worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
index 5db43113f1b4aedea7761cd4ad7bcc3575542919..4453145f690b9a8be8b8da1bbf78fd5626d5fa71 100644 (file)
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -20,8 +20,9 @@
 class QualityScores {
 public:
        QualityScores();
-       QualityScores(ifstream&, int);
+       QualityScores(ifstream&);
        string getName();
+       vector<int> getQualityScores() { return qScores; }
        void printQScores(ofstream&);
        void trimQScores(int, int);
        void flipQScores();
@@ -29,6 +30,10 @@ public:
        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();