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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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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/92c9e36a2464632d6e2562f77d971886c0bfd0a0">92c9e36a</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2021-07-23T21:56:28+02:00</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/92c9e36a2464632d6e2562f77d971886c0bfd0a0#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">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="LC3" class="line" lang="plaintext">1 Jul 2021: Fixed --bcf bug that could result in a spurious out-of-memory error when the file has no INFO entries.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">8 Jun: Fixed multiallelic-variant-writing bug (typically manifesting as a segmentation fault or assertion failure) that could occur with --sort-vars or under low-memory conditions.</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">25 May: .fa loader now tolerates blank lines. gzip files containing multiple streams or trailing garbage should be accepted again.</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">23 May: Fixed FID+IID+SID loading (recent builds were giving an incorrect "SID column does not immediately follow IID column" error).</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">5 May: Fixed --within bug introduced on 16 Jan.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">20 Apr: --het cols= should now work properly.</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">16 Apr: --data/--gen now supports .gen files with 6 leading columns. This format can be exported with "--export oxford-v2".</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">14 Apr: --pmerge-list should no longer be limited by the system's #-of-open-files cap.</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">13 Apr: --glm local-covariate-handling bugfix. Fixed --pmerge[-list] bug that could cause the generated .pgen header to be invalid when multiallelic variants were present.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">6 Apr: --data/--sample now recognizes column type 'C' as a synonym for 'P' (continuous phenotype). (This build has an incorrect "6 Mar" datestamp; sorry about that.)</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 Mar: --sample-counts chrX no-known-males bugfix.</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">25 Mar: --pmerge[-list] .bim-handling bugfix.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">23 Mar: Unbreak --make-pgen + --sort-vars (this was broken by the 28 Feb build).</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">2 Mar: --pmerge[-list] bugfixes (no longer segfaults when all variants are at different positions; if the output .pvar file already exists, it's deleted first instead of appended to; if an input file covers multiple chromosomes, there is no longer a likely assert failure; fixed some issues with merging of same-position same-ID variants).</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">1 Mar: --pmerge-list-dir flag implemented (specifies a common directory prefix for all --pmerge-list entries).</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">28 Feb: --pmerge[-list] can now be used for concatenation-like jobs.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Note that it doesn't necessarily perform pure concatenation on a chromosome-split dataset: if two variants in a file have the same position and ID, they will be merged, in a way that's not compatible with 'split' multiallelic variants sharing a single ID (those must be merged with a dedicated 'join' operation, such as "bcftools norm -m +"). As a consequence, --pmerge[-list] defaults to erroring out when it detects such a split variant. One workaround is to use --set-all-var-ids to assign distinct IDs to each piece of the split variant.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">3 Feb: 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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4
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;"> <span id="LC38" 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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6
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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