Update patches

8 files changed, 79 insertions, 72 deletions

diff --git a/debian/patches/correct_64bit_test b/debian/patches/correct_64bit_test
index acd08cb..f8349f8 100644
--- a/debian/patches/correct_64bit_test
+++ b/debian/patches/correct_64bit_test
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Handle -m64 and -msse2 flags better
 --- a/Makefile
 +++ b/Makefile
-@@ -61,16 +61,13 @@ ifneq (,$(findstring Darwin,$(shell unam
+@@ -61,9 +61,9 @@ ifneq (,$(findstring Darwin,$(shell unam
    endif
  endif
  
@@ -12,7 +12,12 @@ Description: Handle -m64 and -msse2 flags better
 +CXXFLAGS += -fopenmp-simd
 +CPPFLAGS += -Ithird_party
 +ifeq (amd64,$(dpkg-architecture -q DEB_TARGET_ARCH))
-   SSE_FLAG := -msse2
+   ifeq (1, $(SSE_AVX2))
+ 	SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2
+   else
+@@ -71,11 +71,8 @@ ifneq (,$(findstring $(shell uname -m),
+   endif
+ 
    POPCNT_CAPABILITY ?= 1
 -else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le))
 -  BITS := 64
diff --git a/debian/patches/drop-not-needed-js-from-manual.patch b/debian/patches/drop-not-needed-js-from-manual.patch
index fb68ee4..90afdba 100644
--- a/debian/patches/drop-not-needed-js-from-manual.patch
+++ b/debian/patches/drop-not-needed-js-from-manual.patch
@@ -1,9 +1,9 @@
 Description: Remove link to external js lib, not needed as used for ie browsers
 Author: Alex Mestiashvili <amestia@rsh2.donotuse.de>
 Forwarded: not-needed
---- bowtie2.orig/doc/manual.html
-+++ bowtie2/doc/manual.html
-@@ -15,9 +15,6 @@
+--- a/doc/manual.html
++++ b/doc/manual.html
+@@ -20,9 +20,6 @@
      .display.math{display: block; text-align: center; margin: 0.5rem auto;}
    </style>
    <link rel="stylesheet" href="doc/style.css" />
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index e558619..4931103 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -5,7 +5,7 @@ Origin: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Last-Update: Tue, 2 Jan 2018 16:20:02 +0100
 --- a/Makefile
 +++ b/Makefile
-@@ -293,7 +293,9 @@ DEFS := -fno-strict-aliasing \
+@@ -306,7 +306,9 @@ DEFS := -fno-strict-aliasing \
    $(FILE_FLAGS) \
    $(PREF_DEF) \
    $(MM_DEF) \
diff --git a/debian/patches/no_sanity b/debian/patches/no_sanity
index faa9d3f..c7d09f5 100644
--- a/debian/patches/no_sanity
+++ b/debian/patches/no_sanity
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: save resources by not making/testing the -fsantize variants
 --- a/Makefile
 +++ b/Makefile
-@@ -189,15 +189,6 @@ BUILD_CPPS_MAIN := $(BUILD_CPPS) bowtie_
+@@ -202,15 +202,6 @@ BUILD_CPPS_MAIN := $(BUILD_CPPS) bowtie_
  SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
  VERSION := $(shell cat BOWTIE2_VERSION)
  
@@ -18,7 +18,7 @@ Description: save resources by not making/testing the -fsantize variants
  DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
  RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
  NOASSERT_FLAGS := -DNDEBUG
-@@ -217,15 +208,6 @@ BOWTIE2_BIN_LIST_DBG := bowtie2-build-s-
+@@ -230,15 +221,6 @@ BOWTIE2_BIN_LIST_DBG := bowtie2-build-s-
    bowtie2-align-l-debug \
    bowtie2-inspect-s-debug \
    bowtie2-inspect-l-debug
@@ -34,7 +34,7 @@ Description: save resources by not making/testing the -fsantize variants
  
  GENERAL_LIST := $(wildcard scripts/*.sh) \
    $(wildcard scripts/*.pl) \
-@@ -277,10 +259,9 @@ endif
+@@ -290,10 +272,9 @@ endif
  .PHONY: all allall both both-debug
  
  all: $(BOWTIE2_BIN_LIST) ;
@@ -46,7 +46,7 @@ Description: save resources by not making/testing the -fsantize variants
  
  DEFS := -fno-strict-aliasing \
    -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
-@@ -294,18 +275,11 @@ DEFS := -fno-strict-aliasing \
+@@ -307,17 +288,10 @@ DEFS := -fno-strict-aliasing \
    $(CPPFLAGS) \
    $(CFLAGS)
  
@@ -60,13 +60,12 @@ Description: save resources by not making/testing the -fsantize variants
  #
  # bowtie2-build targets
  #
- 
 -bowtie2-build-s-sanitized bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
 +bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
  	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
  		$(CPPFLAGS) \
-@@ -313,7 +287,7 @@ bowtie2-build-s-sanitized bowtie2-build-
+@@ -325,7 +299,7 @@ bowtie2-build-s-sanitized bowtie2-build-
  		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
  		$(LDFLAGS) $(LDLIBS)
  
@@ -75,7 +74,7 @@ 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) \
-@@ -341,7 +315,7 @@ bowtie2-build-l-debug: bt2_build.cpp $(S
+@@ -353,7 +327,7 @@ bowtie2-build-l-debug: bt2_build.cpp $(S
  # bowtie2-align targets
  #
  
@@ -84,7 +83,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
  		$(CPPFLAGS) \
-@@ -349,7 +323,7 @@ bowtie2-align-s-sanitized bowtie2-align-
+@@ -361,7 +335,7 @@ bowtie2-align-s-sanitized bowtie2-align-
  		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
  		$(LDFLAGS) $(LDLIBS)
  
@@ -93,7 +92,7 @@ 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) \
-@@ -379,7 +353,7 @@ bowtie2-align-l-debug: bt2_search.cpp $(
+@@ -391,7 +365,7 @@ bowtie2-align-l-debug: bt2_search.cpp $(
  # bowtie2-inspect targets
  #
  
@@ -102,7 +101,7 @@ Description: save resources by not making/testing the -fsantize variants
  	$(CXX) $(RELEASE_FLAGS) \
  		$(RELEASE_DEFS) $(CXXFLAGS) \
  		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
-@@ -388,7 +362,7 @@ bowtie2-inspect-s-sanitized bowtie2-insp
+@@ -400,7 +374,7 @@ bowtie2-inspect-s-sanitized bowtie2-insp
  		$(SHARED_CPPS) \
  		$(LDFLAGS) $(LDLIBS)
  
@@ -111,7 +110,7 @@ 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 \
-@@ -589,7 +563,7 @@ test: simple-test
+@@ -601,7 +575,7 @@ test: simple-test
  
  .PHONY: clean
  clean:
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index c0cfeff..7665052 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -14,7 +14,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
  BOWTIE_MM := 1
  BOWTIE_SHARED_MEM :=
  
-@@ -205,8 +205,8 @@ DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
+@@ -218,8 +218,8 @@ DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
  RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
  NOASSERT_FLAGS := -DNDEBUG
  FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
@@ -27,7 +27,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
    bowtie2-build-l \
 --- a/bt2_build.cpp
 +++ b/bt2_build.cpp
-@@ -579,15 +579,15 @@ int bowtie_build(int argc, const char **
+@@ -580,15 +580,15 @@ int bowtie_build(int argc, const char **
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -81,7 +81,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
  
 --- a/bt2_search.cpp
 +++ b/bt2_search.cpp
-@@ -5103,15 +5103,15 @@ int bowtie(int argc, const char **argv)
+@@ -5123,15 +5123,15 @@ int bowtie(int argc, const char **argv)
  			} else {
  				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
  			}
@@ -90,19 +90,19 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
 -			cout << "Compiler: " << COMPILER_VERSION << endl;
 -			cout << "Options: " << COMPILER_OPTIONS << endl;
 -			cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
--				 << sizeof(int)
--				 << ", " << sizeof(long) << ", " << sizeof(long long)
--				 << ", " << sizeof(void *) << ", " << sizeof(size_t)
--				 << ", " << sizeof(off_t) << "}" << endl;
-+			//cout << "Built on " << BUILD_HOST << endl;
-+			//cout << BUILD_TIME << endl;
-+			//cout << "Compiler: " << COMPILER_VERSION << endl;
-+			//cout << "Options: " << COMPILER_OPTIONS << endl;
-+			//cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
-+			//	 << sizeof(int)
-+			//	 << ", " << sizeof(long) << ", " << sizeof(long long)
-+			//	 << ", " << sizeof(void *) << ", " << sizeof(size_t)
-+			//	 << ", " << sizeof(off_t) << "}" << endl;
+-			     << sizeof(int)
+-			     << ", " << sizeof(long) << ", " << sizeof(long long)
+-			     << ", " << sizeof(void *) << ", " << sizeof(size_t)
+-			     << ", " << sizeof(off_t) << "}" << endl;
++//			cout << "Built on " << BUILD_HOST << endl;
++//			cout << BUILD_TIME << endl;
++//			cout << "Compiler: " << COMPILER_VERSION << endl;
++//			cout << "Options: " << COMPILER_OPTIONS << endl;
++//			cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
++//			     << sizeof(int)
++//			     << ", " << sizeof(long) << ", " << sizeof(long long)
++//			     << ", " << sizeof(void *) << ", " << sizeof(size_t)
++//			     << ", " << sizeof(off_t) << "}" << endl;
  			return 0;
  		}
  		{
diff --git a/debian/patches/simde b/debian/patches/simde
index 120215c..24aa113 100644
--- a/debian/patches/simde
+++ b/debian/patches/simde
@@ -1,11 +1,11 @@
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Enable SIMDE everywhere
 
---- bowtie2.orig/sse_wrap.h
-+++ bowtie2/sse_wrap.h
-@@ -27,41 +27,7 @@
- #ifndef SSE_WRAP_H_
- #define SSE_WRAP_H_
+--- a/sse_wrap.h
++++ b/sse_wrap.h
+@@ -112,44 +112,12 @@ typedef __m256i SSERegI;
+ 
+ #else /* no SSE_AVX2 */
  
 -#if defined(__aarch64__) || defined(__s390x__) || defined(__powerpc__)
 -#include "simde/x86/sse2.h"
@@ -13,37 +13,40 @@ Description: Enable SIMDE everywhere
 -#include <emmintrin.h>
 -#endif
 -
+ #define NBYTES_PER_REG 16
+ #define BYTES_LOG2_PER_REG 4
+ #define SSE_MASK_ALL 0xffff
+ 
 -#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)
--#define _mm_cmpeq_epi16(x, y) simde_mm_cmpeq_epi16(x, y)
--#define _mm_cmpeq_epi8(x, y) simde_mm_cmpeq_epi8(x, y)
--#define _mm_cmpgt_epi16(x, y) simde_mm_cmpgt_epi16(x, y)
--#define _mm_cmpgt_epi8(x, y) simde_mm_cmpgt_epi8(x, y)
--#define _mm_cmplt_epi16(x, y) simde_mm_cmplt_epi16(x, y)
--#define _mm_cmplt_epu8(x, y) simde_mm_cmplt_epu8(x, y)
--#define _mm_extract_epi16(x, y) simde_mm_extract_epi16(x, y)
--#define _mm_insert_epi16(x, y, z) simde_mm_insert_epi16(x, y, z)
--#define _mm_load_si128(x) simde_mm_load_si128(x)
--#define _mm_max_epi16(x, y) simde_mm_max_epi16(x, y)
--#define _mm_max_epu8(x, y) simde_mm_max_epu8(x, y)
--#define _mm_movemask_epi8(x) simde_mm_movemask_epi8(x)
--#define _mm_or_si128(x, y) simde_mm_or_si128(x, y)
--#define _mm_setzero_si128() simde_mm_setzero_si128()
--#define _mm_shuffle_epi32(x, y) simde_mm_shuffle_epi32(x, y)
--#define _mm_shufflelo_epi16(x, y) simde_mm_shufflelo_epi16(x, y)
--#define _mm_slli_epi16(x, y) simde_mm_slli_epi16(x, y)
--#define _mm_slli_si128(x, y) simde_mm_slli_si128(x, y)
--#define _mm_srli_epi16(x, y) simde_mm_srli_epi16(x, y)
--#define _mm_srli_epu8(x, y) simde_mm_srli_epu8(x, y)
--#define _mm_srli_si128(x, y) simde_mm_srli_si128(x, y)
--#define _mm_store_si128(x, y) simde_mm_store_si128(x, y)
--#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
+-typedef simde__m128i SSERegI;
+-#define sse_adds_epi16(x, y) simde_mm_adds_epi16(x, y)
+-#define sse_adds_epu8(x, y) simde_mm_adds_epu8(x, y)
+-#define sse_cmpeq_epi16(x, y) simde_mm_cmpeq_epi16(x, y)
+-#define sse_cmpeq_epi8(x, y) simde_mm_cmpeq_epi8(x, y)
+-#define sse_cmpgt_epi16(x, y) simde_mm_cmpgt_epi16(x, y)
+-#define sse_cmpgt_epi8(x, y) simde_mm_cmpgt_epi8(x, y)
+-#define sse_cmplt_epi16(x, y) simde_mm_cmplt_epi16(x, y)
+-#define sse_cmplt_epu8(x, y) simde_mm_cmplt_epu8(x, y)
+-#define sse_extract_epi16(x, y) simde_mm_extract_epi16(x, y)
+-#define sse_insert_epi16(x, y, z) simde_mm_insert_epi16(x, y, z)
+-#define sse_load_siall(x) simde_mm_load_si128(x)
+-#define sse_max_epi16(x, y) simde_mm_max_epi16(x, y)
+-#define sse_max_epu8(x, y) simde_mm_max_epu8(x, y)
+-#define sse_movemask_epi8(x) simde_mm_movemask_epi8(x)
+-#define sse_or_siall(x, y) simde_mm_or_si128(x, y)
+-#define sse_setzero_siall() simde_mm_setzero_si128()
+-#define sse_slli_epi16(x, y) simde_mm_slli_epi16(x, y)
+-#define sse_slli_siall(x, y) simde_mm_slli_si128(x, y)
+-#define sse_srli_epi16(x, y) simde_mm_srli_epi16(x, y)
+-#define sse_srli_epu8(x, y) simde_mm_srli_epu8(x, y)
+-#define sse_srli_siall(x, y) simde_mm_srli_si128(x, y)
+-#define sse_store_siall(x, y) simde_mm_store_si128(x, y)
+-#define sse_subs_epi16(x, y) simde_mm_subs_epi16(x, y)
+-#define sse_subs_epu8(x, y) simde_mm_subs_epu8(x, y)
+-#define sse_xor_siall(x, y) simde_mm_xor_si128(x, y)
+-#define sse_set1_epi16(x) simde_mm_set1_epi16(x)
 +#define SIMDE_ENABLE_NATIVE_ALIASES
 +#include <simde/x86/sse2.h>
  
- #endif /* SSE_WRAP_H_ */
+ #else
+ typedef __m128i SSERegI;
diff --git a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
index eb8002d..aaaa0f0 100644
--- a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
+++ b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
@@ -165,7 +165,7 @@ Description: Math::Random is in package libmath-random-perl which is
  print STDERR "DONE\n";
 --- a/Makefile
 +++ b/Makefile
-@@ -515,12 +515,12 @@ install: all
+@@ -527,12 +527,12 @@ install: all
  	done
  
  .PHONY: simple-test
@@ -180,7 +180,7 @@ Description: Math::Random is in package libmath-random-perl which is
  	eval `perl -I $(CURDIR)/.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.tmp` ; \
  	sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
  
-@@ -531,8 +531,7 @@ perl-deps:
+@@ -543,8 +543,7 @@ perl-deps:
  	fi
  	DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate -O-" ) || echo "curl -L") ; \
  	$$DL http://cpanmin.us | perl - -l $(CURDIR)/.tmp App::cpanminus local::lib ; \
@@ -190,7 +190,7 @@ Description: Math::Random is in package libmath-random-perl which is
  
  .PHONY: static-libs
  static-libs:
-@@ -589,7 +588,7 @@ sra-deps:
+@@ -601,7 +600,7 @@ sra-deps:
  	 fi ;
  
  .PHONY: test
diff --git a/debian/patches/use-source-date-epoch-in-Makefile.patch b/debian/patches/use-source-date-epoch-in-Makefile.patch
index 1eb4902..e49bb2e 100644
--- a/debian/patches/use-source-date-epoch-in-Makefile.patch
+++ b/debian/patches/use-source-date-epoch-in-Makefile.patch
@@ -7,7 +7,7 @@ https://reproducible-builds.org/docs/source-date-epoch/
 
 --- a/Makefile
 +++ b/Makefile
-@@ -266,7 +266,7 @@ both-debug: bowtie2-align-s-debug bowtie
+@@ -279,7 +279,7 @@ both-debug: bowtie2-align-s-debug bowtie
  DEFS := -fno-strict-aliasing \
    -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
    -DBUILD_HOST="\"$${HOSTNAME:-`hostname`}\"" \