git: e2110f368446 - main - biology/bcftools: Update to 1.23.1

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.so