fixed some bugs found while testing 1.8

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ddb70290936458fdbc5ca85d550fff1bc1d6ea96..5eb4ff5df0eaf4999808925e658e61c1eedccf31 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -155,11 +155,16 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                delete command;   //delete the old command
                
                //user has opted to redirect output from dir where input files are located to some other place
-               if (outputDir != "") { optionString += ", outputdir=" + outputDir; }
+               if (outputDir != "") { 
+                       if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+                       else { optionString += "outputdir=" + outputDir; }
+               }
                
                //user has opted to redirect input from dir where mothur.exe is located to some other place
-               if (inputDir != "") { optionString += ", inputdir=" + inputDir; }
-
+               if (inputDir != "") { 
+                       if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+                       else { optionString += "inputdir=" + inputDir; }
+               }
                
                if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                    }
                else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                             }