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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/commit/c972f9bc0d9d3838f9eed7bdf5970f9400bb5192">c972f9bc</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-11-20T06:03:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disable all patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/commit/7c671e799caee5625b584ed75fc3fb5ae422c1f6">7c671e79</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-11-20T06:26:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add draft tests
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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</li>
<li class="file-stats">
<a href="#4c7e8d9f8daa46ba62175a9aa219b11664be5e36">
<span class="new-file">
+
debian/tests/output_tests/README
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<li class="file-stats">
<a href="#5a8f7343634c7e2ebe546e8b06d5b58886fd8387">
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+
debian/tests/output_tests/expected.plink.assoc
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</li>
<li class="file-stats">
<a href="#957e79469c6fce463cb6dbed751c23c023e5220d">
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+
debian/tests/output_tests/expected.plink.frq
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<li class="file-stats">
<a href="#5cc37fd93ea78de7fa21d0db40d2e809ed627fc3">
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+
debian/tests/run-sample-analysis
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<h4>Changes:</h4>
<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Fix_Makefile.patch</span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Disable_opt.patch</span></pre>
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<br>
</li>
<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-sample-analysis</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span></pre>
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</li>
<li id="4c7e8d9f8daa46ba62175a9aa219b11664be5e36">
<a href="https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6#4c7e8d9f8daa46ba62175a9aa219b11664be5e36"><strong>debian/tests/output_tests/README</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Output files (i.e. expected.plink.assoc and expected.plink.frq) were generated following:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">wget https://www.cog-genomics.org/static/bin/plink141220/plink_linux_x86_64.zip</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext">unzip plink_linux_x86_64.zip</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">./plink --file toy --freq</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">mv plink.frq expected.plink.frq</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">./plink --file toy --assoc</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">mv plink.assoc expected.plink.assoc</span></pre>
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<li id="5a8f7343634c7e2ebe546e8b06d5b58886fd8387">
<a href="https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6#5a8f7343634c7e2ebe546e8b06d5b58886fd8387"><strong>debian/tests/output_tests/expected.plink.assoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> CHR SNP BP A1 F_A F_U A2 CHISQ P OR </span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> 1 rs0 1000 0 0 NA 1 NA NA NA </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> 1 rs10 1001 2 0.5 0 1 1.333 0.2482 NA </span></pre>
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<li id="957e79469c6fce463cb6dbed751c23c023e5220d">
<a href="https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6#957e79469c6fce463cb6dbed751c23c023e5220d"><strong>debian/tests/output_tests/expected.plink.frq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> CHR SNP A1 A2 MAF NCHROBS</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> 1 rs0 0 1 0 2</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> 1 rs10 2 1 0.25 4</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/compare/02bf6ac56c24dbf785673c92671d6659c313d32f...7c671e799caee5625b584ed75fc3fb5ae422c1f6#5cc37fd93ea78de7fa21d0db40d2e809ed627fc3"><strong>debian/tests/run-sample-analysis</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># http://dep.debian.net/deps/dep8/</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>plink2</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">PLINK2_TEST</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'plink2 --file toy'</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Allele frequencies</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">$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;">$PLINK2_TEST</span> <span class="nt" style="color: #000080;">--assoc</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">diff plink.assoc expected.plink.assoc</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span>/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span></pre>
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