CVS commit: pkgsrc/biology/bcftools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Feb 25 13:56:33 UTC 2023

Modified Files:
        pkgsrc/biology/bcftools: Makefile PLIST distinfo

Log Message:
biology/bcftools: Update to 1.17

Numerous enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/releases


To generate a diff of this commit:
cvs rdiff -u -r1.16 -r1.17 pkgsrc/biology/bcftools/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/bcftools/PLIST
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/bcftools/distinfo

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

Modified files:

Index: pkgsrc/biology/bcftools/Makefile
diff -u pkgsrc/biology/bcftools/Makefile:1.16 pkgsrc/biology/bcftools/Makefile:1.17
--- pkgsrc/biology/bcftools/Makefile:1.16       Wed Dec 28 15:27:15 2022
+++ pkgsrc/biology/bcftools/Makefile    Sat Feb 25 13:56:33 2023
@@ -1,17 +1,21 @@
-# $NetBSD: Makefile,v 1.16 2022/12/28 15:27:15 bacon Exp $
+# $NetBSD: Makefile,v 1.17 2023/02/25 13:56:33 bacon Exp $
 
-DISTNAME=      bcftools-1.15
-PKGREVISION=   2
+DISTNAME=      bcftools-1.17
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_RELEASE=        ${PKGVERSION_NOREV}
+EXTRACT_SUFX=  .tar.bz2
 
 OWNER=         bacon%NetBSD.org@localhost
 HOMEPAGE=      https://www.htslib.org/
 COMMENT=       Tools for manipulating BCF and VCF variant call files
 LICENSE=       mit
 
-USE_TOOLS+=    autoconf automake autoreconf bash gmake perl
-GNU_CONFIGURE= yes
+USE_TOOLS+=            autoconf automake autoreconf bash gmake perl
+GNU_CONFIGURE=         yes
+CONFIGURE_ARGS+=       --with-htslib=system
+MAKE_ENV+=             USE_GPL=1
+TEST_TARGET=           test
 
 SUBST_CLASSES+=                version
 SUBST_STAGE.version=   pre-configure
@@ -30,10 +34,6 @@ REPLACE_PERL+=               misc/plot-vcfstats
 REPLACE_PERL+=         test/test.pl
 REPLACE_PYTHON+=       misc/*.py
 
-CONFIGURE_ARGS+=       --with-htslib=system
-MAKE_ENV+=             USE_GPL=1
-TEST_TARGET=           test
-
 pre-configure:
        cd ${WRKSRC} && autoreconf -if
 

Index: pkgsrc/biology/bcftools/PLIST
diff -u pkgsrc/biology/bcftools/PLIST:1.5 pkgsrc/biology/bcftools/PLIST:1.6
--- pkgsrc/biology/bcftools/PLIST:1.5   Sat Feb 26 23:14:33 2022
+++ pkgsrc/biology/bcftools/PLIST       Sat Feb 25 13:56:33 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2022/02/26 23:14:33 bacon Exp $
+@comment $NetBSD: PLIST,v 1.6 2023/02/25 13:56:33 bacon Exp $
 bin/bcftools
 bin/color-chrs
 bin/gff2gff.py
@@ -31,6 +31,7 @@ libexec/bcftools/impute-info.so
 libexec/bcftools/indel-stats.so
 libexec/bcftools/isecGT.so
 libexec/bcftools/mendelian.so
+libexec/bcftools/mendelian2.so
 libexec/bcftools/missing2ref.so
 libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
@@ -44,5 +45,6 @@ libexec/bcftools/tag2tag.so
 libexec/bcftools/trio-dnm2.so
 libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
+libexec/bcftools/variant-distance.so
 libexec/bcftools/variantkey-hex.so
 man/man1/bcftools.1

Index: pkgsrc/biology/bcftools/distinfo
diff -u pkgsrc/biology/bcftools/distinfo:1.7 pkgsrc/biology/bcftools/distinfo:1.8
--- pkgsrc/biology/bcftools/distinfo:1.7        Sat Feb 26 23:14:33 2022
+++ pkgsrc/biology/bcftools/distinfo    Sat Feb 25 13:56:33 2023
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.7 2022/02/26 23:14:33 bacon Exp $
+$NetBSD: distinfo,v 1.8 2023/02/25 13:56:33 bacon Exp $
 
-BLAKE2s (bcftools-1.15.tar.gz) = 50d87d4463c84dc7a450dba488d79ad43c5ab2a25c10bee92c94b1c3d11e5963
-SHA512 (bcftools-1.15.tar.gz) = fcb8dac8cf28f9c490c14d72a1c9fba027d7224e09ba37f6ab4c940e0a1eec8aef3b439137be013abb97dff492d252492cee4e88325285fc643729042b4fbd07
-Size (bcftools-1.15.tar.gz) = 3347901 bytes
+BLAKE2s (bcftools-1.17.tar.bz2) = 322846c2569abe78d079cadf82e6cb629c064e26161d5a08cdbfc7c45215a6f0
+SHA512 (bcftools-1.17.tar.bz2) = 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68
+Size (bcftools-1.17.tar.bz2) = 7538043 bytes
 SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731