minor mods to seq.error

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index ae85d86199c3ce9fbec09aac5525b17db3c4297a..b23ee1924d1a69ef8783a2d4f343f8b2cec74499 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -376,10 +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;  }
                }       
        }