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[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 0e500d4982d372c95436b99e1ead81cb3c02a9c5..fc4327f210d04241b5c1e7a6056759525998c738 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -115,7 +115,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }