Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 9A3AA85DE8 for ; Sat, 28 Oct 2023 20:35:45 +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 fSoKQW0yu-Ng for ; Sat, 28 Oct 2023 20:35:45 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id ED62084E5D for ; Sat, 28 Oct 2023 20:35:44 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id E6D52FADC; Sat, 28 Oct 2023 20:35:44 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1698525344251600" MIME-Version: 1.0 Date: Sat, 28 Oct 2023 20:35:44 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/fastq-trim To: pkgsrc-changes@NetBSD.org Approved: commit_and_comment Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20231028203544.E6D52FADC@cvs.NetBSD.org> This is a multi-part message in MIME format. --_----------=_1698525344251600 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Sat Oct 28 20:35:44 UTC 2023 Modified Files: pkgsrc/biology/fastq-trim: DESCR Makefile PLIST distinfo Log Message: biology/fastq-trim: Update to 0.1.3 fastq-scum: Add zstd and lz4 support Add low_qual_base_count update for paired end reads Clean up and expand final output format A few other minor improvements Updates for latest libxtend API Improvements to test script Changes: https://github.com/auerlab/fastq-trim/releases To generate a diff of this commit: cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/fastq-trim/DESCR cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/fastq-trim/Makefile cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/fastq-trim/PLIST \ pkgsrc/biology/fastq-trim/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1698525344251600 Content-Disposition: inline Content-Length: 3028 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/fastq-trim/DESCR diff -u pkgsrc/biology/fastq-trim/DESCR:1.1 pkgsrc/biology/fastq-trim/DESCR:1.2 --- pkgsrc/biology/fastq-trim/DESCR:1.1 Sun Nov 6 22:49:37 2022 +++ pkgsrc/biology/fastq-trim/DESCR Sat Oct 28 20:35:44 2023 @@ -1,5 +1,6 @@ -Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads -prior to analyses such as RNA-Seq. it runs in a fraction of the time required -by popular trimmers and uses only a few megabytes of RAM, so it will run -almost entirely in cache. The design supports adding any number of alignment -functions, so it can be easily adapted to any trimming needs. +Fastq-trim is a lightening fast read trimming tool for QA of DNA +and RNA reads prior to analyses such as RNA-Seq. it runs in a +fraction of the time required by popular trimmers and uses only a +few megabytes of RAM, so it will run almost entirely in cache. +The design supports adding any number of alignment functions, so +it can be easily adapted to any trimming needs. Index: pkgsrc/biology/fastq-trim/Makefile diff -u pkgsrc/biology/fastq-trim/Makefile:1.3 pkgsrc/biology/fastq-trim/Makefile:1.4 --- pkgsrc/biology/fastq-trim/Makefile:1.3 Wed Dec 28 15:27:16 2022 +++ pkgsrc/biology/fastq-trim/Makefile Sat Oct 28 20:35:44 2023 @@ -1,6 +1,6 @@ -# $NetBSD: Makefile,v 1.3 2022/12/28 15:27:16 bacon Exp $ +# $NetBSD: Makefile,v 1.4 2023/10/28 20:35:44 bacon Exp $ -DISTNAME= fastq-trim-0.1.2 +DISTNAME= fastq-trim-0.1.3 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/} Index: pkgsrc/biology/fastq-trim/PLIST diff -u pkgsrc/biology/fastq-trim/PLIST:1.2 pkgsrc/biology/fastq-trim/PLIST:1.3 --- pkgsrc/biology/fastq-trim/PLIST:1.2 Sun Dec 11 21:25:47 2022 +++ pkgsrc/biology/fastq-trim/PLIST Sat Oct 28 20:35:44 2023 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.2 2022/12/11 21:25:47 bacon Exp $ +@comment $NetBSD: PLIST,v 1.3 2023/10/28 20:35:44 bacon Exp $ bin/fastq-scum bin/fastq-trim include/fastq-trim-accessors.h Index: pkgsrc/biology/fastq-trim/distinfo diff -u pkgsrc/biology/fastq-trim/distinfo:1.2 pkgsrc/biology/fastq-trim/distinfo:1.3 --- pkgsrc/biology/fastq-trim/distinfo:1.2 Sun Dec 11 21:25:47 2022 +++ pkgsrc/biology/fastq-trim/distinfo Sat Oct 28 20:35:44 2023 @@ -1,5 +1,5 @@ -$NetBSD: distinfo,v 1.2 2022/12/11 21:25:47 bacon Exp $ +$NetBSD: distinfo,v 1.3 2023/10/28 20:35:44 bacon Exp $ -BLAKE2s (fastq-trim-0.1.2.tar.gz) = d86b5a4a59c9b3e82b4a303c272e9818a9b54532e64d7e42e4c89dea34591fc4 -SHA512 (fastq-trim-0.1.2.tar.gz) = e27852410cc0af06e30d06e1266be6639ff2f63cd35c61801817b37241a6feb41ef5efc5e8668333a19d575a7c018a85113b3e6ec618e2fcbdb2572c05be6148 -Size (fastq-trim-0.1.2.tar.gz) = 29796 bytes +BLAKE2s (fastq-trim-0.1.3.tar.gz) = f346e25b1c5d14a532e2611a1a6f3d6c9fef4454e0848f1adbe70e0ee5ee76b2 +SHA512 (fastq-trim-0.1.3.tar.gz) = 7fa94c7f4a97956fef98dbdd233b7628d1a49440fc8ba8e52e06e8e87343555ed325c4361f93865ad82863274018d625397d4b288d096196412865a22a106beb +Size (fastq-trim-0.1.3.tar.gz) = 30596 bytes --_----------=_1698525344251600--