Freshen patches

10 files changed, 229 insertions, 365 deletions

diff --git a/debian/changelog b/debian/changelog
index 7589324..8018b0e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ bowtie2 (2.4.1-1) UNRELEASED; urgency=medium
     2-3+ hours to fail, so lets be nice and skip them.
     Patches to fix 32-bit archs are very welcomed!
   * Standards-Version: 4.5.0 (routine-update)
+  * Freshen patches
 
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 19 Dec 2019 11:52:41 -0800
 
diff --git a/debian/patches/2to3.patch b/debian/patches/2to3.patch
deleted file mode 100644
index 2daaf5f..0000000
--- a/debian/patches/2to3.patch
+++ /dev/null
@@ -1,248 +0,0 @@
-Description: Use 2to3 to port to Python3
-Bug-Debian: https://bugs.debian.org/936233
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
-
---- a/Makefile
-+++ b/Makefile
-@@ -481,11 +481,11 @@
- 
- bowtie2-build.bat:
- 	echo "@echo off" > bowtie2-build.bat
--	echo "python %~dp0/bowtie2-build %*" >> bowtie2-build.bat
-+	echo "python3 %~dp0/bowtie2-build %*" >> bowtie2-build.bat
- 
- bowtie2-inspect.bat:
- 	echo "@echo off" > bowtie2-inspect.bat
--	echo "python %~dp0/bowtie2-inspect %*" >> bowtie2-inspect.bat
-+	echo "python3 %~dp0/bowtie2-inspect %*" >> bowtie2-inspect.bat
- 
- .PHONY: bowtie2-src-pkg
- bowtie2-src-pkg: $(SRC_PKG_LIST)
---- a/scripts/sa.py
-+++ b/scripts/sa.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- 
- """
- sa.py
-@@ -15,7 +15,7 @@
- def loadBowtieSa(fh):
- 	""" Load a .sa file from handle into an array of ints """
- 	nsa = struct.unpack('I', fh.read(4))[0]
--	return [ struct.unpack('I', fh.read(4))[0] for i in xrange(0, nsa) ]
-+	return [ struct.unpack('I', fh.read(4))[0] for i in range(0, nsa) ]
- 
- def loadBowtieSaFilename(fn):
- 	""" Load a .sa file from filename into an array of ints """
-@@ -58,7 +58,7 @@
- 		# Suffix array is in sas; note that $ is considered greater than all
- 		# other characters
- 		if ref is not None:
--			for i in xrange(1, len(sas)):
-+			for i in range(1, len(sas)):
- 				sa1, sa2 = sas[i-1], sas[i]
- 				assert sa1 != sa2
- 				# Sanity check that suffixes are really in order
-@@ -76,4 +76,4 @@
- 			assert sas[-1] == len(ref)
- 	
- 	go()
--	
-\ No newline at end of file
-+	
---- a/scripts/test/README.md
-+++ b/scripts/test/README.md
-@@ -17,7 +17,7 @@
- 
- From root:
- 
--    python scripts/test/regressions.py --verbose
-+    python3 scripts/test/regressions.py --verbose
- 
- Val Antonescu originally set these up.
- 
-@@ -27,7 +27,7 @@
- 
- From root:
- 
--    python scripts/test/large_idx.py --verbose
-+    python3 scripts/test/large_idx.py --verbose
- 
- #### Randomized tests
- 
---- a/scripts/test/benchmark/benchmarks.py
-+++ b/scripts/test/benchmark/benchmarks.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- """
- A few items to deal with sets of benchmarks.
- """
-@@ -57,7 +57,7 @@
-         self.set_idx = 0
-         return self
- 
--    def next(self):
-+    def __next__(self):
-         if self.set_idx == len(self.values):
-             raise StopIteration
- 
-@@ -250,7 +250,7 @@
-                     delta = [0, 1]
-                     logging.debug("%s: missed (pos:%d vs %d)" % (q_name, orig[1], rec.pos))
-                 try:
--                    mapq_summary[rec.mapq] = map(sum, zip(delta, mapq_summary[rec.mapq]))
-+                    mapq_summary[rec.mapq] = list(map(sum, list(zip(delta, mapq_summary[rec.mapq]))))
-                 except KeyError:
-                     mapq_summary[rec.mapq] = delta
- 
---- a/scripts/test/benchmark/run.py
-+++ b/scripts/test/benchmark/run.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- """
-    Runs benchmark sets specified in JSON files.
- 
---- a/scripts/test/benchmark/samreader.py
-+++ b/scripts/test/benchmark/samreader.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- """
- A reader of SAM format.
- 
-@@ -49,7 +49,7 @@
-         self.curr_idx = 0
-         return self
- 
--    def next(self):
-+    def __next__(self):
-         if self.curr_idx == len(self.header_lines):
-             raise StopIteration
-             
-@@ -114,7 +114,7 @@
-         self._source_fh.seek(self.header.end_header_pointer)
-         return self
- 
--    def next(self):
-+    def __next__(self):
-         line = self._source_fh.readline()
-         if not line:
-             raise StopIteration
---- a/scripts/test/bt2face.py
-+++ b/scripts/test/bt2face.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- 
- import os
- import logging
---- a/scripts/test/btdata.py
-+++ b/scripts/test/btdata.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- """
- Note: This would look so much better replaced by XML or at least JSON. But 
-       is not worth to do it for now.
-@@ -6,7 +6,7 @@
- 
- import os
- import gzip
--import urllib2
-+import urllib.request, urllib.error, urllib.parse
- import logging
- 
- 
-@@ -66,14 +66,14 @@
-     def init_data(self):
-         """ Try and init the data we need.
-         """
--        for genome,gdata in self.genomes.iteritems():
-+        for genome,gdata in self.genomes.items():
-             gn_path  = os.path.join(self.data_dir_path,genome)
-             gn_fasta = os.path.join(gn_path,gdata['ref_name'])
-             if not os.path.exists(gn_fasta):
-                 self._get_genome(genome)
-                 self._build_genome(genome)
-         
--        for genome,gdata in self.joint_genomes.iteritems():
-+        for genome,gdata in self.joint_genomes.items():
-             gn_path  = os.path.join(self.data_dir_path,genome)
-             gn_fasta = os.path.join(gn_path,gdata['ref_name'])
-             if not os.path.exists(gn_fasta):
-@@ -103,7 +103,7 @@
-             
-             try:
-                 f = open(fname,'wb')
--                u = urllib2.urlopen(uri)
-+                u = urllib.request.urlopen(uri)
-                 f.write(u.read())
-             except:
-                 f.close()
---- a/scripts/test/dataface.py
-+++ b/scripts/test/dataface.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- 
- import os
- import logging
---- a/scripts/test/large_idx.py
-+++ b/scripts/test/large_idx.py
-@@ -1,8 +1,8 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- 
- import os
- import gzip
--import urllib2
-+import urllib.request, urllib.error, urllib.parse
- import inspect
- import unittest
- import logging
-@@ -69,7 +69,7 @@
-    
- def get_suite():
-     tests = ['test_human','test_mouse','test_large_index']
--    return unittest.TestSuite(map(TestLargeIndex,tests))
-+    return unittest.TestSuite(list(map(TestLargeIndex,tests)))
- 
-     
-             
---- a/scripts/test/regressions.py
-+++ b/scripts/test/regressions.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python3
- 
- import os
- import inspect
---- a/bowtie2-build
-+++ b/bowtie2-build
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- 
- """
-  Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
---- a/bowtie2-inspect
-+++ b/bowtie2-inspect
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- 
- """
-  Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
-@@ -21,7 +21,7 @@
- 
- 
- import os
--import imp
-+import importlib
- import sys
- import inspect
- import logging
diff --git a/debian/patches/correct_64bit_test b/debian/patches/correct_64bit_test
index 55a7313..08451ba 100644
--- a/debian/patches/correct_64bit_test
+++ b/debian/patches/correct_64bit_test
@@ -2,40 +2,48 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Handle -m64 and -msse2 flags better
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -197,31 +197,13 @@
- SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
- VERSION := $(shell cat VERSION)
+@@ -198,38 +198,12 @@
+   SANITIZER_FLAGS := -fsanitize=undefined
+ endif
  
 -BITS := 32
+-SSE_FLAG := -msse2
 -ifeq (x86_64,$(shell uname -m))
--	BITS := 64
--endif
--ifeq (amd64,$(shell uname -m))
--	BITS := 64
--endif
--ifeq (aarch64,$(shell uname -m))
--	BITS := 64
+-  BITS := 64
+-else ifeq (amd64,$(shell uname -m))
+-  BITS := 64
+-else ifeq (aarch64,$(shell uname -m))
+-  BITS := 64
+-  SSE_FLAG :=
+-  CXXFLAGS := -fopenmp-simd
+-  CPPFLAGS := -Ithird_party/simde
+-else ifeq (s390x,$(shell uname -m))
+-  BITS := 64
+-  SSE_FLAG :=
+-  CXXFLAGS := -fopenmp-simd
+-  CPPFLAGS := -Ithird_party/simde
+-  SANITIZER_FLAGS :=
+-else ifeq (ppc64le,$(shell uname -m))
+-  BITS := 64
+-  SSE_FLAG :=
+-  CXXFLAGS := -fopenmp-simd
+-  CPPFLAGS += -Ithird_party/simde
+-  SANITIZER_FLAGS :=
 -endif
 -# msys will always be 32 bit so look at the cpu arch instead.
 -ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
--	ifeq (1,$(MINGW))
--		BITS := 64
--	endif
+-  ifeq (1,$(MINGW))
+-    BITS := 64
+-  endif
 -endif
 -ifeq (32,$(BITS))
 -  $(error bowtie2 compilation requires a 64-bit platform )
--endif
-+M64_FLAG :=
- 
--SSE_FLAG := -msse2
--M64_FLAG := -m64
--ifeq (aarch64,$(shell uname -m))
 +ifeq (amd64,$(dpkg-architecture -q DEB_TARGET_ARCH))
-+	SSE_FLAG := -msse2
-+	M64_FLAG := -m64
++	SSE_FLAG = -msse2
++	M64_FLAG = -m64
 +else
- 	SSE_FLAG =
--	M64_FLAG =
++	SSE_FLAG =
++	M64_FLAG =
  endif
  
- DEBUG_FLAGS    := -O0 -g3 $(M64_FLAG) $(SSE_FLAG)
+ DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
diff --git a/debian/patches/drop-not-needed-js-from-manual.patch b/debian/patches/drop-not-needed-js-from-manual.patch
index 76ecd47..25f7b9f 100644
--- a/debian/patches/drop-not-needed-js-from-manual.patch
+++ b/debian/patches/drop-not-needed-js-from-manual.patch
@@ -3,8 +3,8 @@ Author: Alex Mestiashvili <amestia@rsh2.donotuse.de>
 Forwarded: not-needed
 --- bowtie2.orig/doc/manual.html
 +++ bowtie2/doc/manual.html
-@@ -12,9 +12,6 @@
-       div.column{display: inline-block; vertical-align: top; width: 50%;}
+@@ -14,9 +14,6 @@
+     ul.task-list{list-style: none;}
    </style>
    <link rel="stylesheet" href="doc/style.css" />
 -  <!--[if lt IE 9]>
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index ff9ec2a..e10236e 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -3,18 +3,16 @@ Author: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
         Sascha Steinbiss <satta@debian.org>
 Origin: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Last-Update: Tue, 2 Jan 2018 16:20:02 +0100
-Index: bowtie2/Makefile
-===================================================================
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -332,7 +332,9 @@ DEFS := -fno-strict-aliasing \
-         $(FILE_FLAGS) \
-         $(PREF_DEF) \
-         $(MM_DEF) \
--        $(SHMEM_DEF)
-+        $(SHMEM_DEF) \
-+        $(CPPFLAGS) \
-+        $(CFLAGS)
+@@ -328,7 +328,9 @@
+   $(FILE_FLAGS) \
+   $(PREF_DEF) \
+   $(MM_DEF) \
+-  $(SHMEM_DEF)
++  $(SHMEM_DEF) \
++  $(CPPFLAGS) \
++  $(CFLAGS)
  
  # set compiler flags for all sanitized builds
- $(BOWTIE2_BIN_LIST_SAN): CXXFLAGS += $(SANITIZER_FLAGS)
+ ifdef BOWTIE2_BIN_LIST_SAN
diff --git a/debian/patches/no_sanity b/debian/patches/no_sanity
index aed8eaf..ec58116 100644
--- a/debian/patches/no_sanity
+++ b/debian/patches/no_sanity
@@ -2,41 +2,39 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: save resources by not making/testing the -fsantize variants
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -213,20 +213,6 @@
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(DEBUG_FLAGS) $(CXXFLAGS))\""
- RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(RELEASE_FLAGS) $(CXXFLAGS))\""
+@@ -189,15 +189,6 @@
+ SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
+ VERSION := $(shell cat VERSION)
  
--ifeq (0,$(shell $(CPP) -E -fsanitize=address,undefined btypes.h 2>&1 > /dev/null; echo $$?))
--	SANITIZER_FLAGS := -fsanitize=address,undefined
--endif
--ifndef SANITIZER_FLAGS
--	ifeq (0,$(shell $(CPP) -E -fsanitize=address btypes.h 2>&1 > /dev/null; echo $$?))
--		SANITIZER_FLAGS := -fsanitize=address
--	endif
--endif
--ifndef SANITIZER_FLAGS
--	ifeq (0,$(shell $(CPP) -E -fsanitize=undefined btypes.h 2>&1 > /dev/null; echo $$?))
--		SANITIZER_FLAGS := -fsanitize=undefined
--	endif
+-SANITIZER_FLAGS :=
+-ifeq (0,$(shell $(CXX) -E -fsanitize=address,undefined btypes.h > /dev/null 2>&1; echo $$?))
+-  SANITIZER_FLAGS := -fsanitize=address,undefined
+-else ifeq (0,$(shell $(CXX) -E -fsanitize=address btypes.h > /dev/null 2>&1; echo $$?))
+-  SANITIZER_FLAGS := -fsanitize=address
+-else ifeq (0,$(shell $(CXX) -E -fsanitize=undefined btypes.h > /dev/null 2>&1; echo $$?))
+-  SANITIZER_FLAGS := -fsanitize=undefined
 -endif
 -
- BOWTIE2_BIN_LIST :=     bowtie2-build-s \
-                         bowtie2-build-l \
-                         bowtie2-align-s \
-@@ -239,12 +225,6 @@
-                         bowtie2-align-l-debug \
-                         bowtie2-inspect-s-debug \
-                         bowtie2-inspect-l-debug
+ ifeq (amd64,$(dpkg-architecture -q DEB_TARGET_ARCH))
+ 	SSE_FLAG = -msse2
+ 	M64_FLAG = -m64
+@@ -225,15 +216,6 @@
+   bowtie2-align-l-debug \
+   bowtie2-inspect-s-debug \
+   bowtie2-inspect-l-debug
 -BOWTIE2_BIN_LIST_SAN := bowtie2-build-s-sanitized \
--                        bowtie2-build-l-sanitized \
--                        bowtie2-align-s-sanitized \
--                        bowtie2-align-l-sanitized \
--                        bowtie2-inspect-s-sanitized \
--                        bowtie2-inspect-l-sanitized
+-  bowtie2-build-l-sanitized \
+-  bowtie2-align-s-sanitized \
+-  bowtie2-align-l-sanitized \
+-  bowtie2-inspect-s-sanitized \
+-  bowtie2-inspect-l-sanitized
+-ifndef SANITIZER_FLAGS
+-        BOWTIE2_BIN_LIST_SAN =
+-endif
  
  GENERAL_LIST := $(wildcard scripts/*.sh) \
-                 $(wildcard scripts/*.pl) \
-@@ -301,10 +281,9 @@
+   $(wildcard scripts/*.pl) \
+@@ -289,10 +271,9 @@
  .PHONY: all allall both both-debug
  
  all: $(BOWTIE2_BIN_LIST) ;
@@ -47,14 +45,18 @@ Description: save resources by not making/testing the -fsantize variants
 -both-sanitized: bowtie2-align-s-sanitized bowtie2-build-s-sanitized bowtie2-align-l-sanitized bowtie2-build-l-sanitized ;
  
  DEFS := -fno-strict-aliasing \
-         -DBOWTIE2_VERSION="\"`cat VERSION`\"" \
-@@ -318,14 +297,12 @@
-         $(CPPFLAGS) \
-         $(CFLAGS)
+   -DBOWTIE2_VERSION="\"`cat VERSION`\"" \
+@@ -306,18 +287,11 @@
+   $(CPPFLAGS) \
+   $(CFLAGS)
  
 -# set compiler flags for all sanitized builds
--$(BOWTIE2_BIN_LIST_SAN): CXXFLAGS += $(SANITIZER_FLAGS)
- 
+-ifdef BOWTIE2_BIN_LIST_SAN
+-$(BOWTIE2_BIN_LIST_SAN): CXXFLAGS+=$(SANITIZER_FLAGS)
+-else
+-$(BOWTIE2_BIN_LIST_SAN): $(error "Compiler does not support...")
+-endif
+-
  #
  # bowtie2-build targets
  #
@@ -64,7 +66,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
  		$(CPPFLAGS) \
-@@ -333,7 +310,7 @@
+@@ -325,7 +299,7 @@
  		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
  		$(LDFLAGS) $(LDLIBS)
  
@@ -73,7 +75,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
  		$(CPPFLAGS) \
-@@ -361,7 +338,7 @@
+@@ -353,7 +327,7 @@
  # bowtie2-align targets
  #
  
@@ -82,7 +84,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
  		$(CPPFLAGS) \
-@@ -369,7 +346,7 @@
+@@ -361,7 +335,7 @@
  		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
  		$(LDFLAGS) $(LDLIBS)
  
@@ -91,7 +93,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
  		$(CPPFLAGS) \
-@@ -399,7 +376,7 @@
+@@ -391,7 +365,7 @@
  # bowtie2-inspect targets
  #
  
@@ -100,7 +102,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) \
  		$(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
-@@ -408,7 +385,7 @@
+@@ -400,7 +374,7 @@
  		$(SHARED_CPPS) \
  		$(LDFLAGS) $(LDLIBS)
  
@@ -109,7 +111,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) \
  		$(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \
-@@ -609,7 +586,7 @@
+@@ -601,7 +575,7 @@
  
  .PHONY: clean
  clean:
@@ -120,26 +122,23 @@ Description: save resources by not making/testing the -fsantize variants
  	rm -f core.* .tmp.head
 --- bowtie2.orig/bowtie2
 +++ bowtie2/bowtie2
-@@ -140,7 +140,6 @@
- }
+@@ -122,7 +122,6 @@
+ sub isWrapped($) { return defined($wrapped{$_[0]}); }
  
  my $debug = 0;
 -my $sanitized = 0;
  my %read_fns = ();
  my %read_compress = ();
  my $cap_out = undef;       # Filename for passthrough
-@@ -199,10 +198,6 @@
- 		$debug = 1;
- 		$bt2_args[$i] = undef;
- 	}
--	if(not $debug and $arg eq "--sanitized") {
--		$sanitized = 1;
--		$bt2_args[$i] = undef;
--	}
- 	if($arg eq "--no-unal") {
- 		$no_unal = 1;
- 		$bt2_args[$i] = undef;
-@@ -503,9 +498,6 @@
+@@ -183,7 +182,6 @@
+     "keep"                          => \$keep,
+     "verbose"                       => \$verbose,
+     "debug"                         => \$debug,
+-    "sanitized"                     => \$sanitized,
+     "large-index"                   => \$large_idx,
+     "no-unal"                       => \$no_unal,
+     "un=s"                          => \&handle_un_or_al,
+@@ -450,9 +448,6 @@
  if ($debug) {
      $suffix = "-debug";
  }
@@ -172,7 +171,7 @@ Description: save resources by not making/testing the -fsantize variants
      elif len(argv) >= 2:
 --- bowtie2.orig/bowtie2-inspect
 +++ bowtie2/bowtie2-inspect
-@@ -34,7 +34,6 @@
+@@ -33,7 +33,6 @@
  
      group = parser.add_mutually_exclusive_group()
      group.add_argument('--debug', action='store_true')
@@ -180,7 +179,7 @@ Description: save resources by not making/testing the -fsantize variants
  
      parser.add_argument('--verbose', action='store_true')
      parser.add_argument('--large-index', action='store_true')
-@@ -61,10 +60,6 @@
+@@ -60,10 +59,6 @@
          inspect_bin_spec += '-debug'
          inspect_bin_l += '-debug'
  
@@ -235,3 +234,23 @@ Description: save resources by not making/testing the -fsantize variants
  perl scripts/test/simple_tests.pl \
  	--bowtie2=./bowtie2 \
  	--bowtie2-build=./bowtie2-build \
+--- bowtie2.orig/bt2_build.cpp
++++ bowtie2/bt2_build.cpp
+@@ -144,7 +144,6 @@
+ 	out << "    --large-index           force generated index to be 'large', even if ref" << endl
+ 		<< "                            has fewer than 4 billion nucleotides" << endl
+ 		<< "    --debug                 use the debug binary; slower, assertions enabled" << endl
+-		<< "    --sanitized             use sanitized binary; slower, uses ASan and/or UBSan" << endl
+ 		<< "    --verbose               log the issued command" << endl;
+ 	}
+ 	out << "    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting" << endl
+--- bowtie2.orig/bt2_inspect.cpp
++++ bowtie2/bt2_inspect.cpp
+@@ -78,7 +78,6 @@
+ 		out << "  --large-index      force inspection of the 'large' index, even if a" << endl
+ 			<< "                     'small' one is present." << endl
+ 			<< "  --debug            use the debug binary; slower, assertions enabled" << endl
+-			<< "  --sanitized        use sanitized binary; slower, uses ASan and/or UBSan" << endl
+ 			<< "  --verbose          log the issued command" << endl;
+ 	}
+ 	out << "  -a/--across <int>  Number of characters across in FASTA output (default: 60)" << endl
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index 7406142..d9d88f0 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -5,17 +5,17 @@ Description: make build reproducible
 Author: Sascha Steinbiss <sascha@steinbiss.name>
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -36,7 +36,7 @@
- 	CPPFLAGS += -Ithird_party/simde
- endif
+@@ -31,7 +31,7 @@
+ CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+ CXX ?= $(CPP)
  
 -HEADERS := $(wildcard *.h)
 +HEADERS := $(sort $(wildcard *.h))
  BOWTIE_MM := 1
  BOWTIE_SHARED_MEM :=
  
-@@ -228,8 +228,8 @@
- RELEASE_FLAGS  := -O3 $(M64_FLAG) $(SSE_FLAG) -funroll-loops -g3
+@@ -236,8 +236,8 @@
+ RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
  NOASSERT_FLAGS := -DNDEBUG
  FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
 -DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
@@ -23,11 +23,11 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
 +DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(DEBUG_FLAGS) $(CXXFLAGS))\""
 +RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(RELEASE_FLAGS) $(CXXFLAGS))\""
  
- ifeq (0,$(shell $(CPP) -E -fsanitize=address,undefined btypes.h 2>&1 > /dev/null; echo $$?))
- 	SANITIZER_FLAGS := -fsanitize=address,undefined
+ BOWTIE2_BIN_LIST := bowtie2-build-s \
+   bowtie2-build-l \
 --- bowtie2.orig/bt2_build.cpp
 +++ bowtie2/bt2_build.cpp
-@@ -551,15 +551,15 @@
+@@ -561,15 +561,15 @@
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -81,7 +81,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
  
 --- bowtie2.orig/bt2_search.cpp
 +++ bowtie2/bt2_search.cpp
-@@ -5128,15 +5128,15 @@
+@@ -5145,15 +5145,15 @@
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -108,7 +108,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
  		{
 --- bowtie2.orig/CMakeLists.txt
 +++ bowtie2/CMakeLists.txt
-@@ -276,7 +276,8 @@
+@@ -275,7 +275,8 @@
  
  include_directories(${PROJECT_SOURCE_DIR})
  get_directory_property(COMPILER_DEFS COMPILE_DEFINITIONS)
diff --git a/debian/patches/series b/debian/patches/series
index 9298199..e11a345 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,7 +4,6 @@ hardening.patch
 reproducible.patch
 skip_test_requiring_non-free_libmath-random-perl.patch
 do-not-rebuild-during-test.patch
-2to3.patch
 silence_tbb_deprecation_warning.patch
 simde
 correct_64bit_test
diff --git a/debian/patches/simde b/debian/patches/simde
index 4041221..a02488c 100644
--- a/debian/patches/simde
+++ b/debian/patches/simde
@@ -7,15 +7,13 @@ Description: Enable SIMDE everywhere
  #ifndef SSE_WRAP_H_
  #define SSE_WRAP_H_
  
--#ifdef __aarch64__
+-#if defined(__aarch64__) || defined(__s390x__) || defined(__powerpc__)
 -#include "simde/x86/sse2.h"
 -#else
 -#include <emmintrin.h>
 -#endif
-+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include "debian/include/simde/x86/sse2.h"
- 
--#ifdef __aarch64__
+-
+-#if defined(__aarch64__) || defined(__s390x__) || defined(__powerpc__)
 -typedef simde__m128i __m128i;
 -#define _mm_adds_epi16(x, y) simde_mm_adds_epi16(x, y)
 -#define _mm_adds_epu8(x, y) simde_mm_adds_epu8(x, y)
@@ -44,6 +42,8 @@ Description: Enable SIMDE everywhere
 -#define _mm_subs_epi16(x, y) simde_mm_subs_epi16(x, y)
 -#define _mm_subs_epu8(x, y) simde_mm_subs_epu8(x, y)
 -#define _mm_xor_si128(x, y) simde_mm_xor_si128(x, y)
- #endif
--
--#endif /* SSE_WRAP_H_ */
+-#endif
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include "debian/include/simde/x86/sse2.h"
+ 
+ #endif /* SSE_WRAP_H_ */
diff --git a/debian/patches/wrong-interpreter-path.patch b/debian/patches/wrong-interpreter-path.patch
index a7d3d66..d2abaeb 100644
--- a/debian/patches/wrong-interpreter-path.patch
+++ b/debian/patches/wrong-interpreter-path.patch
@@ -12,16 +12,103 @@ Forwarded: not-needed
 --- bowtie2.orig/bowtie2-build
 +++ bowtie2/bowtie2-build
 @@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python
+-#!/usr/bin/env python3
++#!/usr/bin/python3
  
  """
   Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
 --- bowtie2.orig/bowtie2-inspect
 +++ bowtie2/bowtie2-inspect
 @@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/python
+-#!/usr/bin/env python3
++#!/usr/bin/python3
  
  """
   Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
+--- bowtie2.orig/example/reads/simulate.pl
++++ bowtie2/example/reads/simulate.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ 
+ ##
+ # Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
+--- bowtie2.orig/scripts/sa.py
++++ bowtie2/scripts/sa.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ 
+ """
+ sa.py
+--- bowtie2.orig/scripts/test/benchmark/benchmarks.py
++++ bowtie2/scripts/test/benchmark/benchmarks.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ """
+ A few items to deal with sets of benchmarks.
+ """
+--- bowtie2.orig/scripts/test/benchmark/run.py
++++ bowtie2/scripts/test/benchmark/run.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ """
+    Runs benchmark sets specified in JSON files.
+ 
+--- bowtie2.orig/scripts/test/benchmark/samreader.py
++++ bowtie2/scripts/test/benchmark/samreader.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ """
+ A reader of SAM format.
+ 
+--- bowtie2.orig/scripts/test/bt2face.py
++++ bowtie2/scripts/test/bt2face.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ 
+ import os
+ import logging
+--- bowtie2.orig/scripts/test/btdata.py
++++ bowtie2/scripts/test/btdata.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ """
+ Note: This would look so much better replaced by XML or at least JSON. But
+       is not worth to do it for now.
+--- bowtie2.orig/scripts/test/dataface.py
++++ bowtie2/scripts/test/dataface.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ 
+ import os
+ import logging
+@@ -78,4 +78,4 @@
+ 
+     
+     
+-    
+\ No newline at end of file
++    
+--- bowtie2.orig/scripts/test/large_idx.py
++++ bowtie2/scripts/test/large_idx.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ 
+ import os
+ import gzip
+--- bowtie2.orig/scripts/test/regressions.py
++++ bowtie2/scripts/test/regressions.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ 
+ import os
+ import inspect