working on current change

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index f62bb0ca8bcf0e0cd5b63ca080208af0b1a5d00d..a01441ed7ad6db77aa26b1a147755cd7eaa354bc 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -126,7 +126,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                                designfile = m->getDesignFile(); 
                                if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setDesignFile(designfile); } 
                        
                        //make sure the user has already run the read.otu command
                        sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -136,7 +136,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setSharedFile(sharedfile); } 
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...