X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=392f5877d9099308593d0cba26a8ff7baddd1d3b;hb=55ec7cde88d5512e177fe9488d5ee13793853bad;hp=b4259bfddfa565d1a6982e6583009c3690c90089;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index b4259bf..392f587 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -313,10 +313,10 @@ int SeqErrorCommand::execute(){
 			else{	minCompare.weight = 1;	}
 
 			printErrorData(minCompare, numParentSeqs);
-
+		
 			if(!ignoreSeq){
-				
-				for(int i=0;i<minCompare.total;i++){
+
+				for(int i=0;i<minCompare.sequence.length();i++){
 					char letter = minCompare.sequence[i];
 
 					errorForward[letter][i] += minCompare.weight;
@@ -429,12 +429,13 @@ void SeqErrorCommand::getReferences(){
 			int numAmbigs = currentSeq.getAmbigBases();
 			if(numAmbigs > 0){	numAmbigSeqs++;	}
 			
-			int startPos = currentSeq.getStartPos();
-			if(startPos > maxStartPos)	{	maxStartPos = startPos;	}
-
-			int endPos = currentSeq.getEndPos();
-			if(endPos < minEndPos)		{	minEndPos = endPos;		}
+//			int startPos = currentSeq.getStartPos();
+//			if(startPos > maxStartPos)	{	maxStartPos = startPos;	}
+//
+//			int endPos = currentSeq.getEndPos();
+//			if(endPos < minEndPos)		{	minEndPos = endPos;		}
 			referenceSeqs.push_back(currentSeq);
+				
 			m->gobble(referenceFile);
 		}
 		referenceFile.close();