fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 21de0344e7c856bb83105abe9b51cf8fe5b4a8ec..582da493e4dc5cdf5267d65606181d1594f56a87 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -147,7 +147,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                        // ...at some point should added some additional type checking...
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
-                       else if (namefile == "not open") { abort = true; }      
+                       else if (namefile == "not open") { namefile = ""; abort = true; }       
                        else {  m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
@@ -162,7 +162,10 @@ PreClusterCommand::PreClusterCommand(string option) {
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);
                        
-                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
                                
        }