*
*/
+//DataStructure for a quality file.
+
#include "mothur.h"
#include "mothurout.h"
QualityScores();
QualityScores(ifstream&);
string getName();
+
+ vector<int> getQualityScores() { return qScores; }
void printQScores(ofstream&);
void trimQScores(int, int);
void flipQScores();
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);
+ void setName(string n) { seqName = n; }
+ void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
+
+
private:
double calculateAverage();