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&, int);
25 void printQScores(ofstream&);
26 void trimQScores(int, int);
28 bool stripQualThreshold(Sequence&, double);
29 bool stripQualRollingAverage(Sequence&, double);
30 bool stripQualWindowAverage(Sequence&, int, int, double);
31 bool cullQualAverage(Sequence&, double);
32 void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
33 void updateForwardMap(vector<vector<int> >&, int, int, int);
34 void updateReverseMap(vector<vector<int> >&, int, int, int);
38 double calculateAverage();
46 /**************************************************************************************************/