X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.cpp;fp=chopseqscommand.cpp;h=fc4327f210d04241b5c1e7a6056759525998c738;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=0e500d4982d372c95436b99e1ead81cb3c02a9c5;hpb=23e60689fa4306234b3d05b116f25d198316d1ae;p=mothur.git

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 0e500d4..fc4327f 100644
--- 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);	}