/usr/include/pbihdf/HDFSMRTSequenceReader.hpp is in libpbihdf-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | #ifndef _BLASR_HDF_SMRT_SEQUENCE_READER_HPP_
#define _BLASR_HDF_SMRT_SEQUENCE_READER_HPP_
#include "data/hdf/HDFBasReader.h"
#include "data/hdf/HDFZMWReader.h"
#include "SMRTSequence.h"
template<typename T_SMRT_Sequence>
class HDFSMRTSequenceReader : public HDFBasReader {
public:
HDFZMWReader zmwReader;
bool readQuality;
int Initialize(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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