added N code to flow data. removed changed for trimming of fast=T in trim.flows.

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index ad79783eda2650928a293d45be58fd409ab50689..3abc7609ac85187513f416c378225e726c8bd197 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.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);   }
+                    if(fasta)  { currSeq.printSequence(fastaFile);     }
                     
                     if(allFiles){
                         ofstream output;