Wed Apr 10 12:36:12 2024 UTC (67d)
biology/minimap2: Update to 2.28

Fix --MD flag
Add experimental lr:hqae

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


(bacon)
diff -r1.5 -r1.6 pkgsrc/biology/minimap2/Makefile
diff -r1.3 -r1.4 pkgsrc/biology/minimap2/PLIST
diff -r1.6 -r1.7 pkgsrc/biology/minimap2/distinfo
diff -r1.1 -r1.2 pkgsrc/biology/minimap2/patches/patch-Makefile.simde
diff -r1.1 -r1.2 pkgsrc/biology/minimap2/patches/patch-example.c
cvs diff -r1.5 -r1.6 pkgsrc/biology/minimap2/Makefile (switch to unified diff)

--- pkgsrc/biology/minimap2/Makefile 2024/03/13 13:54:04 1.5
+++ pkgsrc/biology/minimap2/Makefile 2024/04/10 12:36:12 1.6
@@ -1,25 +1,25 @@ @@ -1,25 +1,25 @@
1# $NetBSD: Makefile,v 1.5 2024/03/13 13:54:04 bacon Exp $ 1# $NetBSD: Makefile,v 1.6 2024/04/10 12:36:12 bacon Exp $
2 2
3VERSION= 2.27 3VERSION= 2.28
4DISTNAME= minimap2-${VERSION} 4DISTNAME= minimap2-${VERSION}
5CATEGORIES= biology python 5CATEGORIES= biology python
6MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/} 6MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/}
7GITHUB_TAG= v${VERSION} 7GITHUB_TAG= v${VERSION}
8 8
9MAINTAINER= pkgsrc-users@NetBSD.org 9MAINTAINER= pkgsrc-users@NetBSD.org
10HOMEPAGE= https://github.com/lh3/minimap2 10HOMEPAGE= https://github.com/lh3/minimap2
11COMMENT= Sequence alignment program for noisy, long reads 11COMMENT= Sequence alignment program for noisy, long reads
12LICENSE= mit 12LICENSE= mit
13 13
14USE_TOOLS+= gmake 14USE_TOOLS+= gmake
15MAKE_FILE= Makefile.simde 15MAKE_FILE= Makefile.simde
16 16
17INSTALLATION_DIRS+= bin ${PKGMANDIR}/man1 17INSTALLATION_DIRS+= bin ${PKGMANDIR}/man1
18 18
19do-install: 19do-install:
20 ${INSTALL} ${WRKSRC}/minimap2 ${DESTDIR}${PREFIX}/bin 20 ${INSTALL} ${WRKSRC}/minimap2 ${DESTDIR}${PREFIX}/bin
21 ${INSTALL_DATA} ${WRKSRC}/minimap2.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1 21 ${INSTALL_DATA} ${WRKSRC}/minimap2.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
22 22
23.include "../../devel/zlib/buildlink3.mk" 23.include "../../devel/zlib/buildlink3.mk"
24.include "../../devel/simde/buildlink3.mk" 24.include "../../devel/simde/buildlink3.mk"
25.include "../../mk/bsd.pkg.mk" 25.include "../../mk/bsd.pkg.mk"
cvs diff -r1.3 -r1.4 pkgsrc/biology/minimap2/PLIST (switch to unified diff)

--- pkgsrc/biology/minimap2/PLIST 2024/03/13 13:54:04 1.3
+++ pkgsrc/biology/minimap2/PLIST 2024/04/10 12:36:12 1.4
@@ -1,3 +1,3 @@ @@ -1,3 +1,3 @@
1@comment $NetBSD: PLIST,v 1.3 2024/03/13 13:54:04 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.4 2024/04/10 12:36:12 bacon Exp $
2bin/minimap2 2bin/minimap2
3man/man1/minimap2.1 3man/man1/minimap2.1
cvs diff -r1.6 -r1.7 pkgsrc/biology/minimap2/distinfo (switch to unified diff)

--- pkgsrc/biology/minimap2/distinfo 2024/03/13 13:54:04 1.6
+++ pkgsrc/biology/minimap2/distinfo 2024/04/10 12:36:12 1.7
@@ -1,7 +1,7 @@ @@ -1,7 +1,7 @@
1$NetBSD: distinfo,v 1.6 2024/03/13 13:54:04 bacon Exp $ 1$NetBSD: distinfo,v 1.7 2024/04/10 12:36:12 bacon Exp $
2 2
3BLAKE2s (minimap2-2.27.tar.gz) = 92e09196bf9de2c121ce8a3305200760ff9e8ba83d634b106b33297508b5e01d 3BLAKE2s (minimap2-2.28.tar.gz) = 0a0afd89e588dd0d8a93a562264bb5fdfe50f88a18f5f057bf59be51e16bbe0b
4SHA512 (minimap2-2.27.tar.gz) = fca5983cbd650b81c6a2caff8ad4d47286467df81ab76646e4fa4b113f0a76d16e4cc8cc5e2f4adaf5c06246ffa099c2728cd0dcba87d808980ed78ee3a029d1 4SHA512 (minimap2-2.28.tar.gz) = d8d4bb4381d6effb3eb3e1a66fac7a83bc00c3cf174d2e0537dd4790d0e4a3cc060b92e39ed2e2cafc6e5e713f6fdbee6bac1d279b6b77d4347f77f3e6d3c0d0
5Size (minimap2-2.27.tar.gz) = 259736 bytes 5Size (minimap2-2.28.tar.gz) = 260341 bytes
6SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551 6SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551
7SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c 7SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c
cvs diff -r1.1 -r1.2 pkgsrc/biology/minimap2/patches/patch-Makefile.simde (switch to unified diff)

--- pkgsrc/biology/minimap2/patches/patch-Makefile.simde 2024/03/13 13:54:04 1.1
+++ pkgsrc/biology/minimap2/patches/patch-Makefile.simde 2024/04/10 12:36:12 1.2
@@ -1,70 +1,70 @@ @@ -1,70 +1,70 @@
1$NetBSD: patch-Makefile.simde,v 1.1 2024/03/13 13:54:04 bacon Exp $ 1$NetBSD: patch-Makefile.simde,v 1.2 2024/04/10 12:36:12 bacon Exp $
2 2
3# Respect standard env vars 3# Respect standard env vars
4 4
5--- Makefile.simde.orig 2021-11-18 22:11:48 UTC 5--- Makefile.simde.orig 2021-11-18 22:11:48 UTC
6+++ Makefile.simde 6+++ Makefile.simde
7@@ -1,13 +1,26 @@ 7@@ -1,13 +1,26 @@
8-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra 8-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
9-CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES 9-CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
10-INCLUDES= -Ilib/simde 10-INCLUDES= -Ilib/simde
11-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 \ 11-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 \
12- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o 12- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
13+ 13+
14+# Makefile patches rejected by upstream 14+# Makefile patches rejected by upstream
15+ 15+
16+CFLAGS?= -g -Wall -O2 16+CFLAGS?= -g -Wall -O2
17+CFLAGS+= -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ 17+CFLAGS+= -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__
18+CPPFLAGS?= -DHAVE_KALLOC 18+CPPFLAGS?= -DHAVE_KALLOC
19+OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o \ 19+OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o \
20+ index.o lchain.o align.o hit.o map.o format.o pe.o seed.o \ 20+ index.o lchain.o align.o hit.o map.o format.o pe.o seed.o \
21+ esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o \ 21+ esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o \
22+ ksw2_exts2_simde.o ksw2_ll_simde.o 22+ ksw2_exts2_simde.o ksw2_ll_simde.o
23 PROG= minimap2 23 PROG= minimap2
24 PROG_EXTRA= sdust minimap2-lite 24 PROG_EXTRA= sdust minimap2-lite
25 LIBS= -lm -lz -lpthread 25 LIBS= -lm -lz -lpthread
26  26
27+PREFIX?= /usr/local 27+PREFIX?= /usr/local
28+MAN1DIR?= ${PREFIX}/man/man1 28+MAN1DIR?= ${PREFIX}/man/man1
29+DATADIR?= ${PREFIX}/share/minimap2 29+DATADIR?= ${PREFIX}/share/minimap2
30  30
31+MKDIR?= mkdir 31+MKDIR?= mkdir
32+CP?= cp  32+CP?= cp
33+INSTALL?= install 33+INSTALL?= install
34+STRIP?= strip 34+STRIP?= strip
35+ 35+
36 ifneq ($(arm_neon),) # if arm_neon is defined 36 ifneq ($(arm_neon),) # if arm_neon is defined
37 ifeq ($(aarch64),) #if aarch64 is not defined 37 ifeq ($(aarch64),) #if aarch64 is not defined
38 CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char 38 CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
39@@ -26,7 +39,7 @@ ifneq ($(tsan),) 39@@ -26,7 +39,7 @@ ifneq ($(tsan),)
40 LIBS+=-fsanitize=thread 40 LIBS+=-fsanitize=thread
41 endif 41 endif
42  42
43-.PHONY:all extra clean depend 43-.PHONY:all extra clean depend
44+.PHONY:all extra install install-strip clean depend 44+.PHONY:all extra install install-strip clean depend
45 .SUFFIXES:.c .o 45 .SUFFIXES:.c .o
46  46
47 .c.o: 47 .c.o:
48@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h 48@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
49 $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@ 49 $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
50  50
51 # other non-file targets 51 # other non-file targets
52+ 52+
53+ 53+
54+install: all 54+install: all
55+ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin 55+ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
56+ ${MKDIR} -p ${DESTDIR}${MAN1DIR} 56+ ${MKDIR} -p ${DESTDIR}${MAN1DIR}
57+ ${MKDIR} -p ${DESTDIR}${DATADIR} 57+ ${MKDIR} -p ${DESTDIR}${DATADIR}
58+ ${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin 58+ ${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
59+ ${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin 59+ ${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin
60+ ${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin 60+ ${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin
61+ ${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR} 61+ ${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
62+ ${CP} -R test ${DESTDIR}${DATADIR} 62+ ${CP} -R test ${DESTDIR}${DATADIR}
63+ 63+
64+install-strip: install 64+install-strip: install
65+ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2 65+ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
66+ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite 66+ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
67+ ${STRIP} ${DESTDIR}${PREFIX}/bin/sdust 67+ ${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
68  68
69 clean: 69 clean:
70 rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* 70 rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
cvs diff -r1.1 -r1.2 pkgsrc/biology/minimap2/patches/patch-example.c (switch to unified diff)

--- pkgsrc/biology/minimap2/patches/patch-example.c 2024/03/13 13:54:04 1.1
+++ pkgsrc/biology/minimap2/patches/patch-example.c 2024/04/10 12:36:12 1.2
@@ -1,15 +1,15 @@ @@ -1,15 +1,15 @@
1$NetBSD: patch-example.c,v 1.1 2024/03/13 13:54:04 bacon Exp $ 1$NetBSD: patch-example.c,v 1.2 2024/04/10 12:36:12 bacon Exp $
2 2
3# Fix data type mismatch 3# Fix data type mismatch
4 4
5--- example.c.orig 2021-11-30 15:26:24 UTC 5--- example.c.orig 2021-11-30 15:26:24 UTC
6+++ example.c 6+++ example.c
7@@ -44,7 +44,7 @@ int main(int argc, char *argv[]) 7@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
8 for (j = 0; j < n_reg; ++j) { // traverse hits and print them out 8 for (j = 0; j < n_reg; ++j) { // traverse hits and print them out
9 mm_reg1_t *r = &reg[j]; 9 mm_reg1_t *r = &reg[j];
10 assert(r->p); // with MM_F_CIGAR, this should not be NULL 10 assert(r->p); // with MM_F_CIGAR, this should not be NULL
11- printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]); 11- printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
12+ printf("%s\t%zu\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]); 12+ printf("%s\t%zu\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
13 printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re, r->mlen, r->blen, r->mapq); 13 printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re, r->mlen, r->blen, r->mapq);
14 for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings! 14 for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
15 printf("%d%c", r->p->cigar[i]>>4, MM_CIGAR_STR[r->p->cigar[i]&0xf]); 15 printf("%d%c", r->p->cigar[i]>>4, MM_CIGAR_STR[r->p->cigar[i]&0xf]);