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#ifndef _BLASR_QUALITY_VALUE_VECTOR_HPP_
#define _BLASR_QUALITY_VALUE_VECTOR_HPP_
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <ostream>
#include <pbdata/Types.h>
#include <pbdata/qvs/QualityValue.hpp>
#include <pbdata/utils.hpp>
template <typename T_QV>
class QualityValueVector
{
public:
T_QV *data;
QVScale qvScale;
T_QV &operator[](unsigned int pos) const;
QualityValueVector();
QualityProbability ToProbability(unsigned int pos);
T_QV ToPhred(unsigned int pos);
void Copy(const QualityValueVector<T_QV> &rhs, const DNALength length);
void Copy(const std::string &rhs);
void Free();
void Allocate(unsigned int length);
/// Fill data with value.
void Fill(const T_QV &value);
/// Fill this->data[thisStart...thisStart+fillLength] with
/// rhs->data[rhsStart...rhsStart+fillLength]
void Fill(const DNALength thisStart, const DNALength fillLength,
const QualityValueVector<T_QV> &rhs, const DNALength rhsStart);
bool Empty() const;
void ShallowCopy(const QualityValueVector<T_QV> &ref, int pos, const DNALength &length);
// Reset data pointer to NULL, don't free memory.
// This should be paired with ShallowCopy.
void ResetShallowData(void);
std::string ToString(void);
// Returns data length
DNALength Length(void) const;
private:
DNALength _length;
};
#include "QualityValueVectorImpl.hpp"
#endif // _BLASR_QUALITY_VALUE_VECTOR_HPP_
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