minor mods to seq.error

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 520d0bb56eae9c66a936311ca71aa5330bf29aa1..b23ee1924d1a69ef8783a2d4f343f8b2cec74499 100644 (file)
--- 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
@@ -373,10 +376,11 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
                        if(errorSeq[i] == 'm')          {       qualErrorMap['m'][qScores[qIndex]] += weight;   }
                        else if(errorSeq[i] == 's')     {       qualErrorMap['s'][qScores[qIndex]] += weight;   }
                        else if(errorSeq[i] == 'i')     {       qualErrorMap['i'][qScores[qIndex]] += weight;   }
-                       else if(errorSeq[i] == 'a')     {       qualErrorMap['a'][qScores[qIndex]] += weight;   }
+                       else if(errorSeq[i] == 'a')     {       qualErrorMap['a'][qScores[qIndex]] += weight;   /*if(qScores[qIndex] != 0){     cout << qIndex << '\t';         }*/     }
                        else if(errorSeq[i] == 'd')     {       /*      there are no qScores for deletions      */              }
 
                        if(errorSeq[i] != 'd')          {       qIndex++;       }
+                                               
                        if(qIndex > stop){      break;  }
                }       
        }