Date: Sun, 29 Mar 2026 13:25:35 +0000 From: Jason W. Bacon <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e2110f368446 - main - biology/bcftools: Update to 1.23.1 Message-ID: <69c9284f.211b6.34050a7@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e2110f368446489c356140a7fda592d946153a07 commit e2110f368446489c356140a7fda592d946153a07 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2026-03-29 13:10:48 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2026-03-29 13:25:32 +0000 biology/bcftools: Update to 1.23.1 A few bug fixes, though more changes to underlying htslib Changes: https://github.com/samtools/bcftools/releases New commands: gff2gff and roh-viz --- biology/bcftools/Makefile | 11 +++++++---- biology/bcftools/distinfo | 6 +++--- biology/bcftools/pkg-plist | 3 +++ 3 files changed, 13 insertions(+), 7 deletions(-) diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile index c936d0b210fb..11a2a1f9a31e 100644 --- a/biology/bcftools/Makefile +++ b/biology/bcftools/Makefile @@ -1,6 +1,5 @@ PORTNAME= bcftools -PORTVERSION= 1.22 -PORTREVISION= 1 +PORTVERSION= 1.23.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -24,11 +23,15 @@ GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share SHEBANG_FILES= misc/* test/test.pl -OPTIONS_DEFINE= GPL +OPTIONS_DEFINE= GPL PERL GPL_DESC= Enable modules that rely on GPL code -OPTIONS_DEFAULT= GPL +PERL_DESC= Enable external PERL scripts for advanced filtering +OPTIONS_DEFAULT= GPL PERL GPL_LIB_DEPENDS= libgsl.so:math/gsl +GPL_CONFIGURE_ENABLE= libgsl +PERL_USES= perl5 +PERL_CONFIGURE_ENABLE= perl-filters .include <bsd.port.options.mk> diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo index 187e684df6f4..c92df2732f05 100644 --- a/biology/bcftools/distinfo +++ b/biology/bcftools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1748951423 -SHA256 (samtools-bcftools-1.22_GH0.tar.gz) = 1608e547daf7bd5ab7d52dea57019f57da3fdfb29bc26dece1e8d01a999a9a2d -SIZE (samtools-bcftools-1.22_GH0.tar.gz) = 3751342 +TIMESTAMP = 1774783023 +SHA256 (samtools-bcftools-1.23.1_GH0.tar.gz) = e3b47ff5f771389ba754b12428873642db15ee2baf06cd3ac1a214a39a74ec58 +SIZE (samtools-bcftools-1.23.1_GH0.tar.gz) = 3764835 diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist index 8d7cedf90291..2edeeaca650c 100644 --- a/biology/bcftools/pkg-plist +++ b/biology/bcftools/pkg-plist @@ -1,11 +1,14 @@ bin/bcftools bin/color-chrs +bin/gff2gff bin/gff2gff.py bin/guess-ploidy bin/plot-roh bin/plot-vcfstats +bin/roh-viz bin/run-roh bin/vcfutils +bin/vrfs-variances libexec/bcftools/GTisec.so libexec/bcftools/GTsubset.so libexec/bcftools/ad-bias.sohome | help
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