added modify names parameter to set.dir

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 93e29fd6e4daad8f09c6d373ba3b57e00ea55b52..2ac2eaa6bd2466df296e407e7e67f9c8a095edc3 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -305,7 +305,7 @@ int ClusterCommand::execute(){
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             read->read(ct);
         }else { read->read(nameMap); }
                
@@ -336,10 +336,10 @@ int ClusterCommand::execute(){
                
         map<string, string> variables; 
         variables["[filename]"] = fileroot;
-        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         variables["[clustertag]"] = tag;
         string sabundFileName = getOutputFileName("sabund", variables);
         string rabundFileName = getOutputFileName("rabund", variables);
+        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         string listFileName = getOutputFileName("list", variables);
         
         if (countfile == "") {