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#ifndef _BLASR_BASE_FILE_HPP_
#define _BLASR_BASE_FILE_HPP_
#include <cstdint>
#include <vector>
#include <pbdata/Enumerations.h>
#include <pbdata/SMRTSequence.hpp>
#include <pbdata/reads/HoleXY.hpp>
#include <pbdata/reads/PulseBaseCommon.hpp>
#include <pbdata/reads/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<DNALength> readLengths;
std::vector<DSLength> readStartPositions;
UInt nReads;
DSLength nBases;
bool LookupReadIndexByXY(uint16_t x, uint16_t y, UInt &index);
void CopyReadAt(UInt readIndex, SMRTSequence &read);
// Copy array from fullArray starting from position pos with length length to dest.
template <typename T>
void CopyArray(std::vector<T> &fullArray, DSLength pos, DNALength length, T *dest);
};
#include "BaseFileImpl.hpp"
#endif // _BLASR_BASE_FILE_HPP_
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