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<h3>
Andreas Tille 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/4369d4bac44391070fcb96d97dea6284ed45272c">4369d4ba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-18T11:45:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add some debug code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/8ee51a44dc70e237dbb6ad541c3ad9ee790b78ca">8ee51a44</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-18T12:14:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop debug code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/455de02d54c75ff46199f013fdb8f9bc1a064355">455de02d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-18T12:15:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Normalise name of autopkgtest script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/f4d55d33b65563dd6a0f86983cf0c68d5a5c1a0d">f4d55d33</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-18T12:16:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add some debug output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/bf51ee937473385bc54b5faca553f59e62120fdd">bf51ee93</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-18T12:35:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix check
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#1a0453e516e167132f0f9392c87de0ea5fe79145">
debian/bin/simd-dispatch
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
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</a>
</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
debian/examples
</a>
</li>
<li class="file-stats">
<a href="#159455bee6fdb73e8d11536e0452e47e714f8375">
<span class="new-file">
+
debian/patches/debug.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-sample-analysis
→
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" 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">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span><span class="mf" style="color: #099;">.</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span></pre>
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</li>
<li id="1a0453e516e167132f0f9392c87de0ea5fe79145">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#1a0453e516e167132f0f9392c87de0ea5fe79145"><strong>debian/bin/simd-dispatch</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,4 +28,5 @@ test_and_run_avx2 "@"</td>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>SIMD <span class="k" style="font-weight: 600;">in </span>avx sse4.1 ssse3 sse3 sse2 sse mmx <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>test_and_run <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SIMD</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
29
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29
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fallback to plain option</span></span>
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<td class="old_line diff-line-num new" data-linenumber="31" 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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<td class="new_line diff-line-num new" data-linenumber="31" 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="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
31
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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$BASE</span><span class="s2" style="color: #d14;">-plain"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,7 @@ plink2 (2.00~a3-220129+dfsg-1) UNRELEASED; urgency=medium</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add some debug code</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> TODO: autopkgtest: /usr/bin/plink2: line 8: 156 Segmentation fault "${cmd}" "$@"</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -> see bug #1004037</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</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">@@ -3,5 +3,4 @@ debian/upstream.docs/toy.ped</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">debian/upstream.docs/toy.map</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"># Expected outputs and script for autopkgtest</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">debian/tests/run-sample-analysis</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">debian/tests/output_tests/*</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#159455bee6fdb73e8d11536e0452e47e714f8375"><strong>debian/patches/debug.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 5ee527d39176d5d612014ce39a1e1ecbe59b3d9c Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Christopher Chang <chrchang523@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Thu, 17 Feb 2022 19:08:02 -0800</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] add terminal --debug prints</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Origin: https://github.com/chrchang/plink-ng/commit/5ee527d39176d5d612014ce39a1e1ecbe59b3d9c.patch</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 2.0/plink2.cc | 6 ++++++</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 2.0/plink2_cmdline.cc | 6 ++++++</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 2 files changed, 12 insertions(+)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">diff --git a/plink2.cc b/2.0/plink2.cc</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">index c9ed51a5..83b28814 100644</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/plink2.cc</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/plink2.cc</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -10944,7 +10944,13 @@</span> int main(int argc, char** argv) {</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> reterr = kPglRetWriteFail;</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> }</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> if (bigstack_ua) {</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (g_debug_on) {</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fputs("--debug: Trying to free bigstack_ua.\n", stdout);</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> free(bigstack_ua);</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> }</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (g_debug_on) {</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fputs("--debug: Exiting.\n", stdout);</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> return S_CAST(int32_t, reterr);</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> }</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">diff --git a/plink2_cmdline.cc b/2.0/plink2_cmdline.cc</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">index 4c49ccee..b02aace5 100644</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/plink2_cmdline.cc</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/plink2_cmdline.cc</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -526,9 +526,15 @@</span> BoolErr CleanupLogfile(uint32_t print_end_time) {</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> BoolErr ret_boolerr = 0;</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if (g_logfile) {</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (g_debug_on) {</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf("--debug: g_log_failed = %u.\n", g_log_failed);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> if (!g_log_failed) {</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> logputs_silent("\n");</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> logputs_silent(g_logbuf);</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (g_debug_on) {</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fputs("--debug: Trying to close log.\n", stdout);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> if (unlikely(fclose(g_logfile))) {</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> fflush(stdout);</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> fprintf(stderr, "Error: Failed to finish writing to log: %s.\n", strerror(errno));</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Fix_Makefile.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_packaged_libdeflate.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">baseline</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debug.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: run-<span class="idiff left right">sample-analysis</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-<span class="idiff left right">unit-test</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-sample-analysis</strong>
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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">@@ -4,12 +4,14 @@</td>
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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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></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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11
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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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12
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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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<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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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">plink2 <span class="nt" style="color: #000080;">--debug</span> <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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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> tmp_data.pgen <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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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plink2 failed to create tmp_data.pgen"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">plink2 <span class="nt" style="color: #000080;">--debug</span> <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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">plink2 <span class="nt" style="color: #000080;">--debug</span> <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></pre>
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