From nobody Sat Apr 29 14:53:41 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 4Q7stF5xnvz47r7R; Sat, 29 Apr 2023 14:53:41 +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 4Q7stF5NvBz4HVk; Sat, 29 Apr 2023 14:53:41 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1682780021; 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=nSKiNd96vhWhqLYKfv1reQnQ+kGyhfcqymAUijimVb0=; b=bw9vx73s+HSKkiafSs24L9RziWMpgB2E9ue0A9WeKmwEKm++o71e8yfgYPBHP7ycXn/eaL ONi3d73U+xW60VZ/7QtugMamAlDypzKInvZ28d/3K1TA0BMJdkIjvYOMOdKDE9WkCcX0qp FXetf3B2T46Kg+D7arO4YLVdJUCZV+BpuUtSkD7S1JOjjw8xmpNNgbYZU+sK8leH5pF6HG b3lNVwZTOjHbKzR3n8OOgTBX013Gx5sBgPIoq8xwP3YEqUTcRXMsPTQHvUwId14aF8F+kq k9GgYarzQMMPbyy/xIiE/ArwKpYEiLjwr6WsyTDl7h0Xy3L3CwF0KuAXqo4w+A== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1682780021; 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=nSKiNd96vhWhqLYKfv1reQnQ+kGyhfcqymAUijimVb0=; b=xF6/zQYXfquel3TwY/wXmOcerX8DDymU4Lcui0P6CQ5YXAB6Asiq+RYKfA4ijbJvx4dVM+ uw65nSYGnGlpt8f7tUYd9dlU+f9wTeSwqNVnObcvjBbQQ0ZUPgiHHGb7XztJjVRP53IZvv IX4bTubrGJjAyVIUnjfwxmfELHg/784XxAgEU42VT71ycpbMfBDj7qfd90ghfJwrAjC8gN yo7X6+AELSh6Eop/5gaLO98SYxRpmZl8ZGWR8yZC57DX+UWnvjLnWS6vJdSSik5BquFxU4 dfJ6CrNdvTwHskjyQcJhQtNHRMo6cPeQtXlwhLCYoq65yMtIPX37vxUHEk9J7A== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1682780021; a=rsa-sha256; cv=none; b=s6H4B7KlEx8hKCnCIkPSZZ41gD4ElNgMX2udxGBKRg0uSkpOwkwpeuorlgFW9UKM4hAW0J dlodRcgAClnDPIA9RAfBWN5uFpMFLEzsdj069oU9j7H3VY2d4KSkOTx9bLmjDdLn95DRFF c4mrawKTvGFgzfZ/rGXl1hnkjL3rmdtIKw1AvrQQZvdk6Q28QSIwMeUAq9wUsVJjnzdl+s FaXWBrApyu6N06EAwzP5mucfsO0a3g9QNSCvM+PCXw+kvTiiW2kkM36rOosHrT2Q/OB2Xj aMzGWN870wnssEwdhH8uhzQ6C07kv9bOZWemYZVZWSK8FGyv9mbhf4zdjd4GXQ== 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 4Q7stF4RZLzmCR; Sat, 29 Apr 2023 14:53:41 +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 33TErfl8086555; Sat, 29 Apr 2023 14:53:41 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 33TErfOa086554; Sat, 29 Apr 2023 14:53:41 GMT (envelope-from git) Date: Sat, 29 Apr 2023 14:53:41 GMT Message-Id: <202304291453.33TErfOa086554@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: 57d280a35eb7 - main - biology/minimap2: Update to 2.25 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: 57d280a35eb7d931d7009182b8dd2289c946f391 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=57d280a35eb7d931d7009182b8dd2289c946f391 commit 57d280a35eb7d931d7009182b8dd2289c946f391 Author: Jason W. Bacon AuthorDate: 2023-04-29 14:51:07 +0000 Commit: Jason W. Bacon CommitDate: 2023-04-29 14:53:40 +0000 biology/minimap2: Update to 2.25 New feature to output sequences in secondary alignments Several minor enhancements and fixes Changes: https://github.com/lh3/minimap2/releases Reported by: portscout --- biology/minimap2/Makefile | 2 +- biology/minimap2/distinfo | 6 +++--- biology/minimap2/pkg-descr | 6 ------ 3 files changed, 4 insertions(+), 10 deletions(-) diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile index 83084fd86a16..ff6799f92d2a 100644 --- a/biology/minimap2/Makefile +++ b/biology/minimap2/Makefile @@ -1,6 +1,6 @@ PORTNAME= minimap2 DISTVERSIONPREFIX= v -DISTVERSION= 2.24 +DISTVERSION= 2.25 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo index 65cf355b10a5..7c79ce9501e2 100644 --- a/biology/minimap2/distinfo +++ b/biology/minimap2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1640960772 -SHA256 (lh3-minimap2-v2.24_GH0.tar.gz) = 2e3264300661cf1fce6adabffe6970ec59d46f3e8150dd40fa4501ff4f6c0dbc -SIZE (lh3-minimap2-v2.24_GH0.tar.gz) = 253050 +TIMESTAMP = 1682729894 +SHA256 (lh3-minimap2-v2.25_GH0.tar.gz) = 9742ff0be01e51ea7d65f70c01d1344eee6f0d7b135359e0c00aec30fb74ac38 +SIZE (lh3-minimap2-v2.25_GH0.tar.gz) = 257574 diff --git a/biology/minimap2/pkg-descr b/biology/minimap2/pkg-descr index e4e8dbd749d9..d0a8f4d1b41d 100644 --- a/biology/minimap2/pkg-descr +++ b/biology/minimap2/pkg-descr @@ -1,16 +1,10 @@ Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: - (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome - (2) finding overlaps between long reads with error rate up to ~15% - (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA readsagainst a reference genome - (4) aligning Illumina single- or paired-end reads - (5) assembly-to-assembly alignment - (6) full-genome alignment between two closely related species with divergence below ~15%