diff -Nru jellyfish-2.2.5/configure.ac jellyfish-2.2.6/configure.ac
--- jellyfish-2.2.5/configure.ac	2016-03-11 17:45:08.000000000 +0000
+++ jellyfish-2.2.6/configure.ac	2016-05-25 12:47:28.000000000 +0000
@@ -1,4 +1,4 @@
-AC_INIT([jellyfish], [2.2.5], [gmarcais@umd.edu])
+AC_INIT([jellyfish], [2.2.6], [gmarcais@umd.edu])
 AC_CANONICAL_HOST
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])
diff -Nru jellyfish-2.2.5/debian/changelog jellyfish-2.2.6/debian/changelog
--- jellyfish-2.2.5/debian/changelog	2016-03-13 05:57:53.000000000 +0000
+++ jellyfish-2.2.6/debian/changelog	2016-08-30 12:16:52.000000000 +0000
@@ -1,3 +1,14 @@
+jellyfish (2.2.6-1) unstable; urgency=medium
+
+  * New upstream version
+  * Rename python module from python3-jellyfish to python3-dna-jellyfish
+    (thanks for the patches to "Diego M. Rodriguez" <diego.plan9@gmail.com>)
+    Closes: #819016
+  * cme fix dpkg-control
+  * hardening=+all,-pie
+
+ -- Andreas Tille <tille@debian.org>  Tue, 30 Aug 2016 14:16:52 +0200
+
 jellyfish (2.2.5-1) unstable; urgency=medium
 
   [ Andreas Tille ]
diff -Nru jellyfish-2.2.5/debian/control jellyfish-2.2.6/debian/control
--- jellyfish-2.2.5/debian/control	2016-03-13 05:57:53.000000000 +0000
+++ jellyfish-2.2.6/debian/control	2016-08-30 12:16:52.000000000 +0000
@@ -19,7 +19,7 @@
                dh-python,
                perl,
                chrpath
-Standards-Version: 3.9.7
+Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jellyfish.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/jellyfish.git
 Homepage: http://www.cbcb.umd.edu/software/jellyfish/
@@ -90,7 +90,7 @@
  This package contains the development files (static library and
  header files)
 
-Package: python3-jellyfish
+Package: python3-dna-jellyfish
 Architecture: any-amd64
 Section: python
 Depends: ${python3:Depends},
diff -Nru jellyfish-2.2.5/debian/patches/enable_c++11_error_deprecated-declarations.patch jellyfish-2.2.6/debian/patches/enable_c++11_error_deprecated-declarations.patch
--- jellyfish-2.2.5/debian/patches/enable_c++11_error_deprecated-declarations.patch	2016-03-13 05:57:53.000000000 +0000
+++ jellyfish-2.2.6/debian/patches/enable_c++11_error_deprecated-declarations.patch	1970-01-01 00:00:00.000000000 +0000
@@ -1,42 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 23 Dec 2015 21:01:45 +0100
-Bug-Debian: https://bugs.debian.org/808537
-Description: enable build with c++11 and -Werror=deprecated-declarations compile
- flag (thanks for the hint to Gert Wollny at
-   https://lists.debian.org/debian-mentors/2015/12/msg00360.html
- )
-
-
---- a/jellyfish/merge_files.cc
-+++ b/jellyfish/merge_files.cc
-@@ -35,8 +35,8 @@ using jellyfish::file_header;
- using jellyfish::RectangularBinaryMatrix;
- using jellyfish::mer_dna;
- using jellyfish::cpp_array;
--typedef std::auto_ptr<binary_reader> binary_reader_ptr;
--typedef std::auto_ptr<text_reader> text_reader_ptr;
-+typedef std::unique_ptr<binary_reader> binary_reader_ptr;
-+typedef std::unique_ptr<text_reader> text_reader_ptr;
- 
- struct file_info {
-   std::ifstream is;
-@@ -47,7 +47,7 @@ struct file_info {
-   header(is)
-   { }
- };
--typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr;
-+typedef std::unique_ptr<RectangularBinaryMatrix> matrix_ptr;
- 
- template<typename reader_type, typename writer_type>
- void do_merge(cpp_array<file_info>& files, std::ostream& out, writer_type& writer,
---- a/sub_commands/count_main.cc
-+++ b/sub_commands/count_main.cc
-@@ -245,7 +245,7 @@ int count_main(int argc, char *argv[])
-   if(args.disk_flag)
-     ary.do_size_doubling(false);
- 
--  std::auto_ptr<jellyfish::dumper_t<mer_array> > dumper;
-+  std::unique_ptr<jellyfish::dumper_t<mer_array> > dumper;
-   if(args.text_flag)
-     dumper.reset(new text_dumper(args.threads_arg, args.output_arg, &header));
-   else
diff -Nru jellyfish-2.2.5/debian/patches/rename-python-module-to-dna_jellyfish.patch jellyfish-2.2.6/debian/patches/rename-python-module-to-dna_jellyfish.patch
--- jellyfish-2.2.5/debian/patches/rename-python-module-to-dna_jellyfish.patch	1970-01-01 00:00:00.000000000 +0000
+++ jellyfish-2.2.6/debian/patches/rename-python-module-to-dna_jellyfish.patch	2016-08-30 12:16:52.000000000 +0000
@@ -0,0 +1,139 @@
+Author:  "Diego M. Rodriguez" <diego.plan9@gmail.com>
+Last-Update: Tue, 22 Mar 2016 23:19:15 +0100
+Bug-Debian: https://bugs.debian.org/819016
+Subject: Rename python bindings module name
+
+--- a/swig/python/setup.py
++++ b/swig/python/setup.py
+@@ -12,13 +12,13 @@ from distutils.core import setup, Extens
+ swig_time = os.path.getmtime('../jellyfish.i')
+ older = True
+ try:
+-    older = os.path.getmtime('jellyfish_wrap.cxx') < swig_time or os.path.getmtime('jellyfish.py') < swig_time
++    older = os.path.getmtime('jellyfish_wrap.cxx') < swig_time or os.path.getmtime('dna_jellyfish.py') < swig_time
+ except FileNotFoundError:
+     older = True
+ 
+ if older:
+-    print("Running swig: swig -c++ -python -o jellyfish_wrap.cxx ../jellyfish.i")
+-    os.system("swig -c++ -python -o jellyfish_wrap.cxx ../jellyfish.i")
++    print("Running swig: swig -c++ -python -module dna_jellyfish -o jellyfish_wrap.cxx ../jellyfish.i")
++    os.system("swig -c++ -python -module dna_jellyfish -o jellyfish_wrap.cxx ../jellyfish.i")
+ 
+ jf_include = [re.sub(r'-I', '', x) for x in os.popen("pkg-config --cflags-only-I jellyfish-2.0").read().rstrip().split()]
+ jf_cflags  = os.popen("pkg-config --cflags-only-other jellyfish-2.0").read().rstrip().split()
+@@ -28,7 +28,7 @@ jf_libdir  = [re.sub(r'-L', '', x) for x
+ jf_ldflags = os.popen("pkg-config --libs-only-other jellyfish-2.0").read().rstrip().split()
+ 
+ 
+-jellyfish_module = Extension('_jellyfish',
++jellyfish_module = Extension('_dna_jellyfish',
+                              sources = ['jellyfish_wrap.cxx'],
+                              include_dirs = jf_include,
+                              libraries = jf_libs,
+@@ -36,9 +36,9 @@ jellyfish_module = Extension('_jellyfish
+                              extra_compile_args = ["-std=c++0x"] + jf_cflags,
+                              extra_link_args = jf_ldflags,
+                              language = "c++")
+-setup(name = 'jellyfish',
++setup(name = 'dna_jellyfish',
+       version = '0.0.1',
+       author = 'Guillaume Marcais',
+       description = 'Access to jellyfish k-mer counting',
+       ext_modules = [jellyfish_module],
+-      py_modules = ["jellyfish"])
++      py_modules = ["dna_jellyfish"])
+--- a/swig/python/test_hash_counter.py
++++ b/swig/python/test_hash_counter.py
+@@ -1,20 +1,20 @@
+ import unittest
+ import sys
+ import random
+-import jellyfish
++import dna_jellyfish
+ 
+ class TestHashCounter(unittest.TestCase):
+     def setUp(self):
+-        jellyfish.MerDNA.k(100)
+-        self.hash = jellyfish.HashCounter(1024, 5)
++        dna_jellyfish.MerDNA.k(100)
++        self.hash = dna_jellyfish.HashCounter(1024, 5)
+ 
+     def test_info(self):
+-        self.assertEqual(100, jellyfish.MerDNA.k())
++        self.assertEqual(100, dna_jellyfish.MerDNA.k())
+         self.assertEqual(1024, self.hash.size())
+         self.assertEqual(5, self.hash.val_len())
+ 
+     def test_add(self):
+-        mer  = jellyfish.MerDNA()
++        mer  = dna_jellyfish.MerDNA()
+         good = True
+         for i in range(1000):
+             mer.randomize()
+--- a/swig/python/test_mer_file.py
++++ b/swig/python/test_mer_file.py
+@@ -1,4 +1,4 @@
+-import jellyfish
++import dna_jellyfish
+ import unittest
+ import sys
+ import os
+@@ -6,7 +6,7 @@ from collections import Counter
+ 
+ class TestMerFile(unittest.TestCase):
+     def setUp(self):
+-        self.mf = jellyfish.ReadMerFile(os.path.join(data, "swig_python.jf"))
++        self.mf = dna_jellyfish.ReadMerFile(os.path.join(data, "swig_python.jf"))
+ 
+     def test_histo(self):
+         histo = Counter()
+@@ -46,7 +46,7 @@ class TestMerFile(unittest.TestCase):
+ 
+     def test_query(self):
+         good = True
+-        qf   = jellyfish.QueryMerFile(os.path.join(data, "swig_python.jf"))
++        qf   = dna_jellyfish.QueryMerFile(os.path.join(data, "swig_python.jf"))
+         for mer, count in self.mf:
+             good = good and count == qf[mer]
+             if not good: break
+--- a/swig/python/test_string_mers.py
++++ b/swig/python/test_string_mers.py
+@@ -1,21 +1,21 @@
+ import unittest
+ import sys
+ import random
+-import jellyfish
++import dna_jellyfish
+ 
+ class TestStringMers(unittest.TestCase):
+     def setUp(self):
+         bases = "ACGTacgt"
+         self.str = ''.join(random.choice(bases) for _ in range(1000))
+         self.k = random.randint(10, 110)
+-        jellyfish.MerDNA.k(self.k)
++        dna_jellyfish.MerDNA.k(self.k)
+ 
+     def test_all_mers(self):
+         count = 0
+         good = True
+-        mers = jellyfish.string_mers(self.str)
++        mers = dna_jellyfish.string_mers(self.str)
+         for m in mers:
+-            m2 = jellyfish.MerDNA(self.str[count:count+self.k])
++            m2 = dna_jellyfish.MerDNA(self.str[count:count+self.k])
+             good = good and m == m2
+             count += 1
+         self.assertTrue(good)
+@@ -23,9 +23,9 @@ class TestStringMers(unittest.TestCase):
+ 
+     def test_canonical_mers(self):
+         good = True
+-        mers = jellyfish.string_canonicals(self.str)
++        mers = dna_jellyfish.string_canonicals(self.str)
+         for count, m in enumerate(mers):
+-            m2 = jellyfish.MerDNA(self.str[count:count+self.k])
++            m2 = dna_jellyfish.MerDNA(self.str[count:count+self.k])
+             rm2 = m2.get_reverse_complement()
+             good = good and (m == m2 or m == rm2)
+             good = good and (not (m > m2)) and (not (m > rm2))
diff -Nru jellyfish-2.2.5/debian/patches/series jellyfish-2.2.6/debian/patches/series
--- jellyfish-2.2.5/debian/patches/series	2016-03-13 05:57:53.000000000 +0000
+++ jellyfish-2.2.6/debian/patches/series	2016-08-30 12:16:52.000000000 +0000
@@ -1,5 +1,5 @@
 pkg-config-with-name
-enable_c++11_error_deprecated-declarations.patch
 drop-rpath
 modern-g++
 spelling
+rename-python-module-to-dna_jellyfish.patch 
diff -Nru jellyfish-2.2.5/debian/rules jellyfish-2.2.6/debian/rules
--- jellyfish-2.2.5/debian/rules	2016-03-13 05:57:53.000000000 +0000
+++ jellyfish-2.2.6/debian/rules	2016-08-30 12:16:52.000000000 +0000
@@ -3,16 +3,14 @@
 DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 build3vers := $(shell py3versions -sv)
 
-#export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-#DPKG_EXPORT_BUILDFLAGS = 1
-#include /usr/share/dpkg/buildflags.mk
-#breaks the build
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
 
 export DH_OPTIONS
 export PKG_CONFIG_LIBDIR=${CURDIR}
 export PKG_CONFIG_ALLOW_SYSTEM_LIBS=true
 export PKG_CONFIG_SYSROOT_DIR=${CURDIR}/debian/tmp/
 export PERL_MM_OPT=INSTALLDIRS=vendor
+export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"
 
 %:
 	dh $@ --with autoreconf,python3 #--parallel
@@ -22,8 +20,12 @@
 
 override_dh_install:
 	# dh_install -X*.a -X*.la -Xpkgconfig
-	dh_install -ppython3-jellyfish
-	pybuild -d swig/python --name jellyfish
+	dh_install -ppython3-dna-jellyfish
+	pybuild -d swig/python --name dna-jellyfish
+#	pybuild -d swig/python --name dna-jellyfish --disable test/python3
+#	pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py"
+#	pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py"
+	chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so
 	
 	dh_auto_configure --sourcedirectory=swig/perl5
 	dh_auto_build --sourcedirectory=swig/perl5
@@ -55,7 +57,7 @@
 	    rmdir debian/tmp_save_tests ; \
 	fi
 	rm -f tests/compat.sh
-	rm -f swig/python/jellyfish*
+	rm -f swig/python/jellyfish* swig/python/dna_jellyfish.py
 
 override_dh_auto_build:
 	mkdir -p debian/tmp_save_tests
diff -Nru jellyfish-2.2.5/include/jellyfish/rectangular_binary_matrix.hpp jellyfish-2.2.6/include/jellyfish/rectangular_binary_matrix.hpp
--- jellyfish-2.2.5/include/jellyfish/rectangular_binary_matrix.hpp	2016-03-11 17:45:08.000000000 +0000
+++ jellyfish-2.2.6/include/jellyfish/rectangular_binary_matrix.hpp	2016-05-25 12:47:28.000000000 +0000
@@ -344,9 +344,10 @@
         (((u128)1 << 64) - 1) << 64,
         ((u128)1 << 64) - 1,
         (u128)-1
-      };\
-    u128  res = res ^ res;
+      };
     u128* p   = (u128*)(_columns + _c - 2);
+    u128 res = 0;
+    //    u128  res = res ^ res;
 
     uint64_t j = 0, x = 0;
     for(unsigned int w = 0; w < nb_words(); ++w) {
diff -Nru jellyfish-2.2.5/jellyfish/merge_files.cc jellyfish-2.2.6/jellyfish/merge_files.cc
--- jellyfish-2.2.5/jellyfish/merge_files.cc	2016-03-11 17:45:08.000000000 +0000
+++ jellyfish-2.2.6/jellyfish/merge_files.cc	2016-05-25 12:47:28.000000000 +0000
@@ -35,8 +35,8 @@
 using jellyfish::RectangularBinaryMatrix;
 using jellyfish::mer_dna;
 using jellyfish::cpp_array;
-typedef std::auto_ptr<binary_reader> binary_reader_ptr;
-typedef std::auto_ptr<text_reader> text_reader_ptr;
+typedef std::unique_ptr<binary_reader> binary_reader_ptr;
+typedef std::unique_ptr<text_reader> text_reader_ptr;
 
 struct file_info {
   std::ifstream is;
@@ -47,7 +47,7 @@
   header(is)
   { }
 };
-typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr;
+typedef std::unique_ptr<RectangularBinaryMatrix> matrix_ptr;
 
 template<typename reader_type, typename writer_type>
 void do_merge(cpp_array<file_info>& files, std::ostream& out, writer_type& writer,
diff -Nru jellyfish-2.2.5/sub_commands/count_main.cc jellyfish-2.2.6/sub_commands/count_main.cc
--- jellyfish-2.2.5/sub_commands/count_main.cc	2016-03-11 17:45:08.000000000 +0000
+++ jellyfish-2.2.6/sub_commands/count_main.cc	2016-05-25 12:47:28.000000000 +0000
@@ -245,7 +245,7 @@
   if(args.disk_flag)
     ary.do_size_doubling(false);
 
-  std::auto_ptr<jellyfish::dumper_t<mer_array> > dumper;
+  std::unique_ptr<jellyfish::dumper_t<mer_array> > dumper;
   if(args.text_flag)
     dumper.reset(new text_dumper(args.threads_arg, args.output_arg, &header));
   else
diff -Nru jellyfish-2.2.5/swig/Makefile.am jellyfish-2.2.6/swig/Makefile.am
--- jellyfish-2.2.5/swig/Makefile.am	2016-03-11 17:45:08.000000000 +0000
+++ jellyfish-2.2.6/swig/Makefile.am	2016-05-25 12:47:28.000000000 +0000
@@ -9,7 +9,7 @@
 %/swig_wrap.cpp: $(SWIG_SRC)
 	$(SWIG_V_GEN)$(SWIG) -$(notdir $*) -I$(srcdir)/../include -o $@ $<
 else
-%/swig_wrap.cc:
+%/swig_wrap.cpp:
 	@echo >&2 SWIG >= 3.x.x not found. Make sure it is install and rerun configure
 	@false
 endif