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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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Commits:
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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/ac09b66d6e58edafb5a7d6c3bd202059933f3bdf">ac09b66d</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-03-27T08:45:47+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump changelogs
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<h4>2 changed files:</h4>
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<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/ac09b66d6e58edafb5a7d6c3bd202059933f3bdf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a3-200321+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> Fri, 27 Mar 2020 08:44:27 +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~a3-200217+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"> * New upstream release.</span>
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<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/ac09b66d6e58edafb5a7d6c3bd202059933f3bdf#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">17 Feb 2020: --bcf implemented.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">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.</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 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.</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">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).</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">10 Mar: Fixed --make-pgen segfault that occurred when phased dosages were present without any phased hardcalls.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">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.</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">25 Feb: --ld multiallelic-phased data handling bugfix.</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">22 Feb: --bcf n_allele=1 (ALT='.') bugfix.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">19 Feb: --bcf GQ/DP-filtering bugfixes. --vcf and --bcf now enforce VCF contig naming restrictions.</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">17 Feb: --bcf implemented.</span>
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4
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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5
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">11 Feb: "--vcf-half-call reference" works properly again (it was behaving like "--vcf-half-call error" in recent builds).</span>
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6
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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