X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=d57ef08ae00e6465edf2cdc17a90da26d968d4f5;hb=b1343ad169d7ec5caa2d683ebc562d5423249c4d;hp=6dee9862ec2c7582aa9a56dd2f5e8bd4f2ce9127;hpb=f3edf14c46814ca437960f0e1070abfbea582c26;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 6dee986..d57ef08 100644
--- 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) {