/usr/include/pbseq/hdf/HDFArray.hpp is in libpbihdf-dev 0~20161219-2.
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 72 73 74 75 76 77 78 79 80 81 82 83 84 85 | #ifndef _BLASR_HDF_ARRAY_HPP_
#define _BLASR_HDF_ARRAY_HPP_
#include <assert.h>
#include <iostream>
#include <H5Cpp.h>
#include "HDFConfig.hpp"
#include "HDFData.hpp"
#include "BufferedHDFArray.hpp"
#include "../pbdata/DNASequence.hpp"
#include "../pbdata/FASTQSequence.hpp"
/*
*
* Implementation of a 1-D array for IO from an HDF array.
* This is templated, but specialized for a few data types, so that
* the HDF data types do not need to be specified by anybody.
*
* Two examples of the usage of this class follow:
*
* HDFArray<int> nElemArray;
* nElemArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/NumEvent");
* nElemArray.Read(i, i+1, &nElem);
*
* HDFArray<unsigned char> qualArray;
* qualArray.Initialize(hdfFile, "PulseData/BaseCalls/QualityValue");
* qualArray.Read(cur, cur + nElem, qual);
*
*/
template<typename T>
class HDFArray : public BufferedHDFArray<T> {
public:
HDFArray() : BufferedHDFArray<T>() {}
HDFArray(H5::CommonFG* _container, std::string _datasetName) :
BufferedHDFArray<T>(_container, _datasetName) {}
/*
* An unbuffered write is simply a write immediately followed by a flush.
*/
void WriteToPos(const T*data, int dataLength, UInt writePos) {
this->writeBuffer = (T*) data;
this->bufferIndex = dataLength;
this->bufferSize = dataLength;
this->Flush(false, writePos);
ResetBuffer();
}
void ResetBuffer() {
this->writeBuffer = NULL;
this->bufferIndex = 0;
this->bufferSize = 0;
}
void Write(const T *data, int dataLength) {
this->writeBuffer = (T*) data;
this->bufferIndex = dataLength;
this->bufferSize = dataLength;
this->Flush();
//
// Reset status of buffer so that no methods are tricked into
// thinking this is a valid pointer.
//
ResetBuffer();
}
~HDFArray() {}
};
class HDFStringArray: public HDFArray<std::string> {
public:
void Read(DSLength start, DSLength end, std::string* dest) {
std::vector<char*> tmpDestCharPtrs;
if (end == start) return;
assert(end > start);
tmpDestCharPtrs.resize(end-start);
// ReadCharArray(start, end, (char**) &tmpDestCharPtrs[0]);
ReadCharArray(start, end, dest);
}
};
#endif
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