From owner-freebsd-ports-bugs@freebsd.org Sun Jul 29 23:28:04 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 42FAF1066B2F for ; Sun, 29 Jul 2018 23:28:04 +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 BCCD27F0A1 for ; Sun, 29 Jul 2018 23:28:03 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: by mailman.ysv.freebsd.org (Postfix) id 7E84A1066B2E; Sun, 29 Jul 2018 23:28:03 +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 5C84C1066B2D for ; Sun, 29 Jul 2018 23:28:03 +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 D780F7F0A0 for ; Sun, 29 Jul 2018 23:28:02 +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 11B851B39E for ; Sun, 29 Jul 2018 23:28:02 +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 w6TNS1KF089082 for ; Sun, 29 Jul 2018 23:28:01 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id w6TNS1jQ089081 for ports-bugs@FreeBSD.org; Sun, 29 Jul 2018 23:28:01 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 230171] biology/samtools: Update to 1.9 Date: Sun, 29 Jul 2018 23:28:01 +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 23:28:04 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D230171 Bug ID: 230171 Summary: biology/samtools: Update to 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 195616 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D195616&action= =3Dedit Update Samtools mpileup VCF and BCF output is now deprecated. It is still function= al, but will warn. Please use bcftools mpileup instead. (#884) Samtools mpileup now handles the '-d' max_depth option differently. The= re is no longer an enforced minimum, and '-d 0' is interpreted as limitless (no maximum - warning this may be slow). The default per-file depth is now 8000, which matches the value mpileup used to use when processing a single sample= . To get the previous default behaviour use the higher of 8000 divided by the nu= mber of samples across all input files, or 250. (#859) Samtools stats new features: The '--remove-overlaps' option discounts overlapping portions of templates when computing coverage and mapped base counting. (#855) When a target file is in use, the number of bases inside the target= is printed and the percentage of target bases with coverage above a given threshold specified by the '--cov-threshold' option. (#855) Split base composition and length statistics by first and last read= s. (#814, #816) Samtools faidx new features: Now takes long options. (#509, thanks to Pierre Lindenbaum) Now warns about zero-length and truncated sequences due to the requested range being beyond the end of the sequence. (#834) Gets a new option (--continue) that allows it to carry on when a requested sequence was not in the index. (#834) It is now possible to supply the list of regions to output in a text file using the new '--region-file' option. (#840) New '-i' option to make faidx return the reverse complement of the regions requested. (#878) faidx now works on FASTQ (returning FASTA) and added a new fqidx command to index and return FASTQ. (#852) Samtools collate now has a fast option '-f' that only operates on prima= ry pairs, dropping secondary and supplementary. It tries to write pairs to the final output file as soon as both reads have been found. (#818) Samtools bedcov gets a new '-j' option to make it ignore deletions (D) = and reference skips (N) when computing coverage. (#843) Small speed up to samtools coordinate sort, by converting it to use rad= ix sort. (#835, thanks to Zhuravleva Aleksandra) Samtools idxstats now works on SAM and CRAM files, however this isn't f= ast due to some information lacking from indices. (#832) Compression levels may now be specified with the level=3DN output-fmt-o= ption. E.g. with -O bam,level=3D3. Various documentation improvements. Bug-fixes: Improved error reporting in several places. (#827, #834, #877, cd71= 97) Various test improvements. Fixed failures in the multi-region iterator (view -M) when regions provided via BED files include overlaps (#819, reported by Dave Larson). Samtools stats now counts '=3D' and 'X' CIGAR operators when counti= ng mapped bases. (#855) Samtools stats has fixes for insert size filtering (-m, -i). (#845; #697 reported by Soumitra Pal) Samtools stats -F now longer negates an earlier -d option. (#830) Fix samtools stats crash when using a target region. (#875, reporte= d by John Marshall) Samtools sort now keeps to a single thread when the -@ option is absent. Previously it would spawn a writer thread, which could cause the CPU usage to go slightly over 100%. (#833, reported by Matthias Bernt) Fixed samtools phase '-A' option which was incorrectly defined to t= ake a parameter. (#850; #846 reported by Dianne Velasco) Fixed compilation problems when using C_INCLUDE_PATH. (#870; #817 reported by Robert Boissy) Fixed --version when built from a Git repository. (#844, thanks to = John Marshall) Use noenhanced mode for title in plot-bamstats. Prevents unwanted interpretation of characters like underscore in gnuplot version 5. (#829, thanks to M. Zapukhlyak) blast2sam.pl now reports perfect match hits (no indels or mismatche= s). (#873, thanks to Nils Homer) Fixed bug in fasta and fastq subcommands where stdout would not be flushed correctly if the -0 option was used. Fixed invalid memory access in mpileup and depth on alignment recor= ds where the sequence is absent. --=20 You are receiving this mail because: You are the assignee for the bug.=