/usr/include/pbseq/hdf/HDFPulseDataFile.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 | #ifndef _BLASR_HDF_PULSE_DATA_FILE_HPP_
#define _BLASR_HDF_PULSE_DATA_FILE_HPP_
#include <string>
#include <vector>
#include <H5Cpp.h>
#include "HDFGroup.hpp"
#include "HDFZMWReader.hpp"
#include "HDFScanDataReader.hpp"
class HDFPulseDataFile {
public:
H5::H5File hdfBasFile;
HDFGroup pulseDataGroup;
HDFGroup rootGroup;
HDFGroup *rootGroupPtr;
string pulseDataGroupName;
HDFScanDataReader scanDataReader;
bool useScanData;
bool closeFileOnExit;
// Max number of rows allowed to read into memory at a time.
DSLength maxAllocNElements;
HDFZMWReader zmwReader;
std::vector<DSLength> eventOffset;
UInt nReads;
bool preparedForRandomAccess;
DSLength GetAllReadLengths(std::vector<DNALength> &readLengths);
void CheckMemoryAllocation(long allocSize, long allocLimit,
const char *fieldName = NULL);
HDFPulseDataFile();
void PrepareForRandomAccess();
int OpenHDFFile(std::string fileName,
const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT);
//
// All pulse data files contain the "PulseData" group name.
//
//
int InitializePulseDataFile(std::string fileName,
const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT);
int Initialize(std::string fileName,
const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT);
//
// Initialize inside another open group.
//
int Initialize(HDFGroup *rootGroupP);
//
// Initialize all fields
//
int Initialize();
int InitializePulseGroup();
size_t GetAllHoleNumbers(std::vector<unsigned int> &holeNumbers);
void Close();
};
#endif
|