This is v.1.4.0

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 70094f2f3afe77711dcb4fe7b46d70f3d35f4835..d0f0af0976bd9e2feba32f8757b6b22067eebbc8 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -156,9 +156,9 @@ int ScreenSeqsCommand::execute(){
                        }
                        gobble(inFASTA);
                }       
-               if(namefile != "")              {       screenNameGroupFile(badSeqNames);       }
-               if(groupfile != "")             {       screenGroupFile(badSeqNames);           }
-               if(alignreport != "")   {       screenAlignReport(badSeqNames);         }
+               if(namefile != "" && groupfile != "")   {       screenNameGroupFile(badSeqNames);       }       // this screens both names and groups
+               else if(groupfile != "")                                {       screenGroupFile(badSeqNames);           }       // this screens just the groups
+               if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
                
                goodSeqOut.close();
                badSeqOut.close();