added sorted parameter to get.oturep, added error checking to chimera classes in...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index bf0ffa66009ba7cdc02f46ff4d2c784e58a45a1f..3632e6363b2414eb67b1d90fd958175f7f0bc8aa 100644 (file)
--- 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;