Dylan Aïssi pushed to branch master at Debian Med / plink2
Commits: ac09b66d by Dylan Aïssi at 2020-03-27T08:45:47+01:00 Bump changelogs - - - - - 2 changed files: - debian/changelog - debian/upstream.docs/upstream.changelog Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +plink2 (2.00~a3-200321+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + + -- Dylan Aïssi <[email protected]> Fri, 27 Mar 2020 08:44:27 +0100 + plink2 (2.00~a3-200217+dfsg-1) unstable; urgency=medium * New upstream release. ===================================== debian/upstream.docs/upstream.changelog ===================================== @@ -1,6 +1,22 @@ # Copy/Paste from https://www.cog-genomics.org/plink/2.0/ -17 Feb 2020: --bcf implemented. +21 Mar 2020: Fixed --glm multiallelic-variant handling bugs that could occur when 'genotypic', 'hethom', 'dominant', 'recessive', 'interaction', or --tests was specified, and corrected 'dominant'/'recessive' documentation. It is no longer necessary to trim zero- (or other-constant-) dosage alleles from multiallelic variants to get --glm results for the other alleles. + +14 Mar: --make-pgen/--make-just-pvar 'vcfheader' column set added (this makes it possible to directly generate a valid sites-only VCF). Bgzipping of the .pvar file is not directly supported, but you can use a named pipe to accomplish that with low overhead. + +11 Mar: Fixed --glm segfault that could occur when no covariates were specified. VCF/BCF importers now default to compressing the temporary .pvar file, so that files with lots of INFO field content don't require a disproportionally large amount of free disk space to work with. --keep-autoconv now has a 'vzs' modifier to request compression of the .pvar file (and conversely, when --vcf/--bcf is used with bare --keep-autoconv, the .pvar is not compressed). + +10 Mar: Fixed --make-pgen segfault that occurred when phased dosages were present without any phased hardcalls. + +8 Mar: "--export bcf" implemented. VCF-export multiallelic HDS-force bugfixes. Added missing FILTER:fa header line to whole-genome 1000 Genomes phase 3 annotated .pvar files on Resources page. + +25 Feb: --ld multiallelic-phased data handling bugfix. + +22 Feb: --bcf n_allele=1 (ALT='.') bugfix. + +19 Feb: --bcf GQ/DP-filtering bugfixes. --vcf and --bcf now enforce VCF contig naming restrictions. + +17 Feb: --bcf implemented. 11 Feb: "--vcf-half-call reference" works properly again (it was behaving like "--vcf-half-call error" in recent builds). View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/ac09b66d6e58edafb5a7d6c3bd202059933f3bdf -- View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/ac09b66d6e58edafb5a7d6c3bd202059933f3bdf You're receiving this email because of your account on salsa.debian.org.
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