Merge remote-tracking branch 'origin'

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 58380942b021bfa370d71e5103118826924b5f67..ad79783eda2650928a293d45be58fd409ab50689 100644 (file)
--- 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;