modified seqerror and qualscores

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 6dee9862ec2c7582aa9a56dd2f5e8bd4f2ce9127..d57ef08ae00e6465edf2cdc17a90da26d968d4f5 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -308,6 +308,8 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
        try {
 
                int seqLength = errorSeq.size();
+               cout << start << '\t' << stop << '\t' << seqLength << endl;
+               
                int qIndex = start - 1;
                for(int i=0;i<seqLength;i++){
                        
@@ -318,7 +320,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
                        else if(errorSeq[i] == 'd')     {       /*      there are no qScores for deletions      */              }
 
                        if(errorSeq[i] != 'd')          {       qIndex++;       }
-
+                       if(qIndex > stop){      break;  }
                }       
        }
        catch(exception& e) {