added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 19eaf85bc04fdce079f21a189c7d5bd4baa6eca0..06e627a615dacf69fe80464db0123582bef510ed 100644 (file)
--- 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
@@ -481,12 +489,12 @@ void ClusterCommand::printData(string label){
                loops = 0;
                start = time(NULL);
         
+        oldRAbund.setLabel(label);
         if (countfile == "") {
             oldRAbund.print(rabundFile);
             oldRAbund.getSAbundVector().print(sabundFile);
         }
-        
-        oldRAbund.setLabel(label);
+       
         if (m->isTrue(showabund)) {
             oldRAbund.getSAbundVector().print(cout);
         }