#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