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	pkgsrc-2026Q1:1.3.0.16
	pkgsrc-2026Q1-base:1.3
	pkgsrc-2025Q4:1.3.0.14
	pkgsrc-2025Q4-base:1.3
	pkgsrc-2025Q3:1.3.0.12
	pkgsrc-2025Q3-base:1.3
	pkgsrc-2025Q2:1.3.0.10
	pkgsrc-2025Q2-base:1.3
	pkgsrc-2025Q1:1.3.0.8
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	pkgsrc-2024Q3:1.3.0.4
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	pkgsrc-2024Q2:1.3.0.2
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	pkgsrc-2024Q1:1.1.0.2
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locks; strict;
comment	@# @;


1.3
date	2024.05.18.00.27.16;	author nia;	state Exp;
branches;
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commitid	chrZC1zqPlflKpaF;

1.2
date	2024.04.10.12.36.12;	author bacon;	state Exp;
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commitid	RUc5YNiWp4e30B5F;

1.1
date	2024.03.13.13.54.04;	author bacon;	state Exp;
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commitid	n9gocd8So9chk02F;


desc
@@


1.3
log
@minimap2: Honour LDFLAGS when linking
@
text
@$NetBSD: patch-Makefile.simde,v 1.2 2024/04/10 12:36:12 bacon Exp $

# Respect standard env vars

--- Makefile.simde.orig	2024-03-27 14:57:17.000000000 +0000
+++ Makefile.simde
@@@@ -1,12 +1,25 @@@@
-CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
-CPPFLAGS=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
-INCLUDES=	-Ilib/simde
-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
+
+# Makefile patches rejected by upstream
+
+CFLAGS?=	-g -Wall -O2
+CFLAGS+=	-Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__
+CPPFLAGS?=	-DHAVE_KALLOC
+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
 PROG=		minimap2
 PROG_EXTRA=	sdust minimap2-lite
 LIBS=		-lm -lz -lpthread
 
+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
@@@@ -26,7 +39,7 @@@@ ifneq ($(tsan),)
 	LIBS+=-fsanitize=thread
 endif
 
-.PHONY:all extra clean depend
+.PHONY:all extra install install-strip clean depend
 .SUFFIXES:.c .o
 
 .c.o:
@@@@ -37,10 +50,10 @@@@ all:$(PROG)
 extra:all $(PROG_EXTRA)
 
 minimap2:main.o libminimap2.a
-		$(CC) $(CFLAGS) main.o -o $@@ -L. -lminimap2 $(LIBS)
+		$(CC) $(LDFLAGS) main.o -o $@@ -L. -lminimap2 $(LIBS)
 
 minimap2-lite:example.o libminimap2.a
-		$(CC) $(CFLAGS) $< -o $@@ -L. -lminimap2 $(LIBS)
+		$(CC) $(LDFLAGS) $< -o $@@ -L. -lminimap2 $(LIBS)
 
 libminimap2.a:$(OBJS)
 		$(AR) -csru $@@ $(OBJS)
@@@@ -62,6 +75,22 @@@@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2
 
 # other non-file targets
 
+
+install: all
+	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+	${MKDIR} -p ${DESTDIR}${MAN1DIR}
+	${MKDIR} -p ${DESTDIR}${DATADIR}
+	${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
+	${CP} -R test ${DESTDIR}${DATADIR}
+
+install-strip: install
+	${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*
 
@


1.2
log
@biology/minimap2: Update to 2.28

Fix --MD flag
Add experimental lr:hqae

Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout
@
text
@d1 1
a1 1
$NetBSD$
d5 1
a5 1
--- Makefile.simde.orig	2021-11-18 22:11:48 UTC
d7 1
a7 1
@@@@ -1,13 +1,26 @@@@
d30 1
a30 1
 
d35 1
a35 1
+
a37 1
 	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
d47 14
a60 2
@@@@ -61,6 +74,22 @@@@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
 		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@@
d63 1
a63 1
+
d79 1
a79 1
 
d82 1
@


1.1
log
@biology/minimap2: Update to 2.27

Several new features and bug fixes since 2.24

Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout
@
text
@@