X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=ae85d86199c3ce9fbec09aac5525b17db3c4297a;hb=59814dd1de1def2b7d162c27c21190d8f1199cba;hp=520d0bb56eae9c66a936311ca71aa5330bf29aa1;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 520d0bb..ae85d86 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -286,23 +286,26 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 
 		if(seqLength < windowSize) {	return 0;	}
 			
-		while(start < seqLength){
+		while((start+windowSize) < seqLength){
 			double windowSum = 0.0000;
 
 			for(int i=start;i<end;i++){
 				windowSum += qScores[i];
 			}
 			double windowAverage = windowSum / (double)(end-start);
-			
+				
 			if(windowAverage < qThreshold){
 				end = end - stepSize;
 				break;
 			}
+			
 			start += stepSize;
 			end = start + windowSize;
-			if(end >= seqLength){	end = seqLength - 1;	}
+				
+			if(end >= seqLength){	end = seqLength;	}
+				
 		}
-		
+	
 		if(end == -1){	end = seqLength;	}
 		
 		//failed first window