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

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 996843b7da9a1c246dc6b38310c0e8f35c327c94..d2f3067a3beb153242cfd5c945156e0e11f42b9b 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -95,10 +95,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(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 = ""; }
 
                        templatefile = validParameter.validFile(parameters, "template", true);
                        if (templatefile == "not open") { abort = true; }
@@ -218,7 +215,8 @@ int ChimeraSlayerCommand::execute(){
                        int start = time(NULL); 
                        
                        chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);   
-                                                       
+                       
+                       if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it                               
                        string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras";
                        string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";