X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.cpp;h=223e5dbb86600907fafaafdf5af48ee665adfc5b;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=e32867f3737b27bc3b9e929a73f142fe564d48c4;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index e32867f..223e5db 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -142,7 +142,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}else { m->setFastaFile(fastafile); }	
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
 			
@@ -159,11 +159,15 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);  if (temp == "not found") { temp = "100"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(fastafile);	}
-
+			
+			if (namefile == ""){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {