X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.h;h=f5493eb7517db72c20048da57080a587ae675f7e;hp=065e6b4532e071383c39c54e38047b01a2b45344;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 065e6b4..f5493eb 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -224,7 +224,7 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
 				
 				flowData.printFlows(trimFlowFile);
 				
-				if(pDataArray->fasta)	{	currSeq.printSequence(fastaFile);	}
+				if(pDataArray->fasta)	{	currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);	}
 				
 				if(pDataArray->allFiles){
 					ofstream output;