X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=ad79783eda2650928a293d45be58fd409ab50689;hb=5ca84bbe4393adecc30dc05d64e79091ef35c40f;hp=58380942b021bfa370d71e5103118826924b5f67;hpb=1732ba6a38869c44c703423c3a16f3a6848f3277;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 5838094..ad79783 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -491,7 +491,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                 if (pos == string::npos) {		
                     flowData.printFlows(trimFlowFile);
                     
-                    if(fasta)	{	currSeq.printSequence(fastaFile);	}
+                    if(fasta)	{	currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);	}
                     
                     if(allFiles){
                         ofstream output;