From nobody Thu Jan 05 23:21:36 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Np2Xw5Nf7z2qmGZ; Thu, 5 Jan 2023 23:21:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Np2Xw4y2Gz3sY0; Thu, 5 Jan 2023 23:21:36 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1672960896; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=pTTKr2kyMoWJ3SyrCNvk4AV3419QuYXEslr7DGR9KFc=; b=sr65WD2qD2s5e1DYFz0+jTs9k/wPqUXRLTOdmLVqv3koyLHRsEBcNOUAXCRAo0IMXzpRVA ZeXZMxEJKZrG2xNRqDn7EDTvIbB9BsGZyDglPdJTeoPT5EO0R/VURKdq4RgnRs0vaQSHIK aFki/xJdS6w3h2lN/0csg7eIyjuVaq7YfVF4XMliw1MbQ6mcLzSCATk3N491NLRXcxrhPw jt6wKPzxr3QxFvVNG6lh3TaVwM+V1rdqV8jKj8SwgSIAZ7tHJvp2ND8IGxKBZx9vlHG4Nz SxPRy/wCk3tKmjmtf3KG/kdhDzsTsxFGNflkQPzY2nTMyyEUJ5oR5SXfZ6AIfg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1672960896; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=pTTKr2kyMoWJ3SyrCNvk4AV3419QuYXEslr7DGR9KFc=; b=OGUvSKY6jMY43GCBuC1ipV9aVsWm2du/ZO2Me0XmIwuFGWccrVfBymctV57bxXKFo0dX0f BXPnVL9/lHH5VguNmLl6qTZMDVUYl5vPtTZgnrkwSLCWx7BpF4xeD4U+E8eCP88ER2azzZ pUH8jFWj+EOeHqE2kmxCms0dboEwO25312vk6RklKvbARot4rJlDLOXEaGBdb1d39XPeFF Zc4L5Kes2Sr1w0ooyz8JErQuXsjYboljqSckksF4D4HL/VkD4lm0ADEVGoXfCYPT43iDwK gQCoAuAmKYFvnkcQrnx8mM+xl9Jych7HacN3/AxztfODuSWvE8QUh+3dYn4soQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1672960896; a=rsa-sha256; cv=none; b=V2bPPupK5zgP5dTMxVOL7lUpR/f24j3ERTxXHkgWgD9pPvX4zyNsagAOdddHWU+SwRYkGb Eo5AkaZkpaMnmlWVGitbBSrnh+Ns0AMz0nAX02LsX6JO2aMwtEmjgAvDmpVaQOvsQClQBs Bpv736GcvJZQZ7waayg8XQ9N62idm0zg4f7Ta21kKh9Vd/QtRWYnnrGuGg5MDIzd9J+l7K AVsspD3kWFWoQKv6x9yztMItirz8eminlEVSZ0hGWKWpfkvdMUzwUWXoOhHJK/k9TNAP/5 zFGvQNIuFUcM8UhuiOMI4u2Ybos9U2kPSQpci6/xgOj9ETqhdtdUPZV4iJZuwQ== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4Np2Xw3qFvz17kC; Thu, 5 Jan 2023 23:21:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 305NLaDx003621; Thu, 5 Jan 2023 23:21:36 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 305NLaeL003608; Thu, 5 Jan 2023 23:21:36 GMT (envelope-from git) Date: Thu, 5 Jan 2023 23:21:36 GMT Message-Id: <202301052321.305NLaeL003608@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 193567cc9e20 - main - biology/samtools: Update to 1.16.1 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 193567cc9e20e9ecb305506d92f522fc77dd18e4 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=193567cc9e20e9ecb305506d92f522fc77dd18e4 commit 193567cc9e20e9ecb305506d92f522fc77dd18e4 Author: Jason W. Bacon AuthorDate: 2023-01-05 23:17:34 +0000 Commit: Jason W. Bacon CommitDate: 2023-01-05 23:17:34 +0000 biology/samtools: Update to 1.16.1 New "reference" subcommand to extract CRAM features (1.16) Numerous minor enhancements and bug fixes Changes: https://github.com/samtools/samtools/releases --- biology/samtools/Makefile | 2 +- biology/samtools/distinfo | 6 +++--- biology/samtools/pkg-plist | 1 + 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile index cbdfaa3b607b..64b06bff07e8 100644 --- a/biology/samtools/Makefile +++ b/biology/samtools/Makefile @@ -1,5 +1,5 @@ PORTNAME= samtools -DISTVERSION= 1.15 +DISTVERSION= 1.16.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo index 19439fbc44f5..d0c7b4cbb765 100644 --- a/biology/samtools/distinfo +++ b/biology/samtools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1645831653 -SHA256 (samtools-samtools-1.15_GH0.tar.gz) = 5109a17f221b36291e4bc3ad68a00c28515d4f20a16b4e23806055661ca0df31 -SIZE (samtools-samtools-1.15_GH0.tar.gz) = 4970205 +TIMESTAMP = 1672094602 +SHA256 (samtools-samtools-1.16.1_GH0.tar.gz) = 70a7f358088929272d8c22d6063290ac8420f5351fba237a99fe17851a45d8be +SIZE (samtools-samtools-1.16.1_GH0.tar.gz) = 4992787 diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist index aafc040158e0..1d228254f042 100644 --- a/biology/samtools/pkg-plist +++ b/biology/samtools/pkg-plist @@ -48,6 +48,7 @@ man/man1/samtools-merge.1.gz man/man1/samtools-mpileup.1.gz man/man1/samtools-phase.1.gz man/man1/samtools-quickcheck.1.gz +man/man1/samtools-reference.1.gz man/man1/samtools-reheader.1.gz man/man1/samtools-rmdup.1.gz man/man1/samtools-samples.1.gz