8 * Created by Pat Schloss on 7/12/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 //DataStructure for a quality file.
17 #include "mothurout.h"
18 #include "sequence.hpp"
20 /**************************************************************************************************/
25 QualityScores(ifstream&);
27 int getLength(){ return (int)qScores.size(); }
28 vector<int> getQualityScores() { return qScores; }
29 void printQScores(ofstream&);
30 void trimQScores(int, int);
32 bool stripQualThreshold(Sequence&, double);
33 bool stripQualRollingAverage(Sequence&, double);
34 bool stripQualWindowAverage(Sequence&, int, int, double);
35 bool cullQualAverage(Sequence&, double);
36 void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
37 void updateForwardMap(vector<vector<int> >&, int, int, int);
38 void updateReverseMap(vector<vector<int> >&, int, int, int);
39 void setName(string n);
40 void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
41 vector<int> getScores() { return qScores; }
45 double calculateAverage();
52 string getSequenceName(ifstream&);
55 /**************************************************************************************************/