X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=16348c8d324a962ca336c82a2ad303f156cde9e3;hb=1e8d08e96f4fe99604a6b3502568de464bf60891;hp=cdcc6ca9745d8bdf3509c3505ef5c15dc61fd991;hpb=e51cb7e261265800fa2d2831b6516e33ebc7d78b;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index cdcc6ca..16348c8 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -75,6 +75,7 @@ ClusterCommand::ClusterCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -149,10 +150,10 @@ ClusterCommand::ClusterCommand(string option)  {
 				//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 cluster command."); m->mothurOutEndLine(); 
 						abort = true;