance(nSteps);
zmwReader.Advance(nSteps);
return retVal;
}
};
template <>
int HDFSMRTSequenceReader<FASTASequence>::GetNext(FASTASequence &seq)
{
int retVal;
if (readQuality) {
retVal = HDFBasReader::GetNext(seq);
}
//
// Bail now if the file is already done
if (retVal == 0) {
return retVal;
}
zmwReader.GetNext(seq.zmwData);
return retVal;
}
#endif
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