X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimeraseqscommand.cpp;h=3632e6363b2414eb67b1d90fd958175f7f0bc8aa;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hp=bf0ffa66009ba7cdc02f46ff4d2c784e58a45a1f;hpb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e;p=mothur.git

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index bf0ffa6..3632e63 100644
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -196,7 +196,7 @@ int ChimeraSeqsCommand::execute(){
 		else if (method == "pintail")			{		chimera = new Pintail(fastafile, templatefile);				}
 		else if (method == "ccode")				{		chimera = new Ccode(fastafile, templatefile);				}
 		else if (method == "chimeracheck")		{		chimera = new ChimeraCheckRDP(fastafile, templatefile);		}
-		else if (method == "chimeraslayer")		{		chimera = new ChimeraSlayer(fastafile, templatefile);		}
+		//else if (method == "chimeraslayer")		{		chimera = new ChimeraSlayer(fastafile, templatefile);		}
 		else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;		}
 		
 		//set user options
@@ -227,7 +227,10 @@ int ChimeraSeqsCommand::execute(){
 		
 				
 		//find chimeras
-		chimera->getChimeras();
+		int error = chimera->getChimeras();
+		
+		//there was a problem
+		if (error == 1) {  return 0;  }
 		
 		string outputFileName = getRootName(fastafile) + method + maskfile + ".chimeras";
 		ofstream out;