X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=29c81e295c883bc42d48830b59243f8961a273fb;hb=bbdb72971ea4cd171abe34985af89f97bc2a31d3;hp=dd5d6de8da69a000882eadd86f8d2c50f853454f;hpb=ccaad73f103d8f105264d65491ce19e5df80477d;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index dd5d6de..29c81e2 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -220,8 +220,8 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		int seqLength = sequence.getNumBases();
 		
 		if(seqName != sequence.getName()){
-			m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
-			m->mothurOutEndLine();	
+			m->mothurOut("sequence name mismatch between fasta: " + sequence.getName() + " and qual file: " + seqName);
+			m->mothurOutEndLine();
 		}
 		
 		int end = windowSize;
@@ -237,7 +237,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 			double windowAverage = windowSum / (double)(end-start);
 			
 			if(windowAverage < qThreshold){
-				end = start;
+				end = end - stepSize;
 				break;
 			}
 			start += stepSize;