CVS commit: pkgsrc/biology/minimap2

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Mar 13 13:54:04 UTC 2024

Modified Files:
        pkgsrc/biology/minimap2: Makefile PLIST distinfo
Added Files:
        pkgsrc/biology/minimap2/patches: patch-Makefile.simde patch-example.c
Removed Files:
        pkgsrc/biology/minimap2/patches: patch-Makefile

Log Message:
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


To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/minimap2/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/minimap2/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/minimap2/distinfo
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/minimap2/patches/patch-Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/minimap2/patches/patch-Makefile.simde \
    pkgsrc/biology/minimap2/patches/patch-example.c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/minimap2/Makefile
diff -u pkgsrc/biology/minimap2/Makefile:1.4 pkgsrc/biology/minimap2/Makefile:1.5
--- pkgsrc/biology/minimap2/Makefile:1.4        Mon Aug 14 05:23:51 2023
+++ pkgsrc/biology/minimap2/Makefile    Wed Mar 13 13:54:04 2024
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.4 2023/08/14 05:23:51 wiz Exp $
+# $NetBSD: Makefile,v 1.5 2024/03/13 13:54:04 bacon Exp $
 
-VERSION=       2.24
+VERSION=       2.27
 DISTNAME=      minimap2-${VERSION}
-PKGREVISION=   1
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
 GITHUB_TAG=    v${VERSION}
@@ -13,6 +12,7 @@ COMMENT=      Sequence alignment program for 
 LICENSE=       mit
 
 USE_TOOLS+=    gmake
+MAKE_FILE=     Makefile.simde
 
 INSTALLATION_DIRS+=    bin ${PKGMANDIR}/man1
 
@@ -21,4 +21,5 @@ do-install:
        ${INSTALL_DATA} ${WRKSRC}/minimap2.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
 
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/simde/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/minimap2/PLIST
diff -u pkgsrc/biology/minimap2/PLIST:1.2 pkgsrc/biology/minimap2/PLIST:1.3
--- pkgsrc/biology/minimap2/PLIST:1.2   Sat May 29 17:35:18 2021
+++ pkgsrc/biology/minimap2/PLIST       Wed Mar 13 13:54:04 2024
@@ -1,3 +1,3 @@
-@comment $NetBSD: PLIST,v 1.2 2021/05/29 17:35:18 brook Exp $
+@comment $NetBSD: PLIST,v 1.3 2024/03/13 13:54:04 bacon Exp $
 bin/minimap2
 man/man1/minimap2.1

Index: pkgsrc/biology/minimap2/distinfo
diff -u pkgsrc/biology/minimap2/distinfo:1.5 pkgsrc/biology/minimap2/distinfo:1.6
--- pkgsrc/biology/minimap2/distinfo:1.5        Sun Jul  9 08:37:39 2023
+++ pkgsrc/biology/minimap2/distinfo    Wed Mar 13 13:54:04 2024
@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.5 2023/07/09 08:37:39 nia Exp $
+$NetBSD: distinfo,v 1.6 2024/03/13 13:54:04 bacon Exp $
 
-BLAKE2s (minimap2-2.24.tar.gz) = fad5bbbfd6563f32ffe046528758eca23b071386847b1a93d3388f5be205de5b
-SHA512 (minimap2-2.24.tar.gz) = f53a28ce5cd8624fbc5e964dc58edfa27ecea5f253cd49cb7b57396a40810b673392ebf323f0fb5d3b6ef82d4a9a96b025581aee10246e3c8d59e954819876e7
-Size (minimap2-2.24.tar.gz) = 253050 bytes
-SHA1 (patch-Makefile) = ae4be7748e5ec1e8ed1ff235be5ac6eeeeb0d3b3
+BLAKE2s (minimap2-2.27.tar.gz) = 92e09196bf9de2c121ce8a3305200760ff9e8ba83d634b106b33297508b5e01d
+SHA512 (minimap2-2.27.tar.gz) = fca5983cbd650b81c6a2caff8ad4d47286467df81ab76646e4fa4b113f0a76d16e4cc8cc5e2f4adaf5c06246ffa099c2728cd0dcba87d808980ed78ee3a029d1
+Size (minimap2-2.27.tar.gz) = 259736 bytes
+SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551
+SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c

Added files:

Index: pkgsrc/biology/minimap2/patches/patch-Makefile.simde
diff -u /dev/null pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.1
--- /dev/null   Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/patches/patch-Makefile.simde        Wed Mar 13 13:54:04 2024
@@ -0,0 +1,70 @@
+$NetBSD: patch-Makefile.simde,v 1.1 2024/03/13 13:54:04 bacon Exp $
+
+# Respect standard env vars
+
+--- Makefile.simde.orig        2021-11-18 22:11:48 UTC
++++ Makefile.simde
+@@ -1,13 +1,26 @@
+-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 ($(aarch64),)   #if aarch64 is not defined
+       CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
+@@ -26,7 +39,7 @@ ifneq ($(tsan),)
+       LIBS+=-fsanitize=thread
+ endif
+ 
+-.PHONY:all extra clean depend
++.PHONY:all extra install install-strip clean depend
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+               $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+ 
+ # 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) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
Index: pkgsrc/biology/minimap2/patches/patch-example.c
diff -u /dev/null pkgsrc/biology/minimap2/patches/patch-example.c:1.1
--- /dev/null   Wed Mar 13 13:54:04 2024
+++ pkgsrc/biology/minimap2/patches/patch-example.c     Wed Mar 13 13:54:04 2024
@@ -0,0 +1,15 @@
+$NetBSD: patch-example.c,v 1.1 2024/03/13 13:54:04 bacon Exp $
+
+# Fix data type mismatch
+
+--- example.c.orig     2021-11-30 15:26:24 UTC
++++ example.c
+@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
+                       for (j = 0; j < n_reg; ++j) { // traverse hits and print them out
+                               mm_reg1_t *r = &reg[j];
+                               assert(r->p); // with MM_F_CIGAR, this should not be NULL
+-                              printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
++                              printf("%s\t%zu\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
+                               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);
+                               for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
+                                       printf("%d%c", r->p->cigar[i]>>4, MM_CIGAR_STR[r->p->cigar[i]&0xf]);