added indicator command

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 1ea9c39af69e703f41b0aa7c9e5194eeeb0efcf0..1a3de32088d3bf1351b1005c654ac612fcd27732 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -181,7 +181,11 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                        else if (taxfile == "not found") {  taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine();  abort = true; }
                        
                        string usedDups = "true";
-                       string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
+                       string temp = validParameter.validFile(parameters, "dups", false);      
+                       if (temp == "not found") { 
+                               if (namefile != "") {  temp = "true";                                   }
+                               else                            {  temp = "false"; usedDups = "";       }
+                       }
                        dups = m->isTrue(temp);
                        
                        taxons = validParameter.validFile(parameters, "taxon", false);