fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index dfcf25b4447d28362dae3f27a4e9cfd27e362d8e..9704464bf80326c87d4afa556e3353b95fcbf37e 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -43,7 +43,7 @@ set<string> MothurOut::getCurrentTypes()  {
         types.insert("tree");
         types.insert("flow");
         types.insert("biom");
-        types.insert("counttable");
+        types.insert("count");
         types.insert("processors");
 
                return types;
@@ -79,7 +79,7 @@ void MothurOut::printCurrentFiles()  {
                if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
                if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
         if (biomfile != "")                    {  mothurOut("biom=" + biomfile); mothurOutEndLine();                           }
-        if (counttablefile != "")      {  mothurOut("counttable=" + counttablefile); mothurOutEndLine();       }
+        if (counttablefile != "")      {  mothurOut("count=" + counttablefile); mothurOutEndLine();    }
                if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
                
        }
@@ -1052,6 +1052,9 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
 int MothurOut::renameFile(string oldName, string newName){
        try {
+        
+        if (oldName == newName) { return 0; }
+        
                ifstream inTest;
                int exist = openInputFile(newName, inTest, "");
                inTest.close();