8 * Created by Pat Schloss on 7/12/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
15 #include "mothurout.h"
16 #include "sequence.hpp"
18 /**************************************************************************************************/
23 QualityScores(ifstream&);
26 vector<int> getQualityScores() { return qScores; }
27 void printQScores(ofstream&);
28 void trimQScores(int, int);
30 bool stripQualThreshold(Sequence&, double);
31 bool stripQualRollingAverage(Sequence&, double);
32 bool stripQualWindowAverage(Sequence&, int, int, double);
33 bool cullQualAverage(Sequence&, double);
34 void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
35 void updateForwardMap(vector<vector<int> >&, int, int, int);
36 void updateReverseMap(vector<vector<int> >&, int, int, int);
40 double calculateAverage();
48 /**************************************************************************************************/