From 4522aebe2246c5f47875d5c8cc505f1b615bfc7e Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Mon, 14 May 2012 13:49:25 -0400
Subject: [PATCH] last checkin for 1.25.1

---
 aligncommand.h    | 1 -
 setdircommand.cpp | 2 ++
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/aligncommand.h b/aligncommand.h
index 86bb4d7..7eeaa1e 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -1,6 +1,5 @@
 #ifndef ALIGNCOMMAND_H
 #define ALIGNCOMMAND_H
-//test
 /*
  *  aligncommand.h
  *  Mothur
diff --git a/setdircommand.cpp b/setdircommand.cpp
index b0d12b8..ca8c62d 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -92,6 +92,8 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
 			if (temp == "not found") {  debug = false;  nodebug=true; }
             else {  debug = m->isTrue(temp); }
             m->debug = debug;
+            
+            if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
 				
 			if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {	
 				m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;
-- 
2.39.2