X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=b23ee1924d1a69ef8783a2d4f343f8b2cec74499;hb=f5ef644ce76074de08b2bbb64097619b2b16d60d;hp=ae85d86199c3ce9fbec09aac5525b17db3c4297a;hpb=1a1ed6dda1d655ff006459f15c712f057c93ddaf;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index ae85d86..b23ee19 100644
--- 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;	}
 		}	
 	}