diff -Nru amap-align-2.2/debian/changelog amap-align-2.2/debian/changelog
--- amap-align-2.2/debian/changelog	2013-11-14 13:31:00.000000000 +0000
+++ amap-align-2.2/debian/changelog	2015-12-19 08:19:31.000000000 +0000
@@ -1,3 +1,13 @@
+amap-align (2.2-5) unstable; urgency=medium
+
+  * Moved debian/upstream to debian/upstream/metadata
+  * cme fix dpkg-control
+  * Fix Mayhem issue caused by not using getopt
+    Closes: #715630
+  * DEP5 fix
+
+ -- Andreas Tille <tille@debian.org>  Sat, 19 Dec 2015 09:17:45 +0100
+
 amap-align (2.2-4) unstable; urgency=low
 
   * debian/README.Debian: Mentioning that latest source is not available
diff -Nru amap-align-2.2/debian/control amap-align-2.2/debian/control
--- amap-align-2.2/debian/control	2013-11-14 12:47:35.000000000 +0000
+++ amap-align-2.2/debian/control	2015-12-19 07:46:58.000000000 +0000
@@ -5,10 +5,10 @@
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.4
+Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/amap-align/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/amap-align/trunk/
-X-Homepage: http://bio.math.berkeley.edu/amap/ - upstream seems to be dead
+Homepage: http://code.google.com/p/amap-align/
 
 Package: amap-align
 Architecture: any
diff -Nru amap-align-2.2/debian/copyright amap-align-2.2/debian/copyright
--- amap-align-2.2/debian/copyright	2013-11-14 13:05:36.000000000 +0000
+++ amap-align-2.2/debian/copyright	2015-12-19 08:19:22.000000000 +0000
@@ -3,6 +3,10 @@
 Source: http://bio.math.berkeley.edu/amap/download
         This download area as well as the homepage vanished
 
+Files: *
+Copyright: 2005—2007 Ariel Schwartz <sariel@cs.berkeley.edu>
+License: PD
+
 Files: display/*
 Copyright: © 2007 Michael E. Smoot
 License: GPL-2+
@@ -23,10 +27,6 @@
  On Debian systems, the complete text of the GNU General Public
  License can be found in `/usr/share/common-licenses/GPL'.
 
-Files: *
-Copyright: 2005—2007 Ariel Schwartz <sariel@cs.berkeley.edu>
-License: PD
-
 License: PD
  The current version of AMAP uses the PROBCONS 1.09 code base for some of the
  input/output procedures, and for the calculation of posterior probabilities
diff -Nru amap-align-2.2/debian/patches/mayhem.patch amap-align-2.2/debian/patches/mayhem.patch
--- amap-align-2.2/debian/patches/mayhem.patch	1970-01-01 00:00:00.000000000 +0000
+++ amap-align-2.2/debian/patches/mayhem.patch	2015-12-19 08:16:57.000000000 +0000
@@ -0,0 +1,32 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 19 Dec 2015 08:36:11 +0100
+Bug-Debian: https://bugs.debian.org/715630
+Description: This patch is a bit non-C++-ish but I'm not a C++
+ programmer and considered this at least a solution and code that
+ ignores getopt does not deserve more care. :-(
+
+--- a/align/Amap.cc
++++ b/align/Amap.cc
+@@ -747,6 +747,7 @@ SafeVector<string> ParseParams (int argc
+   SafeVector<string> sequenceNames;
+   int tempInt;
+   float tempFloat;
++  int has_sequence_argument = 0;
+ 
+   for (int i = 1; i < argc; i++){
+     if (argv[i][0] == '-'){
+@@ -1049,9 +1050,14 @@ SafeVector<string> ParseParams (int argc
+       }
+     }
+     else {
++      has_sequence_argument = 1;
+       sequenceNames.push_back (string (argv[i]));
+     }
+   }
++  if (!has_sequence_argument) {
++    cerr << "ERROR: No MFAFILE specified" << endl;
++    exit(1);
++  }
+ 
+   if (enableTrainEmissions && !enableTraining){
+     cerr << "ERROR: Training emissions (-e) requires training (-t)" << endl;
diff -Nru amap-align-2.2/debian/patches/series amap-align-2.2/debian/patches/series
--- amap-align-2.2/debian/patches/series	2013-11-14 13:00:48.000000000 +0000
+++ amap-align-2.2/debian/patches/series	2015-12-19 08:13:21.000000000 +0000
@@ -1,3 +1,4 @@
 fix-gcc-4.3.diff
 fix-gcc-4.6.diff
 hardening.patch
+mayhem.patch
File /tmp/tmpQTvCuV/BVxJoJqkRc/amap-align-2.2/debian/upstream is a regular file while file /tmp/tmpQTvCuV/Nq9Juc86Nk/amap-align-2.2/debian/upstream is a directory