Created attachment 195614 [details] 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. Note 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 stream 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 can be now in a file as, e.g., GT[@samples.txt]="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 some platforms
Hi Nathan, Thanks for the patch. Unfortunately, files/patch-Makefile fails to apply. Would you have a look at it? Thanks.
(In reply to Fernando Apesteguía from comment #1) > Hi Nathan, > > Thanks for the patch. Unfortunately, files/patch-Makefile fails to apply. > > Would you have a look at it? > > Thanks. I will when I get home on pc. Possibly updated ports and it restored the unneeded patch
(In reply to Fernando Apesteguía from comment #1) > Hi Nathan, > > Thanks for the patch. Unfortunately, files/patch-Makefile fails to apply. > > Would you have a look at it? > > Thanks. Should work now. I can’t currentlu attack it to bug report as I’m on my phone but I pastebin it https://pastebin.com/RG1zCjL5
(In reply to Nathan from comment #3) I'll test build tomorrow. Thanks!
Sorry, but the patch in pastebin doesn't touch patch-Makefile and it still fails to apply :-(
(In reply to Fernando Apesteguía from comment #5) > Sorry, but the patch in pastebin doesn't touch patch-Makefile and it still > fails to apply :-( Sigh ok. Will relook at it when I get on my PC
Created attachment 195701 [details] patch for biology/bcftools New patch to update the port to 1.9
I updated a new patch. It builds in {10.4,11.1}{amd64,i386}, 11.2 amd64 and 12-CURRENT. Does it look good?
(In reply to Fernando Apesteguía from comment #8) > I updated a new patch. > > It builds in {10.4,11.1}{amd64,i386}, 11.2 amd64 and 12-CURRENT. > > Does it look good? Looks good to me
I created a review with the refined patch: https://reviews.freebsd.org/D16543 But this PR is actually assigned to wen@ and I dont' want to step into his shoes, so I leave this to him :-)
(In reply to Fernando Apesteguía from comment #10) Now it is yours :) wen
Comment on attachment 195701 [details] patch for biology/bcftools Approved
A commit references this bug: Author: fernape Date: Thu Aug 2 19:30:58 UTC 2018 New revision: 476247 URL: https://svnweb.freebsd.org/changeset/ports/476247 Log: biology/bcftools: update to 1.9 While here: * Update LICENSE handling * Move all commands to bin/ PR: 230169 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16543 Changes: head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/files/patch-Makefile head/biology/bcftools/files/patch-configure.ac head/biology/bcftools/pkg-plist
Committed, Thanks!