added blastlocation to chimera.slayer and fixed issue with clearcut getting current...

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 29a5d725ff121b47b5c8f3132f54776f3e8a34ff..d3c7fa48128246f8f4cb28ad53727329b3de856c 100644 (file)
--- 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;