working on current change

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index a4464692607df14d08384f3cfdf112a4e18debb8..a9bffc6eca25d3ad78ce7b01d96e196ba6308bfb 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -117,11 +117,12 @@ CountSeqsCommand::CountSeqsCommand(string option)  {
                                namefile = m->getNameFile(); 
                                if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all"; }