X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=d3c7fa48128246f8f4cb28ad53727329b3de856c;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=29a5d725ff121b47b5c8f3132f54776f3e8a34ff;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 29a5d72..d3c7fa4 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -166,10 +166,10 @@ ClearcutCommand::ClearcutCommand(string option)  {
 				//is there are current file available for either of these?
 				//give priority to phylip, then fasta
 				phylipfile = m->getPhylipFile(); 
-				if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+				if (phylipfile != "") {  inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 
 					fastafile = m->getFastaFile(); 
-					if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+					if (fastafile != "") { inputFile = fastafile;  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 					else { 
 						m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine(); 
 						abort = true;