X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=b46e1fb14f9aaf9c34a94216ffd5692c4f043148;hb=3c9e8dcf7e1f73e911a52742961c2f9b4c14541d;hp=5a469963875ab3673e4d9b892e9ecf472f5af09e;hpb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 5a46996..b46e1fb 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -154,6 +154,14 @@ ClusterCommand::ClusterCommand(string option)  {
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["name"] = inputDir + it->second;		}
 				}
+                
+                it = parameters.find("count");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["count"] = inputDir + it->second;		}
+				}
 			}
 			
 			//check for required parameters
@@ -304,7 +312,7 @@ int ClusterCommand::execute(){
             ct = new CountTable();
             ct->readTable(countfile);
             read->read(ct);
-        }
+        }else { read->read(nameMap); }
 		
 		list = read->getListVector();
 		matrix = read->getDMatrix();