X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=a422c8883ea9f172fe076961fa7705cb548e767e;hb=15dfbabd5aa00c468a43f1f99cb73b2ebc5b5e3f;hp=097664efc2640af01a0b10cfa3bcd9efcc46d5e3;hpb=1e8d08e96f4fe99604a6b3502568de464bf60891;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 097664e..a422c88 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -305,9 +305,10 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 					
 					templatefile = validParameter.validFile(parameters, "reference", true);
 					if (templatefile == "not open") { abort = true; }
-					else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }	
+					else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true;  }	
 				}
-			}
+			}else if (hasName) {  templatefile = "self"; }
+			else { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }	
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);