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#ifndef _BLASR_QUALITY_VALUE_PROFILE_HPP_
#define _BLASR_QUALITY_VALUE_PROFILE_HPP_
#include <fstream>
#include <alignment/tuples/DNATuple.hpp>
#include <alignment/tuples/TupleMetrics.hpp>
#include <pbdata/matrix/FlatMatrix.hpp>
#include <pbdata/qvs/QualityValue.hpp>
class QualityValueProfile
{
int wordSize;
int numQualityValues;
FlatMatrix2D<int> profile;
int nWords;
TupleMetrics tm;
public:
static const int CDF_GRANULARITY = 10000;
QualityValueProfile(int _wordSize, int _numQualityValues);
void Update(Nucleotide *seq, QualityValue qv);
void Print(std::ofstream &out);
void ProfileToCDF();
};
#endif
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