X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=772113baf83e9fbbd057794103f46ffa21c21fda;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=ad1bd81b4a9d4554751cfbbc5eb836e107e7b53d;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index ad1bd81..772113b 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -147,7 +147,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(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 {  readNameFile(); m->setNameFile(namefile); }
 			
 			string temp;
@@ -157,6 +157,11 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
 			temp = validParameter.validFile(parameters, "percent", false);		if (temp == "not found"){	temp = "0";				}
 			m->mothurConvert(temp, percent);
 			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
+			
 		}
 				
 	}