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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/ec82585d7d4f68303d5c4d21e4ceee0e630bae63">ec82585d</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2019-12-06T21:25:06Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtest
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<strong><a href="https://salsa.debian.org/med-team/plink2/commit/ff817ba6026d5d6a4e045a47e2efee5a2eb24c1f">ff817ba6</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2019-12-06T21:30:33Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to NEW
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#5cc37fd93ea78de7fa21d0db40d2e809ed627fc3">
debian/tests/run-sample-analysis
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink2/compare/4d31a54fed36ec2a2d3db3e87aad44d45b6c1c0f...ff817ba6026d5d6a4e045a47e2efee5a2eb24c1f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a2-191128+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a2-191128+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</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"> * Initial release. (Closes: #858947)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * TODO:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> - add autopkgtest</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="LC7" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> <span class="idiff left right">Wed, 20 Nov 2019 07:00:08</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> <span class="idiff left right">Fri, 06 Dec 2019 22:28:40</span> +0100</span></pre>
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<li id="5cc37fd93ea78de7fa21d0db40d2e809ed627fc3">
<a href="https://salsa.debian.org/med-team/plink2/compare/4d31a54fed36ec2a2d3db3e87aad44d45b6c1c0f...ff817ba6026d5d6a4e045a47e2efee5a2eb24c1f#5cc37fd93ea78de7fa21d0db40d2e809ed627fc3"><strong>debian/tests/run-sample-analysis</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,17 +6,10 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">PLINK2_TEST</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'plink2 --file toy'</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Allele frequencies</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">$PLINK2_TEST</span> <span class="nt" style="color: #000080;">--freq</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">diff plink.frq expected.plink.frq</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Case/control or QTL association</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">$PLINK2_TEST</span> <span class="nt" style="color: #000080;">--assoc</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell">diff plink.assoc expected.plink.assoc</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell">plink2 <span class="nt" style="color: #000080;">--dummy</span> 33 65537 0.1 dosage-freq<span class="o" style="font-weight: 600;">=</span>0.1 <span class="nt" style="color: #000080;">--out</span> tmp_data</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">plink2 <span class="nt" style="color: #000080;">--pfile</span> tmp_data <span class="nt" style="color: #000080;">--export</span> vcf vcf-dosage<span class="o" style="font-weight: 600;">=</span>DS <span class="nt" style="color: #000080;">--out</span> tmp_data2</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">plink2 <span class="nt" style="color: #000080;">--vcf</span> tmp_data2.vcf <span class="nv" style="color: #008080;">dosage</span><span class="o" style="font-weight: 600;">=</span>DS <span class="nt" style="color: #000080;">--out</span> tmp_data2</span>
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20
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span>/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span></pre>
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