added homova command

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 4dd5b38d4f7ab3895d7fa305bdb57f2e9ab5a628..90412c62b6ae20705c0ba1c162c4c73c260d0171 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -271,12 +271,12 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                int start = 0;
                
                if(seqLength < windowSize) {    return 0;       }
-               
+                       
                while(start < seqLength){
                        double windowSum = 0.0000;
 
                        for(int i=start;i<end;i++){
-                               windowSum += qScores[i];                                
+                               windowSum += qScores[i];
                        }
                        double windowAverage = windowSum / (double)(end-start);
                        
@@ -289,10 +289,8 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
                        if(end >= seqLength){   end = seqLength - 1;    }
                }
                
-               
                if(end == -1){  end = seqLength;        }
                
-               
                sequence.setUnaligned(rawSequence.substr(0,end));
                trimQScores(-1, end);