From b1343ad169d7ec5caa2d683ebc562d5423249c4d Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Thu, 3 Mar 2011 21:40:52 +0000
Subject: [PATCH] modified seqerror and qualscores

---
 qualityscores.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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) {
-- 
2.39.2