/usr/include/pbdata/reads/PulseFile.hpp is in libpbdata-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 | #ifndef _BLASR_PULSE_FILE_HPP_
#define _BLASR_PULSE_FILE_HPP_
#include <map>
#include <vector>
#include "Types.h"
#include "Enumerations.h"
#include "DNASequence.hpp"
#include "SMRTSequence.hpp"
#include "PulseBaseCommon.hpp"
#include "ScanData.hpp"
class PulseFile : public PulseBaseCommon {
public:
unsigned int numFrames;
PlatformId platformId;
std::vector<unsigned int> startFrame;
std::vector<uint16_t> plsWidthInFrames;
int midSignalNDims, maxSignalNDims, meanSignalNDims;
std::vector<uint16_t> midSignal;
std::vector<uint16_t> maxSignal;
std::vector<uint16_t> meanSignal;
std::vector<int> numEvent;
std::vector<int> pulseStartPositions;
std::vector<float> classifierQV;
PulseFile(){numFrames = 0; platformId = Springfield;}
void CopySignal(HalfWord *signalData, // either a vector or matrix
int signalNDims,
int pulseStartPos, // 0 if baseToPulseIndex maps to abs position
int *baseToPulseIndex,
Nucleotide *readSeq,
int readLength,
HalfWord *readData);
// plsReadIndex: index of this hole number in /PulseCalls/ZMW/HoleNumber.
// baseToPulseIndex: index from pulse to base from the beginning of the read.
// read: a SMRTSequence.
void CopyReadAt(uint32_t plsReadIndex, int *baseToPulseIndex, SMRTSequence &read);
template<typename T_FieldType>
void StoreField(std::vector<T_FieldType> &source, int *basToPlsIndex, T_FieldType *dest, int destLength);
template <typename T>
bool Realloc(T *&ptr, int length);
};
#include "PulseFileImpl.hpp"
#endif
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