1.19.0

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 3f8722f34f83416aa143f21a5a81e99c7329a7d8..c9c65042843bffddf5c6d3d7acca4ab38754ac5e 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -278,7 +278,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                
                int end = windowSize;
                int start = 0;
-               
+
                if(seqLength < windowSize) {    return 0;       }
                        
                while(start < seqLength){
@@ -300,6 +300,9 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                
                if(end == -1){  end = seqLength;        }
                
+               //failed first window
+               if (end < windowSize) { return 0; }
+                       
                sequence.setUnaligned(rawSequence.substr(0,end));
                trimQScores(-1, end);