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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/ece3ea428e8b7ebd0df387e7a7df7e0ab98a6fb6">ece3ea42</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-06-04T07:58:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.1-180528</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/c5cc8b2bab28ed38b331c9fa6c5c28b06445c538">c5cc8b2b</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-06-04T07:58:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/1.90_b6.1-180528'
Upstream version 1.90~b6.1-180528
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/644b614f638d080e6bd004cc33b968f6e276ebfa">644b614f</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-06-04T08:01:32+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelogs
</pre>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<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
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<li class="file-stats">
<a href="#60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69">
plink_assoc.c
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<li class="file-stats">
<a href="#a8e4f7e2f6aedfa2e57a4b081931760a1e0f1908">
plink_common.c
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<li class="file-stats">
<a href="#ddc87b66f3aa93580d31aff93025241d811cc99e">
plink_common.h
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<li class="file-stats">
<a href="#f101da6685d6d3284ff66b606e058f55eebde6b7">
plink_data.c
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/7c1a905bdc915410076bf26808bc7a627e194c3f...644b614f638d080e6bd004cc33b968f6e276ebfa#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~b6.1-180528-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</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"> -- Dylan Aïssi <bob.dybian@gmail.com> Mon, 04 Jun 2018 07:59:00 +0200</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~b5.4-180410-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream release.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" 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="257" 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">@@ -251,4 +257,3 @@ plink (1.03p1-1) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext"> * Initial release (Closes: #490832).</span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sun, 24 Aug 2008 17:10:55 +0200</span></pre>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="plaintext"></span></pre>
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<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink1-9/compare/7c1a905bdc915410076bf26808bc7a627e194c3f...644b614f638d080e6bd004cc33b968f6e276ebfa#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">10 Apr 2018: --zero-cluster command-line parsing bugfix. --mendel-multigen bugfix.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">28 May 2018: Fixed --file triallelic-variant handling bug which occurred when the .map was unsorted.</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">26 May (beta 6): --merge-equal-pos bugfixes. If you used --merge-equal-pos with .bed+.bim+.fam filesets where allele order may have differed between .bim files, or with any .ped+.map fileset at all, we recommend redoing that run.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">10 Apr: --zero-cluster command-line parsing bugfix. --mendel-multigen bugfix.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">21 Feb: "--indiv-sort file" no longer scrambles the phenotypes when used with --{b}merge or --merge-list.</span>
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<a href="https://salsa.debian.org/med-team/plink1-9/compare/7c1a905bdc915410076bf26808bc7a627e194c3f...644b614f638d080e6bd004cc33b968f6e276ebfa#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 v1.90b<span class="idiff left right">5.4</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 v1.90b<span class="idiff left right">6.1</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;">" (<span class="idiff left right">10 Apr</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">28 May</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/7c1a905bdc915410076bf26808bc7a627e194c3f...644b614f638d080e6bd004cc33b968f6e276ebfa#60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69"><strong>plink_assoc.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">@@ -11236,6 +11236,11 @@ int32_t cmh_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*</td>
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11236
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<pre style="margin: 0;"> <span id="LC11236" class="line" lang="c"> <span class="n" style="color: #333;">c_star</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a1_ctd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a_star</span><span class="p">;</span></span>
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11237
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<pre style="margin: 0;"> <span id="LC11237" class="line" lang="c"> <span class="n" style="color: #333;">d_star</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctrl_ctd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a1_ctd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">a_star</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11238" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC11239" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// concordance fix (25 May 2018): print NA,NA instead of inf,0</span></span>
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<pre style="margin: 0;">+<span id="LC11240" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">a_star</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 class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">b_star</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 class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">c_star</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 class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">d_star</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC11241" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">cmh_assoc_bd_fail</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11242" class="line" lang="c"> <span class="p">}</span></span>
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11243
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<pre style="margin: 0;">+<span id="LC11243" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC11244" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// inverse variance</span></span>
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<pre style="margin: 0;"> <span id="LC11245" class="line" lang="c"> <span class="n" style="color: #333;">dxx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">a_star</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">b_star</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">c_star</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">d_star</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11246" class="line" lang="c"></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">@@ -4902,6 +4902,25 @@ void cleanup_allele_storage(uint32_t max_allele_slen, uintptr_t allele_storage_e</td>
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<pre style="margin: 0;"> <span id="LC4902" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4903" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4904" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC4905" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup_allele_storage2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_storage_entry_ct</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="n" style="color: #333;">allele_storage</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4906" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_storage</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4907" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">one_char_strs_addr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">g_one_char_strs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4908" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">allele_storage_entry_ct</span><span class="p">;)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4909" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">];</span></span>
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4910
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<pre style="margin: 0;">+<span id="LC4910" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cur_entry</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4911" 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">
4911
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<pre style="margin: 0;">+<span id="LC4911" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// --merge-equal-pos hacked entry</span></span>
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4912
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<pre style="margin: 0;">+<span id="LC4912" class="line" lang="c"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4913" 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">
4913
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<pre style="margin: 0;">+<span id="LC4913" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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4914
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<pre style="margin: 0;">+<span id="LC4914" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4915" 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">
4915
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<pre style="margin: 0;">+<span id="LC4915" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// take advantage of unsigned wraparound</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4916" 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">
4916
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<pre style="margin: 0;">+<span id="LC4916" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((((</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">cur_entry</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">one_char_strs_addr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">512</span><span class="p">)</span> <span class="p">{</span></span>
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4917
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<pre style="margin: 0;">+<span id="LC4917" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cur_entry</span><span class="p">);</span></span>
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4918
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<pre style="margin: 0;">+<span id="LC4918" class="line" lang="c"> <span class="p">}</span></span>
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4919
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<pre style="margin: 0;">+<span id="LC4919" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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4920
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<pre style="margin: 0;">+<span id="LC4920" class="line" lang="c"> <span class="p">}</span></span>
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4921
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<pre style="margin: 0;">+<span id="LC4921" class="line" lang="c"> <span class="p">}</span></span>
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4922
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<pre style="margin: 0;">+<span id="LC4922" class="line" lang="c"><span class="p">}</span></span>
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4923
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<pre style="margin: 0;">+<span id="LC4923" class="line" lang="c"></span>
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4905
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4924
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<pre style="margin: 0;"> <span id="LC4924" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">refresh_chrom_info</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Chrom_info</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">chrom_end_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">chrom_fo_idx_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">is_x_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">is_y_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">is_mt_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">is_haploid_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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4906
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4925
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<pre style="margin: 0;"> <span id="LC4925" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// assumes we are at the end of the chromosome denoted by chrom_fo_idx. Ok</span></span>
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4907
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4926
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<pre style="margin: 0;"> <span id="LC4926" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// for chrom_fo_idx == 0xffffffffU.</span></span>
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<a href="https://salsa.debian.org/med-team/plink1-9/compare/7c1a905bdc915410076bf26808bc7a627e194c3f...644b614f638d080e6bd004cc33b968f6e276ebfa#ddc87b66f3aa93580d31aff93025241d811cc99e"><strong>plink_common.h</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">@@ -2266,6 +2266,10 @@ uint32_t allele_reset(const char* newval, uint32_t allele_slen, char** allele_pt</td>
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2266
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2266
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<pre style="margin: 0;"> <span id="LC2266" class="line" lang="c"></span>
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2267
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2267
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<pre style="margin: 0;"> <span id="LC2267" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">cleanup_allele_storage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_storage_entry_ct</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="n" style="color: #333;">allele_storage</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2268" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC2269" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// needed by fixed --merge-equal-pos implementation, which takes more liberties</span></span>
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<pre style="margin: 0;">+<span id="LC2270" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// with allele_storage[]</span></span>
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<pre style="margin: 0;">+<span id="LC2271" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">cleanup_allele_storage2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_storage_entry_ct</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="n" style="color: #333;">allele_storage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2272" class="line" lang="c"></span>
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2269
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2273
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<pre style="margin: 0;"> <span id="LC2273" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// no need for this; code is simpler if we just create a copy of marker_exclude</span></span>
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2270
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2274
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<pre style="margin: 0;"> <span id="LC2274" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// with all non-autosomal loci removed</span></span>
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2271
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2275
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<pre style="margin: 0;"> <span id="LC2275" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<a href="https://salsa.debian.org/med-team/plink1-9/compare/7c1a905bdc915410076bf26808bc7a627e194c3f...644b614f638d080e6bd004cc33b968f6e276ebfa#f101da6685d6d3284ff66b606e058f55eebde6b7"><strong>plink_data.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">@@ -5116,6 +5116,8 @@ int32_t incr_text_allele_str(char* allele_name, uint32_t an_len, Ll_str* allele_</td>
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5116
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5116
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<pre style="margin: 0;"> <span id="LC5116" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Ll_str.next is a pointer to a linked list entry storing the next 1+ allele</span></span>
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5117
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<pre style="margin: 0;"> <span id="LC5117" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// names. Worst case, the linked list is of length 4 (beyond that we error</span></span>
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5118
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5118
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<pre style="margin: 0;"> <span id="LC5118" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// out). Most of the time, it'll be length 0.</span></span>
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<pre style="margin: 0;">+<span id="LC5119" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Allele names are separated by tabs; \0 denotes the end of the allele name</span></span>
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5120
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<pre style="margin: 0;">+<span id="LC5120" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// list.</span></span>
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5121
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<pre style="margin: 0;"> <span id="LC5121" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// This type of function will become more important when it's time to parse</span></span>
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5122
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<pre style="margin: 0;"> <span id="LC5122" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// .vcf files, etc.</span></span>
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5123
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<pre style="margin: 0;"> <span id="LC5123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allele_num</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5147" 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">@@ -5145,30 +5147,29 @@ int32_t incr_text_allele_str(char* allele_name, uint32_t an_len, Ll_str* allele_</td>
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5145
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5147
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<pre style="margin: 0;"> <span id="LC5147" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">an_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">,</span> <span class="n" style="color: #333;">allele_name</span><span class="p">,</span> <span class="n" style="color: #333;">an_len</span><span class="p">)))</span> <span class="p">{</span></span>
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5146
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5148
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<pre style="margin: 0;"> <span id="LC5148" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="n" style="color: #333;">allele_num</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5147
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5149
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<pre style="margin: 0;"> <span id="LC5149" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC5150" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC5151" class="line" lang="c"> <span class="n" style="color: #333;">allele_num</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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5152
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<pre style="margin: 0;">+<span id="LC5152" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">)</span> <span class="p">{</span></span>
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5153
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<pre style="margin: 0;">+<span id="LC5153" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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5154
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<pre style="margin: 0;">+<span id="LC5154" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">)</span> <span class="p">{</span></span>
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5155
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<pre style="margin: 0;">+<span id="LC5155" class="line" lang="c"> <span class="n" style="color: #333;">allele_list_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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5156
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<pre style="margin: 0;">+<span id="LC5156" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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5148
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5157
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<pre style="margin: 0;"> <span id="LC5157" 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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5149
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<pre style="margin: 0;">-<span id="LC5149" class="line" lang="c"> <span class="n" style="color: #333;">allele_num</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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5150
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<pre style="margin: 0;">-<span id="LC5150" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">)</span> <span class="p">{</span></span>
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5151
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<pre style="margin: 0;">-<span id="LC5151" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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5152
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<pre style="margin: 0;">-<span id="LC5152" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">)</span> <span class="p">{</span></span>
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5153
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<pre style="margin: 0;">-<span id="LC5153" class="line" lang="c"> <span class="n" style="color: #333;">allele_list_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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5154
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<pre style="margin: 0;">-<span id="LC5154" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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5158
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<pre style="margin: 0;">+<span id="LC5158" class="line" lang="c"> <span class="n" style="color: #333;">chars_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mh" style="color: #099;">0x7ffffff0</span> <span class="o" style="font-weight: 600;">-</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</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="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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5159
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<pre style="margin: 0;">+<span id="LC5159" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chars_left</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">an_len</span><span class="p">)</span> <span class="p">{</span></span>
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5160
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<pre style="margin: 0;">+<span id="LC5160" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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5161
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<pre style="margin: 0;">+<span id="LC5161" class="line" lang="c"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">allele_name</span><span class="p">,</span> <span class="n" style="color: #333;">an_len</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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5155
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5162
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<pre style="margin: 0;"> <span id="LC5162" 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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5156
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5156" class="line" lang="c"> <span class="n" style="color: #333;">chars_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mh" style="color: #099;">0x7ffffff0</span> <span class="o" style="font-weight: 600;">-</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</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="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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5157
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chars_left</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">an_len</span><span class="p">)</span> <span class="p">{</span></span>
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5158
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5158" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5159" 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">
5159
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5159" class="line" lang="c"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">allele_name</span><span class="p">,</span> <span class="n" style="color: #333;">an_len</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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5160
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5160" 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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5161
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5161" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_llstr</span><span class="p">(</span><span class="n" style="color: #333;">an_len</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="n" style="color: #333;">ll_ptr</span><span class="p">))</span> <span class="p">{</span></span>
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5162
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5162" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">RET_NOMEM</span><span class="p">;</span></span>
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5163
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5163" class="line" lang="c"> <span class="p">}</span></span>
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5164
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5164" class="line" lang="c"> <span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_ptr</span><span class="p">;</span></span>
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5165
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5165" class="line" lang="c"> <span class="n" style="color: #333;">ll_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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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<td class="diff-line-num old old_line" data-linenumber="5166" 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">
5166
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5166" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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5167
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5167" class="line" lang="c"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">,</span> <span class="n" style="color: #333;">allele_name</span><span class="p">,</span> <span class="n" style="color: #333;">an_len</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5168" 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">
5168
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5168" class="line" lang="c"> <span class="p">}</span></span>
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5169
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5169" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="n" style="color: #333;">allele_num</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5170
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<td class="diff-line-num new_line old" data-linenumber="5163" 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="LC5170" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5163" 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">
5163
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<pre style="margin: 0;">+<span id="LC5163" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_llstr</span><span class="p">(</span><span class="n" style="color: #333;">an_len</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="n" style="color: #333;">ll_ptr</span><span class="p">))</span> <span class="p">{</span></span>
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5164
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<pre style="margin: 0;">+<span id="LC5164" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">RET_NOMEM</span><span class="p">;</span></span>
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5165
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<pre style="margin: 0;">+<span id="LC5165" class="line" lang="c"> <span class="p">}</span></span>
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5166
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<pre style="margin: 0;">+<span id="LC5166" class="line" lang="c"> <span class="n" style="color: #333;">allele_list_start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_ptr</span><span class="p">;</span></span>
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5167
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<pre style="margin: 0;">+<span id="LC5167" class="line" lang="c"> <span class="n" style="color: #333;">ll_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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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5168
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<pre style="margin: 0;">+<span id="LC5168" class="line" lang="c"> <span class="n" style="color: #333;">cur_allele_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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5169
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<pre style="margin: 0;">+<span id="LC5169" class="line" lang="c"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele_name_start</span><span class="p">,</span> <span class="n" style="color: #333;">allele_name</span><span class="p">,</span> <span class="n" style="color: #333;">an_len</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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5171
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5170
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<pre style="margin: 0;"> <span id="LC5170" class="line" lang="c"> <span class="p">}</span></span>
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5171
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<pre style="margin: 0;">+<span id="LC5171" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="n" style="color: #333;">allele_num</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5172
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<pre style="margin: 0;">+<span id="LC5172" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5172
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5173
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<pre style="margin: 0;"> <span id="LC5173" class="line" lang="c"> <span class="p">}</span></span>
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5173
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5174
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<pre style="margin: 0;"> <span id="LC5174" class="line" lang="c"> <span class="p">}</span></span>
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5174
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5175
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<pre style="margin: 0;"> <span id="LC5175" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">RET_INVALID_FORMAT</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5443" 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>
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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">@@ -5443,22 +5444,17 @@ int32_t ped_to_bed_multichar_allele(FILE** pedfile_ptr, FILE** outfile_ptr, char</td>
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5443
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<pre style="margin: 0;"> <span id="LC5444" class="line" lang="c"> <span class="p">}</span></span>
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5444
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5445
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<pre style="margin: 0;"> <span id="LC5445" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="p">{</span></span>
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5445
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5446
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<pre style="margin: 0;"> <span id="LC5446" class="line" lang="c"> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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5446
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<pre style="margin: 0;">-<span id="LC5446" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">map_is_unsorted</span><span class="p">)</span> <span class="p">{</span></span>
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5447
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<pre style="margin: 0;">-<span id="LC5447" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: Variant %u (post-sort/filter) %sallelic; setting rarest missing.</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;">map_reverse</span><span class="p">[</span><span class="n" style="color: #333;">marker_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">uii</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"quad"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"tri"</span><span class="p">));</span></span>
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5448
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<pre style="margin: 0;">-<span id="LC5448" 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="LC5449" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: Variant %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" %sallelic; setting rarest alleles missing.</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;">marker_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">uii</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"quad"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"tri"</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC5450" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC5447" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (28 May 2018): do NOT look up map_reverse[] in unsorted case</span></span>
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<pre style="margin: 0;">+<span id="LC5448" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: Variant %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">"%s %sallelic; setting rarest missing.</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;">marker_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">map_is_unsorted</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (post-sort)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">uii</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"quad"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"tri"</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC5449" class="line" lang="c"> <span class="n" style="color: #333;">logerrprintb</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC5450" class="line" lang="c"> <span class="n" style="color: #333;">get_top_two_ui</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_idx</span><span class="p">]),</span> <span class="n" style="color: #333;">uii</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ulii</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">uljj</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC5453" class="line" lang="c"> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map_is_unsorted</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">map_reverse</span><span class="p">[</span><span class="n" style="color: #333;">marker_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">marker_idx</span><span class="p">;</span></span>
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5454
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<pre style="margin: 0;"> <span id="LC5451" 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="LC5452" class="line" lang="c"> <span class="n" style="color: #333;">ulii</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">marker_allele_cts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_idx</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="mi" style="color: #099;">1</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="LC5453" class="line" lang="c"> <span class="n" style="color: #333;">uljj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ulii</span> <span class="o" style="font-weight: 600;">^</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC5457" class="line" lang="c"> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_idx</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC5454" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC5455" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC5460" class="line" lang="c"> <span class="n" style="color: #333;">aptr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_llstr</span><span class="p">((</span><span class="n" style="color: #333;">Ll_str</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_alleles_tmp</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">uii</span></span><span class="p">])),</span> <span class="n" style="color: #333;">uljj</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC5461" class="line" lang="c"> <span class="n" style="color: #333;">aptr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_llstr</span><span class="p">((</span><span class="n" style="color: #333;">Ll_str</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_alleles_tmp</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">uii</span></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="LC5456" class="line" lang="c"> <span class="n" style="color: #333;">aptr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_llstr</span><span class="p">((</span><span class="n" style="color: #333;">Ll_str</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_alleles_tmp</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">marker_idx</span></span><span class="p">])),</span> <span class="n" style="color: #333;">uljj</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC5457" class="line" lang="c"> <span class="n" style="color: #333;">aptr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_llstr</span><span class="p">((</span><span class="n" style="color: #333;">Ll_str</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_alleles_tmp</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">marker_idx</span></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="LC5458" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">aptr1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC5459" class="line" lang="c"> <span class="n" style="color: #333;">aptr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC5460" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5708,7 +5704,7 @@ int32_t ped_to_bed_multichar_allele(FILE** pedfile_ptr, FILE** outfile_ptr, char</td>
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5704
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<pre style="margin: 0;"> <span id="LC5704" class="line" lang="c"> <span class="n" style="color: #333;">g_bigstack_base</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">cur_slen_rdup</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5709" 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">
5709
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<td class="diff-line-num new_line" data-linenumber="5705" 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">
5705
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<pre style="margin: 0;"> <span id="LC5705" class="line" lang="c"> <span class="n" style="color: #333;">logprint</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="5710" 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">
5710
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<td class="diff-line-num new_line" data-linenumber="5706" 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">
5706
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<pre style="margin: 0;"> <span id="LC5706" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">RET_NOMEM</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5711" 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">
5711
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<td class="diff-line-num new_line old" data-linenumber="5707" 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="LC5711" class="line" lang="c"> <span class="n" style="color: #333;">LOGERRPRINTF</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: More than 4 different alleles at variant %u%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;">uii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">map_is_unsorted</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (post-sort<span class="idiff left right">/filter</span>)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5707" 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">
5707
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<pre style="margin: 0;">+<span id="LC5707" class="line" lang="c"> <span class="n" style="color: #333;">LOGERRPRINTF</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: More than 4 different alleles at variant %u%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;">uii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">map_is_unsorted</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (post-sort)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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5712
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5708
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<pre style="margin: 0;"> <span id="LC5708" class="line" lang="c"> <span class="p">}</span></span>
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5713
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5709
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<pre style="margin: 0;"> <span id="LC5709" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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5714
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5710
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<pre style="margin: 0;"> <span id="LC5710" class="line" lang="c"> <span class="nl">ped_to_bed_multichar_allele_ret_INVALID_FORMAT_4:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6107" 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="6103" 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">@@ -6107,11 +6103,7 @@ int32_t ped_to_bed(char* pedname, char* mapname, char* outname, char* outname_en</td>
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6107
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6103
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<pre style="margin: 0;"> <span id="LC6103" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6108" 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">
6108
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<td class="diff-line-num new_line" data-linenumber="6104" 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">
6104
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<pre style="margin: 0;"> <span id="LC6104" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">marker_alleles</span><span class="p">[</span><span class="n" style="color: #333;">marker_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6109" 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">
6109
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<td class="diff-line-num new_line" data-linenumber="6105" 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">
6105
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<pre style="margin: 0;"> <span id="LC6105" 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;">marker_alleles</span><span class="p">[</span><span class="n" style="color: #333;">marker_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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6110
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<td class="diff-line-num new_line old" data-linenumber="6106" 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="LC6110" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">map_is_unsorted</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6111" 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">
6111
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<td class="diff-line-num new_line old" data-linenumber="6106" 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="LC6111" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: Variant %u (post-sort/filter) %sallelic; setting rarest missing.</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;">map_reverse</span><span class="p">[</span><span class="n" style="color: #333;">marker_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"quad"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"tri"</span><span class="p">));</span></span>
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6112
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<td class="diff-line-num new_line old" data-linenumber="6106" 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="LC6112" 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 old_line" data-linenumber="6113" 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">
6113
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<td class="diff-line-num new_line old" data-linenumber="6106" 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="LC6113" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: Variant %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" %sallelic; setting rarest alleles missing.</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;">marker_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"quad"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"tri"</span><span class="p">));</span></span>
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6114
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<td class="diff-line-num new_line old" data-linenumber="6106" 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="LC6114" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6115" 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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6106
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<pre style="margin: 0;">+<span id="LC6106" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: Variant %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">"%s %sallelic; setting rarest alleles missing.</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;">marker_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">map_is_unsorted</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (post-sort)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"quad"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"tri"</span><span class="p">));</span></span>
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6115
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6107
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<pre style="margin: 0;"> <span id="LC6107" class="line" lang="c"> <span class="n" style="color: #333;">logerrprintb</span><span class="p">();</span></span>
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6116
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6108
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<pre style="margin: 0;"> <span id="LC6108" class="line" lang="c"> <span class="n" style="color: #333;">ujj</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;">4</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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6117
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6109
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<pre style="margin: 0;"> <span id="LC6109" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// insertion sort</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15021" 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="15013" 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">@@ -15021,8 +15013,8 @@ int32_t report_non_biallelics(char* outname, char* outname_end, Ll_str* non_bial</td>
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15021
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15013
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<pre style="margin: 0;"> <span id="LC15013" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">retval</span><span class="p">;</span></span>
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15022
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15014
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<pre style="margin: 0;"> <span id="LC15014" class="line" lang="c"><span class="p">}</span></span>
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15023
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15015
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<pre style="margin: 0;"> <span id="LC15015" class="line" lang="c"></span>
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15024
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<td class="diff-line-num new_line old" data-linenumber="15016" 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="LC15024" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">merge_alleles_update_str</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="n" style="color: #333;">marker_allele_ptr</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="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">distinct_allele_ct<span class="idiff left right">_ptr</span></span><span class="p">)</span> <span class="p">{</span></span>
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15025
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<td class="diff-line-num new_line old" data-linenumber="15016" 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="LC15025" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distinct_allele_ct<span class="idiff left right">_ptr</span></span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15026" 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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15016
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<pre style="margin: 0;">+<span id="LC15016" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">merge_alleles_update_str</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="n" style="color: #333;">marker_allele_ptr</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="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">distinct_allele_ct<span class="idiff left right">p</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15017" 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">
15017
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<pre style="margin: 0;">+<span id="LC15017" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distinct_allele_ct<span class="idiff left right">p</span></span><span class="p">;</span></span>
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15026
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15018
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<pre style="margin: 0;"> <span id="LC15018" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allele_idx</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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15027
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15019
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<pre style="margin: 0;"> <span id="LC15019" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">marker_allele_ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g_missing_geno_ptr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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15028
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15020
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<pre style="margin: 0;"> <span id="LC15020" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15033" 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="15025" 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">@@ -15033,33 +15025,52 @@ void merge_alleles_update_str(char* marker_allele_ptr, char** allele_ptrs, uint3</td>
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15033
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15025
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<pre style="margin: 0;"> <span id="LC15025" class="line" lang="c"> <span class="p">}</span></span>
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15034
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15026
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<pre style="margin: 0;"> <span id="LC15026" class="line" lang="c"> <span class="n" style="color: #333;">allele_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15035
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15027
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<pre style="margin: 0;"> <span id="LC15027" class="line" lang="c"> <span class="p">}</span></span>
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15036
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<pre style="margin: 0;">-<span id="LC15036" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distinct_allele_ct<span class="idiff left right">_ptr</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15028
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<pre style="margin: 0;">+<span id="LC15028" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distinct_allele_ct<span class="idiff left right">p</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15037
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<td class="diff-line-num new_line" data-linenumber="15029" 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">
15029
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<pre style="margin: 0;"> <span id="LC15029" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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15038
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15030
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<pre style="margin: 0;"> <span id="LC15030" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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15039
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15031
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<pre style="margin: 0;"> <span id="LC15031" class="line" lang="c"> <span class="p">}</span></span>
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15040
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15032
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<pre style="margin: 0;"> <span id="LC15032" class="line" lang="c"> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">distinct_allele_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptr</span><span class="p">;</span></span>
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15041
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15033
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<pre style="margin: 0;"> <span id="LC15033" class="line" lang="c"><span class="p">}</span></span>
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15042
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15034
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<pre style="margin: 0;"> <span id="LC15034" class="line" lang="c"></span>
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15043
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<pre style="margin: 0;">-<span id="LC15043" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="nf" style="color: #900; font-weight: 600;">merge_alleles</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="n" style="color: #333;">marker_allele_ptrs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">marker_uidx2</span><span class="p">)</span> <span class="p">{</span></span>
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15044
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<pre style="margin: 0;">-<span id="LC15044" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">distinct_allele_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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15045
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<td class="diff-line-num new_line old" data-linenumber="15035" 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="LC15045" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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15046
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<td class="diff-line-num new_line old" data-linenumber="15035" 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="LC15046" class="line" lang="c"> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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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15047
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<td class="diff-line-num new_line old" data-linenumber="15035" 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="LC15047" class="line" lang="c"> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</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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<td class="diff-line-num new old_line" data-linenumber="15048" 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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15035
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<pre style="margin: 0;">+<span id="LC15035" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="nf" style="color: #900; font-weight: 600;">merge_equal_pos_alleles</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="n" style="color: #333;">marker_allele_ptrs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">distinct_allele_ctp</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="n" style="color: #333;">allele_ptrs</span><span class="p">)</span> <span class="p">{</span></span>
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15048
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15036
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<pre style="margin: 0;"> <span id="LC15036" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// reverse order so --keep-allele-order works</span></span>
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15049
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<td class="diff-line-num new_line old" data-linenumber="15037" 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="LC15049" class="line" lang="c"> <span class="n" style="color: #333;">merge_alleles_update_str</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">distinct_allele_ct</span><span class="p">);</span></span>
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15050
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<pre style="margin: 0;">-<span id="LC15050" class="line" lang="c"> <span class="n" style="color: #333;">merge_alleles_update_str</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">distinct_allele_ct</span><span class="p">);</span></span>
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15051
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<pre style="margin: 0;">-<span id="LC15051" class="line" lang="c"> <span class="n" style="color: #333;">merge_alleles_update_str</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">distinct_allele_ct</span><span class="p">);</span></span>
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15052
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<pre style="margin: 0;">-<span id="LC15052" class="line" lang="c"> <span class="n" style="color: #333;">merge_alleles_update_str</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx2</span><span class="p">],</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">distinct_allele_ct</span><span class="p">);</span></span>
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15053
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<td class="diff-line-num new_line old" data-linenumber="15037" 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="LC15053" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">distinct_allele_ct</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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15037
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<pre style="margin: 0;">+<span id="LC15037" class="line" lang="c"> <span class="n" style="color: #333;">merge_alleles_update_str</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="n" style="color: #333;">distinct_allele_ctp</span><span class="p">);</span></span>
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15038
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<pre style="margin: 0;">+<span id="LC15038" class="line" lang="c"> <span class="n" style="color: #333;">merge_alleles_update_str</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">,</span> <span class="n" style="color: #333;">distinct_allele_ctp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC15039" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">distinct_allele_ctp</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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15040
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<pre style="margin: 0;">+<span id="LC15040" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15041
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<pre style="margin: 0;">+<span id="LC15041" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC15042" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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15043
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<pre style="margin: 0;">+<span id="LC15043" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC15044" class="line" lang="c"></span>
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15045
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<pre style="margin: 0;">+<span id="LC15045" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="nf" style="color: #900; font-weight: 600;">save_equal_pos_alleles</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ll_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_pos_stop</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="n" style="color: #333;">equal_pos_allele_ptrs</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="n" style="color: #333;">marker_allele_ptrs</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15046" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">canonical_marker_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC15047" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// (do we really need the reversal in merge_equal_pos_alleles()?)</span></span>
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<pre style="margin: 0;">+<span id="LC15048" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (26 May 2018): forgot about plink 1.9's allele memory management</span></span>
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15049
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<pre style="margin: 0;">+<span id="LC15049" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// strategy.</span></span>
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<pre style="margin: 0;">+<span id="LC15050" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">g_missing_geno_ptr</span><span class="p">;</span></span>
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15051
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<pre style="margin: 0;">+<span id="LC15051" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_reset</span><span class="p">(</span><span class="n" style="color: #333;">new_allele</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">new_allele</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">])))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15052" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15053" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC15054" class="line" lang="c"> <span class="n" style="color: #333;">new_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">g_missing_geno_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15055" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_reset</span><span class="p">(</span><span class="n" style="color: #333;">new_allele</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">new_allele</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">])))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC15056" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC15057" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC15056" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="p">{</span></span>
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15057
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<pre style="margin: 0;">-<span id="LC15057" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// todo: test if this write is inefficient enough that we want to guard it</span></span>
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15058
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<pre style="margin: 0;">-<span id="LC15058" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// with an if statement</span></span>
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15059
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<pre style="margin: 0;">-<span id="LC15059" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx</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="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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15060
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<pre style="margin: 0;">-<span id="LC15060" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_ptrs</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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15061
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<pre style="margin: 0;">-<span id="LC15061" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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15058
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<pre style="margin: 0;">+<span id="LC15058" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">read_pos</span><span class="p">;</span></span>
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15059
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<pre style="margin: 0;">+<span id="LC15059" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">read_pos_stop</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">read_pos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15060" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC15061" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// DIRTY HACK (25 May 2018): save (nullptr, canonical_marker_uidx) tuple,</span></span>
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15062
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<pre style="margin: 0;">+<span id="LC15062" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// and have merge_main() look up the canonical marker_uidx in this case.</span></span>
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15063
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<pre style="margin: 0;">+<span id="LC15063" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// something like this is necessary for mixed .bed/.ped merge +</span></span>
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15064
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<pre style="margin: 0;">+<span id="LC15064" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// --merge-equal-pos to work properly.</span></span>
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15065
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<pre style="margin: 0;">+<span id="LC15065" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (26 May 2018): need to free entries here by hand.</span></span>
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15066
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<pre style="margin: 0;">+<span id="LC15066" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</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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15067
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<pre style="margin: 0;">+<span id="LC15067" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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15062
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15068
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<pre style="margin: 0;"> <span id="LC15068" class="line" lang="c"> <span class="p">}</span></span>
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15069
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<pre style="margin: 0;">+<span id="LC15069" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]</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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15070
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<pre style="margin: 0;">+<span id="LC15070" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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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15071
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<pre style="margin: 0;">+<span id="LC15071" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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15072
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<pre style="margin: 0;">+<span id="LC15072" class="line" lang="c"> <span class="p">}</span></span>
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15073
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<pre style="margin: 0;">+<span id="LC15073" class="line" lang="c"> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">cur_marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</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="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="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">canonical_marker_uidx</span><span class="p">);</span></span>
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15063
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15074
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<pre style="margin: 0;"> <span id="LC15074" class="line" lang="c"> <span class="p">}</span></span>
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15064
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15075
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<pre style="margin: 0;"> <span id="LC15075" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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15065
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15076
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<pre style="margin: 0;"> <span id="LC15076" class="line" lang="c"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15081" 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="15092" 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">@@ -15081,6 +15092,10 @@ static inline uint32_t merge_post_msort_update_maps(char* marker_ids, uintptr_t </td>
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15081
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<td class="diff-line-num new_line" data-linenumber="15092" 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">
15092
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<pre style="margin: 0;"> <span id="LC15092" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_pos</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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15082
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<td class="diff-line-num new_line" data-linenumber="15093" 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">
15093
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<pre style="margin: 0;"> <span id="LC15093" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// may be lower than read_pos due to dups</span></span>
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15083
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15094
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<pre style="margin: 0;"> <span id="LC15094" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">position_warning_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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15095
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<pre style="margin: 0;">+<span id="LC15095" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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15096
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<pre style="margin: 0;">+<span id="LC15096" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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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<td class="diff-line-num new new_line" data-linenumber="15097" 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">
15097
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<pre style="margin: 0;">+<span id="LC15097" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</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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<td class="diff-line-num new new_line" data-linenumber="15098" 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">
15098
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<pre style="margin: 0;">+<span id="LC15098" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">equal_pos_allele_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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15084
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15099
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<pre style="margin: 0;"> <span id="LC15099" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">;</span></span>
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15085
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15100
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<pre style="margin: 0;"> <span id="LC15100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrom_read_end_idx</span><span class="p">;</span></span>
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15086
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15101
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<pre style="margin: 0;"> <span id="LC15101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">llxx</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15096" 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="15111" 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">@@ -15096,6 +15111,7 @@ static inline uint32_t merge_post_msort_update_maps(char* marker_ids, uintptr_t </td>
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15096
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15111
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<pre style="margin: 0;"> <span id="LC15111" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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15097
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15112
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<pre style="margin: 0;"> <span id="LC15112" class="line" lang="c"> <span class="p">}</span></span>
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15098
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<td class="diff-line-num new_line" data-linenumber="15113" 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">
15113
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<pre style="margin: 0;"> <span id="LC15113" class="line" lang="c"> <span class="n" style="color: #333;">unplaced</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">unplaced</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zero_extra_chroms</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">unplaced</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_code</span><span class="p">));</span></span>
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15114
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<pre style="margin: 0;">+<span id="LC15114" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_merge_equal_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merge_equal_pos</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">unplaced</span><span class="p">);</span></span>
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15099
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15115
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<pre style="margin: 0;"> <span id="LC15115" class="line" lang="c"> <span class="n" style="color: #333;">chrom_read_end_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_start</span><span class="p">[</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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15100
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15116
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<pre style="margin: 0;"> <span id="LC15116" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// ll_buf has base-pair positions in high 32 bits, and pre-sort indices in</span></span>
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15101
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15117
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<pre style="margin: 0;"> <span id="LC15117" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// low 32 bits.</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15120" 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">@@ -15104,34 +15120,63 @@ static inline uint32_t merge_post_msort_update_maps(char* marker_ids, uintptr_t </td>
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15104
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15120
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<pre style="margin: 0;"> <span id="LC15120" class="line" lang="c"> <span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)(((</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span><span class="n" style="color: #333;">llxx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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15105
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<td class="diff-line-num new_line" data-linenumber="15121" 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">
15121
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<pre style="margin: 0;"> <span id="LC15121" class="line" lang="c"> <span class="n" style="color: #333;">pos_buf</span><span class="p">[</span><span class="n" style="color: #333;">write_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_bp</span><span class="p">;</span></span>
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15106
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<td class="diff-line-num new_line" data-linenumber="15122" 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">
15122
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<pre style="margin: 0;"> <span id="LC15122" class="line" lang="c"> <span class="n" style="color: #333;">marker_map</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">llxx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15123
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<pre style="margin: 0;">+<span id="LC15123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">equal_pos_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0xffffffffU</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// force initial mismatch</span></span>
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15124
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<pre style="margin: 0;">+<span id="LC15124" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">equal_pos_read_start</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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15107
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15125
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<pre style="margin: 0;"> <span id="LC15125" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chrom_read_end_idx</span><span class="p">;</span> <span class="n" style="color: #333;">read_pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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15108
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15126
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<pre style="margin: 0;"> <span id="LC15126" class="line" lang="c"> <span class="n" style="color: #333;">llxx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span><span class="p">];</span></span>
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15109
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15127
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<pre style="margin: 0;"> <span id="LC15127" class="line" lang="c"> <span class="n" style="color: #333;">presort_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">llxx</span><span class="p">;</span></span>
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15110
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<td class="diff-line-num new_line" data-linenumber="15128" 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">
15128
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<pre style="margin: 0;"> <span id="LC15128" class="line" lang="c"> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)(</span><span class="n" style="color: #333;">llxx</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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15111
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<pre style="margin: 0;">-<span id="LC15111" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// do not merge chr 0 (unplaced).</span></span>
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15112
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<td class="diff-line-num new_line old" data-linenumber="15129" 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="LC15112" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">unplaced</span><span class="p">))</span> <span class="p">{</span></span>
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15113
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<td class="diff-line-num new_line old" data-linenumber="15129" 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="LC15113" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_equal_pos</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">merge_alleles</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">,</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">presort_idx</span><span class="p">))</span> <span class="p">{</span></span>
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15114
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<td class="diff-line-num new_line old" data-linenumber="15129" 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="LC15114" class="line" lang="c"> <span class="n" style="color: #333;">LOGERRPRINTFWW</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --merge-equal-pos failure. Variants '%s' and '%s' have the same position, but do not share the same alleles.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">max_marker_id_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">presort_idx</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">max_marker_id_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">])]));</span></span>
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15115
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<pre style="margin: 0;">-<span id="LC15115" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15116
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<pre style="margin: 0;">-<span id="LC15116" class="line" lang="c"> <span class="p">}</span></span>
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15117
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<pre style="margin: 0;">-<span id="LC15117" class="line" lang="c"> <span class="n" style="color: #333;">LOGPREPRINTFWW</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Variants '%s' and '%s' have the same position.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">max_marker_id_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">presort_idx</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">max_marker_id_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">])]));</span></span>
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15118
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<pre style="margin: 0;">-<span id="LC15118" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">position_warning_ct</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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15119
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<pre style="margin: 0;">-<span id="LC15119" class="line" lang="c"> <span class="n" style="color: #333;">logerrprintb</span><span class="p">();</span></span>
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15120
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<pre style="margin: 0;">-<span id="LC15120" 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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15121
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<pre style="margin: 0;">-<span id="LC15121" class="line" lang="c"> <span class="n" style="color: #333;">logstr</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">);</span></span>
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15122
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<pre style="margin: 0;">-<span id="LC15122" class="line" lang="c"> <span class="p">}</span></span>
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15123
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<pre style="margin: 0;">-<span id="LC15123" class="line" lang="c"> <span class="n" style="color: #333;">position_warning_ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15124
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<pre style="margin: 0;">-<span id="LC15124" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_equal_pos</span><span class="p">)</span> <span class="p">{</span></span>
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15129
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<pre style="margin: 0;">+<span id="LC15129" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// don't care about position conflicts on chr 0 (unplaced).</span></span>
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15130
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<pre style="margin: 0;">+<span id="LC15130" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_merge_equal_pos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15131" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (25 May 2018): previous merge_alleles() usage was broken for</span></span>
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15132
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<pre style="margin: 0;">+<span id="LC15132" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// multiple reasons</span></span>
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15133
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<pre style="margin: 0;">+<span id="LC15133" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">)</span> <span class="p">{</span></span>
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15134
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<pre style="margin: 0;">+<span id="LC15134" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">equal_pos_bp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">prev_bp</span><span class="p">)</span> <span class="p">{</span></span>
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15135
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<pre style="margin: 0;">+<span id="LC15135" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_read_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15136
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<pre style="margin: 0;">+<span id="LC15136" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_bp</span><span class="p">;</span></span>
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15137
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<pre style="margin: 0;">+<span id="LC15137" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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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15138
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<pre style="margin: 0;">+<span id="LC15138" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</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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15139
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<pre style="margin: 0;">+<span id="LC15139" class="line" lang="c"> <span class="n" style="color: #333;">equal_pos_allele_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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15140
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<pre style="margin: 0;">+<span id="LC15140" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_equal_pos_alleles</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">equal_pos_read_start</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">equal_pos_allele_ct</span><span class="p">,</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15141" 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">
15141
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<pre style="margin: 0;">+<span id="LC15141" class="line" lang="c"> <span class="n" style="color: #333;">LOGERRPRINTFWW</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --merge-equal-pos failure: inconsistent alleles at %s:%u.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"?"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">);</span></span>
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15142
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<pre style="margin: 0;">+<span id="LC15142" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15143
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<pre style="margin: 0;">+<span id="LC15143" class="line" lang="c"> <span class="p">}</span></span>
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15144
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<pre style="margin: 0;">+<span id="LC15144" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15145" 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">
15145
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<pre style="margin: 0;">+<span id="LC15145" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_equal_pos_alleles</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">,</span> <span class="n" style="color: #333;">presort_idx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">equal_pos_allele_ct</span><span class="p">,</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15146" 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">
15146
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<pre style="margin: 0;">+<span id="LC15146" class="line" lang="c"> <span class="n" style="color: #333;">LOGERRPRINTFWW</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --merge-equal-pos failure: inconsistent alleles at %s:%u.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"?"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15147" 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">
15147
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<pre style="margin: 0;">+<span id="LC15147" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15148" 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">
15148
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<pre style="margin: 0;">+<span id="LC15148" class="line" lang="c"> <span class="p">}</span></span>
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15125
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15149
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<pre style="margin: 0;"> <span id="LC15149" class="line" lang="c"> <span class="n" style="color: #333;">marker_map</span><span class="p">[</span><span class="n" style="color: #333;">presort_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15126
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15150
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<pre style="margin: 0;"> <span id="LC15150" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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15127
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<pre style="margin: 0;">-<span id="LC15127" class="line" lang="c"> <span class="p">}</span></span>
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15151
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<pre style="margin: 0;">+<span id="LC15151" 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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15152
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<pre style="margin: 0;">+<span id="LC15152" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">equal_pos_bp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prev_bp</span><span class="p">)</span> <span class="p">{</span></span>
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15153
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<pre style="margin: 0;">+<span id="LC15153" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">save_equal_pos_alleles</span><span class="p">(</span><span class="n" style="color: #333;">ll_buf</span><span class="p">,</span> <span class="n" style="color: #333;">equal_pos_read_start</span><span class="p">,</span> <span class="n" style="color: #333;">read_pos</span><span class="p">,</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">,</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">))</span> <span class="p">{</span></span>
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15154
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<pre style="margin: 0;">+<span id="LC15154" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15155
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<pre style="margin: 0;">+<span id="LC15155" class="line" lang="c"> <span class="p">}</span></span>
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15156
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<pre style="margin: 0;">+<span id="LC15156" class="line" lang="c"> <span class="p">}</span></span>
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15157
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<pre style="margin: 0;">+<span id="LC15157" class="line" lang="c"> <span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">;</span></span>
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15158
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<pre style="margin: 0;">+<span id="LC15158" class="line" lang="c"> <span class="p">}</span></span>
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15159
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<pre style="margin: 0;">+<span id="LC15159" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">unplaced</span><span class="p">))</span> <span class="p">{</span></span>
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15160
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<pre style="margin: 0;">+<span id="LC15160" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// shouldn't print warning in --merge-equal-pos case</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15161" 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">
15161
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<pre style="margin: 0;">+<span id="LC15161" class="line" lang="c"> <span class="n" style="color: #333;">LOGPREPRINTFWW</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Variants '%s' and '%s' have the same position.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">max_marker_id_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">presort_idx</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">max_marker_id_len</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ll_buf</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">])]));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15128" 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="15162" 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">
15162
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<pre style="margin: 0;">+<span id="LC15162" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">position_warning_ct</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15128" 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="15163" 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">
15163
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<pre style="margin: 0;">+<span id="LC15163" class="line" lang="c"> <span class="n" style="color: #333;">logerrprintb</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15164" 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">
15164
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<pre style="margin: 0;">+<span id="LC15164" 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 new new_line" data-linenumber="15165" 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">
15165
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<pre style="margin: 0;">+<span id="LC15165" class="line" lang="c"> <span class="n" style="color: #333;">logstr</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15166" 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">
15166
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<pre style="margin: 0;">+<span id="LC15166" class="line" lang="c"> <span class="p">}</span></span>
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15167
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<pre style="margin: 0;">+<span id="LC15167" class="line" lang="c"> <span class="n" style="color: #333;">position_warning_ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15128
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<td class="diff-line-num new_line" data-linenumber="15168" 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">
15168
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<pre style="margin: 0;"> <span id="LC15168" 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 old_line" data-linenumber="15129" 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">
15129
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<td class="diff-line-num new_line old" data-linenumber="15169" 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="LC15129" class="line" lang="c"><span class="idiff left right"> </span><span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">;</span></span>
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15169
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<pre style="margin: 0;">+<span id="LC15169" class="line" lang="c"><span class="idiff left right"> </span><span class="n" style="color: #333;">prev_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">;</span></span>
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15130
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<td class="diff-line-num new_line" data-linenumber="15170" 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">
15170
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<pre style="margin: 0;"> <span id="LC15170" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="15131" 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">
15131
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<td class="diff-line-num new_line" data-linenumber="15171" 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">
15171
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<pre style="margin: 0;"> <span id="LC15171" class="line" lang="c"> <span class="n" style="color: #333;">marker_map</span><span class="p">[</span><span class="n" style="color: #333;">presort_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_pos</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="15132" 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">
15132
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<td class="diff-line-num new_line" data-linenumber="15172" 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">
15172
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<pre style="margin: 0;"> <span id="LC15172" class="line" lang="c"> <span class="n" style="color: #333;">marker_cms</span><span class="p">[</span><span class="n" style="color: #333;">write_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_cms_tmp</span><span class="p">[</span><span class="n" style="color: #333;">presort_idx</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="15133" 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">
15133
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<td class="diff-line-num new_line" data-linenumber="15173" 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">
15173
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<pre style="margin: 0;"> <span id="LC15173" class="line" lang="c"> <span class="n" style="color: #333;">pos_buf</span><span class="p">[</span><span class="n" style="color: #333;">write_pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15134" 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">
15134
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<td class="diff-line-num new_line" data-linenumber="15174" 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">
15174
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<pre style="margin: 0;"> <span id="LC15174" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15175" 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">
15175
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<pre style="margin: 0;">+<span id="LC15175" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">equal_pos_bp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prev_bp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15176" 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">
15176
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<pre style="margin: 0;">+<span id="LC15176" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">save_equal_pos_alleles</span><span class="p">(</span><span class="n" style="color: #333;">ll_buf</span><span class="p">,</span> <span class="n" style="color: #333;">equal_pos_read_start</span><span class="p">,</span> <span class="n" style="color: #333;">read_pos</span><span class="p">,</span> <span class="n" style="color: #333;">equal_pos_allele_ptrs</span><span class="p">,</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15177" 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">
15177
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<pre style="margin: 0;">+<span id="LC15177" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15178" 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">
15178
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<pre style="margin: 0;">+<span id="LC15178" class="line" lang="c"> <span class="p">}</span></span>
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15179
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<pre style="margin: 0;">+<span id="LC15179" class="line" lang="c"> <span class="p">}</span></span>
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15135
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15180
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<pre style="margin: 0;"> <span id="LC15180" class="line" lang="c"> <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_start</span><span class="p">[</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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15136
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15181
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<pre style="margin: 0;"> <span id="LC15181" class="line" lang="c"> <span class="n" style="color: #333;">chrom_start</span><span class="p">[</span><span class="n" style="color: #333;">chrom_idx</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="n" style="color: #333;">write_pos</span><span class="p">;</span></span>
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15137
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15182
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<pre style="margin: 0;"> <span id="LC15182" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15367" 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="15412" 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">@@ -15367,8 +15412,16 @@ int32_t merge_main(char* bedname, char* bimname, char* famname, char* bim_loadbu</td>
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15367
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15412
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<pre style="margin: 0;"> <span id="LC15412" class="line" lang="c"> <span class="n" style="color: #333;">bufptr2</span><span class="p">[</span><span class="n" style="color: #333;">alen1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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15368
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<td class="diff-line-num new_line" data-linenumber="15413" 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">
15413
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<pre style="margin: 0;"> <span id="LC15413" class="line" lang="c"> <span class="n" style="color: #333;">alen2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen_se</span><span class="p">(</span><span class="n" style="color: #333;">bufptr3</span><span class="p">);</span></span>
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15369
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15414
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<pre style="margin: 0;"> <span id="LC15414" class="line" lang="c"> <span class="n" style="color: #333;">bufptr3</span><span class="p">[</span><span class="n" style="color: #333;">alen2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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15370
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<pre style="margin: 0;">-<span id="LC15370" class="line" lang="c"> <span class="n" style="color: #333;">bufptr4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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15371
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<pre style="margin: 0;">-<span id="LC15371" class="line" lang="c"> <span class="n" style="color: #333;">bufptr5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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15415
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<pre style="margin: 0;">+<span id="LC15415" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">;</span></span>
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15416
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<pre style="margin: 0;">+<span id="LC15416" class="line" lang="c"> <span class="n" style="color: #333;">bufptr4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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15417
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<pre style="margin: 0;">+<span id="LC15417" class="line" lang="c"> <span class="n" style="color: #333;">bufptr5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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15418
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<pre style="margin: 0;">+<span id="LC15418" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bufptr4</span><span class="p">)</span> <span class="p">{</span></span>
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15419
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<pre style="margin: 0;">+<span id="LC15419" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// --merge-equal-pos non-canonical index. Retrieve the canonical</span></span>
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15420
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<pre style="margin: 0;">+<span id="LC15420" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// index.</span></span>
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15421
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<pre style="margin: 0;">+<span id="LC15421" class="line" lang="c"> <span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">bufptr5</span><span class="p">;</span></span>
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15422
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<pre style="margin: 0;">+<span id="LC15422" class="line" lang="c"> <span class="n" style="color: #333;">bufptr4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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15423
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<pre style="margin: 0;">+<span id="LC15423" class="line" lang="c"> <span class="n" style="color: #333;">bufptr5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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15424
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<pre style="margin: 0;">+<span id="LC15424" class="line" lang="c"> <span class="p">}</span></span>
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15372
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15425
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<pre style="margin: 0;"> <span id="LC15425" class="line" lang="c"></span>
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15373
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15426
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<pre style="margin: 0;"> <span id="LC15426" class="line" lang="c"> <span class="n" style="color: #333;">last_marker_in_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_in_idx</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15374" 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">
15374
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<td class="diff-line-num new_line" data-linenumber="15427" 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">
15427
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<pre style="margin: 0;"> <span id="LC15427" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cur_sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15531" 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="15584" 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">@@ -15531,7 +15584,7 @@ int32_t merge_main(char* bedname, char* bimname, char* famname, char* bim_loadbu</td>
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15531
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<td class="diff-line-num new_line" data-linenumber="15584" 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">
15584
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<pre style="margin: 0;"> <span id="LC15584" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">umm</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="15532" 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">
15532
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<td class="diff-line-num new_line" data-linenumber="15585" 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">
15585
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<pre style="margin: 0;"> <span id="LC15585" class="line" lang="c"> <span class="n" style="color: #333;">diff_discordant</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15533" 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">
15533
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<td class="diff-line-num new_line" data-linenumber="15586" 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">
15586
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<pre style="margin: 0;"> <span id="LC15586" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15534" 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">
15534
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<td class="diff-line-num new_line old" data-linenumber="15587" 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="LC15534" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_diff_print</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">bufptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[</span><span class="n" style="color: #333;">ujj</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_len</span><span class="p">]),</span> <span class="n" style="color: #333;">ucc</span><span class="p">,</span> <span class="n" style="color: #333;">ucc3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[<span class="idiff left">((</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">])))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15535" 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="15587" 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">
15587
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<pre style="margin: 0;">+<span id="LC15587" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_diff_print</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">bufptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[</span><span class="n" style="color: #333;">ujj</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_len</span><span class="p">]),</span> <span class="n" style="color: #333;">ucc</span><span class="p">,</span> <span class="n" style="color: #333;">ucc3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">canonical_ascii_uidx</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">])))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="15535" 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">
15535
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<td class="diff-line-num new_line" data-linenumber="15588" 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">
15588
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<pre style="margin: 0;"> <span id="LC15588" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15536" 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">
15536
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<td class="diff-line-num new_line" data-linenumber="15589" 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">
15589
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<pre style="margin: 0;"> <span id="LC15589" class="line" lang="c"> <span class="p">}</span></span>
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15537
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<td class="diff-line-num new_line" data-linenumber="15590" 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">
15590
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<pre style="margin: 0;"> <span id="LC15590" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15669" 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="15722" 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">@@ -15669,6 +15722,15 @@ int32_t merge_main(char* bedname, char* bimname, char* famname, char* bim_loadbu</td>
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<td class="diff-line-num old_line" data-linenumber="15669" 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">
15669
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<td class="diff-line-num new_line" data-linenumber="15722" 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">
15722
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<pre style="margin: 0;"> <span id="LC15722" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="15670" 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">
15670
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<td class="diff-line-num new_line" data-linenumber="15723" 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">
15723
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<pre style="margin: 0;"> <span id="LC15723" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// actual relative position</span></span>
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<td class="diff-line-num old_line" data-linenumber="15671" 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">
15671
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<td class="diff-line-num new_line" data-linenumber="15724" 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">
15724
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<pre style="margin: 0;"> <span id="LC15724" class="line" lang="c"> <span class="n" style="color: #333;">marker_out_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_map</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start_marker_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15672" 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="15725" 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">
15725
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<pre style="margin: 0;">+<span id="LC15725" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (25 May 2018): in --merge-equal-pos case, we need to update a</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15672" 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="15726" 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">
15726
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<pre style="margin: 0;">+<span id="LC15726" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// single canonical marker_allele_ptrs[]. We now handle this by</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15672" 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="15727" 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">
15727
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<pre style="margin: 0;">+<span id="LC15727" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// storing nullptr in [0] and the canonical index in [1] when the</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15672" 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="15728" 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">
15728
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<pre style="margin: 0;">+<span id="LC15728" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// current index is non-canonical.</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15672" 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="15729" 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">
15729
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<pre style="margin: 0;">+<span id="LC15729" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">canonical_marker_allele_ptrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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15730
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<pre style="margin: 0;">+<span id="LC15730" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">canonical_marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15731" 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">
15731
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<pre style="margin: 0;">+<span id="LC15731" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">canonical_marker_allele_ptrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15732" 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">
15732
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<pre style="margin: 0;">+<span id="LC15732" class="line" lang="c"> <span class="n" style="color: #333;">canonical_marker_allele_ptrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">canonical_ascii_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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15733
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<pre style="margin: 0;">+<span id="LC15733" class="line" lang="c"> <span class="p">}</span></span>
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15672
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15734
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<pre style="margin: 0;"> <span id="LC15734" class="line" lang="c"></span>
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15673
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<td class="diff-line-num new_line" data-linenumber="15735" 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">
15735
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<pre style="margin: 0;"> <span id="LC15735" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aptr1</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">alen1</span> <span class="o" style="font-weight: 600;">==</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_line" data-linenumber="15674" 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">
15674
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<td class="diff-line-num new_line" data-linenumber="15736" 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">
15736
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<pre style="margin: 0;"> <span id="LC15736" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aptr2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">alen2</span> <span class="o" style="font-weight: 600;">!=</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 unfold js-unfold old_line" data-linenumber="15679" 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="15741" 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">@@ -15679,39 +15741,39 @@ int32_t merge_main(char* bedname, char* bimname, char* famname, char* bim_loadbu</td>
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15679
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<td class="diff-line-num new_line" data-linenumber="15741" 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">
15741
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<pre style="margin: 0;"> <span id="LC15741" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_HALF_MISSING</span><span class="p">;</span></span>
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15680
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<td class="diff-line-num new_line" data-linenumber="15742" 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">
15742
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<pre style="margin: 0;"> <span id="LC15742" 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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15681
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<td class="diff-line-num new_line" data-linenumber="15743" 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">
15743
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<pre style="margin: 0;"> <span id="LC15743" class="line" lang="c"> <span class="n" style="color: #333;">ucc2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// A2 count</span></span>
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15682
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<td class="diff-line-num new_line old" data-linenumber="15744" 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="LC15682" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">]))</span> <span class="p">{</span></span>
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15744
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<pre style="margin: 0;">+<span id="LC15744" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff right">[</span></span><span class="mi" style="color: #099;">1</span><span class="p">]))</span> <span class="p">{</span></span>
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15683
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<td class="diff-line-num new_line" data-linenumber="15745" 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">
15745
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<pre style="margin: 0;"> <span id="LC15745" class="line" lang="c"> <span class="n" style="color: #333;">ucc2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15684
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<td class="diff-line-num new_line old" data-linenumber="15746" 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="LC15684" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">]))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15746" 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">
15746
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<pre style="margin: 0;">+<span id="LC15746" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">]))</span> <span class="p">{</span></span>
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15685
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<td class="diff-line-num new_line" data-linenumber="15747" 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">
15747
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<pre style="margin: 0;"> <span id="LC15747" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// new allele code</span></span>
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15686
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<td class="diff-line-num new_line old" data-linenumber="15748" 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="LC15686" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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15748
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<pre style="margin: 0;">+<span id="LC15748" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff right">[</span></span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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15687
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<td class="diff-line-num new_line" data-linenumber="15749" 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">
15749
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<pre style="margin: 0;"> <span id="LC15749" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// fill A2 first</span></span>
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15688
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15750
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<pre style="margin: 0;"> <span id="LC15750" class="line" lang="c"> <span class="n" style="color: #333;">ucc2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15689
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<td class="diff-line-num new_line old" data-linenumber="15751" 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="LC15689" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15690" 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">
15690
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<td class="diff-line-num new_line old" data-linenumber="15751" 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="LC15690" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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15691
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<td class="diff-line-num new_line old" data-linenumber="15751" 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="LC15691" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15692" 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="15751" 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">
15751
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<pre style="margin: 0;">+<span id="LC15751" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15752" 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">
15752
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<pre style="margin: 0;">+<span id="LC15752" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15753" 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">
15753
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<pre style="margin: 0;">+<span id="LC15753" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15692" 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">
15692
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<td class="diff-line-num new_line" data-linenumber="15754" 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">
15754
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<pre style="margin: 0;"> <span id="LC15754" 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="15693" 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">
15693
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<td class="diff-line-num new_line" data-linenumber="15755" 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">
15755
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<pre style="margin: 0;"> <span id="LC15755" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_NOT_BIALLELIC</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15694" 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">
15694
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<td class="diff-line-num new_line" data-linenumber="15756" 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">
15756
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<pre style="margin: 0;"> <span id="LC15756" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15695" 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">
15695
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<td class="diff-line-num new_line old" data-linenumber="15757" 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="LC15695" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_set</span><span class="p">(</span><span class="n" style="color: #333;">aptr1</span><span class="p">,</span> <span class="n" style="color: #333;">alen1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">ukk</span><span class="p">])))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15696" 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="15757" 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">
15757
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<pre style="margin: 0;">+<span id="LC15757" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_set</span><span class="p">(</span><span class="n" style="color: #333;">aptr1</span><span class="p">,</span> <span class="n" style="color: #333;">alen1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">canonical_</span>marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">ukk</span><span class="p">])))</span> <span class="p">{</span></span>
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15696
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<td class="diff-line-num new_line" data-linenumber="15758" 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">
15758
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<pre style="margin: 0;"> <span id="LC15758" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_NOMEM</span><span class="p">;</span></span>
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15697
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<td class="diff-line-num new_line" data-linenumber="15759" 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">
15759
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<pre style="margin: 0;"> <span id="LC15759" class="line" lang="c"> <span class="p">}</span></span>
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15698
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15760
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<pre style="margin: 0;"> <span id="LC15760" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15699" 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">
15699
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<td class="diff-line-num new_line old" data-linenumber="15761" 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="LC15699" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </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 new old_line" data-linenumber="15700" 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="15761" 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">
15761
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<pre style="margin: 0;">+<span id="LC15761" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff right">[</span></span><span class="mi" style="color: #099;">1</span><span class="p">]))</span> <span class="p">{</span></span>
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15700
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<td class="diff-line-num new_line" data-linenumber="15762" 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">
15762
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<pre style="margin: 0;"> <span id="LC15762" class="line" lang="c"> <span class="n" style="color: #333;">ucc2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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15701
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<pre style="margin: 0;">-<span id="LC15701" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">]))</span> <span class="p">{</span></span>
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15763
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<pre style="margin: 0;">+<span id="LC15763" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">aptr2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">]))</span> <span class="p">{</span></span>
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15702
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<td class="diff-line-num new_line" data-linenumber="15764" 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">
15764
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<pre style="margin: 0;"> <span id="LC15764" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// put A2 check second since the only way A2 will be unset when A1</span></span>
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15703
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<td class="diff-line-num new_line" data-linenumber="15765" 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">
15765
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<pre style="margin: 0;"> <span id="LC15765" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// is set at this point is if it was specified that way in an</span></span>
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15704
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<td class="diff-line-num new_line" data-linenumber="15766" 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">
15766
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<pre style="margin: 0;"> <span id="LC15766" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// earlier binary file.</span></span>
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15705
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<td class="diff-line-num new_line old" data-linenumber="15767" 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="LC15705" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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15706
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<td class="diff-line-num new_line old" data-linenumber="15767" 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="LC15706" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">;</span></span>
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15707
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<td class="diff-line-num new_line old" data-linenumber="15767" 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="LC15707" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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15708
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<td class="diff-line-num new_line old" data-linenumber="15767" 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="LC15708" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15767
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<pre style="margin: 0;">+<span id="LC15767" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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15768
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<pre style="margin: 0;">+<span id="LC15768" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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15769
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<pre style="margin: 0;">+<span id="LC15769" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">canonical_marker_allele_ptrs</span></span><span class="p"><span class="idiff right">[</span></span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">missing_geno_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15770" 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">
15770
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<pre style="margin: 0;">+<span id="LC15770" class="line" lang="c"> <span class="n" style="color: #333;">ukk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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15709
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<td class="diff-line-num new_line" data-linenumber="15771" 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">
15771
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<pre style="margin: 0;"> <span id="LC15771" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (14 Nov 2017): forgot to increment the A2 allele count!</span></span>
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15710
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15772
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<pre style="margin: 0;"> <span id="LC15772" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ucc2</span><span class="p">;</span></span>
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15711
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<td class="diff-line-num new_line" data-linenumber="15773" 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">
15773
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<pre style="margin: 0;"> <span id="LC15773" 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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15712
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15774
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<pre style="margin: 0;"> <span id="LC15774" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_NOT_BIALLELIC</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15713" 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">
15713
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<td class="diff-line-num new_line" data-linenumber="15775" 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">
15775
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<pre style="margin: 0;"> <span id="LC15775" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15714" 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">
15714
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<td class="diff-line-num new_line old" data-linenumber="15776" 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="LC15714" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_set</span><span class="p">(</span><span class="n" style="color: #333;">aptr2</span><span class="p">,</span> <span class="n" style="color: #333;">alen2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">ukk</span><span class="p">])))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15776" 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">
15776
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<pre style="margin: 0;">+<span id="LC15776" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_set</span><span class="p">(</span><span class="n" style="color: #333;">aptr2</span><span class="p">,</span> <span class="n" style="color: #333;">alen2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">canonical_</span>marker_allele_ptrs</span><span class="p">[</span><span class="n" style="color: #333;">ukk</span><span class="p">])))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="15715" 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">
15715
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<td class="diff-line-num new_line" data-linenumber="15777" 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">
15777
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<pre style="margin: 0;"> <span id="LC15777" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15716" 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">
15716
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<td class="diff-line-num new_line" data-linenumber="15778" 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">
15778
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<pre style="margin: 0;"> <span id="LC15778" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="15717" 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">
15717
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<td class="diff-line-num new_line" data-linenumber="15779" 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">
15779
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<pre style="margin: 0;"> <span id="LC15779" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15772" 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="15834" 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">@@ -15772,7 +15834,7 @@ int32_t merge_main(char* bedname, char* bimname, char* famname, char* bim_loadbu</td>
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<td class="diff-line-num old_line" data-linenumber="15772" 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">
15772
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<td class="diff-line-num new_line" data-linenumber="15834" 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">
15834
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<pre style="margin: 0;"> <span id="LC15834" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">umm</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="15773" 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">
15773
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<td class="diff-line-num new_line" data-linenumber="15835" 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">
15835
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<pre style="margin: 0;"> <span id="LC15835" class="line" lang="c"> <span class="n" style="color: #333;">diff_discordant</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15774" 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">
15774
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<td class="diff-line-num new_line" data-linenumber="15836" 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">
15836
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<pre style="margin: 0;"> <span id="LC15836" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15775" 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">
15775
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<td class="diff-line-num new_line old" data-linenumber="15837" 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="LC15775" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_diff_print</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_marker_id_len</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_len</span><span class="p">]),</span> <span class="n" style="color: #333;">ucc2</span><span class="p">,</span> <span class="n" style="color: #333;">ucc3</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">])</span>))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15776" 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="15837" 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">
15837
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<pre style="margin: 0;">+<span id="LC15837" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_diff_print</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_marker_id_len</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_len</span><span class="p">]),</span> <span class="n" style="color: #333;">ucc2</span><span class="p">,</span> <span class="n" style="color: #333;">ucc3</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">canonical_marker_allele_ptrs</span></span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="15776" 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">
15776
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<td class="diff-line-num new_line" data-linenumber="15838" 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">
15838
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<pre style="margin: 0;"> <span id="LC15838" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15777" 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">
15777
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<td class="diff-line-num new_line" data-linenumber="15839" 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">
15839
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<pre style="margin: 0;"> <span id="LC15839" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="15778" 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">
15778
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<td class="diff-line-num new_line" data-linenumber="15840" 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">
15840
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<pre style="margin: 0;"> <span id="LC15840" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15786" 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="15848" 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">@@ -15786,7 +15848,7 @@ int32_t merge_main(char* bedname, char* bimname, char* famname, char* bim_loadbu</td>
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<td class="diff-line-num old_line" data-linenumber="15786" 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">
15786
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<td class="diff-line-num new_line" data-linenumber="15848" 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">
15848
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<pre style="margin: 0;"> <span id="LC15848" class="line" lang="c"> <span class="n" style="color: #333;">diff_not_both_genotyped</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15787" 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">
15787
</td>
<td class="diff-line-num new_line" data-linenumber="15849" 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">
15849
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<pre style="margin: 0;"> <span id="LC15849" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ucc2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ucc3</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="15788" 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">
15788
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<td class="diff-line-num new_line" data-linenumber="15850" 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">
15850
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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="LC15850" class="line" lang="c"> <span class="n" style="color: #333;">diff_discordant</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="15789" 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">
15789
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<td class="diff-line-num new_line old" data-linenumber="15851" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC15789" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_diff_print</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_marker_id_len</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_len</span><span class="p">]),</span> <span class="n" style="color: #333;">ucc2</span><span class="p">,</span> <span class="n" style="color: #333;">ucc3</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">marker_allele_ptrs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uii</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">])</span>))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15790" 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="15851" 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">
15851
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<pre style="margin: 0;">+<span id="LC15851" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_diff_print</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">marker_ids</span><span class="p">[</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_marker_id_len</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_len</span><span class="p">]),</span> <span class="n" style="color: #333;">ucc2</span><span class="p">,</span> <span class="n" style="color: #333;">ucc3</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">canonical_marker_allele_ptrs</span></span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="15790" 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">
15790
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<td class="diff-line-num new_line" data-linenumber="15852" 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">
15852
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<pre style="margin: 0;"> <span id="LC15852" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_main_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="15791" 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">
15791
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<td class="diff-line-num new_line" data-linenumber="15853" 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">
15853
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<pre style="margin: 0;"> <span id="LC15853" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="15792" 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">
15792
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<td class="diff-line-num new_line" data-linenumber="15854" 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">
15854
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<pre style="margin: 0;"> <span id="LC15854" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16648" 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="16710" 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">@@ -16648,7 +16710,11 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>
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16648
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<td class="diff-line-num new_line" data-linenumber="16710" 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">
16710
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<pre style="margin: 0;"> <span id="LC16710" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="16649" 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">
16649
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<td class="diff-line-num new_line" data-linenumber="16711" 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">
16711
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<pre style="margin: 0;"> <span id="LC16711" class="line" lang="c"> <span class="p">}</span></span>
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16650
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<td class="diff-line-num new_line" data-linenumber="16712" 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">
16712
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<pre style="margin: 0;"> <span id="LC16712" class="line" lang="c"> <span class="nl">merge_datasets_ret_1:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16651" 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">
16651
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<td class="diff-line-num new_line old" data-linenumber="16713" 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="LC16651" class="line" lang="c"> <span class="n" style="color: #333;">cleanup_allele_storage</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">tot_marker_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16713" 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">
16713
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<pre style="margin: 0;">+<span id="LC16713" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_equal_pos</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16714" 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">
16714
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<pre style="margin: 0;">+<span id="LC16714" class="line" lang="c"> <span class="n" style="color: #333;">cleanup_allele_storage2</span><span class="p">(</span><span class="n" style="color: #333;">tot_marker_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16715" 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">
16715
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<pre style="margin: 0;">+<span id="LC16715" 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 new new_line" data-linenumber="16716" 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">
16716
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<pre style="margin: 0;">+<span id="LC16716" class="line" lang="c"> <span class="n" style="color: #333;">cleanup_allele_storage</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">tot_marker_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">marker_allele_ptrs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16717" 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">
16717
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<pre style="margin: 0;">+<span id="LC16717" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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16652
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<td class="diff-line-num new_line" data-linenumber="16718" 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">
16718
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<pre style="margin: 0;"> <span id="LC16718" class="line" lang="c"> <span class="n" style="color: #333;">fclose_cond</span><span class="p">(</span><span class="n" style="color: #333;">mergelistfile</span><span class="p">);</span></span>
</pre>
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16653
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<td class="diff-line-num new_line" data-linenumber="16719" 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">
16719
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<pre style="margin: 0;"> <span id="LC16719" class="line" lang="c"> <span class="n" style="color: #333;">fclose_cond</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="16654" 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">
16654
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<td class="diff-line-num new_line" data-linenumber="16720" 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">
16720
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<pre style="margin: 0;"> <span id="LC16720" class="line" lang="c"> <span class="n" style="color: #333;">bigstack_double_reset</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_mark</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_end_mark</span><span class="p">);</span></span>
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