/usr/include/pbdata/reads/BaseFile.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 | #ifndef _BLASR_BASE_FILE_HPP_
#define _BLASR_BASE_FILE_HPP_
#include <stdint.h>
#include <vector>
#include "Enumerations.h"
#include "SMRTSequence.hpp"
#include "HoleXY.hpp"
#include "PulseBaseCommon.hpp"
#include "ScanData.hpp"
class CompareHoleXY {
public:
bool operator()(const HoleXY &lhs, const HoleXY &rhs) const;
};
class BaseFile : public PulseBaseCommon {
public:
std::vector<unsigned char> baseCalls;
std::vector<uint8_t> holeStatus;
std::vector<HoleXY> holeXY;
std::vector<uint16_t> basWidthInFrames;
std::vector<uint16_t> preBaseFrames;
std::vector<int> pulseIndex;
std::vector<unsigned char> qualityValues;
std::vector<unsigned char> deletionQV;
std::vector<unsigned char> deletionTag;
std::vector<unsigned char> insertionQV;
std::vector<unsigned char> substitutionQV;
std::vector<unsigned char> substitutionTag;
std::vector<unsigned char> mergeQV;
std::vector<int> readLengths;
std::vector<int> readStartPositions;
int nReads;
int nBases;
bool LookupReadIndexByXY(uint16_t x, uint16_t y, int &index);
void CopyReadAt(uint32_t readIndex, SMRTSequence &read);
template<typename T>
void CopyArray(std::vector<T> &fullArray, int pos, int length, T*dest);
};
#include "BaseFileImpl.hpp"
#endif // _BLASR_BASE_FILE_HPP_
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