biology/bwa: Update to 0.7.18

Official support for aarch64 (we already had this patched in)
A few minor enhancements and fixes
Changes: https://github.com/lh3/bwa/releases

PR:             282923
Reported by:    alster@vinterdalen.se

4 files changed, 34 insertions, 30 deletions

diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile
index eef1e1a5948d..11d77f255875 100644
--- a/biology/bwa/Makefile
+++ b/biology/bwa/Makefile
@@ -1,35 +1,29 @@
 PORTNAME=	bwa
-PORTVERSION=	0.7.17
-DISTVERSIONPREFIX=v
-PORTREVISION=	2
+DISTVERSIONPREFIX=	v
+DISTVERSION=	0.7.18
 CATEGORIES=	biology
 
-PATCH_SITES=	https://github.com/lh3/bwa/commit/
-PATCHFILES=	2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch:-p1
-
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Burrows-Wheeler sequence aligner
-WWW=		https://sourceforge.net/projects/bio-bwa/
+WWW=		https://github.com/lh3/bwa/
 
 LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/COPYING
 
-BROKEN_mips=		fails to compile: cc1: unrecognized command line option "-msse2"
-BROKEN_mips64=		fails to compile: cc1: unrecognized command line option "-msse2"
+# Recheck these after 0.7.18 update
+BROKEN_mips=	fails to compile: cc1: unrecognized command line option "-msse2"
+BROKEN_mips64=	fails to compile: cc1: unrecognized command line option "-msse2"
 
 BUILD_DEPENDS=	simde>0:devel/simde
 
 USES=		gmake localbase perl5 shebangfix tar:bzip2
-SHEBANG_FILES=	qualfa2fq.pl xa2multi.pl
-USE_PERL5=	run
-
 USE_GITHUB=	yes
 GH_ACCOUNT=	lh3
+USE_PERL5=	run
 
-PLIST_FILES=	bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl share/man/man1/bwa.1.gz
+SHEBANG_FILES=	qualfa2fq.pl xa2multi.pl
 
-# Avoid #error in emmintrin.h
-CFLAGS_i386=	-msse2
-CFLAGS_amd64=	-msse2
+PLIST_FILES=	bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl share/man/man1/bwa.1.gz
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin
diff --git a/biology/bwa/distinfo b/biology/bwa/distinfo
index e4f099c0700c..b9b0548bf588 100644
--- a/biology/bwa/distinfo
+++ b/biology/bwa/distinfo
@@ -1,5 +1,3 @@
-TIMESTAMP = 1598613295
-SHA256 (lh3-bwa-v0.7.17_GH0.tar.gz) = 980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd
-SIZE (lh3-bwa-v0.7.17_GH0.tar.gz) = 232593
-SHA256 (2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch) = 15216a79759a2390bda4a4684af34ff3108f63519d2ec3935754507f3c008da0
-SIZE (2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch) = 709
+TIMESTAMP = 1732300398
+SHA256 (lh3-bwa-v0.7.18_GH0.tar.gz) = 194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870
+SIZE (lh3-bwa-v0.7.18_GH0.tar.gz) = 238036
diff --git a/biology/bwa/files/patch-ksw.c b/biology/bwa/files/patch-ksw.c
index c86cabf2e497..f5314cbe72ce 100644
--- a/biology/bwa/files/patch-ksw.c
+++ b/biology/bwa/files/patch-ksw.c
@@ -1,13 +1,13 @@
---- ksw.c.orig	2021-12-01 13:48:35 UTC
+--- ksw.c.orig	2024-11-22 18:42:53 UTC
 +++ ksw.c
-@@ -26,7 +26,9 @@
- #include <stdlib.h>
+@@ -27,7 +27,9 @@
  #include <stdint.h>
  #include <assert.h>
+ #if defined __SSE2__
 -#include <emmintrin.h>
 +// #include <emmintrin.h>
 +#define SIMDE_ENABLE_NATIVE_ALIASES
 +#include <simde/x86/sse2.h>
- #include "ksw.h"
- 
- #ifdef USE_MALLOC_WRAPPERS
+ #elif defined __ARM_NEON
+ #include "neon_sse.h"
+ #else
diff --git a/biology/bwa/pkg-descr b/biology/bwa/pkg-descr
index 60f539b01220..e0c3d83a0b28 100644
--- a/biology/bwa/pkg-descr
+++ b/biology/bwa/pkg-descr
@@ -1,3 +1,15 @@
-BWA is a program for aligning sequencing reads against a large reference
-genome (e.g. human genome). It has two major components, one for read shorter
-than 150bp and the other for longer reads.
+BWA is a software package for mapping DNA sequences against a large
+reference genome, such as the human genome. It consists of three
+algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
+designed for Illumina sequence reads up to 100bp, while the other two
+are for longer sequences ranging from 70bp to a few megabases. BWA-MEM
+and BWA-SW share similar features such as the support of long reads
+and chimeric alignment, but BWA-MEM, which is the latest, is generally
+recommended, as it is faster and more accurate. BWA-MEM also has
+better performance than BWA-backtrack for 70-100bp Illumina reads.
+
+For all algorithms, BWA first needs to construct the FM-index for the
+reference genome (the "bwa index" command). Alignment algorithms are
+invoked with different sub-commands: "bwa aln/samse/sampe" for
+BWA-backtrack, "bwa bwasw" for BWA-SW, and "bwa mem" for the BWA-MEM
+algorithm.