git: cdd5a51ea04a - main - biology/minimap2: Update to 2.29

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=cdd5a51ea04a82261c18e4dec24539bdd75f8daf

commit cdd5a51ea04a82261c18e4dec24539bdd75f8daf
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-04-20 13:15:13 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-04-20 13:15:13 +0000

    biology/minimap2: Update to 2.29
    
    A few new features and fixes
    Changes: https://github.com/lh3/minimap2/releases
    
    Reported by:    portscout
---
 biology/minimap2/Makefile                   |  5 +++--
 biology/minimap2/distinfo                   |  6 +++---
 biology/minimap2/files/patch-Makefile.simde | 12 ++++++++----
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index 3dca063831be..eb65d48578c5 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.28
-PORTREVISION=		1
+DISTVERSION=		2.29
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -27,6 +26,8 @@ INSTALL_TARGET=	install-strip
 MAKEFILE=	Makefile.simde
 MAKE_ARGS=	MAN1DIR=${PREFIX}/share/man/man1
 
+CFLAGS+=	-DHAVE_KALLOC
+
 pre-build:
 	${REINPLACE_CMD} -e 's|-msse4.1||g' -e 's|-msse2||g' ${WRKSRC}/Makefile.simde
 
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
index 27ba854d0f42..fac01c43c7f5 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1713393837
-SHA256 (lh3-minimap2-v2.28_GH0.tar.gz) = 5ea6683b4184b5c49f6dbaef2bc5b66155e405888a0790d1b21fd3c93e474278
-SIZE (lh3-minimap2-v2.28_GH0.tar.gz) = 260341
+TIMESTAMP = 1745154104
+SHA256 (lh3-minimap2-v2.29_GH0.tar.gz) = 008d5e9848b918e4eb09d054aa3d6c272d50e92b8fc8537abf5081a507019718
+SIZE (lh3-minimap2-v2.29_GH0.tar.gz) = 269107
diff --git a/biology/minimap2/files/patch-Makefile.simde b/biology/minimap2/files/patch-Makefile.simde
index 5d5e0ccf482c..12b989eca82a 100644
--- a/biology/minimap2/files/patch-Makefile.simde
+++ b/biology/minimap2/files/patch-Makefile.simde
@@ -1,4 +1,4 @@
---- Makefile.simde.orig	2021-11-18 22:11:48 UTC
+--- Makefile.simde.orig	2025-04-18 17:41:47 UTC
 +++ Makefile.simde
 @@ -1,13 +1,26 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
@@ -15,7 +15,7 @@
 +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
@@ -32,7 +32,7 @@
  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),)
+@@ -26,7 +39,7 @@ endif
  	LIBS+=-fsanitize=thread
  endif
  
@@ -41,9 +41,13 @@
  .SUFFIXES:.c .o
  
  .c.o:
-@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+@@ -60,7 +73,26 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
  		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
  
++jump.o:jump.c ksw2.h kalloc.h
++		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
++
  # other non-file targets
 +
 +