X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=qualityscores.cpp;h=916dab3a59743e4bcb860bd9891dcfbda74504b4;hp=3a1687bf9e174d77ddded9eaf331d6f1a78da734;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=aca78ed4a47dff8672ea8fd93cef0dfbaf0f7495

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 3a1687b..916dab3 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -23,7 +23,19 @@ QualityScores::QualityScores(){
 		exit(1);
 	}							
 }
+/**************************************************************************************************/
 
+QualityScores::QualityScores(string n, vector<int> s){
+	try {
+		m = MothurOut::getInstance();
+		setName(n);
+        setScores(s);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "QualityScores", "QualityScores");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 QualityScores::QualityScores(ifstream& qFile){
@@ -344,10 +356,9 @@ double QualityScores::calculateAverage(bool logTransform){
         if (logTransform)   {  aveQScore += pow(10.0, qScores[i]);  }
         else                {  aveQScore += qScores[i];             }
 	}
-	aveQScore /= (double) seqLength;
     
-    if (logTransform)   {  aveQScore = log10(aveQScore /(double) seqLength);  }
-    else                {  aveQScore /= (double) seqLength;                 }
+    if (logTransform)   {  aveQScore = log10(aveQScore /(double) seqLength);    }
+    else                {  aveQScore /= (double) seqLength;                     }
 	
 	return aveQScore;
 }
@@ -366,6 +377,8 @@ bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage, bool lo
 			
 		double aveQScore = calculateAverage(logTransform);
 		
+        if (m->debug) { m->mothurOut("[DEBUG]: " + sequence.getName() + " average = " + toString(aveQScore) + "\n"); }
+        
 		if(aveQScore >= qAverage)	{	success = 1;	}
 		else						{	success = 0;	}