working on chimera.uchime change for dereplicate=t bug. added shared file to get...

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 61b19b8dbaa61546c0e984e444fa8ddda5b366f1..7ecdf74916aa6ea61150d0174b685e8987a624c9 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -489,7 +489,7 @@ 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;