trimadap: Update to latest commit, fix license, support non-x86 with SIMDE

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Oct 17 07:15:59 2024 -0500
Changeset:	8d72066c935c4111e37ef8ea6ec6c7cc57c696e1

Modified Files:
	trimadap/Makefile
	trimadap/distinfo
	trimadap/patches/patch-Makefile
	trimadap/patches/patch-kthread.c
Added Files:
	trimadap/patches/patch-ksw.c

Log Message:
trimadap: Update to latest commit, fix license, support non-x86 with SIMDE

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8d72066c935c4111e37ef8ea6ec6c7cc57c696e1

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

diffstat:
 trimadap/Makefile                | 19 +++++++++----------
 trimadap/distinfo                | 11 ++++++-----
 trimadap/patches/patch-Makefile  |  3 ++-
 trimadap/patches/patch-ksw.c     | 16 ++++++++++++++++
 trimadap/patches/patch-kthread.c |  3 ++-
 5 files changed, 35 insertions(+), 17 deletions(-)

diffs:
diff --git a/trimadap/Makefile b/trimadap/Makefile
index 30019e8e03..ada199ce66 100644
--- a/trimadap/Makefile
+++ b/trimadap/Makefile
@@ -1,19 +1,17 @@
 # $NetBSD$
 
-DISTNAME=	trimadap-${PORTVERSION}
+DISTNAME=	trimadap-0.1.4
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
-GITHUB_PROJECT=	trimadap
-GITHUB_TAG=	ddfef210563830d9193b40949da3523b6fb93003
+# GITHUB_PROJECT=	trimadap
+GITHUB_TAG=	ec5a764e1834363ae0c4b52f52bdb114ff7af265
 
-MAINTAINER=	dsiercks%uwm.edu@localhost
-HOMEPAGE=	https://github.com/lh3/seqtk
-COMMENT=	Tool for processing sequences in FASTA/FASTQ format
-LICENSE=	gnu-gpl-v2
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/lh3/trimadap
+COMMENT=	Trim adapter sequences from Illumina data using heuristic rules
+LICENSE=	mit
 
-WRKSRC=		${WRKDIR}/trimadap-${GITHUB_TAG}
-
-PORTVERSION=	0.2.20170211
+# WRKSRC=		${WRKDIR}/trimadap-${GITHUB_TAG}
 
 INSTALLATION_DIRS=	bin
 
@@ -21,4 +19,5 @@ do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/trimadap-mt ${DESTDIR}${PREFIX}/bin
 
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/simde/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/trimadap/distinfo b/trimadap/distinfo
index 13a22b7e64..872402be1d 100644
--- a/trimadap/distinfo
+++ b/trimadap/distinfo
@@ -1,7 +1,8 @@
 $NetBSD$
 
-RMD160 (trimadap-0.2.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 95019d0ed6aa478efa9126a6446afc71ea054f6d
-SHA512 (trimadap-0.2.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 364683285fd5f52df33e637f2ca9756b00a24acb45ea3a9ccddaf4126ee30e3f4e1150f56b0e5404f62b010374000eb6768c16ef17954356ffba7d1f28c01c86
-Size (trimadap-0.2.20170211-ddfef210563830d9193b40949da3523b6fb93003.tar.gz) = 13133 bytes
-SHA1 (patch-Makefile) = 7f66c14aa1ccf67ee94895d03a98aad62e8d0731
-SHA1 (patch-kthread.c) = 40cfaaf734b0eed0da13f698d2e31d55f189f272
+BLAKE2s (trimadap-0.1.4-ec5a764e1834363ae0c4b52f52bdb114ff7af265.tar.gz) = 9ed8c649ba8788fda23840ffa1c0a11b22f3cd272cf52328efc0dc1d5c679a94
+SHA512 (trimadap-0.1.4-ec5a764e1834363ae0c4b52f52bdb114ff7af265.tar.gz) = 671bf4bcfcd0912463cfe3f7b11bdb7b0d7bcdc6a588ef3c54aa24157073779145a033b47dc6674e82075d57c140bdd21c2c024c524e5754766f5eaa40f47e45
+Size (trimadap-0.1.4-ec5a764e1834363ae0c4b52f52bdb114ff7af265.tar.gz) = 13261 bytes
+SHA1 (patch-Makefile) = 749cbfb811f6b88ec90b64f8a10b8f0ee240a20b
+SHA1 (patch-ksw.c) = d6c105d0899570a2c840649afb2a7db436e94d4d
+SHA1 (patch-kthread.c) = 75dec73c5bab03b06d7644541febbbfc00f30e2e
diff --git a/trimadap/patches/patch-Makefile b/trimadap/patches/patch-Makefile
index 91dcd5659a..261eab8b0d 100644
--- a/trimadap/patches/patch-Makefile
+++ b/trimadap/patches/patch-Makefile
@@ -1,6 +1,7 @@
 $NetBSD$
 
-Allow flags & compiler override
+# Respect build env
+
 --- Makefile.orig	2017-02-11 22:31:35 UTC
 +++ Makefile
 @@ -1,10 +1,12 @@
diff --git a/trimadap/patches/patch-ksw.c b/trimadap/patches/patch-ksw.c
new file mode 100644
index 0000000000..afe009ac73
--- /dev/null
+++ b/trimadap/patches/patch-ksw.c
@@ -0,0 +1,16 @@
+$NetBSD$
+
+# Support non-x86 platforms with SIMDE
+
+--- ksw.c.orig	2022-03-17 13:43:27.000000000 +0000
++++ ksw.c
+@@ -26,7 +26,8 @@
+ #include <stdlib.h>
+ #include <stdint.h>
+ #include <string.h>
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+ #include "ksw.h"
+ 
+ #ifdef __GNUC__
diff --git a/trimadap/patches/patch-kthread.c b/trimadap/patches/patch-kthread.c
index 4384b6438c..4b0c6305e0 100644
--- a/trimadap/patches/patch-kthread.c
+++ b/trimadap/patches/patch-kthread.c
@@ -1,6 +1,7 @@
 $NetBSD$
 
-# include inttypes
+# Fix build
+
 --- kthread.c.orig	2017-02-11 22:31:35 UTC
 +++ kthread.c
 @@ -1,6 +1,7 @@