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#ifndef QUALITYSCORES
#define QUALITYSCORES
/*
* qualityscores.h
* Mothur
*
* Created by Pat Schloss on 7/12/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
//DataStructure for a quality file.
#include "mothur.h"
#include "mothurout.h"
#include "sequence.hpp"
#include "utils.hpp"
#include "writer.h"
/**************************************************************************************************/
class QualityScores {
public:
QualityScores();
~QualityScores() = default;
QualityScores(string n, vector<int> qs);
QualityScores(ifstream&);
#ifdef USE_BOOST
QualityScores(boost::iostreams::filtering_istream&);
#endif
int read(ifstream&);
string getName();
int getLength(){ return (int)qScores.size(); }
//vector<int> getQualityScores() { return qScores; }
void printQScores(ofstream&);
void printQScores(ostream&);
void printQScores(OutputWriter*);
void trimQScores(int, int);
void flipQScores();
bool stripQualThreshold(Sequence&, double);
bool stripQualRollingAverage(Sequence&, double, bool);
bool stripQualWindowAverage(Sequence&, int, int, double, bool);
bool cullQualAverage(Sequence&, double, bool);
void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
void updateForwardMap(vector<vector<int> >&, int, int, int);
void updateReverseMap(vector<vector<int> >&, int, int, int);
void setName(string n);
void setScores(vector<int> qs) { qScores = qs; seqLength = (int)qScores.size(); }
vector<int> getScores() { return qScores; }
private:
double calculateAverage(bool);
double calculateExpectedErrors(void);
MothurOut* m;
vector<int> qScores;
Utils util;
string seqName;
int seqLength;
string getSequenceName(ifstream&);
string getCommentString(ifstream&);
#ifdef USE_BOOST
string getCommentString(boost::iostreams::filtering_istream&);
string getSequenceName(boost::iostreams::filtering_istream&);
#endif
};
/**************************************************************************************************/
#endif
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