- bool stripQualRollingAverage(Sequence&, double);
- bool stripQualWindowAverage(Sequence&, int, int, double);
- bool cullQualAverage(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 = qScores.size(); }
+ vector<int> getScores() { return qScores; }
+