bwa: Add support for aarch64

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu May 18 07:37:01 2023 -0500
Changeset:	569bd896e5cc8a7226c4dbf5810b719838a8cead

Modified Files:
	bwa/Makefile
	bwa/distinfo
	bwa/patches/patch-Makefile
	bwa/patches/patch-kopen.c
Added Files:
	bwa/patches/patch-ksw.c
Removed Files:
	bwa/patches/patch-fastmap.c

Log Message:
bwa: Add support for aarch64

Import SIMDE patch from FreeBSD
Clean up other patches

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=569bd896e5cc8a7226c4dbf5810b719838a8cead

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

diffstat:
 bwa/Makefile                |  5 +++--
 bwa/distinfo                | 10 +++++-----
 bwa/patches/patch-Makefile  |  3 ++-
 bwa/patches/patch-fastmap.c | 14 --------------
 bwa/patches/patch-kopen.c   |  2 +-
 bwa/patches/patch-ksw.c     | 17 +++++++++++++++++
 6 files changed, 28 insertions(+), 23 deletions(-)

diffs:
diff --git a/bwa/Makefile b/bwa/Makefile
index 21764627db..e791cf36f9 100644
--- a/bwa/Makefile
+++ b/bwa/Makefile
@@ -2,7 +2,7 @@
 
 DISTNAME=	bwa-0.7.17
 CATEGORIES=	biology
-PKGREVISION=	1
+PKGREVISION=	7
 GITHUB_TAG=	v${PKGVERSION_NOREV}
 MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
 
@@ -17,7 +17,7 @@ REPLACE_PERL=	*.pl
 INSTALLATION_DIRS=	bin ${PKGMANDIR}/man1
 
 # unconditionally uses <emmintrin.h>
-ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-i386 *-*-ia64
+ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-i386 *-*-ia64 *-*-aarch64
 
 CFLAGS.SunOS+=	-Du_int32_t=uint32_t
 LDFLAGS.SunOS+=	-lsocket -lnsl
@@ -28,4 +28,5 @@ do-install:
 	${INSTALL_MAN} ${WRKSRC}/*.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
 
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/simde/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/bwa/distinfo b/bwa/distinfo
index 32f0819e1a..8fafc31d29 100644
--- a/bwa/distinfo
+++ b/bwa/distinfo
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.6 2017/12/27 23:44:01 he Exp $
+$NetBSD: distinfo,v 1.8 2021/10/26 10:03:37 nia Exp $
 
-RMD160 (bwa-0.7.17.tar.gz) = d26a266387dee4fc9fcf6eef4f7ffcc076495c22
+BLAKE2s (bwa-0.7.17.tar.gz) = be24abe7b59b3fddc3360344657c0ea38c1475aa86b9fd1729479f2bd927016d
 SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
 Size (bwa-0.7.17.tar.gz) = 232593 bytes
-SHA1 (patch-Makefile) = 72ac08d92540a88da08bf4d988ca3f6132327a6a
-SHA1 (patch-fastmap.c) = e96f972a65ecc68c92eb82816e9e24b057435d1d
-SHA1 (patch-kopen.c) = ecc92efa3ebe4da484aa6760e23de9437b000644
+SHA1 (patch-Makefile) = 5da1b5453cc4c173e1bc01e37704685357b7a6c9
+SHA1 (patch-kopen.c) = 092cc6c83904aaab737ca6049ea9ee358149a2d7
+SHA1 (patch-ksw.c) = 2e7c655a40b485db99f4f8a7f844078b0065f572
diff --git a/bwa/patches/patch-Makefile b/bwa/patches/patch-Makefile
index 280d2cfa63..e8645a0bae 100644
--- a/bwa/patches/patch-Makefile
+++ b/bwa/patches/patch-Makefile
@@ -1,6 +1,7 @@
 $NetBSD: patch-Makefile,v 1.2 2017/12/17 14:30:36 bacon Exp $
 
-Respect env, add librt for NetBSD
+# Respect env, add librt for NetBSD
+
 --- Makefile.orig	2017-10-23 17:10:17.000000000 +0000
 +++ Makefile
 @@ -1,6 +1,6 @@
diff --git a/bwa/patches/patch-fastmap.c b/bwa/patches/patch-fastmap.c
deleted file mode 100644
index e46d21df34..0000000000
--- a/bwa/patches/patch-fastmap.c
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
---- fastmap.c.orig	2018-04-19 22:02:10.516983388 +0000
-+++ fastmap.c
-@@ -130,7 +130,9 @@ int main_mem(int argc, char *argv[])
- 
- 	aux.opt = opt = mem_opt_init();
- 	memset(&opt0, 0, sizeof(mem_opt_t));
-+	fprintf(stderr, "argc = %d argv[1] = %s\n", argc, argv[1]);
- 	while ((c = getopt(argc, argv, "51qpaMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
-+		fprintf(stderr, "c = %d %c\n", c, c);
- 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
- 		else if (c == '1') no_mt_io = 1;
- 		else if (c == 'x') mode = optarg;
diff --git a/bwa/patches/patch-kopen.c b/bwa/patches/patch-kopen.c
index bf3c18bf71..597a1df1a3 100644
--- a/bwa/patches/patch-kopen.c
+++ b/bwa/patches/patch-kopen.c
@@ -1,6 +1,6 @@
 $NetBSD: patch-kopen.c,v 1.3 2017/12/27 23:44:01 he Exp $
 
-Add includes for getting timevals and select prototype into scope.
+# Add includes for getting timevals and select prototype into scope.
 
 --- kopen.c.orig	2017-10-23 17:10:17.000000000 +0000
 +++ kopen.c
diff --git a/bwa/patches/patch-ksw.c b/bwa/patches/patch-ksw.c
new file mode 100644
index 0000000000..564838b690
--- /dev/null
+++ b/bwa/patches/patch-ksw.c
@@ -0,0 +1,17 @@
+$NetBSD$
+
+# Use SIMDE to support non-x86 architectures
+
+--- ksw.c.orig	2017-10-23 17:10:17.000000000 +0000
++++ ksw.c
+@@ -26,7 +26,9 @@
+ #include <stdlib.h>
+ #include <stdint.h>
+ #include <assert.h>
+-#include <emmintrin.h>
++// #include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+ #include "ksw.h"
+ 
+ #ifdef USE_MALLOC_WRAPPERS