last checkin for 1.25.1

diff --git a/aligncommand.h b/aligncommand.h
index 86bb4d7a4377904f0ca3c2712204d5932fdb46f6..7eeaa1eb7e7bc3e2dc28d144d646b2190eb34983 100644 (file)
--- 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 b0d12b87bc49f4d3b6e9cae63558ba622b199701..ca8c62d43821652d6bf4ea868e9444d54c256ff4 100644 (file)
--- 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;