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

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 7c3b24b8c4595079a053eab7ecd9179a1ac72d69..30136505f2a2136028c392c8e3e346ce878e045d 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -150,10 +150,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(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; }
@@ -287,6 +284,7 @@ int ChimeraPintailCommand::execute(){
                        
                        chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
                        
+                       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])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";