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biology/minimap2: Update to 2.29

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A few new features and fixes
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2025-04-20 08:15:13 -05:00
parent d0be75580f
commit cdd5a51ea0
3 changed files with 14 additions and 9 deletions
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5
biology/minimap2/Makefile
View file

@ -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

6
biology/minimap2/distinfo
View file

@ -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

12
biology/minimap2/files/patch-Makefile.simde
View file

@ -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
+
+