get.oturep ifstream

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index a1d44857531ddea86b025ac1b6d0d888f21df702..4948a1a095343748dde3f467ff59c9ce5e050702 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -27,6 +27,7 @@ vector<string> GetLineageCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetLineageCommand::GetLineageCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -44,7 +45,7 @@ GetLineageCommand::GetLineageCommand(){
 //**********************************************************************************************************************
 vector<string> GetLineageCommand::getRequiredParameters(){     
        try {
-               string Array[] =  {"taxonomy"};
+               string Array[] =  {"taxonomy","taxon"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -181,7 +182,11 @@ GetLineageCommand::GetLineageCommand(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);