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

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 753bc9ad9f43dc1008689ac877aa5c16ca11d0a5..ab10eb8f56bb04dffceb9f4a309ff59157c708d2 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -92,10 +92,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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; }
@@ -192,6 +189,7 @@ int ChimeraCcodeCommand::execute(){
                        if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
                        templateSeqsLength = chimera->getLength();
                        
+                       if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
                        string outputFileName, accnosFileName;
                        if (maskfile != "") {
                                outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";