added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index a504d0b496dec5b23795b546c70b573bc6c0c2ca..5972c62f028100b71b9007785af7c9d4600aaeb4 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -82,10 +82,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
-                               outputDir = ""; 
-                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
-                       }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
@@ -152,7 +149,8 @@ int ChimeraBellerophonCommand::execute(){
                        int start = time(NULL); 
                        
                        chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);     
-                                       
+                       
+                       if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it               
                        string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  "bellerophon.chimeras";
                        string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";