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

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 94da28fdd112dcd7347768088f58164d3973ca05..5fbdfa891db7e57957df05538b5f2f4325684fe4 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -91,6 +91,7 @@
 #include "clusterfragmentscommand.h"
 #include "getlineagecommand.h"
 #include "removelineagecommand.h"
+#include "parsefastaqcommand.h"
 
 /*******************************************************/
 
@@ -186,6 +187,7 @@ CommandFactory::CommandFactory(){
        commands["cluster.fragments"]   = "cluster.fragments";
        commands["get.lineage"]                 = "get.lineage";
        commands["remove.lineage"]              = "remove.lineage";
+       commands["parse.fastaq"]                = "parse.fastaq";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -324,6 +326,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
                else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
                else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
+               else if(commandName == "parse.fastaq")                  {       command = new ParseFastaQCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;