hisat2: Replace with simde-enabled package

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: hisat2: Replace with simde-enabled package
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Wed, 17 May 2023 21:45:28 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed May 17 16:45:28 2023 -0500
Changeset:	de7dee0792ce2422a7172564eef00b849c6552cd

Modified Files:
	Makefile
	hisat2/Makefile
	hisat2/distinfo
Added Files:
	hisat2/patches/patch-aligner__sw.h
	hisat2/patches/patch-sse__util.h
Removed Files:
	hisat2-simde/DESCR
	hisat2-simde/Makefile
	hisat2-simde/PLIST
	hisat2-simde/distinfo
	hisat2-simde/patches/patch-Makefile
	hisat2-simde/patches/patch-aligner__sw.h
	hisat2-simde/patches/patch-hisat2
	hisat2-simde/patches/patch-processor__support.h
	hisat2-simde/patches/patch-sse__util.h

Log Message:
hisat2: Replace with simde-enabled package

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=de7dee0792ce2422a7172564eef00b849c6552cd

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                        |   1 -
 hisat2-simde/DESCR                              |   3 -
 hisat2-simde/Makefile                           |  34 ------
 hisat2-simde/PLIST                              |  67 -----------
 hisat2-simde/distinfo                           |  10 --
 hisat2-simde/patches/patch-Makefile             | 145 ------------------------
 hisat2-simde/patches/patch-aligner__sw.h        |  22 ----
 hisat2-simde/patches/patch-hisat2               |  15 ---
 hisat2-simde/patches/patch-processor__support.h |  25 ----
 hisat2-simde/patches/patch-sse__util.h          |  22 ----
 hisat2/Makefile                                 |   3 +-
 hisat2/distinfo                                 |   2 +
 hisat2/patches/patch-aligner__sw.h              |  22 ++++
 hisat2/patches/patch-sse__util.h                |  22 ++++
 14 files changed, 48 insertions(+), 345 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 3b95eae814..47e0b27589 100644
--- a/Makefile
+++ b/Makefile
@@ -1516,7 +1516,6 @@ SUBDIR+=	higan
 SUBDIR+=	higgsbounds
 SUBDIR+=	hijra
 SUBDIR+=	hisat2
-SUBDIR+=	hisat2-simde
 SUBDIR+=	homeassistant
 SUBDIR+=	honggfuzz-git
 SUBDIR+=	honk
diff --git a/hisat2-simde/DESCR b/hisat2-simde/DESCR
deleted file mode 100644
index b2a627c14e..0000000000
--- a/hisat2-simde/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-HISAT2 is a fast and sensitive alignment program for mapping next-generation
-sequencing reads (both DNA and RNA) to a population of human genomes (as well
-as to a single reference genome).
diff --git a/hisat2-simde/Makefile b/hisat2-simde/Makefile
deleted file mode 100644
index b9f21805da..0000000000
--- a/hisat2-simde/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	hisat2-2.2.1
-PKGREVISION=	2
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=DaehwanKimLab/}
-GITHUB_TAG=	v${PKGVERSION_NOREV}
-
-OWNER=		bacon%NetBSD.org@localhost
-HOMEPAGE=	https://ccb.jhu.edu/software/hisat2/index.shtml
-COMMENT=	Alignment program for mapping next-generation sequencing reads
-LICENSE=	gnu-gpl-v3
-
-# 64-bit code, some assembly language
-ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-aarch64
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	bash gmake perl
-
-REPLACE_BASH=		scripts/*.sh
-REPLACE_PERL=		hisat2 scripts/*.sh scripts/*.pl scripts/*.py
-REPLACE_PYTHON=		*.py scripts/*.py hisat2-build hisat2-inspect
-
-PTHREAD_AUTO_VARS=	yes
-WRKSRC=			${WRKDIR}/hisat2-2.2.1
-
-# Unbreak #include <version> on case-insensitive file systems
-post-patch:
-	${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION
-
-.include "../../devel/simde/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/pthread.buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/hisat2-simde/PLIST b/hisat2-simde/PLIST
deleted file mode 100644
index 96055d08a6..0000000000
--- a/hisat2-simde/PLIST
+++ /dev/null
@@ -1,67 +0,0 @@
-@comment $NetBSD$
-bin/hisat2
-bin/hisat2-align-l
-bin/hisat2-align-s
-bin/hisat2-build
-bin/hisat2-build-l
-bin/hisat2-build-s
-bin/hisat2-inspect
-bin/hisat2-inspect-l
-bin/hisat2-inspect-s
-bin/hisat2-repeat
-libexec/hisat2/convert_quals.pl
-libexec/hisat2/extract_exons.py
-libexec/hisat2/extract_splice_sites.py
-libexec/hisat2/gen_2b_occ_lookup.pl
-libexec/hisat2/gen_occ_lookup.pl
-libexec/hisat2/gen_solqual_lookup.pl
-libexec/hisat2/hisat2_extract_exons.py
-libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
-libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
-libexec/hisat2/hisat2_extract_splice_sites.py
-libexec/hisat2/hisat2_read_statistics.py
-libexec/hisat2/hisat2_simulate_reads.py
-libexec/hisat2/infer_fraglen.pl
-libexec/hisat2/make_a_thaliana_tair.sh
-libexec/hisat2/make_b_taurus_UMD3.sh
-libexec/hisat2/make_bdgp6.sh
-libexec/hisat2/make_bdgp6_tran.sh
-libexec/hisat2/make_canFam2.sh
-libexec/hisat2/make_ce10.sh
-libexec/hisat2/make_dm6.sh
-libexec/hisat2/make_e_coli.sh
-libexec/hisat2/make_grch37.sh
-libexec/hisat2/make_grch37_snp.sh
-libexec/hisat2/make_grch37_snp_tran.sh
-libexec/hisat2/make_grch37_snp_tran_ercc.sh
-libexec/hisat2/make_grch37_tran.sh
-libexec/hisat2/make_grch38.sh
-libexec/hisat2/make_grch38_rep.sh
-libexec/hisat2/make_grch38_snp.sh
-libexec/hisat2/make_grch38_snp_rep.sh
-libexec/hisat2/make_grch38_snp_tran.sh
-libexec/hisat2/make_grch38_snp_tran_ercc.sh
-libexec/hisat2/make_grch38_tran.sh
-libexec/hisat2/make_grcm38.sh
-libexec/hisat2/make_grcm38_snp.sh
-libexec/hisat2/make_grcm38_snp_tran.sh
-libexec/hisat2/make_grcm38_tran.sh
-libexec/hisat2/make_hg19.sh
-libexec/hisat2/make_hg38.sh
-libexec/hisat2/make_hg38_allsnp.sh
-libexec/hisat2/make_hg38_snp.sh
-libexec/hisat2/make_hg38_snp_tran.sh
-libexec/hisat2/make_mm10.sh
-libexec/hisat2/make_mm9.sh
-libexec/hisat2/make_r64.sh
-libexec/hisat2/make_r64_tran.sh
-libexec/hisat2/make_rn4.sh
-libexec/hisat2/make_rn6.sh
-libexec/hisat2/make_rnor6.sh
-libexec/hisat2/make_rnor6_tran.sh
-libexec/hisat2/make_sc3.sh
-libexec/hisat2/make_wbcel235.sh
-libexec/hisat2/make_wbcel235_tran.sh
-libexec/hisat2/make_zm3_snp_tran_ercc.sh
-libexec/hisat2/sa.py
-libexec/hisat2/validate_repeat.py
diff --git a/hisat2-simde/distinfo b/hisat2-simde/distinfo
deleted file mode 100644
index 0f331bc61f..0000000000
--- a/hisat2-simde/distinfo
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD$
-
-BLAKE2s (hisat2-2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c0176a2dfdec51bdb
-SHA512 (hisat2-2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
-Size (hisat2-2.2.1.tar.gz) = 6761242 bytes
-SHA1 (patch-Makefile) = 067b766ecebacd840db4a287bba25d2d2264b339
-SHA1 (patch-aligner__sw.h) = 628c14bfd6b26185eada73013175e35de2b38227
-SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d
-SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af
-SHA1 (patch-sse__util.h) = f0bbe72dfe3a2567e614683e3aecc10f3d6583ef
diff --git a/hisat2-simde/patches/patch-Makefile b/hisat2-simde/patches/patch-Makefile
deleted file mode 100644
index 5615e72d99..0000000000
--- a/hisat2-simde/patches/patch-Makefile
+++ /dev/null
@@ -1,145 +0,0 @@
-$NetBSD$
-
-# Respect env
-
---- Makefile.orig	2020-07-24 20:07:54.000000000 +0000
-+++ Makefile
-@@ -23,9 +23,11 @@
- INC =
- GCC_PREFIX = $(shell dirname `which gcc`)
- GCC_SUFFIX =
--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
--CXX = $(CPP)
-+CC	?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-+CPP	?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-+CXX	?= $(CPP)
-+INSTALL	?= install
-+
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 0
-@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell unam
- 	MACOS = 1
- endif
- 
--EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
-+EXTRA_FLAGS += -std=c++11
- INC += -I. -I third_party 
- 
- MM_DEF = 
-@@ -150,33 +152,11 @@ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) h
- HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp
- 
- SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
--VERSION = $(shell cat VERSION)
--
--# Convert BITS=?? to a -m flag
--BITS=32
--ifeq (x86_64,$(shell uname -m))
--BITS=64
--endif
--# msys will always be 32 bit so look at the cpu arch instead.
--ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
--	ifeq (1,$(MINGW))
--		BITS=64
--	endif
--endif
--BITS_FLAG =
--
--ifeq (32,$(BITS))
--	BITS_FLAG = -m32
--endif
--
--ifeq (64,$(BITS))
--	BITS_FLAG = -m64
--endif
--SSE_FLAG=-msse2
-+HISAT2_VERSION = $(shell cat HISAT2_VERSION)
- 
- DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
--RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
-+RELEASE_FLAGS  = $(CXXFLAGS)
- RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
- NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-@@ -251,7 +231,7 @@ GENERAL_LIST = $(wildcard scripts/*.sh) 
- 	MANUAL \
- 	MANUAL.markdown \
- 	TUTORIAL \
--	VERSION
-+	HISAT2_VERSION
- 
- ifeq (1,$(WINDOWS))
- 	HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat 
-@@ -287,7 +267,7 @@ repeat: hisat2-repeat
- repeat-debug: hisat2-repeat-debug
- 
- DEFS=-fno-strict-aliasing \
--     -DHISAT2_VERSION="\"`cat VERSION`\"" \
-+     -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \
-      -DBUILD_HOST="\"`hostname`\"" \
-      -DBUILD_TIME="\"`date`\"" \
-      -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
-@@ -517,12 +497,12 @@ hisat2-inspect.bat:
- hisat2-src: $(SRC_PKG_LIST)
- 	chmod a+x scripts/*.sh scripts/*.pl
- 	mkdir .src.tmp
--	mkdir .src.tmp/hisat2-$(VERSION)
-+	mkdir .src.tmp/hisat2-$(HISAT2_VERSION)
- 	zip tmp.zip $(SRC_PKG_LIST)
--	mv tmp.zip .src.tmp/hisat2-$(VERSION)
--	cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
--	cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
--	cp .src.tmp/hisat2-$(VERSION)-source.zip .
-+	mv tmp.zip .src.tmp/hisat2-$(HISAT2_VERSION)
-+	cd .src.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
-+	cd .src.tmp ; zip -r hisat2-$(HISAT2_VERSION)-source.zip hisat2-$(HISAT2_VERSION)
-+	cp .src.tmp/hisat2-$(HISAT2_VERSION)-source.zip .
- 	rm -rf .src.tmp
- 
- .PHONY: hisat2-bin
-@@ -530,16 +510,16 @@ hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN
- 	chmod a+x scripts/*.sh scripts/*.pl
- 	rm -rf .bin.tmp
- 	mkdir .bin.tmp
--	mkdir .bin.tmp/hisat2-$(VERSION)
-+	mkdir .bin.tmp/hisat2-$(HISAT2_VERSION)
- 	if [ -f hisat2.exe ] ; then \
- 		zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
- 	else \
- 		zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
- 	fi
--	mv tmp.zip .bin.tmp/hisat2-$(VERSION)
--	cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
--	cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
--	cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
-+	mv tmp.zip .bin.tmp/hisat2-$(HISAT2_VERSION)
-+	cd .bin.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
-+	cd .bin.tmp ; zip -r hisat2-$(HISAT2_VERSION)-$(BITS).zip hisat2-$(HISAT2_VERSION)
-+	cp .bin.tmp/hisat2-$(HISAT2_VERSION)-$(BITS).zip .
- 	rm -rf .bin.tmp
- 
- .PHONY: doc
-@@ -554,6 +534,20 @@ doc/manual.inc.html: MANUAL.markdown
- MANUAL: MANUAL.markdown
- 	perl doc/strip_markdown.pl < $^ > $@
- 
-+# Install per filesystem hierarchy standard:
-+# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
-+
-+.PHONY: install
-+install:
-+	mkdir -p ${DESTDIR}${PREFIX}/bin
-+	${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin
-+	${INSTALL} -c hisat2 hisat2-build hisat2-inspect \
-+		${DESTDIR}${PREFIX}/bin
-+
-+	mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
-+	${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \
-+		${DESTDIR}${PREFIX}/libexec/hisat2
-+
- .PHONY: clean
- clean:
- 	rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \
diff --git a/hisat2-simde/patches/patch-aligner__sw.h b/hisat2-simde/patches/patch-aligner__sw.h
deleted file mode 100644
index 7aba6299e5..0000000000
--- a/hisat2-simde/patches/patch-aligner__sw.h
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD$
-
-# Support non-x86
-
---- aligner_sw.h.orig	2020-07-24 20:07:54.000000000 +0000
-+++ aligner_sw.h
-@@ -66,11 +66,14 @@
- 
- #define INLINE_CUPS
- 
-+#define	SIMDE_ENABLE_NATIVE_ALIASES
-+
-+#include <simde/x86/sse2.h>
- #include <stdint.h>
- #include <iostream>
- #include <limits>
- #include "threading.h"
--#include <emmintrin.h>
-+// #include <emmintrin.h>	// Replace this with simde when possible
- #include "aligner_sw_common.h"
- #include "aligner_sw_nuc.h"
- #include "ds.h"
diff --git a/hisat2-simde/patches/patch-hisat2 b/hisat2-simde/patches/patch-hisat2
deleted file mode 100644
index ea0ed8175d..0000000000
--- a/hisat2-simde/patches/patch-hisat2
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Support BSD, etc.
-
---- hisat2.orig	2018-11-07 21:43:32 UTC
-+++ hisat2
-@@ -45,7 +45,7 @@ while (-f $prog && -l $prog){
- 
- ($vol,$script_path,$prog) 
-                 = File::Spec->splitpath($prog);
--my $os_is_nix   = ($^O eq "linux") || ($^O eq "darwin");
-+my $os_is_nix   = ($^O ne "MSWin32") && ($^O ne "MSWin64");
- my $align_bin_s = $os_is_nix ? 'hisat2-align-s' : 'hisat2-align-s.exe'; 
- my $build_bin   = $os_is_nix ? 'hisat2-build' : 'hisat2-build.exe';               
- my $align_bin_l = $os_is_nix ? 'hisat2-align-l' : 'hisat2-align-l.exe'; 
diff --git a/hisat2-simde/patches/patch-processor__support.h b/hisat2-simde/patches/patch-processor__support.h
deleted file mode 100644
index b882729882..0000000000
--- a/hisat2-simde/patches/patch-processor__support.h
+++ /dev/null
@@ -1,25 +0,0 @@
-$NetBSD$
-
-# Support non-x86
-
---- processor_support.h.orig	2020-07-24 20:07:54 UTC
-+++ processor_support.h
-@@ -12,7 +12,7 @@
- 
- #if defined(__INTEL_COMPILER)
- #   define USING_INTEL_COMPILER
--#elif defined(__GNUC__)
-+#elif defined(__GNUC__) && (defined(__amd64__) || defined(__i386__))
- #   define USING_GCC_COMPILER
- #   include <cpuid.h>
- #elif defined(_MSC_VER)
-@@ -52,8 +52,7 @@ class ProcessorSupport { (public)
- #elif defined(USING_GCC_COMPILER)
-         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
- #else
--        std::cerr << "ERROR: please define __cpuid() for this build.\n"; 
--        assert(0);
-+	return false;
- #endif
-         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
-     }
diff --git a/hisat2-simde/patches/patch-sse__util.h b/hisat2-simde/patches/patch-sse__util.h
deleted file mode 100644
index 22bbf22180..0000000000
--- a/hisat2-simde/patches/patch-sse__util.h
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD$
-
-# Support non-x86
-
---- sse_util.h.orig	2020-07-24 20:07:54.000000000 +0000
-+++ sse_util.h
-@@ -20,11 +20,14 @@
- #ifndef SSE_UTIL_H_
- #define SSE_UTIL_H_
- 
-+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include <simde/x86/sse2.h>
-+
- #include "assert_helpers.h"
- #include "ds.h"
- #include "limit.h"
- #include <iostream>
--#include <emmintrin.h>
-+// #include <emmintrin.h>		// Replace with simde when possible
- 
- class EList_m128i {
- public:
diff --git a/hisat2/Makefile b/hisat2/Makefile
index 4ee939ae2c..b9f21805da 100644
--- a/hisat2/Makefile
+++ b/hisat2/Makefile
@@ -12,7 +12,7 @@ COMMENT=	Alignment program for mapping next-generation sequencing reads
 LICENSE=	gnu-gpl-v3
 
 # 64-bit code, some assembly language
-ONLY_FOR_PLATFORM=	*-*-x86_64
+ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-aarch64
 
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	bash gmake perl
@@ -28,6 +28,7 @@ WRKSRC=			${WRKDIR}/hisat2-2.2.1
 post-patch:
 	${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION
 
+.include "../../devel/simde/buildlink3.mk"
 .include "../../lang/python/application.mk"
 .include "../../mk/pthread.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/hisat2/distinfo b/hisat2/distinfo
index 13767c5c01..0f331bc61f 100644
--- a/hisat2/distinfo
+++ b/hisat2/distinfo
@@ -4,5 +4,7 @@ BLAKE2s (hisat2-2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c
 SHA512 (hisat2-2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
 Size (hisat2-2.2.1.tar.gz) = 6761242 bytes
 SHA1 (patch-Makefile) = 067b766ecebacd840db4a287bba25d2d2264b339
+SHA1 (patch-aligner__sw.h) = 628c14bfd6b26185eada73013175e35de2b38227
 SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d
 SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af
+SHA1 (patch-sse__util.h) = f0bbe72dfe3a2567e614683e3aecc10f3d6583ef
diff --git a/hisat2/patches/patch-aligner__sw.h b/hisat2/patches/patch-aligner__sw.h
new file mode 100644
index 0000000000..7aba6299e5
--- /dev/null
+++ b/hisat2/patches/patch-aligner__sw.h
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Support non-x86
+
+--- aligner_sw.h.orig	2020-07-24 20:07:54.000000000 +0000
++++ aligner_sw.h
+@@ -66,11 +66,14 @@
+ 
+ #define INLINE_CUPS
+ 
++#define	SIMDE_ENABLE_NATIVE_ALIASES
++
++#include <simde/x86/sse2.h>
+ #include <stdint.h>
+ #include <iostream>
+ #include <limits>
+ #include "threading.h"
+-#include <emmintrin.h>
++// #include <emmintrin.h>	// Replace this with simde when possible
+ #include "aligner_sw_common.h"
+ #include "aligner_sw_nuc.h"
+ #include "ds.h"
diff --git a/hisat2/patches/patch-sse__util.h b/hisat2/patches/patch-sse__util.h
new file mode 100644
index 0000000000..22bbf22180
--- /dev/null
+++ b/hisat2/patches/patch-sse__util.h
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Support non-x86
+
+--- sse_util.h.orig	2020-07-24 20:07:54.000000000 +0000
++++ sse_util.h
+@@ -20,11 +20,14 @@
+ #ifndef SSE_UTIL_H_
+ #define SSE_UTIL_H_
+ 
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
++
+ #include "assert_helpers.h"
+ #include "ds.h"
+ #include "limit.h"
+ #include <iostream>
+-#include <emmintrin.h>
++// #include <emmintrin.h>		// Replace with simde when possible
+ 
+ class EList_m128i {
+ public:
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