fixed bug in chimera.uchime

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 097664efc2640af01a0b10cfa3bcd9efcc46d5e3..a422c8883ea9f172fe076961fa7705cb548e767e 100644 (file)
--- 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);