class QualityScores {
public:
QualityScores();
- QualityScores(ifstream&);
+ QualityScores(ifstream&, int);
string getName();
void printQScores(ofstream&);
void trimQScores(int, int);
bool stripQualRollingAverage(Sequence&, double);
bool stripQualWindowAverage(Sequence&, int, int, double);
bool cullQualAverage(Sequence&, double);
+ 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);
+
private:
double calculateAverage();