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
This commit is contained in:
bacon
parent
ce82d407df
commit
36ab0bcd8c
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@ -1,8 +1,7 @@
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# $NetBSD: Makefile,v 1.4 2023/08/14 05:23:51 wiz Exp $
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# $NetBSD: Makefile,v 1.5 2024/03/13 13:54:04 bacon Exp $
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VERSION= 2.24
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VERSION= 2.27
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DISTNAME= minimap2-${VERSION}
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PKGREVISION= 1
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CATEGORIES= biology python
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MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/}
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GITHUB_TAG= v${VERSION}
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@ -13,6 +12,7 @@ COMMENT= Sequence alignment program for noisy, long reads
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LICENSE= mit
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USE_TOOLS+= gmake
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MAKE_FILE= Makefile.simde
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INSTALLATION_DIRS+= bin ${PKGMANDIR}/man1
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@ -21,4 +21,5 @@ do-install:
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${INSTALL_DATA} ${WRKSRC}/minimap2.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../devel/simde/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -1,3 +1,3 @@
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@comment $NetBSD: PLIST,v 1.2 2021/05/29 17:35:18 brook Exp $
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@comment $NetBSD: PLIST,v 1.3 2024/03/13 13:54:04 bacon Exp $
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bin/minimap2
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man/man1/minimap2.1
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@ -1,6 +1,7 @@
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$NetBSD: distinfo,v 1.5 2023/07/09 08:37:39 nia Exp $
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$NetBSD: distinfo,v 1.6 2024/03/13 13:54:04 bacon Exp $
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BLAKE2s (minimap2-2.24.tar.gz) = fad5bbbfd6563f32ffe046528758eca23b071386847b1a93d3388f5be205de5b
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SHA512 (minimap2-2.24.tar.gz) = f53a28ce5cd8624fbc5e964dc58edfa27ecea5f253cd49cb7b57396a40810b673392ebf323f0fb5d3b6ef82d4a9a96b025581aee10246e3c8d59e954819876e7
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Size (minimap2-2.24.tar.gz) = 253050 bytes
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SHA1 (patch-Makefile) = ae4be7748e5ec1e8ed1ff235be5ac6eeeeb0d3b3
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BLAKE2s (minimap2-2.27.tar.gz) = 92e09196bf9de2c121ce8a3305200760ff9e8ba83d634b106b33297508b5e01d
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SHA512 (minimap2-2.27.tar.gz) = fca5983cbd650b81c6a2caff8ad4d47286467df81ab76646e4fa4b113f0a76d16e4cc8cc5e2f4adaf5c06246ffa099c2728cd0dcba87d808980ed78ee3a029d1
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Size (minimap2-2.27.tar.gz) = 259736 bytes
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SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551
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SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c
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@ -1,26 +0,0 @@
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$NetBSD: patch-Makefile,v 1.1 2023/07/09 08:37:39 nia Exp $
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Honour CFLAGS/LDFLAGS. Hopefully fixes building on platforms where zlib
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is installed from pkgsrc.
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--- Makefile.orig 2021-12-26 20:14:54.000000000 +0000
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+++ Makefile
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@@ -1,4 +1,4 @@
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-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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+CFLAGS+= -Wall -Wc++-compat #-Wextra
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CPPFLAGS= -DHAVE_KALLOC
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INCLUDES=
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
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@@ -45,10 +45,10 @@ all:$(PROG)
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extra:all $(PROG_EXTRA)
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minimap2:main.o libminimap2.a
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- $(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
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+ $(CC) $(LDFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
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minimap2-lite:example.o libminimap2.a
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- $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
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+ $(CC) $(LDFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
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libminimap2.a:$(OBJS)
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$(AR) -csru $@ $(OBJS)
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@ -0,0 +1,70 @@
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$NetBSD: patch-Makefile.simde,v 1.1 2024/03/13 13:54:04 bacon Exp $
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# Respect standard env vars
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--- Makefile.simde.orig 2021-11-18 22:11:48 UTC
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+++ Makefile.simde
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@@ -1,13 +1,26 @@
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-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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-CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
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-INCLUDES= -Ilib/simde
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-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 \
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- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
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+
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+# Makefile patches rejected by upstream
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+
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+CFLAGS?= -g -Wall -O2
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+CFLAGS+= -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__
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+CPPFLAGS?= -DHAVE_KALLOC
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+OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o \
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+ index.o lchain.o align.o hit.o map.o format.o pe.o seed.o \
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+ esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o \
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+ ksw2_exts2_simde.o ksw2_ll_simde.o
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PROG= minimap2
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PROG_EXTRA= sdust minimap2-lite
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LIBS= -lm -lz -lpthread
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+PREFIX?= /usr/local
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+MAN1DIR?= ${PREFIX}/man/man1
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+DATADIR?= ${PREFIX}/share/minimap2
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+MKDIR?= mkdir
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+CP?= cp
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+INSTALL?= install
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+STRIP?= strip
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+
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ifneq ($(arm_neon),) # if arm_neon is defined
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ifeq ($(aarch64),) #if aarch64 is not defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
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@@ -26,7 +39,7 @@ ifneq ($(tsan),)
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LIBS+=-fsanitize=thread
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endif
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-.PHONY:all extra clean depend
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+.PHONY:all extra install install-strip clean depend
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.SUFFIXES:.c .o
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.c.o:
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@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
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# other non-file targets
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+
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+
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+install: all
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+ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
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+ ${MKDIR} -p ${DESTDIR}${MAN1DIR}
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+ ${MKDIR} -p ${DESTDIR}${DATADIR}
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+ ${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR}
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+ ${CP} -R test ${DESTDIR}${DATADIR}
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+
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+install-strip: install
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+ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
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+ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
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+ ${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
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clean:
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rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
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@ -0,0 +1,15 @@
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$NetBSD: patch-example.c,v 1.1 2024/03/13 13:54:04 bacon Exp $
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# Fix data type mismatch
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--- example.c.orig 2021-11-30 15:26:24 UTC
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+++ example.c
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@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
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for (j = 0; j < n_reg; ++j) { // traverse hits and print them out
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mm_reg1_t *r = ®[j];
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assert(r->p); // with MM_F_CIGAR, this should not be NULL
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- printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
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+ printf("%s\t%zu\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
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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);
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for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
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printf("%d%c", r->p->cigar[i]>>4, MM_CIGAR_STR[r->p->cigar[i]&0xf]);
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