Received: by mail.netbsd.org (Postfix, from userid 605) id 3489184F69; Sat, 25 Feb 2023 13:53:25 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 4A0D284F7C for ; Sat, 25 Feb 2023 13:53:24 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id eZyXyz4p8bTT for ; Sat, 25 Feb 2023 13:53:23 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 909F484CDC for ; Sat, 25 Feb 2023 13:53:23 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 92105FA93; Sat, 25 Feb 2023 13:52:39 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1677333159238590" MIME-Version: 1.0 Date: Sat, 25 Feb 2023 13:52:39 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/samtools To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20230225135239.92105FA93@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1677333159238590 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Sat Feb 25 13:52:39 UTC 2023 Modified Files: pkgsrc/biology/samtools: Makefile PLIST distinfo pkgsrc/biology/samtools/patches: patch-Makefile Log Message: biology/samtools: Update to 1.17 Numerous enhancements and bug fixes Changes: https://github.com/samtools/samtools/releases To generate a diff of this commit: cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/samtools/Makefile cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/samtools/PLIST cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/samtools/distinfo cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/samtools/patches/patch-Makefile Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1677333159238590 Content-Disposition: inline Content-Length: 3046 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/samtools/Makefile diff -u pkgsrc/biology/samtools/Makefile:1.18 pkgsrc/biology/samtools/Makefile:1.19 --- pkgsrc/biology/samtools/Makefile:1.18 Wed Dec 28 15:27:17 2022 +++ pkgsrc/biology/samtools/Makefile Sat Feb 25 13:52:39 2023 @@ -1,6 +1,6 @@ -# $NetBSD: Makefile,v 1.18 2022/12/28 15:27:17 bacon Exp $ +# $NetBSD: Makefile,v 1.19 2023/02/25 13:52:39 bacon Exp $ -DISTNAME= samtools-1.16.1 +DISTNAME= samtools-1.17 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} GITHUB_RELEASE= ${PKGVERSION_NOREV} Index: pkgsrc/biology/samtools/PLIST diff -u pkgsrc/biology/samtools/PLIST:1.6 pkgsrc/biology/samtools/PLIST:1.7 --- pkgsrc/biology/samtools/PLIST:1.6 Tue Dec 13 10:28:01 2022 +++ pkgsrc/biology/samtools/PLIST Sat Feb 25 13:52:39 2023 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.6 2022/12/13 10:28:01 adam Exp $ +@comment $NetBSD: PLIST,v 1.7 2023/02/25 13:52:39 bacon Exp $ bin/ace2sam bin/blast2sam.pl bin/bowtie2sam.pl @@ -30,6 +30,7 @@ man/man1/samtools-cat.1 man/man1/samtools-collate.1 man/man1/samtools-consensus.1 man/man1/samtools-coverage.1 +man/man1/samtools-cram-size.1 man/man1/samtools-depad.1 man/man1/samtools-depth.1 man/man1/samtools-dict.1 @@ -51,6 +52,7 @@ man/man1/samtools-phase.1 man/man1/samtools-quickcheck.1 man/man1/samtools-reference.1 man/man1/samtools-reheader.1 +man/man1/samtools-reset.1 man/man1/samtools-rmdup.1 man/man1/samtools-samples.1 man/man1/samtools-sort.1 Index: pkgsrc/biology/samtools/distinfo diff -u pkgsrc/biology/samtools/distinfo:1.9 pkgsrc/biology/samtools/distinfo:1.10 --- pkgsrc/biology/samtools/distinfo:1.9 Tue Dec 13 10:28:01 2022 +++ pkgsrc/biology/samtools/distinfo Sat Feb 25 13:52:39 2023 @@ -1,6 +1,6 @@ -$NetBSD: distinfo,v 1.9 2022/12/13 10:28:01 adam Exp $ +$NetBSD: distinfo,v 1.10 2023/02/25 13:52:39 bacon Exp $ -BLAKE2s (samtools-1.16.1.tar.bz2) = 45ca326da1c2aa560fde2d582b58150b71f05d72ff996c9ae97427ef22b018a0 -SHA512 (samtools-1.16.1.tar.bz2) = f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba -Size (samtools-1.16.1.tar.bz2) = 8217689 bytes +BLAKE2s (samtools-1.17.tar.bz2) = 9ab61bddae955190736abf7e9198ee869396a74e195166df38ebb652fe4bc7c7 +SHA512 (samtools-1.17.tar.bz2) = 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3 +Size (samtools-1.17.tar.bz2) = 8605080 bytes SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d Index: pkgsrc/biology/samtools/patches/patch-Makefile diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.4 pkgsrc/biology/samtools/patches/patch-Makefile:1.5 --- pkgsrc/biology/samtools/patches/patch-Makefile:1.4 Sat Feb 26 23:11:43 2022 +++ pkgsrc/biology/samtools/patches/patch-Makefile Sat Feb 25 13:52:39 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-Makefile,v 1.4 2022/02/26 23:11:43 bacon Exp $ +$NetBSD: patch-Makefile,v 1.5 2023/02/25 13:52:39 bacon Exp $ # Respect pkgsrc env --_----------=_1677333159238590--