minimap2: Update to 2.29

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

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sun Apr 20 08:23:40 2025 -0500
Changeset:	9191efea0a0d38c8f47ef7e3800d21e417d10232

Modified Files:
	minimap2/Makefile
	minimap2/distinfo
	minimap2/patches/patch-Makefile.simde

Log Message:
minimap2: Update to 2.29

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9191efea0a0d38c8f47ef7e3800d21e417d10232

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

diffstat:
 minimap2/Makefile                     |  4 +++-
 minimap2/distinfo                     |  8 ++++----
 minimap2/patches/patch-Makefile.simde | 24 ++++++++++++++----------
 3 files changed, 21 insertions(+), 15 deletions(-)

diffs:
diff --git a/minimap2/Makefile b/minimap2/Makefile
index cae3de8f23..6c52ecc48e 100644
--- a/minimap2/Makefile
+++ b/minimap2/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD: Makefile,v 1.4 2023/08/14 05:23:51 wiz Exp $
 
-VERSION=	2.28
+VERSION=	2.29
 DISTNAME=	minimap2-${VERSION}
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
@@ -14,6 +14,8 @@ LICENSE=	mit
 USE_TOOLS+=	gmake
 MAKE_FILE=	Makefile.simde
 
+CFLAGS+=	-DHAVE_KALLOC
+
 INSTALLATION_DIRS+=	bin ${PKGMANDIR}/man1
 
 do-install:
diff --git a/minimap2/distinfo b/minimap2/distinfo
index 514a8eb43b..1f442379ff 100644
--- a/minimap2/distinfo
+++ b/minimap2/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-BLAKE2s (minimap2-2.28.tar.gz) = 0a0afd89e588dd0d8a93a562264bb5fdfe50f88a18f5f057bf59be51e16bbe0b
-SHA512 (minimap2-2.28.tar.gz) = d8d4bb4381d6effb3eb3e1a66fac7a83bc00c3cf174d2e0537dd4790d0e4a3cc060b92e39ed2e2cafc6e5e713f6fdbee6bac1d279b6b77d4347f77f3e6d3c0d0
-Size (minimap2-2.28.tar.gz) = 260341 bytes
-SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551
+BLAKE2s (minimap2-2.29.tar.gz) = 9db51992b4fe24f57a1363d28c2ccb393abd59949543b711902dd1c178e6690e
+SHA512 (minimap2-2.29.tar.gz) = 5f299cf9a268fab2e58fb915ffac139bfc95b237da0dc084298ff085e39e064e8ffa3f4c1d9f7275feefa917ccded6c9e32a8306558a3fe29a3085581f93c69d
+Size (minimap2-2.29.tar.gz) = 269107 bytes
+SHA1 (patch-Makefile.simde) = 2fd6239d148be24692c876bdc44e371f6c1166d9
 SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c
diff --git a/minimap2/patches/patch-Makefile.simde b/minimap2/patches/patch-Makefile.simde
index 2c7b2c5e51..e2938eb192 100644
--- a/minimap2/patches/patch-Makefile.simde
+++ b/minimap2/patches/patch-Makefile.simde
@@ -1,10 +1,10 @@
 $NetBSD$
 
-# Respect standard env vars
+# Respect build env
 
---- Makefile.simde.orig	2021-11-18 22:11:48 UTC
+--- Makefile.simde.orig	2025-04-18 17:41:47.000000000 +0000
 +++ Makefile.simde
-@@ -1,13 +1,26 @@
+@@ -1,12 +1,25 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 -CPPFLAGS=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
 -INCLUDES=	-Ilib/simde
@@ -19,7 +19,7 @@ $NetBSD$
 +OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o \
 +		index.o lchain.o align.o hit.o map.o format.o pe.o seed.o \
 +		esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o \
-+		ksw2_exts2_simde.o ksw2_ll_simde.o
++		ksw2_exts2_simde.o ksw2_ll_simde.o jump.o
  PROG=		minimap2
  PROG_EXTRA=	sdust minimap2-lite
  LIBS=		-lm -lz -lpthread
@@ -27,15 +27,14 @@ $NetBSD$
 +PREFIX?=	/usr/local
 +MAN1DIR?=	${PREFIX}/man/man1
 +DATADIR?=	${PREFIX}/share/minimap2
- 
++
 +MKDIR?=		mkdir
 +CP?=		cp	
 +INSTALL?=	install
 +STRIP?=		strip
-+
+ 
  ifneq ($(arm_neon),) # if arm_neon is defined
  ifeq ($(aarch64),)   #if aarch64 is not defined
- 	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
 @@ -26,7 +39,7 @@ ifneq ($(tsan),)
  	LIBS+=-fsanitize=thread
  endif
@@ -45,11 +44,15 @@ $NetBSD$
  .SUFFIXES:.c .o
  
  .c.o:
-@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+@@ -60,8 +73,27 @@ ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2
+ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
  		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
  
- # other non-file targets
++jump.o:jump.c ksw2.h kalloc.h
++		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
 +
+ # other non-file targets
+ 
 +
 +install: all
 +	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
@@ -65,6 +68,7 @@ $NetBSD$
 +	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
 +	${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
 +	${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
- 
++
  clean:
  		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
+