CVS commit: pkgsrc/biology/bcftools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Oct 11 22:41:14 UTC 2024

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

Log Message:
biology/bcftools: Update to 1.21

Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/bcftools/releases

Reported by:    portscout


To generate a diff of this commit:
cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/bcftools/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/bcftools/PLIST
cvs rdiff -u -r1.8 -r1.9 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:1.18 pkgsrc/biology/bcftools/Makefile:1.19
--- pkgsrc/biology/bcftools/Makefile:1.18       Mon Aug 14 05:23:51 2023
+++ pkgsrc/biology/bcftools/Makefile    Fri Oct 11 22:41:14 2024
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.18 2023/08/14 05:23:51 wiz Exp $
+# $NetBSD: Makefile,v 1.19 2024/10/11 22:41:14 bacon Exp $
 
-DISTNAME=      bcftools-1.17
-PKGREVISION=   1
+DISTNAME=      bcftools-1.21
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 GITHUB_RELEASE=        ${PKGVERSION_NOREV}
@@ -50,7 +49,8 @@ post-install:
        ${MV} ${DESTDIR}${PREFIX}/bin/vcfutils.pl \
                ${DESTDIR}${PREFIX}/bin/vcfutils
 
-.include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../math/gsl/buildlink3.mk"
 .include "../../lang/python/application.mk"
+.include "../../biology/htslib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/bcftools/PLIST
diff -u pkgsrc/biology/bcftools/PLIST:1.6 pkgsrc/biology/bcftools/PLIST:1.7
--- pkgsrc/biology/bcftools/PLIST:1.6   Sat Feb 25 13:56:33 2023
+++ pkgsrc/biology/bcftools/PLIST       Fri Oct 11 22:41:14 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.6 2023/02/25 13:56:33 bacon Exp $
+@comment $NetBSD: PLIST,v 1.7 2024/10/11 22:41:14 bacon Exp $
 bin/bcftools
 bin/color-chrs
 bin/gff2gff.py
@@ -30,7 +30,6 @@ libexec/bcftools/gvcfz.so
 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

Index: pkgsrc/biology/bcftools/distinfo
diff -u pkgsrc/biology/bcftools/distinfo:1.8 pkgsrc/biology/bcftools/distinfo:1.9
--- pkgsrc/biology/bcftools/distinfo:1.8        Sat Feb 25 13:56:33 2023
+++ pkgsrc/biology/bcftools/distinfo    Fri Oct 11 22:41:14 2024
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.8 2023/02/25 13:56:33 bacon Exp $
+$NetBSD: distinfo,v 1.9 2024/10/11 22:41:14 bacon Exp $
 
-BLAKE2s (bcftools-1.17.tar.bz2) = 322846c2569abe78d079cadf82e6cb629c064e26161d5a08cdbfc7c45215a6f0
-SHA512 (bcftools-1.17.tar.bz2) = 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68
-Size (bcftools-1.17.tar.bz2) = 7538043 bytes
+BLAKE2s (bcftools-1.21.tar.bz2) = 517b73f84870fa967e6f7f6241c446131cc54229e7ee446110955e39dfbe2563
+SHA512 (bcftools-1.21.tar.bz2) = f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
+Size (bcftools-1.21.tar.bz2) = 7982173 bytes
 SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731