fixed minor issue with sub.sample command.

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 5021f4085534cfc84a17d5875e449cf90f9f1d53..e8f42dda532fab7f252de8c95e220c8eb27fa8f8 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -189,6 +189,15 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                        else if (namefile == "not found") {  namefile = "";  }  
                        else { m->setNameFile(namefile); }
                        
+                       groupfile = validParameter.validFile(parameters, "group", true);
+                       if (groupfile == "not open") { abort = true; }
+                       else if (groupfile == "not found") {  
+                               //if there is a current group file, use it
+                               groupfile = m->getGroupFile(); 
+                               if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }else { m->setGroupFile(groupfile); }   
+                       
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }