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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/179bb50324fe8f8939714696a3c0e31323b16eb9">179bb503</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-03-08T21:45:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b5.3-180221</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/a142d833e55a935053a3fd49e43f52c9fe43d883">a142d833</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-03-08T21:45:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/1.90_b5.3-180221'
Upstream version 1.90~b5.3-180221
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/2dae8eb547b91229246b3b0a2dd8bd4b46c7b211">2dae8eb5</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-03-08T21:55:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelogs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/caee70d9c7dbb4182e258c36526a41ec825f742c">caee70d9</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-03-08T22:01:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<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>
</li>
<li class="file-stats">
<a href="#f101da6685d6d3284ff66b606e058f55eebde6b7">
plink_data.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c#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~b5.3-180221-1) unstable; 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"> * New upstream release.</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="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <bob.dybian@gmail.com> Thu, 08 Mar 2018 21:50:36 +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">plink1.9 (1.90~b5.2-180109-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<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"> * New upstream release.</span>
</pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Dylan Aïssi <bob.dybian@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11<span class="idiff left right">~</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> help2man,</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"> 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="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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<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c#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">21 Feb 2018: "--indiv-sort file" no longer scrambles the phenotypes when used with --{b}merge or --merge-list.</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">9 Jan 2018: --all-pheno no longer gets into an infinite loop when one phenotype is all-missing.</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">20 Dec 2017: --meta-analysis 'report-all' now reports original stats instead of 'NA' when N=1. Fixed an inaccuracy in --adjust's handling of very small p-values. --make-just-fam works properly with just .fam input again.</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">@@ -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 v1.90b5.<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 v1.90b5.<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">@@ -105,10 +105,10 @@ 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;">" (<span class="idiff left right">9 Jan</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;">" (<span class="idiff left right">21 Feb</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 class="idiff left right"> </span>"</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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112
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef STABLE_BUILD</span></span>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="s" style="color: #d14;">" "</span> <span class="c1" style="color: #998; font-style: italic;">// (don't want this when version number has two trailing digits)</span></span>
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114
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<a href="https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c#f101da6685d6d3284ff66b606e058f55eebde6b7"><strong>plink_data.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16203" 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="16203" 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">@@ -16203,11 +16203,11 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>
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16203
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<td class="diff-line-num new_line" data-linenumber="16203" 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">
16203
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<pre style="margin: 0;"> <span id="LC16203" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="16204" 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">
16204
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<td class="diff-line-num new_line" data-linenumber="16204" 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">
16204
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<pre style="margin: 0;"> <span id="LC16204" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dichot_pheno</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="16205" 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">
16205
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<td class="diff-line-num new_line" data-linenumber="16205" 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">
16205
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<pre style="margin: 0;"> <span id="LC16205" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qsort_ext</span><span class="p">(</span><span class="n" style="color: #333;">sample_fids</span><span class="p">,</span> <span class="n" style="color: #333;">tot_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sample_full_len</span><span class="p">,</span> <span class="n" style="color: #333;">merge_nsort</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">strcmp_natural_deref</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">strcmp_deref</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_c_char</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16206" 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">
16206
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<td class="diff-line-num new_line old" data-linenumber="16206" 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="LC16206" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16207" 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="16206" 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">
16206
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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="LC16206" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
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16207
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<td class="diff-line-num new_line" data-linenumber="16207" 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">
16207
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<pre style="margin: 0;"> <span id="LC16207" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="16208" 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">
16208
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<td class="diff-line-num new_line" data-linenumber="16208" 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">
16208
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<pre style="margin: 0;"> <span id="LC16208" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="16209" 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">
16209
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<td class="diff-line-num new_line" data-linenumber="16209" 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">
16209
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<pre style="margin: 0;"> <span id="LC16209" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qsort_ext</span><span class="p">(</span><span class="n" style="color: #333;">sample_fids</span><span class="p">,</span> <span class="n" style="color: #333;">tot_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sample_full_len</span><span class="p">,</span> <span class="n" style="color: #333;">merge_nsort</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">strcmp_natural_deref</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">strcmp_deref</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pheno_d</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16210" 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">
16210
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<td class="diff-line-num new_line old" data-linenumber="16210" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC16210" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="16211" 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="16210" 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">
16210
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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="LC16210" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16211" 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">
16211
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<td class="diff-line-num new_line" data-linenumber="16211" 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">
16211
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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="LC16211" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16212" 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">
16212
</td>
<td class="diff-line-num new_line" data-linenumber="16212" 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">
16212
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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="LC16212" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16213" 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">
16213
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<td class="diff-line-num new_line" data-linenumber="16213" 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">
16213
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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="LC16213" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_sort</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SAMPLE_SORT_FILE</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16284" 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="16284" 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">@@ -16284,10 +16284,12 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>
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<td class="diff-line-num old_line" data-linenumber="16284" 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">
16284
</td>
<td class="diff-line-num new_line" data-linenumber="16284" 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">
16284
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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="LC16284" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_WRITE_FAIL</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16285" 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">
16285
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<td class="diff-line-num new_line" data-linenumber="16285" 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">
16285
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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="LC16285" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16286" 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">
16286
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<td class="diff-line-num new_line" data-linenumber="16286" 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">
16286
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16286" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dichot_pheno</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="16287" 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">
16287
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<pre style="margin: 0;">-<span id="LC16287" class="line" lang="c"> <span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_c_char</span><span class="p">[</span><span class="n" style="color: #333;">ulii</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC16287" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (21 Feb 2018): need to use the map_reverse index here,</span></span>
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<pre style="margin: 0;">+<span id="LC16288" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// since the phenotypes correspond to ASCII-sorted sample ID order.</span></span>
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<pre style="margin: 0;">+<span id="LC16289" class="line" lang="c"> <span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_c_char</span><span class="p">[</span><span class="n" style="color: #333;">ujj</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC16290" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">?</span> <span class="p">((</span><span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"2"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"-9"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC16291" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC16290" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_d</span><span class="p">[</span><span class="n" style="color: #333;">u<span class="idiff left right">lii</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC16292" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_d</span><span class="p">[</span><span class="n" style="color: #333;">u<span class="idiff left right">jj</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC16293" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC16294" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC16295" class="line" lang="c"> <span class="p">}</span></span>
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