X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=d4cb57a3158a85008d30d9c875e331f5be5801e9;hb=1c898913f53fe4c6574102896b967d9347d1b42a;hp=a47aed0ca840197331cdf251ef48bcb68cf9df56;hpb=1e8d08e96f4fe99604a6b3502568de464bf60891;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index a47aed0..d4cb57a 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -309,9 +309,11 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(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.uchime command."); m->mothurOutEndLine(); abort = true;  }	
 				}
-			}
+			}else if (hasName) {  templatefile = "self"; }
+			else { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.uchime command, unless you have a namefile."); m->mothurOutEndLine(); abort = true;  }	
+
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
@@ -370,7 +372,7 @@ int ChimeraUchimeCommand::execute(){
 			int start = time(NULL);	
 			string nameFile = "";
 			
-			if (templatefile == "self") { //you want to run slayer with a refernce template
+			if (templatefile == "self") { //you want to run uchime with a refernce template
 				
 				#ifdef USE_MPI	
 					int pid; 
@@ -694,6 +696,8 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 		for(int i = 0; i < cPara.size(); i++)  {  delete[] cPara[i];  }
 		delete[] uchimeParameters; 
 		
+		if (m->control_pressed) { return 0; }
+		
 		//create accnos file from uchime results
 		ifstream in; 
 		m->openInputFile(outputFName, in);
@@ -711,7 +715,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 			in >> chimeraFlag >> name;
 			
 			//fix name if needed
-			if (templatefile != "self") { 
+			if (templatefile == "self") { 
 				name = name.substr(0, name.length()-1); //rip off last /
 				name = name.substr(0, name.find_last_of('/'));
 			}