1.22.0

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 378e9186a70b46f8a8c8821b77e3c213b2859990..9742bcbd3b0ea952e3a5b5b54428bee701c5191f 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -232,10 +232,10 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
                                //give priority to column, then phylip
                                columnfile = m->getColumnFile(); 
-                               if (columnfile != "") {  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+                               if (columnfile != "") {  distFile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
                                else { 
                                        phylipfile = m->getPhylipFile(); 
-                                       if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+                                       if (phylipfile != "") {  distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                        else { 
                                                m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the get.oturep command."); m->mothurOutEndLine(); 
                                                abort = true;