X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=qualityscores.h;h=a802636fd364071ab15aa84c148ebb38fead14b4;hp=87699739d34ad012b121a295be53f976b122a5b7;hb=a2cde58c1e72199498a2142983ef040dce36da10;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a

diff --git a/qualityscores.h b/qualityscores.h
index 8769973..a802636 100644
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -30,19 +30,19 @@ public:
 	void trimQScores(int, int);
 	void flipQScores();
 	bool stripQualThreshold(Sequence&, double);
-	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; }
 	
 private:
 	
-	double calculateAverage();
+	double calculateAverage(bool);
 	MothurOut* m;
 	vector<int> qScores;