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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink1-9">Debian Med / plink1.9</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/80f5c46f6644f29ca7176b78fe67df3638c68edf">80f5c46f</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-08-03T05:43:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.3-180717</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/37a7d95a164357fa77d545e4b1937738544ecddf">37a7d95a</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-08-03T05:43:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/1.90_b6.3-180717'
Upstream version 1.90~b6.3-180717
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/aea924912eb3fc1b3d4cb141bf7c9f9cacef00c6">aea92491</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-08-03T05:46:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/changelogs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/c6edf54d8b1ccb7d7165c3e1825b3d9bab4bb07a">c6edf54d</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-08-03T05:54:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version: 4.2.0 (no changes needed)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/52649ac487c085f55bfe80056c6e6ccc8f7bc503">52649ac4</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-08-03T05:56:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ce544ebebfbabf03afff4b98aa2aff1785670f6f">
debian/upstream.docs/upstream.changelog
</a>
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<li class="file-stats">
<a href="#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
plink.c
</a>
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<li class="file-stats">
<a href="#33439c8ad8c4c9294b8ac45b5e66f758606f8a04">
plink_set.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/e7f895321f49209ba13695af080dce89070c192e...52649ac487c085f55bfe80056c6e6ccc8f7bc503#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink1.9 (1.90~b6.3-180717-1) unstable; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</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"> * Bump Standards-Version: 4.2.0 (no changes needed).</span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> -- Dylan Aïssi <bob.dybian@gmail.com> Fri, 03 Aug 2018 07:44:29 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">plink1.9 (1.90~b6.2-180612-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream release.</span>
</pre>
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<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/e7f895321f49209ba13695af080dce89070c192e...52649ac487c085f55bfe80056c6e6ccc8f7bc503#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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="8" 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">@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libatlas-base-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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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<td class="diff-line-num new_line" data-linenumber="9" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> liblapack-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="10" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<td class="diff-line-num new old_line" data-linenumber="12" 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="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.0</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/plink1-9</span>
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<td class="diff-line-num old_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/plink1-9.git</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext">Homepage: https://www.cog-genomics.org/plink/1.9/</span>
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<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/e7f895321f49209ba13695af080dce89070c192e...52649ac487c085f55bfe80056c6e6ccc8f7bc503#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/1.9/</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">12 Jun 2018: "--assoc fisher"'s multiple testing corrections no longer treat zero-MAF variants as valid tests.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">17 Jul 2018: Fixed uninitialized --make-set-border value bug.</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">12 Jun: "--assoc fisher"'s multiple testing corrections no longer treat zero-MAF variants as valid tests.</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">28 May: Fixed --file triallelic-variant handling bug which occurred when the .map was unsorted.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/plink1-9/compare/e7f895321f49209ba13695af080dce89070c192e...52649ac487c085f55bfe80056c6e6ccc8f7bc503#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb"><strong>plink.c</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">@@ -93,7 +93,7 @@</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef STABLE_BUILD</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90b6.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90b6.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90p"</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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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">@@ -105,7 +105,7 @@ static const char ver_str[] =</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="s" style="color: #d14;">" 32-bit"</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="s" style="color: #d14;">" (1<span class="idiff left right">2 Jun</span> 2018)"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="s" style="color: #d14;">" (1<span class="idiff left right">7 Jul</span> 2018)"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="s" style="color: #d14;">""</span></span>
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<a href="https://salsa.debian.org/med-team/plink1-9/compare/e7f895321f49209ba13695af080dce89070c192e...52649ac487c085f55bfe80056c6e6ccc8f7bc503#33439c8ad8c4c9294b8ac45b5e66f758606f8a04"><strong>plink_set.c</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">@@ -25,12 +25,15 @@ void set_init(Set_info* sip, Annot_info* aip) {</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">subset_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_set_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">genekeep_flattened</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (17 Jul 2018): make_set_border not zero-initialized</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">make_set_border</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">;</span></span>
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32
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_test_lambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">sip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// sip->names, sip->setdefs not accessed if ct == 0</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">aip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">aip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">attrib_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">aip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ranges_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>
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