]> git.donarmstrong.com Git - mothur.git/blobdiff - clustercommand.cpp
Merge remote-tracking branch 'origin/master'
[mothur.git] / clustercommand.cpp
index 5a469963875ab3673e4d9b892e9ecf472f5af09e..b46e1fb14f9aaf9c34a94216ffd5692c4f043148 100644 (file)
@@ -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();