biology/minimap2: Update to 2.28 Fix --MD flag Add experimental lr:hqae Changes: https://github.com/lh3/minimap2/releases Reported by: portscoutdiff -r1.5 -r1.6 pkgsrc/biology/minimap2/Makefile
(bacon)
@@ -1,16 +1,16 @@ | @@ -1,16 +1,16 @@ | |||
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 | |||
3 | VERSION= 2.27 | 3 | VERSION= 2.28 | |
4 | DISTNAME= minimap2-${VERSION} | 4 | DISTNAME= minimap2-${VERSION} | |
5 | CATEGORIES= biology python | 5 | CATEGORIES= biology python | |
6 | MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/} | 6 | MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/} | |
7 | GITHUB_TAG= v${VERSION} | 7 | GITHUB_TAG= v${VERSION} | |
8 | 8 | |||
9 | MAINTAINER= pkgsrc-users@NetBSD.org | 9 | MAINTAINER= pkgsrc-users@NetBSD.org | |
10 | HOMEPAGE= https://github.com/lh3/minimap2 | 10 | HOMEPAGE= https://github.com/lh3/minimap2 | |
11 | COMMENT= Sequence alignment program for noisy, long reads | 11 | COMMENT= Sequence alignment program for noisy, long reads | |
12 | LICENSE= mit | 12 | LICENSE= mit | |
13 | 13 | |||
14 | USE_TOOLS+= gmake | 14 | USE_TOOLS+= gmake | |
15 | MAKE_FILE= Makefile.simde | 15 | MAKE_FILE= Makefile.simde | |
16 | 16 |
@@ -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 $ | |
2 | bin/minimap2 | 2 | bin/minimap2 | |
3 | man/man1/minimap2.1 | 3 | man/man1/minimap2.1 |
@@ -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 | |||
3 | BLAKE2s (minimap2-2.27.tar.gz) = 92e09196bf9de2c121ce8a3305200760ff9e8ba83d634b106b33297508b5e01d | 3 | BLAKE2s (minimap2-2.28.tar.gz) = 0a0afd89e588dd0d8a93a562264bb5fdfe50f88a18f5f057bf59be51e16bbe0b | |
4 | SHA512 (minimap2-2.27.tar.gz) = fca5983cbd650b81c6a2caff8ad4d47286467df81ab76646e4fa4b113f0a76d16e4cc8cc5e2f4adaf5c06246ffa099c2728cd0dcba87d808980ed78ee3a029d1 | 4 | SHA512 (minimap2-2.28.tar.gz) = d8d4bb4381d6effb3eb3e1a66fac7a83bc00c3cf174d2e0537dd4790d0e4a3cc060b92e39ed2e2cafc6e5e713f6fdbee6bac1d279b6b77d4347f77f3e6d3c0d0 | |
5 | Size (minimap2-2.27.tar.gz) = 259736 bytes | 5 | Size (minimap2-2.28.tar.gz) = 260341 bytes | |
6 | SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551 | 6 | SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551 | |
7 | SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c | 7 | SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c |
@@ -1,14 +1,14 @@ | @@ -1,14 +1,14 @@ | |||
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 |
@@ -1,14 +1,14 @@ | @@ -1,14 +1,14 @@ | |||
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 = ®[j]; | 9 | mm_reg1_t *r = ®[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! |