Date: Sun, 29 Jul 2018 23:18:21 +0000 From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 230169] biology/bcftools: Update 1.9 Message-ID: <bug-230169-7788@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D230169 Bug ID: 230169 Summary: biology/bcftools: 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 Flags: maintainer-feedback?(cartwright@asu.edu) CC: cartwright@asu.edu Created attachment 195614 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D195614&action= =3Dedit Update Release Notes: annotate REF and ALT columns can be now transferred from the annotation file. fixed bug when setting vector_end values. consensus new -M option to control output at missing genotypes variants immediately following insersions should not be skipped. No= te however, that the current fix requires normalized VCF and may still falsely skip variants adjacent to multiallelic indels. bug fixed in -H selection handling convert the --tsv2vcf option now makes the missing genotypes diploid, "./." instead of "." the behavior of -i/-e with --gvcf2vcf changed. Previously only sites with FILTER set to "PASS" or "." were expanded and the -i/-e options dropped sites completely. The new behavior is to let the -i/-e options control which records will be expanded. In order to drop records completely, one can stre= am through "bcftools view" first. csq since the real consequence of start/splice events are not known, the aminoacid positions at subsequent variants should stay unchanged add --force option to skip malformatted transcripts in GFFs with out-of-phase CDS exons. +dosage: output all alleles and all their dosages at multiallelic sites +fixref: fix serious bug in -m top conversion -i/-e filtering expressions: add two-tailed binomial test add functions N_PASS() and F_PASS() add support for lists of samples in filtering expressions, with many samples it was impractical to list them all on the command line. Samples ca= n be now in a file as, e.g., GT[@samples.txt]=3D"het" allow multiple perl functions in the expressions and some bug fixes fix a parsing problem, @ was not removed from @filename expressions mpileup: fixed bug where, if samples were renamed using the -G (--read-groups) option, some samples could be omitted from the output file. norm: update INFO/END when normalizing indels +split: new -S option to subset samples and to use custom file names instead of the defaults +smpl-stats: new plugin +trio-stats: new plugin Fixed build problems with non-functional configure script produced on s= ome platforms --=20 You are receiving this mail because: You are the assignee for the bug.=
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