made dups=T default in get.seqs

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 68d0d2b4e4a8f9addeb39d4ee853d12aef61592f..6d4bff2c38cf495a843b9c57ff7eff802a7ee72f 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -218,7 +218,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        else if (qualfile == "not found") {  qualfile = "";  }
                        
                        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") { temp = "true"; usedDups = ""; }
                        dups = m->isTrue(temp);
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }