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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>
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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/cce84c08bbabda72d56f0ef78c4056523175bb52">cce84c08</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2021-02-04T12:12:13+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream changelog
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<h4>1 changed file:</h4>
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<a href="#ce544ebebfbabf03afff4b98aa2aff1785670f6f">
debian/upstream.docs/upstream.changelog
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<h4>Changes:</h4>
<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/cce84c08bbabda72d56f0ef78c4056523175bb52#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 Oct 2020: Multipass "--export A" bugfix. If you've previously run plink2 "--export A" on a file too large to fit in memory, we recommend that you rerun with this build.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">3 Feb 2021: Fixed .pvar loading bug that triggered when FILTER values were relevant at the same time as either INFO/PR or CM values. .ped-derived filesets containing variants where both REF and ALT are missing are permitted again (such variants were prohibited in recent builds). --vcf-ref-n-missing flag added to simplify re-import of .ped-derived VCFs. Removed extra tabs from --pgen-diff output.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">23 Jan: --chr-set now sets MT to haploid. ##chrSet .pvar header line without the corresponding command-line flag now initializes chrX, chrY, and MT ploidy correctly.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">18 Jan: ##chrSet .pvar header lines now conform to VCFv4.3 specification (an ID field is included). VCF/BCF export now performs more header validation.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">16 Jan: --update-parents now works properly with 'maybeparents' output column sets in other commands.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">14 Jan: --update-ids now works properly with 'maybefid' output column sets in other commands when it creates a FID column.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">4 Jan: --normalize now properly skips missing and '*' alleles.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">3 Jan: Fixed --bcf bug that affected unphased multiallelic variants (usually resulting in a spurious "GT half-call" crash, but if you suppressed that with --vcf-half-call the data would not be imported correctly). Fixed "--export bcf" bug that occurred on headers with FILTER/INFO/FORMAT keys with identical names, and a crash that occurred on variants with multiple FILTER failures. --output-missing-genotype/--output-missing-phenotype bugfixes/cleanup.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">2 Jan: --pgen-diff multiallelic-variant handling bugfix. --pgen-diff DS comparison implemented. --adjust cols= parsing bugfix ('cols=+qq' should work now).</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">1 Jan 2021: Several SID-handling bugfixes. --sample-diff 'dosage' and 'id-delim=' modifier command-line parsing bugfixes. --sample-diff no longer omits later ALT alleles when they're absent from the samples being compared. --pgen-diff GT comparison implemented (generalization of PLINK 1.x --merge-mode 6/7).</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">12 Dec 2020: --q-score-range score-average, ALLELE_CT, DENOM, and NAMED_ALLELE_DOSAGE_SUM column bugfix.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">28 Oct: Multipass "--export A" bugfix. If you've previously run plink2 "--export A" on a file too large to fit in memory, we recommend that you rerun with this build.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">20 Oct: --fst Weir-Cockerham method implemented. --fst ids= and chrX bugfixes. --fst variant-report OBS_CT is now specific to population pair.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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