From owner-freebsd-ports-bugs@freebsd.org Sun Jul 29 23:22:54 2018 Return-Path: Delivered-To: freebsd-ports-bugs@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 402621066A19 for ; Sun, 29 Jul 2018 23:22:54 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id D06E27E9C3 for ; Sun, 29 Jul 2018 23:22:53 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: by mailman.ysv.freebsd.org (Postfix) id 957771066A18; Sun, 29 Jul 2018 23:22:53 +0000 (UTC) Delivered-To: ports-bugs@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 70A211066A17 for ; Sun, 29 Jul 2018 23:22:53 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mxrelay.ysv.freebsd.org (mxrelay.ysv.freebsd.org [IPv6:2001:1900:2254:206a::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.ysv.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 118E47E9C2 for ; Sun, 29 Jul 2018 23:22:53 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2001:1900:2254:206a::16:76]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.ysv.freebsd.org (Postfix) with ESMTPS id 44F701B398 for ; Sun, 29 Jul 2018 23:22:52 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org ([127.0.1.118]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id w6TNMqts084008 for ; Sun, 29 Jul 2018 23:22:52 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id w6TNMqZf084007 for ports-bugs@FreeBSD.org; Sun, 29 Jul 2018 23:22:52 GMT (envelope-from bugzilla-noreply@freebsd.org) X-Authentication-Warning: kenobi.freebsd.org: www set sender to bugzilla-noreply@freebsd.org using -f From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 230170] biology/htslib: Update 1.9 Date: Sun, 29 Jul 2018 23:22:51 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Only Me X-Bugzilla-Who: ndowens.fbsd@yandex.com X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: ports-bugs@FreeBSD.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter cc flagtypes.name attachments.created Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated MIME-Version: 1.0 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 29 Jul 2018 23:22:54 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D230170 Bug ID: 230170 Summary: biology/htslib: Update 1.9 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: ports-bugs@FreeBSD.org Reporter: ndowens.fbsd@yandex.com CC: cartwright@asu.edu CC: cartwright@asu.edu Flags: maintainer-feedback?(cartwright@asu.edu) Created attachment 195615 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D195615&action= =3Dedit Update The default SAM version has been changed to 1.6. This is in line with the latest version specification and indicates that HTSlib supports the CG tag = used to store long CIGAR data in BAM format. bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner) Faidx can now index fastq files as well as fasta. The fastq index adds an e= xtra column to the .fai index which gives the offset to the quality values. New interfaces have been added to htslib/faidx.h to read the fastq index and retrieve the quality values. It is possible to open a fastq index as if fas= ta (only sequences will be returned), but not the other way round. (#701) New API interfaces to add or update integer, float and array aux tags. (#69= 4) Add level=3D option to hts_set_opt() to allow the compression level= to be set. Setting level=3D0 enables uncompressed output. (#715) Improved bgzip error reporting. Better error reporting when CRAM reference files can't be opened. (#706) Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences. (#716) Efficiency improvements: Small speed-up for CRAM indexing. Reduce the number of unnecessary wake-ups in the thread pool. (#703) Avoid some memory copies when writing data, notably for uncompressed BG= ZF output. (#703) Bug fixes: Fix multi-region iterator bugs on CRAM files. (#684) Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files. (#687) Fixed synced_bcf_reader() bug when reading contigs multiple times. (#69= 1, reported by @freeseek) Fixed bug where bcf_hdr_set_samples() did not update the sample diction= ary when removing samples. (#692, reported by @freeseek) Fixed bug where the VCF record ref length was calculated incorrectly if= an INFO END tag was present. (71b00a) Fixed warnings found when compiling with gcc 8.1.0. (#700) sam_hdr_read() and sam_hdr_write() will now return an error code if pas= sed a NULL file pointer, instead of crashing. Fixed possible negative array look-up in sam_parse1() that somehow esca= ped previous fuzz testing. (#731, reported by @fCorleone) Fixed bug where cram range queries could incorrectly report an error wh= en using multiple threads. (#734, reported by Brent Pedersen) Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files. (#739, reported by @carsonhh) --=20 You are receiving this mail because: You are the assignee for the bug.=