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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/commit/d73f17bbefd9693a4839f75e5c5ebd134cbf294b">d73f17bb</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-01-20T07:43:43+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelogs
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ce544ebebfbabf03afff4b98aa2aff1785670f6f">
debian/upstream.docs/upstream.changelog
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink2/commit/d73f17bbefd9693a4839f75e5c5ebd134cbf294b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a3-200116+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Mon, 20 Jan 2020 07:41:03 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">plink2 (2.00~a2-191128+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Initial release. (Closes: #858947)</span>
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<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink2/commit/d73f17bbefd9693a4839f75e5c5ebd134cbf294b#ce544ebebfbabf03afff4b98aa2aff1785670f6f"><strong>debian/upstream.docs/upstream.changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Copy/Paste from https://www.cog-genomics.org/plink/2.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">28 Nov 2019: Fixed a VCF half-call handling bug introduced last month.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">This is a candidate for the final alpha 2 build (which will remain available for download for several months).</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">16 Jan 2020: --pca allele/variant weight multithreading bugfix.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">14 Jan: --make-king-table rel-check bugfix.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">3 Jan 2020: Fixed --extract-if-info/--exclude-if-info numeric-argument bug introduced in late October.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">30 Dec 2019 (alpha 3): This makes the following potentially compatibility-breaking changes:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> --write-snplist and --indep-pairwise require all variant IDs to be unique. For --write-snplist, this can be overridden by adding the 'allow-dups' modifier.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> .bgen/.gen import commands require the REF/ALT mode to be explicitly declared.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> --glm defaults to 'firth-fallback' mode for binary phenotypes. The old behavior can be requested with the 'no-firth' modifier.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> --glm errors out, instead of just skipping the phenotype and printing a warning, when there's a linear dependency between the phenotype and the covariates. The old behavior can be requested with the 'skip' modifier.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> --pca's 'var-wts' subcommand has been replaced with 'allele-wts', which handles multiallelic variants properly. For datasets that contain only biallelic variants, the old output format can still be requested with 'biallelic-var-wts'.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> PLINK 2 now errors out when you request an LD computation on a dataset with less than 50 founders. This can be overridden with --bad-ld.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> --score's old NMISS_ALLELE_CT column (nonmissing allele count) has been renamed to ALLELE_CT, and the column set renamed accordingly, since in other contexts, 'nmiss' refers to the number of missing values, which is essentially the opposite...</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> --make-king-table's ID{1,2} columns have been renamed to IID{1,2}, for consistency with other PLINK 2 commands.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">In addition, the GRM computation (along with "--pca approx" and "--score variance-standardize") now handles multiallelic variants properly, instead of just collapsing all minor alleles together; --score allows each allele in a multiallelic variant to be assigned its own score; and --glm handles categorical covariates in a manner that's less likely to cause VIF overflow.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">29 Dec: Fixed a bug which affected processing of some heterozygous-double-ALT multiallelic variants, and a bug that caused ALT2/ALT3/etc. allele frequencies to not be properly initialized in some circumstances.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">13 Dec: Fixed bug introduced in 22 Nov build which caused some reported dosages/counts (such as --freq's OBS_CT column) to be doubled. --loop-cats bugfixes.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">28 Nov: Fixed a VCF half-call handling bug introduced last month.</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">26 Nov: Fixed recent bug which caused a segfault when no-duplicate-allowed variant ID lookup was performed with more than 16 threads.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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