pat's slight modifications to trim.seqs

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index dd5d6de8da69a000882eadd86f8d2c50f853454f..29c81e295c883bc42d48830b59243f8961a273fb 100644 (file)
--- 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;